VictorJuiz/thesis huggingface dataset:
Expanding the Applications of Mitochondrial Targeted Delivery Peptides

Mitochondria play a critical role in the generation of cellular energy, the organization of metabolic pathways, and regulation of programmed cell death. The study of these processes is complicated by the impermeability of the mitochondrial membrane, particularly the inner membrane, to chemical agents designed to probe the biochemistry of mitochondria. Previous research conducted in the Kelley lab has led to the development of peptide-based vectors to overcome these limitations. These mitochondria penetrating peptides (MPPs) are capable of transduction through the cell and mitochondrial membranes, concentrating within the mitochondrial matrix with high specificity. MPPs have been used to localize a number of small molecule probes and therapeutics allowing for the study of biological processes which would have previously been impossible. With the basic principles of MPP based mitochondrial study established, herein data is presented on the expansion of the breadth of compounds, organisms, and molecular targets which can be manipulated using MPP conjugates. We describe the development of a releasable linker for MPP conjugation to bioactive cargo in order to release compounds from MPPs following localization in the mitochondrial matrix. This strategy allows for the use of compounds whose activity would otherwise be impacted by MPP conjugation. The co-targeting of bacteria by MPPs based on the physiochemical similarities of bacteria to mitochondria is also investigated. The chemical properties required by MPPs for bacterial and mitochondrial co-targeting as well as methods to control relative affinity towards these targets are presented in order to allow for preferential control of delivery. Finally, initial investigations into the use of MPPs paired with a new class of in cellulo RNA secondary structure probe are presented. The combination of a secondary structure probe and an MPP could potentially lead to new avenues towards understanding the in vivo structure of key structural mitochondrial RNAs such as rRNAs and tRNAs and the biochemical basis in which disease-causing mutations affect their function. Taken together, these findings expand the potential uses for MPPs for biochemical research as well as potential therapeutic applications.

Keywords: Drug Targeting
Mitochondria
Peptide
Advisor: Kelley, Shana O
Investigation of the Mechanism of Idiosyncratic Drug-Induced Liver Injury by Immune System Modulation

Idiosyncratic drug-induced liver injury (IDILI) continues to be an important issue. There is increasing clinical evidence that most IDILI is immune mediated. Extensive mechanistic studies are needed to better understand these reactions; however, it is impossible to do controlled experiments in humans, and previous animal models did not properly model IDILI. If IDILI is immune mediated, and the major factor preventing liver injury in patients is immune tolerance, then a plausible method to develop an animal model of IDILI would be to impair immune tolerance. Therefore, the objectives of my research were to develop a valid animal model of IDILI, use this model to test mechanistic hypotheses, and to develop better ways to predict risk. In my first two papers I show that immunization of mice with drug-modified hepatic proteins prior to drug exposure paradoxically decreased liver injury unless immune tolerance was impaired during the immunization. In my third paper, I show that PD1-/- mice treated with anti- CTLA-4 and amodiaquine can lead to significant liver injury and liver dysfunction, which is mediated by CD8 T cells. In my fourth paper, I show that this impaired immune tolerance model is able to unlock the potential of isoniazid and nevirapine to cause increased liver injury. Finally, in my fifth paper, I show that this impaired immune tolerance model is also able to distinguish the potential for liver injury of chemically similar drugs, where one drug causes IDILI in humans and the other does not (troglitazone/pioglitazone and tolcapone/entacapone). Overall, I have shown that risk of developing IDILI may be influenced by previous exposures, and I have further developed a model of IDILI, showing its potential for other drugs and as a tool for drug screening. Further characterization and validation of these models is required; however, it is likely that they will make it possible to perform mechanistic studies that have been impossible in the past.

Keywords: Animal Models
Idiosyncratic Drug Reactions
Immunomodulation
Advisor: Uetrecht, Jack
High-Fidelity Numerical Modeling and Analysis of Low Reynolds Number Airfoils and Synthetic Jets

The shear layer development over a NACA 0025 airfoil at a low Reynolds number was investigated experimentally and with large-eddy simulation. Two angles-of-attack (AOA) were considered: 5deg and 12deg. Experiments and numerics confirm two flow regimes. The first regime (AOA=5deg) exhibits boundary layer reattachment with formation of a laminar separation bubble. The second regime consists of boundary layer separation without reattachment. The stability equations exhibit significant sensitivity to base flow variations, making experimental-numerical comparisons challenging. Linear stability analysis suggests that the first regime is characterized by high frequency instabilities with low spatial growth, whereas the second regime experiences low frequency instabilities with more rapid growth. Spectral analysis confirms the dominance of a central frequency, and the importance of nonlinear interactions with harmonics during transition. The sensitivity of the Orr-Sommerfeld equation due to base flow deviations was investigated with a Monte Carlo-type perturbation strategy and a Chebyshev collocation method. A separated boundary layer with a nominal shape factor of H=5.9 was perturbed for both velocity and wall-normal position deviations. Wide bands of eigenvalue spectra were obtained due to both perturbations. The standard deviation of the peak growth rate and frequency was found to be independent of Reynolds number. To broaden the results, six boundary layers were investigated with shape factors H=5.9-22. Perturbations resulting in a standard deviation of 1 % of the nominal shape factor were applied. Sensitivities of the peak growth rate and frequency are more pronounced at lower shape factors. The effect of synthetic jet cavity shape was investigated numerically and experimentally. In the examination of three cavities it was found that the cavity with the sharpest nozzle-to-cavity transition transmits the most momentum at the exit. The sharp transition within the cavity results in a stronger vortex, higher self-induced inward velocity, and more room for flow to exit the cavity during expulsion. It is shown that the shape of the internal cavity plays an important role in the flow behaviour at the nozzle exit. From a computational perspective, the flow field within the cavity must be computed to obtain accurate exit conditions for the synthetic jet.

Keywords: Flow control
Flow stability
Large-Eddy Simulation
Advisor: Sullivan, Pierre E
The Institutional Organization of Black Female Child Protection Workers’ (Re)construction of their Role as Carers in Child Protection: An Institutional Ethnographic Inquiry

This institutional ethnographic study explores the coordinated processes that organize Black female child protection workers’ (re)construction of their role as carers in the Ontario child protection system. This examination occurs within the backdrop of colonialism and shifting and unequal power relations in Canada. Absent from social work research is an understanding of the complex sequences of actions in every day child protection activities that authorize colonial ideologies and practices and the impact of Black female child protection workers’ negotiation of this context on their well-being. This study’s informant sample includes 9 Black female child protection workers currently employed at a child protection institution in Ontario. Data was collected from semi-structured interviews and textual analysis. The findings revealed colonialism in the child protection system is maintained through institutional patterns of exclusion and acts of dissimulation in the institutional discourse and practice. In response, Black female child protection workers resist colonial practices through their injection of acts of caring into their work. At the same time, their constant experiences of structural violence lead to institutional trauma. This research highlights a contradiction within the social work framework; the overt espousal of human rights and social justice as ethical priorities, while covertly maintaining colonialism in the child protection system, specifically towards Black female child protection workers and their communities. The findings advance social work knowledge by offering a way to identify the existence and the impact of the colonial context on Black female child protection workers as well as map out the sequences of actions or inactions that embed colonial ideologies and practices in the child protection system.

Keywords: Black
Child
Colonialism
Female
Protection
Workers
Advisor: Williams, Charmaine C
On Love: Between Lacan and Badiou

This thesis considers love through the interlacing of psychoanalyst Jacques Lacan and philosopher Alain Badiou. Engaging with the problematic of love as an in-between (metaxú) in Western thought and intervening in the contemporary scholarship around Lacan and Badiou, this thesis examines love in the works of Lacan and Badiou and conceptualizes the consequences that remain implicit and unexplored in the two authors’ thoughts on love. Chapter 1 addresses love through mathematics. Noting that mathematics plays a pivotal role in Lacan’s and Badiou’s approaches to love, I discuss love through the sexuation formulas, numericity, modality, topology, and knot theory, elaborating the concept of amorous void. Chapter 2 addresses love through politics. Noting that politics resides where the interlacing of Lacan and Badiou reaches a peak, I examine the enigmatic knot between love and politics through the contemporary crisis of love, the reinvention of philia, community, and humanity, elaborating the concept of amorous unpower. Chapter 3 addresses love through antiphilosophy and philosophy. Referring to Japanese writer Murakami Haruki’s Tony Takitani as a facilitator for the dialogue between antiphilosophy and philosophy, I examine how love straddles both the psychoanalytic symptom and the philosophical truth, the analytic act and the philosophical operation. I conclude this chapter by elaborating the concepts of sinthomatic truth and archiamorous acts. Chapter 4 reads Letter to D by French philosopher André Gorz. Discussing Gorz and Dorine’s amorous itinerary from their first encounter to their joint suicide, I address how Gorz and Dorine weave both the Lacanian side and the Badiouian side through their “Bacanian” love. In Conclusion, I revisit love as an in-between in relation to intermediate daemons in Plato’s Epinomis, from which are drawn the interlacing of the analyst as a participant of pain and the philosopher as a discerner of truth. Developing the problematic implied in this interlacing, I argue that the subject of love comes between the enigma of love as the loveless that is indiscernible to love and the principle of love as the love that infinitely surpasses itself.

Keywords: Alain Badiou
Jacques Lacan
Love
Philosophy
Psychoanalysis
Advisor: Kingwell, Mark
Mating costs and gametic barriers to reproduction

Mating is essential to many organisms for their continued existence, and yet mating is costly. However, the fitness costs–which may immediately affect the individuals involved, or may affect their future reproductive output, are not often quantified. I assess costs that are acquired at different periods of the mating process–in search of a mate and gametic interactions after copulation. I first quantify the cost of mate searching of a monogynous spider measured by male longevity and I additionally examine how mate searching affects subsequent mating behaviours and performance. I find evidence for behavioural plasticity in males influenced by mate search duration to maximize female egg laying which may be mediated by male seminal fluids and/or female cryptic choice. I then use transparent organisms, Caenorhabditis nematodes, to identify a novel form of gametic isolation using 10 different species. This sperm mediated form of gametic isolation likely evolved from intra-species sperm competition, resulting in incompatibilities as a byproduct of competitive sperm in inter-species matings that caused early death, sterility, and invasive sperm. I further explored sperm-mediated gametic isolation in Caenorhabditis from the perspective of inter-species interactions by experimentally evolving populations with mixed species for six generations to show reproductive interference at the population level. Finally, I screened 25 genetic mutants and phenotyped 99 nearly isogenic lines of Caenorhabditis to identify genetic contributions to gametic isolation (i.e. speciation genes). I identified candidate genes that fall into two categories of phenotypic defects: ovulation defects increase the incidence of sperm invasion, whereas sperm signaling defects reduce the incidence of sperm invasion. These findings and novel methods add to our understanding of how costly mating can be, and how gametic interactions, in particular, contribute to reproductive isolation in Caenorhabditis.

Keywords: Gametic isolation
Reproductive barriers
Sexual Selection
Speciation
Advisor: Cutter, Asher D
Managing Software Evolution Through Semantic History Slicing

Software change histories are results of incremental updates made by developers. As a byproduct of the software development process, change history is surprisingly useful for understanding, maintaining and reusing software. However, traditional commit-based sequential organization of version histories lacks semantic structure and thus is insufficient for many development tasks that require high-level, semantic understanding of program functionality. In this dissertation, we propose a new semantics-based view of software version histories, where a set of related changes satisfying a common high level property (also known as slicing criteria) is recognized as a semantic history slice. As one concrete instantiation, test cases exercising a software functionality can be used as slicing criteria to identify changes implementing the particular functionality. Specifically, we present a family of automated techniques which analyze the semantics of historical changes and assist developers in many practical software evolution tasks. First, we introduce CSlicer, an efficient static history slicing algorithm which requires only a one-time effort for compilation and test execution. It mostly relies on static analysis of dependencies between change sets and is therefore inexpensive in terms of running time but can be imprecise. Second, we present Definer, a dynamic history slicing algorithm based on delta refinement. It executes tests multiple times and observes the test results while attempting to shorten the history slices iteratively. The semantic slices found by the dynamic approach are guaranteed to be minimal, but the running time can be much longer. Finally, we describe the design and implementation of a Web-based semantic slicing framework CSlicerCloud which aims to find balance between performance and precision, unifies different history slicing algorithms and provides software developers a flexible and ready-to-use environment for various evolution management tasks. We have successfully applied the history slicing techniques in many development tasks including creating focused pull requests, back-porting bug fixes, locating feature implementations and building feature models to assist evolution understanding. For validation, we evaluate our approaches on a benchmark of developer-annotated version history instances obtained from real-world open-source software projects from GitHub.

Keywords: Evolution management
Program analysis
Software changes
Version control
Advisor: Chechik, Marsha
Conceptualization, Measurement, and Association of Underemployment to Mental Health Inequities between Immigrant and Canadian-born Labour Force Participants

This thesis aims to increase understanding of the association of underemployment (unemployment or overqualification) to mental health inequities between immigrant and Canadian-born labour force participants. The first paper provides a theoretical framework to guide design, analyses and interpretation of findings for this thesis, and future research on social determinants of mental health inequities. The second paper uses the Canadian Community Health Survey (CCHS) Cycle 1.2 to assess the construct validity of self-rated mental health (SRMH) for the overall population, and sub-groups by immigrant status and sex. Positive associations between SRMH and a comprehensive array of mental morbidity measures were large and consistent, but a sizeable percentage of respondents with mental morbidity did not rate their mental health as fair/poor. SRMH is useful for assessing social determinants of inequities in general mental health, but not specific mental health morbidities. The third paper uses CCHS Cycle 2.1 (2003) to examine the association of underemployment to fair/poor self-rated mental health (SRMH) in: 1. labour force participants (18-64yrs) in Canada, and 2. between a. immigrants vs. Canadian-born labour force participants, and b. recent immigrant (

Keywords: discrimination
immigrants
mental health
refugees
social determinants
underemployment
Advisor: O'Campo, Patricia
Exploring Functional Neuroplasticity and the Associations with Outcomes of Advanced Gross Motor Interventions for Children with Cerebral Palsy

Improvement of advanced gross motor skills is a key rehabilitation goal of children with cerebral palsy (CP), given their underlying brain injury, motor impairments, and physical activity participation possibilities. Evidence for potential functional neuroplastic change following gross motor training is lacking, and may provide important indicators that could advance intervention design to target children’s goals. This research focused on independently ambulatory children with hemiplegic CP (HCP) (i.e., those with unilateral motor involvement), and with diplegic CP (DCP) (i.e., those with both legs involved). In the first study, an ankle dorsiflexion functional magnetic resonance imaging (fMRI) paradigm was refined and optimized to calculate the ratio of hemispheric activity in the primary motor cortex (M1) and overall M1 activation volume. This fMRI paradigm was then used in two linked studies that explored relationships between changes in M1 activation and changes in advanced motor skills following goal-directed gross motor interventions for children with HCP and DCP. Lower limb M1 functional connectivity was also probed using resting state fMRI. Individual changes in fMRI outcomes were observed, with no significant group change. Three patterns of change in the laterality of M1 activation were identified: maintenance of principally contralateral activation (i.e. typical motor control), increased contralateral activation, or increased ipsilateral activation. Relationships were observed between motor skill gains and M1 activation during ankle dorsiflexion on the more affected/non-dominant side. For children with DCP, increased ipsilateral activity was associated with motor skill improvements. In both HCP and DCP, a smaller cortical activation volume was a predictor of motor skill gains. These exploratory findings suggest that M1 activation may be related to motor skill change. This investigation of lower limb functional neuroplasticity is an important step towards developing evidence of the underlying neural mechanisms of advanced gross motor skill improvement following interventions for children with CP.

Keywords: cerebral palsy
fMRI
functional neuroplasticity
gross motor
Advisor: Wright, Virginia
Fehlings, Darcy
Delineating the Cardio-Myogenic Hierarchy during Mouse Embryonic Development

The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. We have turned to cell surface mass spectrometry to increase the candidate pool of membrane proteins on cardiac progenitor cells (CPCs). Specifically, we examined the expression of surface markers on CPCs using an integrated mass spectrometry and microarray-based approach. We analyzed the genome and surface proteome of cardiac progenitors generated from the stage-specific differentiation of mouse (m) and human (h) pluripotent stem cells (PSCs). We have identified and characterized Frizzled 4 (FZD4) as a new marker for lateral plate mesoderm (LPM). We also utilized FZD4 as a marker, in conjunction with fetal liver kinase 1 (FLK1) and platelet derived growth factor alpha (PDGFRA) and demonstrated an increase in CPC purity and a subsequent increase in cardiomyocyte (CM) enrichment. Additionally, we have found FZD4 is also expressed in the hPSC system and results in a similar enrichment in CM. Furthermore, we showed that NORRIN can be presented to the FZD4 receptor to induce Wingless-related integration site (WNT) signaling-mediated proliferation, resulting in an increase in CM output from CPCs. This demonstrates the value in knowing the set of surface markers present on a cell at a specific stage of development and the potential to leverage that knowledge into more efficient cell differentiation protocols. Further validation of the function of FZD4 is also being established in a preliminary in vivo study. The identified surface markers also have the potential to isolate cell types not only within the CPC stage, but within the PSC, epiblast, and primitive streak stages as well. These markers have been compiled into a preliminary cell-cell communication network model overlaid with an initial alternative slicing analysis to determine potential mechanisms that impact cell signaling during early CPC development. In summary, the application of a systems biology approach as demonstrated in this thesis, greatly expanded the number of surface markers available and upon further characterization and validation, can improve our understanding of cardiac biology.

Keywords: cardiac progenitor cells
cell surface capture
Frizzled 4
mass spectrometry
mouse pluripotent stem cells
Advisor: Zandstra, Peter