VictorJuiz/thesis huggingface dataset:
X-ray crystallographic studies of argininosuccinate synthetase

Argininosuccinate synthetase (AS) is the rate-limiting enzyme of both the urea and arginine-citrulline cycles. In mammals, deficiency of AS leads to citrullinemia, a debilitating and often fatal autosomal recessive urea cycle disorder, whereas its overexpression for sustained nitric oxide production via the arginine-citrulline cycle leads to the potentially fatal hypotension associated with septic and cytokine-induced circulatory shock. C-terminally 6-histidine tagged E. coli AS (EAS) has been expressed in a recombinant bacterial expression system, and isolated by Ni2+ affinity chromatography. The purified protein, a homotetramer of approximately 200 kDa, is enzymatically active and has been crystallized under a number of conditions. Selenomethionine incorporation and the MAD technique were used to determine the crystal structure of the apo-enzyme, which was subsequently refined to 1.6 Å resolution. Structures of EAS in complex with aspartate and citrulline, ATP and citrulline, and ATP alone have also been determined at 2.0 Å resolution. The EAS monomer has two structural domains: a nucleotide binding domain and a catalytic/multimerization domain. The fold of the nucleotide binding domain confirms AS as the fourth structurally defined member of the N-type ATP pyrophosphatases, while the fold of the catalytic/multimerization is novel. The EAS structures identify catalytically important residues and suggest the requirement for a conformational change during the catalytic cycle. Comparisons of the structures provide explanations of some of the observed kinetic properties of the enzyme, and have allowed a detailed enzymatic mechanism of catalysis to be proposed. Furthermore, sequence similarity between the bacterial and human enzymes has been used to provide insight into the structural and functional effects of clinically observed mutations. Collectively, these first AS structures provide valuable insight into the enzymatic mechanism, and will serve as an important prototype for future structural investigations.
Shape-free statistical information in optical character recognition

The fundamental task facing Optical Character Recognition (OCR) systems involves the conversion of input document images into corresponding sequences of symbolic character codes. Traditionally, this has been accomplished in a bottom-up fashion: the image of each symbol is isolated, then classified based on its pixel intensities. While such shape-based classifiers are initially trained on a wide array of fonts, they still tend to perform poorly when faced with novel glyph shapes. In this thesis, we attempt to bypass this problem by pursuing a top-down "codebreaking" approach. We assume no a priori knowledge of character shape, instead relying on statistical information and language constraints to determine an appropriate character mapping. We introduce and contrast three new top-down approaches, and present experimental results on several real and synthetic datasets. Given sufficient amounts of data, our font and shape independent approaches are shown to perform about as well as shape-based classifiers.
Affect change: The increased influence of attitudinal factors on Canadians' support for legal same-sex marriage

Using data from Canadian Election Surveys, this study considers Canadian public opinion on legalizing same-sex marriage with the aim of trying to account for the dramatic shift from minority-support to majority-support that occurred between 1997 and 2004. Evidence is presented that, contrary to what public opinion polls suggest, opinions on same-sex marriage can no longer be justifiably ascribed to demographic origins. In large part, the majority support that citizens held by 2004 came about as the result of shifts in attitudes, values, and beliefs, rather than because of demographic factors. Data also suggest that there was a decrease in the influence that traditional moral values played and an even larger increase in the influence played by one's feelings towards gays and lesbians. This particular change was found to be a fundamental driver behind the dramatic shift to majority support for same-sex marriage that Canadians came to hold by 2004.
Scalability concepts for i* modelling and analysis

We propose an iterative, "one concern at a time" analysis approach and present a set of model decomposition concepts based on the i* model structure and the analysis question at hand, to address complex model reasoning challenges. Additionally, we offer our insights and practical experience results in dealing with complex model development and validation difficulties. Goal and agent oriented modelling techniques represent one of the major accomplishments of the Requirements Engineering research community. As modelling frameworks cross the boundary from research phase prototypes to application in complex real life projects, scalability challenges, which could not be easily anticipated through simple example application, surface. Models, like software products, have their own lifecycle. They go through an initial development phase, are then validated by stakeholders and finally used for reasoning purposes by the analysis team. We argue that each phase entails its own scalability challenges and requires specific mechanisms to address them.
"Mistake of law": The taxpayer's ultimate answer to S. 152(4)(a)(i) of the Income Tax Act. If the shoe fits, wear it ... properly!

This paper identifies three approaches that may be used by taxpayers to prevent the Minister from reassessing beyond the normal reassessment period. One approach consists of arguing that although a mistake may have been committed in filing the return, that mistake cannot be attributed to the taxpayer's neglect, as he/she/it had carefully assessed the situation and had finally adopted a filing position that was reasonable and bona fide. Through a detailed study of eighteen cases, this paper sheds light on the threshold that needs to be met for the taxpayer's filing position to be considered reasonable and bona fide. It demonstrates that when this threshold is met, the argument will assure success to the taxpayer who raises it. This paper also refines the argument. Inter alia, it demonstrates that the argument draws its strength from the purpose of the limitation period, not from a skewed interpretation of the word "misrepresentation."

Keywords: Income tax, Law and legislation
Income tax, Canada
Time (Law), Canada
Mistake (Law), Canada
Tax assessment, Law and legislation
Tax assessment, Canada
Polyethylene/clay nanocomposite foams blown with physical blowing agents (PBA): from microcellular to nanocellular

In order to investigate the effect of clay particles on the cellular structure of polyethylene (PE) foam with different clay contents and to confirm the expected synergistic potential between nanocomposites and microcellular foams, a study of batch and continuous foaming processes with PE/clay nanocomposites was conducted using PBAs. A batch foaming process using HDPE/clay nanocomposites produced a very successful nanocellular structure with a high cell density, 1013 cells/cm3, and an average cell size that was substantially less than 1 mum. The effects of blowing agent type and content, die geometry, clay content and dispersion on the foamability during the continuous extrusion process were studied in detail. Also, this study presents the optimum content of clay required to achieve high quality microcellular LDPE/clay nanocomposite foams when blown with CO2. Moreover, the effects of clay dispersion on mechanical and flame retardant properties were investigated.
Cross-gain modulation and four-wave mixing with picosecond pulses in a quantum-dash waveguide

The processes of cross-gain modulation and four-wave mixing are characterized in a quantum-dash ridge waveguide laser operating near 1590 nm. These processes are observed by means of a nondegenerate pump-probe experiment with 1.6-ps pulses. The probe transmission dynamics exhibit picosecond and nanosecond components. The pico-second component is identified as carrier heating, and its characteristic time is measured to be 2--3 ps. At transparency, the dynamics recover in 8 ps, potentially enabling 100-Gb/s wavelength conversion. A wavelength-insensitive 12-dB extinction ratio is obtained using a pump energy of 50 pJ. The wavelength up-conversion efficiency of four-wave mixing is found to vary from -17.6 to -21.8 dB for detuning from 1.8 to 3.8 THz. The efficiency is found to increase with injection current up to a point of saturation.
Membrane remodelling and signal transduction during phagosome formation and maturation

Phagocytosis of IgG-opsonized pathogens begins when plasmalemmal Fcgamma receptors bind to the microbe, triggering clustering of receptors and receptor-activation. This in turn promotes remodelling of the actin cytoskeleton and plasma membrane leading to protrusion of membrane pseudopods (the phagocytic cup) that surround and engulf the pathogen. The internalized microbe is contained within a distinct organelle called the phagosome, which undergoes a maturation process consisting of sequential fusion and fission reactions with endosomes, culminating in fusion of the phagosome with lysosomes. The resultant phagolysosome is where most pathogens are degraded due to its highly proteolytic and acidic environment. However some microbes, notably M. tuberculosis, survive inside phagocytes by subverting phagosome maturation. In this thesis, we have examined different stages of phagocytosis. Firstly, because the membrane at the phagocytic cup undergoes focal exocytosis, pinocytosis, and other remodelling events, we performed a quantitative assessment of membrane remodelling at the phagocytic cup using multiple fluorescent membrane markers. In addition, we analyzed membrane remodelling during internalization of different-sized particles and demonstrate how, for large particles, focal exocytosis separates the Fc receptor from its effectors. Secondly, while activation of Fc receptors triggers actin polymerization necessary for formation of the phagocytic cup, the signalling events linking receptor activation to actin polymerization are poorly understood. We describe a novel role for the adaptor protein CrkII and the guanine nucleotide exchange factor Dock180 during Fc-mediated phagocytosis. These data establish a link between early Fc-receptor-mediated signalling events and Rac activation, which is necessary for actin dynamics during phagocytosis. Thirdly, although the phagosome undergoes fusion events with endosomes during maturation, it remains a constant size. This implies that fission from the evolving phagosome must occur, although little is known about how this is regulated. We describe a role for ubiquitin and the proteasome in this process, and establish that fusion and fission from the phagosome are regulated separately. Lastly, while it is known that the mycobacterial phagosome avoids fusion with lysosomes, the basis of this evasion remains unclear. We outline preliminary data on the nature of the mycobacterial phagosome inside macrophages, demonstrating that it is not enriched in Rab5 or Rab7.
Oligomerization of the D2 dopamine receptor

Dopamine is the predominant catecholamine neurotransmitter in the brain, where it controls numerous functions. The physiological actions of dopamine are mediated by five G protein-coupled receptors (GPCRs). The D2 dopamine receptor (D2DR) is the model receptor of D2-like subfamily of dopamine receptors and is prototypic of GPCRs that inhibit adenylyl cyclase and activate K+ channels. Taken together, these studies represent a significant characterization of both the function and structure of D2DR oligomerization. The realization that oligomerization is a pivotal aspect of GPCR biology with implications for trafficking, signalling, and pharmacology has provided more intricate models for understanding the physiological roles of these receptors and prompted a re-evaluation of established ideas. The determinations for D2DR oligomers in this study may yield clues to the principles governing the oligomerization of all rhodopsin-like GPCRs and thereby a better understanding of these important proteins. Initial biochemical characterization of D2DR dimerization revealed that there was a robust interaction between receptor monomers that could not be dissociated by chaotropic agents. Further, neither agonist nor antagonist binding to the D2DR affected the extent of receptor dimerization. Interestingly, co-expression of the wild-type D2DR with truncation mutants and some point mutants of the D2DR resulted in inhibition of cell surface expression of the receptor as the result of an interaction between the receptor mutant and the D2DR. This finding suggested that oligomerization of the receptor occurred prior to cell surface trafficking and that a properly arranged oligomeric complex was required for D2DR trafficking. An investigation of the structural assembly of dimeric receptors showed that there are several sites of interaction including transmembrane domain interactions. Specifically, a symmetrical transmembrane domain 4 interface was identified as being one of these sites. Until recently, it has been assumed that GPCRs function as monomers. However, it has become well established that GPCRs can form dimers and oligomers, leading to a re-evaluation of the mechanisms thought to mediate GPCR function. This thesis documents the characterization of the functional role of D2DR homo-oligomers and elucidation of the sites of intermolecular association in D2DR homodimers. It includes experiments performed prior to the first widely accepted published reports on GPCR dimerization and during the explosive period of research when theories concerning oligomerization evolved rapidly.
Disability studies, physical education and change: contextualizing and re-imagining curricular and co-curricular university practices

The text and images of undergraduate courses and campus recreation programs from different universities reveal conflicting approaches in their social construction of disability. The individual model of disability treats disability as a medical condition which is subjected to diagnoses, treatments, and rehabilitation by experts in medicine and education. In contrast, the social model of disability, argues that society sets up disabling barriers that include attitudes, policies, physical facilities, technology, learning environments, work opportunities, and cultural representations. When conflicting approaches exist, the research method of critical interpretative analysis investigates current meanings, and provokes new imaginations. The text and visual images will be drawn from publicly available documents from universities such as academic calendars and promotional websites. In this thesis, the discussions will include: the models of disability, the language of disability, in(ex)clusion in physical education curricular and co-curricular practices, and a proposal on how to imagine new approaches for curriculum development and recreational programs. In building our awareness of the intersection of disability studies and physical education, we can increase our respect and advocacy for bodies of difference, and bodies of knowledge.

Keywords: Physical education for people with disabilities
Disability studies
People with disabilities, Education (Higher)
Universities and colleges, Curricula
Inclusive education
Pre-service geography teachers' self perceptions of readiness for technology implementation

High school geography teachers need adequate skill and confidence levels to integrate technology successfully into the classroom. This study examined the skill and confidence levels of high school geography pre-service teachers with technology integration. Seventy-four pre-service teachers were surveyed from two universities near the end of an eighth month teacher education program. The results indicated that participants perceived high entering and exiting skill levels with basic computer operations, moderate to high skill levels with using the Internet and productivity software, and low skill levels with geotechnologies. Participants who were required to take a computers in education course indicated a greater number of gains in their skill levels than participants who did not take a basic computers course. The majority of participants perceived no gains in their competencies during their teacher education program. Participants reported high confidence levels with using the Internet and low confidence levels with geotechnology curricular integration.

Keywords: Geography, Study and teaching
Educational technology
Teachers, Training of
Student teachers
Molecular cytotoxic mechanims of fructose and some metabolites in isolated rat hepatocytes

Dietary fructose consumption is associated with the development of obesity and hepatic steatosis. A two hit hypothesis has been proposed for the pathogenesis of non-alcoholic steatohepatitis (NASH), the first hit: hepatic steatosis, and second: oxidative stress. In addition, rats fed fructose developed insulin resistance and increased their serum methylglyoxal, a fructose metabolite. As previously reported, glyoxal induced hepatocyte cytotoxicity could be attributed to mitochondrial toxicity. However the toxic mechanism of fructose, a glyoxal precursor has not been investigated. Isolated hepatocytes incubated with different concentrations of fructose were assessed for toxicity and the molecular cytotoxic mechanisms involved were investigated. Fructose itself was toxic at 1.5M, whereas 12mM was toxic when hepatocytes were also exposed to a non-cytotoxic dose of H2O2. The molecular mechanism for fructose cytotoxicity involved oxidative stress as endogenous reactive oxygen species (ROS) and H2O2 formation preceded cytotoxicity. Toxicity was decreased by radical scavengers, ROS scavengers, and lipid antioxidants.
"Thou land of hope for all who toil"? The effects of social resources on job search and job outcome of skilled immigrants in Toronto (Ontario)

Contrary to the expectations of assimilation theory, job contacts used by respondents even for the job at the time of survey remained predominantly co-ethnic. Moreover, with time, there was increasing participation in the ethnic-related economy. Nevertheless, the use of co-ethnic ties led more often to jobs in the mainstream---usually good jobs with high occupational status. But jobs in the ethnic economy at the time of survey, while slightly inferior to mainstream economy jobs, were mainly good jobs, thanks to the almost institutionally complete Chinese ethnic economy in Toronto which provided opportunities in many professions. Distinction between mainstream and ethnic economy jobs was not significant. Previous research indicated that social resources significantly affected job search outcome for the general population. This study tests whether this also holds true for skilled immigrants. Based on a survey and in-depth interviews of university graduates from Hong Kong in Toronto, it finds that social resources were also key to their job search. While these skilled immigrants lacked social resources immediately after settlement, with time, they established ties, especially Canadian work ties. These ties were instrumental in their obtaining jobs that were of higher occupational status and better matches for their skills and work experience. Their job search pattern grew to resemble mid-career job changes among professionals and managers. Evidence points to social resources, especially in the form of contact status reached, acting as an intervening variable between the human capital endowment of the immigrant and his/her job search outcome. The lack of social resources could be an important but rarely explored explanation for the widespread occupational status dislocation and income disparity experienced by immigrants. The study also found that job search outcome was significantly related to the type of occupation held by the respondent, which also impacted on the method of job search. Confirming previous findings, immigrants found accessing managerial jobs and jobs in other people- and service-oriented occupations most difficult. Because these occupations required linguistic and cultural sensitivity, skills were less portable internationally. Immigrants need personal intermediaries to find such jobs precisely because such skills were not evident in their credentials.
Development of metallocene polyethylene foams using rotational molding and compression molding

This thesis focuses on the feasibility study of foaming metallocene polyethylene with chemical blowing agent (CBA) via rotational molding and compression molding processes. This thesis further proposes and verifies a new processing technology for the manufacture of over 10-fold recyclable metallocene polyethylene foams using CBA. Incorporating the newly developed metallocene polyethylene into foaming applications is feasible but challenging. In manufacturing recyclable metallocene polyethylene foams with over 10-fold volume expansion ratio for impact application, the current rotational foam molding and compression foam molding face some fundamental obstacles. Through extensive experiments, these obstacles are identified to be inevitable entrapped air bubbles and predecomposition of the CBA. Based on an ideal model for CBA blown foam molding, a new processing technology is developed to solve these obstacles. The overall strategy of the new technology is to decouple the two stages in foaming, i.e., the preparation of foamable compositions and foaming. Practically, foamable sheets are manufactured to facilitate the foaming, while preventing the formation of entrapped air bubbles and the pre-decomposition of CBA. Through the new compression foam molding technology based on foamable sheet, over 10-fold recyclable metallocene polyethylene foams are successfully manufactured.
Determination of the human perception threshold of phase difference between motion and visual cues in a moving-based flight simulator

A repeated measures, full factorial experiment was run on the UTIAS flight research simulator with nine subjects to study the effect of four factors on the detection of phase difference between motion and visual cues. Motion gain, amplitude, frequency and visual scene complexity were the four factors. Two levels were tested for each factor, resulting in sixteen sessions for each subject. A Kennedy SSQ was administered to the subjects following each session. Simulator motion was limited to sinusoidal pitch. Results from this study indicate a mean phase difference perception threshold of 56.3° with a standard deviation of 5.67°. Motion gain, amplitude, motion gain x frequency and motion gain x frequency x visual complexity were found to have a significant effect (95% confidence) on the perception threshold. Simulator sickness was mild across all the subjects with a total severity sickness score mean value of 1.91. One significant effect on simulator sickness was found: amplitude x frequency x visual complexity.

Keywords: Flight simulators
Visualization, Technique
Human-computer interaction