VictorJuiz/thesis huggingface dataset:
A molecular dynamics study of filamin repeat mechanics

The response of domains of the actin cross-linking protein filamin to mechanical stretching forces has recently been characterized by atomic force microscopy using both wildtype and mutant filamin domains. These mutations may have affected the mechanical behaviour of the filamin domain. To investigate the conclusions of this experimental study without resorting to mutations, we have used a computational approach called molecular dynamics. With respect to the sequence of mechanical unfolding events, computational results were more heterogeneous than the experiment implied, but we argue that this heterogeneity was likely an artefact of the computational approach, and that the conclusions of the experimentalists were most likely correct. In a related line of investigation, we have performed a preliminary characterization of the response of a pair of domains to forces that rotate one domain relative to the other, and we have found that such rotation can occur without distortion of the domains.
A three-dimensional analysis of the innervation to the lateral pterygoid muscle

Problem. Dysfunction within the lateral pterygoid muscle (LP) has been shown to predispose the temporomandibular joint (TMJ) to injury. Objectives. To determine the functional characteristics of the LP using a three-dimensional model of its innervation and morphology. Methods. To create a three dimensional model the nerves innervating the LP, its volume, surrounding bone and the TMJ disc were dissected, digitized and reconstructed using Maya animation software. Results. The superior head of the lateral pterygoid muscle (SLP) and the inferior head of the lateral pterygoid muscle (ILP) receive innervation from the long buccal nerve, the anterior and posterior deep temporal nerves (ADT & PDT) and directly from the mandibular division of the trigeminal nerve. Conclusions. The extramuscular and intramuscular innervation of the LP suggests that the both heads share common innervation. The SLP and ILP are independently innervated by the ADT and PDT and direct branches from the trigeminal nerve respectively.
Attachment and mothers' perceptions of their infants' emotional expressions

According to attachment theory (Bowlby, 1969), mothers' perceptions of their infants' emotional expressions influence maternal sensitivity. Mothers' perceptions have yet to be parsed and studied separately from caregiving behaviours by attachment research. Perceptions of 60 mothers were assessed using the OWNTIES: eight videoclips for each subject's infant expressing positive, negative, neutral and ambiguous emotions. Mothers were grouped as (1) autonomous, dismissing or disengaged on the Adult Attachment Interview (AAI: George, Goldwyn & Main, 1985); (2) balanced, disengaged or distorted on the Working Model of the Child Interview (WMCI: Zeanah, Barton & Benoit, 1993) and (3) secure, avoidant or resistant according to their infants' classification on the Strange Situation Procedure (SSP: Ainsworth, Blehar, Waters & Wall, 1978). The hypotheses suggested that mothers in the autonomous/balanced/secure groups would be most accurate, mothers in the dismissing/disengaged/avoidant groups would be least accurate, and that mothers in the preoccupied/distorted/resistant groups would be inconsistently accurate. Attachment effects were expected to be most pronounced for negative emotions. Attachment effects on accuracy scores were determined by a series of one-way ANOVAs for each attachment measure. WMCI balanced mothers were most accurate overall, particularly for positive emotions. No attachment effects on perception were detected for negative emotions when assessed as a group. The failure to link attachment and accuracy for negative emotions led to exploratory analyses of use of specific emotion labels. Adult attachment effects on interpretations of distress suggested that autonomous mothers used 'fear' labels, dismissing mothers used 'sadness' labels and preoccupied mothers used 'distress' labels most often to describe these clips. The findings of this research support the hypotheses that (a) balanced mothers would be most accurate; (b) for negative emotions, dismissing mothers would be least accurate; and (c) preoccupied mothers would be inconsistently accurate. Surprisingly, accurate perception of distress was not associated with autonomous attachment. This research suggests the need for further study of attachment effects on mothers' perceptions, with a focus on specific interpretations of distress and links between perceptions, interpretations and response choices. (PsycINFO Database Record (c) 2016 APA, all rights reserved)

Keywords: Emotions in infants
Infants, Development
Mother and child
Personality in children
Child psychology
Parenting
A molecular and genetic analysis of drosophila cadherin DCad87A

I helped to improve the annotation of the Drosophila cadherin gene, Dcad87A, identified by the BDGP project. I generated polyclonal antibodies against Dcad87A and used these to analyze the protein distribution during embryogenesis and oogenesis. Dcad87A is mainly found in epithelial tissues. Subcellularly, Dcad87A is predominantly located on the apical membrane and in cytoplasmic vesicles. The distribution between the two subcellular pools is dynamically regulated during morphogenetic processes. Further, there is evidence that suggests that in some tissues Dcad87A is associated with microvilli. To gain an understanding of the function of Dcad87A, I employed different strategies to inactivate the gene function of Dcad87A. First, Dcad87A dsRNA was injected into embryos in order to silence Dcad87A. This did not produce a detectable embryonic or 1st instar larval mutant phenotype suggesting that Dcad87A may not be required for embryogenesis. I also designed and participated in the generation of RNA interference foldback constructs that will be used to silence Dcad87A postembryonically. Second, I analyzed lethal mutations that map to the chromosomal position of Dcad87A but found no evidence that one of those represents a mutation in Dcad87A. A sequence comparison revealed that the closest mammalian homologue to Dcad87A is cadherin23. Mutations of cadherin23 cause defects in the stereocilia (modified microvilli) of the hair cells of the inner ear, which leads to congenital deafness.
Development of processing technology for the production of highly porous nickel materials

This thesis demonstrates a novel processing method for producing porous nickel foams. The method involves three processing steps: (1) compounding of nickel powder with binder and a foaming agent, (2) foaming of nickel-binder mixtures, and (3) debinding and sintering of the nickel-binder foam. Nickel foams with different porosities and cell sizes have been produced to verify the feasibility of this method. Compounding of nickel-binder mixtures was studied using viscosity results, and the effects of stearic acid, nickel loading, and maximum powder loading was observed. Debinding/sintering experiments were conducted with nickel-binder samples to determine the most suitable powder type and content. Nickel-binder mixtures were foamed with a chemical blowing agent and the effect of different amount of wax on cell morphology, density, and cell density were investigated. The sintered nickel foams were characterized in terms of porosity, density, and cell morphology.
Acquisition of reading skills in Russian speaking ESL children

This study investigated the impact of underlying cognitive-linguistic processes, such as phonological awareness and naming speed, on the acquisition of L2 reading skills by ESL children with Russian as their L1. Forty bilingual Grade 1 and 2 students were tested on letter naming, phonological awareness and language proficiency tasks in English and Russian. The results indicated that corresponding English and Russian cognitive-linguistic measures were highly correlated. Multiple regression analyses revealed that the predictive value of phonological awareness and naming speed for reading achievement was higher than that of the oral language proficiency in both languages. They also showed evidence of cross-linguistic transfer of underlying cognitive-linguistic components. Orthography-specific factors in early reading were noted as well. Phonological awareness was a better predictor of basic reading skills in English, whereas naming speed was a more significant factor in predicting Russian basic reading skills, confirming other research findings on regular and “deep” orthographies.

Keywords: English language, Study and teaching
English language, Study and teaching
Reading
Reading, Code emphasis approaches
Psychophysiology of distaste and disgust: Testing a taxonomy of repulsion

Efforts to understand disgust are complicated by the wide variety of disgusting stimuli. In an attempt to explain the range of disgusting objects, Rozin and colleagues have suggested that the function of disgust has expanded from an origin in protecting the body from dangerous ingestants to a derived role in protecting the metaphorical soul from dangerous influences. The aim of this research was to test the base of Rozin's taxonomy: the relationship between distaste and disgust. The facial expressions associated with distaste and disgust were measured using electromyography. Activation of the levator labii muscle, which raises the upper lip and wrinkles the nose, was found to be common to expressions of both disgust and distaste. Given that disgust and distaste are associated with similar expressions, it can be inferred that they activate a common behavioural program and thus may be part of a unitary system, as Rozin's taxonomy suggests.
PQR-trees and undirected path graphs

In [1] Booth and Lueker introduce PQ-trees and an algorithm solving the following problem. Given a set U and a family of subsets {S 0 ..., Sz-1} of U, output a data structure (PQ-tree) capturing all embeddings of U onto a path such that each Si is a subpath of that path. Their algorithm provides a linear time recognition algorithm for interval graphs (intersection graphs of subpaths of a path) which outputs a PQ-tree capturing all subpaths of a path intersection representations of an interval graph. We introduce PQR-trees, generalizing PQ-trees [1], and an algorithm solving a similar problem where U is embedded in a tree and a PQR-tree is produced. Our algorithm provides a new recognition algorithm for path graphs (intersection graphs of paths in a tree) which outputs a PQR-tree capturing all paths in a tree intersection representations of a path graph.
A canine model for assessment of satiety

Overweight and obesity are commonly treated with weight-loss agents that reduce food intake through alternation to the parameters that influence meal ingestion. The mechanism of action, efficacy, and toxicological profiles of these agents are firstly assessed in animals and finally in humans. However, the currently available animal models and methods of assessment are not sufficient and sensitive enough to detect the minute changes in appetite and feeding motivation prior to the observable and quantifiable reduction in food ingestion. Hence, the current study attempts to develop and promote a novel cognitive-based protocol to assess satiety in dogs. The visuospatial memory task used in this protocol was also used to evaluate the satiability of a high-fibre diet and the anorexigenic effect of d-amphetamine. All three experiments demonstrated that the visuospatial memory task was a sensitive and valid method in assessing feeding motivation and comparing the efficacy of potential weight-reducing agents in beagle dogs.
The role of interferon-beta in the attenuation of cardiac fibrosis in coxsackievirus B3-induced myocarditis

Interferon-beta has previously been shown to decrease the development of pathological fibrosis in various profibrotic diseases. Viral myocarditis leading to dilated cardiomyopathy is a condition with high mortality associated with myocyte destruction and fibrosis. To determine if IFN-beta tan attenuate fibrosis in viral myocarditis, and have therapeutic value, we performed experiments whereby coxsackievirus B3 (CVB3) infected mite were randomized to treatment with IFN-beta, or placebo control. We found that IFN-beta administration ameliorated the development of fibrosis, as quantitated by picrosirius red staining, in infected mite at day 7 (15.3% +/- 1.7% vs. 5.8% +/- 0.5%, percent of fibrotic area from baseline, mean +/- SEM, p
Improved amino acid sequence fingerprints to identify proteins with dehalogenase activity through screening of microbial genomes

Dehalogenases are environmentally important enzymes that detoxify organohalogens by cleaving their carbon-halogen bonds. Sequencing of microbial genomes reveals that many harbour enzyme families containing potential dehalogenases. However, characterization of dehalogenases on a greater scale is challenging, because little information is available to pinpoint proteins with this catalytic activity amongst thousands of family members having significant overall sequence similarity while displaying other hydrolytic activities. Reliable sequence markers are needed to fully profit from genome sequencing efforts for accelerating the discovery of novel dehalogenases with improved activities. Using enzymatic screens, 7 dehalogenases, 20 esterases and 32 phosphatases were identified amongst 174 candidates selected from five relevant microbial genomes. Subsequent protein sequence comparisons have identified dehalogenase fingerprints which improved the selection accuracy 16-fold over sequence similarity searches alone. Their broader applicability was demonstrated when an independently performed search discovered 11 dehalogenases from only 27 candidates using the improved procedure identified in this thesis.
Endogenous noradrenergic drive modulates respiratory muscle activity across sleep-wake states

Perfusion of the terazosin into the HMN decreased respiratory-related GG-activity in wakefulness and non-rapid eye movement (REM)-sleep; tonic GG-activity was also decreased in wakefulness. Application of phenylephrine increased GG-activity across all sleep-wake states. There was evidence of an additive effect of combined alpha1-adrenergic and 5-HT2-receptor stimulation at the HMN. These results show the first demonstration of an endogenous drive to respiratory motoneurons that activates GG muscle in wakefulness and non-REM, but not REM-sleep. Withdrawal of this noradrenergic input may be responsible for decreases in GG-activity in sleep. Suppression of respiratory muscle activity in sleep predisposes to sleep-related breathing disorders such as obstructive sleep apnea (OSA). Our laboratory developed a model for manipulation of the hypoglossal motor nucleus (HMN), the source of motor outflow to the genioglossus(GG) muscle, in rats across sleep-wake states. Microdialysis perfused terazosin (alpha1 receptor antagonist), phenylephrine (alpha1-agonist), or a combination of phenylephrine and alpha-methyl-serotonin (5HT2-agonist) into the HMN.
Breaking down barriers: male physical education teachers' and coaches' role in female students' physical education and athletic programs

Sport sociologists and activists have documented female disengagement in physical education classes, low levels of participation in physical activity, and inequitable opportunities in sport. Few studies have considered the role of men's contributions to women's advancement in PE and sport. The objective of this study is to examine how and to what extent male PE teachers and coaches may provide equitable and rewarding experiences for female students and athletes, as one of many strategic approaches aimed at combating sexism in PE and sport. Qualitative methods consisted of individual interviews, a focus group session, and an analysis of the current state of the Ontario educational system and its various educational equity policies. The results show that some male PE teachers and coaches challenge gendered and sexist practices, and that their professional and personal socialization experiences have influenced the beliefs and attitudes required to foster a gender-equitable environment.

Keywords: Physical education teachers
Sexism in education
Physical education for women
Teachers', students', and principals' perspectives on character: their moral reasoning and wisdom : case study at two best practice character schools

The following study concerns the concept, development and education of character as seen by 24 students, 4 teachers, and 2 principals from one elementary and one high school from the York Region School District. Additionally, all participants' moral reasoning and wisdom-related knowledge were assessed in order to consider these concepts developmentally. Both the schools and the individuals were chosen through a "best practice" nomination process. Participants were interviewed using an open-ended questionnaire guide. Results show character-related knowledge and opinions are both similar and different in elementary and high school, and also between students and adults within each school. Adults' wisdom-related knowledge and moral reasoning were the most complex and advanced, followed by the 11th graders' and finally by the 5 th graders'—suggesting that "seeds of wisdom" can be found in children as young as 10 years old. Thus, the design of character education programs should be developmentally appropriate.
A Bayesian approach to multiagent reinforcement learning and coalition formation under uncertainty

Sequential decision making under uncertainty is always a challenge for autonomous agents populating a multiagent environment, since their behaviour is inevitably influenced by the behaviour of others. Further, agents have to constantly struggle to find the right balance between exploiting current information regarding the environment and the rest of its inhabitants, and exploring so that they acquire additional information. Moreover, they need to profitably trade off short-term rewards with anticipated long-term ones, while learning through interaction about the environment and others—employing techniques from reinforcement learning (RL), a fundamental area of study within artificial intelligence (AI). Coalition formation is a problem of great interest within game theory and AI, allowing autonomous individually rational agents to form stable or transient teams (or coalitions) to tackle an underlying task. Agents participating in realistic scenarios of repeated coalition formation under uncertainty face the issues identified above, and need to bargain to succesfully negotiate the terms of their participation in coalitions—often having to compromise individual with team welfare effectively. In this thesis, we provide theoretical and algorithmic tools to accommodate sequential decision making under uncertainty in multiagent settings, dealing with the issues above. Specifically, we combine multiagent Bayesian RL with game theoretic ideas to facilitate the agents' sequential decision making. We deal with popular multiagent problems which were to date not tackled under uncertainty, or more specifically under type uncertainty. In our work, we assume that the environment dynamics or the types (capabilities) of other agents are not known, and thus the agents have to account for this uncertainty, in a Bayesian way, when making decisions. Handling type uncertainty allows information about others acquired within one setting to be exploited in possibly different settings in the future. The core of our contributions lies in the area of coalition formation under uncertainty. We studied several aspects of both the cooperative and non-cooperative facets of this problem, coining new theoretical concepts, proving theoretical results, presenting and evaluating algorithms for use in this context, and proposing a Bayesian RL framework for optimal repeated coalition formation under uncertainty.
Influence of workplace factors on depression-related disability and return to work

The purpose of the present study was to enhance the generalizability and improve the interpretation of results from an administrative database study of depression-related short-term disability in the workplace conducted at three work sites. This multiple-case study included a secondary analysis of data from the administrative database study, which was supplemented by descriptive information using a qualitative approach. Five themes emerged from the qualitative analysis that helped increased the understanding of the similarities in rates of depression-related disability and differences in achievement of the disability outcomes across the three work sites. The five themes consisted of: (1) employee health in a changing environment, (2) leadership with respect to disability management, (3) supportive managers, (4) accountability and (5) cross-functional coordination. The increased understanding of each work site and more specifically of their disability management practices has improved the interpretation of the administrative study. The in-depth descriptions of each work site will assist readers in deciding on the transferability of the findings to other settings.
The emergence of democratic educational and experiential educational philosophies in the practice of outdoor education

This thesis explores whether outdoor educators apply the philosophical frameworks of Experiential Education (EE) and Democratic Education (DE) as a part of their daily practice in Ontario's public secondary schools. The primary research question asks, 'what is a work?' in the OE classroom, by looking at how philosophical paradigms guide OE practitioners in the design and implementation of their programs, in their relationships with students, and in their decisions about curriculum and evaluation. This study operates from a critical-pragmatist perspective and embodies a conceptual framework whose aims are to integrate the experiences of outdoor educators, critical thinking, theory/philosophy, reflection, and suggestions for action. It consists of an extensive review of the literature, as well as six interviews with outdoor educators. Given the data collected, this study proposes that the philosophical tenets of EE and DE emerge in the practice of OE and that, in an effort to reassert the value of threatened OE programs, it would be beneficial for outdoor educators to include theoretical/philosophical arguments in their defense.

Keywords: Outdoor education, Methodology
Outdoor education, Ontario
Student-centered learning, Ontario
Non-formal education, Ontario
Teaching, Ontario
Active learning, Ontario
Experiential learning, Philosophy
Experiential learning, Ontario
Teacher effectiveness, Ontario
Environmental education, Ontario
Outdoor education, Philosophy
Outdoor education, Ontario
Experiential learning, Methodology
Experiential learning, Ontario
Teachers, Ontario
The adjoint method for optimal aerodynamic design on unstructured grids

One of the fastest methods for automated aerodynamic shape optimization is available only on structured grids. It employs a Krylov-subspace solver to solve a set of discrete adjoint equations in ⅕ to ½ the time of a Newton-Krylov flow solve. With the solution to these equations, the optimization method uses the BFGS Hessian-approximation formula and a backtracking line search to efficiently solve many optimization problems based on the Navier-Stokes equations. An extension of this method to unstructured grids for the Euler equations is presented. Aside from the difference in spatial discretization and flow equations, the major difference in the two methods is the grid-movement algorithm, for which an efficient, modified version of a common algorithm is presented. The unstructured optimization method is proven over a number of cases that include drag minimization and inverse design, and it is found to be as efficient as the structured method.

Keywords: Multigrid methods (Numerical analysis)
Aerodynamics, Mathematical models