VictorJuiz/thesis huggingface dataset:
Consequences of Multiple Stability and Connectivity on Coral Reef Ecosystem Dynamics
Keywords: anthropocene
climate change
coral reefs
dispersal
mathematical models
theoretical ecology

Coral larval dispersal networks are changing due to multiple anthropogenic stressors that are destroying coral habitat and shifting reefs from coral-dominated to macroalgal-dominated states that support smaller fish communities. However, it is unclear whether these connectivity changes could themselves propagate or contain shifts to macroalgal-dominated states. My research investigates how the combined effects of connectivity and local multiple stability affect coral persistence with the goal of informing conservation decisions. In Chapter 2, I explore how plausible scenarios of climate-change-induced loss could change coral larval dispersal networks and their reseeding potential. I find that these scenarios of loss (yielding the same number of reefs) lead to vastly different global reef networks, from which full reseeding is impossible. In Chapter 3, I develop a two-reef mathematical model and determine that two connected reefs may exhibit a novel third, mixed coral-macroalgal stable state at low dispersal. Furthermore, I find that high- and low-grazing reefs have stable coral-dominated and macroalgal-dominated states if connected by high dispersal to a low or high-grazing reef (respectively). In Chapter 4, I extend this two-reef model to a model of 75 Fijian reefs to determine the interplay among connectivity, local multiple stability, and management strategies in larger networks across three grazing scenarios spanning the stability regimes elucidated in Chapter 3. I find that increasing the grazing rate of a few reefs leads to higher overall coral cover in the entire network, even in reefs with low grazing rates. I also find evidence that a combined strategy of increasing the water quality and increasing a few reefs’ grazing rates is more effective than either strategy in isolation, across all grazing scenarios. Overall, my research increases our general understanding of how ecosystems with multiple stable states respond to connectivity changes, stresses the importance of collecting connectivity and grazing rate data for coral reefs and pioneers novel methods for informing reef management design. Specifically, my thesis stresses the importance of connectivity and local stability dynamics to coral reef management by showing that natural larval dispersal can tip connected reefs to higher coral states but is not sufficient to restore coral habitat worldwide.
Towards Establishing and Validating an MRI Scoring System for Assessment and Interval Monitoring of Temporomandibular Joints in Juvenile Idiopathic Arthritis
Keywords: Juvenile Idiopathic Arthritis
Magnetic Resonance Imaging
Outcome Measure
Scoring System
Temporomandibular Joints

Background: Contrast enhanced magnetic resonance imaging (MRI) is the most comprehensive diagnostic tool for the evaluation of temporomandibular joints (TMJ) in juvenile idiopathic arthritis (JIA). However, its acquisition and interpretation remain variable across centres. Purpose: 1) To construct a scoring system for the MRI-observable manifestations of JIA in the TMJ (JAMRIS-TMJ), 2) determine and validate its importance weights, and 3) test its reliability. Methods: First, an inter-reader reliability study with 21 cases and 7 readers was done to test the items of three existing TMJ MRI scoring systems. Then, a Delphi and nominal group technique process was used to construct a consensus scoring system (JAMRIS-TMJ) based on the reliability results and expert opinion. An imaging atlas and protocol were developed through subsequent consensus meetings. Next, the relative weights of the JAMRIS-TMJ were determined among experts using an adaptive, partial-profile discrete choice experiment (DCE). Group-averaged weights were validated using a series of 14 image vignettes. Finally, the reliability of JAMRIS-TMJ were tested in a 20-reader reliability study using 31 TMJ MRI exams across different levels of calibration and differences in reader specialty. Results: Consensus process driven by expert opinion and reliability data yielded a scoring system containing 5 inflammatory and 3 damage items in respective domains. DCE showed a homogenous group-level preference on weights, with items ranging from 9% to 49% of domain score. Vignette ranking exercise showed high correlation of vignette ranks between the partial profile, DCE-weighted method and the image-based ranking method, with median Spearman’s ρ of >0.90 for the two domains. Generalizability (G-) coefficients for domain score reliability were 0.61-0.67 for the inflammatory, and 0.66-0.74 for the damage domain, depending on the level of calibration. Atlas and tutorial did not affect agreement within radiologists but improved agreement between radiologists and non-radiologist clinicians. Reliability by G-coefficient reached >0.8 when taking the average of two reads. Conclusion: A multi-center, multi-specialty effort has led to the proposal of JAMRIS-TMJ, which demonstrated construct validity and moderate-to-good reliability.
Hippocampal Inputs to the Anterior Hypothalamus Modulate Defensive Behaviour and Stress Response
Keywords: Anterior hypothalamus
Defensive behaviour
Fear memory
Hippocampus
Instinctive behaviour
Stress

Fearful experiences trigger defensive behaviours and stress hormone release. It has been known that the hippocampus (HPC) is important for mood and cognition via its connectivity to the downstream targets essential for threat integration and stress response. One key region which receives dense inputs from the HPC and is apt to orchestrate defensive behaviors and modulate stress endocrine response is the anterior hypothalamus (AHN). The AHN is an exclusive recipient of the HPC terminals in the medial hypothalamic defensive system (MHDS) and may act as an intermediary control for the hypothalamic-pituitary-adrenal (HPA) axis during psychogenic stress. However, the functional role of HPC-AHN pathway had never been examined. In chapter 2, we aimed to uncover the functional role of the AHN and the HPC inputs to the AHN. Using optogenetics, we compared the behavioural outcomes of the low and high frequency AHN soma and HPC-AHN pathway stimulations. Through a set of behavioural test paradigms, we demonstrated that the AHN stimulations induced robust defensive behaviours (i.e., freezing, running, jumping) with memorable aversion. The HPC-AHN stimulations induced running only yet carried negative valence and induced conditioned place avoidance. Upon shelter availability, HPC-AHN stimulation induced goal-directed escape. Through optogenetic pathway inhibition, we revealed the necessity of the HPC-AHN circuit in the predator cue associated contextual memory retrieval and during the shelter-directed escape evoked by the presentation of an innately threatening auditory cue (20 kHz ultrasound). In chapter 3, we examined the HPC-AHN pathway in modulation of neuroendocrine and behavioural responses to stress in mice. We showed that the GABAergic neurons of the AHN receive inputs from the HPC through a monosynaptic cell-type specific rabies tracing. HPC-AHN pathway inhibition during physical restraint stress led to an abnormal release of corticosterone and increased stress-induced anxiety behaviours. Consistent with the known effects of chronic HPA-axis dysfunction on cognition, the functional loss of AHN GABA synapses induced memory impairments. Our studies clarify the role of HPC inputs to the AHN in mediating context-dependent defensive behaviours and modulating of the psychogenic stress induced activation of the HPA-axis.
Therapist Responsiveness in Couples Therapy: Perceptions of Male and Female Partners
Keywords: couples therapy
gender
process research
therapist responsiveness
therapist training

Responsiveness refers to the ability of the therapist to understand a client’s concerns and convey this understanding through a thoughtfully selected intervention, treatment, or other action. Although a sizeable literature on individual therapist responsiveness exists, a complementary framework to guide responsiveness in couples therapy is absent. This is surprising given that responsiveness becomes appreciably more complex when the therapist must attend to the moment-to-moment needs of both partners and tailor interventions to fit the needs of each individual as well as the couple. The present study sought to understand how individual partners experience therapist responsiveness in the context of couples therapy. One-on-one semi-structured interviews were conducted with eight individuals from four partnerships currently in couples therapy. Transcripts were coded and analyzed following constructivist grounded theory. A hierarchical model of the experience of therapist responsiveness in couples therapy emerged and subsumed a number of categories. Clear differences between male and female partners were inconclusive. By extrapolating principles from this model, a theory was proposed that identifies factors and processes that contribute to the experience of therapist responsiveness in couples therapy. Limitation and directions for future research are presented.
A Machine Learning Approach to Real-time MRI Guidance for Robotic Needle-Based Procedures
Keywords: Machine Learning
MRI
Needle
Prostate
Segmentation
Tracking

Needle-based interventions such as biopsy and brachytherapy play a vital role in the diagnosis and treatment of cancer. Notably, prostate procedures are particularly challenging as they require the insertion of multiple long, flexible needles to access deep-seated targets. Several robotic systems have been developed to aid needle insertion under intermittent MRI-guidance. To realize the full potential of image-guided robotics, there is a need to integrate with real-time imaging for feedback during insertion.This work describes a novel data-driven approach to the integration of real-time imaging for the guidance of multi-needle robotic interventions. Three critical steps in realizing this approach were developed and demonstrated: i) rapid needle segmentation in MR images, ii) a robotic multi-needle insertion strategy and iii) real-time adjustment of MRI scan plane parameters based on image-input. Rapid, automatic segmentation of multiple needles in multi-slice MR image volumes was achieved using a convolutional neural network. The network achieves a 95% detection rate in a test set at a rate of 0.89s/image volume with shaft errors <1mm and tip errors <2.5mm for over 90% of the needles. Next, a robot was designed for the sequential insertion of multiple non-parallel needles. The kinematics, accuracy, and compatibility with real-time MRI were characterized. Finally, needle tracking was achieved using remote scan control to dynamically update the scan plane of a real-time single-slice MR sequence and the automatic needle segmentation algorithm to evaluate the alignment of the scan plane to the needle. A scan plane was purposefully misaligned and allowed to automatically search for a needle in a gelatin phantom. The algorithm achieved a localization accuracy of 2.9±1.8mm in 6.88s compared to 2.1±1.2mm in 39.13s for manual localization using interactive scan plane manipulation with a refresh rate of 0.89s. Overall, this work demonstrated that using rapid needle segmentation and automated scan control, real-time MRI may be used as a tool to track needle insertion for robot-driven multi-needle procedures. To advance the automated image-guided robot-driven platform through the regulatory process and obtain approval for its use in humans, future work employing this system should focus on proving the clinical benefit and safety of the system.
Increasing the Pack Energy Throughput in Electric Vehicles with Impedance-Based Battery Management
Keywords: Battery
Battery Balancing
Battery Management System
Electric Vehicle
Electrochemical Impedance Spectroscopy

Between 2010 and 2021, the global stock of Battery Electric Vehicles grew from 17,000 units to over 10 million. Innovations in Lithium-ion batteries have been the key technological driver of the fast-paced EV growth. As the physical performance limits of Lithium-ion batteries reach a saturation point, the value of system-level battery pack performance improvements is increasing. Battery systems must be designed to utilise as much of the available energy storage and power delivery capacity of cells as possible, without sacrificing safety and reliability. The focus of this thesis is on first identifying the impact of battery cell capacity/resistance imbalance, and inaccurate battery state estimation, on the usable pack energy. This is done by quantifying the single-cycle and cumulative discharge energy metrics, which capture the work done by the EV battery system. It is found that significant cumulative performance loss is experienced under cell imbalance and state estimation inaccuracy. Solutions are then proposed to alleviate the virtual loss of battery performance:\begin{enumerate} \item A new balancing control algorithm is presented, which utilises a Linearised Equivalent Circuit Model (L-ECM) to capture the capacity and resistance equalisation effect of active balancing systems. The L-ECM control is shown to provide up to 47\% cumulative energy improvement, compared to a time-to-balance SOC equalisation scheme. \item In-situ Electrochemical Impedance Spectroscopy (EIS) architectures are developed and demonstrated experimentally. It is found that performing vehicle-level EIS through the dc charging port captures the high-voltage power electronics impedance, in addition to the battery pack impedance. The feasibility of sub-module-level impedance measurement with a pack-level current perturbation is also demonstrated. \item Battery Equivalent Circuit Model (ECM) extraction techniques are evaluated based on their accuracy in the presence of noisy impedance phasor measurements. A total of 53 ECMs for 20 battery sub-modules are extracted from an experimental in-situ EIS setup across temperatures ranging from 15$^\circ$C to 35$^\circ$C. Approximately 8-11\% improvement in the state-of-power estimation accuracy is identified through a model prediction accuracy analysis. \end{enumerate}
Mind and Prejudice: Cognitive Improvement in the Philosophies of René Descartes and Mary Astell
Keywords: Astell
Descartes
Education
Habit
Prejudice
Women

This dissertation examines the philosophies of René Descartes and Mary Astell with the aim of answering the question: what makes cognitive improvement possible? Both Astell and Descartes acknowledge prejudice as a significant barrier to cognitive improvement such that the possibility of cognitive improvement depends in part on routing such prejudices and their effects. However, for Descartes, part of what explains the challenge presented by prejudices also explains the possibility of cognitive improvement: humans are susceptible to habituation. In chapter one, I argue that Descartes should be read as appropriating a scholastic notion of habitus in accounting for both the challenge of prejudice as well as the goal of cognitive improvement, namely, better cognitive habits. Yet, merely being susceptible to habituation cannot fully explain cognitive improvement. In chapter two, I argue that another significant feature of Descartes’s account of cognitive improvement is what I call Rational Self-Confidence: a subject’s confidence in their ability to use and improve the cognitive capacities. Still, recognizing the importance of rational self-confidence for cognitive improvement suggests another barrier to such projects: not all subjects possess this confidence. In chapter three, I argue that Astell recognizes how a peculiar prejudice, what I call the Women’s Defective Will Prejudice [WDWP], can undermine the rational self-confidence of women especially – those cognitive subjects that most concern Astell. The effect of this prejudice on a subject’s rational self-confidence leads to what I call the Astellian Circle: the apparent truth of the WDWP can undermine a subject’s rational self-confidence and inhibit subjects from pursuing activities that would cultivate their cognitive capacities, thus further reinforcing the apparent truth of the WDWP and so on in circulo. Significantly, a subject caught in this circle is unlikely to engage in projects of cognitive improvement. Accordingly, chapter four argues that Astell’s account of cognitive improvement addresses precisely the influence and effects of the WDWP and the Astellian Circle. In particular, I contend that Astell’s social solutions stand to promote a subject’s rational self-confidence, thus supporting their engagement in projects of cognitive improvement. By recognizing and addressing a more preclusive barrier to cognitive improvement, Astell develops an account of cognitive improvement that expands the pool of potential subjects that could succeed in such projects.
Third-party Arrangements between Private and Public Colleges in Ontario: Benefits, Threats, Implications for Policy
Keywords: Marketization
Ontario Colleges
Privatization
Strategic risk
System Design

Ontario’s Colleges of Applied Arts and Technology (CAATs) were established more than 50 years ago as an alternative public postsecondary choice for students to provide vocational education programs grounded in general education. The CAAT system was positioned as a public good, envisioned to serve individuals and society. In the past 20 years, governments have implemented neoliberal policies requiring CAATs to be more entrepreneurial, efficient, and fiscally sustainable amid declining funding and domestic enrolment, and increased regulation. These pressures, coupled with burgeoning demand from international students motivated to study in and immigrate to Canada, led some colleges to enter third-party arrangements (TPAs) with for-profit private career colleges (PCCs). The PCC partner delivers the public college curriculum to international students at the PCC campus, located in the Greater Toronto Area (GTA), who earn their credentials from the public college. This research study examined the development, growth and impact of TPAs between 2005 and 2019, using an exploratory, descriptive, qualitative research design to understand the factors that led to the TPAs, their impact on public colleges and the implications of these arrangements on the future of Ontario’s public college system. Two overarching theoretical frameworks grounded the research: historical institutionalism (Streeck & Thelen, 2005) and Principal-Agent Theory (PAT) (Mitnick, 1973; Ross, 1973). Three complementary theoretical frameworks were used to situate findings. Data were collected in two phases (1) document analysis and (2) 25 semi-structured interviews with system and policy leaders. Data were used to elucidate the trajectory of the formation, growth and cementing of TPAs into the Ontario college system. Four inflection points, each representing the culmination of various environmental factors, were conceptualized to explain how decisions and conditions contributed to the trajectory. Interviewees identified competition, marketization of higher education, economics, demographics and policies as contributing to the formation, growth and formalization of the TPAs. Interviewees perceived TPAs to introduce significant risks to public colleges, including financial, labour, relational, reputational and quality. More critical are strategic risks posed by the TPAs concerning future funding and enablement of PCCs, which have implications for system design, including further marketization and privatization of Ontario’s public college system.
Singularity Analysis in Mean Curvature Flow
Keywords: ancient solutions
mean curvature flow
singularity analysis

In this thesis, we investigate the formation of singularities in mean curvature flow. Specifically, we study ancient asymptotically cylindrical flows, i.e. ancient solutions whose tangent flow at $-\infty$ is a round shrinking cylinder $\mathbb{R}^{k}\times S^{n-k}(\sqrt{2(n-k)|t|})$, where $1\leq k\leq n-1$. While in the neck case, i.e. for $k=1$, a complete classification has been obtained in several breakthroughs, a classification for the case $2\leq k\leq n-1$ until recently seemed out of reach. To analyze ancient asymptotically cylindrical flows for $2\leq k\leq n-1$, we consider the cylindrical profile function $u$ that measures the deviation of the renormalized flow from the round cylinder. We prove that for $\tau\to -\infty$ we have the asymptotics $u(y,\omega,\tau)= (y^\top Qy -2\textrm{tr}(Q))/|\tau| + o(|\tau|^{-1})$, where $Q$ is a constant symmetric $k\times k$-matrix whose eigenvalues are quantized to be either 0 or $-\sqrt{(n-k)/8}$. We then focus on the extremal rank cases. Under the natural noncollapsing condition, we obtain a classification of all solutions with $\textrm{rk}(Q)=0$, and establish $\textrm{SO}(n-k+1)$-symmetry and unique asymptotics in the case $\textrm{rk}(Q)=k$, also known as the $k$-oval case. Next, we confirm a conjecture by Angenent-Daskalopoulos-Sesum about uniqueness of $\textrm{O}(k) \times \textrm{O}(n-k+1)$-symmetric ancient ovals and more generally classify all $\textrm{O}(k) \times \textrm{O}(n-k+1)$-symmetric ancient noncollapsed solutions. On the other hand, for every $2\leq k\leq n-1$ we construct a $(k-1)$-parameter family of ancient ovals that are only $\mathbb{Z}^{k}_{2}\times \mathrm{O}(n-k+1)$-symmetric, giving counterexamples to another conjecture of Daskalopoulos. We then investigate ancient ovals without any symmetry assumption. Specifically, we prove that any $2$-oval in $\mathbb{R}^4$, up to scaling and rigid motion, either is the unique $\textrm{O}(2)\times \textrm{O}(2)$-symmetric ancient oval constructed by White and Haslhofer-Hershkovits, or belongs to our new one-parameter family of $\mathbb{Z}_2^2\times \textrm{O}(2)$-symmetric ancient ovals. In particular, this seems to be the first instance of a classification result for geometric flows that are neither cohomogeneity-one nor selfsimilar. Finally, as an application of the theory of ancient solutions, we prove that for the mean curvature flow of closed embedded hypersurfaces the intrinsic diameter stays uniformly bounded as the flow approaches the first singular time, provided all singularities are of neck or conical type. In particular, our analysis yields sharp curvature bounds improving prior results by Head and Cheeger-Haslhofer-Naber.