VictorJuiz/thesis huggingface dataset:
Everyday Tragedies: People with Severe Traumatic Brain Injury in the Liminal Spaces of a Level I Trauma Centre

Sustaining a severe traumatic brain injury (sTBI) can have a devastating and permanent impact on a person’s ability to function, on their selfhood, on their families, and on the spaces where they can exist in the world. Individuals with sTBI in Ontario are often transported to Level I Trauma Centres, as textually mediated by the provincial Life or Limb Policy, to ensure access to expert lifesaving medical care. After entering these trauma centres, transitions across the spaces of the trauma centre, from critical care to intensive care to a trauma ward, can signify recovery through decreased reliance on medical technology and medical care. Rehabilitation is required as individuals with sTBI become medically stable to ensure further improvement. This rehabilitation is needed to prepare these individuals to move to other healthcare spaces, such as inpatient rehabilitation, repatriation hospitals, or to return home. Textually mediated institutional relations through the Ministry of Health and Long-Term Care (MOHLTC), specifically the Acquired Brain Injury (ABI) Resource Rehab Tool, ignite sites of struggle in the provision of rehabilitation for individuals with sTBI. These sites of struggles reveal ruling relations that remain hidden until the institution is brought into view using an empirical method of inquiry, institutional ethnography. Specific methods in this dissertation included: participant observation, interviews, a focus group, and analysis of texts. Findings of this study suggest language in the ABI Resource Rehab Tool, specifically the discursive organizer “rehab ready” cleaves individuals with sTBI into two groups: (1) those with faster recoveries able to gain access to inpatient rehabilitation, and (2) those with slower recoveries who do not meet these restrictive guidelines and become unaccounted for in healthcare spaces, with limited options for rehabilitation. Trauma centres are medicalized spaces, whereby provincial funding is distributed on the basis of medical procedures, not rehabilitation. One notable contradiction in funding is revealed for individuals with stroke, who access beds for rehabilitation in acute care and other initiatives outlined by the provincial stroke strategy. No such provincial strategy exists for individuals with sTBI, leaving these individuals marginalized through more limited access to rehabilitation within the healthcare continuum.

Keywords: institutional ethnography
liminality
qualitative research
rehabilitation
social relations
traumatic brain injury
Advisor: Rappolt, Susan G
Bisaillon, Laura
States and Fates of Primitive Neural Stem Cells and Their Progeny in the Mammalian Brain

The mature brain contains an incredible number and diversity of cells that are produced and maintained by heterogeneous pools of neural stem cells. Two distinct types of neural stem cells (NSCs) in the developing and adult mouse brain include primitive (p)NSCs and definitive (d)NSCs. PNSCs form clonogenic neurospheres when grown in LIF, arise ~E5.5, and persist into the adult brain. In this and other work we show adult pNSCs are very rare and quiescent, express Oct4, and give rise to GFAP+ definitive (d)NSCs that form neurospheres in EGF and FGF2. While pNSCs can serve as a reserve pool for an ablated dNSC population in the adult brain, characterization of this activation process remains of interest, and herein I propose this occurs through transition between unique molecular states. To better understand the functions of NSCs embryonically, we performed clonal lineage tracing within neurospheres grown in either LIF or EGF/FGF2, to enrich for neural progenitor cells (NPCs) directly downstream pNSCs or dNSCs, respectively. These clonal progenitor lineage tracing data allowed us to construct a hierarchy of progenitor subtypes downstream of pNSCs and dNSCs that were validated using single cell transcriptomics. Combined, these data provide single cell resolution of NPCs downstream of rare pNSCs that would likely be missed from population level analyses in vivo.

Keywords: Development
Lineage analysis
Neural stem cells
Neuroscience
Quiescence
Stem Cells
Advisor: van der Kooy, Derek
Essays on Experimentation

This thesis studies different directions of experimentation in contests (Chapter 1), experimentation in a principal-agent environment (Chapter 2), and information acquisition during the experimentation process (Chapter 3). While Chapter 1 and Chapter 3 focus on how players choose between different risky arms in different environments, Chapter 2 analyzes how to induce the agent to conduct the efficient amount of experimentation using retention policies. Chapter 1 studies firm innovation in terms of different directions of experimentation, where directions that expedite innovation success are often more costly. In a winner-takes-all contest where player action choices are public, players choose the faster but socially less efficient arms, leading to over-investment in inefficient directions of experimentation. We find that a social planner can restore full efficiency by setting a dynamic reward structure that offers a relatively small share of the prize to the winner initially, when players are still optimistic, and gradually increases the winner's prize share as beliefs drop over time in absence of a success. Finally, while information disclosure makes no difference in a two-armed bandit model winner-takes-all contest, we find that concealing player action choices in a three-armed bandit model improves efficiency. Chapter 2 studies a dynamic principal-agent problem where a principal hires an agent to experiment. We study how the principal can employ a retention policy to induce the agent to make the optimal decision in strategic experimentation, and show that, if the principal cannot commit to a retention policy, efficient experimentation cannot be achieved. However, when the principal can commit to a retention policy upfront, with probationary periods followed by infinite tenure, efficient experimentation can often be achieved. Chapter 3 builds an exponential bandit model with an experimentation arm and an information arm, where the information arm provides positive but inconclusive evidence about the state of the world, to study whether and when an agent would benefit from acquiring information. We find that a pessimistic agent often chooses the information arm as a last-ditch effort before he quits. Moreover, the presence of the information arm induces the agent to experiment more than what he would have otherwise.

Keywords: Experimentation
Advisor: Shi, Xianwen
Interactions between the Structural Domains of the Hedgehog-ligand Receptor, Patched-1, Mediate its Distinct Activities

The Hedgehog (Hh)-signalling pathway is a crucial, evolutionarily conserved signalling cascade important in animal development and de-regulated in oncogenic diseases. Central to this pathway is the principal receptor for Hh-ligands, Patched-1 (Ptch1), which in the absence of ligand, acts to repress the pathway via an indirect repression of Smoothened (Smo). Mammals also express a second Patched isoform, Ptch2, which is non-essential during development and for which the role in Hh-signalling is less characterized. Ptch1 is a 12-pass transmembrane receptor containing distinct structural modules which include two luminal “loops” responsible for binding to Hh-ligand, three large intrinsically-disordered cytoplasmic domains, and two five-pass transmembrane sterol-sensing domains (SSDs) found in a family of proteins involved with cholesterol transport and homeostasis. Despite the central role of Ptch1 in controlling the Hh-pathway, the structural aspects that determine its activities remain largely uncharacterized. The Ptch1 cytoplasmic domains, two of which (the “middle loop” (ML) and C-terminus) mediate formation of Ptch1 multimers, are unnecessary for the core functions of Ptch1. A mutant of Ptch1 lacking both of these domains is still able to repress Smo and respond to Hh-ligand. Nonetheless, these domains may have a role in regulating canonical Hh-signalling as Ptch1 missing only the ML domain acts as a constitutively active mutant which cannot be repressed by Shh-ligand. This constitutive activity is reversed upon subsequent deletion of the Ptch1 C-terminus. The two halves of Ptch1 can interact non-covalently to mediate ligand-dependent regulation of Hh-signalling. However, both Ptch1 SSDs are required for repression of Smo. Despite the high level of sequence conservation between the SSDs of Ptch1 and the cholesterol transporter NPC1, these domains are not functionally interchangeable. Finally, we describe the structural foundations for the differences in activity of Ptch1 and Ptch2. This difference in activity is not dependent on the transmembrane or luminal domains as these appear to be functionally interchangeable between Ptch1 and Ptch2. The differences in function are determined by their cytoplasmic domains, which are sufficient to allow Ptch2 to repress Smo. These observations begin to define how interactions between the structural domains of Ptch1 contribute to its functions.

Keywords: Hedgehog
Patched
Ptch1
Advisor: Hamel, Paul A
Sex-Specific Behavioural Traits of the Sirtuin-3 Knockout Mouse Model

The NAD+-dependent mitochondrial deacetylase sirtuin-3 (SIRT3) has been recognized to regulate a number of metabolic processes in peripheral tissues, however its role in the brain remains less well investigated. The results of this thesis show that sirtuin-3 displays a unique temporal and spatial pattern of mRNA and protein expression in the developing, adult, and aged brain, that encompasses both neurons and astrocytes. These data indicate sirtuin-3 is a potentially targetable product in the brain for pharmacological interventions. SIRT3 activity does influence brain function, as behavioural alterations were observed in both male and female Sirt3-KO mice. Interestingly, only female Sirt3-KO mice were found to display hyperlocomotor and exploratory behaviour in the open field, reduced anxiety-like behaviour in plus maze and light/dark paradigms, and impaired balance on the accelerated rotarod task. These observed phenotypes were also progressive across age. In addition, both male and female Sirt3-KO mice demonstrated hyper-sensitivity to low dose amphetamine treatment compared with wild-type animals, as increased locomotor responses and lowered anxiety responses were evident in the mutants but absent in wild-type mice. These behavioural alterations correlated with an upregulation of the mTORC1 signaling pathway in the cortex in the female Sirt3-KO mice, which could underlie the observed novelty-driven hyperactive phenotype. In summary, this thesis discloses an as-yet unrecognized role for sirtuin-3 in the regulation of behavioural activity, anxiety and motor functions that is sex-dependent and influenced by both age and environment.

Keywords: Behaviour
Genetics
Mice
mTOR
SIRT3
Sirtuins
Advisor: Eubanks, James H
Measurement of the Higgs boson produced in association with a Z boson and decaying to WW∗ with a leptonic final state in pp collisions at √ s = 13 TeV with the ATLAS detector

An analysis of the Higgs boson produced in association with a Z boson, with the Higgs decaying to WW∗ and the W and Z bosons decaying leptonically — i.e. the ZH → ZWW∗ → ```ν`ν process — is presented, using the combined 2015 and 2016 datasets from the ATLAS experiment, totalling 36.1 fb−1 of data from pp collisions at √ s = 13 TeV. Control region normalisation and a data-driven technique are employed alongside Monte Carlo estimation to predict the number of signal and background events. A cut-based approach is used to discriminate signal events from background, with cut values optimised to maximise expected significance. A statistical fit of the data, including thorough treatment of sources of systematic uncertainty, is performed, yielding a signal strength of µZH = 3.0 +1.9 −1.4 , where the Standard Model prediction is µZH = 1.

Keywords: Associated production
ATLAS
Higgs physics
HWW
Standard Model
ZH
Advisor: Krieger, Peter
Principal Leadership for Teacher Collaborative Inquiry

This study investigated principal leadership for Collaborative Inquiry (CI) as a strategy for teachers’ ongoing professional learning and school improvement. A qualitative methodology was employed to generate insight into how the Ontario elementary school principals have led and supported this strategy in their school contexts. The findings show that principals’ roles in the CI process include (1) fostering the CI culture; (2) providing teachers with time and resources; (3) acting as an active co-learner, co-facilitator, and coach; (4) supporting models of shared decision-making and distributed leadership; (5) adapting CI to the school context; (6) setting the direction for the CI inquiry teams; and (7) sustaining CI. The capacity principals need to lead and support CI includes knowledge of CI and data, facilitation skills, and a growth mindset and perseverance for CI, which can be acquired in various ways including: reading CI resources, engaging in the CI process, attending professional learning sessions, accessing Ministry resources, participating in professional networks of colleagues, and listening to teachers who are involved in the CI process. The challenges and barriers principals encounter include (1) lack of time and resources for the teachers to conduct CI, (2) facilitation skills to develop a culture of inquiry and learning, (3) getting teachers to buy into the CI culture, (4) embedding a true learning CI culture at school, and (5) the stance of teacher unions which is claimed to be one source of teachers’ resistance to engagement in the CI process. To overcome these barriers and challenges, principals use some common strategies such as (1) finding time creatively for the teachers to conduct CI, (2) keeping things as focused and practically manageable as possible, (3) setting norms for building trust and ensuring a variety of opinions, (4) not using the term CI but associating CI with the existing norms and practices of collaboration and learning at school. Overall, the findings of this study corroborate and extend upon findings in the literature indicating how principals lead and support CI endeavors in schools.

Keywords: Leadership
Principals
Professional Learning for Teachers
Teacher Collaborative Inquiry
Teachers
Advisor: Anderson, Stephen
Interactome Analysis Identifies Novel Targets of Phosphoinositide 3-kinase (PI3K) that Mediate Astrocyte Neuroprotection

In a homeostatic state, astrocytes can support neuronal survival and function through a range of secreted signals that protect against neurotoxicity, oxidative stress, and apoptotic cascades. Thus, the analysis of astrocyte conditioned media (ACM) may provide valuable insight into the nature of these protective mechanisms, and how they might be promoted. Previously, we characterized a potent neuroprotective activity mediated by ACM in neurons and the retina in metabolic stress models. However, the molecular entity and mechanism underlying this activity remained unclear. Here, a chemical genetics screen revealed phosphoinositide 3-kinase (PI3K) as a central player transducing ACM-mediated neuroprotection. To identify additional proteins contributing to the protective activity, endogenous neuronal PI3K was immunoprecipitated from astrocytes exposed to ACM or control media, and MS/MS analyses were undertaken. MS data analyses pointed toward only five additional proteins that co-immunoprecipitated with PI3K and were regulated by the ACM signal. These hits included expected PI3K interactors, such as the platelet-derived growth factor receptor A (PDGFRA), and novel interactors, such as the zinc finger CCCH-type containing 14 (ZC3H14). ZC3H14 has recently emerged as an important RNA binding protein that modifies poly-adenosine tail lengths on nascent mRNA transcripts. In downstream validation studies we show that Platelet Derived Growth Factor-BB (PDGF-BB) strongly activates PI3K signaling to protect neuronal cells. Finally, PDGF-BB treatment induced recruitment of ZC3H14 to PI3K, and inhibiting this interaction eliminated ACM-mediated neuroprotection. Thus, we identified a novel ACM- and PDGF-induced neuroprotective signaling cascade mediated through PI3K that involves recruitment of ZC3H14. Enhancing this pathway may present a promising strategy to promote astrocyte-secreted neuroprotective signals.

Keywords: Astrocyte
Astrocyte Conditioned Media
Glaucoma
Neuroprotection
PI3K Interactome
ZC3H14
Advisor: Sivak, Jeremy
Engineered In Vitro Models of Human Skeletal Muscle for Drug Testing, Developmental Biology, and Physiology Studies

Skeletal muscle is the most abundant tissue in the lean human body and is responsible for all motor functions such as locomotion, speech, and respiration. During development, myogenic progenitor cells fuse to form multinucleated muscle fibers that are innervated by the motor neurons of the spinal cord to form functional motor units. Various genetic and acquired diseases of motor neuron, neuromuscular junction (NMJ), and skeletal muscle affect motor unit function with significant effects on patients’ quality of life. Recent advancements in the field of tissue engineering now enable precise control of microenvironment and biochemical cues that emulate physiological conditions and have led to the successful formation of functional human skeletal muscle and neuromuscular tissues in vitro. In 2013 when I initiated my Ph.D. studies, the field had yet to establish parameters to produce engineered human skeletal muscle tissue in a dish capable of responding to electrical and biochemical stimuli. Further, human neuromuscular co-culture models to study NMJ transmission and diseases impacting this critical structure were replete. Since 2013, my work and that of other researchers has overcome barriers to forming functional of human-cell derived skeletal muscle and neuromuscular tissues in vitro. The work in this thesis leveraged, extended, and then applied prior advancements in tissue engineering and engineering techniques, in general, to improve our understanding of skeletal muscle, the neuromuscular junction formation and the maturation of each, in vitro. An important goal of my studies was to encourage widespread adoption of methods I developed by researchers and industry. As such, the tools and technologies were engineered to be simple and integrate into current standard operating procedures and the experimental studies were focused on uncovering biological inquiries that were new and/or were not possible to study with other currently available culture or animal models.

Keywords: Drug Testing
Exercise
Neuromuscular Junction
Optogenetics
Skeletal Muscle
Tissue Engineering
Advisor: Gilbert, Penney M
Investigating the Role of Wnt Signalling and Identifying of Novel Fitness Genes in Glioblastoma

Glioblastoma (GBM) is the most common malignant tumour of the central nervous system and in spite of aggressive treatment, recurrence remains high. Glioblastoma stem cells (GSCs) have the ability to self-renew and differentiate into the different cell types observed in the tumour and have decreased sensitivity to chemotherapy and radiotherapy. Thus, characterization of GSCs can provide insights into targeted therapy that are tailored to each individual and that will prevent relapse. The Wnt signalling pathway is essential during embryonic development and tissue homeostasis to control stem cell renewal, proliferation and differentiation and is involved in maintaining cancer stem cells in many organs and tissues. Using an orthotopic Wnt reporter model we showed that GBM cells with higher Wnt activity have a higher self-renewing ability relative to cells with lower Wnt activity. In my work I identified a subset of GSCs that are dependent on Wnt signalling for self-renewal and a subset that is independent. Characterization of these subtypes discovered that the Wnt-dependent subset had a gene signature similar to the proneural subtype of GBM and relies on the canonical Wnt signalling pathway whereas the Wnt-independent subtype was similar to the mesenchymal subtype. Xenograft models also demonstrated that inhibition of Wnt signalling reduced tumour burden using Wnt-dependent GSCs but not in Wnt-independent GSCs. We also showed that dual inhibition of Wnt/-catenin and Notch signalling pathways in Wnt-dependent GSCs increased neuronal differentiation and reduced self-renewal. This first project in my thesis identified new contexts for Wnt modulation in GBM specifically its role in self-renewal and differentiation. In my second thesis project we identified context-specific genetic vulnerabilities in GSCs using CRISPR-Cas9 approaches. Specifically we characterized members of the SOX transcription factor family and cholesterol biosynthesis pathway as essential for GSC proliferation. This study provided a large data set that remains to be explored for additional therapeutic targets. In summary, this thesis identified and characterized a subset of GSCs dependent on Wnt signalling for survival and discovered novel genetic vulnerabilities in a panel of GSCs using CRISPR-Cas9 screens.

Keywords: CRISPR-Cas9
genome-wide screens
Glioblastoma
Notch signaling
self-renewal
Wnt signaling
Advisor: Angers, Stephane
Dynamics of Sediment-Laden Gravity Currents; Influences of Sedimentation and Coriolis Force

When a sediment-laden river enters a stratified lake or the coastal ocean, the density difference between the river and the ambient determines whether a surface, sub-surface or bottom-hugging turbidity current can form. In this thesis, I will explore the sedimentation mechanisms occurring beneath surface and sub-surface currents, and how Coriolis force can potentially modify sedimentation patterns from the bottom hugging turbidity currents. It is shown that when a sediment-laden plume overlies a salty ambient, both processes of double-diffusive convection and settling-driven convection can increase the settling rate of particles. Direct velocity measurements found that the velocity of sinking sediment fingers are always larger than the Stokes settling velocity. The parameter that controls the dynamics of settling is density ratio, defined as the ratio of density differences due to the added salt and sediment. For 7.8 µm Silicon Carbide particles, sediment fingering only dominates when the density ratio is near one; otherwise settling-driven convection is the dominant sedimentary process. Thus, sediment fingers control sedimentation beneath lake interflows, whereas settling-driven convection dominates in most oceanic overflows. Furthermore, scaling is developed for the propagation length-scale over which sediment particles fall out of suspension beneath a buoyant sediment-laden river plume due to vigorous settling-driven convection of sediment. When density ratio is close to one, settling-driven convection is vigorous and the propagation length-scale is very small. Finally, in order to understand how the Earth’s rotation might influence erosion and depositional patterns in large oceanic channels, the world’s largest rotating platform was used to show the influence of Coriolis force on the near-bed velocity structure in oceanic density currents flowing in straight and sinuous channels. The experiments were quantified in terms of a dimensionless Rossby number defined in terms of either the channel width (for straight channels) or the radius of channel curvature (for bent channels). Coriolis force can change the direction of the near-bed flow when the bend Rossby number is less than +0.8. Using these results, coupled with changes in density fields, a process model of the evolution of sinuous channels is developed under the effect of Coriolis force in different latitudes.

Keywords: Coriolis force
Double-diffusive convection
Ekman layer
Sediment-laden gravity currents
Settling-driven convection
Sinuous submarine channels
Advisor: Wells, Mathew G