VictorJuiz/thesis huggingface dataset:
Exploring the Connections between Linguistic Inference and Linguistic Perspective Taking
Keywords: cognition
communicative competence
experimental
inference
language
perspective taking

Linguistic inference and linguistic perspective taking are two aspects of cognition that both involve the ability to identify and draw on information not explicitly provided in text or speech, in turn contributing to the successful comprehension of communicated information. There are abundant scientific literature investigating linguistic inference and linguistic perspective taking separately which often use an individual differences approach to assess the links between these abilities and general aspects of cognition. However, no study to date has directly explored the possible relationship (or lack thereof) between linguistic inference and linguistic perspective taking, which would provide important evidence about the basis of these abilities. The current thesis measured individual differences in linguistic inference and linguistic perspective taking simultaneously in an integrated reading paradigm. Results showed that linguistic inference and linguistic perspective taking, as measured in the current paradigm, were not related. Interpretations and theoretical implications are discussed.
Introducing a New Performance Metric to Quantify the Risk of Exposure to Infection Using Electronic Monitoring Systems
Keywords: activity recognition
hand hygiene
healthcare-acquired infections
indoor localization

Healthcare-acquired infections (HAIs) are infections that were not present or incubating at the time of patient admission and are contracted during the process of care. These infections contribute to significant morbidity and mortality each year. Hand Hygiene (HH) is one of the most effective ways to prevent HAIs. The measures used to calculate and report HH performance are not able to fully benefit from the high-resolution data collected by electronic monitoring systems. This work leverages the advancement of intelligent systems to bridge the gap between HH reports and the risk of acquiring infections for patients. This thesis introduces a metric for estimating the risk of exposure to infections for patients in healthcare settings using the existing electronic monitoring systems. The proposed metric can be used to measure the risk of infection for healthcare workers who are at a high risk of infection.
Knowledge Building with Low Proficiency English Language Learners: Facilitating Metalinguistic Awareness and Scientific Understanding in Parallel
Keywords: English Language Learner
Knowledge Building
Metalinguistic Awareness
Scientific Understanding

Two studies were conducted to explore theoretical, pedagogical, and technological issues for advancing language/literacy and scientific understanding in parallel in knowledge building communities. Findings from the initial analysis of student change over 5-years indicated a possible cumulative gap between lexically, orthographically, and conceptually high and low achieving students. A pilot study was conducted subsequently with two Japanese children (grade 4 and 7), both having limited English language proficiency. The goal was to explore the possibility of deepening language and subject knowledge through pedagogical and technological supports. The two children wrote in English in Knowledge Forum®, technology designed to support Knowledge Building, with support from translator and specially designed dictionary. Results revealed student use of translators as a “theory-testing tool,” enabling them to experiment with Japanese and English versions of their ideas and texts. The study informed design possibilities for future work to advance linguistic and subject matter understanding in parallel.
The Roles of Transcription Factors (TF)EB and E3 in the Host Defense Against Invading Bacterial Pathogens: Novel Insights into Bacterial Recognition and the Transcriptional Induction of the Anti-bacterial Response in Non-immune Cells
Keywords: Host-Pathogen Relationship
Infection
Innate Immunity
TFEB

Upon pathogen infection, innate signaling cascades are induced to initiate the transcription of immune effectors. Transcription factors (TF) EB and E3, master regulators of lysosomal biogenesis and autophagy, were recently found to be novel regulators of innate immunity in both C. elegans and mammals. Despite TFEB and TFE3 participating in pathogen recognition and the transcriptional response to infection, little is known about their roles in the infected epithelium. In this thesis we demonstrate that TFEB and TFE3 are activated in non-immune cells upon infection with bacterial pathogens and their ligands by both mTORC1-dependent and -independent mechanisms. Additionally, we characterize a novel mechanism of bacterial recognition dependent on membrane damage, amino acid starvation, mTORC1 inactivation and TFEB nuclear import. Finally, we present data suggesting that although TFEB does not affect bacterial killing or load, it alters the host transcriptome upon infection thus promoting the transcription of cytoprotective and antimicrobial genes.
Neural Correlates of Visual Stimulus Encoding and Verbal Working Memory Differ between Cochlear Implant users and Normal-hearing Controls
Keywords: Cochlear Implant
Cogntion
Connectivity
Hearing Loss
Neural Oscillations
Speech Perception

A common concern for individuals with severe-to-profound hearing loss fitted with cochlear implants (CIs) is difficulty following conversations in noisy environments. Recent work has suggested that these difficulties are related to individual differences in verbal working memory and the degree of cross-modal reorganization of auditory areas for visual processing. However, the neural basis for these relationships is not fully understood. Here, we investigated neural correlates of visual-verbal working memory and sensory plasticity in 14 CI users and age-matched normal-hearing (NH) controls using high-density electroencephalogram (EEG). Participants completed a modified Sternberg visual working memory task where results suggested that CI users had comparable behavioral working memory performance compared to NH. However, CI users had more pronounced neural activity during visual stimulus encoding, including stronger visual-evoked activity in auditory and visual cortices, larger modulations of neural oscillations, and increased frontotemporal connectivity. In contrast, during memory retention of the characters, CI users had descriptively weaker neural oscillations and significantly lower frontal-temporal connectivity. We interpret the differences in neural correlates of visual stimulus processing in CI users through the lens of cross-modal and intra-modal plasticity.
The Effect of Repetitive Transcranial Magnetic Stimulation on Suicidality in Patients with Treatment Resistant Depression
Keywords: Brain stimulation
Depression
Repetitive transcranial magnetic stimulation
Suicidality

Objective: To investigate the effect of 10Hz repetitive transcranial magnetic stimulation (rTMS) and intermittent theta-burst stimulation (iTBS) on suicidality in patients with treatment resistant depression (TRD).Methods: Data from a three-site randomized clinical trial comparing 10Hz and iTBS rTMS applied to the left dorsolateral prefrontal cortex in patients with TRD was analyzed. The effect of 10Hz rTMS and iTBS on suicidality was compared as measured by the suicide item of the Hamilton Depression Rating Scale 17-item (HDRS-17). Results: Suicidality remitted in 71 (43.7%) of participants randomized to 10Hz stimulation and 91 (49.1%) of participants randomized to iTBS. The difference between the proportions in the two groups (X2 = 0.674, df = 1, p = 0.4117) was not significant. Conclusions: Both 10Hz and iTBS rTMS were effective in reducing suicidality in TRD. Further investigation into the effect of rTMS on suicidality is warranted.
Enhancement of a HSP90 Inhibitor through Development of Thermosensitive Liposomes and in vitro Combinations
Keywords: combination chemotherapy
heat shock protein 90 inhibitors
luminespib
nanomedicine
non-small cell lung cancer
thermosensitive liposomes

The heat shock protein 90 inhibitor, luminespib, has demonstrated potent preclinical activity against numerous cancers, yet clinical translation has been unsuccessful due to dose-limiting toxicities. Thermosensitive liposomes are proposed as a drug delivery strategy capable of delivering high concentrations of luminespib to the tumor in combination with other chemotherapeutic molecules. This work establishes that luminespib exhibits synergistic activity in lung cancer in combination with standard of care drugs, cisplatin and vinorelbine. While thermosensitive liposomes containing cisplatin or vinorelbine have previously been developed, this work presents the first liposomal formulation of luminespib. The physicochemical properties and heat-triggered release of the formulation were characterized. Cytotoxicity assays were used to determine the optimal drug ratios for treatment of luminespib in combination with cisplatin or vinorelbine in non-small cell lung cancer cells. The formulation and drug combination work presented offer the potential for resuscitation of the clinical prospects of a promising anticancer agent.
Exploring Genetic and Metabolic Factors of Neisseria gonorrhoeae using Genomic Datasets
Keywords: Disseminated gonococcal infection
Gonorrhea
Metatranscriptomics
Microbiome
Neisseria gonorrhoeae
Population genomics

Neisseria gonorrhoeae has evolved a suite of factors that allow it to survive in the various niches of the human host, from the genital mucosa to the bloodstream. In this thesis, I use genomic datasets to investigate the genetic factors that allow N. gonorrhoeae to persist in diﬀerent host niches. Whole genome sequences of N. gonorrhoeae isolates from Canada are used to identify genomic features associated with disseminated gonococcal infection, where I identify the porBa allele and other genes as important factors. Next, I use metatranscriptomic datasets of male and female genital tracts with gonorrhea to investigate the gene expression of the microbiota, N. gonorrhoeae and the host. Here, I identify diﬀerences in metabolic expression between N. gonorrhoeae and the microbiota of female subjects with bacterial vaginosis. These analyses contribute to a more complete understanding of the lifestyle of N. gonorrhoeae and its interactions with the host and the microbiota.
Thermal Pulse Induced by Emplacement of Ramba Leucogranites in Southern Tibet
Keywords: Contact aureole
Diffusion
Garnet
Himalayan leucogranites
Ramba Dome
RSCM

The thermal histories of Himalayan leucogranites provide critical information of the post-collisional geodynamics. The Ramba Dome is located at the intersection of the Tethyan Himalaya leucogranite belt and Yadong-Gulu Rift, hosts the youngest endmembers of Himalayan leucogranites (8 Ma, Liu et al., 2014) and provides a good opportunity to constrain the thermal history of the aureole. In the first part of this study, we focus on the carbonaceous staurolite schist at ~1.3 km from the intrusion. Our results from the phase equilibria modeling and the RSCM thermometer indicate a consistent peak metamorphic condition of 550 °C, 3.5-4 kbar. The garnet core composition yields a P-T condition 525 °C, 2.5-3 kbar, with a overstep of ~45 °C corresponds to a 5 kJ/mol (12 O) chemical affinity of garnet nucleation. The sharp dendritic zoning of the garnet core suggests that the duration of the thermal pulse was within 1.4 m.y. In the second part, we focus on the 8 Ma garnet leucogranite dykes, to test the hypothesis of rapid transportation and emplacement of the leucogranitic magma. The diffusion modeling on garnet yields a short timescale of transportation and emplacement (0.25 Ma) which indicates that the transport from the depth of garnet incorporation in leucogranite magma to the final crystallization level was fast. The rapid cooling of the Ramba Dome marked the cessation of Himalayan leucogranite magmatism, which reflects the termination of deep heat source.
A The Sustainability of Moving towards Healthy Plant-based Dietary Patterns
Keywords: environmental footprint
greenhouse gas emissions
plant-based diets
sustainability
sustainable diets
therapeutic diets

A synthesis of the literature on diet-related environmental impacts is needed. We therefore conducted a scoping review to assess the environmental impacts of moving towards plant-based diets. We concluded that shifting toward more plant-based diets can reduce diet-related greenhouse gas emissions (GHGE), land use, water use, energy use, and biodiversity impacts. However, there is a lack of assessment of therapeutic plant-based diet patterns and their human environmental impacts, particularly in real-life settings. Therefore, a randomized controlled trial was analyzed to determine the difference in GHGE between a more plant-based dietary pattern, the Portfolio diet, and the Dietary Approaches to Stop Hypertension (DASH). This is the first study to demonstrate how reductions in diet-related GHGE and some cardiometabolic risk factors can be achieved through well-planned therapeutic diets, using past clinical trials. Future research should analyze the many human health and environmental effects of moving towards more plant-based diets in real-life settings.
A Vote of Conscience: Investigating the Early Development of Guilt and Shame in an Online Context
Keywords: Children
Guilt
Other-Orientation
Reparation
Self-conscious Emotions
Shame

In the second year of life, children begin to respond to transgressions with guilt-motivated reparative behaviour or shame-motivated avoidance. Yet, questions remain regarding when and whether guilt and shame are separable, whether the way guilt and shame are measured may lead to different response patterns, and the mechanism underlying reparative responses. Here, 24 two- year-olds’ guilt and shame were assessed through a virtual experimental task, a parent-report questionnaire, and a parent interview question; we hypothesized that other-orientation (measured through children’s memory for the experimenter’s appearance) would predict their reparative behaviour. None of our measures were reliable in distinguishing guilt-specific responses from shameful behaviours and few relations were found across tasks, but admissions of guilt on the paradigm were linked to admissions of guilt on the questionnaire. Other-orientation was found to be unrelated to both guilt and shame across all measures. Implications for future research on early self-conscious emotional expressions are discussed.
The Institutionalization of New Equity, Diversity, and Inclusion Positions and Practices in Ontario Student Affairs and Services
Keywords: Equity
diversity
and inclusion
Higher education
Student affairs and services

This study investigated the emergence of new equity, diversity, and inclusion (EDI) positions developed in student affairs and services divisions at universities in Ontario, Canada. Most Canadian universities now espouse the values of EDI, though identifying and addressing persistent systemic barriers experienced by undergraduate students from equity-deserving groups has received limited attention. Based on semi-structured interviews with seven student affairs and services staff and directors from three universities, the multiple case study analysis reveals the institutional conditions and factors contributing to staff and student agency that facilitated the development of new EDI-focused positions and practices. The results of this study highlight the importance of understanding and responding to changes in the institutional environment as a critical factor in motivating change to systemic inequities within Canadian universities.
A Study on Water Recovery from Industrial Effluents via Forward Osmosis
Keywords: forward osmosis
membranes
mining
water

Water removal from aqueous effluents in the mining and metals processing industry poses a unique challenge due to the high concentration of dissolved ions. Forward Osmosis (FO) is a membrane technology, which employs a concentrated draw solution to osmotically draw water through a semi-permeable membrane, that can operate on high dissolved ion feeds. FO operation relies on using a draw solution of higher osmotic pressure to extract water while managing concentration polarization which limits the water flux of the membrane. This investigation evaluated how flow rates, draw salt type and membrane orientation impact FO performance on solvent extraction raffinate and mine water effluent samples under osmotic gradient equivalent scenarios for a flat-sheet commercial FO membrane. The type of feed, osmotic gradient and flow rate were found to have the largest impact on water flux while only the feed type impacted the separation efficacy of the FO membrane.
Affective Encounters and Activist Subjectivities
Keywords: Activism
Affect
Autoethnography
Burnout
Relational ontology
Subjectivity

In this thesis, I explore the ways in which notions of activism can be extended by a closer attention to affect from a relational-ontological perspective. Through an autoethnographic study of my own experiences with various forms of activism, I analyze the ways in which different affects emerging from processes of activism may have an impact on activist journeys and subjectivities. Analyzing the affective state of hopelessness or alienation that is often classified as activist burnout, I explore the openings it may present for transformation of self and work. Describing my own ways of addressing such “feelings out of place,” I point to the role of shifting notions of efficacy, time, and belonging in building “infrastructures of response-ability” that are dynamic and attentive to the rewards and strains of activism.
A Systematic Investigation of Anti-phage Defense in Pseudomonas aeruginosa
Keywords: aeruginosa
anti-defense
Bacteriophage
defense
Phage
Pseudomonas

Phages are obligate parasites that kill bacteria through their lytic life cycle. This constant selective pressure causes coevolution, which has been described as an “evolutionary arms race”. To evade phage predation, bacteria have evolved “defense systems”. To counter these bacterial mechanisms, phages contain reciprocal “anti-defense systems”. With the growing rise of antibiotic resistance, finding alternative ways to treat pathogenic bacterial infections is becoming more pressing. Phage therapy is one such alternative. Pseudomonas aeruginosa is a multidrug-resistant, opportunistic pathogen. I aimed to study the intracellular defense/anti- defense interactions of P. aeruginosa strains/phages, in vivo, as a greater knowledge of these interactions will hopefully allow for more successful phage therapy. I conducted a screen to assess the ability of a large collection of phages to replicate on diverse P. aeruginosa strains. In cases where a phage did not replicate on a strain, I determined whether the phage in question was able to adsorb to the strain. If adsorption did occur, it was likely that phage replication was being blocked by anti-phage defense systems operating within the cell. Since these types of systems are of greatest current interest, we conducted further studies on these phage/host combinations. In the hope of finding phage genes involved in anti-defense, I expressed several phage moron genes within P. aeruginosa strains being infected by phages that could adsorb but not replicate. I identified one phage protein, gene product 15 from Pseudomonas phage JBD26, the expression of which decreased phage resistance.
Investigating the Temporal Dynamics of SMX Assembly and Disassembly throughout the Cell Cycle
Keywords: Cell cycle
Homologous recombination
SLX4

Genome instability is a hallmark of cancer. The accurate removal of replication and recombination intermediates is essential for maintaining genome stability. Structure-selective endonucleases, such as the SMX complex, are required to resolve such structures. SMX is composed of three structure-selective endonucleases called SLX1-SLX4, MUS81-EME1, and XPF-ERCC1. Human SLX4 provides the scaffold for assembling these proteins into a tri- nuclease complex. SMX is formed predominately in prometaphase, however, it is still unclear how this complex disassembles in humans. The goal of my thesis was to determine when and how the SMX complex disassembles in human cells. My work showed that the assembly of SMX peaks in early mitosis and then declines in late mitosis. This suggests that the SMX complex does not have an “on” and “off” switch for assembly and disassembly. Future experiments are required to understand the molecular mechanism that triggers SMX disassembly.
Multivariate Associations between White Matter and the Cognitions in Schizophrenia
Keywords: Canonical correlation analysis
Cognition
Multivariate statistics
Schizophrenia
Tractography
White matter

Deficits in “the cognitions” are important contributors to functional outcomes in schizophrenia. An unanswered question of considerable import is if neurocognitive and social cognitive deficits arise from overlapping or distinct white matter impairments. By applying dimensional multivariate statistical analyses to the Social Processes Initiative in the Neurobiology of the Schizophrenia(s) (SPINS) dataset, the present thesis establishes that white matter circuitry is related to both neurocognition and social cognition. In particular, the uncinate fasciculus and the rostral body of the corpus callosum may assume a “privileged role” subserving both. Further, we found that participant-wise estimates of white matter microstructure, weighted by cognitive performance, do not reveal novel biotypes, but are largely consistent with participants’ categorical diagnosis, and predictive of functional outcome. In tandem, our results underscore the promise of white matter and cognitive assessment to identify biomarkers of functioning, with potential prognostic and therapeutic relevance.
Cryogenic Characterization and Modelling of FinFET Technology
Keywords: characterization
coulomb blockade
cryogenic
finfet
modelling
quantum computing

This thesis investigates the performance of commercial 5nm and 7nm FinFET technology from room temperature down to cryogenic temperatures for quantum computing and other low-temperature applications. DC characteristics and high-frequency figures of merits show significant improvement in all devices at cryogenic temperaturecompared to room temperature, with 5nm devices performing better than 7nm devices. Furthermore, all measured devices exhibit quantum dot (QD) behaviour when biased in the subthreshold region up to 35K, suggesting the potential of commercial FinFET technologies for monolithic quantum processors where the semiconductor qubits are integrated with the control electronics on the same die. A novel compact analytical model is developed to capture the effect of bias and temperature on the QD characteristics, required to develop a complete simulation environment for designing monolithic quantum processors.
Bacteriopheophorbide Nanoemulsions as Photodynamic Therapy Agents
Keywords: Nanoemulsion
Photodynamic therapy

Bacteriochlorins exhibit ideal photosensitizer properties: they have near-infrared excitation wavelengths, large molar extinction coefficients, and intersystem crossing quantum yields approaching unity. By loading bacteriochlorins into a nanoparticle, it may be possible to extend the circulation kinetics of this otherwise potent agent, allowing for cell-targeted photodynamic therapy. Nanoemulsions were first evaluated in solution and found to be colloidally stable. The droplets also behaved as off-on probes, becoming fluorescent and photoactive upon particle disruption. Cellular studies revealed that cells rapidly uptake the nanoemulsion, and treated cells are very sensitive to subsequent photodynamic therapy. Confocal imaging showed that the nanoemulsion is diffused throughout the cytosol. Unfortunately, in vivo experiments revealed no improvement in circulation kinetics, with droplets clearing very rapidly from circulation. Although this work was unable to improve the circulation kinetics of bacteriopheophorbide, it marks an important step in the development of bacteriochlorin-based nanomedicines, especially with respect to nanoemulsions.