VictorJuiz/thesis huggingface dataset:
A Spatio-temporal Phylogenetic Approach to Community Ecology

Ecologists seek to explain the causes and consequences of species diversity patterns through the interactions of species with each other and their shared environment. Species diversity is however inherently complex because various processes influence species at different spatial and temporal scales. To examine the contribution of both evolutionary and ecological processes, ecologists often measure the phylogenetic relationships between interacting species. However since various processes drive species assembly at different scales, phylogenetic relationships vary with spatial and phylogenetic scale. In my thesis, I address how phylogenetic relationships at different spatial and temporal scales can inform both the ecological and evolutionary processes which affect assembly patterns. For montane plant communities in Colorado, I show that different spatial and phylogenetic scales produce different phylogenetic patterns for the trait, "elevational range size". From my findings, I caution against the use of a single spatial or phylogenetic scale, as it may lead to different conclusions about the data. For angiosperms in a plant community in Toronto, I show that species trait and phylogenetic relationships are spatially-dependent within the community level. For my system, multiple processes likely co-occur within the community and influence species assembly patterns at different spatial scales. I find evidence of competitive interactions at small spatial scales, which then transitions to environmental filtering at broad spatial scales. Therefore studies which select communities at a fixed spatial size are biased toward observing certain patterns and may subsequently overlook spatially-dependent processes. Finally, for angiosperm plant communities in Colorado, I demonstrate how phylogenetic relationships within communities can provide insights on macroevolutionary events. I find patterns consistent with niche conservatism and adaptive radiation, where the environmental gradient associated more with turnover of recently diverged lineages than with ancestral lineages.

Keywords: angiosperms
coexistence
community assembly
community phylogenetics
plant diversity
spatial scale
Advisor: Cadotte, Marc W
Fortin, Marie-Josée
Pitch Processing Experience: Comparison of Musicians and Tone-language Speakers on Measures Auditory Processing and Executive Function

Psychophysiological evidence supports an association between music and speech such that experience in one domain is related to processing in the other. Musicianship has been associated with benefits to auditory processing and executive function. It is unclear, however, whether pitch processing experience in nonmusical contexts, namely speaking a tone language, has comparable associations with auditory processing and executive function. The present investigation aimed to clarify this association, with the overarching goal of better understanding how two different types of pitch processing are linked to perceptual and cognitive processing. If pitch-processing experience gained via musicianship or tone-language use shapes perceptual and cognitive processes in similar ways, then musicians and tone-language speakers (nonmusicians) should outperform controls without music training or tone-language experience. This hypothesis was tested in a series of experiments that measured behavioural and neural responses of tone-language speakers and musicians on tasks of perception (pitch discrimination, pitch encoding, i.e., representation of pitch-relevant information) and cognition (pitch memory, visual working memory). Collectively, the findings reveal that benefits to auditory processing are more closely associated with music training than with tone-language use. When musicians and tone-language speakers performed comparably on behavioural tasks, this occurred at the perceptual level (i.e., sound discrimination). Differential responsiveness of tone-language speakers or musicians was evident at the neural level (i.e., event-related potentials, brain-signal variability). Neither musicianship nor speaking a tone language was associated with a benefit to visual working memory. These results are discussed in relation to the respective contributions of nature and nurture to auditory processing and visual working memory in musicians and tone-language speakers.

Keywords: auditory
EEG
music
perception
pitch
tone language
Advisor: Alain, Claude
McIntosh, Anthony R
Investigation of the Ribosome Independent mRNA Localization to the Endoplasmic Reticulum

Localization of mRNA to various subcellular compartments is a widespread phenomenon in both prokaryotes and eukaryotes. One group of mRNAs that exhibit this organelle specific localization are mRNAs encoding secreted, organellar and membrane-bound proteins. These mRNAs are localized on the surface of the plasma membrane in prokaryotes and on the endoplasmic reticulum (ER) in eukaryotes. Previously, these mRNAs were thought to target and later be maintained on the surface of the ER through information that is present in the encoded polypeptide. However, here I provide direct visual evidence that a subset of these mRNAs can be targeted and also later maintained on the ER independently of translation. I also identified an mRNA receptor on the ER, p180, which anchors mRNAs on the ER via a highly positively charged lysine-rich region. Subsequently I identified a region in the placental alkaline phosphatase (ALPP) mRNA, the region that encodes the transmembrane domain (TMD), that is required and sufficient to anchor mRNAs to the ER in a p180-dependent manner. Finally, I demonstrate that certain mRNAs encoding tailed anchored (TA) proteins are also anchored to the ER in a translation-independent manner. Overall my work provides the first mechanistic insight into RNA-mediated targeting of mRNAs to the ER, suggesting a more complex role for the ER in the post-transcriptional control of genes encoding secretory proteins.

Keywords: Endoplasmic Reticulum
mRNA Localization
Tail Anchored Proteins
Advisor: Palazzo, Alexander F
Targeting and Specificity of RNA-binding Proteins

RNA-binding proteins (RBPs) are critical parts of the gene regulatory framework, but the vast majority have unknown specificity for RNA. In this thesis I undertook three projects aimed at identifying the determinants of RNA specificity. First, I describe the creation of a database of experimental RNA-binding data that catalogues metazoan RBPs and published measurements of RNA binding. This catalogue allowed me to identify that the RNA-binding specificity of only a small fraction of RBPs was known. In collaboration with other members of the Hughes and Morris labs, I employed RNAcompete, an in vitro microarray-based method for determining the sequence specificity of RBPs, to over 200 eukaryotic RBPs. In order to determine the optimal modelling framework, I performed a systematic comparison of motif-finding methods on the RNAcompete data. The resulting motifs capture a wide range of RNA-binding specificities and allow for the inference of motifs for 20% of metazoan RBPs. In the last data chapter I describe a methodology, termed RNAcompete-S, that I developed for experimentally testing and computationally identifying the sequence and secondary structure preferences of RNA-binding proteins. Applying this method to a panel of RBPs with diverse RNA-binding domains and strategies allowed me to identify the known sequence and structural specificities of these proteins. Specifically, I was able to identify de novo an 18-nt motif matching the conserved SLBP binding site. I also developed an extension of the position weight matrix (PWM) motif model called sequence-structure motifs (SSMs), which allow both visualization of sequence and structural preferences in a way similar to standard sequence logos, and allow scanning of genomic and mRNA sequences. The work described here represents a small step toward understanding of protein specificity for RNA sequences and structures. Further refinements of the methods and models I present are described in the concluding chapter. The RNA-binding specificities discovered, and the experimental and computational methods developed, should help identify binding sites in targets of RBPs to understand their function in living cells.

Keywords: Computational biology
RNA-binding proteins
RNA secondary structure
Stem-loop binding protein
Advisor: Hughes, Timothy R
Ritual, Materiality and Memory in an Iroquoian VIllage

This study has sought to demonstrate that analyses of Iroquoian ceramics that focus on technological practices can provide new insights into Iroquoian materiality and ritual. Implicit in this approach is the notion that many objects contain within them a record of human decisions that articulate with social practices. I have examined four types of ceramic objects typically recovered from Ontario Iroquoian villages: smoking pipes, pots, juvenile pots, and fired clay lumps. Through the application of novel methods of ceramic petrography to the objects recovered from Holly, an early 14th century AD Iroquoian village, I documented the technological choices made during Iroquoian engagement with ceramic objects throughout their biographies, and related them to social practices using contextual and spatial data. When viewed as a whole, the evidence presented suggests that the ceramic objects at Holly were made in several overlapping but distinct communities of practice. In particular, pottery vessels were made by a smaller group of experienced craftspeople, using a restricted palette of materials and techniques. Smoking pipes, however, were made by larger numbers of people of differing skill levels, using a wider range of materials. The patterned use of dark-coloured rock temper in smoking pipes and pottery embodied the intentionality of their creators or users and served as a symbolic referent to Iroquoian cosmological beliefs. The deliberate fragmentation and preferential deposition of dark-tempered smoking pipes in the structured deposits of de-commissioned sweat lodges served as symbolic referents to two types of memories: both at the object level, where dark-tempered pipes were deliberately broken, exposing their black temper that had been hidden since manufacture, thereby revealing (or perhaps confirming) their symbolically informed production history; and in the built environment of a longhouse, where deposition in a socially sanctioned space might have served to create appropriate memories of the transactions taking place that were associated with darkness, smoking, and the spirit-world. In this way, material qualities precipitated remembrance. For its occupants, the space inside an Iroquoian longhouse was filled with invisible deposits associated with objects, materials, and memories that reflected and reified Iroquoian cosmologies, and influenced quotidian social practices.

Keywords: experimental archaeology
Huron-Wendat
Iroquoian
materiality
petrography
shamanism
Advisor: Miller, Heather M.-L.
Associative Learning as a Source of Visual Bias

The visual system does not encounter isolated visual features, but sets of features that bind together and constitute complex perceptual events. Visual features are also typically accompanied by the observer's own movements, and it is believed that these movements are also included in the representation of events. In the present thesis, argue that the units of attentional selection are such multi-featured events. This means that learning the regularities in the relation among features can guide visual attention toward multiple features that belong to the selected event. Through a series of experiments, I demonstrate how visual bias for colour is influenced by the selection associated features, such as a shape or a manual movement. In all instances, I argue, selecting or inhibiting one feature impacts the treatment of the associated colour feature. In short, feature association can extend the impact of feature-based attention across multiple dimensions, which supports the idea that events, not features, are units of attentional selection.

Keywords: Attention
Bias
Cueing
Memory
Advisor: Pratt, Jay
ESL Education for Social Transformation

If one considers the colonial history of TESL, its ties to imperialism, and capitalism’s need for a cheap labour force which instigates movement of both people and corporations, one will see that TESL is a very social and political activity. Furthermore, since our current social organization and economic model are guided by capitalist social relations, it is crucial to place teaching ESL within these relations in order to shed light on its role in capitalism’s reproduction. In this study, I focus on the learner as a social being and investigate the potential of English language learning as a social and political act for the purpose of social change. My main research question is: What is English language learning from the perspective of the learner who is motivated by pursuing social transformation? What would an ESL class aimed at social change look like from the perspective of the learners and teachers of this study and a dialectical theoretical framework? To what degree are ESL teachers and institutions aware or accommodating to these learners’ needs? To pursue these questions, I have conducted a qualitative research study to explore the barriers and successes that ESL teachers attempting to do critical work have had. I have also interviewed ESL learners who are motivated by their desire to be politically and socially active in order to gain insight about their English language learning and their ESL classes. My theoretical conceptualization has allowed me to see how our actions as ESL teachers and theorists at times reproduce capitalist social relations and at other times challenges and disrupts them. It is my hope that this study will generate theory in the field of language education that helps other language learners and educators to politicize, decolonize, and radicalize the field of ESL.

Keywords: Activism
Education
ESL
Social Change
Social Transformation
Advisor: Mojab, Shahrzad
Essays in Asset Pricing

In this thesis I study the relationship between investor behavior and asset pricing from two aspects: First, I examine how investors' learning about a firm's stock price in the presence of noisy information impacts the firm's stock return volatility. Second, my co-authors and I investigate how institutional investors vary in the type and extent of skill they exhibit based on prudency requirements and active management. In the first chapter, I examine the relationship between investor learning and firm volatility. Price return volatility is excessive relative to fundamentals (Shiller 1981) and exhibits persistence (Engle 1982). However, empirical research has not focused on providing an explanation that simultaneously addresses both stylized facts. I use a simple rational learning model to predict that the level of return volatility is positively related to the level and uncertainty of cash flow growth rates, and that the dynamics of return volatility reflect the dynamics of investors' uncertainty about cash flow growth rates. Proxying for growth rate variables using analyst earnings forecasts, I show that the data support model predictions. In the second chapter, my co-authors, Mikhail Simutin and Kent Womack, and I examine the relationship between prudency requirements, active management, and the assessment of institutional skill. We hypothesize that the type of skill an institution exhibits depends on how constrained it is by prudency requirements, while the extent of its skill is related to how actively it is managed. We conjecture that less constrained institutions such as hedge funds exhibit skill by trading on near-term information, whereas more constrained institutions such as bank trusts exhibit skill by generating abnormal returns in bad states of the economy. The results from our analysis offer evidence supporting these hypotheses. We employ active share and holdings churn as competing measures of active management and, after controlling for prudency, we find that high active share level is more indicative of skill based trading, whereas high churn level is more consistent with momentum based trading.

Keywords: Institutions
Investing skill
Learning
Parameter uncertainty
Prudency
Volatility
Advisor: Han, Bing
Kan, Raymond M.
Student Engagement: A Qualitative Study Of Extracurricular Activities

This study explores how students engaged with sports and citizenship clubs. Data was generated through semi-structured interviews with students, teachers and the principal, and observations of four extra-curricular clubs. The data revealed that clubs play important roles in students’ educational lives. The study found that students were empowered in all the clubs’ activities and decision-making, and shared and learned from each other’s knowledge and strengths. It also revealed that club leaders had a significant impact on student engagement within the clubs and the entire school. Students engaged in dialogue, shared ideas, and learned from each other. Unlike other studies in the area of extracurricular activities (ECA), this study illustrates just how the interactions of students in the ECA generate community building within the clubs and the entire school. This research does so by featuring students’ own points of view about the support, challenges, and impact of ECA.

Keywords: community building
extracurricular activities
leadership
motivation
relationships
student engagement
Advisor: Ryan, James
Learning in a Militarized Context: Exploring Afghan Women’s Experiences of Higher Education in ‘Post-Conflict’ Afghanistan

This study examines the repercussions of the war on terror and subsequent occupation of Afghanistan, on the daily (gendered) life experiences of Afghan women. I argue that such wars are markers of the shifts in global capitalist accumulation processes, from exporting ‘goods’ to the Global South, to now exporting capitalism. Specifically, the war on terror is the latest manifestation of monopoly finance capitalism, which leverages wars and insecurity in the Global South as lucrative sites for accumulating profits and (re)investments. Democratic ideals provide a ‘moral’ justification for mass militarism, human rights violations, torture and erosion of existing social and economic inequalities. Notions of freedom, equality or classlessness, which are important objectives of formal democracy, as well, colonialist and racist ideologies of Others have become effective mechanisms for capitalism to sustain and reproduce capitalist class relations. Education is an important site for socializing citizens toward accepting and participating as human capital in monopoly finance capitalism. Through the World Bank, higher education reforms in Afghanistan are endorsing neoliberal policies, even as these policies continue to contradict and exacerbate existing inequalities. Specifically, female education has become a key strategy in continued militarization and occupation in the country. In this study, I examine the contradictory ways in which female university students navigate through an increasingly militarized, violent and patriarchal terrain. Guided by a transnational feminist approach and a dialectical historical materialist framework, 19 female university students from 5 public and private universities were interviewed in Afghanistan. Findings suggest that the university is a contradictory site where participants mobilize new and old strategies for addressing gendered constraints in their lives, while simultaneously creating new ones. The implications of these findings suggest a need for extensive institutional and ideological support for women’s learning, and also improving home-school connections. The participants’ desire to learn and their concerns over increasing violence and insecurity, reveal the militarized nature of their learning, as well, the possibility for critical and transformative learning against imperialism, patriarchy and class relations.

Keywords: Afghanistan
Colonialism
Educational policies
Gender
Higher education
Patriarchy
Advisor: Magnusson, Jamie-Lynn
A Surface Chemistry Approach to Enhancing Colloidal Quantum Dot Solids for Photovoltaics

Colloidal quantum dot (CQD) photovoltaic devices have improved rapidly over the past decade of research. By taking advantage of the quantum confinement effect, solar cells constructed using films of infrared-bandgap nanoparticles are able to capture previously untapped ranges of the solar energy spectrum. Additionally, films are fabricated using simple, cheap, reproducible solution processing techniques, enabling the creation of low-cost, flexible photovoltaic devices. A key factor limiting the creation of high efficiency CQD solar cells is the short charge carrier diffusion length in films. Driven by a combination of limited carrier mobility, poor nanoparticle surface passivation, and the presence of unexamined electrically active impurities throughout the film, the poor diffusion length limits the active layer thickness in CQD solar cells, leading to lower-than-desired light absorption, and curtailing the photocurrent generated by such devices. This thesis seeks to address poor diffusion length by addressing each of the limiting factors in turn. Electrical transport in quantum dot solids is examined in the context of improved quantum dot packing; methods are developed to improve packing by using actively densifying components, or by dramatically lowering the volume change required between quantum dots in solution and in solid state. Quantum dot surface passivation is improved by introducing a crucial secondary, small halide ligand source, and by surveying the impact of the processing environment on the final quality of the quantum dot surface. A heretofore unidentified impurity present in quantum dot solids is identified, characterized, and chemically eliminated. Finally, lessons learned through these experiments are combined into a single, novel materials system, leading to quantum dot devices with a significantly improved diffusion length (enhanced from 70 to 230 nm). This enabled thick, high current density (30 mA cm-2, compared to typical values in the 20-25 mA cm-2 range) devices, and the highest reported solar power conversion efficiency to date.

Advisor: Sargent, Edward H