VictorJuiz/thesis huggingface dataset:
Phage-mediated Mobile Genetic Elements Identified in Dehalococcoidia, Chloroflexi Bacteria used for Bioremediation
Keywords: bioremediation
chlorinated ethenes
horizontal gene transfer
mobile genetic elements
phage satellites

Chlorinated compounds, such as vinyl chloride (VC), are persistent, carcinogenic soil and groundwater contaminants. Organohalide-Respiring Bacteria (OHRB) are used for their ability to detoxify these chlorinated compounds from soil and groundwater in a process called bioremediation. Dehalococcoidia, including Dehalococcoides and Dehalogenimonas, are deep- branching bacteria from the Chloroflexi phylum and are obligate OHRB. Dehalococcoidia use reductive dehalogenase enzymes, RdhA, for organohalide respiration which are encoded by reductive dehalogenase homologous genes, rdhA. There is substantive evidence that certain rdhA were acquired by horizontal gene transfer, found on Genomic Islands (GIs), Integrative and Mobilizable Elements (IMEs), transposable elements, and bacteriophages (phages). However, no mechanism of horizontal gene transfer has been identified to date. VC reductase-encoded genomic islands, vcrA-GI and bvcA-GI, were the focus of this work. Experiments were designed to selectively induce the vcrA-GI to characterize the mechanism of horizontal gene transfer. While there was evidence for replication and circularization of the vcrA-GI, there was no evidence to support the selective induction of the vcrA-GI nor gene transfer for over 4 years of study. On the other hand, the bvcA-GI was predicted to be incorporated in a phage genome in Dehalococcoides, prompting the isolation and sequencing of phage fractions of Dehalococcoides-containing cultures. A hybrid metagenome sequencing approach was used because it combines short- and long-read technologies for a cost-effective, high-quality assembly. The bvcA-GI was not found in a phage genome but a sub-group of IMEs, called IME1s, were found in extremely high abundance in the metavirome. Upon bioinformatic inspection, IME1s shared a conserved structural organization and met the criteria of phage satellites. Phage satellites are a well-studied class of genetic elements which manipulate the phage lifecycle for their benefit and package into phage particles. Six new IME1s were identified in Dehalococcoides and Dehalogenimonas and were re-categorized as a new subclass of phage satellites called Dehalococcoidia Chromosomal Islands (DeCIs). This work revealed the first horizontal gene transfer mechanism in Dehalococcoidia and advances our understanding of horizontal gene transfer in OHRB which are difficult to study using classical approaches. An improved understanding of their lifecycle will enhance the efficiency of bioremediation of contaminated sites globally.
Neutral pH Ion-Conducting Polymer Electrolytes for Solid-state Electrochemical Capacitors
Keywords: Electrochemical Capacitors
Neutral pH
Polymer Electrolytes
Sulfates
Supercapacitors

Thin, solid, flexible, safe, and reliable electrochemical capacitors (ECs) are in demand to power up next generations of wearable electronics and Internet-of-Things devices. Polymer electrolytes are key enablers for the development of solid-state capacitive devices. In this thesis, neutral pH ion-conducting polymer electrolytes (NPPEs) have been developed for ECs using either Li2SO4 or Na2SO4 ionic conductor and polyacrylamide (PAM) host. The optimized NPPEs exhibit: (i) wide electrochemical stability window, (ii) high ionic conductivity with low activation energy for conduction, (iii) long-shelf-life, (iv) good interfaces with EDLC electrodes, and (v) wide-range thermal stability. An in-depth investigation on material properties affecting electrolyte performance has been conducted for NPPEs. Through correlative studies between vibrational spectroscopic and electrochemical measurements, ion hydration was determined as crucial factor affecting ion conductivity and performance stability. Fully solvated ions are necessary to maintain stable performance over time, while smaller hydration shell allows for fast ion mobility. Meanwhile, at low temperatures below freezing point, EDLC interface can only be maintained with NPPE containing fewer crystallized water. Anti-icing additives possessing deep eutectic properties with water, e.g., DMSO, can widen the lower limit of operating temperatures of the NPPE. These correlations are essential considerations for developing future generations of NPPE. In carbon-based solid EDLC devices, both Li2SO4-PAM and Na2SO4-PAM demonstrated a stable 1.8 V cell voltage, much wider than those cells with proton- or hydroxide-ion based electrolytes which allows for significantly higher energy and power densities. Adding DMSO, the ternary system enabled the operating temperature of solid EDLC cells to -20 °C, beyond the typical limit in most aqueous-based systems. The effects of carbon loading on NPPE-based EDLCs were studied using two types of carbon with different pore structures to understand the limitations in designing solid capacitive devices. Although increasing carbon loading leads to higher capacitance, there are two possible adverse effects: (1) lower electrolyte penetration from highly viscous NPPE precursor solution; and (2) increased diffusion limitation, leading to lower material utilization which can be aggravated at faster rates, low temperatures, or with closed micropore-rich materials. These insights can be added to the guiding principle for design and develop solid EDLCs.
The Role of Narrative Competence in French Immersion: A Detailed Investigation of Macro-and Micro-structural Skills on Language Development Micro-structural Skills and Reading Comprehension
Keywords: Bilingual Education
Bilingualism
French Immersion
Language Development
Narrative Competence
Reading Comprehension

This dissertation is comprised of two separate studies that assess narrative competence in a French Immersion setting. The first examined an array of macro- and micro-structural skills in English and French and further compared the development of these skills between two language groups: Children who speak English as their first language and French as their second language (FL2s) and minority language speakers who speak English as their second language and French as their third language (FL3s). There were no differences in narrative microstructural or macrostructural skills between language groups. In contrast, vocabulary was demonstrated to develop differently among both language groups in English, with FL2 children outperforming FL3 children. No such distinctions were observed in French. The results suggest that narrative skills develop at similar rates in FL2 and FL3 children in a French Immersion setting. The second study investigated the role of macro- and micro-structural skills on the development of reading comprehension, again in a French Immersion setting. The contributions of these skills to reading outcomes were assessed in a combined group of Grade 3 and 4 students, through concurrent analyses. Story grammar, grammaticality and productivity were shown to be significant predictors of reading comprehension. The findings present new evidence of the facilitative role that both macro- and micro-structural narrative skills play in the development of reading skills in French. Together, these studies provide a comprehensive understanding of the relationship between narrative competence and literacy outcomes in French Immersion. These results can also positively impact the French Immersion curriculum, encouraging educators to provide more focused support for narrative skills at grade levels where these skills are evidenced to contribute to literacy development. The findings of this research indicate that FL3 children can develop their English narrative skills well in French Immersion programs; these results in turn suggest that French Immersion is a viable option for FL3 children.
Bubble Dynamics in High-pressure Foam Injection Molding
Keywords: bubble dissolution
bubble dynamics
bubble growth
high-pressure foam injection molding
polymer foaming

Foam injection molding (FIM) is utilized in many industries. Despite its flourish, the understanding of the cell dynamics in FIM is still lacking. This work aims to improve the fundamental understanding of cell growth, dissolution, and elongation phenomena during FIM, to expedite the foam structure design for the industry via correlating the processing parameters with the final morphology.A model that predicts the cell growth tailored to high-pressure FIM (HP-FIM) processes during the entire processing period is presented. The model captures the fluid flow and the transport phenomenon during cell growth facilitated by the Simha-Somcynsky equation of state and realistic material properties for the PS/CO2 mixture. The proposed model predicted the cell growth profile for its entire lifespan under different HP-FIM conditions and was validated by comparison with the visualization experimental data. Moreover, a study on the critical, but often overlooked, cell dissolution and its relation to the packing/holding stage is presented. The dissolution of cells in the packing stage decouples the foaming and filling steps in FIM and lays the foundation for the consistent production of uniform foam structures. Systematic experiments were conducted using a visualization mold to study the effect of various processing parameters on the packing efficiency to determine the time required to fully dissolve the gate-nucleated cells. A simulation attempt was made to predict the evolution of cell size during packing. Moreover, a sensitivity analysis showed the model’s response to the changes in various parameters, and echoed the experimental observations. In the end, a study that attempted to correlate the mold opening (MO) parameters to the final foam structure is discussed. Visualized HP-FIM experiments demonstrated that the removal of the gate-nucleated cells could effectively prevent cell coalescence and collapse during MO. Besides the packing pressure, the packing time also dictated the structure by affecting the melt strength and gas diffusion coefficient. Moreover, employing the cell model, we were able to accurately predict the cell growth for a small MO distance and validated the results with experimentally measured growth data. For large MO distances, the simulated results demonstrated qualitative agreement with experimental observations.
Delineating the Conformational Landscape of the Adenosine A2A Receptor-G Protein Signaling Complex
Keywords: Adenosine A2A receptor
Conformational landscape
G protein
G protein-coupled receptor
Membrane protein
Nuclear magnetic resonance spectroscopy

G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors in eukaryotes. Their canonical activation involves binding by an extracellular ligand, conformational changes in the receptor, and complexation with a G protein inside the cell. The adenosine A2A receptor (A2AR) is a prototypical GPCR and a drug target for the treatment of inflammation, cancer, diabetes, and Parkinson’s disease. The allosteric interplay between ligand, receptor, membrane, and the G protein is key to determining the pharmacological outcome of a signaling event, which may be characterized by basal activity, inverse agonism, partial and full agonism, and varied signaling pathways. Here, biochemical and biophysical approaches were taken to investigate the conformational ensemble of both the receptor and the G protein in the context of signaling. Fluorine nuclear magnetic resonance (19F NMR) spectroscopy was key in identifying specific functional states. The results provided insights into mechanisms concerning efficacy and allostery, as well as protein-protein and protein-membrane interactions that play important roles in modulating the conformational dynamics and hence, the signaling of this complex.
Global Health Promotion and Arts Approaches in Goma, Democratic Republic of Congo: A Focus on Strengthening Community Action for Health
Keywords: Arts Approaches
Community Action for Health
Critical Social Sciences Research
Global Health
Health Promotion
Qualitative Health Research

Goma, in the Democratic Republic of Congo (DRC), is largely dominated by the presence of international non-governmental organizations (INGOs), many of whom work with global health promotion (GHP) researchers and/or practitioners. Until recently, ongoing colonial dynamics shaping this work has been largely overlooked. This dissertation aims to contribute to ongoing calls to decolonize the GHP field.Arts approaches have become common in GHP, but they are less commonly examined from a critical and/or decolonial perspective. I propose that GHP workers adopt a ‘critical social science perspective influenced by an applied decolonial framework for health promotion’ (CSSP-ADF) when engaging in arts approaches to help re-shape relationships among actors and facilitate the integration of core GHP community concepts (GHPCCs) – such as community participation, community ownership, and community assets – in order to strengthen community action for health. Grounded in the Goma context, I explore these key concepts and relationships across three papers. In the first paper, I provide a reflexive account of my experiences of co-creating the documentary film Kwa Nini Art? in Goma with arts and cultural centre Yole!Africa. I conclude that collaborative documentary filmmaking can be considered a promising CSSP-ADF arts-based research approach in GHP. In the second paper, I engage in a multimodal critical discourse analysis of the audio and visual discourses in the film Kwa Nini Art?. I conclude that decolonial discourse in arts-based INGO collaborations can contribute to fostering core GHPCCs. In the third paper, I engage in a qualitative textual thematic analysis and a critical visual analysis of data generated during a project in Goma implemented by the INGO Colors of Connection. I conclude that the broader neocolonial context fundamentally shaped the three core GHPCCs. In my final dissertation chapter, I highlight the theoretical, methodological, and practical contributions of this work to GHP, while also noting some of its key limitations. I provide a set of reflexive questions (organized thematically and grounded in a CSSP-ADF) that international GHP workers can engage with when seeking to employ arts approaches in their research and/or practice to strengthen community action for health.
Advances in Knowledge-based Planning for Radiotherapy with an Open Framework
Keywords: Computer vision
Generative models
Inverse optimization
Knowledge-based planning
Open data
Radiotherapy

Automated radiotherapy planning is on the verge of transforming personalized cancer treatment, and it will likely help address the growing global cancer burden. The most common type of automated planning is knowledge-based planning (KBP), which can generate treatment plans for radiotherapy without human intervention. In general, KBP is implemented as a two-stage pipeline that first predicts the dose that should be delivered to a patient, and then an optimization model converts that prediction into a treatment plan. Although KBP research is flourishing, it is largely limited to institution-specific datasets and evaluation metrics, which makes comparing competing approaches difficult. The purpose of this thesis is to develop state-of-the-art KBP methods and an open framework for the KBP research community to benchmark new contributions. In this thesis, we developed the first generative adversarial network for KBP dose prediction, which outperformed several baselines. Next, we launched the OpenKBP Grand Challenge, which was the first platform that enabled researchers to compare KBP prediction methods fairly, and helped democratize KBP research by making it accessible to everyone. Next, we found that there were interaction effects between the two stages in KBP and that the choice of both stages can contribute to considerable variations in plan quality. To explore this further, we developed new plan optimization methods using open data and the dose predictions from the OpenKBP Grand Challenge. Overall, we improved KBP methods and promoted more collaboration within the KBP research community.
Development of a Next-generation Rechargeable Aluminum Battery Technology
Keywords: Aluminum-ion battery
Chloroaluminate ionic liquid
Electrical and transport properties
Rechargeable aluminum battery
trimethylamine hydrochloride
urea

This dissertation is focused on the development of next-generation rechargeable aluminum batteries. Two approaches are taken to achieve the main objective: i) development of new electrolytes chemistries that are more environmentally sustainable and economic than the state-of-the-art, and ii) comprehensive investigation of electrolyte properties and charge storage mechanisms to gain fundamental insights into designing/engineering high-performance electrode materials. Dialkylimidazolium chloride-based chloroaluminate ionic liquids have been highly popular in the research and development of room-temperature rechargeable aluminum batteries due to their high conductivity, high ionicity, and wide liquidus range. However, their high cost associated with small-scale production and potential environmental concerns, greatly diminish the practicability of resulting battery systems. On the other hand, chloroaluminate ionic liquids are known to function simultaneously both as a medium for ion transportation and as electroactive materials (anolytes) in many existing chemistries. This unique dual functionality fundamentally governs several key battery performance metrics including capacity, energy- and power densities. In this dissertation, first, a rechargeable aluminum battery employing natural graphite cathode and an ionic liquid analog made of aluminum chloride-urea anolyte is developed. Fundamental investigations reveal a new aluminum electrodeposition/stripping mechanism. The achievable capacity and energy density of aluminum chloride-urea|graphite battery are assessed and in-depth characterizations are performed to gain insights into the physicochemical properties of aluminum chloride-urea ionic liquid analog. In the subsequent work, the research focus is extended to Lewis organic bases beyond urea. A novel chloroaluminate ionic liquid made of aluminum chloride and low-cost trimethylamine hydrochloride is identified. In addition to the cost advantage of trimethylamine hydrochloride over existing dialkylimidazolium chlorides, the resulting ionic liquid electrolyte/anolyte also demonstrates improved electrochemical stability window, specific- and volumetric anodic capacities. To investigate the limitations of existing chloroaluminate ionic liquids, electrical and transport properties of trimethylamine hydrochloride-based and dialkylimidazolium chloride-based ionic liquids are investigated. In addition, the research is further expanded to understanding of fundamental properties and charge-storage mechanisms of graphitic- and organic cathode materials in chloroaluminate melts. Lastly, critical assessments of concepts, proposed mechanisms, performance metrics, and key challenges of existing rechargeable aluminum batteries are conducted to provide future guidance for the research community.
Peripheral Skeletal Muscle Structure and Contractile Function in Adults with Cystic Fibrosis
Keywords: Cystic fibrosis
Muscle composition
Muscle Contractile function
Muscle Contractility
Muscle size
Skeletal muscle

Genetic mutations in cystic fibrosis (CF) result in dysfunction of the CF transmembrane conductance regulator (CFTR) protein. As people with CF are living longer, issues regarding skeletal muscle performance have become more prominent. Limb muscle structure and contractile function in adults with CF are not well characterized and their associations with patient demographics and clinical features have not been adequately evaluated. CFTR protein is expressed in human skeletal muscle, but its role is unknown. This thesis was undertaken to characterize limb muscle structure and contractile function in people with CF, to examine their associations with demographic and clinical variables in people with CF, and to delineate the impact of abnormalities of CFTR protein on skeletal muscle structure and contractile function in people with CF. A systematic review and meta-analysis (Study 1) found adults with CF to have thigh muscle atrophy, and a subgroup had quadriceps weakness. Also, adults with CF had lower handgrip strength, especially in females, and it was associated with lower lung function. A prospective study designed to investigate the association between CFTR protein dysfunction and muscle structure (Study 2) demonstrated no differential impact of the extent of diminished CFTR protein activity on quadriceps size or muscle quality, as determined by ultrasound measures. Upper and lower limb muscle strength, determined by dynamometry, and leg muscle power assessed with stair climb power test (Study 3) showed no relationships between CFTR protein dysfunction and impairment in muscle strength or muscle power. Nevertheless, quadriceps muscle contractility was found to be lower in people with severe CFTR protein dysfunction. In conclusion, adults with CF are confirmed to have impairment in their limb muscle size and muscle strength, and CFTR protein plays a role in muscle contractility, which needs to be confirmed with cellular and molecular studies in humans with CF. Future studies are needed to examine the implications of these results on ventilatory muscle contractility, and how CFTR modulator therapies affect muscle contractility in adults with CF. Furthermore, upper limb muscle structure and contractile function, and other aspects of muscles, e.g. muscle architecture, need further exploration in adults with CF.