VictorJuiz/thesis huggingface dataset:
Investigating the Role of a Cation Channel-like Protein NCA-1 in Regulating Synaptic Activity and Development in Caenorhabditis elegans
Keywords: NCA-1
cation channels
C. elegans
synaptic activity

NCA-1 (putative nematode calcium channel) and NCA-2 are two cation channel-like proteins in Caenorhabditis elegans that function redundantly to regulate locomotion through unknown mechanisms. A recent study from our lab showed that in vivo Ca2+ imaging analyses of egg-laying neurons in nca-1 loss- and gain-of-function mutants implicate that NCA channels regulate Ca2+ flux at synapses, without affecting Ca2+ dynamics in neuron somas. Furthermore, we observed that NCA-1 localizes to non-synaptic region along axons, strongly suggesting that NCA channels propagate electrical signals from cell bodies to synapses. To identify molecular components that function in the nca-1 genetic pathway, I performed a genetic suppressor screen that led to the identification of behavioral suppressors of nca-1 gain-of-function mutant. Possible NCA auxiliary subunits, UNC-79 (uncoordinated) and UNC-80, were identified from this screen. Molecular characterization of other suppressors will help to identify other regulators and downstream signaling components through which NCA channels transmit electrical signals.
Open Source 3D Reconstruction
Keywords: vision
reconstruction
open source
evaluation
multiview
matchmoving
tracking
camera calibration

A new open source 3D reconstruction and evaluation pipeline is described, with a thorough description of the algorithms employed. A new evaluation framework is introduced, which is easy to use for comparison of state-of-the-art multiview reconstruction algorithms. The evaluation framework also includes tools for creating data sets which have ground truth. The source code is available under the GPL; a first for a complete end-to-end reconstruction system.
Participatory Governance in Public Housing? Understanding Spaces for Participation and Empowerment through the Tenant Representative Role
Keywords: Participatory democracy
Empowerment
Housing
citizenship learning

In order to address the disconnection between the governing and the governed in our democracies and bureaucracies, many practitioners and academics are looking at models such as participatory governance to increase empowerment and foster better decision- making. Although this model has some encouraging possibilities, there are challenges to implementing an empowering and participatory process. To better understand these issues, this research focused on tenant representatives’ understanding and experience of their role in a recently implemented participatory process in the Toronto Community Housing Corporation. Representatives reported taking on extensive responsibilities to improve their communities and interviews with tenants suggested empowerment and citizenship were often products of tenant participation. The research also found limitations on empowerment and the extent to which tenants saw themselves as agents and decision-makers in the Tenant Participation System. The paper connects how structure and education impacts the possibilities for agency and empowerment of participants.
Characterization of APLF in the Nonhomologous End-joining Pathway
Keywords: DNA Repair
NHEJ

Nonhomologous end-joining (NHEJ) is a major DNA double-strand break (DSB) repair pathway. NHEJ is initiated through DSB recognition by the DNA end-binding heterodimer, Ku, while end-joining is accomplished by the XRCC4-DNA ligase IV (X4L4) complex. This thesis reports that APLF (Aprataxin and Polynucleotide kinase-Like Factor), an endo/exonuclease with a forkhead-associated (FHA) domain and two unique zinc fingers (ZF), interacts with both Ku and X4L4. The APLF-X4L4 interaction is FHA- and phospho-dependent, and is mediated by CK2 phosphorylation of XRCC4 in vitro. APLF binds Ku independently of the FHA and ZF domains, and complexes with Ku at DNA ends. APLF undergoes ionizing radiation induced ATM-dependent hyperphosphorylation and ATM phosphorylates APLF in vitro. Downregulation of APLF is associated with defective NHEJ and impaired DSB repair kinetics. These results suggest that APLF is an ATM target that is involved in NHEJ and facilitates DSB repair, likely via interactions with Ku and X4L4.
Reduced Sulphur Compounds in Ambient Air and in Emissions from Wastewater Clarifiers at a Kraft Pulp Mill
Keywords: Environmental Engineering
Chemical Engineering
Reduced Sulphur Compound

Small quantities of reduced sulphur compounds (RSCs) emitted from Kraft pulp mills can affect air quality due to low odour thresholds. Chromatographic methods were developed for individual RSCs at ppt to ppb concentrations. Analyses of ambient air samples showed that while H2S, CH3SH, DMS and DMDS were linked to the pulp mill, the majority of COS and CS2 was due to other sources unrelated to the mill. The fluxes of individual RSCs from kraft wastewater clarifiers were quantified for the first time. DMDS and DMS were the major RSCs emitted from the primary and secondary clarifiers, respectively. RSC fluxes were one to three orders of magnitude higher at the primary clarifier than at the secondary one. Clarifier emissions were, however, insignificant compared to point sources in the mill. Statistically significant correlations were found between the DMS emission and BOD, COD, as well as TSS in the secondary treatment system.
Inadequate Empiric Antibiotic Therapy among Canadian Hospitalized Solid-Organ Transplant Patients: Incidence and Impact on Hospital Mortality
Keywords: Antibiotics
Infection
Solid Organ Transplantation

Background: The incidence of inadequate empiric antibiotic therapy (IET) and its clinical importance as a risk factor for hospital mortality in Canadian solid-organ transplant patients remains unknown. Methods: This retrospective cohort study evaluated all patients admitted to a transplant unit from May/2002-April/2004. Therapy was considered adequate when the organism cultured was found to be susceptible to an antibiotic administered within 24 hours of the index sample collection time. Univariate and multivariate regression analyses were conducted to determine associations between potential determinants, IET, and mortality. Results: IET was administered in 169/312 (54%) transplant patients. Regression analysis demonstrated that an increasing duration of IET (adjusted OR at 24h, 1.33; p < 0.001), ICU-associated infections (adjusted OR, 6.27; p < 0.001), prior antibiotic use (adjusted OR, 3.56; p = 0.004), and increasing APACHE-II scores (adjusted OR, 1.26; p < 0.001), were independent determinants of hospital mortality. Conclusions: IET is common and appears to be an important determinant of hospital mortality in the Canadian transplant population.
Model-Theoretic Analysis of Asher and Vieu's Mereotopology
Keywords: mereotopology
representation theorem
pseudocomplemented lattice
orthocomplemented lattice
first-order ontology
characterization as graphs of lattices
connection structure
characterization up to isomorphism
axiomatic theory
p-ortholattices

In the past little work has been done to characterize the models of various mereotopological systems. This thesis focuses on Asher and Vieu's first-order mereotopology which evolved from Clarke's Calculus of Individuals. Its soundness and completeness proofs with respect to a topological translation of the axioms provide only sparse insights into structural properties of the mereotopological models. To overcome this problem, we characterize these models with respect to mathematical structures with well-defined properties - topological spaces, lattices, and graphs. We prove that the models of the subtheory RT− are isomorphic to p-ortholattices (pseudocomplemented, orthocomplemented). Combining the advantages of lattices and graphs, we show how Cartesian products of finite p-ortholattices with one multiplicand being not uniquely complemented (unicomplemented) gives finite models of the full mereotopology. Our analysis enables a comparison to other mereotopologies, in particular to the RCC, of which lattice-theoretic characterizations exist.
Norfloxacin For Hepatopulmonary Syndrome: A Pilot Study of a Rare Disease
Keywords: hepatopulmonary syndrome
rare diseases
pulmonary vascular disease
nitric oxide
cirrhosis

Norfloxacin For Hepatopulmonary Syndrome: A Pilot Study of a Rare Disease Samir Gupta, Masters of Science, 2008 Graduate Department of Health Policy, Management and Evaluation University of Toronto Introduction: Hepatopulmonary Syndrome is a rare disease characterized by abnormal gas-exchange and a poor prognosis, with no known effective medical therapy. A rat model and preliminary human data suggest that this disease may be caused by intestinal bacterial overgrowth, systemic endotoxemia and increased nitric oxide. Methods: We conducted a pilot crossover randomized controlled trial of norfloxacin versus placebo over four weeks, in seven subjects with HPS or a milder condition called pre-HPS, with a primary outcome of alveolar-arterial oxygen gradient (AaDO2). Results: There was no trend toward improved AaDO2, this outcome and other intermediate outcomes were highly variable, and results suggested that a longer treatment course might be necessary. We identified multiple obstacles to recruitment. Conclusion: We believe that a full-scale study of norfloxacin therapy for HPS will require 1) a six-month therapeutic period, 2) more specific HPS diagnostic criteria for clinical and study populations, and 3) creative recruitment maneuvers.
Chemical Composition Fluctuations in the Gaseous and Particulate Phases of Urban Aerosols
Keywords: urban aerosols
aerosol chemistry

From June 2006 to March 2007, the concentrations of water soluble inorganic particulates and their associated precursor gases were semi-continuously measured adjacent to a high traffic street in downtown Toronto, Canada. Measurements underwent extensive quality assurance and control protocols. Seasonal and diurnal variations in HNO3 and NH3 partitioning to NH4NO3 were observed. Long range transported air masses from southwest of Toronto were the predominant source of measured SO4 2- for all seasons. The contributing sources of PM2.5 nitrate mass fluctuated between seasons: pNO3- was predominantly locally derived in the summer and resulted from long range transport in the winter. Comparison between measurements and ISORROPIA thermodynamic model predictions identified model weaknesses and was used to explore the effect of modulating primary gas concentrations on consequent particulate levels. SO2 emissions reductions were the most influential and direct method to reduce overall PM2.5 concentrations; however, limiting ammonia emissions was also another successful strategy.
Investigating the Neural Correlates of Crossmodal Facilitation as a Result of Attentional Cueing: An Event-Related fMRI Study
Keywords: human event-related fMRI
crossmodal (audio-visual) facilitation
attention

Investigating the Neural Correlates of Crossmodal Facilitation as a Result of Attentional Cueing: An Event-Related fMRI Study. Degree of Masters of Science, 2008 Zainab Fatima Institute of Medical Science, University of Toronto ABSTRACT Attentional cueing modulated neural processes differently depending on input modality. I used event-related fMRI to investigate how auditory and visual cues affected reaction times to auditory and visual targets. Behavioural results showed that responses were faster when: cues appeared first compared to targets and cues were auditory versus visual. The first result was supported by an increase in BOLD percent signal change in sensory cortices upon cue but not target presentation. Task-related activation patterns showed that the auditory cue activated auditory and visual cortices while the visual cue activated the visual cortices and the fronto-polar cortex. Next, I computed brain-behaviour correlations for both cue types which revealed that the auditory cue recruited medial visual areas and a fronto-parietal attentional network to mediate behaviour while the visual cue engaged a posterior network composed of lateral visual areas and subcortical structures. The results suggest that crossmodal facilitation occurs via independent neural pathways depending on cue modality.
A Nonlinear Framework for Facial Animation
Keywords: Computer Animation
Facial Animation
Nonlinear Dimensionality Reduction
Manifold of Faces

This thesis researches techniques for modelling static facial expressions, as well as the dynamics of continuous facial motion. We demonstrate how static and dynamic properties of facial expressions can be represented within a linear and nonlinear context, respectively. These two representations do not act in isolation, but are mutually reinforcing in conceding a cohesive framework for the analysis, animation, and manipulation of expressive faces. We derive a basis for the linear space of expressions through Principal Components Analysis (PCA). We introduce and formalize the notion of "expression manifolds", manifolds residing in PCA space that model motion dynamics for semantically similar expressions. We then integrate these manifolds into an animation workflow by performing Nonlinear Dimensionality Reduction (NLDR) on the expression manifolds. This operation yields expression maps that encode a wealth of information relating to complex facial dynamics, in a low dimensional space that is intuitive to navigate and efficient to manage.
Modernization And The Institutionalization Of Differentiation: The Quebec Case
Keywords: Sociology
Social sciences

The aim of this thesis is to study the institutionalization of differentiation in the Quebec of the sixties. In order to do so a theoretical model of structural change is put forward, specific propositions are derived from it and verified through an analysis of relevant historical material. Quebec society and the modernization of its fiduciary and political subsystems constitute the empirical referent. Quebec's school reform of the sixties is viewed essentially as a process involving differentiation of religious and educational roles, collectivities and institutional norms. Building on Parsons' and Bellah's evolutionary writing as well as Rueschemeyer's exploratory essay on partial modernization, its causes and consequences we seek to situate the post-war Quebec within the framework of partial modernization and the so-called Quiet Revolution within that of a movement toward a more complete form of modernity. Partial modernization is conceptualized as the co-existence of modern and pre-modern or traditional patterns side by side within the society. A pattern is considered modern to the extent that it increases the level of rationalization of the system in question.
Structural And Functional Analysis Of N-Acetylglucosamine-1- Phosphotransferase And β- Hexosaminidase A
Keywords: Molecular biology
Genetics
Biochemistry

To gain a better insight into the complex process of sorting and delivery of lysosomal enzymes into lysosomes, in this thesis, the focus was on understanding the structure-function relationships of GlcNAc-1-phosphotransferase, the enzyme responsible for tagging the soluble lysosomal enzymes with mannose-6-phosphate (M6P), and also on β-hexosaminidase A, an enzyme that utilizes M6P receptor dependent pathway of delivery to lysosomes, and responsible for degradation of GM2 ganglioside. Mucolipidosis II and III, lysosomal storage disorders result from mutations in GNPTAB and GNPTG genes encoding the αβ- and γ-subunits of the G1cNAc-1-phosphotransferase, respectively. In Chapter 2, four MLII and three MLIII cell lines were screened for the presence of mutations and 22 novel genetic variants in GNPTAB gene and 2 previously reported mutations (one in GNPTAB and another in GNPTG) including several potential polymorphic sites in GNPTAB gene were identified. In addition, it was also shown that mutations in one subunit affect the assembly and intracellular distribution of the other subunits. Further, phenotypic correction of defect of MLII and MLIIIC fibroblasts was demonstrated by in vitro transfection with wild type cDNAs encoding the α/β- and γ-subunits of G1cNAc-1-phosphotransferase, respectively. Primary sequences of soluble lysosomal enzymes have not revealed any common targeting motif for their recognition by G1cNAc-1-phosphotransferase. Since the recognition site resides in the γ-subunit of G1cNAc-1-phosphotransferase (Protein id: NP_115909), structural studies were undertaken to better understand how the enzyme recognizes its substrates. Accordingly in Chapter 3, a number of physical characteristics of the expressed, in vitro folded γ-subunit, a 305 amino acid soluble glycoprotein responsible for substrate recognition were studied. The main focus of Chapter 4 was on β-hexosaminidase A that requires GM2 activator protein to hydrolyze the GM2 ganglioside substrate. The studies of refinement of the molecular model created for the interaction of β-hexosaminidase A and its substrate-specific cofactor, GM2 activator protein, indicated the necessity of the α-loop (α280GSEP 283) for functional interaction between β-hexosaminidase A and GM2 activator proteins in hydrolyzing GM2 ganglioside. In conclusion, this thesis enriches the current view of structure-function analysis of the proteins responsible for lysosomal trafficking and degradation.
Analysis of the TGF- β Family Ligand UNC-129 as a Novel Regulator of Netrin Signaling in Caenorhabditis elegans
Keywords: Molecular biology

UNC-129 is a TGF-β family ligand that regulates ventral to dorsal migration of commissural motor axons in C. elegans. Mutations in unc-129 result in motor axons that do not accomplish normal ventral to dorsal migration, but instead deviate from their proper course. Genetic evidence demonstrates that UNC-129 does not function as other TGF-β family ligands, through the classical type I and type II serine/threonine kinase receptors, but instead regulates axon guidance through a novel signaling pathway. Genetic interactions between null alleles of unc-129 and unc-5, unc-40 and unc-6 revealed that unc-129 acts within the UNC-5 signaling pathway to regulate axon guidance, cell migration and patterning of the male tail. Analysis of unc-40 and unc-129 compound null mutants demonstrates that UNC-129 acts specifically to promote UNC-5+UNC-40 signaling. In contrast, overexpression studies using ectopically expressed UNC-129 suggest that UNC-129 acts to inhibit UNC-40 independent UNC-5 signaling. BMP7, a human BMP protein similar to UNC-129, was able to directly interact with UNC-5 and its mammalian homologue RCM. Together, these data suggest a model where UNC-129 regulates the decision between UNC-40 dependent and independent UNC-5 signaling. The result of this, for cells and axons migrating along the ventral-dorsal axis, is to increase the sensitivity of cells and axons to decreasing levels of UNC-6/Netrin by switching from UNC-5 signaling to UNC-5+UNC-40 signaling. To further examine the mechanism of UNC-129 function on UNC-5 signaling, I examined candidate receptors that might function with UNC-129 to regulate UNC-5. In addition, I performed a genetic screen to isolate suppressors of distal tip cell defects resulting from the ectopic expression of UNC-129 that implicates EGF receptor signaling in the ventral to dorsal migration of Distal Tip Cells. Further analysis of these components of UNC-129 signaling will contribute to our understanding of UNC-129 function and regulation and broaden our understanding of how axonal migration is controlled over long distances.
Re-situating Learning
Keywords: Learning
Teaching
Philosophy of mind
Education, Philosophy

In this dissertation I examine the Theory-Theory (T-T). I argue that T-T represents the orthodox conception of learning in today's psychological literature. T-T theorists hold that human beings come "equipped" with innate representations that are "a theory." Theorists believe that this innate theory guides our relations to the world. If T-T theorists are correct, learning amounts to theory-revision. Hence, T-T brings together (roughly) two commitments: (1) innate knowledge and (2) theory-revision. In this dissertation, I show that T-T depends on a reading of Plato's Meno to buttress its commitment to innate knowledge. For (2), T-T depends on aspects of W. V. Quine's philosophy. Theorists think that Quine's naturalised epistemology is central to their position. I show that T-T's dependence on Meno depends on a rough interpretation of the dialogue. Furthermore, I suggest while in some sense Quine's philosophy can accommodate innate knowledge, T-T theorists do not make a sufficient case for such an accommodation. By reconsidering Meno I wish to question T-T's dependence on what may not be in fact a case for innate knowledge. Later I show that no clear case has been made that Quine's philosophy is compatible with the sort of innate knowledge theorists require. I suggest that re-thinking Plato's dialogue cannot save T-T. For T-T theorists must provide a clear case of how innate knowledge is clearly compatible with Quine's philosophy. I argue that too much requires reworking in T-T, and that such a reworking is not necessary because an alternative conception of learning is possible. As an alternative, I argue that learning depends on factors that are not primarily innate but social. In terms of the social aspects of learning, I argue that an important condition of human learning involves being initiated into a set of social practices. Those practices are constitutive of meaningful behaviour that is inherently tied to the histories of those who live and work within these boundaries. Here we can read "history" as "having a tradition." This latter position stands, I suggest, in stark contrast to the view of T-T theorists and is far more plausible in providing an account of learning.