VictorJuiz/thesis huggingface dataset:
Manipulating a "cocaine-cue engram" in mice

Experience with drugs of abuse (such as cocaine) produces powerful, long-lasting memories that may be key in the development and persistence of drug addiction. The neural mechanisms that mediate how and where these cocaine-cue memories are encoded, consolidated, and stored in the brain are unknown. Here we used cocaine-induced conditioned place preference to examine the precise neural circuits that support a cocaine-cue memory (cocaine-cue “memory trace” or “engram”) in mice. We found that a small population of neurons (~10%) in the lateral nucleus of the amygdala (LA) was recruited at the time of cocaine-conditioning to become part of the cocaine-cue engram supporting that memory. Moreover, neurons with increased levels of the transcription factor CREB (cAMP response element-binding protein) were preferentially recruited or allocated to the cocaine-cue engram. Pre-test ablation or silencing of neurons overexpressing CREB (but not a similar number of LA neurons not allocated to the cocaine-cue memory engram) disrupted the expression of a previously acquired cocaine-cue memory, suggesting that neurons overexpressing CREB become critical nodes in the LA of what is likely a larger (perhaps brain-wide) cocaine-cue engram. Previous research has suggested that coordinated post-encoding reactivation of neurons within an engram or cell assembly is crucial for memory consolidation (Marr, 1971; Buzsáki, 1989; Wilson McNaughton, 1994; McClelland et al., 1995; Girardeau et al., 2009; Dupret et al., 2010; Carr et al., 2011). Consistent with this, we also found that post-training suppression or non-discriminate activation of CREB overexpressing neurons impaired consolidation of the cocaine-cue memory. We also showed that these neurons were important for the reinstatement of a cocaine-cue memory. Following extinction of a cocaine-cue memory, re-exposure to cocaine may reinstate the original memory (Brown et al., 2010; Bilbao et al., 2008; Mueller Stewart, 2000). These results suggest that those neurons that are initially important in a cocaine-cue memory continue to be important to that memory, even following extinction. Finally, we found that in the LA, neurons that have relatively higher levels of neuronal excitability are more likely to be recruited to an engram supporting a cocaine-cue memory. Together, these findings reveal mechanisms underlying how and where drug memories are encoded and stored in the brain.

Keywords: Amygdala
Cocaine
Conditioned place preference
Memory
Advisor: Josselyn, Sheena
Abiotic and Biotic Leaching Characteristics of Pyrrhotite Tailings From the Sudbury, Ontario Area

The present study investigated the abiotic and biotic leaching characteristics of nickeliferous non-upgraded pyrrhotite (Po) tailings (0.6 wt% Ni), and upgraded Po tailings (1 wt% Ni) produced by Vale Base Metals in the Sudbury Basin of Ontario, with the aim of maximizing Ni and S0 recoveries. Mineralogical characterization of the tailings revealed the deportment of Ni to be similar in the non-upgraded and upgraded tailings, with 60% of the total Ni locked in Po, and the balance 40% associated with pentlandite (Pn). Application of a bacterial adaptive evolution protocol on 1%-20% (w/v) non-upgraded Po tailings, showed that the extent of Ni dissolution is positively correlated with microbial activity. Subsequently, a selective-dissolution protocol was developed to relate the overall Ni dissolution with the individual terminal dissolution extent of Po and Pn as functions of four leaching regimes: ‘anoxic acid’ (with and without pH control), ‘oxic acid’ (O2 sparging), ‘oxic acid’ (air sparging), and ‘oxic ferric’ (air sparging). The results showed that the maximum Ni dissolution (94%) was obtained during the pH controlled oxic acid leach with O2 sparging at pH 1.5, while the anoxic acid leach at pH 1.5 resulted in minimum Ni dissolution (10-15%) from Po. Application of the selective dissolution protocol to leach residue samples showed that Po and Pn dissolve simultaneously in the presence of Fe(III) and O2, in contrast to the preferential dissolution of Po in the absence of Fe(III). The maximum yield of elemental sulfur (65%) was obtained during the oxic Fe(III) leach at pH 0.6. However, the oxic ferric leach tests did not result in increased Ni dissolution due to the formation of a protective sulfur coating around Po grains. Thus, the present study has shown that the recovery of Ni and the yield of S0 cannot be maximized simultaneously under the experimental conditions tested; thereby, leading to the identification of operating conditions that maximize the oxidative-dissolution kinetics of Po and Pn (oxic acid leach with O2 sparging at pH 1.5), and the yield of elemental sulfur (oxic ferric leach at pH 0.6).

Keywords: Bioleaching
Nickel
Pyrrhotite
Sudbury
Sulfur
Advisor: Papangelakis, Vladimiros
Mahadevan, Radhakrishnan
Climate Change Impacts on Mercury Cycling in Peatlands

Climate change, through hydrological impacts and shifts in vascular plant communities, may significantly affect the strength of peatlands as sinks of inorganic mercury (Hg) and downstream sources of neurotoxic methylmercury (MeHg). Four complementary studies were conducted at the PEATcosm (Peatland Experiment at the Houghton Mesocosm Facility) and SPRUCE (Spruce and Peatland Responses Under Climatic and Environmental change) sites to investigate the anticipated effects on Hg cycling. Lowered, more variable water tables and the removal of Ericaceae shrubs in the PEATcosm mesocosms significantly enhance Hg and MeHg mobility in peat pore waters as well as export from the peat in runoff during the snowmelt period. Mercury is mobilized in association with dissolved organic carbon leached from the peat as a result of increased aerobic decomposition. Enhanced Hg and MeHg solid phase peat concentrations are observed within the zone of the lowered, fluctuating water tables due to translocation within the peat profile. This shift in peat concentrations does not correspond to any significant differences in Hg methylation or MeHg demethylation. The strongest trend of Hg deposition to peat occurs with increased sedge cover, possibly as a result of coincidental shuttling of Hg to the peat by aerenchymous tissues. Different plant functional groups alter the pathway of gaseous Hg exchange, with greater Hg sorption to leaf surfaces and accumulation in leaf tissues by stomatal uptake for the Ericaceae shrubs as compared to the sedges. Total gaseous Hg fluxes increase marginally with deep soil warming. Isotopic analyses demonstrate differences in Hg depositional sources to the two peatland sites, likely due to differences in snow accumulation, and provide insight into the mechanisms governing Hg cycling in peatlands. Collectively, these studies demonstrate that anticipated climate change may significantly affect peatland Hg mobility and cycling within and among the terrestrial, atmospheric and hydrological pools.

Advisor: Mitchell, Carl PJ
Contributions to Tensor-based Stress Variability Characterisation in Rock Mechanics

In situ stress is an important parameter in rock mechanics, but localised measurements often display significant variability. To incorporate such stress variability into probabilistic related analyses in rock mechanics, robust approaches for stress variability characterisation are essential components and prerequisites. Currently, variability of stress is customarily characterised by processing principal stress magnitude and orientation separately using scalar and vector related approaches, respectively. This is erroneous, as stress is a second order tensor and should be processed using tensorial approaches. However, tensorial approaches are poorly developed. The result is that to date there seems to have been no mathematically rigorous proposal for and systematic analysis of stress variability characterisation in rock mechanics. This work presents a mathematically robust approach to characterise stress variability. The work commences with an examination of the customary scalar/vector approach, and demonstrates why stress data should be processed in a tensorial manner. From this, fully tensorial approaches are proposed for calculating the mean stress (Euclidean mean), obtaining the statistical distribution model (multivariate distribution of distinct tensor components), assessing scalar valued stress dispersion (effective variance) and generating random stress tensors (generating multivariate random vector and forming the random stress tensor). The transformational consistency, or invariance, of these with respect to coordinate system change is derived in an analytical manner. A systematic examination of the applicability and efficacy of the proposed fully tensorial approaches for stress variability characterisation is presented using synthetic, actual and numerically simulated stress data. The calculations show that both the customary scalar/vector approach, which treats principal stress magnitudes and orientations as independent quantities, and existing quasi tensorial applications, which ignore the correlation between tensor components, may give incorrect results. The recommendation is thus made that stress tensors are referred to as comprising â six distinct componentsâ , rather than the customary â six independent componentsâ . This leads to the conclusion that stress variability should be characterised using multivariate statistics of the distinct tensor components referred to a common Cartesian coordinate system. Finally, transformational consistency, or invariance, of the proposed fully tensorial approaches is demonstrated, and this allows stress variability to be characterised in any convenient coordinate system.

Keywords: Mean stress
Random stress tensor
Rock mechanics
Statistics
Stress dispersion
Stress variability
Advisor: Harrison, John P.
Thermo-oxidation of undoped and W-doped carbon co-deposited films: a study of erosion behaviour and reaction product formation

The goal of the study is to determine the effect of W-doping on the thermo-oxidation of carbon co-deposited films. W-doped carbon-deuterium co-deposited films are generated on Si wafers, varying the W-content and co-deposit structures. The D retention after oxidation is examined as a function of W-content and compared against undoped specimens. Three cycles of plasma deposition and thermo-oxidation take place, to determine any trends over time and with the varying W-content. Finally, the reaction products are observed and compared between the oxidation of a batch of undoped films and W-doped films. For the W-doped films, it was found that higher %W films (a few at. %) with moderate thickness (330 nm) show strong oxidation-inhibition behaviour when compared to undoped films under oxidation at 2 Torr O2, 350 oC, for 8 h. No concentrated surface layer of W or WO3 is observed on the surface. This uniform-depth oxidation behaviour suggests the absence of any kind of “blocking layer”, but rather, since the oxidation-inhibiting action occurred throughout the depth, it is proposed here that during film formation, the amount of W acts to create different film structures – more or less susceptible to oxidation. Repeating the deposition and oxidation across several cycles does not show any enhanced retention, likely due to the inconsistency in the W-content between film applications. Products are the same for W-doped and undoped films.

Keywords: co-deposit
fusion
oxidation
plasma-facing materials
surface
tritium
Advisor: Davis, James W
Haasz, Anthony A
DOES INITIAL TEACHER EDUCATION AFFECT TEACHER CANDIDATE BELIEFS ABOUT EQUITY AND DIVERSITY?: DEVELOPMENT AND USE OF THE TEACHER CANDIDATE BELIEFS ABOUT EQUITY AND DIVERSITY MEASURE

Abstract What teacher candidates believe â and whether those beliefs change during their initial teacher education â has important implications for their future students. In this three paper dissertation, the first two papers describe the development, refinement, and psychometric properties testing of the Teacher Candidate Beliefs about Equity and Diversity (TCBED) measure. The TCBED was designed to answer the main research question â does initial teacher education (ITE) affect teacher candidate beliefs about equity and diversity? The third paper presents the findings from administering the TCBED at the beginning and ending of an initial teacher education (ITE) program. More than 150 teacher candidates attending a large one-year consecutive ITE program in 2012-2013 answered the TCBED measure at both the beginning and end of the program. Most teacher candidates had moderately to very positive beliefs about teaching for social justice, their equity and diversity beliefs, and their sense of selfefficacy regarding teaching for social justice, and showed little change in their beliefs. To better understand the teacher candidates who did not fit this pattern, several who had consistently low scores across parts of the TCBED measure and across time or who varied in their scores were selected for closer analysis of their responses to open-ended items on the TCBED measure. In general, the ideas teacher candidates wrote about did not change over time except to show some development of already expressed beliefs. Implications of the findings and usefulness of the TCBED measure are discussed.

Keywords: development
equity and diversity
measure development
social justice
teacher candidate beliefs
teacher education
Advisor: Childs, Ruth A.
Informing Identities: Religious Conversion Experiences of Muslims in the Toronto Area

The purpose of this dissertation is to explore the ways in which information seeking, evaluation, and sharing practices mediate the conversion experiences of Muslims living in the Greater Toronto Area (GTA). This research contributes to Information Studies and interdisciplinary literature on conversion by adding insight into information practice in a religious context, particularly one that is characterized by a critical transition and situated within a contentious political landscape. Research was guided by an interpretive ethnographic approach. Data collection involved participant observation at religious conventions, education classes, discussion groups, and social gatherings hosted by convert support organizations over a 14-month period; semi-structured narrative interviews with 13 Muslim converts and two of their spouses; timeline drawings with ten research participants; a guided tour with one pilot study participant; and journal entries written by three pilot study participants. Findings are framed by three themes: navigation, authority, and expression; these themes correspond with the concepts of seeking, evaluating and sharing information. They describe participantsâ experiences of finding their way through new information systems and social networks; assessing sourcesâ trust, relevance, and authenticity; and presenting religious commitments through their bodies, vocabulary, and creative pursuits. Findings suggest that rather than being peripheral to religious experience, information practice is integral to how participants develop their religious identities and articulate their connection to local and global Muslim communities. This study extends the idea that everyday information practices involve not only interactions with written documentary sources such as books, websites, and social media, but also embodied forms of expression such as clothing, movements, words, and verbal references to key issues and debates, historical moments, influential figures, social norms and activities in the communities with which people identify.

Keywords: ethnography
information practice
Islam
Muslim converts
religious conversion
Toronto
Advisor: Hartel, Jenna
AN ANALYSIS OF THE TEACHING AND LEARNING OF ACADEMIC LITERACIES IN ONLINE BOOK CLUBS

English for academic purposes (EAP) students require opportunities to practice and develop their English computer mediated communication to interact effectively in university contexts where English is the medium of instruction (EMI). In 2014 a literacy activity that used Facebook Groups to host student online book clubs was introduced into the curriculum of a 24 week EAP program at a major Canadian university. Informed by sociocultural theory this thesis presents insights gained through a multi-method qualitative study of the book clubs and their participants over the course of the program. The Community of Inquiry framework (Garrison, Anderson Archer, 2000) was employed to conduct a content analysis of five Facebook book club groups. The content analysis data were then analyzed with the data collected from multiple interviews with three case study students who participated in the five book clubs, a student questionnaire (n=58), and interviews with four book club instructors. The COI framework was used to record and interpret how instructor choices, actions and interventions affected social and cognitive presence of the studentsâ participation and practices in the book clubs. The interview and questionnaire data enabled me to elucidate the content analysis data and gain insights into how instructor online behaviour mediated student perceptions about their learning and participation in the activity. The thesis findings indicate that instructor book selection, scaffolding, modelling, and manner significantly mediated student perceptions regarding their engagement, participation, and interaction in the activity, specifically, whether students thought that they: (1) read extensively, and practiced essential academic reading strategies; (2) demonstrated high cognitive presence in their written comments; (3) and interacted and scaffolded each otherâ s learning. This thesis contributes to the L2 online learning literature in significant ways. The multi-method approach over 24 weeks provides an in-depth understanding of teaching and learning processes in an EAP online learning context that is currently absent in the literature. The study also draws attention to a need to better understand the influence and impact of politeness and pragmatics in interactive online activities such as book clubs, both between students, and between instructors and students.

Keywords: COI
Facebook
Literacy
Online
Politeness
Sociocultural
Advisor: Brett, Clare
Claiming Places: An Exploration of People's Use of Locative Media and the Relationship to Sense of Place

This dissertation explores the role of locative media in people’s place-making activities and sense of place. Sense of place is a human need that entails people’s meanings, memories, and feelings for a location. Recent technological and market developments have introduced powerful geographic information tools and place-related media. By identifying a user’s location, locative media deliver geographically relevant content that enable people to capture and preserve place information, virtually append it to space, and broadcast it to others. Despite locative media’s growing prominence, the influence on sense of place is not well understood. A major finding of this research is that use of locative media can contribute meaningfully to a person’s positive sense of place, including fostering existential connection. This study refutes scholarly and popular dismissals of the medium as only detracting from sense of place. Locative media was found to enable people to make spaces their own by offering geographic relevant information and experiences, recording and sharing place-related impressions, and presenting places in new and enjoyable ways, such as through defamiliarization and decommodification. This study demonstrates the importance of access to our hybrid spaces, unfettered by corporate restriction, to create meaningful place relationships. However, it was also found that locative media can distract from sense of place through the loss of serendipitous discovery. This study used qualitative field reports and semi-structured interviews with 22 people, predominantly from Ontario, Canada. Participants reported using 44 locative media applications in a variety of contexts and locations. Crawford’s urban counter dynamics (2012) and Bott’s sense of place work (2000) were employed as analytical frameworks. Methodologically, this study demonstrates the utility of Bott’s sense of place framework and provides an effective mix of methods for future studies. This research contributes to place theory and mobile media studies by examining the role of locative media in sense of place. From an information studies perspective, it offers evidence of the use and value of geographic relevance and vocality of information. Design guidelines are offered to aid the development of locative media to foster user engagement and conservation attitudes towards place.

Keywords: geographic relevance
location based services
locative media
mobile media
place
sense of place
Advisor: Phillips, David J
Asymmetry in the Partitioning of Surfactants into Lipid Membranes

The emergence of modern standards of public sanitation and personal hygiene was promoted by the invention and mass production of synthetic detergents/surfactants. Detergents insert into and permeabilize cell membranes, and solubilize them completely at higher concentrations; a thorough understanding of these phenomena is particularly important for the agriculture, pharmaceutical, and cosmetics industries. The complex cell membrane is often modelled with liposomes; detergent–membrane interactions have been described by a three-stage model, which assumes equilibrated interactions in that detergents flip-flop rapidly within the membrane bilayer. However, many detergents flip-flop slowly and become asymmetrically distributed in the membrane upon insertion (e.g., sodium dodecyl sulphate at room temperature). The works presented in this thesis aim to further our understanding of asymmetric detergent–membrane interactions and to advance the methodology of characterizing them. The methods applied in these works are spectroscopic and calorimetric in nature, and extended here by developments in quantitative analysis. They were used to investigate three very different detergents: surfactin, a lipopeptide that is negatively charged near neutral pH; 12:0 lysophosphocholine (12:0 LPC), a zwitterionic product of membrane lipid metabolism; and digitonin, a nonionic surfactant often used in membrane protein studies. These detergents share the common thread of asymmetry, but interact with and solubilize membranes in different ways: Surfactin equilibrates in the membrane upon reaching a threshold content in the outer leaflet; 12:0 LPC and digitonin stay in the outer leaflet and do not solubilize the membrane even at high concentrations (digitonin being more persistent in this than 12:0 LPC). As such, all equilibrating detergent–lipid interactions are alike, in that they can be described by the three-stage model; every nonequilibrating detergent–lipid interaction is asymmetric in its own way.

Keywords: detergents
dynamic light scattering
isothermal titration calorimetry
partitioning
solubilization
zeta potential
Advisor: Heerklotz, Heiko