VictorJuiz/thesis huggingface dataset:
Dissecting The Differential Functions of the Two Isoforms of the Essential Argonaute CSR-1 Throughout Caenorhabditis elegans Development
Keywords: Argonautes
C. elegans
CSR-1
sRNA

Endogenous small RNA pathways play vital roles in regulating gene expression to ensure germline integrity across animal species. The key effectors of these pathways are Argonaute proteins (AGOs), which utilize small RNA partners to identify target transcripts in a sequence-specific manner. The Caenorhabditis elegans genome encodes nineteen functional AGOs that use 22G-RNAs, 26G-RNAs, miRNAs or piRNAs to regulate target transcripts. Only one Argonaute is essential under normal laboratory conditions: CSR-1. Although AGOs predominantly downregulate their targets, the essential C. elegans AGO CSR-1 has been shown to promote and fine-tune germline gene expression. While CSR-1 has been studied widely, nearly all studies have overlooked the fact that the csr-1locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR1a. Using a series of transgenes (MosSCI), endogenously GFP::3xFLAG-tagged strains (CRISPR/Cas9), and two different antisera that recognize 1) both isoforms of CSR-1 or 2) CSR-1a only, I have identified key differences between the CSR-1 isoforms. I found that CSR-1a is expressed during spermatogenesis and in several somatic tissues, including the intestine. CSR-1b is expressed constitutively in the germline. Phenotypic analyses reveal that the essential functions of csr-1 described in the literature coincide with CSR-1b, while CSR1a plays tissue-specific functions. Although my data also suggest CSR-1a can compensate for CSR-1b’s absence if expressed throughout the germline. small RNA sequencing of CSR-1 complexes shows that they interact with partly overlapping sets of 22G-RNAs. CSR-1a integrates into an sRNA regulatory network with spermatogenic AGOs ALG-3, ALG-4 and WAGO-10 that is necessary for fertility at 25˚C. Meanwhile CSR-1b functions alongside the spermatogenic AGOs, but also targets oogenic genes along with WAGO-4. In the intestine, CSR-1a silences immunity and pathogen-responsive genes, and its loss results in improved survival from the pathogen Pseudomonas aeruginosa. My findings functionally distinguish the CSR-1 isoforms and highlight the importance of studying each AGO isoform independently.
Mitochondrial Damage and Dysfunction in Severe Malnutrition
Keywords: INTESTINAL BARRIER
MALNUTRITION
MITOCHONDRIA
ORGANOID
SEVERE WASTING
TIGHT JUNCTION

Background: Globally, undernutrition contributes to over 45% of deaths in children under five years of age. Hospital mortality rates for children with severe malnutrition remain high. Progress to improve mortality is hindered by a lack of understanding of the organ dysfunctions that underly severe malnutrition. Children with severe malnutrition suffer from metabolic disturbances and an enteropathy that contribute to a heightened mortality risk. Interestingly, children with complicated severe malnutrition have altered protein metabolism and reduced serum tryptophan levels. Disturbances in the tryptophan pathway and consequent mitochondrial dysfunction have been implicated in other intestinal disorders and malnutrition induced hepatic stress, however this pathway has never been studied in a model of severe malnutrition.Objective: The first objective was to determine if, and how, tryptophan pathway disturbances and downstream alterations in mitochondrial homeostasis were associated with malnutrition enteropathy. The second objective was to validate the existence and degree of mitochondrial alterations in severely malnourished patient samples. Methods: In the first study, mice were randomized into two dietary groups: control diet, low protein diet (LPD). Subsets of mice were treated with modulators of downstream tryptophan pathway components. In the second study, an intestinal organoid model of malnutrition enteropathy was generated. Intestinal permeability, mitochondrial parameters, and downstream targets of the tryptophan-NAD+ pathway were assessed. In the last study, post-mortem tissue biopsy samples were used to examine the degree of mitochondrial damage through histological techniques. Results: In the first study, feeding a LPD resulted in intestinal barrier dysfunction that was associated with disturbances in mitochondrial biogenesis, clearance, and function. This was improved through treatment with an NAD+ precursor, nicotinamide. In the second study, mitochondrial reactive oxygen species were elevated in organoids deprived of amino acids, causing impaired paracellular barrier function. In the last study, mitochondrial morphology was altered in the liver of children with severe malnutrition and was most severely perturbed in patients with edematous severe malnutrition. Significance: This study improves the current understanding of severe malnutrition induced enteropathy and points to the mitochondria as an important mediator of severe malnutrition organ dysfunction, potentially leading to the development of novel targeted treatments to reduce mortality.
What on ice is going on here? How Chemical Morphology Controls Reactivity
Keywords: Chemical morphology
Hydroxyl radicals
Ice morphology
Interfacial chemistry
Phase
Surface reactions

Interfaces play a crucial role in mediating chemical reactions. This is especially true in the atmosphere, where reagents gather on surfaces, and reactions can be either facilitated or inhibited depending on the surface interactions. At the surface of ice, there have been several surprising results where OH radicals, a highly reactive species contributing significantly to the oxidative capacity of the atmosphere, did not react with species which one would normally expect them to oxidize. I provide a review of the literature on surface mediation of OH radical reactions. Tantalizing evidence suggests that ice surfaces may play a direct role in the reactions of a variety of species from chloride ions to large hydrocarbons. In order to examine the chemical morphology of the ice surface in the simple case of a nitrate solution, I use Raman microscopy to directly probe the distribution of nitrate salts and show that they exist in three distinct forms near the surface of ice crystals: as solvated salts in a liquid-like environment, as quasi-solids, and in crystalline form. This result helps to explain the sharp difference in rate of nitrate photolysis on the ice surface (fast) vs on the liquid water surface (negligibly slow). Likewise, I show that even hydrogen peroxide is not uniformly distributed at the ice surface. I extend this research to directly compare OH radical reactions at ice and liquid water surfaces for two aromatic pollutants, pyrene and coumarin. Although both react readily with OH radicals at the liquid water surface, hydrophobic pyrene forms clumps at the ice surface which inhibits its reaction, while relatively hydrophilic coumarin is spread over the ice surface and continues to react readily. Finally, I present experimental results pertaining to the possibility of the formation of OH radicals at the freezing edge of water ice, where electrical potentials high enough to split water have been observed, and upper bound the extent to which OH radicals may be formed by this process. A detailed understanding of these reaction mechanisms is essential to provide accurate models of environmental degradation of pollutants and other interface-mediated reactions.
B Cell Responses During Obesity-Associated Non-Alcoholic Fatty Liver Disease and Age-Related Decline
Keywords: Adaptive Immunity
Aging
B Cells
Immunology
Metabolism
Non-Alcoholic Fatty Liver Disease

Chronic systemic low-grade inflammation is an underlying feature that drives the onset of various pathological manifestations associated with obesity and aging. Accordingly, the development of this inflammatory state has been linked to alterations in the composition and functional properties of the immune system. B cells are lymphocytes belonging to the adaptive immune compartment that are best recognized for their ability to generate a humoral response against an infectious agent, however, emerging evidence posits them as key drivers of inflammation during obesity-associated metabolic syndrome and age-related decline in mammalian health. In this thesis, I initially characterize B cell functions during non-alcoholic fatty liver disease, the hepatic manifestation of metabolic syndrome, and uncover a disease-associated expansion of pro-inflammatory B cells in the liver that subsequently promotes intrahepatic T cell activation, and perpetuates local inflammation, fibrosis, hepatocellular injury, and metabolic dysregulation. Next, I uncover alterations to the aged adaptive immune compartment, and provide evidence for a role of B cells in facilitating T cell immunosenescence, inflammation, fibrosis, metabolic dysfunction, and frailty with age. Cumulatively, with an emphasis on B cell dysfunction, this work may lead to novel diagnostic biomarkers and therapeutic modalities for chronic diseases that manifest with obesity and age.
Making Sense of Compulsory Schooling: Ontario Secondary School Graduation Requirements and Transitions to Postsecondary Education
Keywords: capabilities approach
education policy
graduation requirements
Ontario education
purposes of education

This thesis investigates the graduation requirements in Ontario’s publicly funded education system in Canada since the beginning of the twenty-first century, to shed light on the purposes of education and how education might contribute to human flourishing. The two-part study applies the capabilities approach, informed by critical race theory and the historical context of settler colonialism. The first part engages in a post-structural policy analysis of the secondary school graduation requirements to explore “What’s the problem represented to be?” in terms of the purposes of compulsory schooling. The analyses are based on over 300 Ontario policy texts from when the requirements were established by the Progressive Conservative government in 1999 through the Liberal government (2003 to spring 2018). In the present study, graduation requirements are used as proxies for the purposes of schooling as they define the policy context for the upper boundaries of compulsory school completion. Although individual actors within the education system have diverse purposes for the actions taken in the context of schooling, the policy context introduces inherent constraints. If the purposes are defined, it may empower actors within and outside the system to engage with compulsory schooling differently. The second part of the study examines the effects of the graduation requirement policies on students’ graduation and transitions to further education. The quantitative analyses focus on a cohort of students who began secondary school in 2013 in the Toronto District School Board (TDSB), which was the last cohort of grade 9 students to attend the 4-year secondary program during the previous Liberal minority government. Analysis of the associated effects of the graduation requirements on students’ graduation and transition to further education is essential for grounding the qualitative analysis of the requirements. In other words, how do the requirements relate to graduation and transition to further education? This study may contribute to the literature on transitions to postsecondary education through an examination of how policy may or may not contribute to changes in desired student outcomes. Ultimately this thesis sets out to explore why we have compulsory schooling, to inform how it might contribute to human flourishing.
A Look into Child Welfare Cases: Risk and Re-reports in the Context of Intimate Partner Violence
Keywords: child exposure to intimate partner violence
child welfare services
intimate partner violence
risk assessment

Child welfare services receive a large proportion of referrals due to concerns about child exposure to intimate partner violence (CEIPV). Fathers, cohabitating and non-cohabitating boyfriends, and stepfathers are disproportionately the perpetrators of CEIPV. Assessment of CEIPV within child welfare services does not include an examination of IPV-specific risk factors found to predict recidivism and dangerous violence in other public sectors. The objectives of my dissertation were to: (1) Describe the profiles and characteristics of fathers and determine what is known about child and IPV risk among fathers transferred to ongoing services following verified CEIPV; (2) Examine whether level of risk was associated with child welfare workers’ decisions on level of involvement with fathers as part of ongoing services; (3) Examine which case characteristics were associated with a new report that was investigated and verified (i.e., verified re-report) by child welfare within two years of transfer to ongoing services, and (4) Determine whether IPV-specific risk factors predicted verified re-reports relative to the risk factors commonly assessed by child welfare. The sample included 231 cases verified for father-perpetrated CEIPV. Results confirmed the presence of moderate to high numbers of IPV-specific risk factors in verified cases of CEIPV; however, cumulative IPV risk did not predict level of worker involvement with fathers. Cumulative child risk significantly predicted worker level of involvement, such that higher risk predicted less worker involvement with fathers. At the bivariate level, fathers’ living status (i.e., whether or not he lived with a child) was negatively associated with cumulative child risk, such that more risk was related to fathers not living with their child. Examining outcomes over two years found that 22.5% of families received a verified re-report to child welfare services, with most re-reported for verified CEIPV. Surprisingly, IPV risk level was not associated with verified re-reports for cases involved in ongoing services. Given the overrepresentation of racialized minorities in the child welfare system, follow-up exploratory analyses were conducted to examine possible differences between race groups on what predicts workers’ involvement and verified re-reports to child welfare. The implications of this study and future directions are discussed, with the overarching suggestion that valid risk assessment tools are needed to help direct practice to meet the safety needs of diverse children and mothers facing IPV.
Ontario College Media Professor Careers Across Five Decades
Keywords: College Media Professors
Intersectionality and Feminist
Neo-Weberian Closure Theory
Ontario Colleges Media Programs
Professional Usurpation
Professions and Professionalism

This exploratory research analyses the careers, teaching practices, and self-assessments of Ontario college media teachers in three parts of the Province and three time periods (those hired in the 1970s and 1980s, 1990-2007, and 2007-2022). I interviewed 15 retired media teachers and academic managers; also, 42 current instructors and academic managers answered a survey about their professional experiences. My analysis uses a feminist model of closure theory from the neo-Weberian sociology of professions (Witz, 1992) along with intersectional writing on identity to explain the gendered and racialized nature of the labour market in these geographically-and historically-specific areas and eras. At the beginning of the first period, privileged white middle class men with connections to education and industry experience founded the programs, eventually hiring privileged white women with relevant credentials, all teaching full-time. In the 1990s, the neoliberal practice of hiring substantial cohorts of non-fulltime (NFT) teachers, and a demand for graduate university credentials can be linked to the advent of joint university-college media programs and an increase in hiring of administrative staff (Mackay, 2014). In the programs themselves, I found that the institutionalized apprenticeship model of the early college changed to a skills-based curriculum, the current emphasis in all college programs. In hiring, gender parity for white heterosexual women has been achieved in the central hub, and consciousness of race has grown over time. However, media teachers still do not match the intersectional diversity of their students due to credentialist and legislative professional closure in hiring and promotion among fulltimers. I theorize that this closure operates by requiring credentials for fulltime positions that are not available to all, depending on intersectional class, race, sexuality, disability, neurodiversity, and age.
Inverse and Robust Models for Optimization with Objective Uncertainty
Keywords: algorithm design
inverse optimization
mathematical programming
robust optimization

Optimization models have become a cornerstone of the operations research and prescriptive analytics community. In practice, model parameters are seldom known with certainty and must instead be estimated from data. In this thesis, we present new algorithms for estimating and solving optimization problems when certain model parameters are unknown. This thesis is comprised of four main chapters. The first three chapters focuses on inverse optimization, which describes a model fitting problem where parameters of an optimization model must be estimated based on a data set of solutions. The first chapter provides a comprehensive survey of recent theoretical, methodological and applications-oriented developments, and represents the first such literature survey in the last two decades. The next chapter focuses on inverse optimization for mixed integer programming problems, which are prevalent in practice but notoriously difficult to solve. In this context, we derive new theoretical insights, propose a novel cutting plane algorithm, and show that this algorithm outperforms existing state-of-the-art methods by orders of magnitudes. In the third chapter, we examine inverse optimization problems for large data sets. We propose a generalized cutting plane algorithm as well as data reduction methods, and evaluate the performance of these methods across a series of inverse knapsack problems. In the fourth and final chapter, we shift our attention to robust optimization with objective uncertainty. We focus specifically on a class of adaptive robust binary optimization problems. We derive new techniques to reformulate these two-stage problems as constrained network flow problems, which we show are easy-to-implement and provide clear computational advantages compared with existing solution methods.
Binary Sparse Modelling for Localization Using WiFi Channel State Information
Keywords: Channel State Information
Ising Model
Localization
Multipath
Optimization
WiFi

Channel state information (CSI) captures the complex signal attenuation between pairs of transmit and receive antennas at each subcarrier frequency. Localizing a target using CSI from commercial WiFi anchors requires that multipath propagation and hardware effects be taken into account. To resolve multiple coherent scatterers, we propose solving the sparse modelling-based localization problem using a binary program, constraining the decision variables to take on values of 0 or 1, and we derive conditions under which this conversion perfectly recovers the signal support. This approach is motivated by the recent proliferation of highly effective binary programming solvers. We address localization errors due to hardware impairments by introducing the accordance function, by which we are able to formulate a multi-anchor localization problem constrained only on the angle of arrival parameters. We then see that triangulation is an asymptotic approximation to this formulation. Finally, under the orthogonal time frequency space (OTFS) waveform, we show that clock drift manifests as a Doppler source. Leveraging this observation, we develop a sparse modelling approach to localize a user using a single anchor. Throughout this thesis, systems that account for multipath propagation effects and hardware impairments have been developed, so that CSI may be used for localization without modifying the existing WiFi protocol or adding dedicated hardware infrastructure.
The Utility of Social Identity Interventions for Reducing Interfaith Prejudice in the United States
Keywords: atheists
Christians
common ingroup identity
intervention research
prejudice
social identity complexity

Social identity complexity (SIC)is the degree of overlap that an individual perceives between their various social identities. High social identity complexity suggests that an individual recognizes that an ingroup member on one social dimension (e.g., religion) is likely to be an outgroup member on another social dimension (e.g., race). Previous research has shown that there is a relationship between social identity complexity and prejudice. However, this relationship has not been investigated extensively for interfaith prejudice between atheists and Christians in the United States. Therefore, the goal of Study 1 was to assess the relationship between SIC and prejudice for atheists and Christians. Results indicated that higher SIC in Christians was associated with lower levels of prejudice, but SIC was unrelated to prejudice for atheists. Therefore, Study 2 tested the utility of an SIC intervention for reducing prejudice in Christian participants. The intervention increased SIC to a small degree, but only trended in reducing prejudice toward atheists. Next, to test the utility of a more traditional social identity intervention, Study 3 relied on a common ingroup identity intervention, where atheists and Christians were primed to reflect on the importance of their superordinate American identity above their religious differences. The intervention was ineffective at prejudice reduction for both groups. Lastly, a mini meta-analysis assessed the relationship between SIC and prejudice across all three studies. The results fully replicated Study 1, where social identity complexity was negatively related to prejudice for Christians, but unrelated to prejudice for atheists. This line of work was an important first step in determining the utility of SIC interventions for interfaith prejudice reduction in atheists and Christians in the United States. The findings suggest that SIC interventions may be well-suited for reducing prejudice in Christians, but future researchers will need to use methods that can be tested longitudinally for greater impact. The findings also suggest that different interventions may need to be used on atheists due to SIC not being related to prejudice in atheists as well as a common ingroup identity intervention also not being effective for this group.