VictorJuiz/thesis huggingface dataset:
Elucidating the Reprogramming Mechanism: Selection Pressures Direct a Poised Subpopulation of Somatic Cells to an Induced Pluripotent Stem Cell State
Keywords: Cellular competition
Cellular fitness
Cellular heterogeneity
Induced pluripotent stem cell
Reprogramming
Systems biology

Through the overexpression of key transcription factors – Oct4, Klf4, c-Myc, and Sox2 (OKMS) – mouse somatic cells can be reprogrammed to an induced pluripotent stem cell (iPSC) state, enabling them to give rise to all cell types of the body. However, the process of reprogramming has remained elusive and it is unclear whether all somatic cells traverse the same trajectory following OKMS transgene overexpression. The reprogramming process has been mapped by conducting ‘omics analyses of bulk reprogramming culture over time. These population-averaged datasets describe reprogramming as a stepwise process where somatic cells transition through a (transgene-dependent) pre-iPSC state to finally stabilise in a (transgene-independent) iPSCs state. On the other hand, single mouse somatic cells reprogrammed in isolation exhibit stochastic reprogramming latencies. As a result, cells experiencing asynchronous reprogramming dynamics are expected to give rise to heterogeneity in bulk reprogramming culture. Here, we aim to consolidate the apparent dichotomy between stepwise cell state changes observed in population reprogramming with the stochasticity of isolated clonal reprogramming by investigating heterogeneity in mouse reprogramming culture. We first develop a surface marker strategy to track transgene-dependent and -independent iPSCs, enabling us to assess heterogeneity with ease. This marker strategy also shows utility in separating naïve and primed pluripotent states in mouse and human culture. We next combine this surface marker-based approach with clonal tracking and mathematical modeling to investigate the reprogramming trajectory of individual reprogramming clones in bulk culture. In doing so, we uncover clonal competition as a novel driver of population reprogramming dynamics. In fact, we show that a subset of poised somatic cells gives rise to clones that have an elite propensity to dominate bulk reprogramming culture and contribute to the iPSC fraction. We also show, for the first time, that a few clones overtake population reprogramming culture, thus making population-averaged data clonally biased. This work provides novel insights into the role of cell competition in driving heterogeneity in reprogramming culture, providing a new lens with which to interpret population-averaged ‘omics datasets. Taken together, we show that not all reprogramming clones exhibit equivalent behaviour in multicellular contexts, underscoring the need to consider the competition potential of iPSCs.
Malignancy and Solid Organ Transplantation: Evaluating Cancer Mortality, Pretransplant Malignancies, and Cancer Screening
Keywords: malignancy
mortality
screening
transplantation

This thesis explores the intersection of malignancy and solid organ transplantation. First, establishing that solid organ transplant recipients (SOTRs) are at risk of cancer mortality and cancer is the second leading cause of death in this population. Second, exploring pretransplant malignancies (PTM): our systematic review identified a lack of clear and consistent recommendations for cancer evaluation of transplant, with only one in every four clinical practice guidelines (CPGs) including recommendations for cancer evaluation. Most recommended cancer screening as per the general population, which might be not adequate to ensure transplant candidates they are free of occult neoplasms. We also found that recipients with PTM in remission are at increased risk of all-cause mortality compared to recipients without prior history of cancer, with increased risk not only of cancer-specific mortality but also non-cancer death. However, when stratified by type of PTM, only those with high-risk PTM had worse outcomes. Lastly, this dissertation explores recommendations for cancer screening in SOTRs and their uptake. A systematic review of CPGs identified several weaknesses in the available recommendations for cancer screening, including variable screening recommendations, lack of recommendations for non-kidney recipients, and paucity of involvement of relevant stakeholders. Our population-based study found that the uptake of cancer screening uptake in SOTR was low; most SOTR had periods when they were non-adherent to screening recommendations during follow-up, and in fact, many recipients were never screened. In addition, we identified that recipients with visits to primary care physicians were more likely to become up-to-date with cancer screening. Overall, the results of this thesis provide compelling evidence that SOTRs are at increased risk of dying from cancer and highlight the role of cancer evaluation of transplant candidates and cancer screening recipients as a strategy to reduce the burden of cancer in this population.
Identity Politicking: New Candidacies and Representations in Contemporary Canadian Politics
Keywords: Canadian Politics
Gender
Identity
Political Leadership

This dissertation centres on the candidacies and leaderships of three politicians—Justin Trudeau, Olivia Chow, and Kathleen Wynne. It examines the ways in which gender, race, sexuality, and other salient aspects of politicians’ identities are strategically negotiated and mobilized by politicians, political actors, the media, and the grassroots. The cases herein question the extent to which identity matters in Canadian electoral politics at the municipal, provincial, and federal levels, bridging sociological understandings of power and authority with feminist analyses of identity. The project engages broadly with qualitative methods—discourse analysis, media analysis, participant observation, and interviewing. The research contributes to understandings of: (1) the durability of masculinity in Canadian electoral politics; (2) dispositional requirements for leaders; (3) the compensatory labour that minority politicians perform; (4) alignments and allegiances between politicians and grassroots movements.The first case of the dissertation examines media coverage of a charity-boxing match between Liberal Member of Parliament Justin Trudeau and Conservative Canadian Senator Patrick Brazeau. It offers the concept recuperative gender strategies to describe how political leaders work to restore their public gender identities. The second case is focused on the candidacy of visible minority Toronto mayoral candidate, Olivia Chow. The case offers three concepts that illuminate forms of identity work that minority politicians navigate on the campaign trail: dispositional requirements, ideological alignment, and political compensatory labour. The final case analyzes social movement actors’ assessments of Premier Kathleen Wynne—the first woman and openly lesbian premier of Ontario—and presents a typology of words and deeds to map the terms under which social movement actors judge progressive politicians.
Development and Evaluation of a High Fidelity Cleft Palate Simulator for Surgical Training and for Development of a Robotic Approach to Infant Cleft Palate Surgery
Keywords: Cleft palate surgery
Surgical learning curve
Surgical robotics
Surgical simulation

Cleft palate is one of the most common birth defects requiring surgical repair for proper speech development and feeding. The surgical procedure is challenging due to the small confines of the infant oral cavity, as well as the delicate tissue handling and dissections required. Surgical access, visualization and instrument manipulation is limited. As a result, cleft palate repair is both difficult to learn with limited teaching opportunities as well as technically challenging to perform. A simulator that incorporates the fidelity necessary to capture the critical steps of cleft palate surgery is a valuable training tool providing a safe environment to practice. In addition, a surgical robot provides improved access, visualization and precision within small workspaces that may overcome the challenges of using traditional instruments. The objectives of this work are to develop and evaluate a high fidelity cleft palate simulator to enhance cleft palate surgery training and to develop a robotic approach to infant cleft palate repair using the simulator as a test bed. The simulator was evaluated and found to be an effective, anatomically accurate and valuable training tool that enhances training metrics such as technical performance. The simulator was utilized to perform infant robotic cleft palate surgery using the latest da Vinci速 robotic surgical systems. Overall, the robotic procedures provide superior visualization and access. The da Vinci速 testing guided development of a novel instrument wrist mechanism with more optimal design characteristics for the infant oral cavity workspace and cleft palate surgery.
Novel Roles of GLP-1 and GLP-2 in the Regulation of Hepatic Lipid/Lipoprotein Homeostasis and the Involvement of BAT Activation
Keywords: Brown Adipose Tissue
Diabetes
Dyslipidemia
Fatty Liver
Glucagon-like peptide
Lipoproteins

Major complications of insulin resistance and type 2 diabetes (T2D) include the development of non-alcoholic fatty liver disease (NAFLD) and an atherogenic fasting dyslipidemic profile, primarily due to increases in hepatic very low density lipoprotein (VLDL) production. Recent studies have implicated neuronal signalling in the control of hepatic lipid metabolism and VLDL production. The gut derived hormones glucagon-like peptide (GLP)-1 and GLP-2 have been shown to signal through neuronal pathways and display postprandial hypolipidemic and hyperlipidemic actions respectively. Furthermore, activation of brown adipose tissue (BAT) through the sympathetic nervous system also displays hypolipidemic actions and has recently been shown to be activated by GLP-1. We hypothesized that GLP-1 and GLP-2 will play opposing roles by decreasing and increasing VLDL production and NAFLD respectively. We further hypothesized that the effects of GLP-1 in modulating lipid metabolism occur through the activation of BAT. Using the Syrian Golden hamster, we showed that the GLP-1 receptor (GLP-1R) agonist exendin-4 decreased body weight, fasting dyslipidemia and VLDL overproduction by enhancing lipid utilization and decreasing hepatic de novo lipogenesis. These effects occurred through a vagal signalling pathway and were independent of changes in food consumption. To assess the involvement of BAT in the hypolipidemic actions of GLP-1, we first characterized the hamster as a novel and effective model of BAT activation. Î˛3-adrenergic receptor (Î˛3-AR) agonism activated hamster BAT, induced browning of WAT and prevented diet-induced NAFLD. The hypolipidemic actions of GLP-1R agonism were partially mediated by BAT as shown in hamsters that underwent BAT removal. Conversely, the sister peptide GLP-2 increased VLDL production and hepatic steatosis in hamsters and mice. Interestingly, GLP-2R knockout (KO) mice were protected against diet-induced dyslipidemia but displayed enhanced hepatic lipid accumulation. An observed reduction in VLDL-TG levels indicated that the enhanced hepatic lipid levels may be due to decreased VLDL production. Taken together, this thesis demonstrates that GLPs play critical but opposing roles in regulating hepatic lipid accumulation and VLDL production. Modulating the balance of GLPs in vivo may be a potential therapeutic approach to correct the dyslipidemia and NAFLD commonly associated with the metabolic syndrome.
FPGA-based Real-Time Simulation Platform For Power Grids Including Multiple Converters
Keywords: Coupled power grid
Electrical Machine
FPGA-based Computing
Power Electronic Converters
Real-time simulation
Transmission Line

This thesis develops an FPGA-based real-time simulation platform for power grids including multiple Power Electronic Converters (PECs) and other classical components, which in contrast to the classical systems do not include long transmission lines for mathematical decoupling of systems for efficient simulation. The presence of short transmission lines creates a large set of network equations that can not be decoupled. Handling the large admittance matrix, representing the large set of network equations, requires floating-point numerical representation which is associated with large latencies and high resource utilization in FPGAs. In addition, the presence of high switching frequency PECs imposes small simulation time-step requirement and therefore high computational burden. Accurate representation of PECs, using two-value resistor model, results in time-variant admittance matrix which also increases computational burden. This thesis proposes Reformulated Modified Nodal Analysis (RMNA) for solution of network equations to enable (i) parallelism between the simulation task of solving network equations and those of other power system component models to achieve small simulation time-steps and (ii) design of a low-latency floating-point matrix-vector multiplication hardware module to efficiently solve relatively large set of network equations associated with systems targeted in this work. An FPGA-based partitioning method is proposed to enable simulation of multiple PECs and representing power switches by two-value resistor model without significantly increasing the computational burden. This overcomes the issues associated with the existing real-time Associate Discrete Circuit (ADC) switch model, i.e., artificial switching loss and numerical oscillation. A new FPGA-based Electrical Machine (EM) Constant-Parameter-Voltage-Behind-Reactance (CPVBR) model is proposed to enable real-time simulation of different types of EMs, i.e., Induction Machine (IM), Synchronous Machine (SM) and Permanent Magnet Synchronous Machine (PMSM), under all test scenarios and regardless of their dynamic saliency and system configuration. Moreover, this thesis develops Inter-Hardware Universal Line Model (IHULM) to enable parallel simulation of distribution system, which includes short transmission lines, in the FPGA-based platform and the rest of the system in commercially available simulation platforms, e.g., RTDS. The platform developed in this work accurately simulates power grids with up to 160 nodes/outputs, four PECs, three EMs and one IHULM using a small real-time time-step of micro-second. Moreover, it features fixed-hardware design to avoid FPGA code compilation time. A model preparation script is developed to calculate the study system parameters based on the modeling approaches devised in this work.
Tools for Point-of-Care Digital Microfluidics
Keywords: diagnostics
microfluidics
point-of-care

Digital microfluidics (DMF) is a liquid handling technology for the manipulation of discrete droplets on a generic array of hydrophobic insulated electrodes. In DMF, protocols are generated through software and are independent of the microfluidic architecture. DMF can be used to miniaturize and automate routine assays. Of interest are miniaturized medical diagnostic assays that could be performed in an automated fashion and can take place close to the point of need. This thesis describes the development of several tools for the realization of this description. The feasibility of performing clinical assays with DMF outside of the laboratory was demonstrated for the first time. DMF immunoassays for anti-measles IgG and anti-rubella IgG were performed in Kakuma, a refugee camp in northwestern Kenya. Custom-built open-source control systems and low-cost inkjet-printed cartridges were used to perform up to four chemiluminescent immunoassays simultaneously. 144 samples were tested and the clinical sensitivities and specificities of the DMF immunoassays were shown to be good (>80%). Having taken DMF out of the laboratory, new tools and detection methods were developed. First, nanostructured microelectrodes (NMEs) for electrochemical analysis were integrated with a DMF device. This was then applied to an immunoassay for anti-rubella IgG. Performance comparable to chemiluminescent methods was achieved. A second tool developed was a method entitled pre-concentration by liquid intake by paper (P-CLIP). Functionalized magnetic microparticles are captured from large (50-300 ÂľL) volumes of liquid and are resuspended in a much smaller volume (1-2 ÂľL). P-CLIP was used with an immunoassay for Pf lactate dehydrogenase and shown to improve signals up to 30-fold. The last tool for DMF clinical assays was the integration of low-cost commercial electrodes. Established methods for integrating sensing electrodes with DMF are costly and have low fabrication throughput. A plastic-based DMF top plate that can receive commercial biosensors and screen-printed electrodes was demonstrated. The sum of the innovations described in this thesis suggest that DMF is a viable platform for point-of-care analysis. Advancement to the tools already described will enable DMF to be used for analysis of a wide range of non-invasive samples such as finger-prick blood samples and saliva samples.
Processes and Structures of Care for Critically Ill Patients with Acute Brain Injury
Keywords: Acute brain injury
Critical care structure
Processes of care

Background: Examining the differences in quality and intensity of care within the context of ICU structure is needed to better understand the mortality differences observed between centers, and may help to improve the design of future trials for this neurocritically ill patient population. Methods: This dissertation uses several methods to examine the relationship between processes, organization of care and outcome for critically ill patients with acute brain injury. Results: First in a cohort study, I evaluated the association between centers rendering early decisions to withdraw life-sustaining therapies in severe traumatic brain injury (sTBI), as measured by time until death, and overall risk-adjusted mortality. After adjustment for case mix, care in a center with a preponderance of early deaths (within the first 5 days of ICU admission) was not associated with increased odds of death (adjusted odds ratio (OR) 0.95; 95% confidence interval (CI) 0.83-1.09). Secondly in a meta-analysis, I examined the relationship between the timing of tracheostomy in acutely brain injured patients and mortality. Early tracheostomy was associated with lower long-term mortality (risk ratio [RR] 0.57. 95% CI 0.36-0.90), reduced duration of mechanical ventilation (mean difference [MD] -2.72 days, 95% CI -1.29 to -4.15) and ICU length of stay (MD -2.55 days, 95% CI -0.50 to -4.59), but, was not associated with lower short-term mortality (RR 1.25; 95% CI 0.68-2.30), and, as expected, increased the probability of ever receiving a tracheostomy (RR 1.58, 95% CI 1.24-2.02). Lastly in a cohort study combined with survey data, I examined the association between dedicated neurocritical care units, the presence of standardized management protocols for sTBI, and mortality. Care in a dedicated neurocritical care unit was not associated with a lower risk-adjusted in-hospital mortality (OR 0.97 (95% CI 0.80-1.19), but the utilization of standardized TBI management protocols for these patients was associated with lower risk-adjusted in-hospital mortality (OR 0.77; 95% CI 0.63-0.93). Conclusions: Using several analytical approaches, these findings highlight important opportunities to reduce variability in care negatively impacting on acute brain injury outcomes.
The Bioengineering of Annulus Fibrosus Tissues Using Phenotypically Distinct Inner and Outer Annulus Fibrosus Cells on Oriented Nanofibrous Polyurethane Scaffolds
Keywords: Biomaterials
Intervertebral Discs
Regenerative Medicine
Tissue Engineering

As the current treatments for chronic neck or low back pain do not restore the full functions of degenerated intervertebral discs (IVD), the replacement of degenerate discs with a bioengineered IVD is an approach of great interest. Owing to the complex structure of the IVD, various engineered tissue components of the IVD require proper integration for mechanical functionality. The aim of this thesis is to improve the fieldâ s understanding of tissue engineering strategies necessary for generating a biological IVD replacement. A protocol was developed to generate a multiphasic IVD implant in vitro composed of multilamellated annulus fibrosus (AF) tissues engineered using nanofibrous aligned polycarbonate urethane (PU) scaffolds and nucleus pulposus (NP) tissues engineered on calcium polyphosphate (CPP) bone substitute. The engineered AF tissues were characteristic of the outer annulus fibrosus (OAF) tissues. Integration between different engineered tissues occurred, forming interfaces with mechanical strength. At one month post-implantation, the AF tissue remained adherent to the bone substitute but inadequate graft fixation resulted in the subsidence of the implant. The absence of the inner annulus fibrosus (IAF) component which can lead to inadequate transmission of compressive forces may have contributed to the loss of the NP tissues. It was hypothesized that OAF and IAF cells would generate tissue in vitro that maintained their distinct extracellular matrix (ECM) compositions. A culture protocol restoring the accumulation of appropriate ECM in multilamellated IAF tissues without altering the composition of multilamellated OAF tissues was identified. The restoration of ECM characteristic of IAF was dependent on the activation of glucocorticoid receptor signalling, which also increased the mitochondrial activity. Potential mechanism(s) of the mitochondria in the regulation of proper ECM accumulation for IAF and OAF tissues should be further investigated. Dynamic loading in vitro was explored as a strategy to improve the mechanical functions of these tissues for withstanding in vivo loads after implantation. As OAF and IAF tissues did not show further increase in ECM accumulation when dynamically loaded individually in vitro, the integration of various IVD components may be required for proper load distribution, warranting further studies into the effect of loading on engineered multiphasic tissues.