VictorJuiz/thesis huggingface dataset:
Soil Methane Dynamics of Skid Trails and Landings in Managed Northern Hardwood Forests

Skid trails and landings are the portions of harvested forests that are used by forestry vehicles; skid trails are the network of trails used to transport logs to the landing, a central storage point where logs are processed and stacked. Soils in these features are highly impacted by the traffic they experience, and often sustain long-lasting changes to soil properties. While temperate forest soils tend to act as a methane (CH4) sink, these altered soil properties can influence soil CH4 dynamics, weakening their strength as a sink or causing a shift to CH4 emissions. This phenomenon has been documented in experimental settings but very few have studied it in situ in harvested forests as well as the soil drivers that contribute to it. We studied soil CH4 fluxes from skid trails and landings in a selection-managed forest in central Ontario, Canada, as well as the properties that may contribute to the observed flux. One-year-old skid trails exhibited high CH4 emissions, particularly from intensively used primary trails that were low-lying and wet. These emissions were correlated to low surface soil porosities and high soil moisture contents. Landings one year after harvest had significant spatial variation but had some strong “hotspots” of high CH4 emissions. CH4 flux on landings was correlated to soil pH and quantities of buried woody residues. On a broader scale, within the first year after harvest emissions from skid trails and landings respectively offset the strength of the CH4 sink from the surrounding untrafficked soils within a harvest area by ~45 and 12%. A chronosequence of skid trails and landings found that highest CH4 emissions occurred one year after a harvest event then began to decrease in the following years. Eventually soils returned to consuming CH4, however in the 15-year study period these soils never recovered to consuming CH4 at the same rate as unharvested soils. Temperate forest soils are an important global CH4 sink, and these findings contribute to the understanding of the effects of forest management on forest CH4 budgets. The results also inform prevention and remedial practices in climate smart forestry practices.

Advisor: Thomas, Sean C.
Essays on Behavioural Strategy at the Firm-Society Interface

This dissertation examines relationships between firm decision makers and stakeholders in light of societal issues. In three sets of studies, I examine different strategic decisions in which stakeholder beliefs and identities are salient. In the first project, I examine why organizational decision makers choose to take sociopolitical stances as part of their business strategies. In an online experiment, I find that higher monetary incentives, cause-individual value alignment, and consequentialist ethics lead to more stance-taking, while credible stakeholder pushback leads to less stance-taking. Liberals tend to view stance-taking as fundamental to the corporation’s social role while conservatives view stance-taking as a means to improve financial performance. These results show that various market and individual-level factors have a nuanced impact on stance-taking decisions. In the second project, my co-authors and I examine how organizational justifications for diversity impact hiring and promotion decisions. In a field experiment with recruiters and a vignette experiment with managers, we find that moral cases for diversity result in greater hiring and promotion of underrepresented minorities than business cases for diversity. In two follow-up studies, we find that a separate set of online participants find moral and legal cases for diversity more effective than the business cases. However, counter to our findings, they predict that managers in our experiments viewed the business cases as more effective than the moral cases. These results show that moral cases may be effective in promoting diversity concerns in personnel decisions and that managers may overestimate the effectiveness of business cases, which could slow efforts to diversify organizations. In the third project, I examine how charitable giving incentives impact group coordination compared to direct monetary payment. I run lab experiments that show that donating participants’ small incomes to a widely admired charity may result in lower group performance compared to using similar-sized monetary incentives. In a follow-on survey, outside observers tend to predict higher coordination rates for those in the charity condition compared to the monetary incentive condition. These results suggest that expectation-setting properties of charitable incentives may impede creation of stable, informal coordination norms in certain settings.

Advisor: Lacetera, Nicola
User Recognition System based on PPG Signal

People are connected to various online and off-line systems that facilitate their interactions performed on a daily basis. In all these activities, individuals use their credentials to create, share and pay which could be related to the individual’s information. This sensitive data should be highly secured and thus, user recognition systems are highly empowered and invested recently.Biometric system is a technology which takes an individual’s traits as input and identifies the individual as a genuine or malicious user. In this work, our goal is to develop the verification system based on a physiological signal which has unique properties for each individual and simultaneously ensures the liveness of user since it is one of its inherent characteristics. Among diverse physiological signals, we focus on the photoplethysmography (PPG) since it can be acquired from low cost, more accessible and portable devices. The advantages correlated to the PPG signal bring it more practical and appealing to be utilized in real applications. However, the PPG signal has theoretical challenging aspects to be considered which include time variability and inherent randomness. To this end, we focus on investigating the feasibility of employing the PPG signal for person verification by developing time-stable and distinguishable features. To achieve our goal, there are five main objectives to be considered. First, a large and reliable PPG database with multi-sessions should be recorded to investigate the time stability of verification system. Second, the appropriate pipeline of PPG verification system needs to be suggested. Third, the conventional machine learning and deep learning models are investigated to understand the suitable model for PPG verification. Fourth, we develop the Generative Adversarial Network which generates the synthetic PPG with holding the unique and time-stable features. Last, we proposed the score-level fusion method of single modality (PPG) with different representations to achieve the better results with less complexity. In the collected database, we achieved up to 11.5% Equal Error Rate (EER) whereas recent works in the literature showed 23.2%, 19.1% EER in their databases. The obtained results guarantee that our PPG verification system has a high possibility to be considered in real world.

Keywords: Biometrics
Deep Learning
Fusion
Generative Models
PPG
Advisor: Hatzinakos, Dimitrios
Methane Fluxes from Living and Dead Trees in a Temperate Forest

Trees have been identified as an important source of methane in forest ecosystems, but little research exists on fluxes beyond their stems, such as those from foliage, branches, wounds, and coarse woody debris. Recent instrumentation advances allow rapid and accurate measurements of relatively low methane flux rates in-situ; this thesis takes advantage of such technology to explore methane fluxes from these tree components in northern hardwood forests of central Ontario, Canada. Foliage was found to represent a substantial component of forest methane budgets, acting as a sink in upland forests and a source in lowland forests (averages = -0.54, 6.06 nmol m-2 s-1; n = 27, 12, respectively). Uptake is hypothesized to occur through methanotrophs within foliage, and emissions from channelling of methane that originates in soil. In an upland site tree branches, wounds, and stems emitted methane (averages = 0.61, 10.58, 0.59 nmol m-2 s-1; n = 18, 83, 79, respectively), and at the stand scale represented 83%, 8%, and 9% of emissions from trees respectively. Emissions are hypothesized to occur through anoxic decomposition within the tree, which often occurs due to wounding. Coarse woody debris was found to act as a methane source in early decay classes and a sink in later decay classes (average flux rates ranged from 0.78 to -1.58 nmol m-2 s-1; n = 94). Immediately after harvest there was a large pulse of emissions from the cut surfaces of trees (>4000 nmol m-2 s-1 for Acer saccharum boles), but on average coarse woody debris was a methane sink in both managed and unmanaged stands. These results represent some of the first and most comprehensive in-situ methane flux measurements from tree branches, wounds, foliage, and coarse woody debris, and help to improve estimates of forest methane budgets. Inclusion of wounds and branches into calculations of tree methane fluxes will increase net emissions, but inclusion of upland foliage and dead wood as methane sinks can offset them. Strengthening forest methane sinks and reducing sources is an attractive policy option for “climate-smart” forestry, and this research can be built upon to support future efforts in this field.

Keywords: Forestry
Methane budgets
Methane sink
Methane source
Methanogens
Methanotrophs
Advisor: Caspersen, John P
Thomas, Sean C
A ‘Truly European Language:’ Europeanization and Supranational Language Regimes in the Case of Romani Language, 1998-2018

What impact has integration with Europe had on state language regimes in Central and Eastern European countries? This dissertation investigates supranational and state treatment of Romani – the language spoken by many Roma communities in Europe – through an illustrative study of the Council of Europe and case studies of Slovakia and Croatia. Changes in state treatment of Romani in both countries have been significant on paper. In reality, however, implementation is limited or nonexistent. What explains this superficial and attenuated change? The Council of Europe’s language regime, centred on its valuation of diversity, led the organization to support Romani and push member states to do the same. In the context of Central and European countries’ integration into the EU, and into ‘Europe’ more generally, the mechanisms of Europeanization have resulted in the diffusion of elements of this supranational language regime to the domestic level. First, normative pressure and membership conditionality from European institutions have led to increased 'paper promises' – legal and policy commitments to support Romani – that follow the norms and standards of the supranational language regime at the Council of Europe. Secondly, Europeanization has resulted in new tools, opportunities, and political space for Romani language advocates within each country. But the penetration of such of supranational language regimes is also limited by two factors. State resistance emerges from the continued durability of state traditions that delegitimize Romani and exclude it from minority language rights frameworks. Secondly, the remedies for linguistic minorities proposed by both state and supranational language regimes are often a poor fit for Roma communities. Studying state treatment of Romani language helps illustrate the impact of integration with Europe on what I term marginal policy areas: those domestic policy areas which are subject to European pressure but not directly subject to EU rules. I also contribute to recent literature on continuity and change within state language regimes. The study of the politics of Romani language illuminates not only the situation of a specific minority language, or even linguistic minorities more generally, but also the complex interactions between institutions and actors at the state and supranational levels in Europe.

Keywords: Council of Europe
Europeanization
language policy
Roma
Romani
Advisor: Jung, Courtney
The Acute Effects of Alcohol on Response Inhibition: An Evaluation of Meta-analytic and Laboratory-based Outcomes

Individuals with and without an alcohol use disorder frequently report loss of control over alcohol use, described as escalations of drinking both within a drinking episode and across time. Dual-process and triadic neurocognitive models provide explanatory frameworks of loss of control. Within these frameworks, response inhibition – the ability to withhold a prepotent response – figures prominently. Alcohol is postulated to acutely impair response inhibition, thereby contributing to loss of control over alcohol use. The effect of alcohol on response inhibition has been extensively studied in the literature. Discrepant findings have been reported, particularly around the magnitude of this effect. Recent extensions of dual-process models postulate a role of interoception – the perception of internal bodily states – in regulating alcohol use behaviour. In the triadic model, the product of the interoceptive system, alcohol craving, is thought to reduce cognitive resources available for cognitive control, resulting in attenuated response inhibition ability and higher levels of alcohol consumption. Partial support for the triadic neurocognitive model is evident in the literature, but central hypotheses from this model have yet to be tested empirically in the laboratory. Therefore, the present work has two aims: (1) to meta-analytically aggregate the literature on the acute effects of alcohol on response inhibition, and; (2) test the hypothesis that interoceptive sensitivity moderates craving elicited by alcohol, and that heightened craving results in diminished response inhibition, and increased alcohol consumption in a laboratory setting. The meta-analysis revealed a detrimental effect of acute alcohol administration on response inhibition, and this effect was moderated by intoxication level, indicators of task difficulty, and comparison type (Stop Signal Task only). The laboratory-based study failed to identify any significant effects, perhaps due to the use of a low priming dose and/or limited statistical power. The current work reinforces extant research showing a detrimental acute effect of alcohol on response inhibition and establishes the size and moderators of this effect. Ultimately, this work furthers the understanding of the potential mechanisms underlying loss of control over alcohol use in a drinking episode and to this end, the findings herein may be used in future studies to examine this construct.

Keywords: Alcohol
Meta-Analysis
Response Inhibition
Advisor: Hendershot, Christian
Bagby, R Michael
Some Topics in the Arithmetic of Hodge Structures and an Ax-Scanuel Theorem for $GL_n$

In the first part of this thesis, we consider smooth projective morphisms $f:X\rightarrow S$ of $K$-varieties with $S$ an open curve and $K$ a number field. We bound the Weil height $h(s)$ polynomially from above by $[K(s):K]$ at points $s\in S(\bar{K})$ that are ``exceptional'' with respect to the variation of Hodge structures $R^n(f^{an}_{\mathbb{C}})_{*}(\mathbb{Q}_{X^{an}_{\mathbb{C}}})$, where $n=\dim X-1$. For this variation, we assume that its generic special Mumford-Tate group is $Sp(\mu,\mathbb{Q})$, that it degenerates strongly over some point $s_0$ of a curve containing $S$, the Hodge conjecture holds, and that what we define as a ``good arithmetic model'' exists for the morphism $f$ over $\mathcal{O}_K$.\\ In the second part of this thesis, we prove an Ax-Schanuel type result for the exponential functions of general linear groups over $\mathbb{C}$. We prove the result first for the group of upper triangular matrices and then for the group $GL_n$ of all $n\times n$ invertible matrices over $\mathbb{C}$. As a corollary we obtain Ax-Lindemann type results for these maps, characterizing the bi-algebraic subsets of these maps.

Keywords: Ax-Schanuel
Height bounds
Unlikely Intersections
Variations of Hodge structures
Zilber-Pink
Advisor: Tsimerman, Jacob
Investigating Regulation of Cyclin-Dependent Kinases by SCF Ubiquitin Ligases and Pharmacological Kinase Inhibitors

Cyclin-dependent kinases (CDKs) are serine/threonine protein kinases that control both transcription and progression through the cell cycle. CDKs are catalytically inactive as monomers and only become fully active upon heterodimerization with cyclin proteins and phosphorylation of their activation segment. Conversely, CDKs can be inhibited by binding to CDK inhibitor proteins and phosphorylation of the glycine-rich loop of the kinase domain. Whether or not a particular CDK is active depends on the abundance of their intermolecular regulators, which is controlled by the ubiquitin-proteasome system. Because CDKs play important roles in directing cell cycle events, dysregulation of their kinase activity is commonly associated with many cancers. For this reason, it is important to understand the biology underlying CDK regulation during the cell cycle and how CDKs can be targeted by small molecule kinase inhibitors. The work conducted in this thesis focuses on two different CDKs, namely CDK2 and CDK11. In Chapter 2, I investigated the binding between the CDK2-cyclin A complex and the F-box protein Skp2. Skp2 is the substrate recognition subunit of the multi-subunit E3 ubiquitin ligase, SCFSkp2. SCFSkp2 regulates CDK2 by ubiquitinating CDK inhibitor proteins. Aside from the domains required for E3 ubiquitin ligase function, Skp2 contains a disordered N-terminus that is known to bind CDK2-cyclin A via cyclin A. The functional significance of this interaction is unknown. I determined a crystal structure of the N-terminus of Skp2 bound to cyclin A and investigated how Skp2 binding cyclin A affects CDK2-cyclin A kinase activity. In Chapter 3, I focused on determining how the small molecule inhibitor OTS964 binds CDK11. OTS964 is the first reported CDK11 specific inhibitor; however, how OTS964 achieves its CDK11 specificity is unclear. To answer this question, I solved a crystal structure of OTS964 bound to CDK11 and investigated the basis of the selectivity of OTS964 by mutagenesis both in vitro and in cells.

Keywords: Cell cycle
Kinase
Kinase inhibitor
Structural biology
Ubiquitin
X-ray crystallography
Advisor: Sicheri, Frank
Clinically Relevant Statin-drug Combinations to Potentiate Breast Cancer Cell Death

Statins are widely prescribed cholesterol-lowering drugs that inhibit HMG-CoA reductase (HMGCR), the rate-limiting enzyme in the metabolic mevalonate pathway. Multiple lines of evidence suggest that certain cancers depend on the mevalonate pathway for growth and survival and are therefore vulnerable to statin therapy. These immediately available, well-tolerated and inexpensive drugs have yet to be successfully integrated into cancer patient care. For statins to be repurposed for personalized treatment in cancer, we must first better understand how best to administer statins in combination with other agents to maximize therapeutic response. In this thesis, my specific objectives have been to identify compounds that synergize with statins and decrease the pro-apoptotic dose of statins to clinically achievable cholesterol-lowering doses. To this end, we first developed an integrative pharmacogenomics pipeline to identify compounds similar to dipyridamole at the level of drug structure, cell line sensitivity and molecular perturbation. We validated top-ranked compounds, nelfinavir and honokiol, and identified that low expression of the canonical epithelial cell marker, E-cadherin, was associated with statin-dipyridamole, statin-nelfinavir and statin-honokiol synergy. Analysis of the remaining prioritized hits led to the validation of additional compounds, clotrimazole and vemurafenib. Thus, our computational pharmacogenomic approach identified novel, actionable compounds with mevalonate pathway-specific activities. Next, we used a genome-scale approach to identify chemogenomic potentiators of fluvastatin sensitivity. Statin treatment in combination with squalene epoxidase (SQLE) inhibition induced a robust pro-apoptotic cell death response in a panel of breast cancer cell lines and patient-derived breast cancer organoids. This combination therapy provides a strong rationale to combine these two clinically approved agents for the treatment of breast cancer. Taken together, the work presented in this thesis reveals several promising opportunities for the repurposing of statins in combination with additional, clinically approved drugs to treat breast cancer. Since statins are already approved for the prevention of cardiovascular disease, and are available as generic drugs, they offer an immediate, safe, and cheap opportunity to improve cancer patient care and treatment outcome.

Advisor: Penn, Linda Z
Transplanting Immortal Orexin Cells in Narcoleptic Mice Rescues Cataplexy

The sleep disorder narcolepsy is characterized by highly diminished or entirely absent levels of the neuropeptide orexin in the central nervous system. This loss manifests in symptoms such as cataplexy, a sudden and involuntary loss of muscle tone during wakefulness. To address this loss, I performed orexin cell transplants in a mouse model of narcolepsy (orexin-knockout; orexin-/-) to explore cell replacement therapy as a therapeutic strategy for narcolepsy. Here, I validate the phenotype of a novel immortal orexin cell line that exhibits genomic, proteomic and neurosecretory properties consistent with hypothalamic orexin neurons. When the designer receptor hM3Dq is expressed in cultured orexin cells activation and orexin release is increased via the ligand clozapine-N-oxide (CNO). To determine if the CNS of the orexin-/- mouse is still responsive to the orexin peptides, I performed intracerebroventricular infusion. I found that cataplexy was significantly reduced but not abolished when orexin was infused to the lateral ventricles. Because cataplexy is a behaviour exhibiting high variation, I next aimed to delineate a new method to identify cataplexy enabling experimental conditions that boost cataplexy presentation. I found that visual identification of cataplexy was accurate and that pair-housed non-instrumented animals have significantly more cataplexy than those instrumented for iii electrophysiological recordings. I next addressed the central goal of my project by transplanting orexin cells to the lateral hypothalamus of orexin-/- mice, finding no change in cataplexy. However, when orexin cells were transplanted to the dorsal raphe a substantial reduction in cataplexy in narcoleptic mice was observed. CNO-mediated activation of hM3Dq-expressing orexin cells further reduces cataplexy in the orexin-/- mouse, in line with my in vitro data. Overall, this thesis provides evidence towards the use of cell replacement therapy as a therapeutic strategy for narcolepsy, and the potential for using an immortal cell line to accomplish this specifically.

Keywords: Cataplexy
Cell transplants
Narcolepsy
Orexin
Sleep disorders
Advisor: Peever, John H