VictorJuiz/thesis huggingface dataset:
Bridging the Gap: Exploring the Treatment Experiences of Children and Youth with Medulloblastoma
Keywords: Attachment
Child Development
Healthcare
Information and Communication Technologies
Isolation
School

Diagnosis and treatment of childhood cancer can be an exceptionally difficult and stressful experience for children and their families. Of all childhood cancers, brain tumours are the second most common, with medulloblastoma the most frequently occurring malignant brain tumour among children. Very aggressive and difficult to cure, medulloblastoma warrants unique and intensive treatment Protocol SJMB03 which typically combines surgery, radiation, and chemotherapy, including high dose chemotherapy with autologous stem cell rescue. During treatment, children and youth are usually required to stay in a protective isolation room in hospital to guard against infections. Visiting policies are strict, typically limiting visitors to parents or caregivers only. Children are unable to see peers in person during this period, which can last from weeks to many months. To address this ethically complex issue, the overall goal of this dissertation is to give voice to children and youth treated with this protocol in order to better understand their experiences. To meet this goal, the objectives of this dissertation are to explore: 1) how children and youth diagnosed with medulloblastoma and treated with protocol SJBM03 perceive the experience of protective isolation in hospital; 2) the social and academicimplications of their treatment experience; 3) children and youths’ use of cyber technologies to bridge communication with peers during treatment; 4) children and youths’ knowledge of and experience with traditional bullying and cyber bullying; and 5) the experience of returning to school following completion of this treatment protocol. This dissertation provides findings that are timely and significant, as the COVID-19 pandemic has highlighted the moral and ethical responsibility to better understand and address the impact of isolation for children and families. Considerations for hospital and school social workers to promote relationships and connection, while facilitating a smooth transition as these vulnerable children and youth return to school are included.
Plastid Genome Evolution in the Parasitic Genera Cuscuta (Convolvulaceae) and Krameria (Krameriaceae)
Keywords: Convolvulaceae
Cuscuta
Heterotroph
Parasite
Plastid
Plastome

Almost all plants are primary producers and many of their phenotypic and genotypic features are centered on the ability to conduct photosynthesis. Variation in these features is rare across green plants due to the degree of selective pressure imposed by primary production. This is particularly true for plastid genomes (plastomes) given that chloroplasts are the primary site of photosynthesis in the cell and that plastomes encode key portions of the photosynthetic apparatus.In only a handful of embryophyte lineages, however, a heterotrophic lifestyle has evolved and reliance on photosynthesis for resource acquisition is reduced or completely absent. In these plants, the selective pressure imposed by primary production is lifted and previously conserved features are able to evolve more freely, including the plastid genome. The genus Cuscuta is one such lineage. It contains c. 200 obligate branch parasite species, diverse in terms of the degree of their heterotrophy: some can conduct limited photosynthesis whilst others are entirely nonphotosynthetic. In chapters 2-4, I assembled and analyzed plastomes from each section of Cuscuta in order to comprehensively characterize the patterns in their evolution across the genus. I found that most species retain the bulk of their photosynthesis genes and, therefore, at least some aspect of the bioenergetic pathway remains available for them to use. In plants forming two clades within Cuscuta, however, there was a wholesale loss of plastid genes encoding the photosynthetic machinery. The genus Krameria contains 18 species of root hemiparasites and they, like Cuscuta, represent an additional independent transition from autotrophy to heterotrophy. In chapter 5, I assembled the plastid genome of one Krameria species and analyzed it along with two previously reported plastid genomes from the group. I found that these species exhibit sweeping retention of plastid genes, unprecedented amongst parasitic angiosperms, and do not appear to have been impacted by the transition to heterotrophy the same way that other parasitic lineages have been. By characterizing plastomes in these two genera, my thesis contributes to our growing understanding of how heterotrophic plants, and genomes, change due to a reduction (or complete loss) of the selective pressure imposed by photosynthesis.
Water Vapour and Ozone: Measuring Key Trace Gases in Challenging Regions
Keywords: Arctic
FTIR
Ozone
Remote Sensing
UTLS
Water Vapour

This thesis focuses on characterizing water vapour and ozone in difficult to measure regions using ground-based and space-borne instruments. The regions of interest are the Upper Troposphere - Lower Stratosphere (UTLS), made challenging due to the dynamic and chemical complexity endemic to the region; the Arctic, due to its remoteness and extreme temperatures; and the mesosphere, due to low gas concentrations and the dearth of satellite instruments capable of measuring over its altitude range. The focus on these gases arises from their importance in the atmosphere due to the numerous chemical and climate interactions in which they participate. The first two studies focus on measurements made by PARIS-IR in the Canadian Arctic, with the first focused on developing a novel water vapour product, with emphasis on systematically evaluating different retrieval parameters in order to optimize this new set of water vapour profile estimates. The second is focused on expanding a prior study of eight trace gases with an additional four years of measurements. Both studies involve the comparison of PARIS-IR measurements to coincident trace gas measurements made by other instruments, such as a second ground-based FTIR or ACE-FTS. The third study focuses on water vapour and ozone in the UTLS using the ACE-FTS, MAESTRO, and OSIRIS satellite instruments along with the CMAM39-SD chemistry-climate model. This study involved the creation of zonal-mean multiyear-mean climatologies from measurements made by these satellite instruments, and employed CMAM39-SD as a means of robustly characterizing the differences in these climatologies, free of the influence of measurement sampling patterns. The final study examines mesospheric water vapour from ACE-FTS over solar cycle 24. Herein the response of water vapour to the 11-year solar cycle and dynamical forcers was examined. Emphasis was placed on the trend in mesospheric water vapour and its response to the solar cycle. The trend was found to peak near the mesopause at about 0.6±0.2% per year. Water vapour was found to be anti-correlated over the upper mesosphere with the solar cycle but exhibited a positive response between 50–65 km, and a set of catalytic reactions have been suggested as the potential source of this behaviour.
Dopaminergic Modulation of Ionotropic Transmission in the Anterior Cingulate Cortex in Naïve and Inflammatory Pain States
Keywords: ACC
CRISPR/Cas9
Dopamine
Electrophysiology
Inflammation
Pain

Pain modulation of dopamine (DA) producing nuclei is known to contribute to the affective component of chronic pain. The anterior cingulate cortex (ACC) is a brain region critical for processing acute and chronic pain. Anatomical studies have established bidirectional connectivity between the ACC and ventral tegmental area (VTA) as nodes within the mesocortical pathway with function in regulating motivation. DA modulates behaviour and synaptic transmission by signalling through D1- and D2-like receptors in target areas. I initially sought to characterize the function of the D1R subtype, a receptor imperative for learning and synaptic plasticity. In this regard, I characterized behaviour in a CRISPR/Cas9 mediated somatic knockout of the D1Rs in all neuronal subtypes of the ACC and found enhanced mechanical sensitivity of the hindpaws. Further, patch-clamp electrophysiology on ACC slices from mice revealed that D1R agonists inhibit basal α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) currents in the ACC., while co-application of D1R antagonists with D1R agonists paradoxically produced robust synergistic depression of AMPAR currents in the ACC. At a fundamental level, DA release in the ACC would modulate behaviour by modulating ionotropic synaptic transmission. Thus, I explored the role of ACC dopaminergic modulation of excitatory and inhibitory ionotropic transmission in naïve mice and mice with inflammatory pain. With slice electrophysiology, I demonstrated that DA inhibits both glutamatergic and GABAergic transmission in ACC neurons through a postsynaptic G-protein mechanism. In naïve mice, DA induced synaptic inhibition in majority of the ACC neurons by shifting the E/I balance towards inhibition via exerting greater inhibition of excitatory over inhibitory transmission. However, in mice with inflammatory pain, I observed decreased dopaminergic-mediated inhibition of AMPAR-mediated currents. ACC dopaminergic function was also examined by quantifying the expression of DA receptor proteins and neurotransmitter concentrations in the ACC. In mice with CFA treament, DA receptor expression was enhanced three- and four-days post-CFA treatment in the ACC. In addition, onset of inflammation upregulated DA neurotransmitter concentraion in the ACC. These results demonstrate that acute phase of inflammation may upregulate DA activity in the ACC and persistent inflammation may induce activity-dependent changes in DA receptor expression and signalling in the ACC.
Banking on Equity: Bay Street and Black Women's Leadership in Banks©
Keywords: Anti-Black Racism
Sexism and work
Black Canadian Feminist Thought
Black Women and Leadership
Diversity
Equity
Inclusion
Mentors
Sponsorship
and Networks
Race
Gender
and Leadership

This qualitative research study examines Black women’s leadership experiences in Canadian banks and their perceptions about opportunities for mobility and advancement to executive management positions. The purpose of this research study is to explore and contextualize the epistemic complexities of Black women’s leadership experiences in the Toronto banking sector. The study’s data are collected through in-depth interviews and focus groups with Black women working in leadership positions. Further, this study seeks to examine: (1) the lived experience of Black women’s leadership in Canadian banks; (2) the perceived incongruity between Black women as leaders and those who are seen as possessing characteristics, qualities, and social capital for leadership roles; and (3) how the discourse of multiculturalism, employment equity policies, and corporate climate has impacted Black women’s mobility and advancement opportunities to executive management positions. This study utilizes theoretical frameworks of Critical Race Theory, Black Canadian Feminist Thought, and Intersectionality Theory to explore and examine Black women’s leadership experiences. My analysis engages with discussions of race, gender, class, sexism, and how the construction of whiteness is manifest in institutional power, and how that construction is written and read upon Black women’s leadership to understand the absence of Black women in executive management positions. The findings indicate that being Black and a woman in banking sector negatively impacts their career mobility and advancement. Black women remain locked out of leadership opportunities as they encounter institutional climate of anti-Black racism and sexism, which deems them unfit and incompetent for senior and executive roles based on negative racial stereotypes and lack of sponsorship. Ultimately, these findings relate to the factors and conditions that make Black women’s executive leadership in the Toronto banking sector so exceedingly rare. This study is one of the few Canadian examinations of Black women’s leadership experience in the banking sector.
Exploring the Boundaries of Emotion and Language: Elementary School Newcomers with Emerging Print Literacy as Co-researchers
Keywords: Emotion
Identity
Limited prior schooling
Literacy
Refugees
Translanguaging

The participants in this study are students in Grades 4 to 6 who arrived in Canadian elementary schools with emerging print literacy not having had the right to learn to read and write before migrating to Canada. The research questions that guide this study are: Who are newcomers with emerging print literacy in elementary schools? What emotions are associated with and shape the students’ identities and literacy practices? And how do the students understand the relationship between these emotions and their identities and literacy practices? To answer these questions, this research combines the theories of translanguaging, which views language as being socially constructed and complex (García & Wei, 2014); identity as social positions through which the self is developed (Hall, 1996; Moje, Luke, Davies & Street, 2009); and the sociality of emotion where emotions create the boundaries of what a person or idea is (Ahmed, 2004). Employing a humanizing methodological design (Paris, 2011), I utilized qualitative critical case studies to work with the students in co-creating oral and written texts as well as co-researching with the students to identify and analyze themes of emotions found in each-other’s texts. Each of the three case studies took place at a different school site and included four to six students and their teachers. Key components of the students’ identities are plurilingualism, racialization, low socio-economic status, English-only writers, avid video-game players and social media users, regional migrators and sophisticated consumers of various cultural experiences. The student identified themes include love of family and friends, safety in religion, anger with writing and shyness about videos, which were interwoven with other themes from the data including trauma, print literacy humiliation and safety in Canada. This research shows how plurilingual children who are in the process of learning to read and write can participate meaningfully in the research process. Emotions and translanguaging combine to take us deeper into understanding how the pedagogical incorporation of the students’ plurilingualism and previous experiences, especially with family, are essential to a classroom without humiliation that is truly culturally sustaining and trauma-informed.
Design Principles for Engineering Dynamic Control of Metabolism in Microbes for Chemical Production
Keywords: Computational Biology
Dynamic Control
Lab Automation
Metabolic Engineering
Synthetic Biology
Toggle Switch

Microbial production of chemicals through metabolic engineering has garnered significant interest in recent years due to growing concerns over the sustainability of conventional chemical production processes. Biochemical production offers an environmentally benign alternative through the use of renewable substrates and the ability to catalyze reactions at mild reactor conditions. While advances in bioengineering and systems biology have enhanced our understanding of microbial metabolism and led to the development of tools and techniques for strain design, several rounds of the design-build-test-learn cycle of strain engineering are necessary before a strain with commercial viability can be realized. Bioprocesses with decoupled growth and chemical production stages – where metabolic states are dynamically controlled, have been proposed as a solution to low chemical productivity. In this work, we explore the design principles that govern the effective implementation of such dynamic control strategies and two-stage chemical production processes to develop bioprocesses that offer optimal Titer, Rate, and Yield (TRY) values. To this end, we first build a computational framework that predicts novel two-stage chemical production processes that use a growth-coupled chemical production stage to outperform one-stage alternatives over a wide range of substrate uptake concentrations. Further, this algorithm also predicts optimal operating points that result in enhanced chemical production characteristics and reveals some common features of ideal production stage flux distributions. Next, in order to facilitate the characterization of large strain and genetic circuit libraries required to validate our experimental hypotheses, we develop an eco-friendly automation platform that effectively characterizes cellular phenotypes. Then, we used a model-based design strategy to improve the switching characteristics of a genetic toggle switch – a gene regulatory device that allows the experimental implementation of dynamic control strategies. Specifically, we were able to improve switching speeds and show a trade-off between the speed and the robustness of the switch. Finally, we validated our model findings by building a large library of toggle switch variants that offer a wide range of switching speeds. We anticipate that these design principles along with the switch library will facilitate the widespread implementation of two-stage chemical production processes.
Towards Reliably Handling Inputs Not From the Training Distribution
Keywords: Deep Learning
Generative Models
Machine Learning
Outlier Detection

Deep learning methods today are exceptional at handling test inputs coming from the training distribution. This makes them effective for automating processes in a controlled and closed environment, like in a lab or a factory. To broaden their applicability, we need to develop systems that can act safely in open environments, where they may face ``unexpected’’ inputs. One strategy to handle unexpected inputs is to abstain from making a decision. For example, an image classifier trained to recognize animals in photographs should abstain from assigning a label when the input image contains a building. Bayesian neural networks are promising candidates to make deep classifiers better at detecting such unexpected inputs. The first part of the thesis presents a new variant of Bayesian neural networks that provides computational savings while performing well on benchmark tasks that simulate detecting unexpected inputs. Another strategy to handle unexpected inputs is to estimate how likely an input is from the training distribution. This view decouples the capability of a classifier from how unexpected a test input is. An ideal method can identify whether an input comes from the training distribution and only pass down inputs from the training distribution, effectively creating a closed environment. Deep generative models are good surrogates to the training distribution, hence are promising methods to enable this strategy. We study different types of generative models, identify one practical issue with a popular class of density models built on invertible neural networks, and show promising results for using unnormalized density models for detecting unexpected inputs. The last strategy to cope with inputs not from the training distribution is to adapt to them, using transfer learning and few-shot learning. We first demonstrate that modern generative models are capable of generating images of concepts not present in the training set using auxiliary information. Then, we show two novel applications of few-shot learning. Finally, we propose a benchmark and a baseline method for anomaly detection in the few-shot classification setting. The goal of this last study is to facilitate research on improving the reliability of machine learning models in the increasingly popular few-shot setting.
Uncovering Outdoor Mobility Behaviours of Older Adults With and Without Dementia from GPS Data
Keywords: Automobile Driving
Dementia
Global Positioning System
Machine Learning
Outdoor Mobility
Spatial Analytics

One of the greatest health challenges of the growing ageing population is dementia. Currently, there is no way to stop the progression of dementia or reverse its physiologic changes, and thus, there is an acute need for (1) supporting people with dementia to maintain a healthy lifestyle, and (2) making early diagnosis of the disease. A key determinant of a healthy and active lifestyle is outdoor mobility. However, dementia affects complex activities such as navigation by impairing cognitive and functional abilities, making outdoor mobility particularly challenging for individuals. In addition, with certain dementias such as Alzheimer’s disease, navigational impairment is considered to be one of the earliest signs of the disease process. In this context, characterizing and supporting outdoor mobility for older adults with dementia is of great significance. Global positioning system (GPS) provides an avenue for addressing outdoor mobility challenges in dementia, and its application in dementia detection has become an area of increased interest. Therefore, the overarching aim of this thesis is to provide means to better understand and support outdoor mobility of people with dementia by using passively collected data from GPS. To operationalize this goal, Chapter 2 and 3 of this work present a new outlook on outdoor mobility patterns in dementia by developing a framework for classifying higher complexity mobility behaviours, ranging from temporal characteristics such as the timing of the user’s trips to semantic characteristics such as the user’s transportation modes and activity types. Chapter 4, then, evaluates the extent to which one can predict the future whereabouts of people with dementia by learning from their past mobility behaviours captured by the GPS-based framework. Finally, Chapter 5 explores driving behaviours, the most common form of transportation among older adults, by modelling older adults’ driving behaviours in naturalistic settings using GPS. In summary, this thesis is an attempt toward developing a comprehensive GPS Mobility Construct for understanding and supporting the complex and interconnected relationship between older adults with dementia and their environment.