VictorJuiz/thesis huggingface dataset:
Development of Optical Methods for Interrogating Neurovascular Coupling in Health and Disease

The communication between neurons and blood vessels to supply cells in the brain with energy is a complex interaction called neurovascular coupling (NVC) that is critical for healthy brain function. Its understanding is crucial for the interpretation of functional brain imaging signals in humans such as blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI), however its underlying mechanisms are presently not fully described. The present work implements combined optical stimulation and recording methods using optogenetics and two-photon fluorescence microscopy (2PFM) to interrogate neurovascular coupling in vivo with high spatiotemporal precision. We present a focused optogenetic stimulation paradigm to excite precise volumes of brain tissue to localize neuronal excitation to nearby vessels, combined with simultaneous, high-throughput single vessel recordings to characterize red blood cell (RBC) speed responses to local NVC cascades. This paradigm was first applied in mice to cortical penetrating arterioles and venules, major regional supply and draining vessels to the cortex respectively, and found that arterioles have higher absolute and lower relative RBC speed responses to focused photostimulation than venules, wider regional dependencies of arterioles over venules, and larger, more reliable neuronal and vascular responses to focused photostimulation versus conventional fibre-optic photostimulation. This paradigm was applied to a mouse model of repeated mild traumatic brain injury (mTBI) that also introduced a GABAA receptor (GABAAR) inverse agonist as a pharmacological intervention and showed neuronal hyporeactivity and venular hyperreactivity 2 weeks post-injury, which were resolved via GABAAR inverse agonism. Lastly, we expanded on the present methodology to characterize RBC speed responses to local neuronal activation along the arteriovenous axis and describe a volumetric functional readout using a machine learning vascular segmentation algorithm. This elucidated larger RBC speed responses in precapillary arterioles than capillaries and a positive linear correlation with distance from photostimulation in the former, and described differential contributions to the volumetric CBV response among different vessel diameters. Combined, these studies reveal novel characteristics of NVC in vivo based on high spatiotemporal control of neuronal activation. Furthermore, these methods have sufficient sensitivity to describe novel functional changes in mTBI, highlighting the efficacy of focused photostimulation for interrogating NVC.

Keywords: Neurovascular coupling
Optogenetics
Traumatic brain injury
Two-photon fluorescence microscopy
Advisor: Stefanovic, Bojana
Sled, John G
The Well-Being of Community-Residing Not Criminally Responsible Patients: Recognizing Ethical Dimensions

In Canada, community-residing not criminally responsible (CR-NCR) patients are provided treatment to reduce their public safety risk and assist their reintegration into society; however, it is unclear whether the social circumstances of these patients sufficiently support this rehabilitative process. Previous research findings suggest deficiencies exist in CR-NCR patients’ well-being, but further work is required to better understand how their circumstances are socially arranged and to examine the pertinent ethical dimensions.Using the theoretical work of Powers and Faden (2006; 2019), the empirical aim of this critical ethnography was to explore the lives of CR-NCR patients for the purposes of developing an understanding of the interplay between the social factors present in the community settings in which they live and their well-being. The corresponding normative aims include examining theoretically the adequacy of patients’ socially arranged well-being, elucidating the justness of their circumstances, and considering the implications of this on their societal reintegration. A total of 23 go-along interviews with CR-NCR patients (N=10) were conducted. These data, along with field notes and relevant documents, were analyzed using a multi-stage, iterative process of deconstructing and reconstructing meaning, with ethical evaluations supported by the practice of reflective equilibrium. The findings reveal that CR-NCR participants were situated unfairly in circumstances that almost invariably resulted in deficiencies in their well-being and undermined their efforts to reintegrate. Recommended remedial changes include enhancing the respectful, patient-centred, and recovery-oriented aspects of care. Further studies are needed to more comprehensively understand the impact of social arrangements on the lives of CR-NCR patients and to examine in greater detail the consequences these arrangements have on the rehabilitative aims of the forensic mental health system.

Keywords: community mental health
forensic mental health
not criminally responsible
public health ethics
social justice
well-being
Advisor: Peter, Elizabeth
Investigating the Sources of Mesenchymal Cells that Contribute to Adult Murine Digit Tip Regeneration

While regeneration of appendages is relatively common among invertebrate, it is relatively restricted in mammals. Adult murine distal digit tip regeneration is one example of mammalian multi-tissue regeneration. Blastema formation is the critical step distinguishing regenerative from non-regenerative amputations. While the sources of the blastema cells in other regenerative vertebrates such as amphibians and zebrafish have been widely studied, the cellular origin and phenotypic identity of mammalian blastema cells are not well understood. In this thesis, using adult mouse digit tip regeneration as a model, I investigate the origin and nature of the mammalian blastema cells. First, I show that distinct Pdgfra-expressing mesenchymal cells in the uninjured distal digit tip contribute to the majority of the mouse blastema. Single cell profiling indicates that the Pdgfra-expressing blastema mesenchymal cells acquire a precursor-like transcriptional state distinct from both the uninjured and developing digit tip mesenchymal cells. Thus, digit tip regeneration occurs via a distinct adult mechanism. Second, I show that various differentiated Pdgfra-expressing mesenchymal cells in the uninjured digit tip, such as the bone lineage cells and nail bed dermal cells, upon contribution to the blastema, lose their differentiated phenotypes, re-enter the cell cycle and acquire the blastema transcriptional signature, suggesting dedifferentiation of cells during regeneration. Third, transplantation studies indicate that the regenerating environment dictates the blastema transcriptional state and confers mesenchymal lineage plasticity to some blastema mesenchymal cells. This allows these select cells to contribute to multiple mesenchymal tissues irrespective of their own tissue-of-origin. Fourth, I show that certain cells such as the nail bed dermal cells show spatial restriction in the regenerating blastema and regenerated digit tip suggesting that some cells might harbour positional memory during mammalian tissue regeneration. Finally, we show that the non-regenerating tissue acquires some aspects of the regenerative blastema transcriptional state. These findings lay the groundwork for further research investigating the differences between regenerative and non-regenerative responses with the hopes of enhancing mammalian tissue repair and regeneration.

Keywords: Development
Mesenchymal Cells
Single cell RNA sequencing
Stem Cells
Tissue Regeneration
Tissue Repair
Advisor: Miller, Freda D
Theory of Electronic Response to Electromagnetic Fields in Crystalline Solids

In a classical theory of light-matter interactions, the introduction of macroscopic polarization and magnetization fields, and free charge and current densities, provides physical insight into the distribution and the dynamics of the charges that constitute a material medium. Here we consider a semi-classical theory of such interactions in crystalline materials and introduce microscopic polarization and magnetization fields, and free charge and current densities, from which the macroscopic analogues can be found. We do so by identifying "sites" in an extended system with respect to which spatially localized portions of the charge and current densities can be associated, and define "site" polarization and magnetization fields from them. The sum of these "site quantities" are taken to constitute the microscopic polarization and magnetization fields. The identification of such site quantities employs a set of spatially localized basis functions, which additionally allow the identification of free charge and current densities that are here associated with charge movement from site to site. In the beginning chapters of this thesis we present the formalism and consider various limiting cases. We consider the "molecular crystal limit" of the more general expressions and recover the expected results. We also consider the linear response of an insulator in the "long-wavelength limit", and find the well-known electrical conductivity tensor. Finally, we consider the macroscopic ground state polarization and magnetization of an "ordinary" insulator, and find agreement with the expressions of the "modern theories of polarization and magnetization". In the chapters that follow we implement this formalism to study various phenomena in a class of insulators, including the orbital magnetoelectric effect and optical activity. The linear response of such systems is captured by that of the microscopic polarization and magnetization fields; from the multipole moments of the macroscopic analogues of these fields, we identify the relevant susceptibility tensors. At various levels of approximation, we show that these general tensors reduce to known results. We also consider the optical response of metallic systems, for which the induced free charge and current densities play a nontrivial role. We derive the usual conductivity tensor, which involves both "Drude" and "anomalous Hall" contributions.

Keywords: Condensed matter physics
Optical properties of solids
Theoretical physics
Advisor: Sipe, John E
How the Role of the Pharmacist is Negotiated in Ontario Family Health Teams: A Multiple Case Study

Including pharmacists on interprofessional primary care teams has demonstrated improvements in patient safety and clinical outcomes but there are concerns about under-utilization. Using Goffman’s micro-sociological theories of self and impression management, this dissertation explored the negotiation of the pharmacists’ role in Ontario Family Health Teams (FHTs). This dissertation used a multiple case study per Yin. Recruitment of five cases was used to ensure cross-case analysis. Cases were varied on geography, FHT size, and team tenure. Data was collected using both semi-structured interviews and document analysis. At least four participants were interviewed in each case. All data was stored in MAXQDA. Thematic analysis was completed using the Quality Analysis of Leuven (QUAGOL) framework. Positionality was completed through reflection and assisted by Social Identity Map. Three cases were recruited and analyzed. Case A demonstrated the organization led the negotiation of the pharmacist’s role, Case B demonstrated that physicians led, and Case C demonstrated a lack of active negotiation of the pharmacist’s role. The cross-case analysis highlighted pharmacists were not actively involved in negotiating their role due to their professional identities. This led to uncertainties of who should lead role negotiations. Organizations with more formal procedures tended to have proactive pharmacist’s roles including independent access to patients. The pharmacists’ supportive identity and ongoing comparison to physicians may have resulted in their lack of archetype. This contributed to unclear goals for role negotiation. Additionally, this contributed to physicians being the audience for the pharmacist’s role and a focus on tasks and delivery that physicians valued. Most patient-care decisions were referred back to physicians. The lack of focus on patients’ experiences and outcomes was likely an important aspect of role negotiation. Stakeholders such as patients, pharmacists, their institutions, and organizations, can use these results to negotiate roles efficiently. Organizations could use programming to assign new tasks to the pharmacist for successful implementation. Future research should look at the pharmacist’s professional identity and its relationship to patient-centered care.

Keywords: Collaboration
Health Care
Organizational behaviour
Pharmacy Practice
Role Negotiation
Advisor: Austin, Zubin
Barnsley, Janet
Fate of Food Cooking Emissions in the Atmosphere

Food cooking emissions represent an important source of particulate matter in urban areas, contributing 10-35% of total organic aerosol. Cooking emissions also contribute significant levels of volatile organic compounds (VOCs) such as carbonyls which are important precursors to formation of secondary organic aerosol (SOA). In this work, I use heated cooking oils as a model to investigate the reaction pathways that drive formation of VOCs and cooking organic aerosol (COA), and their evolution in physicochemical properties. I demonstrate that VOCs and primary COA emissions are driven by autoxidation reactions involving radical species, and the composition of cooking oils strongly influences the reaction mechanisms. Antioxidants, routinely employed in food industry to delay oil oxidation have complex effects on autoxidation reaction mechanisms. Furthermore, in this work, physicochemical properties and chemistry of COA are investigated. I demonstrate that evaporation of oxidized cooking oil particles is much slower than unoxidized oil particles, despite containing a higher fraction of volatile reaction products than unoxidized cooking oil particles. Additionally, a new analytical approach was developed to characterize the chemical composition of SOA. It is shown that SOA formed from cooking oil vapors undergo fragmentation reactions with increasing atmospheric oxidative aging. Moreover, detailed chemical speciation and total production of SOA from heated cooking oils are explained from aldehydes and its oxidation products which are significant contributors to VOCs from cooking emissions. Overall, knowledge about both oxidation pathways provide useful insights into the importance of fragmentation reactions during evolution of cooking emissions in the atmosphere.

Keywords: Aldehydes
Cooking emissions
Evaporation rates
Primary organic aerosol
Secondary organic aerosol
Advisor: Chan, Arthur
A χαλεπὸν καὶ ἀμυδρὸν εἶδος: Plotinus’ Theory of Matter

I put forward a unified account of Plotinus’ theory of matter with a focus on why it is necessary to explain how things exist at each level of his metaphysics. I argue that matter is a quasi-principle, insofar as it is a necessary condition for the generation of all products of the One, the first principle. It is not a principle on a par with the One, however, because matter is itself generated by the One. It is also not on a par with the One because matter, as non-being, does not make a causal contribution to the generation of all existents. I arrive at this conclusion by investigating what Plotinus says about the role that matter plays in the generation of the sensible realm. The existents in the sensible realm are bodies, which are composed of qualities and extended in three dimensions. I argue that Plotinus thinks bodies can only exist if there is a matter that exists to receive all these qualities, while nonetheless never joining with any of them. The bodies in the sensible realm also undergo change by losing and gaining the qualities. I claim that Plotinus explains this by rejecting the Aristotelian idea that matter becomes a numerical unity with the forms it receives. I also explain how matter can be understood as responsible for the existence of evil in bodies and souls, despite its lack of causal influence. The evils that exist in the sensible realm are a necessary result of the proliferation of goodness, which matter makes possible by providing a space for the higher principles to produce in. I also examine what Plotinus says about matter as it exists in the intelligible realm, where the Intellect and the intelligible Beings reside. I show that previous assumptions about the nature of this matter are wrong and that we must presuppose that the same matter exists among the intelligibles as exists among the bodies of the sensible realm. I then explain how matter – both sensible and intelligible, since they are the same – is generated directly from the One as a place for its product.

Keywords: Matter
Neoplatonism
Plotinus
Advisor: Gerson, Lloyd P
Bayesian Inference for Extended Latent Gaussian Models

Additive regression models cover the analysis of many types of data which exhibit complex dependence structures. Models for continuous, bounded or unbounded count, multivariate and multinomial, time-to-event, and other types of data exhibiting nonlinear covariate effects, group-specific dependence as well as serial dependence in time and space, and other types of complexities can all be fit under this single framework. Such generality is handled using a Bayesian hierarchical model which accommodates quantification of uncertainty for all unknown parameters but introduces computational challenges. In this thesis I introduce a novel class of additive models called Extended Latent Gaussian Models and an algorithm for fitting these models using approximate Bayesian inference. The new class covers a much broader range of models than previous classes and the new algorithm is faster and scales to larger datasets than previous algorithms. I implement the method in open-source software which is transparent and accessible to statisticians and include a detailed discussion of the theoretical properties of the approximations, a subject which has remained unaddressed in the literature for similar existing approaches. I demonstrate the utility of the new model class and algorithm in seven substantial examples. To illustrate the breadth of the ELGM class specifically I fit a fully Bayesian log-Gaussian Cox process for inferring the spatial pattern in Malaria risk in Madagascar at a high resolution where the observed data are aggregated to predefined administrative regions; a Cox Proportional Hazards model with partial likelihood and a latent spatial process for inferring the spatial pattern in Leukemia survival times in Northern England; and a multivariate model for estimating the mass of the Milky Way Galaxy accounting for measurement uncertainties. I then fit four additional examples more briefly to illustrate the use of the new software: a simple model for infectious disease spread; another astrophysical model; an over-dispersed, zero-inflated mixed Poisson regression where the mean, dispersion, and zero-inflation parameters depend on covariates and random effects; and a zero-inflated geostatistical binomial regression for mapping the spatial pattern in risk from a tropical disease in West Africa, for which no Bayesian implementation previously existed.

Keywords: Approximate
Bayesian
Quadrature
Spatial
Advisor: Stafford, Jamie
The Role of Notch Signaling on Recent Thymic Emigrant Cell Maturation and Function in a T Cell Transfer Model of Colitis

Recent thymic emigrants (RTE) are a distinct subset of T cells that leave the thymus and enter the periphery where they undergo further post-thymic maturation. RTE cells play a crucial role in neonatal life as well as during adult lymphopenia. As such, it is important that we understand the events that govern their maturation and functionality. In this thesis, I investigated whether there was any role for Notch signaling during RTE and RTE-regulatory T cell (Treg) maturation andfunctionality. In order to address this question, we used an RBPJind mouse model, in which Notch responsiveness and, in effect, T cell development are under the control of Doxycycline, to generate various RTE and RTE-Treg subsets. We then used these newly generated cells in a T cell transfer model of colitis to test their immunocompetence. Here, I show that maturing RTE cells display a significant bias towards IL-17 production, a bias that is completely Notch-dependent and that is lost at the next developmental stage. In addition, I found that extrathymic Notch signaling is one of the pathways that contributes to RTE and RTE-Treg maturation. I also showed that the loss of Notch responsiveness impacts the pathogenicity of developing RTE cells and RTE-Treg regulatory capacity. Furthermore, I demonstrated a time-specific role for Notch signaling in RTE-Treg regulatory ability, with this sensitivity to Notch signals being lost upon full maturation to Treg cells. In summary, this body of work has contributed to our understanding of RTE and RTE-Treg biology and shown a critical role for Notch signaling in mediating their cellular maturation and functionality.

Advisor: Zuniga-Pflucker, Juan Carlos
Genetic Analysis of Triple-Negative Breast Cancer and Pineoblastoma

Metastatic triple-negative breast cancer (TNBC) is a devastating disease affecting relatively young women. The tumor suppressor genes TP53 and RB1 are commonly lost together in a subset of TNBC with exceedingly poor prognosis. The identification of oncogenic drivers that cooperate with p53/Rb-loss in TNBC may uncover novel therapeutic modalities. Here, I employed sleeping beauty (SB) mutagenesis screens to identify oncogenic drivers that cooperate with p53- versus p53 plus Rb-deletion to promote primary mammary tumors and lung metastases, using a WAP-Cre deleter line to induce transposon mobilization. SB mutagenesis accelerated tumorigenesis in the absence of functional p53 or p53 plus Rb. 66.7% of metastases formed in p53/Rb-deficient mice had transposon insertions in genes involved in the Ras pathway (Hras1 and Sos2) or cell motility/migration (Rock2, Fam19a5, and Ntn1). In accordance, bioinformatic analysis revealed that the Ras pathway is enriched in TNBC samples and cell lines. Inhibition of ERK1/2 via ulixertinib suppressed growth of TNBC cell lines with high Ras activity; suppression was more pronounced in cells with stable RB1 knocked-down relative to parental RB1 wild-type cells. These results suggest that alterations in genes involved in Ras pathway activation and motility promote metastatic p53/Rb-deficient TNBC, and point to ERK1/2 inhibitors as potential therapeutic intervention for this subgroup of metastatic TNBC patients. I also used WAP-Cre to generate a mouse model for Pineoblastoma (PB), a lethal pediatric brain cancer. Germline mutations in RB1 and DICER1 have been implicated in the etiology of PB, and deletion of Rb and p53 via WAP-Cre has been shown to induce pineal tumors that resemble human PB with 100% penetrance. Here, I inactivated Dicer1 plus p53 or Dicer1 plus Rb and p53 in the pineal gland via WAP-Cre. Dicer1/p53 and Dicer1/Rb/p53-deficient mice developed PB with 33.3% and 93.8% penetrance, respectively. These tumors clustered close to human PB, and exhibited sensitivity to the tricyclic antidepressant drug nortriptyline in vitro. This study describes the first mouse model for Dicer1-deficient pineoblastoma, demonstrates that WAP-Cre can be used to target the cell-of-origin of distinct PB subtypes, and identifies nortriptyline as a potential new therapeutic for children with DICER1-deficient pineoblastoma.

Keywords: Breast Cancer
Nortriptyline
Pineoblastoma
Sleeping Beauty
Triple-Negative Breast Cancer
Advisor: Zacksenhaus, Eldad