VictorJuiz/thesis huggingface dataset:
The Plot of Attentional Transformation: Literature and History in the Victorian Novel

This dissertation tracks the history of a formal phenomenon that is prevalent across nineteenth-century British novels, but which has gone largely overlooked by previous scholars. This is what I call the plot of attentional transformation, and it comprises two chief elements: a narrative agon that arises when the protagonist adopts an abject mode of attention such as inattention, distractibility, or absorption; and a denouement that takes place when the protagonist shakes off this abject condition to assume an antithetical, idealized attentional state. I argue that if nineteenth-century novelists as diverse as Walter Scott, W.M. Thackeray, George Eliot, Wilkie Collins, Robert Louis Stevenson, and William Morris all invoked this plot form, it is because it served a valuable organizing and coordinating function. At the same time as the attentional plot allowed these novelists to organize the fates of their differently classed and gendered characters into single teleological history, it also enabled them coordinate their otherwise independent and unrelated narrative interventions into social and literary politics into one coherent historical narrative. In analyzing how concepts of attention structure the Victorian novel, my project contributes to the area of attentional formalism—a body of research that studies connections between forms of human attention and the form of Victorian literature. But whereas previous scholars have analyzed the Victorian novel’s attentional form primarily in relation to contemporary psychological and technological discourses, and largely by drawing on physiological and temporal models of attention, I take a different tack here. I study how authors such as Scott, Thackeray, Eliot, Collins, Stevenson, and Morris used representations of everyday objects, and engaged with discourses around aesthetics, linguistics, and typography, to imagine attention chiefly as a spatial and object-oriented—as opposed to a psychological, somatic, and temporal—concept. I also intervene in this established research by extending our understanding of what attention is. My dissertation asks us to think of attention not only as a psychological faculty or as a construct of technological modernity but also as a narrative function that has the power to organize and give structure to large and complex master narratives of social and cultural change.

Keywords: Attention
Genre
Literary History
Narrative form
Plot
Victorian novel
Advisor: Schmitt, Cannon
Osteohistological Reconstruction of Body Mass Growth Curves in Extant and Extinct Tetrapods

Body mass growth curves have been reconstructed in numerous extinct animals, especially non-avian dinosaurs, based on growth marks preserved in the cross sections of limb bones. Utilizing the parameters obtained from the growth curves, recent studies have quantitatively estimated the physiology and life history of extinct animals. Growth curve reconstructions based on growth marks need two estimated parameters: body mass estimation with consideration of ontogeny, and the number of missing growth marks (age) of the samples. Several estimation methods for age and mass have been proposed and used in previous studies, but their performance has never been evaluated using extant tetrapods. Thus, the accuracy of reconstructed body mass growth curves still has considerable uncertainties. In order to address this issue, this thesis focuses on evaluating age and mass estimation methods and the overall performance of growth curve reconstruction based on growth marks using a dataset of extant tetrapods. The results in this thesis indicate that body mass can be reliably estimated using Developmental Mass Extrapolation, and the age can be reliably estimated by growth-model-fitting methods. The results also show that the combination of these age and mass estimations can approximate body mass growth of extant animals adequately. Finally, the most appropriate reconstruction method was applied to samples of a non-avian dinosaur, Centrosaurus apertus. The results demonstrate that the parameters based on some of the previously proposed methods are vastly different from the ones from the most appropriate method. In addition, the best method reveals large growth variations in a single population of Centrosaurus, and small and large individuals co-existed. The size variation in adults might be related to the presence/absence of sexually dimorphic features. This thesis strongly recommends the use of proper growth reconstruction methods to investigate the biology and potential dimorphic patterns of fossil tetrapods in future studies.

Advisor: Evans, David C
Selection, Constraint, and Adaptation in the Visual Genes of Neotropical Cichlid Fishes and Other Vertebrates

The visual system serves as a direct interface between an organism and its environment. Studies of the molecular components of the visual transduction cascade, in particular visual pigments, offer an important window into the relationship between genetic variation and organismal fitness. In this thesis, I use molecular evolutionary models as well as protein modeling and experimental characterization to assess the role of variable evolutionary rates on visual protein function. In Chapter 2, I review recent work on the ecological and evolutionary forces giving rise to the impressive variety of adaptations found in visual pigments. In Chapter 3, I use interspecific vertebrate and mammalian datasets of two visual genes (RH1 or rhodopsin, and RPE65, a retinoid isomerase) to assess different methods for estimating evolutionary rate across proteins and the reliability of inferring evolutionary conservation at individual amino acid sites, with a particular emphasis on sites implicated in impaired protein function. In Chapters 4, and 5, I narrow my focus to devote particular attention to visual pigments in Neotropical cichlids, a highly diverse clade of fishes distributed across South and Central America. In Chapter 4, I find accelerated evolutionary rates in RH1 are associated with cichlid colonization of Central America. I experimentally characterize a South American cichlid rhodopsin pigment and assess the functional consequences of a unique amino acid variant. Finally, in Chapter 5, I examine diversity in UV, violet, and blue-sensitive opsins across the Neotropical cichlids. I identify several putative pseudogenization events in the UV opsin, as well as complete loss of this opsin in several South American cichlid species. Conversely, the UV opsin was under strong purifying selection in Central American cichlids. My results also indicate a burst of episodic positive selection in the blue-sensitive opsin at the base of an ancient adaptive radiation in South American cichlids. This thesis combines computational and experimental work investigating visual pigment evolution in Neotropical cichlid fishes. More broadly, this thesis also considers the evolutionary forces governing visual gene loss and inactivation, as well as the molecular mechanisms mediating visual protein function and adaptation.

Keywords: fish evolution
molecular evolution
opsins
sensory systems
visual ecology
Advisor: Chang, Belinda SW
Lopez-Fernandez, Hernan
Transgenerational Effects of Antenatal Synthetic Glucocorticoid Exposure on Transcription and Methylation in the Developing Brain

The early environment has long term influences on future health that are heritable over multiple generations via maternal and paternal lineages. Antenatal synthetic glucocorticoids (sGC) are administered to women at risk for pre-term delivery because they reduce the morbidity and mortality associated with newborn respiratory distress syndrome. However, the administration of multiple courses of antenatal sGC results in long-term programing of behavioral and physiological responses to stress. In this research, we performed transcriptomic and epigenomic analyses to ascertain the long-term programming effects of antenatal sGC in the brains of first generation (F1) juvenile males and three generations of juvenile female offspring of the paternal lineage. We hypothesized that antenatal sGC exposure results in transgenerational changes in transcription and DNA methylation in the hypothalamic paraventricular nucleus (PVN), prefrontal cortex (PFC) and hippocampus, due to their role in the regulation of the HPA-axis. We observed that antenatal sGC results in generation-, sex-, and brain region-specific changes in gene expression and DNA methylation in three generations juvenile female offspring of the paternal lineage. In the PVN, exposure to sGC programmed large transgenerational changes in gene expression, including type II diabetes, thermoregulation, and collagen formation gene networks. The PFC was the only brain region to show overlap in the significantly differentially expressed genes across all three generations of juvenile females and F1 males. In the PFC, the expression of four genes that were significantly decreased in sGC offspring explained 20-29% of the variability in locomotor behavioral phenotypes. Epigenetic analyses of the hippocampus identified significant changes in CpG methylation in regulatory regions of small non-coding RNAs involved in transcription and splicing. These findings may implicate alternative splicing as a mechanism involved in the transgenerational transmission of the effects of antenatal sGC. This is the first study to show that antenatal sGC exposure, a clinically relevant treatment, results in transgenerational changes in gene expression, and methylation over three generations, via paternal transmission.

Keywords: Epigenetics
Neural Development
Prenatal Glucocorticoids
Transgenerational Transmission
Advisor: Matthews, Stephen G
Challenging Assumptions: Using Research to Evaluate Child Welfare Worker Qualifications

Child welfare workers are the conduit between child welfare systems and children and their families. Required qualifications for practice include certain educational and practice experiences, skills, and knowledge. The overall goal of this dissertation is to increase understanding of the child welfare workforce. To meet this goal, the objectives of this dissertation are: 1) to assess the evidence for the necessary education and training qualifications required for child welfare practice; 2) to examine how worker qualifications have shifted in response to changes in child welfare system mandates and child and family needs; and 3) to contribute to the understanding of the role worker characteristics play in the ongoing services provision. Three studies were undertaken to meet the goal of this dissertation. The first paper is a synthesis of a portion of the child welfare workforce literature and reveals a lack of evidence regarding the specific educational background, skills, and experience that best equip child welfare workers for the demands of practice. Paper two is the first provincial study in Canada to examine how the profile of workers who conduct child maltreatment investigations has changed alongside shifts in child welfare legislation and mandate. Ontario data over the past 20 years illustrate changes in caseload size, training attendance, pre-service education, ethnicity, and years of child welfare worker experience. Paper three, the final study of this dissertation, uses multilevel analyses to examine the decision to transfer a family for ongoing services. Findings reveal that clinical and organizational characteristics predict this service provision, whereas worker characteristics (i.e., education, training attendance, experience, age, position, caseload size) did not. Overall findings suggest that there is little empirical evidence to suggest that valued qualifications actually equip workers with the skills and knowledge for effective child welfare practice and that the efficacy of these qualifications are based primarily on assumptions. Recommendations for future research and practice are provided.

Keywords: child welfare
child welfare worker
qualifications
workforce
Advisor: Mishna, Faye
Fluke, John
Get to the tumour! Transporting nanoparticles past predatory biological barriers

Specific delivery of therapeutic and diagnostic agents to the disease tissue is an essential step for their successful translation into the clinic. In the recent years, nanomedicine has become a promising concept for the delivery of therapeutic molecules and contrast agents to the tumour. However, the body is riddled with many intrinsic biological barriers at the systemic, organ, and the cellular level. These barriers can redirect, hinder, and reduce the transport of nanomaterials to the cancer cells, thus limiting the clinical success of nanomedicine. The purpose of this thesis is to investigate the biological barriers that hinders nanoparticle delivery to tumours. To this end, we 1) examined the nanoparticle adsorption of blood serum proteins on reducing the nanoparticle targeting specificity to cancer cells; 2) the hindrance of extracellular matrix and tumour associated macrophages on the transport of nanoparticles in the tumour; and 3) the variability of tumour pathophysiology on the transport of intratumoural nanoparticles. The knowledge presented from this thesis can be used to improve delivery efficiency to the cancer cells via 1) manipulating the biological system, and 2) improve the design of nanomaterials to avoid biological barriers.

Keywords: Cancer
Drug delivery
Nanoparticle
Advisor: Chan, Warren CW
Bone Microstructure and Changes in Tissue Mineralization throughout Adulthood

This research aims to explore the global variability in the structural and material properties of mid-thoracic ribs within a large (n=213) sample of known age, sex, and government “race” designation from apartheid South Africa [DOD 1967-1998]. Most individuals in the study sample were non-white, and inferred to be of poor socioeconomic status. Using linearly polarized light microscopy (LPLM) on the full sample, and back-scattered scanning electron microscopy (BSE-SEM) on a subset (n=143), histomorphometric parameters, and the average tissue mineralization of the cortical and trabecular bone compartments were assessed in photomontages of transverse rib cross-sections. The influence of body size on bone mass and histomorphometry was first considered. Tissue-level changes were then interpreted in a biosocial context, exploring variation associated with adverse apartheid living conditions and adult life history. Body size does not appear to correlate with either bone mass or histomorphometry, suggesting that size-standardization may not be necessary in studies of rib bone microstructure. Compared to the women in the research sample, men exhibited delayed peak bone mass attainment, lower osteocyte densities, and lower average tissue mineralization. Women achieved peak bone mass when anticipated. Relative cortical area, osteon area, bone tissue mineralization, and cortical porosity were the best histological indicators of menopause in women. Poorer bone health indices in males infer greater systematic marginalization under apartheid rule. Men in this sample may have been more susceptible to dietary deficiencies and substance abuse issues, leading to compromised bone mass and quality. This research demonstrates that osteoporosis risk is not just a concern of the aged, white female population in South Africa. It provides novel data on an understudied population, and underscores the importance of skeletal research collections for the study of contemporary epidemiological issues.

Keywords: Adult body size
Bone histomorphometry
BSE-SEM
Osteoporosis
Skeletal health
South African Apartheid
Advisor: Pfeiffer, Susan K
Structural Insights into Biosynthesis and Export of the Pseudomonas aeruginosa Pel Biofilm Exopolysaccharide

Pseudomonas aeruginosa is an opportunistic pathogen that causes chronic pulmonary infections in cystic fibrosis patients. This bacterium forms biofilms at the infection site, which contributes to increased antibiotic tolerance and promotes immune evasion. Exopolysaccharides are a critical component of P. aeruginosa biofilms. The cationic polysaccharide Pel engages in ionic interactions with extracellular DNA, and provides protection against aminoglycoside antibiotics. Despite the importance of Pel in antibiotic resistance, little is known about its biosynthesis. The process begins in the cytoplasm where nucleotide-sugar precursors are synthesized. Given the monosaccharide analysis, we suspect Pel is synthesized from UDP-N-acetylgalactosamine (UDP-GalNAc) and UDP-N-acetylglucosamine (UDP-GlcNAc). In several proteobacteria a gene adjacent to the pel locus is predicted to encode a nucleotide-sugar epimerase, which we propose is involved in UDP-GalNAc synthesis. We characterized the protein product of this gene from Pseudomonas protegens, PelX. The crystal structure coupled with 1H NMR established that PelX is a UDP-GlcNAc C4-epimerase. We showed that Pel is a major constituent of P. protegens biofilms; however, deletion of pelX does not affect biofilm formation. Because UDP-hexose C4-epimerases are required in other biosynthetic pathways, we conclude that redundant epimerases located elsewhere in the genome may compensate for the absence of PelX. Following precursor polymerization, Pel is transported to the periplasm where it is modified by the bifunctional enzyme PelA. We showed that PelA is recruited to the outer membrane through a direct interaction with the PelB tetratricopeptide repeat domain, and that disrupting this interaction abrogated Pel-dependent biofilm formation. Furthermore, the interaction altered PelA’s enzymatic activities, which may serve to promote the efficient deacetylation of Pel. Once modified, Pel is secreted across the outer membrane. PelC and PelB have each been suggested to form the export channel. We solved the crystal structure of PelC, which revealed a twelve-subunit ring-shaped oligomer, that in vivo disulfide-crosslinking suggests is the physiological arrangement of PelC. We demonstrated that the negative charge within the PelC pore is critical for biofilm formation and proposed that PelC is a molecular funnel that guides the positively charged Pel towards the PelB β-barrel. Together, this work provides insight into a unique polysaccharide secretion pathway.

Keywords: Biofilm
Exopolysaccharide
Pseudomonas aeruginosa
X-ray crystallography
Advisor: Howell, P. Lynne
Kiyokewin: Urban Indigenous Kinship-Visiting Methodology Approach for Urban Indigenous Youth

My research presents urban Indigenous kinship-visiting as a methodology, analytical lens, a deliberative approach and forum. An Indigenous kinship-visiting approach emphasizes the second step of R v. Gladue: how the legal community responds to the collective harms against Indigenous peoples and the present-day rehabilitative healing needs that colonialism has created. My research demonstrates an urban Indigenous kinship-visiting approach is beneficial to ensure a more thorough implementation of the Gladue decision and the Youth Criminal Justice Act. In bringing to bear an Indigenous kinship-visiting approach, I focus on Cree, Métis, and Saulteaux laws including: wahkotowin (laws of kinship relationships) and kiyokewin (laws of visiting). Through these Indigenous legal principles, I suggest a viable urban Indigenous kinship-visiting procedural and deliberative approach. An Indigenous-led kinship-visiting approach assists urban Indigenous youth to connect and build kinship relationships with the urban Indigenous community. My case study focuses on urban institutions serving Indigenous youth in Toronto: Aboriginal Legal Services and the Aboriginal Youth Court. They represent two institutions that are visiting with each other to improve the healing services to urban Indigenous youth. Both urban institutions respond to the unique needs of urban Indigenous youth and both are committed to connecting urban Indigenous youth with Indigenous-led talking circles and wellness programs. The intention is for urban Indigenous youth to feel a sense of belonging within the urban Indigenous community. The success of the Aboriginal Youth Court lies in the healthy partnership with, and informal transfer of jurisdiction to, Aboriginal Legal Services to provide Indigenous-led consensus-based deliberation and healing options. Finally, based on the United Nations Declaration of the Rights of Indigenous Peoples and the Calls to Action of the Truth and Reconciliation Commission, I consider future Indigenous Law Institutes where unique Indigenous juridical systems and urban Indigenous kinship-visiting approaches can be respected.

Keywords: Criminal
Gladue
Indigenous
Kinship
kiyokewin
wahkotowin
Advisor: Nedelsky, Jennifer
Selves and Subjectivities in Medieval North Atlantic Verse

This thesis explores the construction of speaking-subjects and their subjectivities in medieval North Atlantic verse. Although first-person poetry in medieval Irish and Welsh, Old English, and Old Norse-Icelandic has enjoyed a good deal of critical attention, little of it, with the exception of the Old English material, has focused on the strategies and rhetoric poets employed in the creation of lyric poetry’s speaking personas. The intent of this project is thus to analyze, discuss, and highlight the creativity and skill with which North Atlantic poets brought the speaking-subjects of their poetry to life. “Subject” and “subjectivity” are understood in psychoanalytical terms, primarily through the narrative of signification articulated by Julia Kristeva. In particular, Kristeva’s understanding of the formation of subjectivity through the interaction of the semiotic and the symbolic order forms both the thesis’s primary tool of analysis – along with close reading – and its organizing principle. The lyric poems under consideration here are thus organized into chapters according to the relationship of the semiotic and symbolic in the formation of their speaking-subjects. The first chapter, then, examines how Irish monastic poets constructed a Christian subjectivity in which the semiotic, bodily drives of the speaking-subject – in its ideal form – ran in perfect accord with the Christian symbolic order. The second chapter takes up the theme of consolation, and examines how Old English, Irish, and Norse verse could be used as a therapeutic tool to end a speaking-subject’s alienation by modelling a process through which the subject signifies himself within an alternative symbolic order, one which enables the speaker to understand his or her subject-position in a more positive light, thus bringing semiotic and symbolic closer to accord. The third and final chapter turns to those alienated speaking-subjects for whom there is no hope of achieving accord between the semiotic desires of the body and the symbolic order, or of finding even consolation. The chapter explores some of the topoi of alienation – eros, old age, illness – prevalent in North Atlantic verse, examining the conditions through which these lyric speakers have become alienated, and what strategies poets employed to represent their estranged state.

Keywords: Medieval Irish literature
Medieval Welsh literature
Old English literature
Old Norse-Icelandic literature
Poetry
Subjectivity
Advisor: Dooley, Ann