VictorJuiz/thesis huggingface dataset:
The Comparative Evolution of the Floral Traits of Island Angiosperms
Keywords: angiosperms
island biogeography
island floral syndrome
island floras
islands
island syndromes

Island biotas show parallel changes in community assembly and the evolution of species traits, which are referred to as “island syndromes.” My thesis investigates the evolution of floral traits on islands to test the “island floral syndrome,” which posits that island angiosperms evolve smaller, less showy flowers compared to mainland relatives. To test this hypothesis, I utilize a phylogenetic comparative approach, in which I compare the flower size of 136 island-mainland pairs of sister taxa across seven islands. I found that on average island angiosperms did not evolve smaller flowers relative to their mainland sister taxa. However, I did find that there was significant variation in the evolution of flower size among islands and among taxonomic families, such that, specific island floras and taxonomic families showed evolutionary trends consistent with and in opposition to the island floral syndrome. My thesis contributes to our understanding of the evolution of island floras.
Validation of Dimethyl-Ether (DME) Combustion Models for use in Internal Combustion Engines
Keywords: biofuel
combustion
Dimethyl-Ether
DME
flame speed
ignition delay

From an environmental point of view, CI engines running on diesel fuel are considered harmful and experimental research has shown that Dimethyl Ether (DME) has the potential to become the fuel of the future due to its clean properties. Ignition delay and laminar flame speed (SL) measurements are some of the important parameters for effective engine design and chemical kinetics modelling. In this study, several chemical models of DME were considered. First, they were validated for ignition delay analysis. The model that was most valid throughout was used for comparison to new experimental measurements of laminar flame speeds of DME and methane-air mixtures in a controlled laboratory environment. Overall, the chemical models of DME, especially the Aramco 2.0 mechanism, showed good agreement with the experimental data sets of ignition delay and SL studies.
Characterization of White Adipose Tissue Depots After Burn
Keywords: adipose tissue
browning
Burn
ER Stress
fat
lipolysis

Burn injury results in a vast and prolonged hypermetabolic state that is characterized by hyperglycemia, cachexia, organ dysfunction, and death. Recently, the adipose has been identified as a major mediator in the activation of the hypermetabolic response. However, the fat, and in particular, the visceral fat, has been largely ignored within this context. Here, we aimed to characterize and compare some of the hallmark responses of burn injury by examining the largest visceral (eWAT) and subcutaneous (iWAT) depots in our murine model. After a 30% burn, we observed the activation of ER stress, lipolysis and browning in different depots. Administration of propranolol (10 mg/kg) for 5 days attenuated these responses. We conclude that burn studies that examine the fat should be mindful of the depot they survey and be careful not to generalize results. Our findings also highlight the use of propranolol as an adjunct treatment for burn injury.
Predicting Active Enhancers From Chromatin Accessibility and RNA-seq Datasets
Keywords: bioinformatics
chromatin accessibility
ExtraTrees
machine learning
RNA-seq

Genomic annotation tools transform vast amounts of genomic data into interpretable labels, and help identify regulatory elements. As genomic assays improve to probe smaller samples of fewer cells, they become capable of characterizing new cell types. Genomic annotation methods must adapt to make sense of this wealth of new information despite the relative dearth of data on protein-DNA interactions on these new cell types, especially for use in locating regulatory elements. This project investigates the effectiveness of Segway, a genomic annotation tool, on minimal amounts of information. This project aims to improve upon existing methods by investigating two new supervised approaches to predict specific regulatory regions (enhancers), elucidating their location given only chromatin accessibility and RNA-seq data. The results show that out of the algorithms available from scikit-learn, an extremely randomized trees classifier is most capable of locating enhancers using minimal data (auPR 0.65).
Onboard Image Processing Algorithms for the BRITE Mission and Development of a Navigation System for Upcoming Formation Flying Missions
Keywords: BRITE
formation flying
image processing
nanosatellites
navigation

This thesis presents contributions to the BRight Target Explorer (BRITE) mission and operational formation flying missions developed at the Space Flight Laboratory. Onboard image processing algorithms were developed to increase science data throughput for the BRITE mission. The algorithms were adapted from a sophisticated ground-based data reduction pipeline developed in parallel with a new operating mode that mitigates the effects of radiation damage to the instrument detector. Onboard processing enables photometric data to be downlinked to the ground rather than entire images, increasing the number of stars that can be observed. The development of the navigation component for a ground-based GNC system for formation flying missions is also presented, focusing on an investigation into the feasibility of commercial orbit determination software for missions with moderate intersatellite baselines and control accuracy requirements. The orbit determination scheme implemented is presented and validated using on-orbit data from the CanX-4/-5 formation flying technology demonstration.
A Psychoeducational Intervention for People Affected by Pancreatic Cancer
Keywords: advanced cancer
implementation science
palliative care
pancreatic cancer
psychoeducation
supportive care

The two aims of this thesis were to: (1) develop an interdisciplinary psychoeducational intervention for people affected by pancreatic cancer; and 2) evaluate the feasibility, acceptability, and preliminary efficacy of its implementation. All stages of research were informed by implementation science principles. In Study One, we developed Living Well with Pancreatic Cancer—an empirically-based, single session, manualized group intervention focused on supportive care needs in pancreatic cancer. Study Two was a mixed methods study to examine early phase implementation of our intervention in a pancreatic oncology clinic. Content and delivery were acceptable to patients, caregivers, and health care professionals (HCPs). Benefits included improved relationships with HCPs and knowledge of palliative and supportive care. Implementation was feasible, facilitated by stakeholder commitment and research support; however, additional human resourcing is required for sustainability. This research presents an innovative approach to operationalize supportive care and promote uptake of complex interventions into practice.
Fabrication and Evaluation of PVA Modified Hydrophilic Cellulose Membrane and TiO2/FAS Modified Superhydrophobic PVDF Electrospun Nanofiber Membrane for Applications in Membrane Bioreactor and Membrane Distillation
Keywords: Desalination
Electrospun Nanofiber Membrane
Membrane Bioreactor
Membrane Distillation
Superhydrophobicity
Water and Wastewater Treatment

In this study, two novel membranes were fabricated for membrane-based water and wastewater treatment processes. A PVA modified hydrophilic cellulose membrane was developed for membrane bioreactor, and the fabrication process is based on hand sheet making and dip-coating process. The membrane performance was evaluated based on flux-step experiments and long-term filtration tests. The results suggested that the modified membranes can operate up to 185 hours, and can provide a MLSS rejection that up to 99.9%. A TiO2/FAS modified superhydrophobic PVDF ENM was fabricated for membrane distillation process, and the manufacture process includes electrospinning, heat-pressing, and dip-coating. The membrane surface properties were investigated via SEM, XPS, and the membrane hydrophobicity was determined based on the apparent contact angle measurement. The superhydrophobic membrane was tested on a bench-scale VMD system, and the results suggested that the membrane was able to effectively treat different feed solutions, and can provide a stable performance.
Mental Illness Diagnoses After Intensive Care
Keywords: intensive care medicine
long-term ICU complications
mental illness
post intensive care syndrome

Background: Survivors of critical illnesses that require intensive care unit (ICU) admission may be at risk of developing new mental illness diagnoses. Methods: Population-based study (2005-2015) of adult ICU survivors in Ontario, Canada, excluding patients with prior mental illness diagnoses. The primary outcome was new mental illness diagnosis during 1-year follow-up, measured using multivariable models that adjusted for potential confounders and the competing risk of death. Results: Overall, the 121,125 patients who survived an ICU admission during the study period had higher adjusted risk of mental illness diagnoses compared to hospitalized controls (HR1.08, 95%CI 1.07-1.10; p
Optimization Application of Acellular Oxidative Potential Measurements to Urban Ambient Particulate Matter
Keywords: air quality
exposure
oxidative burden
oxidative potential
particulate matter
urban

Oxidative potential (OP) and oxidative burden (OB) are emerging metrics for assessing air pollution hazard and risk. Three acellular assays were tested and recommendations were made for standard, reproducible approaches. Standardized practices for choosing analysis concentrations, incorporating standards and controls, and mixing reduced inter-experimental variability and facilitated identification of failed assays. These methods were applied to samples collected from across Toronto, Canada to assess the spatial and seasonal variability in OP and OB of fine particulate matter (PM2.5). OP and OB exhibited greater spatial variability than PM2.5 mass, and OPDTT exhibited greater seasonal variability than PM2.5 mass. Finally, associations between chemical composition and OP suggest that OP may capture the influence of local emissions, such as those from brake wear and road dust. Future work should focus on testing standardized protocols across laboratories to facilitate inter-lab collaborations, and investigating OP associations with a broader suite of chemical species.
Plasmodesmatal Density and Cell Wall Architecture Across the C3 to C4 Evolutionary Gradient in Flaveria
Keywords: C4 photosynthesis
flaveria
photosynthesis
pitfield
plasmodesmata
transport

High plasmodesmatal density between mesophyll and bundle sheath cells is of importance in C4 plants, where rapid intercellular movement of metabolites is required for efficient operation of C4 photosynthesis. Using the genus Flaveria, I evaluate the hypothesis that plasmodesmatal density gradually increases in C3-C4 intermediate species at the bundle sheath and mesophyll cell interface. Results show that plasmodesmatal density gradually increases as the C4 cycle strengthens in parallel to a reduction in bundle sheath and mesophyll cell contact area. In contrast, absolute number of plasmodesmata does not significantly increase until the C4-like transitional stage. Based on these results, I conclude that plasmodesmatal density gradually increases as a byproduct of other anatomical changes, while elevation of plasmodesmata is punctual, occurring at the C4-like transitional stage.
Examining Effects of Early Life Stress and Moderating Influences of Current Life Stress on Reward Processing in Young Adults
Keywords: Adversity
Motivation
Reward
Reward processing
Reward sensitivity
Stress

This study investigated whether high levels of perceived life stress (Perceived Stress Scale; PSS) moderate the relationship between higher levels of childhood adversity (Childhood Trauma Questionnaire; CTQ) and reduced reward processing functions in a university sample. It was hypothesized that early life adversity and perceived stress would lead to reduced reward sensitivity, measured through performance on the Monetary Incentive Delay Task (MIDT). Further, early life adversity was predicted to reduce motivational behaviours, measured through performance on the Effort Expenditure for Rewards Task (EEfRT). While results did not reveal a significant interaction between childhood adversity and current life stress on reward processes, higher CTQ scores were associated with reduced accuracy in the MIDT. Participants in the high stress group also demonstrated increased reaction times across MIDT trials. There were no significant effects on the EEfRT. These results demonstrate independent associations between early life adversity, current perceived stress, and reduced reward sensitivity.
The Three I's of Diabetes Integration in Emerging Adulthood: Developing a Framework to Individualize Diabetes Care
Keywords: Emerging adulthood
Health care transition
Narrative research
Self-management
Type 1 diabetes

Transition to adult diabetes care occurs during a challenging stage of life known as emerging adulthood. As emerging adults are tasked with increased responsibility for diabetes management, they are faced with competing demands in work and education. This study employed a narrative approach to elucidate the lived experiences of emerging adults with Type 1 diabetes. In-depth interviews were performed with 33 participants (18 to 24 years of age). Narrative analysis defined story typology and themes across first-hand accounts. Participants narrated life with diabetes through one of three ‘lenses’: ingrained (n=14), intrusive (n=12) and inconspicuous (n=7). Participants conveying an ingrained lens described actively integrating diabetes within their lives. Through an intrusive lens, participants described struggles trying to accept diabetes and striving for control. Participants conveying an inconspicuous lens expressed a desire to minimize attention towards diabetes to protect their normalcy. This conceptual framework presents opportunities to individualize support accordingly.
Microrobots with Programmable Three-dimensional Magnetizations and Motions
Keywords: magnetic materials
magnetization patterning
microrobots
programmable morphology
soft actuators

Flexible magnetic small-scale robots use patterned magnetization to achieve fast transformation into complex three-dimensional shapes, and thereby achieve locomotion capabilities and functions. These capabilities address current challenges for microrobots such as drug delivery, object manipulation, and minimally invasive procedures. However, possible design options are limited by the existing capabilities of patterning magnetic particles in flexible materials. Here, we report a method for patterning hard magnetic microparticles in an elastomer matrix. This method, based on UV-lithography, uses controlled reorientation of magnetic particles and selective exposure to UV light to encode magnetic particles in planar materials with arbitrary orientation with a geometrical feature size as small as 100 µm. The patterned 3D magnetization profile allows higher-order and multi-axis bending, large-angle bending, and combined bending and torsion in one sheet of polymer, creating previously unachievable shape changes and micro-robotic locomotion mechanisms such as multi-arm power grasping and multi-legged crawling.
Differential Regulation of Cx43 Expression and Gap Junction Formation by Progesterone Receptor A and B in Breast Cancer Cells
Keywords: Breast Cancer
CRISPR
Cx43
in vitro
Progesterone

Progesterone (P4) imparts distinct effects in the breast via its progesterone receptors (PRs) PRA and PRB. Since the gap junction and tumour suppressor protein Connexin 43 (Cx43) is differentially regulated by P4 via PRA/B in human myometrial cells, we sought to delineate the roles of PRA/B on Cx43 in breast cancer cells. We hypothesize that, similar to myometrial cells, the two PRs differentially affect Cx43 expression, trafficking, and gap junction intercellular communication (GJIC) in breast cancer cells. In this project, I have shown that in the luminal A cell line MCF7, PRA promotes Cx43 expression, trafficking (similarly observed in the cell line MFM223), and GJIC whereas PRB inhibits these processes. Conversely, in the basal-like cell line MDA-MB-231, P4 inhibits Cx43 expression, intracellular trafficking, and GJIC through both PRs. These data provide insight as to how PRs differentially regulate the same gene, Cx43, in contrasting in vitro models of breast cancer.
Engineering Ca2+-activated Control of Ras Family GTPases
Keywords: calcium signaling
cell-based therapies
cellular reprogramming
genetics
protein
ras

Reprogrammed cells are capable of sensing specified biomarkers for targeting disease sites. My work aims to rewire mammalian cells to use Ca2+ signaling to respond to a broad spectrum of stimuli. Previously, a Ca2+-CaM system replaced the GTP/GDP switch in Rho-GTPases such that increased intracellular Ca2+ leads to protein activation. This work applied the same strategy to a Rab and Ras GTPase, Rab5 and Ras, respectively. Ca2+-activated Rab5 (called Raber) induces cell retraction, whereas, Ca2+-activated Ras (called Raser) induces focus formation. To demonstrate rewiring potential to Ca2+ mobilizing proteins, Raber and Raser were co-expressed with either ChR2 or VEGFR2 to indirectly activate them with light and VEGF, respectively. This work demonstrates the potential for these proteins to be activated by any external stimuli via Ca2+ rewiring. In regards to cell-based therapies, Raber can enable cellular detachment, encouraging migration, whereas Raser can enable cells to form foci, accumulating at target sites.
Examining the Relations among Autobiographical Memory Recall Types, Quality of Descriptions, and Emotional Arousal
Keywords: Autobiographical Memory Recall
Depression
Emotional Arousal
Psychotherapy
Quality of Descriptions

Recalling specific or episodic (rather than generic) memories and using descriptive language in psychotherapy sessions have been shown to be two ways of enhancing clients’ emotional arousal. This study’s aim was to test the relationships among depressed clients’ types of memory recall, quality of language, and emotional arousal in psychotherapy. As predicted, correlation analyses revealed a positive relationship between clients’ quality of language and emotional arousal and a negative relationship between clients’ pre-therapy level of depression and proportion of their specific memory recalls. However, contrary to the prediction, pairwise comparisons revealed that recalls of generic memories were significantly higher in their ratings of emotional arousal than recalls of specific memories, and clients’ post-therapy levels of depression were unrelated to both their in-session levels of emotional arousal and quality of descriptions. These findings hold theoretical and clinical implications for understanding the relationships among types of memory recall, quality of language, and emotional arousal in the context of psychotherapy for depression.
Evaluating the Clinical Utility of Long Non-coding RNAs as Prognostic Biomarkers in Cancer
Keywords: Cancer
lncRNA
Prognostic
RNA
Survival

Cancer patient risk stratification remains a significant challenge in the clinic. Molecular profiles of protein-coding genes have showed limited clinical utility as diagnostic or prognostic biomarkers. Long non-coding RNAs (lncRNAs) are increasingly associated with diverse cellular functions and disease mechanisms and their expression is often dysregulated in cancer. Thus, a systematic analysis of lncRNA expression in cancer is likely to lead to clinically relevant and biological insights. Here, we evaluated the expression of 5,785 lncRNAs in relation to overall patient survival across 28 cancer types and 8,454 patients. We implemented regularized survival models and cross-validation to identify the most representative lncRNA candidates. We compiled a catalogue of 166 unique lncRNAs across 22 cancer types and summarized their survival prediction performance relative to nearby protein-coding genes and previously defined prognostic features. We highlighted several high-confidence candidates with potential prognostic value and further predicted the molecular processes they may be involved in.
How Can Researchers and Research Users Initiate Integrated Knowledge Translation (IKT) Partnerships?
Keywords: Health services research
Integrated knowledge translation

Integrated knowledge translation (IKT) describes researcher and research user partnerships formed with the long-term goal to increase knowledge uptake. Research shows that processes for initiating IKT partnerships are still developing and initiation remains challenging. The purpose of this thesis was to explore IKT partnership initiation to understand and provide guidance on how to optimize the process. Phase 1, a meta-narrative review of the literature guided by RAMESES reporting standards, described how IKT initiation was undertaken by others. Phase 2, semi-structured interviews guided by the COREQ checklist, explored IKT initiation processes, enablers, and barriers. Six narratives describing IKT initiation were identified from the literature: IKT, action research, stakeholder engagement, knowledge transfer, team initiation and shared mental models. Twenty-two Canadian experts in IKT were interviewed. Data from the two phases were blended to create a summary of inputs, processes, influencing factors and outputs of IKT initiation. Practice and research implications were suggested.
Polypyrrole-Chitosan Hydrogel Functions as a Semi-conductive Bridge Within Fibrotic Matrix and Cardiac Tissue
Keywords: Arrhythmia
Biomaterials
Electrophysiology
Myocardial Infarction
Tissue Engineering

Myocardial infarction(MI) results in myocardial fibrosis leading to cardiac arrhythmia. We previously developed conductive biomaterial, polypyrrole-chitosan(PPY:CHI), which can prevent arrhythmias after MI. However, mechanism is unknown. I hypothesized that PPY:CHI reduces myocardial fibrotic tissue(FT) resistance to enhance myocardial conduction. To investigate electrical improvements of FT, PPY:CHI was added into Invitro and Ex-vivo FT matrix models. Three studies were performed to evaluate effect of PPY:CHI on fibrotic matrix, 1)impedance analysis using impedance spectroscopy; 2)electrical potential analysis using multi-electrode arrays(MEA), and 3)conduction velocity analysis using MEA. The research results showed 1)PPY:CHI reduced the impedance of the FT to a level like healthy myocardium; 2)PPY:CHI influenced the FT to transmit field potentials to a level like healthy myocardium; and 3)PPY:CHI influenced the FT to generate a velocity to a level like healthy myocardium. Addition of PPY:CHI to the FT models improved electrical conduction and transferred electrical potentials at a distance.
Accumulating Multimorbidity: the Role of Depression, Socioeconomic Status, and Other Factors
Keywords: depression
multimorbidity
socioeconomic status

Multimorbidity is a significant challenge facing patients, clinicians, and the healthcare system. This study examines whether depression and socioeconomic status are associated with incident physical illness and multimorbidity, after controlling for potential sociodemographic, behavioural, and clinical confounders. This is a longitudinal retrospective cohort study. Cohorts were derived by linking adult respondents to three population health surveys to health administrative databases in Ontario and were followed for ten years. Cox proportional hazards regression was used to examine the rate at which participants developed illnesses, and Poisson regression was used to examine the number of conditions developed after ten years. In this study, depression increased the risk of accumulating multimorbidity, in terms of both time to development of conditions and number of conditions accumulated after ten years. Higher household incomes were protective against developing a second and subsequent physical illness, but not the first incident illness in a disease-free cohort.