VictorJuiz/thesis huggingface dataset:
Multi-Source Remote Sensing Data for Automated Extraction of Fine-scale Attributes in a Northern Hardwood Forest

Forest resources require careful management and planning as they are under increasing pressure to support wood industry and conservation needs. The management of structurally complex, uneven-aged, deciduous-dominated forests requires detailed and accurate data on fine-scale forest attributes (e.g., gap dynamics, crown sizes, species distributions). New advances in remote sensing techniques will transform traditional forest inventory practices that have relied on expensive ground-based measurements or less accurate interpretation of aerial photography. Recently, multiple sources of high spatial resolution remote sensing data have demonstrated great potential for automated extraction of fine-scale forest attributes. In this context, my PhD research aims to utilize multi-source high spatial resolution remote sensing data to develop methods for automated extraction of fine-scale forest attributes in deciduous-dominated forests, including canopy gap identification, crown delineation, and species classification. This study was carried out in Haliburton Forest and Wildlife Reserve, an uneven-aged, deciduous-dominated forest located in the Great Lakes-St. Lawrence region of Central Ontario, Canada. Specifically, the thesis first quantified the accuracy of canopy gap segmentation and classification by integrating optical and LiDAR data. Thereafter, the thesis proposed a novel method for individual tree crown (ITC) delineation, involving multispectral watershed segmentation and multi-scale fitting. Finally, the thesis explored the feasibility of using multi-seasonal WorldView-3 images to map tree species using the delineated ITCs. Results indicated that: (1) the independent use of LiDAR data performed the best segmentation of canopy gaps while the synergistic use of optical and LiDAR data provided higher classification accuracy for non-forest and forest gap identification; (2) the proposed multispectral watershed segmentation and multi-scale fitting method was able to produce ITC maps of higher quality; (3) the combined use of late-spring, mid-summer, and early-spring images substantially improved the accuracy of individual tree-based species classification. The goal of this study was to develop automated methods for extracting fine-scale forest attributes for operational purposes. Although the proposed methods were mainly designed for temperate deciduous-dominated forests, they could be implemented in other types of temperate or boreal forests, such as coniferous-dominated forests.

Advisor: He, Yuhong
Caspersen, John P.
The Regulation of Occupations and Labour Market Outcomes in Canada: Three Essays on the Relationship between Occupational Licensing, Earnings and Internal Labour Mobility

The thesis begins with an introductory chapter that discusses the current state of occupational licensing research and motivates the analysis through the importance of occupational licensing, similar to unionization, to both labour market theory and public policy. The first paper in this thesis asks whether or not Canadian licensed workers earn higher wages than unlicensed workers. The paper also compares licensing pay premium to union wage premium. Based on longitudinal data from the Canadian Survey of Labour and Income Dynamics (SLID) from 1993 to 2011, a pay premium of approximately 12.0% is estimated for occupational licensing, slightly higher than the union wage premium, as 9.0%. These results are based on a cross-section of respondents using Ordinary Least Square (OLS) estimates. Fixed-effect estimates from the longitudinal data (2.6% and 4.0% for licensing and unionization, respectively), however, are much lower than the OLS amounts, suggesting the importance of unobservable factors that are correlated with licensing and union status in determining the wage premium of workers. The second paper further investigates whether or not wage premiums are uniform across the wage distribution. Using unconditional quantile regression methods, I investigated how occupational licensing and unionization impact the wage distribution of Canadian workers between 1998 and 2014. Unionization decreases wage inequality in upper-wage earners, but increases wage inequality in lower-wage earners. Occupational licensing, on the other hand, increases inequality across the entire wage distribution. The third paper focuses on the impacts of occupational licensing and unionization on young workers inter-provincial mobility decision. Using Canadian Longitudinal data from the Canadian Survey of Labour and Income Dynamics (SLID) from 1993 to 2010, the results of both multilevel modeling analysis and linear probability models with clustered standard errors show that, unlike unionization which restricts labour mobility, individualsâ licensing status is not correlated with the likelihood of moving across provincial boundaries for young Canadians aged 21-34. The final component of the thesis is an Appendix that presents a newly constructed occupational licensing index, which is based on an authoritative Canadian jurisdictional review. I define occupational licensing based on the exclusive-right-to-practice clause, and occupational certification based on the exclusive-right-to-title clause in the legislation, and construct licensing indicators to carry the empirical analyses of the effects of occupational licensing in Canada.

Keywords: earning inequality
internal mobility
Occupational licensing
Unionization
wage premium
Advisor: Gunderson, Morley K
Gomez, Rafael
Early Opioid Prescriptions for Work-Related Musculoskeletal Disorders of the Low Back: Understanding Dispensing Patterns, Their Determinants, and Their Impact on Work Disability

Opioids are prescribed early for low back pain (LBP), despite little evidence supporting this practice. The dissertation objective was to understand factors associated with early opioid provision after a LBP workersâ compensation claim and their relationship with work disability. A systematic review (Manuscript 1) found evidence of a positive association between early opioids and prolonged work disability for musculoskeletal disorders, but internal validity was jeopardized by exposure measurement and confounding biases. Informed by review findings, an historical cohort study was conducted of workersâ compensation claimants with LBP using dispensing data on LBP-indicated drug classes: opioids, nonsteroidal anti-inflammatory drugs (NSAIDs), and skeletal muscle relaxants (SMRs). Opioids, NSAIDs, and SMRs were dispensed to 19.7%, 21.2%, and 6.3% of claimants, respectively, one year pre-injury, and 39.0%, 50.2%, and 28.4% one year post-injury (Manuscript 2). Dispensing was stable pre-injury, increased within eight weeks post-injury, and declined thereafter, although not to pre-injury levels. A small subgroup demonstrated prolonged dispensing, suggesting delayed recovery. Claimant factors associated with early post-injury dispensing included pre-injury days supplied with the three drug classes, prior adjuvant medication dispenses, diagnosis, prior health care, age, sex, and occupation (Manuscript 3). Prescriber sex, birth year, and specialty were associated with drug class(es) at first prescription and the prescriber accounted for 25-36% of outcome variability. Examining the relationship between these drug classes dispensed within eight weeks post- injury and wage replacement benefits after eight weeks (Manuscript 4) revealed claimants receiving opioids, particularly with NSAIDs and/or SMRs, were more likely to receive benefits compared to NSAIDs/SMRs only. Strong and weak opioid combinations and days supply for all classes were positively associated with receiving benefits. There is evidence of increased opioid, NSAID, and SMR dispensing within eight weeks of a LBP claim. Early dispensing is multifactorial and prescribers play a role in dispensing variation. Early opioids compared to NSAIDs/SMRs appear to confer a greater risk of work disability. Methodological strengths include capturing pre-injury factors and all prescriptions and partially addressing confounding by indication/severity. However, residual confounding remains concerning. Consideration of severity, prescriber, and system/workplace measures is needed to advance understanding of opioid use for LBP and work disability.

Keywords: occupational injury
opioids
work disability
Advisor: Hogg-Johnson, Sheilah
Automatic Segmentation and Classification of Cervical Accelerometry Signals: Towards the Instrumental Detection of Unsafe Swallowing

Dual-axis cervical accelerometry has been proposed as a method for non-invasive clinical evaluation of swallowing function in people with risk for dysphagia (swallowing impairment). Acceleration signals in anterior-posterior and superior-inferior anatomical directions are processed and automatically segmented for use in classification experiments. However, automatic segmentation is often too liberal, admitting both pre- and post-swallowing activity and non-swallow segments. These segmentation shortcomings adversely affect feature extraction and ultimately classification of swallowing function. We propose a kernel density estimation-based algorithm to adaptively trim the swallow segments, and energy and noise-floor algorithms to reduce the number of false positive swallow segments. Dramatic reductions (-85.4%) in false positives can be achieved with a moderate loss of true positives (-15.1%). Furthermore, we propose a detection system for instructed and reflexive coughs, discriminating accelerometry signals associated with coughs from those representing swallows, tongue movements, and speech. Using binary genetic feature selection and a support vector machine, the proposed system achieved a cough detection accuracy of 99.26±0.12% when discriminating between instructed cough and rest state accelerometry signals. An accuracy of 90±13.9% was achieved using elastic net feature selection and a support vector machine when classifying reflexive coughs and rest signals. When discriminating instructed and reflexive coughs from all other non-cough artefacts, the proposed system achieved accuracies of 90.2±3.6% and 80.3±10.5%, respectively. Additionally, all previous cervical accelerometry studies have relied on videofluoroscopy-demarcated segments rather than the automatic localization of segments of interest, which precludes direct translation of these algorithms into a stand-alone tool. Moreover, previous studies have adopted an ipsative classification paradigm, wherein, for every unseen case, the classifier must make a forced choice (e.g. between safe and unsafe swallowing). To address these shortcomings, bolus length estimation and instance selection were introduced as enhancements to swallowing accelerometry classification, on one hand liberating classification algorithms from manual segmentation of swallows and secondly affording the classifier the freedom to abstain from a decision in the face of uncertainty. We demonstrated that together these enhancements lead to an improvement in area under the curve (83.6±5.7%) in the discrimination between safe and unsafe swallows in a sizable clinical data set.

Keywords: Algorithm development
Dual-axis accelerometry
Dysphagia
Machine Learning
Segmentation
Signal Processing
Advisor: Chau, Tom
Neurobiological Mechanism and Treatment Targets of Magnetic Seizure Therapy for Resolution of Suicidal Ideation in Treatment-Resistant Depression

Background: Major depressive disorder affects 16% of the general population and is associated with increased risk of suicidal ideation. Up to 40% depression patients do not respond to two or more antidepressant trials and are referred to as having treatment-resistant depression (TRD). Magnetic Seizure Therapy (MST) is a promising intervention for TRD patients and may be effective at targeting their suicidal ideation. Methods: To better understand the mechanism of MST and to identify potential biomarkers, TRD patients were recruited from an open label MST trial and assessed before and after the treatment course with measures of transcranial magnetic stimulation and electroencephalography (TMS-EEG) in the dorsolateral prefrontal cortex (DLPFC). Objectives/Hypotheses: 1) To evaluate if higher GABAergic inhibition (measure: N100 peak and long-interval cortical inhibition (LICI)) at baseline is effective at predicting suicidal ideation resolution (SI-resolution) after MST; 2) To determine if MST produces neuroplasticity (measure: cortical evoked activity) while decreasing GABAergic inhibition (measure: LICI); 3) To check if MST works by decreasing the strength of the DLPFC to subgenual cingulate (SGC) connection (measure: significant current scatter). Results: 1) Higher prefrontal GABAergic inhibition at baseline predicted SI-resolution after MST with 89% accuracy. 2) MST produced neuroplasticity in tandem with individual specific reductions in GABAergic inhibition that are indicative of SI-resolution after treatment. 3) Stronger DLPFC to SGC connection at baseline was able to predict SI-resolution with 83% accuracy, while the connectivity was significantly decreased after the treatment course. Conclusion: MST works by producing neuroplasticity in TRD patients with individual variations in suicidal ideation reduction governed by differences in GABAergic inhibition, both at baseline and in the process of treatment. The neuroplasticity produced by MST involved a neural circuit component part of the limbic-cortical network, specifically the DLPFC to SGC connection, which determined the efficacy of MST at baseline and is modified by the seizure treatments.

Keywords: Cortical Inhibition
Magnetic Seizure Therapy
Neuroplasticity
Subgenual Cingulate
Suicidal Ideation
TMS-EEG
Advisor: Daskalakis, Zafiris J
Wong, Willy
Doing It by the Book: Teaching Sexuality in the Twelfth-Century Classroom

This dissertation demonstrates the extent to which concepts of sexuality were intertwined with teaching and learning in twelfth-century French schools, making a vital connection between the history of education and that of gendered sexuality. Learning, enculturation and socialization were combined in the new urban schools of the twelfth century, in which boys underwent rigorous grammatical and moral training while forming homosocial bonds with their classmates and teachers. Students in their early- to mid- teens would routinely read sexually explicit texts, such as Ovid’s Ars amatoria and Remedia amoris, Terence’s Eunuchus, Statius’ Achilleid, and Juvenal’s satires, as part of their training in Latin literacy. These classical Latin texts were categorized by medieval teachers as “ethical” despite the fact that they contain depictions of rape, adultery, prostitution, cross-dressing and male sodomy. I argue that such discussions of sexuality were incorporated into the program of mores which traditionally accompanied early education in grammatica. My research presents a new perspective on socialization in medieval schools, using classroom texts and commentaries which have rarely been examined as sources for the history of sexuality. Starting with an overview of the role of the medieval school in male social formation, I uncover the pedagogical discourse which connects grammar with sexuality, and with the sexual status of the medieval adolescent student. While Ovid identifies himself as a schoolteacher and establishes “rules” for love and sex with the help of his medieval commentators, and Alan of Lille describes sexual deviance as the result of mislearning the “grammar” of sex, Statius and Terence highlight the inherent gender fluidity and erratic sexual behaviour of adolescent boys, casting doubt on the stability of the boundaries established by such regulatory mechanisms. Juvenal and his twelfth-century commentators add to this discourse by implying that male sodomy is taught through homosocial networks, and identifying adolescent boys as especially prone to learning sodomy, with the school as the site of particular anxiety. These perspectives reflect twelfth-century anxieties about clerical celibacy and homosociality and demonstrate a medieval recognition of the social forces which underpin both education and sexuality.

Keywords: Adolescence
Latin auctores
Masculinity
Medieval education
Medieval literacy
Sexuality
Advisor: Ross, Jill
Townsend, David
Life on the Periphery, Life at the Crossroads: A Zooarchaeological Perspective on Late Bronze and Early Iron Age Animal Utilization at Kinet Höyük (Turkey).

This study examines faunal skeletal remains from Kinet Höyük, a small harbour site in the Plain of Issos in the northeast corner of the Mediterranean. The faunal material in this study covers the period of approximately six and a half centuries in the long history of the site, spanning from the Late Bronze Age I through Late Bronze Age II, when the site was under Hittite control, and ends with the Early Iron Age. It aims to contribute to the growing body of environmental studies helping to understand and reconstruct events that mark the collapse of Late Bronze Age polities, and the following era of transformation and formation of new political and geographical entities. Based on the analysis of nearly 35,000 animal bones, I argue that the local population continued occupation of the site and adjusted their subsistence strategies to the changing geopolitical, economic and climatic conditions, despite a decline observed toward the end of the Late Bronze Age, and that the modifications seen in animal husbandry and exploitation of wild fauna reflect a period of hardship, rather than influx of new settlers. This thesis also represents the first major report on the Late Bronze and Early Iron Age faunal remains from Kinet Höyük, and it revises conclusions drawn from the very preliminary data published previously. Legal, administrative, ritual and economic texts dealing with the treatment and purchase of animals or animal products, known mainly from the Late Bronze Age Hittite archives and from a limited number of texts dated to the earlier phases of the Iron Age, are also examined in light of the results of this zooarchaeological analysis. This unconventional interdisciplinary approach yielded some interesting insights, and offered a novel perspective on both the bioarchaeological and textual materials from this eventful period in the history of the eastern Mediterranean.

Keywords: animal utilization
Hittites
skeletal faunal remains
subsistence strategies
Advisor: Harrison, Timothy P.
Characterization of NLRP1B Inflammasome Activation

An inflammasome is a multi-protein complex that consists of a sensor protein, caspase-1, and often an adaptor protein ASC. An inflammasome assembles in response to microbial or danger signals and the assembly leads to autoproteolysis of pro-caspase-1 and, consequently, to processing of the inflammatory cytokines pro-IL-1Î˛ and pro-IL-18 and to a type of cell death called pyroptosis. NLRP1B is a cytosolic protein that forms an inflammasome in response to anthrax lethal toxin or reduction in cytosolic ATP levels. NLRP1B detects anthrax lethal toxin when the toxin cleaves an amino-terminal fragment from the protein. The mechanism by which NLRP1B senses reduction in cytosolic ATP is unknown. In chapter 3, I addressed whether the amino-terminal region of NLRP1B also serves as a sensor of reduced ATP levels. I found that an NLRP1B mutant lacking the amino- terminal region exhibited some spontaneous activity and failed to be further activated by lethal toxin, but was still activated by metabolic inhibitors, indicating that the amino-terminal region is not the sole sensing domain of NLRP1B. Comparison of NLRP1B alleles that differed in their response to metabolic inhibitors, but not to lethal toxin, led to the finding that a repeated sequence in the FIIND facilitated detection of ATP depletion. NLRP1B might sense ATP depletion as a way of sensing microbial infections. In chapter 4, I show that an infection with an intracellular pathogen, Listeria monocytogenes caused a reduction of cytosolic ATP levels and activation of the NLRP1B inflammasome in a reconstituted system. NLRP1B activation was dependent on Listeriaâ s expression of a protein required for vacuolar escape, listeriolysin O. Furthermore, I show that infection with Listeria monocytogenes and Shigella flexneri also caused reduction of ATP and activation of NLRP1B in the murine RAW264.7 macrophage cell line.

Keywords: ATP depletion
Inflammasome
Listeria
NLRP1B
Advisor: Mogridge, Jeremy
How Open Data Entrepreneurs Advance Institutional Change

Openness is one of the fundamental principles of scientific inquiry and the benefits of open research data include accountability, transparency, and efficiency. Change is also an expected prerequisite for scientific progress, yet, despite recent technological advances enabling open data not all data generated during scientific inquiry is normally available. This thesis examines the institutional work of open science entrepreneursâ efforts to introduce open data practices, thus advancing institutional change in science. Through a multi-case study of five institutional entrepreneurs, this study is guided by the question â How do open data entrepreneurs institutionalize a new open data practice? First, the background of open data as a scientific practice is presented, highlighting the obstacles to its adoption. Second, the theoretical framework of institutional entrepreneurship and work are discussed, along with concepts of multilevel institutional work. The findings indicate that open data entrepreneurs actively advance change by persevering in conducting a variety of institutional work such as counterfactual thinking, disassociation, creation of standards of practice, mobilization of resources, forging new relations, and alliances, and advocacy. They are adept at strategizing iteratively between institutional levels, fluidly mediating between their organization, scientific communities, and broader societal levels. Theorization of open data occurs at all levels, with an expanding set of specifications and justifications attuned to each level. The outcome of their work is distinct at each level: individual opportunity recognition; development and establishment at the organization level; legitimation and diffusion at the scientific community level; and policy change at the societal level. The study casts light on the nature of science-based institutional entrepreneurship and contributes to the study of agency and multilevel institutional change. The iterative, multilevel institutional work of the open data entrepreneurs provides support to the recursive change models that highlight the interplay of both bottom-up and top-down processes. As research funding agencies, professional societies, and policy bodies are increasingly enacting open data and data sharing policies, the findings from this study are significant in demonstrating importance of open data legitimation and diffusion at the level of the scientific community for the successful adoption of open data by researchers.

Keywords: data sharing
institutional entrepreneurship
institutional theory
open data
open science
science policy
Advisor: Sรก, Creso