VictorJuiz/thesis huggingface dataset:
Genomic Causes and Consequences of the Evolution of Self-fertilization in the Flowering Plant Genera Capsella and Collinsia
Keywords: Mating system evolution
Genomic causes and consequences

The shift in mating system from outcrossing to selfing is associated with many evolutionary changes including reduced flower size and changes in sex allocation, leading to a suite of morphological characteristics known as the selfing syndrome. Furthermore, the evolution of selfing is expected to have important effects on genetic variation and the efficacy of natural selection. However, the underlying genomic causes of morphological evolution and the extent of relaxed selection remain unresolved. In this thesis I use new genomic approaches to investigate the genetic basis of floral evolution as well as the consequences of the evolution of selfing in the genus Capsella (Brassicaceae), in which the highly selfing C. rubella evolved recently from the self-incompatible, obligately outcrossing C. grandiflora. Quantitative trait locus (QTL) mapping results suggest that few loci with major effects on multiple floral phenotypes underlie the evolution of the selfing syndrome. Patterns of neutral diversity in QTL regions from both resequencing and next-generation transcriptome sequencing suggest an important role for positive directional selection in the evolution of the selfing syndrome. Combined with the identification of differentially expressed genes, the signals of positive selection provide candidate regions for identifying the causal evolutionary changes. Analysis of whole-transcriptome polymorphism patterns shows a significant increase in the ratio of unique nonsynonymous to synonymous polymorphism in C. rubella, consistent with a genome-wide relaxation of selection. To investigate the evolution of selfing in the genus Collinsia, I combined transcriptome sequencing with Sanger resequencing of multiple populations of the large-flowered Collinsia linearis with its small flowered, more highly selfing sister species Collinsia rattanii. Patterns of nucleotide diversity suggest the recent divergence of C. rattanii associated with a severe population bottleneck. C. rattanii showed an increased proportion of nonsynonymous polymorphism, consistent with a relaxation of natural selection following the population bottleneck and shift to selfing. In general, my results using combined genome-wide polymorphism, QTL mapping and gene expression data allow for a powerful approach to investigate the targets of adaptive evolution following the shift to selfing, and highlight the potential for relaxation of selection associated with this transition
The Order of St John of Jerusalem in London, Middlesex, and Surrey, c.1128–c.1442: A Social and Economic Study Based on The Hospitaller Cartulary, British Library Cotton MS Nero E vi
Keywords: Hospitallers
Templars
Military Orders
London
Middlesex
Surrey
Southwark
Medieval England
New Temple
Indulgences

This dissertation is a socio-economic analysis of the Knights Hospitallers’ estate management in London, Middlesex, and Surrey. It is based on the examination of 372 charters that trace the social, legal, administrative, and economic history of the Order in England between c.1128 and c.1442. The Hospitallers’ involvement in London’s property market is placed within the larger social and economic context of the city. The evolution of the Order’s administrative policy from serving largely as an absentee landlord, to one entangled in litigation to recover rents in arrears, allowed the Order to more than double its income from urban and suburban possessions between the twelfth and fifteenth centuries. Regarding the rural Middlesex estates, it is argued that the Hospitallers tailored their administrative tactics to suit local social and economic conditions. They developed new estates with aggressive solicitation of properties and manorial assets, and expanded pre-existing manors by purchasing scattered properties and quit-claims from the descendants and widows of tenants. In response to fourteenth-century population decline and rising prices and wages, the Order shifted to long-term leasehold tenancies, removing themselves ii from the direct management of the properties. Social tensions after 1381, moreover, resulted in shorter leases, and the emergence of copyhold tenancies in the early fifteenth century. A comparative analysis of the Templars’ urban and rural possessions, and of the Hospitallers’ administration thereof following the dissolution of the Templars in 1312, is included in this dissertation. It is argued that the Hospitallers’ acquisition of Templar possessions increased not only their economic standing in England, but also positively impacted the spiritual profile of the priory church at Clerkenwell, London. This dissertation is the first of its kind to examine the corpus of charters pertaining to the Hospitallers’ estate management in London, Middlesex, and Surrey. It is a valuable contribution to our understanding of one of the most important medieval military orders in Europe, and its relationship with London. It is also of interest to scholars of the social and economic history of England. The charters that serve as the basis for this dissertation have been edited, and are included here as an appendix.
"Incongruent Bedfellows": Physics and Medicine in the Formation of North American and British Radiology, 1896-1930
Keywords: History of Science
History of Medicine

The announcement of the discovery of x-rays in 1896 sparked great excitement among physicists who rushed to replicate Wilhelm Röntgen’s experiments, hoping to make sense of the properties of this new disturbance in the aether. The medical world was equally entranced by the x-ray pictures that circulated in the press. The diagnostic possibilities were clear, and within a few months, doctors were able to purchase equipment to begin their own x-ray investigations. Physicists and doctors asked very different kinds of questions of these new rays, and the medical and physical investigations were largely separate. There were, however, a number of points of contact between these two worlds. Physicists were members of the first x-ray societies alongside doctors, and, by the 1920s, a small number of physicists were employed in the United States and Britain in hospitals and medical schools. In this study, I trace the contributions of these few physicists in medicine in order characterise the professional relationships that developed between doctors and physicists, individuals from very different disciplinary cultures. I show that the physicists’ values of objectivity and precise measurement, along with their deep belief in regularity, often clashed with the culture of individualism in early 20th century medicine. The first doctors to use x-rays expressed faith in their own, unique clinical art, and emphasized bodies’ idiosyncratic responses to radiation. These conflicting attitudes were evident in debates surrounding the best way to measure therapeutic x-rays, and I argue that the eventual adoption of the röntgen as the international unit of x-ray measurement in 1928 represents a victory of the values of physics. I link the increasing authority awarded to physicists in the American and British x-ray communities to the particular leadership roles taken on by these individuals as physics teachers and safety inspectors.
The Biased Mirror: A Functional Approach to Intergroup Motor Resonance
Keywords: motor resonance
prejudice
mu-suppression

Similar neural circuits are activated during action and during the observation of action, and such motor resonance is said to support action understanding and could potentially facilitate affect sharing, communication, cooperation and interpersonal coordination. Here I describe a line of research that uses suppression of electroencephalographic mu-oscillations as an indicator of motor resonance to look at motor resonance in an intergroup context. In study 1 I find that group categorization and intergroup biases can restrict motor resonance to the ethnic ingroup, potentially making it unavailable during cross-group interactions. In study 2 I investigate a reduction in affect sharing as a potential consequence of group biases in motor resonance. Using EEG prefrontal asymmetry patterns as an indicator of negative affect and avoidance tendencies, I show that participants do not share the sadness of outgroup members. Finally, I present two studies that test the boundary conditions of the ingroup bias in motor resonance. Study 3 shows that when motivational relevance of the outgroup is increased, because participants are in an inclusive, perspective taking mindset, group biases in motor resonance disappear. Similarly, study 4 shows that when the situation is highly motivationally relevant, such as when the behavior poses a potential threat; people will show motor resonance in response to anyone independent of group membership.
Ottoman Constructions of the Morea Rebellion, 1770s: A Comprehensive Study of Ottoman Attitudes to the Greek Uprising
Keywords: The Morea Rebellion
Ottoman
Greek
Russia
Millet
Nationalism

The topic of our dissertation concerns the Greek uprisings against the Ottoman Empire, which took place in the context of the Ottoman-Russian struggle of 1768-1774. That is, our research focuses on the Morea Rebellion which is often claimed as not only the first crucial step on the way towards creating an independent Greek state, which came into being in 1829 with the treaty of London, but also occasionally as one of the most significant turning points both for the history of the Ottoman Empire and for the struggle of Greek independence. The meaning of the Morea Rebellion has long been under discussion among Greek historians. While we will deal with Ottoman side of the issue, this study will shed light on matters of Greek historiography which has been generally been created without taking account of the Ottoman side of the story. In the light of Ottoman archival documents as well as writings of earlier, more contemporary sources, we will argue for the complexity and intricacy of the Morea Rebellion, as reflected in the Ottoman documents, many of which have not been used before. We have tested the veracity of narratives in contemporary chronicles, many of which have been subsumed into the narratives that are current still, by comparing them in Ottoman archival documents. Accordingly, we have revisited many widely accepted assumptions, such as those describing Ottoman society of the time as being divided into homogenous groups clearly defined religion, nation or other identity. In opposition to the earlier explanations of this uprising, our primary sources lead us to see the Morea Rebellion as predominately an international issue. Our conclusions invalidate the long held assumption that the Ottomans were ignorant of Russian initiatives in the Morea. Last but not least, the Ottoman attitudes towards the rebels as well as Ottoman preoccupation with Russia long after the collapse of the rebellion are considered in greater detail. On balance, we believe that, with the help of a better analysis of the secondary literature and the major new primary sources, we have provided an original and comprehensive story of the Morea Rebellion.
An Investigation of the Journey of Care Related to Secondary Health Conditions for Community-dwelling Persons with Spinal Cord Injury
Keywords: spinal cord injury
health services

This thesis comprises an in-depth analysis of the journey of care in managing secondary health conditions (SHCs) for community dwelling persons with a spinal cord injury (SCI) in Ontario. Persons with SCI are at high risk of preventable secondary health conditions. The Network Episode Model was used to help conceptually guide the thesis. To determine whether potentially preventable SHCs may be related to emergency department (ED) use, in the first study, I examined patterns of emergency department use (ED) such as the number of visits by year post injury and characteristics of these visits (e.g., acuity level, timing of visits, reasons for visits). Results from this study suggest that the ED is being used as an inappropriate substitute for primary health care for individuals with traumatic SCI. In the second study, to better understand care provision in the community, I examined the caregiving networks, in particular the structure and roles of informal care. While networks are smaller for persons with SCI compared to the general population, these ties are strong, which is essential when the roles involve a level of trust and flexibility. These informal networks serve as critical key players and secondary team members. Finally, in the third study, the journey of care related to SHCs was examined at the micro (individual level), meso (care provider level) and macro (health system level). Significant challenges at the macro health system level were identified such as rigid policies, wait-times for services, funding and social inequities. These analyses have led to a better understanding of the journey of care, which seems to be a challenging and an uphill struggle for persons with SCI, care providers, and community-based advocates. If we are to make significant gains in minimizing the incidence and severity of SHCs, we need to tailor efforts at the health system.
Multi-agent Reinforcement Learning for Integrated Network of Adaptive Traffic Signal Controllers (MARLIN-ATSC)
Keywords: Traffic Signal Control
Multi-Agent Reinforcement Learning

The population is steadily increasing worldwide resulting in intractable traffic congestion in dense urban areas. Adaptive Traffic Signal Control (ATSC) has shown strong potential to effectively alleviate urban traffic congestion by adjusting the signal timing plans in real-time in response to traffic fluctuations to achieve the desired objectives (e.g., minimizing delay). Efficient and robust ATSC can be designed using a multi-agent reinforcement learning (MARL) approach in which each controller (agent) is responsible for the control of traffic lights around a single traffic junction. Applying MARL approaches to ATSC problem is associated with a few challenges as agents typically react to changes in the environment at the individual level but the overall behaviour of all agents may not be optimal. This dissertation presents the development and evaluation of a novel system of Multi-Agent Reinforcement Learning for Integrated Network of Adaptive Traffic Signal Controllers (MARLIN-ATSC). The MARLIN-ATSC control system is developed to provide a self-learning ATSC using a synergetic combination of reinforcement learning approaches and game theory. MARLIN-ATSC operates in two modes: (1) independent mode, i.e. each intersection controller operates independently of other agents; and (2) integrated mode, where each controller coordinates the signal control actions with the neighbouring intersections. The system was tested on three networks (i.e., small, medium, large-scale) to ensure seamless transferability of the system design and results. The large-scale application was conducted on a computerized testbed network of 60 intersections in the lower downtown core of the City of Toronto for the morning rush hour handling 25,000 trips. The results show unprecedented reduction in the average intersection delay ranging from 27% in mode 1 to 39% in mode 2 at the network level; and travel time savings of 15% in mode 1 and 26% in mode 2, along the busiest routes in downtown Toronto. The thesis shows how mathematical modelling of the traffic control problem as a stochastic control problem, combined with the utilisation of artificial intelligence techniques such as reinforcement learning in a game-theory setup, can provide highly useful and economically inexpensive solutions to real-life problems such as urban traffic congestion.
Modulation of Clr-b Ligand for the Inhibitory NKR-P1B NK Cell Receptor in Response to Transformation and Genotoxic Stress
Keywords: NK cell
genotoxic stress
transformation
missing-self recognition

Innate immunity is an important first-line defense against infectious disease and malignancies. Natural killer (NK) cells are large granular lymphocytes that are critical for the innate immune response. NK cells recognize target cells undergoing pathological alterations such as viral infection and transformation, through germline-encoded receptors. The recognition of targets undergoing genotoxic stress or transformation by NK cells has been limited to the upregulation of stimulatory NKG2DL and “missing-self” recognition of MHC-I. The ligand pair NKR-P1B:Clr-b participates in “missing-self” recognition of tumour and infected cells, but the role of this axis in sensing stressed cells remains unknown. This thesis focuses on the modulation of Clr-b by genotoxic stress and transformation In the first data chapter, we show that Clr-b is downregulated at the transcript and protein level upon genotoxic stress, in a time- and dose-dependent manner in tumour cells and fibroblasts. This loss occurs upon exposure to a variety of genotoxic agents with the exception of γ-irradiation and radiomimetics. The loss of surface Clr-b results in disinhibition of target cells using 51Cr-release assays and BWZ reporter assays. ii In the next chapter, we investigate the mechanism(s) by which this phenotype occurs. Genotoxic stress-induced Clr-b downregulation is not modulated entirely by classical DNA damage response effectors including ATM, ATR, Chk1, Chk2 and p53. Furthermore, the loss of transcript can by uncoupled from the loss of surface protein following administration of proteasomal inhibitors. Lastly, inhibition of the autocatalytic hammerhead ribozyme harboured within the 3’UTR of the Clr-b transcript can abrogate genotoxic stress-induced Clr-b downregulation. In the final chapter, we investigate the effect of oncogenic stress mediated through H-RasV12 on Clr-b expression in NIH3T3 fibroblasts. H-RasV12-mediated Clr-b downregulation occurs through the MEK-Erk pathway and can be inhibited through pharmacological inhibition of MEK1/2 or shRNA knockdown of Erk2. However, Erk2 alone is not sufficient to induce Clr-b downregulation and requires activation from upstream signals. All together, our results explore the role of genotoxic stress and transformation on the modulation of Clr-b, ligand for the NKR-P1B. This work begins to shed light on the role of NKR-P1B:Clr-b system in “missing-self” recognition of target cells undergoing pathological alterations.
"When you witness an evil act, you should stop it with your hand." Citizenship Learning and Engagement of Muslim Youth Activists in Toronto, Canada
Keywords: Muslim youth
Citizenship
Youth citizenship
Citizenship learning
Citizenship education
Social activism
Political activism
Immigrant youth
Muslim diaspora
Muslims in Canada
Muslim feminisms
Citizenship education in Canada
Transnational Communities

This thesis is about being young, Muslim and politically engaged in contemporary Toronto, Canada. Young Muslims attempting to come to terms with the complex and contradictory promises of Canadian citizenship must confront what it means to "be Canadian"—a national identity marked by historical legacies of oppressions, and shaped by ideals of western liberal democracy. Post-9/11 Canada is marked by intensified suspicion and repression of Muslims and those who “look like” Muslims. This thesis examines how 18 young people, ages16 to 29, who self-identity as “Muslim” and “activist” learned “to reflect and act upon the world in order to transform it” (Freire, 1970). Through life history interview methods, this study attempts to capture how the participants had come to their political activism, critical experiences of learning inside and outside of schools that they understood as influential in shaping their political subjectivities and practices, the range of issues of injustice that concerned them, and the various actions they took to address those issues. The young Muslims expressed concern for and acted on access to quality affordable housing, police brutality, gender-based violence, Islamophobia and other forms of hate, and the question of Palestine. Their actions included creating safe spaces, (dis-) engaging formal systems of governance and public authority, providing public education, producing cultural narratives, and engaging in various forms of direct action. Their voices and stories maintain centrality throughout this work. This thesis is based on a broad definition of “education” that encompasses formal and non-formal education and informal learning. It is also based on the premise that “all education is citizenship education.” It demonstrates how the young Muslims’ multiple learning experiences in families, neighborhoods, communities, youth subcultures, social movements and school--embedded in histories of war and migration—enable them to name and to take action to transform the concrete situations of oppression that impact them and their communities. Particularly important for the young Muslims were the cultural and political spaces in which they were able to critically and collectively explore and question their lived experiences, identities, and binding solidarities.
Pierre-Yvon Barré, ses collaborations et la (re)naissance du vaudeville : l’hybridité d’un répertoire dramatique protéiforme
Keywords: Vaudeville
Hybridité
Hybridité matérielle
Hybridité générique
Hypertextualité
Métathéâtralité
Interthéâtralité
Pièces en vaudevilles
Comédies-parades
Airs et timbres musicaux
Pièces à hommages (Voltaire, Rousseau, Racine)
Apothéoses dramatiques (Scarron, Favart, Lesage, Vadé)
Théâtre du Vaudeville (1792)
Pierre-Yvon Barré
Pierre-Antoine-Augustin de Piis
Jean-Baptiste Radet
François-Georges Fouques Deshayes dit Desfontaines
Vaudevillistes
Ancien Régime
Révolution française
Théâtre de la Foire
Théâtre des Boulevards

La liberté des théâtres français déclarée après la Révolution engendre l’ouverture de multiples salles de spectacle, dont le Théâtre du Vaudeville (1792). Cette thèse met en lumière les débuts du vaudeville en tant que genre dramatique qui se développe sur cette scène si peu explorée, jusqu’à date, par les critiques du théâtre. C’est ici qu’à la fin de l’Ancien Régime, des auteurs comme Barré, Piis, Radet et Desfontaines, entre autres, produisent un vaste répertoire de pièces en vaudevilles, ouvrages hybrides où sont visibles les marques d’un passé forain mélangées à des éléments annonçant le vaudeville du XIXe siècle. Notre étude se penche sur l’hybridité matérielle des comédies en vaudevilles (issue du mélange de prose et de musique les caractérisant) et sur l’hybridité générique (provenant de l’emploi intertextuel et hypertextuel d’œuvres savantes au sein de pièces dites légères). Afin de mieux cerner le vaudeville tel qu’il se présente à l’époque qui nous intéresse (1780-1807), cette thèse offre, tout d’abord, un aperçu qui se veut complet des origines du vaudeville et des différentes influences ayant agi sur lui selon le contexte historique, dramatique et politique dans lequel il s’était retrouvé. Deuxièmement, l’étude des comédies-parades nous laisse explorer la fonction de la chanson dans ce corpus où figurent de vieux timbres populaires et des airs de compositions plus récentes, d’opéras-comiques principalement. Troisièmement, nous analysons des pièces à hommages engendrés principalement par l’emploi d’érudits comme personnages référentiels (Voltaire, Rousseau, Racine). Finalement, nous présentons des analyses de ce même type d’apothéoses dramatiques adressées à la scène comique (Scarron, Favart, Lesage, Vadé). Nos recherches montrent qu’une véritable interthéâtralité s’établit entre les différentes salles de l’époque par des renvois plus ou moins explicites au sein des pièces à des représentations sur d’autres scènes parisiennes, amplifiant le caractère anecdotique de ce genre connu comme étant un théâtre d’actualité.