VictorJuiz/thesis huggingface dataset:
APOE genotype and concussion in varsity athletes: Can genetics predict brain injury

Concussion is a common sport-related injury and it is hypothesized that an epsilon-4 allele in the apolipoprotein E gene (APOE egr;4) may increase concussion susceptibility. Understanding the association between APOE egr;4 and concussion may be useful for targeting prevention strategies to APOE egr;4 carriers. The association between the presence of an APOE egr;4 allele in the APOE genotype and the incidence of concussion was studied in a prospective cohort study conducted from September 2002 to April 2006. Participants included University of Toronto varsity athletes participating in sports deemed high risk for concussion. Full informed consent was volunteered from 318 athletes with no concussion in the two years prior. Collected blood samples were genotyped and the presence of APOE egr;4 was described dichotomously. There was no loss to follow-up. Full informed consent involved agreement not to receive individual genetic results. A framework was developed using ethical principles to assist in the decision not to disclose individual genetic information to participants. The main outcome measure in the cohort study was time-to-concussion. It was measured two ways: athletic-exposures (number of games and practices) and number of games played. Only the first concussion sustained by an individual was included in the analysis. Sport-medicine professionals present on the sidelines identified the concussions. To assess misclassification, athletes self-reported if they incurred a concussion missed by the sport-medicine professional. The unadjusted hazard for concussion was 18% greater in APOE egr;4 carriers than in those without the APOE egr;4 allele (Hazard ratio (HR): 1.18 (95% confidence interval (CI): 0.52, 2.69)). Adjustment for sex, weight, height, and team type resulted in a HR of 1.06 (95% CI: 0.41, 2.72) indicating little effect from confounding factors. The HR including the self-reported concussions was 0.96 (95% CI: 0.50, 1.85) for the unadjusted HR and 0.81 (95% CI: 0.38, 1.73) for the adjusted HR. The number of games exposure measure produced similar results. In conclusion, no evidence for an association between the presence of an APOE egr;4 allele in the APOE genotype and the incidence of concussion was found. At this time, we do not recommend pre-season genetic testing for varsity athletes as a mechanism for targeting prevention strategies.
Protein complexes and epistatic mini-array profiles (E-MAPs) reveal pathways involved in chromatin function

Proteins are being systematically TAP-tagged in the budding yeast Saccharomyces cerevisiae, then purified and identified by mass spectrometry in order to define the stably associated components of protein complexes and weak interactions among protein complexes. In order to initiate a systems biology approach to chromatin metabolism and the transcription apparatus for RNA polymerase II, including initiation factors, elongation and termination factors, RNA processing proteins, and chromatin modifying proteins, we are combining the clustered protein purification data with synthetic genetic array (SGA) analysis and microarray analysis of gene deletion mutants. SGA analysis was used to define proteins that are genetically linked to known components of the RNA polymerase II transcriptional apparatus and chromatin modifiers, and all the resulting proteins were subsequently tagged and purified. Deletion mutants for all the non-essential proteins in this genetic and biochemical network were then assembled into a 384 gene deletion E-MAP (epistatic mini-array profile) where quantitative measures of negative (aggravating) or positive (buffering or alleviating) interactions between gene pairs were obtained. The protein complexes were then organized into putative pathways according to the similarity of their genetic interaction profiles and through buffering interactions. Proteins and protein complexes were also organized into putative pathways by clustering the gene expression profiles of a large number of gene deletion mutants. Experimental tests of the organization of pathways containing newly discovered chromatin modifying complexes and other proteins are described in this thesis.
Characterization of recycled paper mill sludge and evaluation of potential applications

This research addresses re-use of recycled paper mill sludge (RPS), a waste by-product of recycled paper manufacturing. The growth of the paper recycling industry over the past 15 years has led to ecological benefits; however it is estimated that over 9 million tonnes of sludge by-product are produced each year in North America, with limited use in beneficial applications. Recycled paper mill sludges that represent a significant segment of the recycling industry were used in this work. Sludges were prepared using a novel kinetic de-watering system that dried and fiberized the material. The unique constitution of the dry sludge overcame constraints of failed utilization attempts of the past. Comprehensive physical and chemical characterization elucidated differences in the sludges based on generating process and raw furnish. Differences in organic content, fibre length, inorganic content and fibre chemistry were found to be strongly influenced by the recycling processes. Fibre contained in recycled newsprint manufacturing sludge had characteristics similar to TMP/mechanical fibre, while the fibre contained in recycled tissue manufacturing sludge were more similar to chemically prepared fibre.

Keywords: Chemical engineering
Wood, Research
Materials science
An incremental elicitation approach to limited-precision auctions

Auction-based mechanisms are increasingly being used for automating resource allocation among large numbers of agents. To make these sort of mechanisms viable one needs to consider the issues of communication and computation expenditure required by these protocols as well as their stability. In this thesis we study limited-precision, iterative mechanisms with dominant strategy equilibria designed for allocation of a single good. Our goal is to limit the communication between the players and the mechanism, reduce the amount of information revealed by the players, as well as minimize the players' computational costs. We accomplish this by placing a number of operational constraints that permit the above objectives. We prove several necessary conditions that severely restrict the space of mechanisms satisfying our criteria. We develop a number of mechanisms and show that with a large and variable number of players, in the case of limited-precision, iterative mechanisms are superior to single-shot mechanisms.
Effects of methanogenic effluent recycle on fermentative hydrogen production

A laboratory-scale, two-phase, hydrogen-producing system was inoculated with unpasteurized anaerobic digester sludge, started up, and operated for 120 days. The hydrogen reactor was operated at 35°C, pH 5.5, and a 10.2-hour SRT. The methanogenic reactor was an up-flow type operated at 28°C and an HRT of 2.7 days. The system was operated with and without methanogenic effluent recycle. A 34--45% reduction in NaOH use for pH control was realized with recycle. Recycle also reduced the dissolved hydrogen concentration, acetic and n-butyric acid concentrations, hydrogen productivity, and hydrogen recovery. The dissolved hydrogen, methane, and carbon dioxide concentrations were supersaturated with respect to their equilibrium concentrations, irrespective of the recycle ratio. The use of recycle also reduced the methane reactor effluent pH and increased the effective organic loading rate to each reactor. Gravity settling of the recycle stream had no effect on the hydrogen reactor performance.
Application of a discursive model of democracy to assess the legitimacy of the exclusion of political groups from the Genocide Convention's definition of genocide

The Genocide Convention's lack of protection for political groups has garnered a great deal of criticism and has resulted in divergent understandings of genocide in law, other fields and broader society. This thesis explores this issue and employs the theory of discursive democracy to determine whether the exclusion of political groups from the definition of genocide contained in the Genocide Convention results in a legitimacy problem. It critically examines the arguments for and against genocide protection for political groups in order to identify underlying discourses and ideologies and ascertain the role that they played in the issue of genocide protection for political groups. The thesis argues that the definition of genocide suffers from a lack of legitimacy because it is inconsistent with shifts that have occurred in discourses. The thesis proposes a method by which to resolve the alleged legitimacy problem of the definition of genocide.
1. Synthetic applications of aziridines: New approaches to the development of asymmetric catalysts. 2. Studies of new reactivity fo p-tolylsulfinayl amides towards olefins

The new N,N-ligands have been synthesized. It was shown that Cu(I) coordinates to the ligands. Enantiomerically pure forms of this ligand were obtained and applied to the cyclopropanation reaction, where the copper catalyst revealed unexpectedly high diastereoselectivity in comparison with the ruthenium catalyst. Observed diastereoselectivities are superior to the known copper catalyzed cyclopropanation. New reactivity of the sulfinyl amide was discovered. Reaction between alkenes and sulfinyl amides in the presence of POCl3 was found to proceed with the formation of β-chlorosulfides. Optimized reaction conditions were applied to a wide range of substrates. In the absence of nucleophile under Lewis acid conditions p-tolylsulfinyl amide reacted with α-methylstyrene with the formation of allylsulfoxide. This chemistry provides a reasonable alternative to currently used oxidative methods of sulfoxides synthesis.
Ultrafast vibrational dynamics of liquid water

Multidimensional IR spectroscopy has the power to demystify molecular dynamics in the liquid phase. It allows a glimpse beneath the broadened spectral lineshapes of molecular liquids giving insight into the internal mechanisms of energy transfer and decoherence. An excellent candidate of this technique is liquid H2O, whose importance to chemistry and biology cannot be understated. Little is known about the time resolved dynamics of this liquid and the hydrogen bonding network which is responsible for its anomalous properties. This lack of previous experimental work is due to the inherent difficulty of performing ultrafast studies on the vibrational transitions of H2O in the condensed phase. In this work, two-dimensional infrared photon echo measurements of the OH stretching vibration in liquid water are performed at various temperatures. The temperature dependence of energy dynamics is of particular interest because it can isolate the effect of the hydrogen bonding network on the intermolecular dynamics. New insight into the hydrogen bonding network are revealed by the spectroscopic behaviour of this hydrogen bonded liquid. It is found that within the pure 'liquid spectral diffusion and resonant energy transfer occur on a time scale much shorter than the average hydrogen bond lifetime. Room temperature measurements show a loss of frequency and, thus, structural correlations on a 50 fs timescale. Weakly hydrogen bonded OH stretching oscillators absorbing at high frequencies undergo slower spectral diffusion than strongly bonded oscillators. With decreasing temperature the loss in memory slows down. Near freezing the frequency correlations in the OH stretch vibration persist beyond sim; 200 fs, pointing to a reduction in dephasing by librational excitations. Polarization resolved purnp-probe studies give a resonant intermolecular energy transfer time of 80 fs which is unaffected by temperature. At low temperature, structural correlations persist longer than the energy transfer time, suggesting new evidence for a delocalization of OH stretching excitations over many water molecules and exciton-like behaviour for the primary excitation of water, a distinctly quantum mechanical effect.
Possible worlds and the problem of evil

The core of classical theism is the belief that an omnipotent, omniscient, perfectly good being—God—exists. Many have urged that belief in God is irrational or philosophically untenable, since theism is disconfirmed by the presence of evil in the world. Efforts to make good this claim are called arguments from evil. I examine the best contemporary arguments from evil, and I conclude that while they may justify disbelief in God, they do not show that theistic belief is irrational or philosophically untenable. Implicitly or explicitly, arguments from evil depend on comparisons between the actual world and alternative possible worlds that an omnipotent, omniscient, perfectly good creator could have made actual. I argue that possible worlds have axiological status, and, after considering some good making and bad-making characteristics of worlds, I conclude that either there are infinitely many axiologically-unsurpassable worlds that an omnipotent being would have the power to actualize, or else there are no such worlds. On each view, arguments from evil take a common form. They typically urge that if God exists, the actual world lacks gratuitous evil: evil which (roughly) serves no outweighing or justifying good. They next suggest that since the actual world likely features gratuitous evil, probably, God does not exist. Such arguments can succeed only if God and gratuitous evil are logically incompatible, but this has been denied. I examine and reject the most influential contemporary such denial, and I endorse the view that God and gratuitous evil are logically incompatible. If the actual world features gratuitous evil, then, theism is disconfirmed. Efforts to disconfirm theism generally turn on one of these inferences: (1) evil E appears to be gratuitous; therefore, probably, evil E is gratuitous; and (2) we know of no outweighing good served by E; therefore, probably, there is no such good Both are controversial. After considering numerous features of our epistemic situation with respect to these inferences, I conclude that entitlement to these moves is subject- and context-specific. I maintain that while one may be so entitled, theists may be rational in resisting these inferences, and (hence) the atheistic conclusion they suggest.
"Environmental refugees": does international law fail to offer them legal protection?

"Environmental refugees" are people forced to seek refuge in another State, due to such environmental degradation of their traditional home land that renders it impossible for them to survive there. Under international law, "environmental refugees" are not refugees and thus, are not entitled to legal protection when in a host State. This thesis examines whether "environmental refugees" can be afforded legal protection under current norms of international law. While international refugee law, international human rights law and the principle of international responsibility to protect fail to offer legal protection to "environmental refugees", the rules on State responsibility can be successfully applied to protect "environmental refugees" in refuge. The author illustrates that under these rules, the international community of States has the obligation to repair damages it caused by breaching the erga omnes obligation to protect the environment in the form of offering legal protection to "environmental refugees."

Keywords: Disaster relief, Law and legislation
Disaster victims, Legal status, laws, etc
Refugees, Legal status, laws, etc
Pollution
Human ecology
Power grid verification

Full-chip verification requires one to check if the power grid voltage drop does not exceed a certain threshold. The traditional simulation-based solution to this problem is computationally expensive, because of the large variety of possible circuit behaviors that would need to be simulated; it also has the disadvantage that it requires full knowledge of the details of the circuit attached to the grid, thereby precluding early verification of the grid. We propose a power grid verification technique that can be applied before the complete circuit has been designed and without exact knowledge of the circuit currents. We use current constraints; which are upper bound constraints on the currents that can be drawn from the grid, as a way to capture the uncertainty about the circuit details and activity. We propose one technique where we verify the worst case voltage as an optimization problem. Using this voltage verification and the constraints we also check the worst case delay of critical paths within the design. Lastly we implement a method of partitioning that allows us to verify grids of an industrial size within reasonable simulation times.
Strategy-based peer tutoring for adolescents with learning disabilities

The current investigation evaluates a peer-tutoring program called Promoting Achievement and Success at School (PASS) developed for students at the secondary school level, who have learning disabilities. The PASS program uses a strategy-based model of teaching higher-order cognitive strategies to adolescents, using a scaffolding approach. The first objective of the study was to examine whether students in the PASS program would outperform control participants on measures of grades, writing skills, numerical operations, and self-ratings of metacognitive awareness, strategy use, motivation/effort and academic self-concept using a randomized experimental design. The results indicated that the PASS students showed a significant improvement in their writing skills compared to control participants by the end of the study, while other areas, such as overall grades, did not show an improvement. The second objective of the study was to explore process factors, such as students' motivation and the relationship between tutor and tutee, to determine whether certain conditions, traits, skills or dynamics were more conducive to academic gains than others. Overall, there were characteristics of both tutors and tutees that predicted better outcomes for the tutees involved in the PASS study. First, tutors who were on task according to their tutees had tutees who made more academic gains. Second, tutees with higher metacognitive skills were more likely to have ii bonded with their tutors and were the students who asked more questions during tutoring. Additionally, students who made gains in their metacognitive skills and who had higher self-ratings of motivation and effort, rated themselves as making gains in their academic abilities by the end of the program. Implications for future research are discussed.
Edible backyards: Residential land use for food production in Toronto

Food security is a fundamental element of community health. Informal house-lot food growing, by providing convenient access to diverse varieties of affordable and nutritious produce, can provide an important support for community food security. With the objective of developing an exploratory assessment of the contribution home food gardening makes to community food security in Toronto, in-depth interviews were conducted with gardeners in two contrasting neighbourhoods. A typology of food gardeners was developed, and this qualitative understanding of residential food production was then assessed from a community food security perspective. It was found that growing food contributes to food security at all income levels by encouraging and enabling a more nutritious diet. The sustainability of household food sourcing and gardeners' overall health and well-being also increased with food production. Secure access to suitable land to grow food and gardening skills were the most significant barriers to residential food production found.
School readiness: the contributions of parent self-reported beliefs/practices and child preschool participation

This study examined the contributions of parent self-reported beliefs and practices and preschool participation to the school readiness of children in Northumberland County, Ontario. The concept of school readiness in Canada was framed in a 1997 federal Speech from the Throne. In the province of Ontario early years policy was further shaped by the McCain and Mustard (1999) Early Years study, which concluded that the period between birth and age six is critical for linguistic and cognitive skill development. A theoretical model of factors influencing the school readiness of young children was developed, including an initial framework of six latent factors. The Preparation for School Experiences (PSE) survey was developed to measure these factors, along with family demographic information and child participation in preschool opportunities. Data were collected from the preschool providers through a preschool opportunity provider survey and analyzed using mixed methods analysis. Seventy-eight parent survey items were pilot tested and findings from an exploratory factor analysis provided evidence for a five factor solution. A refined PSE parent survey comprising 34 items was administered during the main study phase. Results from exploratory and confirmatory factor analyses provided evidence for a further refined 4-factor solution. High internal consistency scores supported the retention of 4-factors (literacy-numeracy development, social interaction, child independence and parent trust for school) and low internal consistency scores supported the removal of the physical development factor from the PSE survey. Initial evidence of predictive validity of the PSE survey was presented based on structural modeling of survey results on a subsample of scores from the Peabody Picture Vocabulary Test (PPVT-III). Parent practices that supported the development of a child's literacy skills were a significant predictor of school readiness, as measured by the PPVT-III. Significant relationships of certain preschool opportunities to the school readiness of children in Northumberland County were also demonstrated through general linear modeling techniques.
The impact of acute live-trapping stress on the hippocampal-hypothalamic-pituitary-adrenal axis of wild snowshoe hares (Lepus americanus)

There is a critical gap in our understanding of how stressors affect brain organization in natural populations. My objective was to examine the impact of the stress associated with live-trapping on the hormonal and molecular changes of the stress axis of wild snowshoe hares. Capture in live-traps for a short duration (