VictorJuiz/thesis huggingface dataset:
Structural Neuroimaging to Generate Biomarkers of Response to Deep Brain Stimulation

Deep Brain Stimulation (DBS) is the use of continuous, typically high-frequency direct electrical current, delivered through neurosurgically implanted electrodes, aimed at altering activity within dysfunctional brain circuits. DBS is now an established therapy for several neurological conditions such as Parkinson’s Disease, dystonia, and tremor, and is emerging as a viable therapy in several others including depression and disorders of memory. However, the response to DBS is highly variable across individuals with the same disease, a fact often attributed to clinical factors such as age or illness severity, or to technical factors such as DBS electrode position. The central hypothesis underlying this thesis is that brain structure, as evaluated by structural magnetic resonance imaging (MRI), is also a key factor influencing clinical response to DBS therapy across various neurological and psychiatric diseases. The specific aims of the thesis project were to determine: 1) whether pre-DBS brain structure relates to, or predicts, eventual clinical response to DBS; and 2) whether ongoing DBS therapy produces detectable structural changes in the brain that may influence clinical response. In study #1, we demonstrate that in patients undergoing DBS of the subcallosal cingulate region (SCG) for depression, future response to DBS is predicted by pre-treatment variations in brain structure, especially volume of the SCG, thalamus, and the total volume of cortical grey matter. Studies #2 and #3 provide preliminary, first-in-human evidence, in two different patient populations (Parkinson’s Disease and Alzheimer’s Disease), that DBS is associated with structural neuroplasticity demonstrable on post-operative MRI scans, and may even result in the reversal of focal atrophy in selected patients. Study #4, however, illustrates the difficulties inherent in replicating these results on a larger scale because of methodological concerns related to the reliability and concordance of automated algorithms currently used to analyze structural neuroimaging data. Despite these concerns, this thesis illustrates that structural neuroimaging with MRI indeed has the potential to generate clinically useful biomarkers of response to DBS therapy, which may ultimately influence patient selection for DBS, guide DBS programming, and inform prognosis after DBS implantation.

Keywords: biomarker
Deep Brain Stimulation
magnetic resonance imaging
Advisor: Lozano, Andres M
Rapid Prediction of Lipid/Protein Interactions by Molecular Dynamics Simulation

Membrane proteins (MP) are a class of biomolecules responsible for important biological processes in living organisms; malfunction of MPs triggers pathological development in the human body. Since the properties of MPs are coupled to membranes, efforts have been devoted to study the interaction of MPs with membranes to reveal the solvation, fold, and function of MPs in the native/membrane environment. However, the chemically-heterogenous biological membrane usually hampers the application of biophysical techniques. This is particularly true for computer simulation approaches such as molecular dynamics (MD) simulations, where a large amount of computations are required to derive meaningful information at the atomic level. Here, I present an MD protocol to accurately predict the interaction of peptides and proteins with membranes in short computation times. The protocol is comprised of a physically-reasonable yet computationally-efficient model representation of membranes by using an octane membrane mimetic and efficient conformational sampling based on an ensemble of MD simulations. This approach is shown to predict the solvation, orientation, and self-assembly of helical peptides into bundles, peptide-mediated pore formation, as well as protein-protein interactions in membranes. I first validate the protocol by predicting the interaction of an amphipathic peptide with membranes. This work leads to identifying four orientation states of melittin in the membrane and spontaneous peptide-mediated pore formation on a short time scale, demonstrating the accuracy and efficiency of the protocol. I then use the method to predict the structure of α-helical MPs based on the spontaneous self-assembly of transmembrane (TM) helices in membranes. The structure and aggregation number of a homotetramer, the M2 channel, are correctly predicted. Simulations containing four M2 and two glycophorin A helices show that the approach captures the selectivity of helix-helix association . I finally apply the protocol to predict the structures of two homo-dimers, Rcf1 and Rcf2, in membranes. Results demonstrate unique solvation patterns suggesting that these two proteins adopt the monomeric form when bound to membranes. The aforementioned applications demonstrate the power and domain of application of the method for predicting lipid/protein interactions.

Keywords: helix self-assembly
membrane mimetics
membrane protein
molecular dynamics
oligomerization state
structural prediction
Advisor: Pomès, Régis RP
Endovascular Optical Coherence Tomography Imaging in Cerebrovascular Disease

Neurointerventional surgery is a subspecialty focused on the diagnosis and treatment of vascular diseases of the central nervous system. The appeal of treating vascular diseases through minimally invasive techniques without the need for open surgery has led to continued technological innovation and device development. Endovascular optical coherence tomography (OCT) is the highest resolution intravascular imaging modality available, utilizing near-infrared light with a wavelength of approximately 1300 nm and excellent spatial resolution of 10µm is achievable. With near histologic resolution, OCT has been described as an optical biopsy modality. The adoption of endovascular OCT imaging in the evolving field of neurointerventional surgery seems instinctive. The goal of this doctoral thesis was to utilize OCT as an adjunct in the diagnosis and treatment of cerebrovascular diseases. Towards that goal, preclinical animal and human investigations were performed. We assessed the feasibility of OCT imaging in quantifying vascular injury after endovascular thrombectomy (EVT) in a swine model. OCT was found to be feasible in assessing vascular injury after EVT with histological accuracy. Varying degrees of vessel wall injury occur after EVT, and residual luminal thrombus was present despite complete angiographic revascularization. Next, we designed a preclinical swine model of cerebral venous sinus thrombosis (CVST) with subsequent EVT and OCT imaging. OCT revealed that residual bridging cortical vein thrombus may be present despite complete sinus recanalization on angiography. This thrombus may be the etiology of poor clinical outcome despite technical success. Establishing preclinical feasibility with novel findings of undetected residual thrombus allowed for research ethics board approval for human OCT imaging. OCT imaging in patients with basilar stroke was undertaken. OCT was safe and capable of producing cross-sectional images displaying evidence of endothelial injury and residual thrombus. OCT may guide future antithrombotic treatment for patients with demonstrated residual thrombus. OCT carries great promise in the future of neurointerventional surgery.

Advisor: Yang, Victor XD
Roles of Phosphatidylinositol 4-phosphate in Secretory Granule Biogenesis

Professional secretory cells are responsible for regulated secretion of biologically active molecules to maintain homeostasis. These molecules, which include neuropeptides, digestive enzymes, and hormones, are stored in long-lasting secretory granules (SGs) that undergo exocytosis in response to external stimuli. The molecular mechanisms of SG biogenesis are poorly understood. Using Drosophila larval salivary glands as a model system, our laboratory has previously discovered that the type II phosphatidylinositol 4 kinase (PI4KII) is required for normal SG biogenesis. PI4KII is responsible for the generation of phosphatidylinositol 4-phosphate (PI4P) from phosphatidylinositol (PI) at the trans-Golgi network (TGN) and endosomes. To examine how PI4KII and its product PI4P regulate SG biogenesis, I employed genetic approaches and cell biology techniques to identify and characterize potential factors acting in this pathway. I discovered that Past1, syntaxin-16 (Syx16) and oxysterol binding protein (Osbp) are regulators of PI4KII and PI4KII-mediated SG maturation. I conducted a candidate RNA interference (RNAi) screen that identified many endocytic genes needed for proper SG maturation, suggesting that SG maturation requires endocytic contribution. A secondary screen suggested that Past1 and Syx16 are potential factors acting in the same pathway as PI4KII to facilitate SG maturation. Further characterization demonstrated that both PI4KII-dependent early endosomal sorting and accumulation of PI4P on SG membranes are associated with proper SG maturation. In addition, Past1 and Syx16 are needed for formation of PI4KII-positive endosomal tubules involved in this process. I also examined Osbp, which is a PI4P effector that regulates non-vesicular transport of PI4P and cholesterol across membrane contact sites (MCS). Loss of Osbp resulted in lowered levels of PI4P on SG membranes and an absence of PI4KII-positive tubules, similar to Past1 null mutants. Moreover, a cholesterol probe, D4H, showed that these tubules are enriched in cholesterol. My results indicate that Osbp is required for cholesterol accumulation at endosomal membranes to enable formation of PIKII-positive and cholesterol-rich membrane tubules. Overall, my results establish Past1, Syx16 and Osbp as regulators of PI4KII and describe a novel PI4KII-mediated early endosome retrograde trafficking pathway important for cellular PI4P distribution and SG maturation.

Keywords: membrane lipids
membrane trafficking
organelle biogenesis
Advisor: Brill, Julie A
Investigation of Amorphous Solid Dispersions for Solubility Enhancement of Poorly Water-soluble Drugs: Understanding the Effect of Material Properties on Amorphous Drug Crystallization and the Impact on Formulation Performance

The preparation of amorphous solid dispersions (ASDs) has enabled the development of oral dosage forms for many poorly water-soluble compounds. The aim of the work presented in this dissertation is to advance our understanding of ASDs, specifically their long-term stability with respect to crystallization and the implications of instability on product performance. Advancing knowledge in these areas is pivotal for the pharmaceutical industry and its efforts in drug discovery. Much of our understanding of ASD stability results from empirical or extrapolative models that have been applied to describe stability. Their application has been limited and they do not provide fundamental insights into the recrystallization process to aid in the rationale development in ASDs. Notably, they fail to consider supersaturation as the driving force for crystallization, diffusivity in viscous systems, and interfacial effects. The works presented in this dissertation model the mechanisms of crystal nucleation and growth in ASDs by incorporating these concepts, develop and apply characterization tools to determine critical model parameters, and study the effects of crystallization on product performance.

Keywords: Amorphous Solid Dispersion(s) (ASD)
Crystallization
Mechanistic modeling
Nucleation
Physical stabilit
Solubility
Advisor: Lee, Ping I
The Politics of Funding Urban Infrastructure in Canada and the United States: Implications for Resilience and Sustainability

Infrastructure is a core municipal expenditure and an important component of local climate change strategies. There is a general consensus that cities never have enough funding to meet their infrastructure needs. Attention is rarely paid, however, to how cities fund and finance infrastructure, which can vary meaningfully between cities in different jurisdictions. While U.S. cities are highly reliant on issuing voter-approved municipal bonds to finance infrastructure, Canadian cities often depend on transfers from higher levels of government. This dissertation uses a mixed-method comparative approach to investigate how the policies governing cities’ capital revenue sources (which I label “multilevel fiscal institutions”) shape local infrastructure policy processes and climate change outcomes. Using an original dataset of infrastructure investments in four North American cities dating back to 1957 (Calgary, Edmonton, San Antonio and Austin) and drawing on in-depth qualitative interview data from Calgary, AB, and San Antonio, TX, I argue that how cities fund and finance infrastructure is critical to what they build, with important implications for local investments in sustainability and resilience. Multilevel fiscal institutions set the capital revenue options available to cities, which in turn influence accountability channels and power distribution. I find that local policy actors (namely, local bureaucrats) respond to these power and accountability dynamics by shaping policy processes and structuring investment choices in order to advance the projects that are best poised to secure the highest levels of funding. Because different projects are more likely to advance under different capital revenue arrangements, multilevel fiscal institutions have important consequences for infrastructure outcomes and how cities choose to advance their sustainability objectives. These findings highlight the various democratic trade-offs involved in different multilevel fiscal arrangements and push back against the commonly held assumption that more fiscal autonomy is inherently good. While local fiscal autonomy and voter approval requirements can heighten citizen influence and accountability over infrastructure investment processes, they may not be conducive to equity and sustainability over the long-term. I close with policy recommendations and areas for further research.

Keywords: Infrastructure
Intergovernmental transfers
Multilevel governance
Municipal bonds
Sustainability
Urban policy
Advisor: Stren, Richard
Living in the In-between: Implications of Counter Narratives of Immigrant Youth with Disabilities in the Canadian Nation State

In 2016, the Provincial Advocate for Children and Youth published a longitudinal study sharing the stories of children and youth with disabilities across Ontario, Canada. Largely missing were the stories of LGBT+, Indigenous, newcomer and/or racialized youth with disabilities. This is a common practice, which continues to erase those who experience a confluence of systemic barriers. When disabled youth are written about it is usually from a service user perspective, especially regarding mental health (see Beiser et al., 2011; Shakya, Khanlou, Gonsalves, 2010; Simich, Beiser, Stewart, Mwakarimba, 2005) through a biomedical lens. Moreover, there is a dominant practice to write about disability as a single identity that defines the experiences of the individual. This leaves out attention to the migration experiences of racialized immigrant youth with disabilities. The study used open-ended semi-structured interviews with 10 (5 males and 5 females) racialized immigrant youth (ages 16-24) with disabilities living in the Greater Toronto Area in Ontario, Canada. Participants illustrate how dominant discourses of disability as a deficit, burden, and undesirable impacts their sense of self-worth, which is intrinsically tied to their employment, their educational journey and how they do/not access navigate health and social services. Their stories also bring to the forefront the complexity of migration pathways and signals the need to rethink migration as occurring on multiple planes leading many to occupy an in-between space. This study contributes to our understandings of disability as they are shaped by changes in Canada’s Immigration and Refugee Protection Act that continues to define and classify disabled people and the lack of critical scholarly research in the critical disability studies and immigrant youth literature in Canada. Through first-person storytelling, this study challenges racism and ableism.

Keywords: Critical Disability Studies
Disability
Immigration
Youth
Advisor: McCready, Lance T
Osteocyte Form and Function in Loading and Unloading Environments

Long-term human spaceflight presents unprecedented challenges to the human body, such as microgravity-induced bone loss. Without intervention, astronauts lose between 1 – 2% bone mineral density per month in weight bearing bones and the cellular mechanisms involved in this process are still poorly understood. To date, the most abundant cell of bone, the osteocyte, has rarely been subjected to spaceflight. Yet osteocytes are known to be important regulators of bone loss in immobilized and elderly people. The first objective of this thesis was to develop novel 3D culture methods to study osteocytes using the Rotary Cell Culture System (RCCS). This device is commonly used for both suspension culture and simulated microgravity by clinorotation. The second objective was to investigate morphological and gene expression changes in MLO-Y4 cells following suspension culture or clinorotation. We found that the ideal 3D scaffold consisted of 2% type I collagen mixed with 6% synthetic hydroxyapatite (collagen-HA). The scaffold was successfully formed into droplets for suspension culture, whereas it was adhered to the RCCS vessel walls for clinorotation. After 3 days of suspension culture, MLO-Y4 cells embedded in the collagen-HA droplets showed reduced expression of the mechanosensitive genes DMP1, E11, IL-6, and RANKL and the number of cells was elevated compared to the static control. We estimated that the drag force acting on the aggregate of droplets was in the range of 2.1 – 4.4 dynes/cm2, speculated to provide a small but significant stimulatory effect on the cells located on the surface, which may de-sensitize them over the course of 3 days. Following clinorotation for 3 days, MLO-Y4 cells showed reduced expression of DMP1 and E11 genes while the cell number was unchanged compared to the static control. Since clinorotation and spaceflight cause the de-differentiation of other bone cells, we speculated that our MLO-Y4 cells were also de-differentiating during clinorotation, resulting in the lower expression of osteocyte-specific genes.

Keywords: bioreactor
bone
microgravity
osteocyte
synthecon
Advisor: Harrison, Rene E.
The Role of Adaptor Protein 3BP2 in CD36-mediated Modified Lipid Uptake and Macropinocytosis

Macrophages are defined by their ability to survey, sample and recognize pathogens within their environment. They can achieve this through several modes of internalization, including constitutive macropinocytosis. Constitutive macropinocytosis relies on a sequence of tightly regulated signalling events at the plasma membrane, ultimately culminating in a wave of actin polymerization, membrane ruffling, and bulk fluid-phase internalization of soluble ligands. Adaptor proteins are vital to facilitating the spatial and temporal organization of signaling modules that regulate membrane internalization pathways and membrane dynamics. Adaptor protein SH3-Domain Binding Protein 2 (3BP2) functions in this way and is capable of coordinating and amplifying signalling cascades in macrophages, affecting transcriptional regulation reorganization of the actin cytoskeleton. In this dissertation, I explore how modulation of Src family kinase activity by 3BP2 regulates the macropinocytic internalization pathway in macrophages. In Chapter 1, I discuss the relevant background pertaining to immune surveillance, macrophage function and internalization pathways, as well as atherosclerotic progression. Chapter 2 outlines the rationale and aims of my work. In Chapter 3, I uncover the role of constitutive macropinocytosis in oxidized low-density lipoprotein internalization and foam cell formation. Additionally, I highlight the mode of scavenger receptor CD36 regulation at the plasma membrane. I document the novel role of 3BP2 as a tunable variable that regulates Src-family kinase (SFK) signalling and constitutive macropinocytosis that ultimately affects the progression of inflammation and atherosclerosis in vivo. Finally, in Chapter 4, I discuss the implications of these findings and future research that should be considered. Taken together, this dissertation highlights the ability for 3BP2 to act as a biochemical rheostat for SFK activation and the role of constitutive macropinocytosis in oxLDL uptake and foam cell formation in the progression of atherosclerosis. Macrophages are defined by their ability to survey, sample and recognize pathogens within their environment. They can achieve this through several modes of internalization, including constitutive macropinocytosis. Constitutive macropinocytosis relies on a sequence of tightly regulated signalling events at the plasma membrane, ultimately culminating in a wave of actin polymerization, membrane ruffling, and bulk fluid-phase internalization of soluble ligands. Adaptor proteins are vital to facilitating the spatial and temporal organization of signaling modules that regulate membrane internalization pathways and membrane dynamics. Adaptor protein SH3-Domain Binding Protein 2 (3BP2) functions in this way and is capable of coordinating and amplifying signalling cascades in macrophages, affecting transcriptional regulation reorganization of the actin cytoskeleton.

Advisor: Rottapel, Robert K
The Stable Rank of Diagonal ASH Algebras

Building on the work of Lutley in [Lut17b], we study a certain subclass of recursive subhomogeneous algebras, called DSH algebras, in which the pullback maps are all diagonal in a suitable sense. We examine inductive limits of DSH algebras, where each bonding map is itself diagonal in an appropriate way, and show that every simple algebra thus obtained has stable rank one. We are therefore able to show that every simple dynamical crossed product has stable rank one and that the Toms-Winter Conjecture holds for such algebras. We also introduce the class of non-unital DSH algebras and make partial progress towards showing that inductive limits of such algebras with diagonal maps have stable rank one. Moreover, we investigate more intrinsic notions of a diagonal map and matrix unit compatibility and show that in the full matrix algebra setting they agree with their usual (global) counterparts.

Keywords: C*-Algebras
Functional Analysis
Advisor: Elliott, George A