VictorJuiz/thesis huggingface dataset:
“Nosotros no comemos caña”: Defence of Territory and Agrarian Change in the Polochic Valley, Guatemala
Keywords: critical agrarian studies
development studies
land grabbing
land reform
political economy
territorialisation

Since the turn of the 21st century, the establishment and subsequent expansion of three (agro)extractive industries – sugarcane, oil palm, and nickel mining – in the Polochic valley lowlands of northern Guatemala has reduced local indigenous Q’eqchi’ campesino (peasant) communities’ access to farmland. Over the years, campesino groups and their allies have engaged in various forms of political contestation in “defence of territory”. In 2015, Chabil Utzaj, the sugarcane company, ceased operations following a second mass occupation of its plantations. As a result, over 800 campesino households now each have access to around 3.5 ha of farmland. In this dissertation, I employ an extended livelihoods approach consisting of archival research, oral histories, key informant interviews, and household surveys grounded in agrarian political economy to explore how the struggle for defence of territory has contested this latest wave of territorialisation driven by (agro)extractive industries and affected the trajectory of agrarian change in the Polochic valley lowlands. First, I find that while the struggle has produced remarkable achievements of immense intrinsic value to campesinos, household incomes remain, on average, well below national and international poverty lines. Campesino households with access to land by and large provide cheap labour, cheap wage goods, and cheap commodities (including environmental services) that sustain the national plantation-based agro-export industry and related global circuits of accumulation. The campesino struggle thus ultimately co-produced a pattern of uneven development characterised by functional dualism. Second, I argue that campesinos and their allies made effective use of available political opportunities, both toeing the line of “acceptable” politics and strategically transgressing its boundaries when necessary, to contest the reterritorialisation process under way. However, the nature of Guatemala’s elite-dominated political spaces limits the scope of the transformation that can be achieved. While campesinos were able to contest property relations and liberate much-needed spaces of social reproduction, the broader structures that shape labour regimes, income distribution, and social reproduction have remained largely intact. The long-term goal of sustainable agrarian change will remain conditional on a radical transformation of power relations and political spaces within Guatemala – a transformation that would require rethinking the scope of territorial struggles.
Developing a Direct Neuronal Reprogramming Strategy to Improve Motor Function in Amyotrophic Lateral Sclerosis
Keywords: ALS
Gene therapy
Neuronal reprogramming
Proneural genes

An estimated 3,000 Canadians suffer from Amyotrophic Lateral Sclerosis (ALS), a disease associated with the degeneration of upper motor neurons in deep cortical layers and lower motor neurons in the spinal cord. In both human patients and rodent models, there is evidence for a dying-forward model in which brain pathology precedes spinal cord motor neuron loss. There are no curative strategies for ALS, with current drugs (Riluzole, Edaravone) extending a patient’s life-expectancy only 2-3 months. During my thesis project, I investigated the potential of direct neuronal reprogramming in vivo as a potential therapeutic strategy to replace lost upper motor neurons and delay disease progression. My hypothesis was that astrocyte-to-neuron lineage conversion would replace lost neurons and delay disease progression in a mouse model of ALS. To test this hypothesis, I first demonstrated that a mutated version of the proneural gene Ascl1, containing six serine-to-alanine (SA) phosphosite mutations (Ascl1SA6), was more efficient than Ascl1 at converting motor cortex astrocytes to induced neurons (iNeurons) in vivo. I also found that a short version of the glial fibrillary acid promoter (GFAP) had increased astrocyte specificity compared to a longer GFAP promoter, and that adeno-associated virus with capsid 5 (AAV5) was better than AAV8 at targeting astrocytes (Chapter 2). Next, I used spatial transcriptomics to create a molecular map of neuronal reprogramming in vivo. Here, I identified the gene regulatory networks associated with neuronal lineage conversion and identified Zbtb18 and Id2 as critical hub transcription factors that are also turned on during in vitro neuronal reprogramming (Chapter 3). Finally, I expressed Ascl1SA6 in motor cortex astrocytes in hSOD1G93A mice, a model of ALS, and demonstrated that this therapeutic approach could increase lifespan and improve motor behaviour compared to a control vector in male and to a lesser extent female mice (Chapter 4). Given the promising therapeutic impact of Ascl1SA6 astrocyte-to-neuron lineage conversion in hSOD1G93A mice, in vivo neuronal reprogramming has potential to become a novel therapeutic strategy for ALS.
The Evaluation of Bundled Care for Patients with Congestive Heart Failure and Chronic Obstructive Pulmonary Disease
Keywords: Bundled Care
Chronic Disease Management
Chronic obstructive Pulmonary Disease
Congestive Heart Failure
Integrated Care
Readmission

Bundled care, also known as the Integrated Funding Model initiative, was implemented by the Ontario Ministry of Health for patients with chronic obstructive pulmonary disease (COPD) and congestive heart failure (CHF). The intervention focused on integrating acute and home care for up to 60 days post-discharge. This thesis generated evidence with three studies to inform health care administrators’ and policymakers’ decisions to scale, spread, or redesign bundled care for patients with COPD and CHF. The first study applied machine learning (ML) approaches to predict 90-day unplanned readmission or death in patients with CHF and compared their performance with a commonly used regression model called the LACE+ index. Overall, the ML models showed modest model discrimination. The gradient boosting machine model had the best discrimination with an Area Under the Receiver Operating Curve (AUROC) of 0.700, which was marginally better than the logistic regression model (AUROC: 0.695) and moderately better than the LACE+ index (AUROC: 0.648). The second study conducted an effectiveness and cost-effectiveness evaluation of the bundled care program among patients hospitalized for COPD and CHF within a 24-month follow-up. In patients with COPD, bundled care was associated with a decrease in the risk of death and an increase in unplanned readmission, but no difference in the risk of emergency department visits within 24 months. In patients with CHF, there were no differences in these outcomes. Participation in the program was cost-effective for both conditions and resulted in significant cost savings in patients with CHF but not significant in COPD. The third study examined bundled care’s level of intervention fidelity for patients with COPD and CHF, and whether it was associated with unplanned readmission within 12 months of follow-up. This analysis suggests that while in aggregate, the intervention fidelity of bundled care for patients with COPD and CHF was not associated with readmission within a 12-month follow-up, specific intervention components were associated with reduced readmission. As healthcare leaders and administrators seek to improve patient outcomes as they transition from hospital to home, evidence from this thesis can inform decision-making regarding the implementation of bundled care in Ontario.
Evaluating the Acoustic Performance of Multi-unit Residential Buildings and the Associated Effects of Noise Exposure on Occupants' Comfort
Keywords: Acoustic comfort
Airborne noise
Environmental noise
Impact noise
Noise annoyance

Exposure to noise can cause annoyance, disturbance of daily activities and increase the risk of adverse health issues. Despite these recognized risks, exposure to high levels of noise is increasing due to population growth and urbanization. Occupants who live in multi-unit residential buildings (MURBs) are at an increased risk because, in addition to outdoor noise, they can be exposed to noise from various indoor sources, such as neighbours, elevators, and heating, ventilation and air conditioning (HVAC) systems, which can increase occupants’ overall noise exposure. Compared to single-family homes, MURB occupants also have very limited noise mitigation strategies available to them which can worsen their perception of their acoustic environment. To enhance current knowledge on acoustic comfort in MURBs, surveys and field measurements of sound insulation and outdoor noise levels were used in this dissertation to examine the effects of noise on occupants and explore acoustic and non-acoustic factors that affect occupants’ perception of noise. The results showed that indoor noise from neighbours and HVAC systems, and outdoor noise from traffic and construction are the most problematic noise sources. The analysis identified annoyance, effects on work performance at home and sleep disturbance as key effects of noise. However, there was a weak correlation between measured acoustic conditions and reported annoyance levels. Occupants in buildings with low indoor noise levels (LAeq,24h = 35.7–36.8 dB) expressed higher outdoor noise annoyance levels than those with LAeq,24h above 40 dB. Similarly, occupants in a building with a high impact sound insulation level (AIIC 62) had similar impact noise annoyance levels to those in buildings with AIIC 31–32. Exposure to outdoor noise was identified as an important factor that can provide a masking effect to indoor noise and reduce reported annoyance due to indoor noise. The effects of outdoor noise however depend on suite location. The results also showed that AIIC correlates better with the perceived effect on work performance compared to annoyance level. The finding suggests that disturbance of work and other activities can be used as additional metrics to assess the relationship between acoustic comfort and sound insulation.
Rethinking Emotions: A Phenomenological, Photo-Elicitation Study of Individuals Living with Cancer
Keywords: Arts-Based Research
Cancer
Emotion
Habitus
Perception
Phenomenology

The dominant discourse on emotions constructs them as irrational, psychological states. This perspective is rooted in Western philosophy, which tends to assume that the body is an unfeeling, material object, separate from and governed by the mind. The field of oncology is also rooted in this philosophy in that it predominantly characterizes distressing emotions as cognitive disturbances that require mitigation and prioritizes cognitive reflections upon inner feelings as a means to access, identify, and measure distressing emotions. However, I argue that this narrow focus produces a limited and sterile account of emotional experiences that is detached from how they are felt and lived.In contrast to the Cartesian mind-body dualism, I apply a synthesis of Merleau-Ponty’s reconceptualization of perception, and Pierre Bourdieu’s theoretical notion of habitus to the phenomenon of emotions, to generate an alternative conceptualization of emotions that captures the full complexity of their experience and expression. I do so through an analysis of findings drawn from a qualitative, arts-based photo-elicitation study in which I explore in depth the experience and expression of emotions, of 10 individuals living with cancer. Based on my analysis I argue that emotions are inextricably interwoven in the fabric of our relationships and constitute an embodied way of knowing that can bring into being new possibilities for one’s growth and development in the experience of illness. There is a particularly transformative aspect to emotions in that they can move us to express ourselves differently and in so doing, mobilize new ways of relating to ourselves, the world, and others. My research not only enriches the discourse on emotions in the context of cancer, but also informs the broader scholarship on emotions by bringing in the body in a way that respects the existential immediacy of the body, without rendering the socio-cultural world peripheral. Recognizing the interrelationship between emotions, the body, and society opens new possibilities for understanding how emotions might reflect and reinforce the productive and materializing effects of caring relations and health care practices, but also how they might serve to reimagine them in more humanistic ways.
Exploiting Structure to Mitigate Risk in Real-world Financial Control Problems
Keywords: Financial Engineering
Machine Learning
Portfolio Management
Quantum Computing
Reinforcement Learning
Systemic Risk

Many researchers have been applying a variety of machine learning tools to a variety of financial control problems. Reinforcement learning would seem to be the most appropriate tool for portfolio management and related problems which involve interaction between an agent and an environment but the applications of this tool have been limited. We studied the challenges for the application of reinforcement learning to real world problems and developed solutions for these challenges. Along the way, we developed a theoretical framework for understanding the performance of reinforcement learning for time series data which incorporates concepts from operations research. We found that incorporating prior knowledge as structure in the reinforcement learning algorithm improves performance. Our research identified four different ways of incorporating structure from the real world into control algorithms. One of the most important challenges for financial control problems is optimizing the trade off between risk and return. We formulated risk as structure in our reinforcement learning framework to encourage the learning algorithms to meet a risk goal or to balance risk and return. Adding financial structure helped improve learning leading to more reliable and sample efficient algorithms with reduced variance, and better performance in terms of total return. This real-world reinforcement learning framework deals with portfolio management from the perspective of a portfolio manager at an institution with a local point of view and a local understanding of risk. The collective behavior of many institutions gives rise to global risks that cannot be evaluated or mitigated by individual institutions, so a global viewpoint of risk is required. We extended our investigation of risk to include global risk management and developed a computational systemic risk environment to model the interaction between institutions and simulate cascade failures in financial networks. To control cascade failures in financial networks, we developed a two-stage network optimization algorithm using quantum partitioning and showed that the algorithm successfully delays cascade failures. The cost function for this algorithm incorporates features related to the structure of the financial network and leads to partitions that tend to confine contagion within their boundaries.
‘We vote for good things’: The moral economy of voting in South Africa, 2009-2019
Keywords: Economic Freedom Fighters
Moral economy
Political behaviour
Political Parties
Populism
South Africa

South Africa has witnessed the emergence of electoral competitiveness between 2009-2019 as the dominance of the African National Congress (ANC) began to decline. During this time there was an increase in both abstention and opposition party support, making it a fruitful time to interrogate how voters make the decisions which ultimately determine the trajectory of democracy - supporting the ruling party, abstaining, or voting for the opposition. In contrast to the dominant explanations of ‘rational’ economic voting in political science and neopatrimonialism in the African context, this study finds that voters evaluate their options based upon both strategic and affective considerations. Voters assess the likelihood that political parties will provide them with material benefits but are also influenced by party loyalty and perceptions about the credibility of parties in promoting the ‘just’ distribution of public goods. Amid declining ANC loyalty and corruption scandals, abstention was the dominant trend among voters who did not see any opposition parties as viable alternatives. Both voters and local activists wanted to support parties which showed a commitment to do ‘good things’ in their policy-orientations and actions, so opposition parties were most successful among young people when they appeared to be a credible and efficacious voice for the ideas and frustrations of their generation. The Economic Freedom Fighters (EFF) gained members and supporters with its populist political style, purporting to represent the interests of Black youth, mineworkers, and informal settlements. This strategy of opposition party building was effective where it could establish ideological and affective linkages among local activists who, in turn, could enhance the party’s reputation for contributing to the public ‘good’. In a context of vast inequality, urbanization, and single-party dominance, appropriating local struggles was a cost-effective strategy of opposition party building because it gave them a presence in the communities they claim to represent. Political ideas were packaged with a political style that projected efficacy, helping to recruit young people and build a partisan identity for those who felt excluded from the economic policies and political career pathways controlled by the ANC.
Rethinking Clinical De-identification
Keywords: Clinical De-identification
Natural Language Processing

The restricted availability of free-text clinical notes and embedding-models trained on clinical notes is a bottleneck in deploying machine learning in clinical settings. To ameliorate concerns regarding the confidentiality of patient data, researchers are developing methods which automatically remove sensitive personal information from notes. While these methods appear to perform exceedingly well, often with reported precision and recall well above 95%, automated approaches for de-identification are still not trusted by clinicians because there remains non-zero risk. In this work, we present fundamental limitations associated with current approaches to de-identification that cannot be solved by incremental improvements to model performance. These limitations stem from the fact that current approaches are all trained in a supervised manner. To address these limitations, this thesis proposes the first unsupervised approach to the de-identification on free-text clinical notes. The proposed algorithm replaces all tokens with other tokens pseudo-randomly sampled from trained embeddings and is most useful for tasks where humans are not required to read the de-identified notes (e.g., training word embeddings for public release, piloting the feasibility of end-to-end machine learning models). Our approach successfully side-steps the issues facing supervised approaches (e.g., having to decide what constitutes sensitive personal information). The second part of the thesis argues for an expansion to the scope of clinical de-identification. Whereas existing de-identification approaches focus solely on protecting patients’ identities, we argue that de-identification should also focus on protecting the identity of healthcare providers. First, we demonstrate that authorship attribution in clinical notes is a very easy task when compared to many traditional author attribution datasets. Despite the need for specialized and improved author obfuscation techniques, the data to develop such techniques is difficult to obtain due to privacy concerns; it is impractical to manually label paired sentences and difficult to crowd-source the task given data-sharing limitations. To enable the development of automated means of evaluating semantic relatedness, we developed a novel sentence-pair dataset ordered by semantic relatedness. This dataset can serve as a catalyst for future author obfuscation evaluation, and we draw insights from this dataset to better understand existing work.
Brain Maturation and Sex Hormones duringA adolescence
Keywords: cerebral cortex
face processing
functional connectivity
puberty
sex hormone binding globulin
testosterone

The second decade of life is a critical period of transition: it involves a series of biological and psychosocial changes that are essential for learning and adaptation to adult life, as well as for the development of a healthy brain. The body of work presented in this doctoral thesis aims to investigate the maturation of the brain during puberty and the possible role of testosterone in shaping the brain; it extends what is known about the hormonal events during puberty. By integrating multi-modal datasets of brain structure and function and longitudinal data on pubertal testosterone, this thesis first revealed the relationship between pubertal testosterone and brain structure, which was modulated by the timing of the testosterone surge; an earlier peak in the change in testosterone levels predicted a stronger relationship. Then it revealed that the cumulative exposure to testosterone during puberty moderated the relationship between adult testosterone and brain response to faces. Using data acquired with functional magnetic resonance imaging (fMRI) in two large cohorts (the Avon Longitudinal Study of Parents and Children, IMAGEN) with the same face paradigm, we have also revealed robust canonical connectivity of the face network that was invariant across populations and developmental stages (i.e., from adolescence to young adulthood). When assessing this network at an individual level, connectivity profiles of individual participants deviated from the canonical one, with the magnitude of this deviation relating to the presence of psychopathology. Lastly, moving the focus from the brain to the body, we have clarified the nature of the relationship between testosterone and sex hormone-binding globulin (SHBG) and body mass index throughout puberty. Combining phenotypic and genetic data, our findings support a hypothesis that high SHBG leads to high total testosterone through a functional hypothalamic-pituitary-gonadal axis.Taken together, these findings indicate a possible organizational effect of pubertal hormones and suggest that consideration of the organizational effects of pubertal hormones is required to reveal the complex relationship between testosterone and social cognition later in life. In addition, we suggest that the relationship between testosterone and the brain may involve multiple biological and psychosocial factors.