VictorJuiz/thesis huggingface dataset:
Network Improvement and Evaluation in Datacenters and Chip-Multiprocessors
Keywords: Chip-multiprocessor
Collective communication
Datacenter
Fault-tolerance
Network
Simulation

Datacenters are vitally important in the information era in which we currently live. Datacenters are the key enabler of cloud computing, and host many important applications including web service and machine learning. To deliver superior application performance, it is imperative to carefully design and optimize networks in datacenters. we improve the network design in datacenters at two granularities. At the high level, we optimize datacenter networks to better handle collective communication and network failures. At a lower level, we propose sampled approaches to enable fast and accurate evaluation for Network-on-Chips (NoCs) that are widely used in Chip-Multiprocessors (CMPs). Current datacenters rely on IP multicast and TCP incast to support collective communication, or one-to-many and many-to-one traffic. However, they struggle to meet the latency, throughput and scalability requirements posed by modern datacenters. We present McLink and rMcLink, an efficient and scalable collective communication solution. In McLink, we distribute multicast packets in a table-free, tree-based manner. rMcLink aggregates incast packets on-the-fly as they travel towards their destination, reducing network bandwidth consumed by incast traffic. Our simulation results show that McLink reduces multicast packet delay by 16%, and rMcLink improves incast TCP flow finish time by 82%. Datacenter networks are subject to failures. In this work, we design a fault-tolerant routing protocol, GatewayPath. We propose a graph-partitioning based algorithm to forward packets around failures. It also allows further optimization to be applied towards shortest path or load balance. Our evaluation shows that GatewayPath improves convergence time by more than 80%; meanwhile the packet delay is on par with that of a traditional link-state fault-tolerant routing protocol. For CMPs used in datacenter servers, full system simulations are widely used to evaluate their performance. Full system simulations are accurate but prohibitively slow, limiting the range and depth of design space exploration. We focus on accelerating NoC simulation via the use of sampling techniques. We propose NoCLabs and NoCPoint, two sampling methodologies utilizing statistical sampling theory and traffic phase behavior, respectively. Experimental results show that NoCLabs and NoCPoint estimate NoC performance with an average error of 7% while achieving one order of magnitude speedup.
Non-Suicidal Self-Injury and Suicidal Behaviours among Children and Adolescents: The Role of Adverse Childhood Experiences and Bullying Victimization
Keywords: adverse childhood experiences
bullying victimization
child abuse and neglect
mental health services
non-suicidal self-injury
referral

This three-paper dissertation examined non-suicidal self-injury among children and adolescents referred to community and inpatient mental health settings in Ontario, and the association between suicidal behaviours and referral for mental health services among children involved in the child welfare system in Ontario. The first paper examined the effect of adverse childhood experiences on non-suicidal self-injury. The results of this paper indicated that children and adolescents who were physically abused had 49% higher odds of engaging in non-suicidal self-injury and children and adolescents who were sexually abused had 60% higher odds of engaging in non-suicidal self-injury, when compared to their non-abused counterparts. The second paper examined the effect of bullying victimization on non-suicidal self-injury and the mediating effect of depressive symptoms on the relationship between bullying victimization and non-suicidal self-injury among adolescents. The results indicated that the effect of bullying victimization on non-suicidal self-injury was partially mediated by depressive symptoms after adjusting for the effect of demographic characteristics, number of childhood abuse, social support, and mental health diagnoses. The third paper examined the association between suicidal behaviours and referral for mental health services among children involved in the Child Welfare System in Ontario. Data for this paper were obtained from the Ontario Incidence Study of Reported Child Abuse and Neglect 2013. Results indicated that children who expressed suicidal thoughts had more than twice the odds of being referred for mental health services and children who engaged in self-harm behaviour had 44% higher odds of being referred for mental health services. Assessment procedures for indicators of mental health, particularly among children and adolescents with a history of maltreatment, should also take into account non-suicidal self-injury. The dissertation concludes by summarizing the results and implications for social work and childrenâ s mental health research.
Functional Consequences of Mammalian-Specific Alternative Splicing Events in RNA Binding Proteins
Keywords: Alternative splicing
Bioinformatics
Evolution
hnRNPs
PTBP1
RNA splicing

Alternative splicing (AS) greatly increases transcriptome diversity by allowing individual transcripts to be processed into multiple mature RNAs. Advances in RNA sequencing technology have revealed that transcripts from nearly all multi-exon genes in vertebrates are subject to AS, and that patterns of AS change during development and in response to environmental stimuli and disease. Transcriptomic analyses of diverse vertebrate species have provided global insight into AS evolution, revealing an expanded role for this process in mammals and showing that AS patterns have diverged more rapidly than changes in gene expression. While these studies uncovered an extensive number of species- and lineage-specific splice variants, the molecular function of these isoforms and their contribution to phenotypic change remain largely unexplored. In this thesis, I describe a detailed investigation of the functional consequences of splice isoform evolution in multiple RNA binding proteins. I show that mammalian-specific skipping of exon 9 in the PTBP1 splicing factor alters its regulatory activity, and engineered skipping of the orthologous exon in chicken is sufficient to induce a large number of mammalian-like changes in the transcriptome. The inclusion of this exon is regulated during neurogenesis, and significantly impacts the kinetics of activation of neural-specific splicing programs. Subsequent analysis of all mammalian-specific AS events revealed that they are enriched among glycine- and tyrosine-rich, intrinsically disordered protein domains. Such exons affect nearly all members of the heterogeneous nuclear ribonucleoprotein (hnRNP) A and D protein family members, which have diverse functions in RNA biology. At the transcript level, their regulation requires formation of long-range, intramolecular, mammalian-specific RNA duplexes. At the protein level, their inclusion facilitates higher-order hnRNP assemblies on substrate pre-mRNAs that are required for regulation of target AS events. Together, my thesis work demonstrates how splice isoform evolution in RNA binding proteins can expand the regulatory capabilities of mammalian cells, and reveals how these changes can influence evolution of developmental processes.
"The Chiaroscuro Technique in the Works of W. G. Sebald"
Keywords: Black and White Photography
Chiaroscuro
European History of Destruction
Holocaust
Rembrandt/Paintings
World Wars

Abstract W. G. Sebald’s writing has often been observed to have a unique quality, a “Sebald effect”. But what is this effect? In asking about it, I was struck by the fact that, even though chiaroscuro (Italian for light and dark) is widely used in the visual arts an appreciated by many due to its mysterious quality, it is also present in Sebald’s work. Yet, it is ignored by all the literary criticism on him. Because of this discrepancy, in my dissertation I explore this artistic technique which is a key concept in creating a peculiar atmosphere because personal and historical aspects are illuminated or hidden in a similar fashion as those in a chiaroscuro composition. In fact, the latter is not only an effect of the visual arts but also of prose. In the same way as the Dutch master, Rembrandt, Sebald has placed black and white in conversation while adjusting the shades of grey to the desired density for form, texture and substance. In my thesis I argue that a deeper meaning behind this technique is not produced by a strong black and white distinction, but by observing how one gradually blends with the other. This blend gives the composition a symbolic quality as it allows the artist to set up patters of both showing and hiding and makes any symbolism of light/white and dark/black complex. The viewer is, thus, compelled to look in-between those tonal shades to find the deeper meaning behind the work. Since the Dutch painter was important to the German author he stands as a significant model for all his oeuvre. In my dissertation I begin by explaining chiaroscuro in art, then I show how it can be applied to photography. After that, I analyze chiaroscuro in Sebald’s photographs, then in his prose. In conclusion, I argue that it is this technique which holds the fabric of his works intact through an invisible thread and gives his prose “a Sebald effect.” With this study I have given an analytical theory for future research and have contributed to the larger body of literature scholarship.
Kinase Inhibitors and Nucleoside Analogues as Novel Therapies to Inhibit HIV-1 or ZEBOV Replication
Keywords: c-SRC
HIV-1
kinase
nucleoside analogue
PTK2B
ZEBOV

Without a vaccine for Human Immunodeficiency Virus type 1 (HIV-1), or approved therapy for treating Zaire Ebolavirus (ZEBOV) infection, new means to treat either virus during acute infection are under intense investigation. Repurposing tyrosine kinase inhibitors of known specificity may not only inhibit HIV-1 replication, but also treat associated inflammation or neurocognitive disorders caused by chronic HIV-1 infection. Moreover, tyrosine kinase inhibitors may effectively treat other infections, including ZEBOV. In addition, established nucleoside/nucleotide analogues that effectively inhibit HIV-1 infection, could also be repurposed to inhibit ZEBOV replication. In this work the role of two host cell kinases, cellular protoncogene SRC (c-SRC) and Protein Tyrosine Kinase 2 Beta (PTK2B), were found to have key roles during early HIV-1 replication in primary activated CD4+ T-cells ex vivo. siRNA knockdown of either kinase increased intracellular reverse transcripts and decreased nuclear proviral integration, suggesting they act at the level of pre-integration complex (PIC) formation or PIC nuclear translocation. c-SRC siRNA knockdown consistently reduced p24 levels of IIIB(X4) and Ba-L(R5) infection, or luciferase activity of HXB2(X4) or JR-FL(R5) recombinant viruses, prompting further drug inhibition studies of this kinase. Four c-SRC kinase inhibitors (dasatinib, saracatinib, KX2-391 and SRC Inhibitor-1) significantly reduced HXB2 and JR-FL infection in primary CD4+ T-cells. Thus, these potent c-SRC inhibitors should be further evaluated in humanized mouse models of HIV-1 infection. During 2014-16, the Ebola outbreak in West Africa prompted us to rapidly assess whether conventional nucleoside analogs could inhibit in vitro ZEBOV replication. Employing a new lifecycle model of ZEBOV infection in level 2 biocontainment, combinations of nucleoside analogues and interferons were found to synergistically inhibit ZEBOV replication. These included zidovudine, lamivudine and tenofovir, confirmed to show antiviral activity against fully infectious ZEBOV-GFP in level 4 biocontainment. Findings from this thesis provided the rationale for further preclinical development of nucleoside analogue combination treatments, and a phase II EVD trial evaluating recombinant interferon in Guinea. Pre-clinical results using c-SRC kinase inhibitors also suggest that this approach could also be effective in EVD.
Properties of Stellar Remnants: Rotational and Magnetic Evolution of Their Progenitors
Keywords: Black holes
Magnetic fields
Neutron stars
Rotation
White dwarfs

The rotation and magnetic evolution of stars is examined in detail. Advection of angular momentum by convective plumes is a source of differential rotation, which both reduces the angular momentum loss to stellar winds and spins up the inner regions. This spin up not only affects the rotation of the stellar remnant, but also facilitates the winding of magnetic field lines necessary to amplify a seed field. In radiative regions we demonstrate that an embedded magnetic field can effectively mix angular momentum, as well as sustain coupling with adjacent convective zones. In addition to the resulting angular momentum transport model, we consider a mechanism for rotationally-induced winding of a seed magnetic field. When this mechanism operates at a convective-radiative boundary which moves in a Lagrangian sense towards the convection zone, net helicity is left behind in the newly radiative material. We employ this model of angular momentum transport and helicity deposition in stellar models of a wide range of masses. Our aim is to gauge the effect on the evolution of rotation and the impact on the properties of stellar remnants. In low- and intermediate-mass stars we find a quantitative agreement between the predicted and observed core and surface rotation rates, during both the sub-giant and helium-burning phases. Continuing the evolution to the ejection of the envelope, we are able to reproduce the spin periods and magnetic fields of highly magnetic white dwarf remnants. We find similar success in massive stellar models, by being able to reproduce both the spin periods and magnetic fields of pulsars. And in progenitors of black holes with sufficiently high angular momentum pre-core-collapse, a portion of the infalling material can reach rotational support. This quenches the accretion onto the newly formed black hole, and may result in observable phenomena, such as high energy jets.
Examining Changes in Spatialized Geometry Knowledge for Teaching as Early Years Teachers Participate in Adapted Lesson Study
Keywords: Geometry
Lesson Study
Professional Development
Spatial Reasoning
Teacher Learning

Background: Research suggests there is a crucial need for improved teaching of geometry and spatial reasoning in early years classrooms; however, limited teacher knowledge of geometry and spatial reasoning are noted to be significant challenges to this goal. Aims: This dissertation investigated teacher learning about spatialized geometry when participating in an adapted lesson study. The analyses focused on growth in teachers’ gains in knowledge of students, their knowledge of teaching, and growth in their content knowledge of spatialized geometry. Teacher perceptions of the adaptations to lesson study were also examined. Intervention: Teachers participated in an adapted lesson study, which added clinical interviews, exploratory lessons, and resource creation to the traditional Japanese lesson study model (goal setting, lesson design, lesson implementation, and lesson debriefing). Sample: This case study examined the learning of five teachers within one lesson group. Design and methods: Data included pre- and post-questionnaires and geometry inventories, video-recordings of nine meetings over seven months, and artifacts and videos from activities within the teachers’ own classes. Teacher learning was then analyzed through a new construct—spatialized geometry knowledge for teaching (SGKT)—which encompassed learning about students and teaching as well as about specific geometry concepts. Results: The teachers demonstrated substantial expansion of their SGKT including an increased awareness and knowledge of students’ strategies, challenges, and abilities to succeed in spatialized geometry tasks. The teachers also gained substantially increased knowledge for teaching as evidenced by their increased sophistication in designing and implementing quality geometric tasks. Finally, the teachers credited the expanded lesson study structure, in particular the addition of clinical interviews and exploratory lessons, for their considerable learning. Conclusion: The substantial learning about SGKT evidenced in this case study suggests that the adapted lesson study model has potential to address the limited geometry knowledge typically found in early years teachers.
FAITH AND FEMINISM IN PAKISTAN: Religious Agency or Secular Autonomy?
Keywords: Feminism
Islam
Muslim women's agency
Pakistan
Secular autonomy

Numerous post 9/11 ethnographic studies on Islamist/Muslim women have focused almost exclusively on their piety, spiritual drive, agency and subjectivities. Against this trend, the academic and political interest of Faith and Feminism is to recall attention to the political ideologies and routine struggles of women in Muslim majority contexts. This thesis tracks some epistemological tensions that define the growing antagonism between faith-based and secular feminist politics in Pakistan. It argues that there are serious limitations to the religious agency sometimes celebrated by scholars in Western academia as a manifestation of Muslim women’s imaginaries or subjectivities (Abu-Lughod 2013, Jamal 2013, Iqtidar 2011, Mahmood 2005). The influence of postsecularist scholarship that discredits secular feminisms and liberal aspirations is studied with reference to Pakistan. The thesis finds that such criticism relies on a forfeiture of equality and freedoms for Muslim women and minorities only and offers a rationalisation of patriarchy and conservatism. At the same time, this study also recognises the limitations and ineffectual strategies of liberal resistance to Islamic conservatism; the ideological tensions amongst feminists; and the futile dependence on popular culture as a mode of resistance. The post 9/11 developmental model of “donor-driven Islam” (as a strategy of embedding progressive Islam under the guise of servicing gender empowerment while promoting a communalised ‘Muslim human rights’) is found to hinge on postsecularist arguments. In contrast to the above trends, this thesis documents and analyses some examples of the nation-wide working women’s movements in Pakistan that were active through the decade of the “War on Terror” (2001 – 2013). These struggles and campaigns have been secular, or free of theological underpinnings, motivations, slogans or props, and have taken no recourse from faith or religious debates, yet they remain the direct targets of Islamist conservatism and militancy. The thesis argues for political investment in these movements of secular resistance for meaningful feminist progress.
Beyond 'Passion Versus Reason': Identifying Person and Feature Attributes that Predict Deontological and Consequentialist Moral Judgment
Keywords: Moral judgment

The Central Tension Principle asserts that characteristically deontological judgments are preferentially supported by automatic emotional responses, whereas characteristically consequentialist judgments are supported by conscious reasoning and cognitive control. Although a large body of research supports this claim, there are reasons to be skeptical. In Chapter 1 I will outline several criticisms of the Central Tension Principle and propose an alternate framework. In Chapter 2 I will demonstrate that consequentialist moral judgments vary as a function of attachment insecurity, a need to belong, discomfort caring for others, empathy for the group (or individual), and the desires of the people involved in the situation. These data support the idea that to understand moral judgment, one must move beyond the emotion vs. reason dichotomy and take into account other features of the situation. In addition, it highlights an emotional route to consequentialist judgment. In Chapter 3 I will demonstrate that deontological and consequentialist responders use equal amounts of emotional language overall when justifying a moral judgment, but deontological responders use more anger language and consequentialist responders use more sadness language. In Chapter 4 I will demonstrate that another feature that influences moral judgment is the amount of effort the protagonist exerts to arrive at a moral conclusion. I will provide evidence that when the actor exerts little effort, participants judge a deontological actor to be morally superior to a consequentialist actor, but at high effort, this difference is eliminated or attenuated. This effect is mediated by changes in the perceived moral character of the actor. Taken together, the accumulated data suggest ways in which the field may move beyond â emotion vs. reasonâ by highlighting the importance of features of the actor, features of the victims, and features of the beneficiaries.
Corneal reinnervation to treat neurotrophic keratopathy
Keywords: Cornea
Corneal neurotization
Nerve Regeneration
Neurotrophic Keratopathy
Peripheral Nerve
Wound Healing

Patients lacking corneal sensation develop neurotrophic keratopathy (NK). NK is characterized by recurrent breakdown of the corneal epithelium, resulting in scarring of the cornea and permanent vision loss. Even with optimal ophthalmic management, corneal epithelial breakdown and vision loss in patients with advanced NK is inevitable. Conventional treatments protect the cornea from injury but fail to prevent vision loss as they do not address the underlying lack of corneal innervation. Success in treating other nerve palsies surgically with nerve grafts and transfers provides a strong rationale for investigating surgical reinnervation of the cornea in patients with NK. We demonstrate in a prospective clinical study that a novel surgical procedure to reinnervate the cornea improves corneal sensation and ocular surface health in patients with NK. Furthermore, we document reinnervation of the cornea using immunohistochemistry, magnetoencephalography and in vivo confocal microscopy of the cornea. We developed a novel rat model of NK and corneal reinnervation with nerve grafts and transfers to further investigate how foreign axons influence corneal epithelial healing. In this model, we demonstrated that corneal reinnervation improves corneal healing after injury, suggesting that the donor nerves that reinnervate the cornea contain neuromediators necessary to promote corneal epithelial healing. There are several challenges limiting axon regeneration and recovery when using nerve grafts and transfers. In the final chapter, investigation of retrograde neuronal death after neonatal peripheral nerve injury demonstrated that N-acetyl cysteine decreases motor neuron death but fails to prevent sensory neuron death after injury. The promising clinical results and animal studies presented as part of this thesis suggest reinnervation of the cornea with nerve grafts and transfers results in corneal reinnervation, restoring corneal sensation and nerve-derived trophic support, which in turn, improves corneal epithelial maintenance and repair after corneal injury in the context of NK. With this work, we have introduced an animal model that will allow investigation of the mechanisms by which corneal reinnervation influences the corneal epithelium and vision.