VictorJuiz/thesis huggingface dataset:
Pharmacologic Inhibition of Ubiquitin Activation as a Novel Therapeutic Strategy in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy for which new therapeutic approaches are required. One such potential therapeutic strategy is to target ubiquitin-like modifier activating enzyme 1 (UBA1), the initiating enzyme in the ubiquitylation cascade in which proteins are tagged with ubiquitin moieties to regulate their degradation or function. Here, we evaluated TAK-243, a first-in-class UBA1 inhibitor, in preclinical models of AML and identified potential determinants of sensitivity to this drug. In AML cell lines and primary AML samples, TAK-243 induced cell death and inhibited clonogenic growth. In contrast, normal hematopoietic progenitor cells were more resistant. TAK-243 preferentially bound to UBA1 over the related enzymes UBA2, UBA3 and UBA6 in intact AML cells. Inhibition of UBA1 with TAK-243 decreased levels of ubiquitylated proteins, increased markers of proteotoxic stress and DNA damage stress. In vivo, TAK-243 reduced leukemic burden and targeted leukemic stem cells without evidence of toxicity. We selected populations of AML cells resistant to TAK-243 and identified missense mutations in the adenylation domain of UBA1. To identify the determinants of TAK-243 sensitivity, we conducted a genome-wide CRISPR/Cas9 knockout screen in AML cells in the presence of TAK-243. We identified BEN domain-containing protein 3 (BEND3), a transcriptional repressor and a regulator of chromatin organization, as the top gene whose knockout conferred resistance to TAK-243 in vitro and in vivo. BEND3 knockout dampened TAK-243 effects on ubiquitylation, proteotoxic stress and DNA damage response. It also upregulated the ABC efflux transporter breast cancer resistance protein (BCRP) resulting in increased efflux of TAK-243 out of the cells. In addition, TAK-243 sensitivity correlated with BCRP expression in cancer cell lines of different origin and chemical inhibition of BCRP sensitized intrinsically resistant high-BCRP cells to TAK-243. Thus, our data demonstrate that TAK-243 targets AML cells and stem cells and support a clinical trial of TAK-243 in this patient population. We also provide insights into potential mechanisms of acquired resistance to TAK-243. Moreover, our data demonstrate that BEND3 regulates the expression of BCRP for which TAK-243 is a substrate. Therefore, BCRP expression could serve as a predictor of TAK-243 sensitivity in different malignancies.

Keywords: ABCG2
AML
BEND3
TAK-243
UBA1
Ubiquitin
Advisor: Schimmer, Aaron D
Reduced-order Modeling in the Finite-difference Time-Domain Method

The finite-difference time-domain (FDTD) method is a well-known numerical algorithm. Despite its many advantages, FDTD becomes time-consuming when applied to multiscale problems, where sharp field variations or fine geometrical details impose a very fine grid, at least locally. Grid refinement affects computational cost in two ways: it increases the number of fields to update at each iteration, and it reduces the maximum timestep allowed by the Courant-Friedrichs-Lewy (CFL) stability limit. Our goal is to investigate how model order reduction (MOR) can be leveraged to address both computational issues associated with grid refinement, and devise accelerated FDTD schemes for multiscale problems. In the envisioned approach, multiscale objects are initially meshed with a locally-refined grid, while the rest of the domain is meshed with a coarse grid. Then, the FDTD update equations of each refined region are processed to generate a reduced-order model, which is finally coupled to the surrounding coarse grid. To achieve this vision, two main issues had to be addressed: i) how to generate FDTD-compatible reduced-order models, and ii) how to guarantee that the final FDTD scheme with embedded reduced models will be stable under a known CFL limit. Our first major contribution is to devise a new theoretical framework to create FDTD-like schemes with provable stability, based on the dissipativity theory. We show that most FDTD schemes can be seen as the connection of different subsystems, such as reduced-order models. We determine the conditions under which these FDTD-like subsystems are dissipative, and prove that, if each subsystem is dissipative, then the whole scheme will be dissipative, and thus stable. This theory provides a systematic way to create a variety of FDTD schemes with provable stability, from simple subgridding algorithms to the advanced FDTD schemes with embedded reduced-order models. Another major contribution is to generate reduced-order models compatible with FDTD simulations, and capable of accurately capturing the electromagnetic behaviour of a given volume enclosing arbitrary objects. The proposed models can be instantiated into a coarser FDTD grid and are compatible with leap-frogging. Through the dissipativity theory, we rigorously prove the stability of the proposed FDTD algorithms with reduced models.

Keywords: CFL limit
FDTD
model order reduction
stability analysis
subgridding
Advisor: Triverio, Piero
Enhancing our Understanding of Outcomes and Determinants of Outcomes Following Proximal Humerus Fractures in Adults

There remains significant debate surrounding the optimal management strategies for proximal humerus fracture (PHF) patients. High quality evidence summarizing and appraising the measurement properties and concepts reflected by outcomes used to evaluate recovery, and predictors of outcomes following PHF is needed. Objectives: To summarize and appraise 1) outcome measures; and 2) predictors of outcomes following PHF; and 3) develop novel risk tools to predict subsequent surgery following PHF. Methods: I performed four systematic reviews to discern 1) the measurement properties of outcomes; 2) identify the concepts reflected by these outcomes; and 3) summarize and appraise predictors of i) patient-reported functional disability, and ii) subsequent surgery following initialtreatment. I used these data to develop a population-based cohort of PHF patients, and novel risk tools to predict subsequent surgery following initial treatment. Results: The Disabilities of the Arm, Shoulder and Hand (DASH), Shoulder Function Index, and Euro-Quol-5D scores appear to have the best measurement properties to evaluate PHF patients.The DASH, American Shoulder and Elbow Surgeon’s, and Oxford Shoulder Scores appropriately address limitations in daily activities. While evidence surrounding predictors of outcomes was somewhat conflicting, there were trends toward worse outcomes in patients who were older (primarily in those treated with fixation), injured their dominant arm, and whosefracture had a varus fracture neck shaft angle, or a disrupted medial hinge. My risk tools identified the use of a bone graft, and fixation with a nail or wire (vs. a plate) in patients treated with fixation, poor bone quality in patients treated with replacement, and younger age, as well asdischarge to a destination other than home in patients treated non-surgically as predictors of subsequent surgery. The tools showed good to strong discriminative ability for patients treated with fixation and non-surgically. Conclusion: This thesis generated important new knowledge surrounding the outcomes and predictors of outcomes following PHF. My outcome studies can help clinicians choose measures for evaluating recovery, and for future research. My systematic reviews to identify predictors of outcomes can help select variables potentially associated with poor outcomes. My risk tools can identify patients at risk for subsequent surgery.

Keywords: outcomes
predictors
Proximal humerus fractures
Advisor: Schemitsch, Emil H
Mamdani, Muhammad
A Paper Examining Reactive Attachment Disorder and the Canadian Criminal Justice System

Reactive attachment disorder (“RAD”) is a recognized behavioural disorder arising from the failure to develop an “attachment” to a primary caregiver in early childhood. RAD can most often be traced to neglect or abuse or both in a child’s first 5 years of life. Some relevant symptoms are incessant lying, a lack of conscience and often a complete inability to have or to show empathy or remorse. The relevance to the operation of our criminal justice system is that the impressions left as a result of these traits are critical to the eventual outcome. From the moment the accused is interviewed and then throughout the process, their demeanor is being scrutinized. Their level of emotion and the “correctness” of that emotion and especially their ability to express empathy and remorse are judged during each phase. The problem is that these behaviours can lead to wrong impressions and, therefore, mistakes and injustice.

Advisor: Friedland, Martin L
Roach, Kent
Vascular Effects of Low-Molecular Weight Heparin in Pregnant Women at High-Risk of Preeclampsia

Preeclampsia (PE) is a hypertensive disorder of pregnancy characterized by new-onset hypertension with evidence of organ injury. Women with severe PE demonstrate cardiovascular impairment during pregnancy and are at higher risk of cardiovascular disease postpartum. There is currently no effective therapy for the prevention of PE in high-risk pregnant women. Low-molecular weight heparin (LMWH) has been investigated for the prevention of severe PE, although the underlying mechanisms of action are unknown. The objective of the first experiment was to assess cardiovascular function in pregnant women at high-risk of PE compared with low-risk pregnant controls at 24 weeksâ gestation. High-risk women demonstrated a lower cardiac output, higher resistance hemodynamic profile with impaired radial artery flow-mediated dilation (FMD), compared to controls. Baseline plasma and urine levels of placental growth factor (PlGF) were significantly lower in high-risk women compared with controls. These findings demonstrate that pregnant women at high-risk of PE exhibit impaired endothelial function prior to the clinical presentation of PE. The acute cardiovascular effects of LMWH in pregnant women at high-risk of PE were then investigated. LMWH significantly increased FMD in high-risk women and maternal plasma levels of PlGF, suggesting that LMWH may exert beneficial effects on maternal endothelial function. To further elucidate the effects of LMWH on the maternal endothelium, the effects of patient serum and LMWH on in vitro endothelial cell function were investigated. Serum from high-risk women impaired angiogenesis and increased PlGF-1 and PlGF-2 expression compared to serum from low-risk subjects. Co-exposure of high-risk serum with LMWH improved the angiogenic response, such that it was equivalent to that of low-risk serum, and promoted PlGF secretion from endothelial cells. These observations provide further evidence that LMWH modifies endothelial cell function, possibly through enhanced PlGF bioavailability. In conclusion, the present experiments indicate that LMWH improves endothelial function in pregnant women at high-risk of developing PE, possibly mediated through increased PlGF bioavailability. These findings are consistent with previous clinical studies in non-pregnant populations and animal studies in which LMWH improved endothelial function. Future trials are needed to assess the effectiveness of LMWH for the prevention of severe PE in high-risk women.

Advisor: Parker, John D
Kingdom, John CP
Morality Police: Sexuality Governance at the League of Nations

During the interwar period, the international community was zealously involved in the regulation of sexuality and vice under the auspices of the League of Nations. The roaring twenties had ushered with it a revival of morality policing in Europe and North America. The League of Nations Sex Trafficking Committee, led by social purity reformers and religious organizations, operated to create policy aimed at eliminating vice districts, music halls, and cabarets. Once this international policy was issued, volunteer organizations (spread literally around the globe) would carry out the carceral policy directives. Morality Police is the first genealogy of this remarkable period, providing an “ontology of ourselves” that seeks to expose the disreputable origins of anti-sex trafficking campaigns. This project narrates how the international community policed morality, following the twists and turns as they occurred on the Sex Trafficking Committee and at local levels from France to India. Drawing on over 10,000 archival documents collected from the League of Nations archive, this project argues that rather than being primarily concerned with abolishing state regulated prostitution, the Sex Trafficking Committee more insidiously engaged in a campaign of sexuality governance. While this campaign to halt changing sexual and cultural norms was ultimately unsuccessful, it was remarkably effective at repressing and disciplining sexual outlaws during its tenure. This project concludes with a stark reminder that while the campaign to stamp out vice and immorality in the interwar period was ultimately a failure, its legacy is still with us. Arguing that the laws and propaganda campaigns during this period created stories of international trafficking that were so powerful, the narratives became folklore that survived generations awaiting another eruption of moral panic.

Keywords: Interwar Period
Magdalene Asylum
Moral Panic
Morality Police
Surveillance
Women's History
Advisor: Cossman, Brenda
Blossoming Multiliteracies: Stories of How W̱SÁNEĆ, Quw’utsun, Gitga’at, and Líl̓wat Nations Reclaim Indigenous Languages and Food Systems through Pedagogies of the Land

Indigenous languages are windows into a myriad of worldviews (Simpson, 2011). They are repositories of botanical, environmental, and kinship knowledges, and, perhaps more importantly, are central to Indigenous identity (McCarty et al., 2018). As W̱SÁNEĆ, Quw’utsun, Líl̓wat and Gitga’at communities (re)inhabit social, physical, spiritual, and emotional spaces to speak their languages of SENĆOŦEN, Hul’q’umi’num’, Ucwalmícwts, and Sm̓algya̱x, respectively, they use pedagogies of the land. Teaching styles are grounded in Indigenous land education (Calderon, 2014; Goodyear-Ka‘ōpua, 2013) and decolonizing botanical knowledges (Geniusz, 2009) as (w)holistic curricula, upholding ontologies of lands and waters. As a settler researcher on these lands, I engaged in conversations with nine Elders and educators from Coast Salish (SȾÁUTW̱, W̱JOȽEȽP, W̱SÍKEM, Quw’utsun), Gitga’at, and Líl̓wat First Nations, and two settlers. Research questions inquired into how youth and Elders approach language reclamation. I learned pedagogies of the land are a return to ancestral ways of being, counter-hegemonic actions that pull children and adults towards nature-based spaces, nurturing whole beings. Conceptual frameworks integrate anti-colonial (Carlson, 2016), Indigenous-centred methodologies (Smith, 2012). Conscious of “unsettling” (Regan, 2010) my positionality as active witness (Atkinson, 2001), I gathered knowledges through conversational interviews (Kovach, 2010) and storywork (Anderson, 2011; Archibald, 2008), contributing through eco-cultural restoration. Knowledge Keepers shared stories of teaching on the land, drawn to sacred places through keystone food systems, interweaving Oral Histories with Indigenous languages. Stories are linked thematically through an iterative framework, and shed light into how Indigenous languages are transmitted intergenerationally, grounded in local epistemologies. Findings show how first (L1) and second (L2) language acquisition connects with ethnobotanical knowledges; blending mariculture, prayer names, traditional practices, and songs. Foods and medicines are harvested in reciprocal acts of gratitude. Through this work, multiple layered literacies develop, with students learning and speaking Indigenous languages through (w)holistic, land-centred education (heart- and community-literacies), while regenerating lands, waters, and medicines (food- and ecological-literacies). Languages grow as part of linguistic ecologies (Twitchell, 2017), thriving within the seen and unseen, more than human world. This thesis may interest those in the fields of language revitalization; food sovereignty, security, and native plants; language policy; eco-justice; and land-based Indigenous pedagogies.

Keywords: Education
Ethnobotany
Indigenous
Land
Language
Reclamation
Advisor: Restoule, Jean-Paul
Electrochemical Study of Proteins using Electrode with Modified Surfaces

Some different aspects of proteins properties as well as nanostructures were studied using various electrochemical approaches in this thesis. Electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), differential pulse voltammetry (DPV) were employed as well as many other analytical tools and methods to explore some structures of our interest. In the first chapter, the above-mentioned electrochemical methods along with some fundamental background of electrochemistry were reviewed. The chapter, also, reviews some aspects of membrane proteins, membrane double layers and chemistry of diazonium compounds which were employed in our studies. The structure of a novel (and patented) nanostructure and mainly its response to electrochemical impedance spectroscopy was studied and discussed in chapter 2. We showed how we can isolate the response of this nanosensor to a small change of the dielectric constant of the material entraps in the nanogap of the sensor. In chapter 3, we used DPV and CV methods to investigate nitrite reduction activity of human hemoglobin. We proposed -for the first time- a complete reaction mechanism for the electrochemical reactions taking place on the surface of modified glassy carbon electrodes. We showed how these electrochemical results were comparable to spectroscopic methods and can be used for future studies of hemoglobin nitrite reduction studies. In chapter 4, we developed a novel platform for preparing a hybrid bilayer (HBM) for electrochemical studies of membrane proteins. We used diazonium chemistry to graft the first layer of the HBM covalently to the glassy carbon electrode. We demonstrated the flexibility of our platform for developing various bilayers with relatively predictable characteristics using molecules with desired properties as the first and second layer in HBM. We used two different electrochemical probes with opposite charges to show how differently the HBM responded to these probes depending of the charge of the polar groups on the second layer. We used amyloid-β42 to demonstrate the application of this platform to study protein aggregation processes. In chapter 5, we discussed some future directions for all previously discussed chapters and mentioned some potential studies which may follow these studies.

Keywords: Bilayer
Diazonium salt
Electrochemistry
Hemoglobin
Impedance Spectroscopy
Protein
Advisor: Kerman, KAgan
The Effect of Hyperthermia on Nanomedicine Efficacy

Chemotherapy remains a cornerstone of oncology and is used to treat the majority of cancer patients. Hyperthermia is a powerful cancer treatment modality, capable of altering tumor physiology and molecular biology, thereby modifying the distribution and efficacy of chemotherapy drugs. In the last 25 years, nanomedicine chemotherapies have become entrenched within the medical oncology field due to decreased side effects compared to the standard of care. The integration of hyperthermia and nanomedicine chemotherapy has the potential to significantly impact patient outcomes. The goal of this thesis is to combine in vitro cytotoxicity and molecular biology assays with nanomedicine drug development and characterization and in vivo medical imaging in order to optimize the therapeutic efficacy of strategies combining hyperthermia with various nanomedicine chemotherapies. Specifically, the ability of hyperthermia to modulate interstitial fluid pressure and nanomedicine accumulation and distribution is demonstrated using computed tomography imaging and correlated with increased efficacy of Doxil®, the most common clinically administered nanomedicine chemotherapy. Currently undergoing Phase III clinical trials, ThermoDox® is a doxorubicin-containing nanomedicine formulation similar to Doxil, but which undergoes heat-triggered release when exposed to hyperthermic temperatures. Research presented within this thesis builds on the successful development of the ThermoDox technology by substituting the drug encapsulated within. The ability of heat-triggered release to increase the tumor accumulation and efficacy of cisplatin is exhibited in multiple preclinical animal models. The ability of hyperthermia to impair a fundamental DNA damage repair pathway of cancer cells is demonstrated to be a contributing factor. A companion therapeutic to ThermoDox that contains a cytotoxic heat shock protein inhibitor was designed and characterized in vitro and in vivo. The heat shock protein inhibitor was selected due to cytotoxic synergy with doxorubicin and physicochemical similarities that allow for comparable formulation strategies. Both formulations were demonstrated to have similar stability and drug release profiles and deliver drug to the tumor with similar efficiency. The results of these studies demonstrate the positive, multifactorial impact that hyperthermia can exert on nanomedicine chemotherapies.

Keywords: drug characterization
drug delivery
drug formulation
hyperthermia
nanomedicine
oncology
Advisor: Allen, Christine
Imaging Immune Functions Induced by Focused Ultrasound and Microbubble Treatments to Increase Blood-brain Barrier Permeability

Treatment of neurological diseases is limited by the blood-brain barrier (BBB). The BBB controls the exchange of compounds between the brain parenchyma and systemic circulation. One method to bypass the BBB is to use focused ultrasound (FUS). FUS, used in conjunction with preformed microbubbles (MBs), can transiently enhance BBB permeability by increasing transcellular and paracellular transport across the brain endothelium. While FUS+MB BBB treatments have been shown to be an effective method to deliver agents to the brain, the use FUS+MB BBB alone, without additional therapeutics, have also been observed to result in various downstream effects, including the reduction of β-amyloid (Aβ) plaque load in animal models of Alzheimer’s disease. The characteristics of this induced clearance response have yet to be fully elucidated. In this thesis, the time course of the effects of FUS+MB BBB and induced recruitment of peripheral immune cells are investigated using two-photon fluorescence microscopy. Thermal effects of two-photon fluorescence microscopy were assessed to evaluate whether experimental parameters affected the brain milieu. Brain temperatures were moderately hypothermic following cranial window implantation and increased linearly with laser power during imaging. Temporal characteristics of induced Aβ plaque load clearance were investigated by monitoring the size of Aβ plaques following one FUS+MB BBB treatment in the TgCRND8 mouse model of Alzheimer’s disease. Aβ plaque reduction was observed between 2 to 14 days following treatment, and repeated biweekly treatments significantly reduced plaque load. The efficiency of plaque clearance suggested the involvement of peripheral phagocytic immune cells. Blood flow perturbations were observed immediately before and after the onset of sonication, and motile cells were recruited intravascularly within seconds following increase in BBB permeability. Neutrophils were identified to be one of the participating cell types. FUS+MB treated brain hemispheres harboured significantly more neutrophils compared to the contralateral hemispheres, and to control animals. However, the participation of neutrophils in clearing Aβ plaques may be transient, as neutrophil counts in treated brain tissue were not significantly different from control animals following biweekly FUS+MB treatments. The characteristics of immune functions provided in this thesis further inform understanding of biological responses induced by FUS+MB BBB treatments.

Keywords: Alzheimer's disease
blood-brain barrier
neuroimmunology
two-photon imaging
ultrasound
Advisor: Hynynen, Kullervo