VictorJuiz/thesis huggingface dataset:
Modeling Neotropical Ecosystems during the Last Glacial Maximum

Rich biodiversity and biogeochemical significance has long motivated research on Neotropical ecosystems, though regionally-focused modeling studies remain relatively sparse and limited in scope. Three individual projects were performed to address potential issues in the modeling of Neotropical ecosystems in past and present contexts with particular emphasis on the Last Glacial Maximum. The first project was focused on discerning the effects of low atmospheric carbon dioxide and temperature on the carbon exchange of a well-watered tropical forest using a canopy-scale ecophysiological model. The radiative transfer regime and canopy energy balance were used to interpret the effect of environmental variables on carbon fluxes, as well as the reproduction of an observed phenomena where leaf temperature drops below air temperature. The second project was an analysis of a four-year data set of ecosystem fluxes designed to assess the seasonal patterns of carbon uptake and the impacts of drought from a tropical dry forest site in Santa Rosa National Park, Costa Rica. A hyperbolic light response function was used to partition net ecosystem exchange into gross primary productivty and ecosystem respiration, while extracting estimates of ecosystem-level photosynthetic radiation and saturated rates of uptake. Bursts of carbon dioxide were observed at the onset of the rainy season suggesting the occurrence of the `Birch Effect' within tropical dry forest ecosystems. The third project was a regional-scale modeling study of vegetation cover in the Neotropics during the Last Glacial Maximum, focusing on the individual and interactive effects of fire and low carbon dioxide on biome distribution and tree cover. Inclusion of fire and the effects of low carbon dioxide improved agreement with pollen records and suggest the past prevalence of grassier, more open ecosystems. Modeling evidence was found to support the existence of hypothesized routes and barriers to dispersal during the Last Glacial Maximum, bolstering theories of range expansion and diversification over Pleistocene climatic oscillations.

Keywords: biodiversity
ecology
palaeoecology
Advisor: Cowling, Sharon A
Barriers to Access to Breast Reconstruction in Ontario

Background: Breast reconstruction (BR) surgically restores the breast mound and provides long-term quality of life benefits. Despite these benefits, BR fails to be consistently integrated as part of the treatment of breast cancer (BC) patients, in part due to inequitable access to BR. Methods: I first performed a systematic review of the literature to comprehensively summarize the known barriers to BR. Access was defined as “the degree of fit between the [patient] and the system”. The access to care framework by Penchansky served as mid-level theory to inform this research. Then, in order to extend knowledge of barriers to BR access in Ontario, I performed semi-structured interviews with key stakeholders (BC patients as well as providers and administrators responsible for the delivery of BR) to explore their perceptions of BR access. Qualitative descriptive methodology guided this research. Results: The systematic review identified 99 articles published between 1996 and 2016 discussing barriers to BR access. Barriers were related to the six Penchansky access to care domains: accessibility, availability, awareness, affordability, acceptability, and accommodation. Interviews with 28 patients, 22 clinicians and 8 administrators (58 total) revealed two novel barriers to BR access in Ontario. Barriers were lack of BR acceptability to patients and lack of interprofessional collaboration among physicians. For BC patients, the main barrier to BR access was their lack of acceptability of the procedure. Although patients could recognize the value of BR, many felt judged when thinking or selecting to undergo BR. These negative perceptions of BR as a “vain” or “cosmetic” procedure could impact access to BR. For providers, ineffective interprofessional collaboration amongst the interprofessional BC team was perceived as a barrier to BR delivery. No clearly identified clinician leader as well as tensions regarding the role of plastic surgeons negatively influenced collaboration. Without effective collaboration between physicians, the delivery of BR could be adversely affected. Conclusions: This research improves our understanding of barriers faced by BC patients when attempting to access BR. Future studies that engage with key stakeholders are needed in order to develop targeted interventions which will facilitate BR access for all BC patients.

Keywords: Access to Care
Breast Cancer
Breast Reconstruction
Advisor: Zhong, Toni
Baxter, Nancy N
Evaluating the Clinical Impact of Timing of Aneurysmal Treatment following Subarachnoid Hemorrhage

The projects in this thesis addressed the knowledge gap regarding optimal timing of aneurysm treatment following subarachnoid hemorrhage (SAH) by evaluating whether earlier aneurysm treatment improves clinical outcomes. This was first examined in a meta-analysis synthesizing evidence from observational studies on timing of endovascular coiling of ruptured aneurysms. The results informed a cohort study using Ontario registry and administrative data evaluating timing of surgical or endovascular aneurysm treatment in SAH, where early treatment within one calendar date of SAH was compared to later treatment. The use of administrative data for evaluation of outcomes in SAH was bolstered by external validation of the Nationwide Inpatient Sample Subarachnoid Hemorrhage Severity Score (NIS-SSS), as well as a modified version of the NIS-SSS (m-NIS-SSS). The meta-analysis of observational studies demonstrated a possible but inconsistent benefit of treatment within 1 day of SAH. Treatment

Keywords: Administrative health data
Endovascular aneurysm repair
Meta-analysis
Subarachnoid hemorrhage
Surgical aneurysm repair
Treatment timing
Advisor: Laupacis, Andreas
Standardizing Injustice in Transition-related Medicine?: An Institutional Ethnography of How Assessment Protocols Coordinate Inequitable Access to Hormones and Surgeries in Canada

Transgender (trans) people experience barriers to transition medicine such as cross-sex hormones and sex reassignment surgeries. In response, standardized care protocols, such as the World Professional Association of Transgender Health standards of care (WPATH-SOC), are recommended to improve gaps in care. To better understand how standardized care protocols shape access to transition medicine in Canada, I draw on institutional ethnography as a critical research strategy. In this dissertation I thus explicate how the main protocols used to assess trans people’s psychosocial readiness for hormones or surgeries serve a powerful coordinating function. Although significant advocacy targets the Diagnostic and Statistical Manual for Mental Disorders for pathologizing trans identity through the gender dysphoria diagnosis, my research demonstrates that the WPATH-SOC standardizes an entire model of care based in pathologization. This research project uses data obtained through talking with twenty-two trans people, clinicians, clinician-educators, and hospital administrators, observing clinician-education workshops, and analyzing pertinent assessment protocols and healthcare policy texts. My dissertation makes three substantive contributions to the areas of public health, trans studies, and health professions education research. First, I show that standardized readiness assessments previously understood as innocuous instead contribute to inequities and further pathologize trans people. Second, I argue that in the absence of trans health in the formal health professions education curricula, standardized assessment protocols serve as a form of curriculum, coordinating how health professionals learn and teach this clinical sub-specialty. Third, the results of this research hold the potential to bolster trans health advocacy efforts by identifying how assessment protocols rule health professionals’ and trans people’s resistance practices. In the spirit of activist institutional ethnography this dissertation concludes with a discussion on recommended future advocacy and systems change in the areas of policy, education, and practice.

Keywords: health professions education
hormone therapy
mental health
transgender studies
transition-related surgery
Advisor: Ross, Lori E
Shape-specific Patterning of Polymer-functionalized Nanoparticles

It has been shown that polymers end-tethered to a two-dimensional substrate will collapse into so-called “pinned micelles” upon exposure to poor solvency conditions. These structures consist of polymer-dense cores surrounded by stretched polymer “legs” as a result of constrained de-wetting. This thesis transfers this known phenomenon to a three-dimensional system: nanoparticles end-grafted with polymer ligands, as a unique strategy to surface pattern nanoparticles with polymer patches. Using spherical gold nanoparticles functionalized with thiol-terminated ligands (mainly polystyrene), the quality of the solvent was reduced and as a response, the uniformly thick polymer brush layer collapsed. In this process, polymer patches are formed to reduce unfavorable interactions at the polymer-solvent interface. The size, distribution, and number of pinned micelles were controlled by three factors: (i) polymer molecular weight, (ii) polymer grafting density, and (iii) nanoparticle diameter. Each factor played a role in the resulting surface free-energy of the system, based on the gain in energy from the polymer-polymer interaction within the micelle core and the energetic cost of stretching the polymer tethers required to form the pinned micelles. The nanoparticle shape played a role in controlling or directing the patches onto specific regions of the nanoparticle surface. For nanoparticles which have various regions of local curvature (e.g. nanocubes, triangular prisms, nanodumbbells, and nanorods), the patches were found to be more stable in regions of higher curvature such as edges, vertices, and tips of various nanoparticle geometries (i.e. predicable localization of polymer patches). Interestingly for nanorods, which exhibit different curvatures along their longitudinal and transverse axes, there is an asymmetric polymer stretching, yielding a unique helicoidal wrapping of the polymer patches. Finally, the stability of the polymer patches was studied for various temperature conditions. The patches are stable over several days at 23 and 40 degrees Celsius, however at 80 degrees Celsius, the patches merge and as a result, the number of patches per nanoparticle decreases. Eventually, the thiol-terminated polymer detaches from the nanoparticle surface. These effects emphasize the lability of the thiol-terminated polymer ligands, given that sufficient energy is applied to the system.

Keywords: Gold
Nanoparticles
Patches
Polymer
Shape
Advisor: Kumacheva, Eugenia
Hippocampal Contributions to Structuring and Segmenting Experience

The hippocampus plays a key role in establishing spatial and event boundaries, crucial for constructing and maintaining cognitive maps in spatial and non-spatial domains. The present set of studies investigated these processes in the context of navigating large-scale, virtual spaces (Google Street View) and viewing visual narratives (film). The first study is composed of two behavioural experiments that highlight the representational priority of turns along travelled routes. Locations associated with turns were recollected better and produced a temporal overestimation bias, compared with locations following turns. The second study presents an fMRI investigation of the interactions between hippocampal representations of decision points and navigational goals along familiar routes. The relationship between decision points and goal representations was modulated by goal proximity, and developed with experience in the virtual environment. This experience-related development suggests that hippocampal representations are reconfigured to represent the most relevant aspects of the environment. The third study presents an fMRI investigation of a large cross-sectional adult lifespan sample in which participants watched a movie. The hippocampus was the only region that consistently represented within-event details as unrelated or dissimilar, in a manner that was distinct from the neocortex. While most neocortical representations remained stable with age, the pattern overlap in the hippocampus, the anterior temporal lobe, and the orbitofrontal cortex increased significantly, suggesting a loss of precision and a potential susceptibility to interference. Together, these studies provide evidence that the representation and segmentation of the temporal flow of experience are key organizational features of episodic memory and navigation. These dimensions are captured in moment-to-moment hippocampal dynamics and malleable by different contexts.

Keywords: Hippocampus
Memory
Spatial navigation
Virtual reality
Advisor: Barense, Morgan D
Moscovitch, Morris
Nursing Professionalization, Gender Equality, and the Welfare State: Identifying Macro-level Factors that Advance Nursing Professionalization

Nursing professionalization has important benefits for the nursing workforce, patients, and health systems. Given the large number of associated goals, the process is ongoing and of continuous relevance to all countries where nursing is practiced. Although the body of research focusing on this topic is vast, the macro-level structural determinants of this process are currently less understood. The objectives of this thesis were to examine the effects of (a) welfare state and gender regimes and (b) measures of education, health, family, labour market, and gender policies on nursing professionalization in high-income countries. The literature review conducted synthesised health and socio-political studies, bringing attention to key links between nursing professionalization and welfare state policies. The empirical analysis consisted of two studies, the first one focused on the welfare state and the second one on gender equality, both using a time-series, cross-sectional design and fixed-effects linear regression models. The analysis covered 16 years and 22 countries. The findings suggest that both the average regulated nurse and the nurse graduate ratios differ among welfare state and gender regimes. In addition, the following policy measures were found to be predictive of (a) the regulated nurse ratio: total government expenditure on education, total and public health care spending, length of paid paternity leave, female share of tertiary education graduates, female share of employment in managerial positions, gender wage gap, and female share of seats in national parliaments; and of (b) the nurse graduate ratio: total government expenditure on education, total health care spending, length of both paid maternity and paid paternity leaves, female share of employment in managerial positions, gender wage gap, female share of seats in national parliaments, and female labour force participation rate. This study’s findings could add to existing upstream advocacy efforts to strengthen nursing and the nursing workforce through healthy public policy.

Keywords: gender equality policies
nursing human resources
nursing professionalization
structural political and economic factors
time-series cross-sectional design
welfare state regimes and policy
Advisor: Muntaner, Carles
Detail and Temporal Structure in Memory for Real-world Experiences: Age- and Time-related Changes

Episodic memory was initially defined as our ability to relive event-specific details and to remember the temporal context in which those details occurred. A rich tradition of laboratory studies has focused on memory organization, but the to-be-remembered stimuli bore little resemblance to real-world experiences. Conversely, autobiographical memory studies provide greater ecological validity but are limited in their measurement of recall organization. In this dissertation, I report three behavioural experiments that examine temporal structure in memory for real-world episodes, its relation to memory detail, and how these dimensions change with increasing age and remoteness. Chapter 2 describes an experiment probing remote temporal order and item recognition memory for objects encountered in a museum exhibit, using photographs of the exhibit and similar lures. Lure discrimination declined more than temporal order memory across a lifespan sample, although aging was associated with decreased flexibility in reconstructing order. Chapter 3 investigated how memory for the details and temporal structure of a single extended event change over time, using verbal true/false tests and a within-subjects delay manipulation. Memory for specific details declined rapidly whereas memory for temporal order was stable from 1 hour to 1 month and increased significantly overnight. Aging was associated with a marked decline in order memory at all delays, in contrast to a subtler and time-dependent decline in detail memory. Chapter 4 describes a study examining spontaneous temporal organization in free recall of extended real-world episodes. Younger and older adults tended to cluster their recall according to temporal proximity with a forward-going bias, extending principles of recall dynamics in laboratory studies to autobiographical-like memory. Moreover, more temporally organized memories were also denser in episodic detail, suggesting a relationship between structure and phenomenology within single recall narratives. Overall, these studies bridge a gap between laboratory memory and autobiographical memory literatures and methods, and provide a richer picture both of how we remember past episodes, and how we fail to do so. More specifically, they suggest that temporal organization is a critical determinant of memory success and quality over long timescales and is particularly vulnerable to age-related decline.

Keywords: aging
context
memory
recollection
Advisor: Levine, Brian
Performance and Stability of Electron-Accepting Boron Subphthalocyanines in Organic Photovoltaics

Boron subphthalocyanine (BsubPc) is a promising organic material with favourable optical and electronic properties for application in organic photovoltaics (OPVs). These properties can be tuned by chemically modifying the peripheral and axial substituents of the BsubPc. In this thesis, the influence of different substituents on the OPV performance of BsubPc as an electron acceptor was assessed using a standardized OPV configuration. Substitution of the BsubPc peripheral hydrogens with chlorines is used to adjust the voltage output of OPVs, but the ability to tune the voltage output using pure BsubPc is quantized based on the number of peripheral positions. Mixtures of compounds with different degrees of peripheral chlorination were found to behave as electronic alloys, providing infinite degrees of material tunability. The effects of axial substitution with phenyl and phenoxy groups were also explored and showed promising time-zero OPV performances. Phenoxy-BsubPcs provided a unique platform to study halogen bonding within OPVs, which were observed to influence molecular orientation and significantly impact OPV performance. The stability of the most promising BsubPcs was assessed and compared in OPVs. Outdoor testing revealed that peripheral chlorination and the addition of benzene rings (boron subnaphthalocyanine) have minimal impact on stability, but axial phenylation and phenoxylation dramatically reduce stability. Given the freedom to peripherally halogenate a BsubPc without impacting stability, these conclusions lay the foundation for the development of new BsubPcs and BsubPc alloys. Through strategic halogen placement, energy levels and molecular orientation can be controlled simultaneously to achieve the ideal materials for OPVs.

Keywords: organic
photovoltaic
solar
stability
subphthalocyanine
Advisor: Bender, Timothy P.
Investigation of Escherichia coli [NiFe]-Hydrogenase Maturation

[NiFe]-hydrogenases catalyze the reversible oxidation of hydrogen gas at a bimetallic active site and are important enzymes in bacteria and archaea for anaerobic growth and pathogenesis. The maturation of [NiFe]-hydrogenase requires at least seven dedicated accessory proteins to assemble and insert the components of the NiFe(CN)2CO catalytic site. The penultimate maturation step is the delivery of nickel to a primed hydrogenase precursor protein, a process that is accomplished by the metallochaperone proteins HypA, HypB, and SlyD. This delivery process is supported by proteins that import, export, regulate, and store nickel to ensure a sufficient supply while also mitigating the innate toxicity of this transition metal. In this work, nickel delivery to the [NiFe]-hydrogenase in Escherichia coli was examined using microbiological, biochemical, spectroscopic, and computational methods. The results demonstrate that protein-protein interactions between the metallochaperones afford layers of nickel selectivity. The protein complexes HypA-HypB and SlyD-HypB are modulated by the GTPase cycle of HypB and mediate the selective release of nickel over zinc. In addition, characterization of the metal-binding sites of HypA and HypB revealed different binding modalities, suggesting distinct acquisition and release mechanisms for these metallochaperones. This thesis also describes the development and employment of a high-throughput whole-cell [NiFe]-hydrogenase assay. The assay was used to screen the Keio collection of single gene deletion strains of E. coli and uncovered, for the first time, eutK as a component of the nickel delivery pathway and nickel homeostasis. The assay was also used to determine extracellular nickel concentrations required to bypass the nickel uptake and delivery processes to validate those systems as potential therapeutic targets, setting the stage for the search for small molecules that inhibit the biosynthesis of [NiFe]-hydrogenase. Together, this work gives insight into several aspects of the crucial nickel delivery process that bacteria use to produce [NiFe]-hydrogenase.

Keywords: Escherichia coli
Hydrogenase
Metal Homeostasis
Metallochaperones
Nickel
Advisor: Zamble, Deborah B
An Integrative Modelling Approach for Disordered Proteins using Single-molecule Fluorescence Spectroscopy

The primary sequences of Intrinsically Disordered Proteins (IDPs) encode for relatively flat, but not featureless, energy landscapes. Consequently, characterizing their conformational properties is non-trivial due to their heterogeneity and interconversion of conformations. I developed experimental protocols and data analysis tools to study IDPs using single-molecule Förster Resonance Energy Transfer (smFRET) with Multiparameter Fluorescence Detection (MFD). Using multiple parameters of fluorescence is necessary to make accurate and unambiguous distance measurements using the mean transfer efficiency

Keywords: Ensemble modelling
Integrative structural biology
Intrinsically disordered proteins
Multiparameter fluorescence detection
Polymer physics
Single molecule biophysics
Advisor: Gradinaru, Claudiu C