VictorJuiz/thesis huggingface dataset:
Growth of the Mammalian Golgi Apparatus during Interphase
Keywords: Golgi apparatus
Golgi growth
Interphase
Mammalian system
Organelle growth

The Golgi apparatus is an important processing station in all eukaryotic cells, where proteins and lipids are glycosylated and sent to their final destinations. For this reason, it is expected that the Golgi apparatus must be duplicated during the cell cycle to ensure subsequent daughter cells have sufficient Golgi content following mitosis. In mammalian systems, extensive research has been focused on the Golgi apparatusâ inheritance process during mitosis, yet research investigating its growth during interphase has been limited. Challenges in monitoring mammalian Golgi growth have been attributed to its elaborate ribbon structure, thus any theories of its growth have mostly been based on observations in lower eukaryotes. The aims of my thesis were to definitively characterize the growth of the mammalian Golgi apparatus during interphase, and elucidate the underlying mechanisms regulating this process. To circumvent the challenges associated with the intricacies of the mammalian Golgi structure, I employed a combination of flow cytometry, fluorescent microscopy and transmission electron microscopy to measure different aspects of its growth. Here I demonstrate the growth of the mammalian Golgi apparatus in its protein content and volume during interphase. Through ultrastructural analyses, physical growth of the mammalian Golgi apparatus was revealed to occur by cisternal elongation of the individual Golgi stacks contrary to previous speculations. By examining the timing and regulation of Golgi growth, I establish that Golgi growth starts after passage through the cell growth checkpoint at late G1 phase and continues growing in a manner highly correlated with cell size growth. Finally, by identifying S6 kinase 1 as a major player in Golgi growth, I reveal the coordination between cell size and Golgi growth via activation of the protein synthesis machinery in early interphase.
A study of the inclusion of students' perspectives in Ontario school board improvement planning through student trustee representation
Keywords: inclusion of students' perspectives
school board improvement planning
student trustees

Students are the largest stakeholders in education and school board improvement plans have a direct impact on their educational experience. This study examined the inclusion of students’ perspectives in improvement planning as represented by student trustees. Based on an adaptation of Fielding’s (2012) framework for student engagement. The study was guided by the assumption that the nature of student trustee engagement in the improvement planning process related to the ways in which education leaders created the conditions to invite students’ input. Responses to on-line questionnaires completed by a sample of 26 English school board supervisory officers and 28 former student trustees all of whom served in their respective roles prior to September 2014 in English school boards in the province of Ontario provided the primary source of data. Both supervisory officers and former student trustees indicated a high level of agreement about the importance of including students’ perspectives in improvement planning. However, overall, across all phases of the board improvement planning process, both supervisory officers and former student trustees indicated that student trustees were not very involved. The study concluded that both supervisory officers and former student trustees would like to see a more participatory role of student trustees in informing the improvement planning process. To do so would require overcoming the challenges identified by these groups. Articulating an appropriate and meaningful role for student trustees in an improvement planning process will be an important consideration when thinking about modifications to existing practices. Provision should be given for enhanced interaction between student trustees and their fellow peers and between student trustees and school board staff when developing improvement plans. Education leaders are encouraged to use an expanded framework for student trustee representation to include opportunities for student trustees to co-lead and co-learn with their fellow peers and staff. Student trustees are encouraged to advocate locally within school boards and provincially through student trustee organizations to elevate the importance of including students’ perspectives in the improvement planning process from students themselves in order to achieve a more authentic response to improving student achievement and well-being in Ontario’s publically funded school system.
Responsiveness to Infant Cues in Postpartum Depressed and Non-Depressed Mothers: Functional Neural Correlates and Their Relation to Behaviour
Keywords: Amygdala
fMRI
Mothering
Postpartum Depression

Postpartum depression (PPD) is the most common maternal birth complication, affecting approximately 5-20% of women. PPD disrupts the normal repertoire of parenting abilities and is thought to have long-term consequences for the developing infant, even after the mothers’ depression remits. Despite its prevalence and potentially enduring effects, we understand very little about the neural correlates of PPD. Recent evidence suggests that postpartum depression (PPD) is associated with reduced amygdala (AMY) response to negative stimuli. However, given the anhedonic features of PPD, it is also important to consider the brain response of depressed mothers specifically to positive infant stimuli and to other positively valenced stimuli. In the current work, mothers with clinically determined PPD (n=31) and without PPD (n=23) viewed smiling pictures of infants (both their own and other), and positive non-infant stimuli during an fMRI. Four studies were completed which examined: 1) multidimensional measures such as current parenting stress, early experiences (e.g., being parented themselves as well as experiences of trauma), current mood and anxiety levels, and relationship satisfaction to better characterize our sample of mothers with and without PPD, 2) PPD and Non-PPD mothers’ response to infants and other positive non-infant stimuli, using AMY region-of-interest as well as amygdala connectivity analyses, 3) subregion-level differences in AMY response and connectivity during the viewing of infant and non-infant stimuli 4) whether and/or how behavioural measures of maternal sensitivity and responsiveness (quality of mother-infant interaction) relate to brain response in the AMY as a whole as well as at the subregion level. Knowing how a depressed mother’s brain responds to her own and other infants is critical as many of the symptoms of PPD focus on the mother-infant dyad and involve a subjective evaluation of one’s parenting abilities. This work adds to the existing literature that examines the brain response of mothers with PPD to various stimuli. Furthermore, it has the long-term potential to inform treatment and intervention programs designed for PPD.
Reproducing Care: Changing Geographies of Nursing Work in the United States
Keywords: care
health
labour
nursing
social reproduction

Nurses provide essential care to people in their most vulnerable times and perform myriad tasks that support the healthcare system as a whole. In spite of their essential role, nurses in the United States have been subject to devaluation individually and systemically, through underinvestment in nurse training, understaffing of facilities, and a lack of recognition for the work that they do. This dissertation is a qualitative study of nursing work in the US, focusing on nursesâ experiences of their jobs since the 2008 financial crisis until 2014. I base my argument on interviews I conducted with 37 nurses working in New York City and St Louis, Missouri. I also analyzed a variety of texts including media stories, union publications, and discussion boards, as a complement to nursesâ own stories. I examine three means of managing nursing work: the restructuring of the built environment of health services, the lengthening of the working day, and the changing modes of measuring and counting nursing work. I demonstrate different ways and scales at which nursesâ work and working conditions are changing during a dynamic period of restructuring in US health care. By drawing on interviews with nurses working in the New York and St Louis metropolitan regions, complemented with secondary textual analyses, I examine how broader changes to the political economy of health care, specifically the built environment, shift length, and ways of measuring work, impact the mundane and everyday aspects of the nursing job. Through these three means of governing nursing work, I add texture to theories of social reproduction. Social reproduction, or the reproduction of people and of everyday life and institutions, includes historically feminized work that sustains life, such as nursing work. Health and health care work, however, are under-theorized in the social reproduction literature. This dissertation contributes to feminist geography by foregrounding nursing work and the workplace of the hospital. While there is a rich literature in geography on the global migration of nurses and on the gendered dynamics of work, few scholars have engaged with the everyday experiences of nurses in their most common worksite. Furthermore, health geography has paid scant attention to the crucial roles that health care workers play in the making of health. Therefore, in this dissertation, I contribute to these literatures by focusing on the workers, how they and their work are regulated, and their subjectivities in relation to their work as it is restructured.
Alterations in Transcription and Connectivity in Stem Cell-Derived Neurons of Children with Neurodevelopmental Disorders
Keywords: autism spectrum disorder
CRISPR
human neuron
induced pluripotent stem cell
SparCon
Williams-Beuren disorder

Many neurodevelopmental disorders (NDD) have a genetic etiology. Some arise from mutations at a specific locus whereas others are polygenic. For example, Williams-Beuren Syndrome (WBS) is caused by hemizygous deletions at 7q11.23 that result in intellectual disability and increased socialization. In contrast, autism spectrum disorder (ASD) is common, results in impaired socialization, and has a polygenic, sex-dependent pattern of inheritance. While these NDDs involve genes in transcription and synapse function, it has been challenging to discover associated neuronal phenotypes owing to a lack of suitable human tissue. The recent development of human induced pluripotent stem cells (IPSC) allows to bridge this gap by providing a renewable source of neurons specific to individuals with NDDs. To examine transcription, I used IPSCs from a child with WBS and two children with ASD with mutations at the PTCHD1/PTCHD1AS locus, which encodes a protein and long non-coding RNA (lncRNA) of unknown function. In WBS neurons, I found an overall reduction in expression of synapse, voltage-gated potassium channel and extracellular matrix genes. In ASD neurons, I found a reduction in genes involved in RNA splicing, export, cellular respiration, and an increase in extracellular matrix genes. The large range of transcriptional alterations suggests that mechanisms of disease in these NDDs are complex and varied. To assess synaptic connectivity in ASD, I compared IPSC-derived neurons from two cases with mutations in SHANK2, a synaptic scaffolding gene, and engineered SHANK2 knockouts to parental and isogenic controls. Because heterogeneity among IPSC-derived neurons can compromise connectivity comparisons, I developed a Sparse coculture for Connectivity (SparCon) assay that increases statistical power by sparsely plating differentially labeled control and mutant neurons onto a lawn of unlabeled control neurons. Using SparCon, I found that dendrite complexity and total synapse number are increased in SHANK2 mutant cells, which was paralleled by increased excitatory synaptic activity. These findings are the first example of excitatory hyperconnectivity in IPSC-derived neurons from subjects with ASD and provide evidence that SHANK2 functions in early neuronal development as a suppressor of dendrite branching. In summary, IPSC-derived neurons are beginning to reveal transcriptional and synaptic neuronal phenotypes in vitro that are associated with NDDs. As the model system matures, methodological refinements like SparCon will further increase the ability of this system to discover disease phenotypes. Investigating alterations in transcription of synaptic genes in WBS, RNA splicing in PTCHD1/PTCHD1AS ASD, and hyperconnectivity in SHANK2 ASD will yield further insight into the pathophysiology of these NDDs.
Studies of Atmospheric Ozone and Related Constituents in the Arctic and at Mid-latitudes
Keywords: Arctic
Bromine
MAX-DOAS
Ozone
profile retrieval
UV-visible spectroscopy

Two UV-visible differential absorption spectroscopy (DOAS) ground-based spectrometers (GBSs) were installed at the Polar Environment Atmospheric Research Laboratory (PEARL) in the Canadian High Arctic (80.1o N, 86.4o W). These two instruments have been used to measure stratospheric trace gases since 1999 and 2006 respectively. In 2010 and 2014, two solar-tracking systems were integrated with the GBSs to make tropospheric trace gas measurements. One goal of this work was to study surface ozone depletion events (ODEs) in the Arctic, using data from the GBSs. The measurements of ozone and BrO, combined with model results, indicate that both high wind/blowing snow and low wind/stable boundary layer are favorable environmental conditions for bromine explosion events, and in some cases, the combination of these two conditions will extend the lifetime of a bromine explosion event. In addition, during a strong surface ODE (ozone VMR
Data Plane Traffic Engineering in Multimedia Communications using Software-Defined Networking
Keywords: Computer Networks
Multimedia Communications
Network Criticality
Software Defined Networking
Traffic Engineering

The quality of multimedia communications heavily relies on the condition of the end-to-end network. Sub-optimal resource allocation may deplete certain links sooner, making the network less resilient to link failures, traffic fluctuation or random traffic spikes. Regulating traffic can improve the media quality, but is not an easy operation to do in legacy IP networks. The maturing Software Defined Networking (SDN) technology provides the support for an unprecedented centralized solution in this regard: making it possible to deploy the optimal embedding of data flows via the central SDN controller. Thus the biggest challenge is to calculate such an optimal embedding for the data flows. This thesis presents our design of traffic engineering in multimedia communications which addresses to the resource allocation concerns in the data plane. Given the physical network, our objective is to allocate the network resource and embed the multimedia data flows in the way such that the total throughput is maximized. To achieve this, we introduce a Centralized Data Flow Routing Module into the control plane of the system. The Module employs a Two-Phase flow embedding procedure: Phase \RNum{1} is a global planning subroutine, periodically invoked. Given the traffic input of an extended time period, it produces and installs the optimal end-to-end tunnels between each pair of communication endpoints. Phase \RNum{2} is a Traffic Engineering (TE) subroutine, always active. It receives the individual data flow requests, and selects one of the pre-installed tunnels to embed the flow. For Phase \RNum{2}, first we propose a greedy-based TE algorithm. We investigate its performance and compare it with the performance if a Dijkstra-routing algorithm is employed. We show that the proposed heuristics outperform the Dijkstra's in three different metrics: session accept rate, maximum/average physical link utilization, and network criticality. In a second attempt, we present an incremental TE algorithm for Phase \RNum{2}. We numerically evaluate it and compare it with (\RNum{1}) Dijkstra algorithm and (\RNum{2}) the greedy-based TE heuristics. We show that the incremental TE excels in all three metrics: session accept rate, throughput, and link utilizations, under a wide spectrum of various network conditions and traffic conditions.
Analysis and Design of Staircase Codes for High Bit-Rate Fibre-Optic Communication
Keywords: coding theory
error correcting code
fiber-optical networks
graph theory
low-density parity-check codes
spatial coupling

Low-complexity, iterative hard-decision decoded staircase codes for hard-decision optical transport-networks (OTNs) are designed, with overheads (OH) between 6.25% and 33.3%. Extensive software simulations are performed for all code designs. Net coding gain gaps to hard-decision capacity are found to range from 0.45 dB at 6.25% OH to 1.38 dB at 33.3% OH. All code designs with
Single-Molecule Spectroscopy of Disordered States and Dynamics in Proteins
Keywords: Conformations
Dynamics
Fluororescence
Intrinsically disordered protein
Protein folding
Single molecule

Single-molecule fluorescence techniques, such as Fรถrster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS), were applied to investigate the conformations, dynamics and interactions of disordered protein systems using custom-built confocal and total internal reflection microscopes. Conformational states of the N-terminal Src-homology-3 domain of downstream of receptor kinases (drkN SH3) were characterized. Both folded and unfolded states of drkN SH3 were detected under non-denaturing conditions. When exposed to high concentrations of urea and GdmCl denaturants, the protein still exhibits two distinct smFRET populations. We propose that the high-FRET population corresponds to denaturation-induced looped conformations. FRET experiments in formamide and DMSO suggest that interactions between hydrophobic amino-acid groups in the distal regions are involved in the formation of the looped state. To gain more insight into the determinants of unfolded protein structures, we studied an intrinsically disordered protein (IDP), the eukaryotic initiation factor 4E (eIF4E) binding protein 2 (4E-BP2). Nanosecond-scale dynamics was observed by FCS and was tentatively assigned to local peptide chain contact formation. Our data suggest that multi-site phosphorylation of the protein slows down the proximal chain motions and modulates the kinetics of distal regions. Segmental rotational correlation times and wobbling cone angles provided a rigidity map of the protein at different sites and were used to evaluate the binding mode to eIF4E. smFRET analysis reveals changes in the conformational ensemble responding to phosphorylation, denaturation, salt and pH. It is shown that both hydrophobic and electrostatic interactions play vital roles in determining the conformations of 4E-BP2. Encapsulating proteins into lipid vesicles has been widely used in studying their structural properties and the kinetics of protein-protein interactions. False signals will be introduced in these studies if the fluorescent probe itself interacts with the lipid wall. We employed the FCS method to systematically quantify the interaction between commonly used fluorophores and lipids and proposed mechanisms for the underlying interactions. This study offers a baseline correction for non-specific interactions and can be used to guide the pairing of dyes and lipids in the single-molecule fluorescence studies.
Exploratory High-Fidelity Aerostructural Optimization using an Efficient Monolithic Solution Method
Keywords: Aerostructural Optimization
Aircraft Design
Computational Fluid Dynamics
Coupled adjoint
Geometry Parameterization and Mesh Movement
Monolithic Solution Algorithm

This thesis is motivated by the desire to discover fuel efficient aircraft concepts through exploratory design. An optimization methodology based on tightly integrated high-fidelity aerostructural analysis is proposed, which has the flexibility, robustness, and efficiency to contribute to this goal. The present aerostructural optimization methodology uses an integrated geometry parameterization and mesh movement strategy, which was initially proposed for aerodynamic shape optimization. This integrated approach provides the optimizer with a large amount of geometric freedom for conducting exploratory design, while allowing for efficient and robust mesh movement in the presence of substantial shape changes. In extending this approach to aerostructural optimization, this thesis has addressed a number of important challenges. A structural mesh deformation strategy has been introduced to translate consistently the shape changes described by the geometry parameterization to the structural model. A three-field formulation of the discrete steady aerostructural residual couples the mesh movement equations with the three-dimensional Euler equations and a linear structural analysis. Gradients needed for optimization are computed with a three-field coupled adjoint approach. A number of investigations have been conducted to demonstrate the suitability and accuracy of the present methodology for use in aerostructural optimization involving substantial shape changes. Robustness and efficiency in the coupled solution algorithms is crucial to the success of an exploratory optimization. This thesis therefore also focuses on the design of an effective monolithic solution algorithm for the proposed methodology. This involves using a Newton-Krylov method for the aerostructural analysis and a preconditioned Krylov subspace method for the coupled adjoint solution. Several aspects of the monolithic solution method have been investigated. These include appropriate strategies for scaling and matrix-vector product evaluation, as well as block preconditioning techniques that preserve the modularity between subproblems. The monolithic solution method is applied to problems with varying degrees of fluid-structural coupling, as well as a wing span optimization study. The monolithic solution algorithm typically requires 20%-70% less computing time than its partitioned counterpart. This advantage increases with increasing wing flexibility. The performance of the monolithic solution method is also much less sensitive to the choice of the solution parameter.
The Future of Canada's Medical Assistance in Dying (MAID) for the Mentally Ill and Physically Disabled
Keywords: assisted dying
bill c-14
carter
euthanasia
health law
medical assistance in dying

Canada's Medical Assistance in Dying (MAID) law continues to be a dividing issue. While it has been decided that only a few qualifying Canadians suffering from severe conditions may request assistance in dying, barriers currently in place may inevitably be lifted as legal challenges are brought against Bill C-14 for potential discrimination towards parties excluded from qualifying under the billâ s eligibility criteria. There is a potential of using the Charter as a force to expand assisted dying which may likely have negative implications on two of the most vulnerable groups in society, those living with a mental illness or physical disability. Studies on controversial practices emerging within the most liberal assisted dying regimes in Europe, Belgium and the Netherlands, may inform Canadian lawmakers on issues to avoid when possibly enacting a broader legalized practice in the near future.