VictorJuiz/thesis huggingface dataset:
Assessing Bibliometrics for the Automation of Technology Readiness Level Assessments
Keywords: Bibliometrics
Technology life cycle
Technology maturity assessment
Technology Readiness Levels

Technology Readiness Levels (TRL) are used to assess technology maturity, an important factor in technology investment and onboarding decisions. Expertly assessed TRLs are time-consuming, financially demanding, and subject to bias. While quantitative TRL assessment tools have been suggested, their accuracy is yet to be confirmed. To address this, we explore an existing method that used prevailing bibliometric models of maturity to assess TRLs. We automated and replicated the method and investigated its reliability by estimating the TRLs of 23 technologies. We show that the results of the automated method do not agree with expertly assessed TRLs and we offer hypotheses as to why bibliometrics fail to provide accurate technology maturity estimates. We argue that the single indicator model commonly used to assess technology life cycle stages must be revised. Finally, we suggest machine learning and Natural Language Processing tools to replace outdated models of maturity and automate TRL assessments.
Temporal Control over Biochemical Cues to Recapitulate Dynamic Tissues
Keywords: Epidermal Growth Factor
Hyaluronic Acid
Hydrogels
Photoactivation
Photocaging

Hydrogels are powerful materials that more accurately mimic the cellular microenvironment over static two-dimensional culture. Photochemical strategies enable dynamic complexity to be achieved within hydrogels to better mimic the extracellular matrix; However, many photochemical systems to pattern proteins are complicated by long reaction times to immobilize these proteins wherein the protein can lose activity to cells. As proof-of-concept, we demonstrate an elegant method where photo-caged proteins are immobilized in hydrogels and then directly photo-activated. Specifically, we immobilized streptavidin-ortho-nitrobenzyl-modified epidermal growth factor (EGF) to crosslinked hyaluronan hydrogels and cultured both EGF-responsive breast cancer and lung cancer cells therein. We used light to temporally uncage and control EGF activation, thereby inducing cell death in breast cancer cells and proliferation in lung cancer cells. These results show how temporal, photochemical protein activation influences cellular response and lays the foundation for further advances in manipulating the in vitro environment to control cellular response.
The Impact of Cognitive and Physical Enrichment on Contextual Fear Memory Retention the Contribution of Oligodendrogenesis and Myelination
Keywords: Contextual Fear Conditioning
Enrichment
Memory
Myelin
Oligodendrogenesis

Memories are encoded in patterns of neural activity deemed “engrams” and are recalled when this network is reactivated. Physical and cognitive enrichment have been shown to increase neurogenesis and myelinogenesis which can alter the stability of the engram. We housed mice in both physical enrichment and a combination of physical plus cognitive enrichment and found that both caused forgetting of a contextual fear memory if housing occurred after conditioning, but improved memory recall if done beforehand. However, combining physical and cognitive enrichment caused a greater change in freezing behaviour relative to physical enrichment alone, only when housing was done after conditioning. Mice in which oligodendrogenesis was halted exhibited a trend of freezing less than mice with functioning oligodendrocytes regardless of enrichment, though this was not considered statistically significant. These results are consistent with the theory that enrichment exerts its effect on memory retention by altering engram stabilization during memory consolidation.
Cultivating Care: Backyard Hens and the Changing Geography of Human-Chicken Relations in Toronto
Keywords: animal geographies
backyard chickens
care ethics
human-animal relations

This project examines the changing geography of human-chicken relationships in Toronto, Ontario. Anchoring my project to themes of care and belonging, I first explore the city’s historical live animal debates through textual news media to highlight how arguments about the inhumane treatment and slaughter of urban chickens informed the expulsion of farm animals from residential and market spaces in the late-twentieth century. I then use contemporary media, documents, and semi-structured interviews with participants of the municipal pilot UrbanHensTO to consider how chickens are making a visible return to Toronto. My study shows that urban chicken-keeping is working in the city in transformative and subversive ways; it is allowing residents to cultivate a companionable ethic of care that brings the individuality, lifeworlds, joy, and suffering of chickens into focus. Importantly, these companionable backyard relations are challenging the ethical invisibility of farm animals while making chickens matter as more-than-producers and other-than-food.
Identifying Candidate Quality Indicators of Knowledge Translation Practice Tools that Support the Practice of Sustainability: A Scoping Review
Keywords: Implementation Science
Knowledge Transfer
Knowledge Translation

Knowledge translation (KT) and implementation science (IS) aim to bridge the research gap between what we know (research evidence) and what we do (practice and policy) in health. KT practice tools (KT-PTs) provide methods guidance across a wide range of KT domains such as dissemination, implementation, sustainability, scalability, and IKT. There is limited evidence-based guidance to determine which KT-PTs are the most relevant for their needs and help assess the overall quality of KT-PTs. As a first step, a scoping review was conducted to identify candidate quality indicators of KT-PTs, focusing on the sustainability domain of KT. The scoping review was guided by the Joanna Briggs Institute methodology for scoping reviews. The review identified and characterized 35 KT-PTs. 17 candidate quality indicators were identified across four categories. Findings of this scoping review will guide next steps and future studies to develop and evaluate a quality assessment tool for KT-PTs.
Deconstructing and Reconstructing Content and Language Integrated Learning (CLIL) in a Public System of Mexican Higher Education: An Autoethnography
Keywords: Autoethnography
CLIL
Dynamic Bilingualism
Plurilingualism
Translanguaging

This thesis explores how a dynamic CLIL project problematized “weak” and “strong” CLIL approaches and deficit discourse of learners and teachers in Mexican (language) education. The study draws from the researcher’s personal and professional challenges as an entry point to analyze language planning and policy in Mexican higher education and to interrogate dominant monolingual ideologies to open spaces for equity-based and inclusive language policy and practice.The study uses layered autoethnographic narratives that integrate experiences as a language educator, literature on CLIL, and primary and secondary sources of language planning and policy. The theoretical framework is grounded on the construct of problematization that derives from critical social theory. Ruiz´s language orientations (1984) guide the analysis of life stories, on-the-ground discourse and policy texts. The study concludes by envisioning a dynamic, critical and plurilingual approach to CLIL that builds on students’ and teachers’ diverse language repertoires and affirms their bi/plurilingual identities.
Partners in Life and Online Search: An Investigation on Older Couples’ Collaborative Information Behaviour
Keywords: Collaborative information seeking
Collaborative search
Human-Computer Interaction
Information behaviour
Technology for older adults

Online search is not always a solitary activity. While past research has investigated collaborative information seeking (“CIS”) among certain demographics, how older couples search online together has not been explored. To address this research gap, a qualitative research study is conducted using semi-structured interviews. Research data is analyzed using thematic analysis.Our analysis suggests that older couples engage in CIS for daily tasks, interests, and to fulfill curiosity. Our findings also suggest that older couples’ CIS is primarily a relationship maintenance behaviour. The trust, care and knowledge developed for each other during their lifelong relationship are essential to understand their communication, decision-making, and various strategies employed during their collaboration. Older couples’ relationship also appears to affect their technology adoption, as couples tend to share the same views about technology despite their individual differences. A few design considerations are recommended for systems aimed to facilitate older couples’ collaborative information seeking.
Host Specificity of Pseudomonas syringae in Common Bean Plants (Phaseolus vulgaris)
Keywords: Bean
Infection
Machine Learning
P. syringae
P. vulgaris

Pseudomonas syringae is a phytopathogenic bacterial species with a wide host-range, encompassing numerous plants of agricultural importance. Here, I make use of machine learning and host-range testing to analyze the host specificity of P. syringae in common bean plants in order to understand the evolution of bean isolation. The first method that I used was to analyze gene content using random forest machine learning. The model identified type 3 secretion as an important predictor for determining if a P. syringae is able to grow on bean plants. AvrB is interesting since it elicits an immune response in soybean and common bean varieties, but this immune response can be prevented when HopF2 is present. I also designed a new method of bean infection with the goal of using it in order to screen the P. syringae species complex on bean plants, taking advantage of the seedborne nature of bean pathogens.
Characterizing Novel ATRX-Associating Proteins – CCDC71 and FAM207A
Keywords: ATRX
BioID
CCDC71
FAM207A
Heterochromatin
HP1

ATRX is an ATP-dependent chromatin remodeling/helicase protein with a number of established cellular functions that depend on its protein-protein interactions, notably with DAXX, a histone chaperone. ATRX maintains heterochromatin stability and repression over repetitive DNA elements, including pericentric heterochromatin and telomeres. According to current models, ATRX resolves aberrant DNA structures and then enforces heterochromatin stability through DAXX-dependent deposition of histone variant H3.3. How ATRX further promotes chromatin compaction and telomere homeostasis is not well understood. To investigate this, we defined the ATRX interactome and identified two novel and uncharacterized interactors of ATRX: CCDC71 and FAM207A. Here, I show that FAM207A locates to the nucleolus, where it associates with nucleolar proteins. CCDC71 is, however, chromatin-bound and dispersed across the nucleus. It associates with Heterochromatin Protein 1 (HP1), suggesting that ATRX likely functions with CCDC71 to maintain heterochromatin.
The Effect of Cell to Cell Communication on Differentiation and Integration of Human Induced Pluripotent Stem Cell-derived Neural Progenitor Cells
Keywords: neural stem cells
regenerative medicine
spinal cord injury

Spinal cord injuries (SCI) have devastating impacts due to paralysis and lack of spontaneous repair. It has been shown in a rat model of cervical SCI that forelimb function can be improved by transplanting neural progenitor cells (NPC) obtained from human-induced pluripotent stem cells (hiPSCs). However, molecular mechanisms behind NPC-mediated recovery remain unclear. To overcome this knowledge gap, we have engineered hiPSC-NPCS with inducible tetanus toxin light chain expression to prevent cellular communication via blocking neurotransmitter and/or growth factor release. The resulting NPC line retained progenitor cell properties and the NPCs were able to differentiate to functional neurons, astrocytes, and oligodendrocytes. TeTxLC expression didn’t have a significant effect on NPC differentiation, reduced neuronal soma size and neurite length, and was successful in abolishing synaptic function in vitro. A preliminary proof-of-concept study showed that the inducible expression was successful in vivo as well as in vitro, highlighting the potential for this cell line to be used to study the effect of cellular communication between transplanted NPCs on NPC-mediated functional recovery after spinal cord injury.
Recapitulating Nutritionally Regulated Human Muscle Protein Metabolism In vitro using Humanized Cell Media
Keywords: Amino acids
Anabolism
mTOR
Muscle
Nutrition
protein synthesis

Most in vitro models used to study the effects of nutrients on skeletal muscle protein metabolism use supraphysiological concentrations of nutrients and amino acids, making translation of their findings to humans difficult. Therefore, there is a need to develop an in vitro model that uses physiological nutrient concentrations. This study used a humanized fasted and fed media, modeled after human plasma fasted and fed amino acid concentrations, to study in vitro protein metabolism and anabolic signalling following nutrient withdrawal and refeeding compared to typical supraphysiological withdrawal and refeeding. In all outcomes measured, there was a similar knockdown of protein synthesis and anabolic signalling in both models. Further, refeeding generally resulted in similar phosphorylation responses in the proteins measured despite protein synthesis differing between the two models. These findings suggest that a humanized media may be a useful tool to study skeletal muscle physiology in vitro.
Comparative Analysis and Demonstration of Monolithic Integration in High-voltage Gallium Nitride Processes
Keywords: Gallium Nitride
gate-driver
HEMT
PMIC
power converter
power electronics

Gallium Nitride (GaN) power e-HEMT, a popular alternative to Si in high temperature and high voltage power applications, can be monolithically integrated with low-voltage HEMTs, passive components and diodes. Through comparative analysis between the experimental performance of LV circuits, fabricated using ON Semiconductor’s 650-V GaN-on-Si and imec’s 200-V GaN-on-SOI process, and simulated results from their BCD-counterparts, this thesis identifies the types of circuits that are suitable for monolithic GaN integration based on the processed-power and operating frequency of an application. Using the GaN-on-SOI technology, a binary-weighted segmented gate-driver is fabricated with a power-HEMT, controlling the HEMT’s voltage slew-rate and overshoot. The power-HEMT has embedded current and temperature sensing structures. A monolithic high-voltage floating level-shifter and a programmable deadtime generation circuit, as building blocks to a GaN half-bridge IC controlled using a single low-side gating signal, are built and tested.
Size Characterization of Biofiltration-related N-nitrosodimethylamine (NDMA) Precursors
Keywords: Backwash
Biofiltration
Dissolved NDMA precursors
Filter ripening
N-nitrosodimethylamine (NDMA)
Particulate NDMA precursors

Previous studies have reported variable removals or even contributions of N-nitrosodimethylamine (NDMA) precursors during biofiltration. To better understand the source of these biofiltration-related NDMA precursors, it is imperative to quantify their state (i.e., dissolved or particulate). This study characterized biofiltration-related NDMA precursors according to their size as well as quantified their removal by examining them in backwash remnant water. Biofiltration-related particulate precursors were the primary contributor (43-64%) to the total NDMA precursor level in the influent, while dissolved precursors were the dominant size fraction (56-83%) in the effluent. Although near-complete removal (80-91%) of particulate precursors was observed during filter ripening, dissolved precursors were removed to a lesser extent (22-31%), indicating their greater potential for a breakthrough. In the event of a breakthrough of dissolved NDMA precursors, turbidity may not be an effective parameter to evaluate backwash performance.
Designing a Synthetic Biology Modulator using Structural Mimicry of Homeodomain-zipper Proteins
Keywords: Biology
DNA-binding
Modulator
Synthetic

In synthetic biology, an organism’s genome can be re-engineered to produce substances outside of its natural capabilities. This is achieved by incorporating exogenous DNA circuitries into the host. We designed a minimalist “franken-protein” termed HinZip that binds to a unique DNA sequence comprising two 12 base-pair half-sites. HinZip combines motifs from eukaryotic and prokaryotic proteins to structurally mimic homeodomain-zipper (HD-Zip) proteins, which is a transcription factor family observed only in plants. HinZip has shown good binding affinity and DNA sequence specificity in vivo. These results provide a promising start to designing synthetic biology circuitries controlled by HinZip.
Field Trips From Home: Exploring how Online Museum-based Learning can Help International Graduate Students Meet their Language Goals in the Time of COVID-19
Keywords: Informal learning
Language learning
Museum-based learning
Online museum
Social isolation
Virtual exhibits

Museums are known as exemplary sites of informal learning and more recently are understood to foster positive social outcomes for visitors, like reduced social isolation and improved wellbeing. As museums and university campuses are closed due to COVID-19 provincial lockdown measures, this thesis asks: how might online museum-based learning support international graduate students in their language learning goals, at a time of physical and social isolation? Using a grounded theory approach, I draw on existing literature on museum-based learning and social outcomes, and bring informal learning theories to bear on the online museum experience. The interviews and group discussions with eight participants revealed that online museum experiences supported formal language improvement, self-reflection and enjoyment, but fell short of supporting informal language practice. The research identifies that a critical pedagogical approach to the development of online museum programs could more robustly meet the needs of international students and language learners alike.
Semantic Processing in Children with ASD: Differences in underlying Neural Processing in Children with High Language vs. Low Language Capabilities
Keywords: auditory
Austim
children
EEG
language
semantics

The primary objective was to investigate semantic neural processing in children with autism spectrum disorder (ASD) as impairments in this domain have been shown in this patient population. Typically developing (TD) children and children with ASD with varying language ability did an auditory semantic categorization task. Only children with ASD with low language ability had semantic neural processing deficits, indexed by a late onset and smaller N400 component compared to TD children when the N400 component was evoked, although it was not evoked to all auditory stimuli. There were negligible neural processing differences between children with high language ability and TD children. In children with ASD, the smaller N400 component predicts lower language ability and the smaller N400 component is predicted by deficits in cortical auditory processing indexed by a smaller P1 component. Thus, language deficits in children with ASD are predicted by semantic and cortical auditory processing deficits.
Development, Validation, and Implementation of a Clinical Decision Tool for Blood Pressure Management in Patients on Hemodialysis
Keywords: Clinical decision tool
Hemodialysis
Hypertension

Hypertension is a strong risk factor for cardiovascular disease and remains uncontrolled in a large proportion of patients on hemodialysis. Management requires a multifactorial approach involving optimization of hemodialysis specific factors and medications. The objective of this study was to develop, validate, and implement a clinical decision tool to help improve blood pressure control for patients on hemodialysis. A clinical decision tool was developed and assessed for face and content validity. The tool was then implemented in a cohort of patients on hemodialysis. Blood pressure control was similar pre and post implementation and without a greater incidence in adverse events compared to the control group. A number of blood pressure related interventions were made including the discontinuation and dose reduction of antihypertensive medications. Implementation of the tool in a larger cohort of patients for an extended time period is required to further assess implications of the tool in clinical practice.
Aqueous Proton Conducting Polymer Electrolytes as Gate Dielectrics for Organic Field-effect Transistors
Keywords: organic thin film transistor
phosphoric acid
polymer electrolyte
Printed electronics
proton conducting
transistor

The vast majority of solid electrolyte-gated field-effect transistors (EGFETs) use ionic liquid or lithium ion conducting electrolytes. However, other classes of solid electrolytes have seen little attention for use in EGFETs despite their promising properties. In particular, proton conducting polymer electrolytes have great potential due to their high ionic conductivity, specific capacitance, and environmental stability. In this work, strong acid based proton conducting polymer electrolytes comprised of either phosphoric acid (H3PO4) or sulphuric acid (H2SO4) in a polyvinyl alcohol (PVA) polymer host were investigated as potential gate dielectrics. The resulting proton conducting polymer electrolyte gated EGFET devices exhibited promising performance with sub 1 V operation, a high ON/OFF ratio >105 and a low subthreshold swing of 90 mV/decade, which demonstrates the viability of using proton conducting polymer electrolytes as gate dielectrics in organic thin-film transistors (OTFTs).
Embodied Energy and Reaction Calorimetry of Boron Subphthalocyanine Derivatives
Keywords: boron subphthalocyanine
embodied energy
reaction calorimetry

This thesis is a culmination of my work in advancing the fields around boron subphthalocyanine materials and their applications. First, it details the methods and results from modelling the embodied energy of chloro-boron subphthalocyanine using an established baseline reaction. It then analyzes the opportunity to reduce the embodied energy through process and solvent modifications by swapping from 1,2-dichlorobenzene to 2,4-dichlorotoluene (2513 MJ/kg versus 64 MJ/kg, respectively). Second, this thesis provides calorimetry results for a variety of bromo- and chloro-boron subphthalocyanine reactions. An alternative method for chloro-boron subphthalocyanine was proposed and tested that incorporated scale-up design principles. These pathways were assessed on their applicability for scale-up based on the measured reaction enthalpy and criticality classes. The work compiled in this thesis serves to highlight the positive aspects of boron subphthalocyanines from an environmental viewpoint through embodied energy modelling and provides strong evidence for their near-term ability for scale-up to commercial reaction sizes.