VictorJuiz/thesis huggingface dataset:
The Colombian Forest Sector Model – An analysis of forest plantation policy in Colombia

An economic model for the Colombian forest sector (Colombian Forest Sector Model – CFSM) is developed and used to analyse Colombia´s commercial forest plantation policy covering the 2018 – 2038 horizon (PFCm policy). The CFSM is a structural partial equilibrium econometric model that forecasts quantities and prices for the Colombian forest product markets using the neoclassical theory of competitive markets. Phase I of the CFSM (CFSM-I), developed in detail in this dissertation, includes a simulator of growth and yield for the Colombian forest plantations and two market (sub)models: for Unprocessed Wood and for Manufactured Wood Products. Using the CFSM-I, two PFCm policy goals were simulated to unveil their impacts on the Colombian forest sector. Simulations of an expansion of Colombia’s forest plantation current area (0.3 million hectares, Mha, on Dec 2015) to 1.5 Mha by 2025 indicate that Colombia would increase the 2015-2047 volume available of industrial wood in plantations by 5 times (annually 20.8 million cubic meters of underbark roundwood, on average). In monetary values, this expansion would importantly impact the unprocessed wood market. Supply and exports of wood would multiply by 2.5 and 14.5 times in the next 25 years meanwhile its price of supply would drop by 24%, respectively, and on average, compared to the scenario of no expansion of the current plantations. Simulations of a 2023-2038 5.5-times expansion of the current (2022) production capacity of Colombia’s manufactured wood forest products industry show that on average in the next 25 years and compared to the no expansion scenario, consumption of unprocessed wood and manufactured wood products of the pulp and paper industry would increase by 8% each, and the imports of the latter and of manufactured products of the furniture industry would decrease by 35% and 25%, respectively. Alternative policies of plantation area expansion (0.45 Mha, 0.765 Mha, and 2.0 Mha under sustained rotation, and 0.3 Mha harvested without replanting) also simulated enrich the set of information for policy makers and other stakeholders in preparation for the first round of the PFCm policy evaluation, scheduled for 2023 after the completion of its first implementation period in December 2022.

Keywords: Colombia
Forest Economics
Forest Plantations
Forest Sector Model
Forest Sector Modelling in the Tropics
Growth and Yield Simulators
Advisor: Kant, Shashi
‘Nothing about us Without us’ – Development of a Patient- centered Digital Health Self-care Program for Marginalized, Underserved Populations with Heart Failure

Heart failure (HF) is a global pandemic affecting over 26 million people worldwide. In high-income-countries (HICs), the use of evidence-based self-care models has led to a decline in HF prevalence. However, these improvements are less evident in low-and-middle-income countries (LMICs) and marginalized subgroup populations in HICs, like the Indigenous People, due to factors related to poor disease control and the disparities in a population’s social determinants of health. With the inequitable distribution of health services, digital health has been offered as an avenue to assist populations with limited resources. While mobile phones have become increasingly utilized, many digital health interventions have failed to be adopted, as they have been designed for usage in high-resource settings. With the current mismatch between technological innovation and local community priorities, this research sought to 1) evaluate the state of heart health within the remote communities in Northern Ontario and Northern Uganda, 2) investigate the contextual requirements to design of a community-based digital health program, and 3) adapt the program according to the identified design requirements. In Study 1a, we established that Indigenous communities and LMICs valued the use of digital tools, but its adoption would be dependent on its cultural compatibility. To better understand how cultural context should be integrated within digital tool design, Study 1b explored how various community engagement strategies could be utilized. Using these findings, in Study 1c, a research partnership was established with each community. In Study 2, a community-based needs assessment was conducted to evaluate the contextual influencers impacting community heart health. In Study 3, we developed a series of design requirements focused on empowering existing community resources and cultural values. In a society where the distribution of wealth is heavily unbalanced, there is concern that the digital divide will compound the effects of socioeconomic divisions. While the COVID-19 pandemic triggered the momentum for digital health, populations with a history of being overlooked, continue to be left with minimal support. As such, to close the gap associated with the digital divide, interventions need to be designed in reflection of the contextual circumstances contributing to a population’s poorer health outcomes.

Keywords: community-based research
digital health
health equity
health services research
heart failure
Indigenous health
Advisor: Cafazzo, Joseph A
The Hunt for Immune Biomarkers during Chronic Hepatitis B Infection

Current treatment options against chronic hepatitis B virus (HBV) infection are rarely curative and represent a significant global health burden. Novel therapeutic approaches directly target the immune system or indirectly enhance antiviral immunity through impeding with viral antigen production or viral lifecycle, yet immunological biomarkers are highly lacking beyond clinical assays for antibodies to HBsAg and HBeAg. In order to characterize immunological mechanisms of action and guide clinical decisions for the use of immunotherapeutic agents, immune assays that can measure T cell functionality or predict liver inflammation are highly sought after. Overall, our work builds upon the current understanding of host immunology during CHB infection and aims to establish immunological biomarkers in pursuit of defining curative strategies against HBV infection.

Advisor: Gehring, Adam
Feld, Jordan
Modern Iran, Republican Nationalism, Empire and Social Movements: Outlines of a Theory of Protest Cycles

This dissertation focuses on the political transitions and quest for self-determination in modern Iran through the prism of successive social movements in Iran since the beginning of 20th century. I argue the process of democratization in Iran was frustrated by competing domestic and imperial forces. Thus, the unfolding of the democratic process remains impeded despite recurring mass uprisings — a phenomenon I’ve theorized as “protest cycles”. By understanding how these internal and external forces have limited the trajectory of Iran’s quest for self-determination and manifested in protest cycles, I worked to develop a theory of collective social action in the region and beyond. This research builds on work I published in 2018 — “The Iranian Green Movement of 2009: Reverberating Echoes of Resistance” —resulting from my York University MA thesis, in which I examined the quest for self-determination of the Green Movement and developed rudimentary concepts for theory of ‘protest cycles’. In the work before you, I am expanding on the theory of ‘protest cycles’ by conducting a socio-historical analysis of Iranian social movements, focusing on the voices and the narratives of the subaltern: women, minoritized ethnics, and the working class. My research is anchored in critical theory and draws on principles of Marx’s historical materialism, Parsons’ theory of social systems, and Giddens’ theory of structuration. Corpus of data comes from a variety of archival and primary textual sources including newspapers, leaflets, and slogans — analyzed based on principles of critical hermeneutics. I map the core dimensions of protest cycles, based on my empirical analysis of three major uprisings in: The Constitutional Revolution, the Oil Nationalization Movement, and the Islamic Revolution. A Causal Loop Model is used to illustrate a complex set of positive and negative influences: overall, Republicanism & Citizenship and Reclamation of National Wealth play a generative role in motivating uprisings; and Oppressive Ideologies, Dislocations & Marginalization (including women and ethnics), and the Islamic Regime were negatively influential.

Keywords: ethnic
Iran
protest
social action
Social movements
theory of protest cycles
Advisor: Portelli, John P
Ngwenyama, Ojelanki
Towards Automated Toxicity Testing Using Novel Technologies to Reduce Spectral Overlap and Address Sensitivity Limitations in Environmental In-Vivo NMR

Toxicity testing of living organisms has been undergoing a paradigm shift over the last decade. Focus has moved from examining apical endpoints such as death or reproduction, to measuring sub-lethal impacts from a biochemical perspective, with future aspirations to automate the approach. One of the ways this is examined is through metabolomics, the study of the impacts to an organism’s metabolic system as a result of an external stressor, such as a potential toxin. Recently, the field of in-vivo nuclear magnetic resonance (NMR) spectroscopy to study metabolomics has provided breakthroughs in toxicity testing information. Much of this work has been done with the aquatic organism Daphnia magna, a model organism for aquatic toxicity studies. While robust, NMR suffers from a lack of sensitivity and heavy spectral overlap in complex systems, such as living organisms. Thus, this thesis introduces novel technologies which help address sensitivity limitations and remove overlap in in-vivo NMR while working towards creating an automated dosing platform in line with the paradigm shift of toxicity testing. First, a new holistic approach to testing is examined which uses three NMR techniques in tandem, providing complementary information of toxin interactions including binding, physical partitioning, and biochemical response inside living organisms. Binding with the organism’s outer shell and metabolic oxidative stress responses were measured, which could not have been examined independently. Additionally, two new NMR pulse sequences are introduced. The first examines new bond formation between different nuclear isotopes (13C-12C), and food incorporation into living biomass of D. magna was examined. In the second sequence, suites of molecules chosen by the user can be isolated from an unchanged matrix, while focusing increases sensitivity over traditional 1H NMR. Four metabolites indicative of oxidative stress were monitored in D. magna simultaneously, while the unselected signals were filtered out. Finally, an automated dosing platform was created by the combination of digital microfluidics (DMF) and NMR to keep D. magna alive for prolonged periods using automated movement of food and water. Moving forward, these four new approaches could be used in tandem to increase sensitivity, reduce overlap, and automate the toxicity testing process.

Keywords: Daphnia magna
Digital Microfluidics
Environmental Toxicity
In-Vivo Metabolomics
Nuclear Magnetic Resonance Spectroscopy
Pulse Sequences
Advisor: Simpson, Andre
Development of a Human Precision Cut Intestinal Slice Model of Acute IgE-Mediated Food Allergy

Food allergy is a potentially life-threatening disorder that affects both children and adults. There are no definitive prevention strategies in place, and treatments remain limited. Models of food allergy are needed to further understand the cause and underlying cellular mechanisms of this disorder, and to develop and test preclinical therapeutics. Current models of food allergy are limited in their ability to reflect the complexity of this disease in human mucosal tissue. Therefore, the aim of this thesis project was to generate a novel model of IgE-mediated food allergy using precision cut intestinal slices (PCIS). PCIS are live pieces of intestinal tissue of a fixed thickness that maintain the cellular diversity and function of the organ. We optimized the generation of PCIS using intestinal tissue from mice, rats, pigs, and humans. Viability and metabolic activity were maintained for up to 24h. Rodent and human PCIS were passively sensitized using plasma or serum from allergic donors and the smooth muscle contraction reactions that occurred following stimulation with allergen or controls were filmed. These contractions functioned as a readout of the allergic response. To quantify these responses, a novel video analysis software was created that measured muscle contraction in free-floating PCIS. We verified these responses were due to mast cell-derived mediator release by measuring allergen-specific increases in tryptase concentration in the culture supernatant. We showed that treating rodent and human PCIS with commonly used antihistamines could block contraction responses. We also found that plasma from peanut allergic patients who were successfully desensitized by oral immunotherapy could suppress allergen-specific contraction responses in human PCIS. Using single nucleus RNA sequencing we confirmed the presence of all expected cell subsets including stromal cells, epithelial cells, and key immune cell populations. We demonstrated that human PCIS can be used to observe tissue-specific changes in gene expression patterns following stimulation with allergen or controls. Through this thesis research, we established PCIS as a novel complementary tissue-based model to study acute, IgE-mediated food allergic responses, to assess current and preclinical therapeutics, and to investigate the complex network of reactions that occurs within intestinal tissues during an allergic reaction.

Keywords: Allergy
Allergy model
Food allergy
Intestine
Advisor: Eiwegger, Thomas
Carving Space for Staff Agency in a Faculty of Medicine: A Foucauldian-inspired Discourse Analysis of Administrative Staff and Faculty Relations

Administrative staff in higher education have been described as invisible (Eveline, 2004; Szekeres, 2004) and often characterized as being “non-academic, non-faculty, non-teaching, [and] non-professional” (Losinger, 2015, p. 157). These characterizations manifest within health professions education (HPE) contributing to the undervaluing of staff and staff contributions. While administrative staff are present on campuses or within the virtual workspace, staff often remain absent when it comes to HPE documents, literature, and reports. With few exceptions, if staff appear in the HPE literature it is as a passive object, often as a resource, a possession, or a liability. If staff appear in institutional reports, it is often within an acknowledgement section rather than a list of authors. These absences are also felt in the everyday staff experience: staff are sometimes overlooked in meetings, may not feel comfortable contributing knowledge, and may feel devalued or invisible in their roles. At the same time, the neoliberal university system has led to the increasing professionalization of staff roles, occurring as health professionals experience their own shifts in power and prestige. These changes affect staff and faculty relationships in the health professions education space at times, leading to tensions if not toxicity. Throughout this thesis I build and examine an archive of published literature, archival documents, interview data, and my reflections and lived experience as a staff member to conduct a Foucauldian-inspired discourse analysis. Specifically, I conduct a “history of the present” (Foucault, 1977; Garland, 2014) to identify discourses that regulate the work of and power relations between administrative staff and faculty in a faculty of medicine. I discuss what these discourses make possible for staff to do, be, or say and what these discourses now make impossible. I explore the material effects of discourse, very purposefully centering staff voices within this text. Using feminist and decolonial critical theories throughout my analysis, I engage with the historic and hierarchical structure of academic medicine that constructs the largely feminized administrative staff cohort as having limited agency in HPE. To navigate the tensions produced by discourses and structure, I work to rebuild agency through staff voices, resistance, and recommendations for practice.

Keywords: administrative staff
critical theory
Foucault
health professions education
higher education
power
Advisor: Kuper, Ayelet
Gender Inequality in the Labor Market: Trends and Mechanisms

Despite significant gains made over the last decades, women—and mothers in particular—are still disadvantaged in the labor market. For example, women are less likely to be employed in the most prestigious occupations, such as managerial and professional occupations (MPOs), especially those that have been historically dominated by men. Moreover, women are more likely than men to reduce their work hours or exit the labor market after the transition to parenthood. Consequently, women more often work in position with lower levels of autonomy, lower salaries, and less beneficial working conditions. In this dissertation, I examine social change in women’s participation in (male-dominated) MPOs and illuminate two prevalent factors that past research has identified as impacting women’s participation in those occupations: motherhood and overwork. In addition, I investigate the role of the male partner’s involvement in domestic work on women’s employment after the transition to parenthood among heterosexual couples. My findings suggest that women are more likely to work in historically male-dominated MPOs with each successive cohort, although participation rates for MPOs overall have been stalling among the youngest cohorts. The prevalence of motherhood does not differ between male-dominated MPOs, non-male dominated MPOs, and other types of occupations, but women working in historically male-dominated MPOs are less likely to have more than one child. My findings further show that overwork is more prevalent in male-dominated MPOs throughout time and across all cohorts, and may be a barrier for having more than one child. Lastly, my results demonstrate that mothers who are most disadvantaged on the labor market benefit most from their partner’s involvement in child care in terms of their labor force participation. Taken together, my findings show a positive development in terms of women’s participation in the most prestigious occupations—i.e., historically male-dominated MPOs—but also suggest that gendered assumptions in the home and in the workplace still create barriers for women’s employment participation. Lastly, my results indicate that the prevalence and impact of those gendered norms varies by women’s labor market (dis)advantages.

Advisor: Schafer, Markus
Ecology and Sensitivity to Environmental Change of a Northern Population of Spotted Salamander, Ambystoma maculatum

Amphibians perform numerous ecological roles—as predators and prey, as connectors of energy flow between aquatic and terrestrial landscapes, and as sizable contributors to vertebrate biomass—in wetland and forest ecosystems. Amphibians are also modern “canaries in the coal mine”, serving as a barometer for assessing environmental health. The Spotted Salamander (Ambystoma maculatum) is geographically widespread in eastern North America and is well-studied. This research arises from long-term monitoring of Spotted Salamanders at Bat Lake in Algonquin Provincial Park, Ontario, Canada, approaching the species northern climatic range edge. In 2008, monitoring efforts were formalized into a capture-mark-recapture study, collecting morphological, reproduction, and population data. The long-term aims of this project are to monitor baseline population vital rates and assess the effects of climate (change) on a northern salamander population. Chapter One introduces salamanders as research subjects and the ecology of Bat Lake. Chapter Two presents a synthesis of Spotted Salamander biology based on 15-years of monitoring data, including phenology of spring breeding and post-metamorphic dispersal, operational sex ratio, early life survival, body size of adults and metamorphic juveniles, age and size at maturity, longevity, and spatial habitat use. These findings are paired with a literature review to compare the natural and life history of Bat Lake salamanders to other populations. Chapter Three estimates population vital rates, including adult survival and abundance, and provides suggestions on how to sample the Bat Lake salamander population to inform continued long-term ecological and demographic study. Chapter Four investigates the influence of seasonal climate on body condition, reproductive output, and breeding phenology. Breeding body condition declined over a 12 year monitoring period (2008–2019) with warmer summer temperatures at least partly responsible for the observed decline in body condition, highlighting the vulnerability of fossorial taxa and subterranean environments amid accelerating climate change. This dissertation contributes to our understanding of salamander ecology and begins to address a knowledge gap about the consequences of climate (change) for amphibian populations.

Keywords: Algonquin Provincial Park
amphibian
climate change
demography
ecology
salamander
Advisor: Rollinson, Njal
Inverse Design of Metasurfaces Using Machine Learning Techniques

These days, devices employing electromagnetic waves, such as antennas, have been intertwined with everyday life such that they are now unrecognizable by a general user. Despite the advancement of these technologies in the past few decades, in recent years, electromagnetic metasurfaces have introduced an unprecedented potential to not only tackle the problems of the conventional systems, but also create new applications for them. These engineered two-dimensional materials offer complete and intimate control over the electromagnetic fields involved through their constituent, judiciously designed meta-atoms. In recent years, in response to emerging applications for these surfaces, there have been tens of proposed meta-atoms that compete in performance, while the search for new applications is ongoing to date. Considering the revolution caused by these structures in different fields, ranging from micro-sized cameras to intelligent buildings, the significance of automated and efficient approaches to design and discover new metasurfaces is undeniable. Inspired by the breakthrough of machine and deep learning methods in other fields, generative machine learning networks such as variational autoencoders and generative adversarial networks are employed to explore the high-dimensional solution space of the meta-atoms composed of metallic and/or dielectric scatterers. Based on the presented generative methods, periodic and quasi-periodic single-layer and multilayer transverse-electric and transverse-magnetic metasurfaces are designed for different applications, including but not limited to frequency selectivity and wideband linear-to-circular polarization conversion. An end-to-end approach involving predicting the dispersive properties of bianisotropic meta-atoms via machine learning surrogate models for a beam-splitting metasurface is also presented. The functionalities of the presented metasurfaces are validated through full-wave simulation tools and experimental measurements. Lastly, future opportunities and design considerations are outlined. While the presented machine learning methods for the design of metasurfaces in this thesis serve as early attempts to tackle the problem, the achieved results demonstrate the capability and versatility of data-driven techniques for different applications of metasurfaces. Due to these remarkable abilities, machine learning will undoubtedly become an indispensable tool for solving increasingly challenging electromagnetic metasurface problems in the near future.

Keywords: machine learning
metasurfaces
optimization
polarizers
wave transformation
Advisor: Hum, Sean V.