VictorJuiz/thesis huggingface dataset:
Modeling the Development of Human Atrial and Ventricular Cardiomyocyte Lineages from Human Pluripotent Stem Cells
Keywords: atrial cardiomyocyte
heart
Human pluripotent stem cell
regenerative medicine
ventricular cardiomyocyte

The ability to direct the differentiation of human pluripotent stem cells (hPSCs) to the different cardiovascular lineages is a prerequisite to modeling specific forms of cardiovascular disease in vitro and for developing novel therapies to treat them. Here we have investigated the development of human atrial and ventricular lineages and demonstrated that retinoic acid (RA) signaling is critical for the atrial fate specification. Insights into the origin of RA signaling has led us to identify that the atrial and ventricular cardiomyocyte lineages develop from distinct mesoderm populations that are marked by the expression of RALDH2 and CD235a, respectively. The RALDH2+ cells give rise to highly enriched atrial cardiomyocytes in the presence of retinol, suggesting that these progenitors can both produce and respond to RA in an autocrine fashion. Analyses of derivative cardiomyocyte populations have demonstrated that the generation of highly enriched, functional cardiomyocyte subtypes depend on the appropriate patterning of early progenitor populations. Based on these findings, we have initiated two independent analytical approaches, the CD-antibody library screen and single cell RNA-seq (scRNA-seq) analyses, to gain better insights into these progenitor populations. Analyses from the antibody screen has identified a new cell surface marker CD324 that has uniquely marked the transition from CD235a+ mesoderm to the early NKX2-5+ cardiomyocyte progenitor stage. We hypothesize that CD324 expression marks the formation of the cardiac crescent-like population from hPSCs. From the same study, we have identified that NOTCH2 and -3 receptors are expressed on the ventricular but not atrial mesoderm populations, suggesting a lineage-specific role of this signaling pathway. Preliminary analyses of scRNA-seq study has also demonstrated heterogeneity within the ventricular progenitor population. Together, these findings provide novel insights into the earliest stage of human heart development that enable the generation of highly enriched cardiomyocyte subtypes for future therapeutic applications.
An Examination of the role of MicroRNA-21 in the Pathobiology of Degenerative Cervical Myelopathy Using Human and Animal Data
Keywords: Biomarkers
Cervical Myelopathy
Inflammation
Microglia
MicroRNA-21

MicroRNA-21 (miR-21) is upregulated in multiple models of traumatic and neuroinflammatory CNS injury. Here, we sought to evaluate the role of miR-21 in the most common form of adult spinal cord dysfunction, degenerative cervical myelopathy (DCM). Using a mouse model of DCM where the spinal cord is progressively compressed over multiple weeks, we found elevated expression of miR-21 in both spinal cord and plasma at 6 weeks and 12 weeks after onset. Deletion of miR-21 in a null mutant mouse strain significantly preserved locomotor function on the rotarod and forced swim tests, but at the cost of increased neuropathic pain. Preservation of motor function was attributed to reduced inflammation, denoted by the approximately 50% reduction in stereological counts of Iba1-positive activated microglia in miR-21 knockout spinal cord sections. In vitro experiments using primary microglia found that miR-21 is induced under pro- or anti-inflammatory conditions, but that miR-21 deletion did not affect the cells natural reaction to these stimuli. Target prediction algorithms identified the IL-6/STAT3 pathway as a potential downstream target of miR-21, and subsequent in vitro testing found that components of the IL-6 receptor complex, IL-6ra, and IL-6st were significantly higher in miR-21 knockout microglia. Finally, to determine whether miR-21 and other microRNAs related to human DCM could be used as biomarkers, we examined plasma microRNA expression in a human DCM cohort. Expression of miR-21 and other microRNAs were found to be correlated to current patient symptoms. In the surgical cohort, baseline levels of miR-132-3p and miR-34a were found to predict surgical outcome, while miR-21 approached a statistically significant correlation with post-operative lower motor function (p=0.05). In aggregate, we find that miR-21 may have a pro-inflammatory role in the DCM microglial response, and that miR-21 expression may be related to the manifestation of motor deficits.
ESSENTIAL COFACTORS IN ANAEROBIC MICROBIAL CONSORTIA USED FOR BIOREMEDIATION: BIOSYNTHESIS, FUNCTION AND REGENERATION
Keywords: Anaerobic bioremediation
Biosynthesis
Cofactors
Cross-feedings
Environmental microbiology
Organohalide respiration

Most microorganisms in nature live in communities and have developed tightly coordinated metabolism via metabolite exchanges. Cofactors are “helper molecules” in all cells, modulating the activity of many enzymes or serving as the electron shuttle. However, biosynthesis of cofactors, such as cobamides, is sometimes accomplished by only one specific phylogenetic group of microorganisms. Therefore, cofactors and their producers play pivotal roles in the functionality, metabolic rates, and population structure of a microbial community. This thesis focuses on three types of cofactors: (i) cobamides, (ii) NADPH, and (iii) prenylated flavin mononucleotide (prFMN) that are involved in anaerobic bioremediation of chlorinated solvents and aromatic pollutants. Cobamides are a family of cobalt-containing tetrapyrroles involved in biochemical reactions including methyltransfer reactions, isomerizations, and reductive dehalogenation. This thesis reports the identification of a functional cobamide prosthetic group in tetrachloroethene dehalogenases (PceA) of Desulfitobacterium hafniense and Geobacter lovleyi using a tiered blue-native polyacrylamide gel electrophoresis (BN-PAGE) and liquid chromatography-mass spectroscopy (LC-MS) method. The metabolic annotations of Dehalobacter restrictus (Dhb), a model organism for bioremediation of chlorinated solvents, were experimentally verified. The verified annotations were written into a constraint-based metabolic model, which identified that NADPH regeneration and de novo serine biosynthesis could be bottlenecks in Dhb metabolism. Using an integrated computational/experimental approach, the stringent nutrient requirements of Dhb were characterized. Further experimental analysis on the Dhb-enriched ACT-3 consortium has revealed an interspecies malate-pyruvate shuttle system between Dhb and its syntrophic partner. prFMN is a newly identified cofactor of UbiD reversible aromatic decarboxylases that are involved in ubiquinone biosynthesis, biological decomposition of lignin monomers, and anaerobic biodegradation of aromatic pollutants. We discovered that in Escherichia coli, dimethylallyl-monophosphate (DMAP), the prenyl donor of prFMN, can be produced from either prenol phosphorylation or from dimethylallyl-pyrophosphate dephosphorylation. In conclusion, this thesis reports biosynthesis and function of new cofactors as well as new mechanisms for reconciling cofactor regeneration in anaerobic microbial communities. Realizing these metabolic interdependencies generates opportunities to manipulate the microbiomes for better outcomes in bioremediation and industrial biotechnology. Interestingly, the identified interspecies cofactor exchange mechanism also provides insights into how life gradually evolved into complexity.
A Mixed Method Exploration of Suicidality in Clients with Intellectual Disability
Keywords: Developmental disability
Intellectual disability
Suicide
Suicide assessment
Suicide prevention
Suicide screening

The goal of this dissertation was to investigate suicidality in individuals with intellectual disability (ID). Study 1 reviewed files of adolescent clients at an agency that serves individuals with ID to estimate the prevalence of suicidality, identify factors associated with suicidality, and describe clinical practices regarding suicidality. Study 2 used in-depth interviews with clinicians, which were analyzed qualitatively, to explore their experiences with suicidality in their clients with ID and their practices to address clients’ suicidality. The results of both studies were integrated using a mixed-methods approach. In study 1, 192 case files of adolescent clients aged 12 to 17 were systematically reviewed using a researcher-generated coding scheme. Data was collected on variables that spanned demographic information, mental and physical health, personal characteristics and experiences, family stressors, and suicidality domains. Adequate inter-rater reliability of data collection was achieved. The estimated suicidality prevalence was 13.0%. Factors associated with suicidality included abuse history, trauma history, psychopathology in the family, and higher functioning (i.e., borderline intelligence and mild ID). These factors provided some support for diathesis-stress models of suicide in youth with ID. Files infrequently documented clinical practices addressing client suicidality. In study 2, semi-structured interviews with 10 clinicians were analyzed using Grounded Theory to create an explanatory framework for understanding clinicians’ experiences with suicidality in their child, adolescent, and adult clients with ID. Although aspects of responding to suicidality in clients with ID were similar to that of clients without ID, the process was more complex due to the inadequacy of the mental health system to address clients’ needs, and clients’ cognitive and communication difficulties made it more difficult to assess suicidality and implement interventions. Suicidality in clients also put an inordinate burden on their caregivers, and the clinicians felt that they were facing the unknown when they worked with these clients.
Negotiating the Zone of Proximal Development in a Pre-University Advanced Academic Writing Classroom
Keywords: English as a Second Language
English for Academic Purposes
Second Language Writing
Socio-cultural Theory
Zone of proximal development

Grounded in sociocultural theory (SCT) of mind and a social-constructivist view of learning, the present study analyzed in depth the construction of Zones of Proximal Development (ZPD) among an experienced teacher and her students over the duration of a pre-university academic English writing course. The research (a) investigated the teacher’s perceptions of the factors that facilitated the creation of opportunities for learning, (b) analyzed classroom dynamics, participation, and interaction patterns over time to identify the instructional choices most conducive to learning, and (c) examined the factors that facilitated or hindered 3 focal students’ take up of opportunities for learning. Multiple sources of data included in-depth teacher interviews, observation and coding of 70 hours of classroom instruction, the teacher’s and students’ stimulated recalls on selected episodes of classroom interactions, and documents such as handouts, students’ assignments, and the teacher’s feedback on students’ writing. The teacher’s interviews revealed a dialectic relationship between two types of facilitative factors she implemented: (a) emotional sustenance, achieved by building rapport with students, maintaining dependable codes of academic behavior, and balancing senses of challenge and attainment in students and (b) four instructional design and pedagogical choices: establishing continuity between course components, monitoring students’ progress, providing several types of assistance, and then later withholding assistance to encourage students’ self-regulation. A microgenetic analysis of two instructional units showed how continuity was established through the use of advanced organizers and clear intertextual links. The gradual decrease of teacher talk over the units gave room for active student participation and engagement. Case studies of 3 focal students revealed that these students valued different mediational tools according to their individual developmental histories and goals. They all showed evidence of investment and intentionality with stronger students commanding a larger repertoire of strategies and showing more understanding of the course design and the teacher’s goals. In sum, the findings indicate that opportunities for learning within the ZPD were constructed through the overlap of multiple interacting factors including emotional sustenance, effective instructional practices, individualized support, and students’ self-regulation and investment. Implications are suggested for deconstructing the ZPD, understanding academic writing teaching and learning, and further research.
Sonic Poetics of Home and the Art of Making Do in Sinophone Toronto
Keywords: CANADA
DIASPORA
ETHNICITY
EVERYDAY LIFE
SINOPHONE
SOUND

This dissertation is an ethnography of the “homes” imagined and practiced through sound and music in Chinese-speaking immigrant communities of Toronto. The notion of “home” and the social imaginary of homelands have been theorized extensively as important linchpins for forming diasporic identities and cohering transnational migrant communities. Music plays a vital role in these processes, as the ethnomusicology of diaspora has demonstrated. Although important, the dominance of formal musical performance in both academic and popular discourses tend to eclipse the fine-grained work of everyday life in contemporary immigrant experiences. This dissertation offers a complementary alternative, arguing that diasporic subjectivities emerge more from accumulations of everyday practices than through self-conscious memorialization of the lost homelands. Based on ethnographic research, I examine how homeland imaginaries mediate diasporic experiences of “home” in everyday singing, speaking, and modes of listening. I also explore how a person’s sonic expressivity interacts with conditioning contexts such as Canada’s multicultural ideology. In the first of three case studies, I explore how ethnic and age identities were contested through sounding and listening in a Chinese nursing home. The second case study focuses on an apartment where queer immigrants gathered for respite from the palpable heteronormativity and homophobia of Toronto’s Chinese diaspora. The final case study follows a young woman as she aurally forged diasporic intimacy in ethnic retail spaces, a boarding house, and a kitchen. Each case study considers the emergence of a particular kind of diasporic subjectivity through accumulations of everyday sonic practices where mediations between public and private, and collectivity and individuality occur. Re-orienting toward the cumulative effects of everyday life, this dissertation reveals how diasporic “homes” can be unsettling and fractured. It also shows, by the same token, how senses of belonging are born out of continuous negotiations, and should not be taken for granted.
Choosing Service Providers: What Clients Want and Service Providers Do
Keywords: choice
honesty
judgment and decision making
mindset
service

A large component of marketing communication consists of service providers trying to persuade clients to use their services. This persuasive information frequently takes the form of service providers’ past experience, some of which is highly relevant to the clients’ interest and others less so. Two essays investigated how different ways of describing the work experience of service providers influence clients’ choices. The first essay examined how service providers and clients chose between two work descriptions which described the less relevant work experience using either a specific (e.g., fund manager) or general (e.g., financial service) job category. Findings show that service providers choose a specific description of their work experience with more information than clients would want to see. It was because service providers judged presenting specific descriptions as a signal of their transparency more than clients judged it. Specific descriptions were judged as transparent when participants considered that a service provider could have described the same experience using a less-revealing general description. Considering that the service provider could have chosen a less transparent description was easier for service providers whereas this same transparency is more difficult for clients to observe. The second essay identified two types of experience, broad and deep, and examined whether and when each type of experience is evaluated more favorably. Drawing upon the theory of mindset, I found that deep experience is evaluated highly when clients adopt an implemental mindset. Clients evaluated a service provider with deep experience more favorably when they need someone to implement a task than when they need someone to consult with to find a solution for their problem. Moreover, a service provider with deep experience was evaluated highly when clients needed the service immediately and reviewed implemental steps for solving their problem. The current research contributes to the literature by showing that evaluation of a specific information format and an information format highlighting depth of experience depends on the type of viewer and implemental mindset. Furthermore, the findings offer insights into service literature by showing transparency inferred from self-description and depth of experience as factors influencing choice.
Development of Coping Strategies and Sexual Subjectivity among Female Youth in the Northwest Territories, described through Body Mapping
Keywords: arts-based research methods
body mapping
Indigenous populations
mental health
sexual subjectivity
youth

Background: The sexual and mental health of young women in the Northwest Territories (NWT) is a serious public health concern. In response, I developed an arts-based intervention called FOXY (Fostering Open eXpression among Youth). FOXY is grounded in social ecological theory and guided by a trauma-informed lens. Objectives: To learn about sexual and mental health from young women in the NWT attending FOXY, using the arts-based method of body mapping. Specifically, to 1) describe and evaluate body mapping an as approach for educational intervention and research data collection with young NWT women; 2) discover the self-identified strategies that young women in the NWT use to cope with mental health issues; and 3) explore how young NWT women develop their sexual subjectivity within the context of contraception use and access. Results: 41 female FOXY youth (aged 13 to 17 years) from six NWT communities completed in-depth interviews, and seven FOXY facilitators provided written reflections. Body mapping was an intervention tool that supported and encouraged participant self-reflection, introspection, personal connectedness, and processing difficult emotions. The process catalyzed data collection that enabled trust and youth voice in research, reduced verbal communication barriers, and facilitated collection of rich data regarding personal experiences. Participants used five mental health coping strategies: grounding via nature, strength through Indigenous cultures, connection with God and Christian beliefs, expression using the arts, and relationships with social supports. Barriers to the development of sexual subjectivity included a culture of stigma and shame surrounding sexuality; pervasive alcohol use in communities; predatory behaviours by older men; poor quality sexual health education offered in schools; and, issues with accessing health services. Comprehensive sexual health education; widespread access to free condoms; and, positive health support networks with female relatives, peers, and some teachers were identified as facilitators for the development of sexual subjectivity. Conclusion: A trauma-informed, holistic, culturally relevant framework of multiple intervention strategies at the intrapersonal, interpersonal, community, and societal levels within a comprehensive social ecological model can address the complex interplay of sexual and mental health needs of young NWT women.
Utilizing Combinatorial Screening Platforms and Modelling Techniques to Predict Optimal Design Conditions for 3D Mesenchymal Stromal Cell Based Heart Valve Tissue Engineering
Keywords: 3D
combinatorial screening
heart valve
microenvironment
response surface
tissue engineering

Microenvironmental factors such as biomaterial physical and chemical properties, mechanical stimuli, and soluble chemical cues integrate in vivo to direct the differentiation of mesenchymal stromal cells (MSCs). Identifying what factor combinations best promote the differentiation of MSCs into myofibroblasts (tissue-synthetic cells of developing valves), but not into osteoblasts, is challenging when designing for heart valve tissue engineering (HVTE). To date, select combinations of microenvironmental factors have been studied in two-dimensional (2D) culture, but systematic consideration of the integration of factors in 3D culture has not been explored fully. We first developed a screening platform using polyethylene glycol norbornene (PEG-NB) as a model biomaterial with which the polymer wt% (to control elastic modulus), adhesion peptide types (RGD, DGEA, YIGSR) and densities, and soluble TGF-β1 could be controlled independently and combinatorially in arrays of 3D hydrogels. We then utilized a deformable membrane platform to screen those same factors under dynamic mechanical stimulation. In a static system, low PEG-NB wt% materials with high concentrations of RGD permitted significant spreading and expression of myofibroblastic markers (α-SMA and collagen type I) in the presence of TGF-β1. In the dynamic system, multiple metrics for α-SMA and collagen type I expression converged to show that mechanical stimulation and TGF-β1 can have different individual and integrated effects on myofibrogenesis depending on the presence of other factors (most notably, PEGNB or RGD), meaning that design decisions could be erroneous if made based on experiments that do not consider integrative effects. When combined with a design of experiments approach, statistical modelling defined previously undescribed response relationships that predicted conditions (subsequently experimentally validated) that promoted maximal α-SMA and collagen expression beyond the initial screening data. Modelling complex interactions has the potential to reveal key regulatory pathways for myofibrogenesis, which has implications for study in other areas like pathological fibrosis and cancer research.