VictorJuiz/thesis huggingface dataset:
The Complicity of GABAergic Neurotransmission in Ictogenesis during Acute Hyperexcitabilty

The observations of GABAergic interneurons leading the transition into seizure events is antithetical to the current framework that seizures (“ictogenesis”) manifest from excessive excitation in the brain. This study utilized optogenetic tools to investigate the paradoxical role of interneurons in mediating ictogenesis in the in vitro cortical 4-AP seizure model. It was discovered that the brief activation of GABAergic interneurons can reliably initiate ictal events in an all-or-none fashion. It was discovered that GABA-initiated ictal events were dependent on bicarbonate, likely for efflux via GABAA receptors to mediate synaptic depolarization. It was also discovered that there are multiple mechanisms to ictogenesis, co-existing at different orders of preference, in the same brain tissue. A secondary pathway to ictogenesis was dependent on K-Cl Co-transporter 2 (KCC2) activity, likely for its role in extracellular potassium accumulation which can non-synaptically depolarize surrounding neurons. Accordingly, the partial downregulation of KCC2 and carbonic anhydrase (to reduce bicarbonate regeneration) reliably thwarted ictogenesis, and most remarkably, completely restored normal activity in the in vitro 4-AP seizure model. Collectively, these findings suggest that ictogenesis can manifest from the pathologically heightened activity of GABAergic interneurons because they activate downstream GABAA receptors in parallel and cause excessive ion fluxes that result in EGABA breakdown (loss of GABA-mediated hyperpolarization) on the post-synaptic neuron. During EGABA breakdown, the subsequent activation of GABAA receptors can mediate depolarization, synaptically and non-synaptically, via downstream carbonic anhydrase and KCC2 activity. This effectively converts intrinsic feedback inhibition circuits into feedforward excitation circuits, facilitating ictogenesis. In summary, the findings in this thesis demonstrate that GABAergic interneurons are complicit in mediating ictogenesis during acute hyperexcitable conditions, such as some cases of drug-induced seizures.

Keywords: 4-AP
Artificial Intelligence
Epilepsy
Optogenetics
Seizure
Seizure Detection Algorithm
Advisor: Valiante, Taufik A
Uncovering Signalling Pathways Mediating Gastrointestinal Morphogenesis and Tumorigenesis

The gastrointestinal system undergoes remarkable morphogenesis during development, in which a simple, smooth tube rapidly rearranges to form millions of finger-like projections called villi that line the entire intestinal tract. While gastrointestinal development requires precisely coordinated intercellular communication via signalling pathways, mechanisms underlying intestinal morphogenesis remain unclear. The Hedgehog signalling pathway is critical for many aspects of gut development, however, its downstream transcriptional targets allowing for complex cell behaviours during villus formation are poorly understood. By uncovering the Hedgehog targetome in vivo, we revealed GLI2 transcriptional activation of atypical cadherin and planar cell polarity genes in the mesenchyme. Moreover, by using a combination of mouse genetics, live imaging and 3D-culture based approaches, I have demonstrated a requirement for planar cell polarity in instructing organized cell migration for mesenchymal clustering, which is critical for each emerging villus. Therefore, mesenchymal planar cell polarity induced by Hedgehog signaling drives morphogenetic cell behaviours required for proper villus formation. While developmental signalling pathways are essential for instructing the formation of complex organ systems, their reactivation later in life can result in disease. Indeed, recent work has revealed reactivation of developmental signalling pathways in many human gastrointestinal cancers. YAP is a co-transcriptional activator in the Hippo signalling pathway, and is frequently upregulated in gastric cancer, however, its role in tumorigenesis is unclear. By investigating the function of activated-YAP, I have shown its ability to induce gastric adenocarcinoma in a cell type-specific manner. Moreover, Yap deletion in a pre-clinical model of gastric cancer results in suppression of tumorigenesis, implicating YAP as a potential therapeutic target. Together, my results demonstrate that Yap is a potent oncogene in stomach tissue, highlighting the importance for strict regulation of Hippo signalling during adult homeostasis. Collectively, my work has defined the mechanisms by which Hedgehog and planar cell polarity pathways mediate intestinal morphogenesis, as well as YAP in driving gastric adenocarcinoma, which contributes to our understanding of how aberrant developmental signalling can drive disease.

Keywords: Development
Gastric cancer
Morphogenesis
PCP
YAP
Advisor: Kim, Tae-Hee
Rhodium(II)-catalyzed Ring-opening of Cyclopropenes for Dearomative Cyclopropanations, and Synthesis of Pro-Nematicides with Imidazothiazole Core

The use of transition metals for the dearomative functionalization of planar aromatic systems has been applied in the synthesis of complex 3D structures that find application throughout the pharmaceutical and agrochemical industry. Several reports from the Lautens group have demonstrated this concept, with a focus on the palladium- and nickel-catalyzed dearomative difunctionalization of indoles.Chapter 1 describes the rhodium(II)-catalyzed dearomative cyclopropanation of benzofurans, indoles and styrene derivatives from the ring-opening of cyclopropenes. Using cyclopropenes as the carbene precursor leads to the formation of a donor vinyl carbene, which can be difficult to synthesize by other methods. This approach offers a complementary one to the classic methods of cyclopropane synthesis, that are typically not amenable to the synthesis of vinyl cyclopropanes. The method described requires mild conditions, and the catalyst loading was further lowered on scale-up without any effect on yield or stereoselectivity. In Chapter 2, the ring-opening of cyclopropenes for the dearomative cyclopropanation of naphthols using rhodium(II) and acid catalysis is described. In contrast to the reactivity of naphthols previously reported, this methodology allows for functionalization at the 3- and 4-positions of naphthols instead of the 1-position. The various sites of reactivity in the vinyl cyclopropane products could be uniquely exploited with several transformations, forming new carbon-carbon or carbon-heteroatom bonds. Substrate modification can allow for the formation of the [4+1]-cycloaddition product between the in-situ generated rhodium carbene and ortho-quinone methide intermediates. Experimental evidence for the proposed mechanism is described. Chapter 3 describes the synthesis of imidazothiazole compounds for control of plant parasitic nematodes, an ongoing collaboration with the Roy group at the University of Toronto. The synthesis of a putative bioactive metabolite and various derivatives was conducted, and the compounds were tested against the free-living nematode Caenorhabditis elegans by the Roy group. Many analogues in the unsaturated imidazothiazole series were synthesized and tested against the plant parasitic nematode Meloidogyne incognita by the Roy group, with some derivatives showing excellent activity and selectivity towards the target organism. The lead and parent compounds in the series were synthesized on larger scale for rat oral toxicity assays.

Keywords: cycloaddition
cyclopropane
cyclopropene
dearomative
nematicide
rhodium
Advisor: Lautens, Mark
Reproducing, Resisting, Challenging, and Changing: Intersectionality and Narratives of Women School Principals in Turkey

This dissertation explores the experiences of female school leaders in Turkey within the framework of Intersectional Feminist Theory and Bourdieu’s Theory of capital using a narrative approach and focusing on the continuum of their past, present, and future. Data collection included semi-structured interviews with fifteen women school principals from three different regions of Turkey (West, Central, and Southeast Anatolia) and demographic information form, document analysis, and fieldnotes. Age, marital status, socioeconomic status, ethnic background, political background, religious background, and social background emerged as the seven primary identity markers intersecting with gender. The study revealed that participants come from low, lower-middle, and middle socioeconomic backgrounds, with most of them from lower-middle backgrounds. Their economic and cultural capital played a significant role in their educational path and choosing teaching as a career. Despite familial and institutional support they received, household and institutional barriers hindered their leadership paths and experiences. In addition, two other significant discourses emerged, which I categorized as “being in between support or a barrier.” These discourses were significant in terms of depicting the construction of gender norms and roles and how participants hover between praise and blame for being a woman, and how they start to “act like a man,” or their hard work is praised by “seeing them as a man but not a woman.” The study also revealed that the intersection of gender with religious and political background played a significant role in participants’ leadership experiences. Besides, the old-boys’ club emerged as an important discourse regardless of time and place. In addition to its common association, the old-boys’ club is mainly expressed in relation to women’s sexuality in men’s eyes in the Turkish context. Last but not least, the participants’ narratives showed that they had complex and contradictory thoughts regarding gender roles. Regardless of their backgrounds, they can propound conflicting and complicated ideas regarding gender norms and reproduce gender stereotypes. On the other hand, they resist, challenge, and are eager to change hegemonic gender norms in society.

Keywords: Education
Intersectionality
Leadership
Narrative Approach
Turkey
Women
Advisor: Joshee, Reva Dr.
Distance Protection of Systems with Inverter-based Resources

This dissertation focuses on the challenges faced by distance relays and their supervising elements, including directional, phase-selection, and loss-of-voltage (LOV) elements, in the systems with inverter-based resources (IBRs). A comprehensive dual current control scheme is proposed for IBRs during the low-voltage ride-through (LVRT) mode to address the challenges. This method addresses the shortcomings of existing solutions and enables correct operation of distance, directional, and phase-selection elements during all types of faults. The proposed method controls the IBR to operate as a voltage source behind a virtual impedance in the positive-sequence circuit and a single inductive virtual impedance in the negative-sequence circuit, thereby emulating the phase angles of an SG's fault current. The proposed method also maximizes the active and reactive current generation of the IBR during faults and emulates the relative incremental sequence current magnitudes of an SG. It is unveiled, for the first time, in this dissertation that IBRs can jeopardize the security of the LOV detection element, which is another supervising element for distance relays. A new LOV detection method is proposed to address this problem. The proposed solution centers around the fault current signature of IBRs and performs superior to the existing LOV detection elements. This method operates reliably regardless of the type of generation units in the system and is sufficiently fast to prevent relay misoperation during LOV conditions. The impact of different implementations of distance element on protection of systems with IBRs is also investigated in this dissertation. The focus is on the relays implemented using the phase comparators and the reactance method. It is unveiled, for the first time, that the ground and phase elements of a distance relay that uses these methods are prone to under-/over-reach in the systems with IBRs. A detailed analysis on the root causes of the problems as well as the measures to alleviate them is provided. Besides, it is shown that IBRs can adversely impact the operation of not only the distance relay that protects their tie-line but also the relays of the neighboring lines. The above studies are all supported by hardware-in-the-loop testing of commercial relays.

Keywords: distance relay
inverter
inverter-based resources
power system protection
protective relay
renewable energy
Advisor: Hooshyar, Ali
Iravani, Reza
The Neurobiological Correlates of Structural Covariance Networks

There exist many studies examining population-level correlations between the cortical thickness or volumes of brain structures. Yet, the reasons for why these correlations—termed structural covariance—form are unclear. Current thoughts on the formation of these correlations can be broadly grouped into two hypotheses. The first hypothesis posits that regions that correlate in their structural properties do so because they are connected by bundles of neurons, and plasticity acting along this structural backbone causes regions to grow or shrink in a coordinated manner. The second hypothesis suggests that regions found to correlate in their structural properties are those that grow together during neurodevelopment. In this thesis, I examine structural covariance in the mouse brain, with the goal of comparing these two mechanisms. I show that in adult mice, structural covariance networks are associated with both structural connectivity and transcriptomic similarity, and that structural covariance is already present at birth and generally decreases over neurodevelopment. I then specifically focus on the thalamus and its connections to the cortex and show that cortical structural covariance reflects the functional organization of the thalamus, and is sensitive but not specific to structural connectivity. Additionally, I show that plasticity (resulting from exercise) decreases thalamocortical structural covariance. Finally, I show (using multiple models of agenesis of the corpus callosum) that structural covariance is preserved in the absence of structural connectivity. I end the thesis with a discussion on the plausible mechanisms underlying the formation of structural covariance, and considering all the results presented in this thesis, I make the case that it is the intrinsic coordinated neurodevelopment of structures that results in the main patterns of structural covariance seen in later life.

Keywords: Anatomical covariance
Connectivity
Mouse
MRI
Neurodevelopment
Structural covariance
Advisor: Lerch, Jason P
Tonian Macroalgae from the Mackenzie Mountain Supergroup in the Wernecke Mountains, Yukon Territory

Early eukaryotic fossils are crucial to understanding the evolution of the Earth's biosphere and geosphere. Molecular clock estimates suggest that crown-group members of key algal lineages evolved and diversified by the Tonian Period (1000 to 720 Ma), but this diversification is poorly reflected in the fossil record. Previously undocumented, centimeter-scale macrofossils were recovered from the outer shelf marine facies of the ca. 950 Ma Dolores Creek Formation, Wernecke Mountains (northwestern Canada, Chapter 2). Three distinct size classes were identified. The larger fossils are interpreted as eukaryotic macroalgae with a likely green algal affinity, making them among the oldest macroalgae yet recognized and filling a critical gap in algal evolution. Analytical microscopy, including scanning electron microscopy and tomographic x-ray microscopy, were used to investigate fossil preservation and develop a taphonomic model (Chapter 3). The fossil preservation consists of pyritization and aluminosilicification, similar to accessory mineralization observed in the Paleozoic Burgess Shale-type preservation. The macroalgae are defined as a new genus and species based on their morphology including an unbranching, uniseriate thallus with uniform width and elliptical to globose holdfasts (Chapter 4). Larger specimens are classified as probable vendotaenids while smaller mm-scale specimens display branching but remain undefined as a form taxon as theylack distinguishing morphological characteristics. The unstable redox conditions that defined the macroalgae's paleoenvironment in the Wernecke Mountains were constrained using geochemical analyses (Fe speciation, major/trace elements, and TOC, Chapter 5). Considering the macroalgae within a paleoenvironmental context allows us to place realistic constraints on these organism's paleoecology and paleobiology. The Dolores Creek macroalgae along with the recently reported ca. 1000 Ma multicellular chlorophyte from North China and ca. 1000 Ma photosynthetic, eukaryotic algae from the Congo Basin, provide evidence that benthic green algae colonized shallow marine habitats by the early Tonian Period. These discoveries indicate that there are glaring omissions in the fossil record that need to be addressed in future studies by recovering new fossils and characterizing their habitats to aid in reconstructing the late Proterozoic biosphere.

Keywords: Mackenzie Mountain Supegroup
Macroalgae
taphonomy
Tonian
Advisor: Laflamme, Marc
The Economic Evaluation of Adult Immunization Programs: The Importance of Local Context and the Example of Pneumococcal Vaccination

Infectious diseases represent a unique challenge in healthcare policy decision-making, as the risk of disease is subject to change based on factors specific to the local context, which can evolve over time. Given this dynamic nature, it is critical to tailor economic evaluations of interventions targeting these diseases to the jurisdiction and timeframe in which they will be applied. The research comprising this thesis sought to address these challenges through a systematic review, population-based studies of health administrative data, and an economic evaluation. This was implemented through the example of evaluating a potential pneumococcal vaccination program, with a specific focus on publicly funding the 13-valent pneumococcal conjugate vaccine (PCV13) for older adults (65+). Streptococcus pneumoniae is a gram-positive bacterium that represents one of the most common causes of community-acquired pneumonia (CAP), imposing a significant health and financial burden across the world. Due to the decline in vaccine-type pneumococcal disease among older adults since PCV13's inclusion in the Ontario infant immunization program, the cost-effectiveness of publicly funding PCV13 for immunocompetent older adults remains unclear. The first study was a systematic review examining the impact of pneumococcal disease on health state utility values, focusing specifically on the syndromes of acute otitis media, CAP, bacteremia and meningitis. The second study was a population-based retrospective matched cohort study assessing the incidence of disease and healthcare costs attributable to CAP from the Ontario healthcare payer perspective using health administrative data. Exposed subjects were found to have substantially higher healthcare costs than comparable unexposed subjects for up to one year post index date. The third study applied the data developed in the first two studies to conduct an economic evaluation of adding PCV13 to the current immunization program in Ontario. The cost-utility analysis employed a microsimulation health state transition model, with the results indicating that adding PCV13 is unlikely to be cost-effective due to the substantial decline in disease caused by vaccine serotypes. Overall, this thesis demonstrates an approach to assessing the cost-effectiveness of vaccination programs, highlighting the influence of local factors such as serotype distribution on cost-effectiveness.

Keywords: Economic Evaluation
Health Technology Assessment
Pneumococcal Disease
Public Health
Vaccination
Advisor: Sander, Beate
The Ion Channel TRPV5 Regulates B Cell Signalling and Activation

B cell activation leads to the production of antibodies that protect us from infection. Recognition of antigen by B cells begins with the B cell receptor (BCR) recognizing and binding antigen, which initiates BCR signalling and antigen internalization. Calcium is an important secondary messenger during B cell activation and calcium signalling in B cells is best characterized by the store operated calcium entry (SOCE) pathway that triggers ion channels on the plasma membrane, predominantly known to be calcium release-activated calcium (CRAC) channels. Patients that have mutations in the proteins of this pathway present with severe immunodeficiency; however, murine B cells deficient in CRAC channel components mount normal antibody responses, suggesting that alternative channels may be important. We identified a member of the calcium permeable transient receptor potential (TRP) ion channel family, TRPV5, as a candidate channel expressed in B cells by a qPCR screen. We found TRPV5 polarized to BCR clusters upon stimulation in a RhoA dependent manner and siRNA knockdown of TRPV5 in a murine B cell line impaired calcium flux upon BCR stimulation. To further investigate the role of TRPV5 in B cell responses, we generated a murine TRPV5 knockout (KO) by CRISPR-Cas9. TRPV5 KO mice had normal B cell development and mature B cell numbers. TRPV5 KO B cells had impaired spreading and contraction in response to membrane-bound antigen. Surprisingly, calcium influx upon BCR stimulation in primary TRPV5 KO B cells was not impacted; however, differential expression of other calcium-regulating proteins, such as ORAI1, which we found was expressed 5-fold higher in TRPV5 KO B cells than WT B cells, may contribute to a compensatory mechanism. Despite no difference in calcium signalling, BCR signalling measured by phospho-tyrosine residues was reduced in TRPV5 KO B cells. Consistent with this, immunization induced T-dependent (TD) antigen-specific antibody titers were reduced in TRPV5 KO mice compared to WT mice. Thus, our findings identify a role for TRPV5 in BCR signalling and B cell activation.

Keywords: B cells
Calcium
Ion channels
TRP channels
Advisor: Treanor, Bebhinn L