Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

Cognitive coaching : a multiple case study /

The purpose of this qualitative study was to investigate the application of Cognitive Coaching as a school-based professional development program to improve instructional thought and decision making as well as to enhance staff perceptions, coUegiality and school culture. This topic emerged from personal and professional issues related to the role ofthe reflective practitioner in improving the quality of education, yet cognizant of the fact that little professional development was available to train teachers to become reflective. This case study, positioned within the interpretive sciences, focused on three teachers and how their experiences with cognitive coaching affected their teaching practices. Their knowledge, understanding and use of the four stages of instructional thought (preactive, interactive, reflective and projective) were tested before and at the end of eight coaching cycles, and again after two months to determine whether they had continued to use the reflective process. They were also assessed on whether their attitude towards peer coaching had changed, whether their feelings about teaching had become more positive and whether their professional dialogue had increased. Three methods of data collection were selected to assess growth: interviews, observations and joumaling. Analysis primarily consisted of coding and organizing data according to emerging themes. Although the professed aim of cognitive coaching was to teach the process in order that the teachers would become self-analytical and self-modifying, this study found that the value of the coaching, after trust had been established in both the coach and the process, was in the dialoguing and the time set aside to do it. Once the coaching stopped providing the time to dialogue, to examine one's meanings and beliefs, so did the critical self-reflection. As a result ofthe cognitive coaching experience though, all participants grew in their feelings of efficacy, craftsmanship, flexibility, consciousness and interdependence. The actual and potential significance ofthis study was discussed according to implications for teacher supervision, professional development, school culture, further areas of research and to my personal growth and development.

Rights jurisprudence and the charter : evaluating the changing structure of Canadian federalism /

Abstract . Rights jiirisprudence in Canada dates back as far as Confederation in 1867. Between this date and 1982, the organizing principle of Confederation - federalism - has kept this jurisprudence solely within the supremacy of Parliament, subject to its confines and division of powers. After 1982, however, a new constitutional organizing principle was introduced, when Prime Minister Pierre Trudeau introduced the patriation initiative, touted as the "people's package". Individual rights and freedoms were now guaranteed by the Constitution. Citizens of Canada now had a direct link to the Constitution via the Charter and there were now two significantly different organizing principles within the constitutional order widch created an unstable coexistence. This instability has led to a clash between judicially enforced Charter rights and federalism. The Charter has since had both a nationalizing and centralizing effect on Canadian federalism. This thesis explores the relationship between rights and federalism in Canada fix)m Confederation to present day by comparing the jurisprudence of pre and post Charter Canada. An analysis of Supreme Court's (and its predecessor's, the JCPC) decisions shows the profound effect the Charter has had on Canadian federalism. The result has been an undermining of federalism in Canada, with Parliamentary Supremacy replaced by Constitutional supremacy, and ultimately. Judicial Supremacy. Moreover, rights discourse has largely replaced federalism discourse. Canadians have become very attached to their Charter, and are unwilling to allow any changes to the constitution that may affect their rights as political elites discovered the hard way after the collapse of the Meech and Charlottetown Accords. If federalism is to remain a relevant and viable organizing principle in the Constitution, then governments, especially at the provincial level, must find new and iimovative ways to assert their importance within the federation.

Fade to black : picturing mortality in contemporary popular film /

This thesis attempts to understand representations of death in contemporary popular film within a framework that posits mortality as a category of particular social and political importance for the way we understand both individual subjectivity and social responsibility in the postmodern cultural moment. It addresses concerns over the social organizing categories of time and space, and performs a sustained consideration of predominant themes related to the popular representation of death, such as contingency, existential.meaning, and temporal finitude. Death consciousness and social consciousness are shown to be not just intertwined, but also vitally dependent on one another, and the analyses undertaken are ultimately aimed at making these intersections explicit in order • l to think through their potential implications for challenging consumer capitalist hegemony and envisioning the possibility of progressive social change through the lens of our mortality.

Teaching media literacy skills about commercials: a comparative analysis of media literacy instruction /

In this study, methods of media literacy instruction including analytic activities, production activities, and a combination of analytic and production activities were compared to determine their influence on grade 8 students' knowledge, attitudes, and behaviours towards commercials. The findings showed that media literacy instruction does improve media literacy skills. Specifically, activities that included an analytic component or an analytic and production component were significantly better than activities that included a production component. Participants that completed analytic or analytic and production activities were able to discern media-related terms, target audience, selling techniques, social values, and stereotypes in commercials better than participants that completed only production activities. The research findings also showed obstacles when teaching media literacy. When engaged in analytic activities, the difficulties included locating suitable resources, addressing the competition from commercials, encouraging written reflection, recognizing social values, and discussing racial stereotypes. When engaged in production activities, the difficulties were positioning recording stations, managing group work, organizing ideas, filming the footage, computer issues, and scheduling time. Strategies to overcome these obstacles are described.

The nature of the highly artistic student in visual arts at secondary school /

This qualitative investigation examined the nature of 7 highly artistic visual arts students at 2 secondary schools in southcentral Ontario. Through interviews, questionnaires, observations, and artwork documents, this study attempted to understand these highly artistic students in terms of creativity, motivation, social and emotional perspectives, and cognitive processes. Data collection occuned over a 3-monlh period. and the data analysis program NVivo 7 was used for coding to develop themes and categories for organizing data. The findings of this study illustrate the significant place that \ isual arts can lake in the growth and development for the youth of today. Participants idcniificd dcxclopnig critical thinking and problem-solving skills, taking risks, and meeting challenges ilirouuh their engagement in the creative process. The transferability of these skills \\ as referenced to numerous aspects of their lives. By enhancing individual perspectives through the study of visual arts, their local and world connections were extended, and environmental and societal concerns evolved. In addition, the communicative opportunities that visual arts provided for these students in terms of personal expression provided emotional health and paths of personal discovery. Through the participants' production of artwork with the many stages this involves, combined with insight into their needs, the participants relayed miportant suggestions for programming enhancements and educational settmgs lor \ isiial arts classrooms. These suggestions are meaningful for educators and curriculum developers of the future.

Conformational analysis of antibody binding site using EDMA methods /

Euclidean distance matrix analysis (EDMA) methods are used to distinguish whether or not significant difference exists between conformational samples of antibody complementarity determining region (CDR) loops, isolated LI loop and LI in three-loop assembly (LI, L3 and H3) obtained from Monte Carlo simulation. After the significant difference is detected, the specific inter-Ca distance which contributes to the difference is identified using EDMA.The estimated and improved mean forms of the conformational samples of isolated LI loop and LI loop in three-loop assembly, CDR loops of antibody binding site, are described using EDMA and distance geometry (DGEOM). To the best of our knowledge, it is the first time the EDMA methods are used to analyze conformational samples of molecules obtained from Monte Carlo simulations. Therefore, validations of the EDMA methods using both positive control and negative control tests for the conformational samples of isolated LI loop and LI in three-loop assembly must be done. The EDMA-I bootstrap null hypothesis tests showed false positive results for the comparison of six samples of the isolated LI loop and true positive results for comparison of conformational samples of isolated LI loop and LI in three-loop assembly. The bootstrap confidence interval tests revealed true negative results for comparisons of six samples of the isolated LI loop, and false negative results for the conformational comparisons between isolated LI loop and LI in three-loop assembly. Different conformational sample sizes are further explored by combining the samples of isolated LI loop to increase the sample size, or by clustering the sample using self-organizing map (SOM) to narrow the conformational distribution of the samples being comparedmolecular conformations. However, there is no improvement made for both bootstrap null hypothesis and confidence interval tests. These results show that more work is required before EDMA methods can be used reliably as a method for comparison of samples obtained by Monte Carlo simulations.

Enhancing pnemonia surveillance in acute care facilities in post SARS era : a Canadian hospital surveillance study, 2003-2004 influenza season

A retrospective study of patients hospitalized with influenza and/or pneumonia in a Niagara area community hospital for the influenza season 2003-04 was designed with the main goal of enhancing pneumonia surveillance in acute care facilities and the following specific objectives: 1) identify etiologies, factors, and clinical presentation associated with pneumonia; 2) assess the ODIN score on ICU patients to predict outcomes of severe pneumonia; 3) identify the frequency of pneumonia and influenza in a hospital setting; and 4) develop a hospital pneumonia electronic surveillance tool. A total of 172 patients' charts (50% females) were reviewed and classified into two groups: those with diagnosis of pneumonia (n=132) and those without pneumonia (n=40). The latter group consisted mainly of patients with influenza (85%). Most patients were young (<10yrs) or elderly (>71yrs). Presenting body temperature <38°C, cough symptoms, respiratory and cardiac precomorbidities were common in both groups. Pneumonia was more frequent in males (p= .032) and more likely community-acquired (98%) than nosocomial (2%). No evidence of ventilator-associated pneumonia was found. Microbiology testing in 72% of cases detected 19 different pathogens. In pneumonia patients the most common organisms were Streptococcus pneumoniae (3%), Respiratory syncytial virus (4%), and Influenza A virus (2%). Conversely, Influenza A virus was identified in 73% of non-pneumonia patients. Community-acquired influenza was more common (80%) than nosocomial influenza (20%). The ODIN score was a good predictor of mortality and the new electronic surveillance tool was an effective prototype to monitor patients in acute care, especially during influenza season. The results of this study provided baseline data on respiratory illness surveillance and demonstrated that future research, including prospective studies, is warranted in acute care facilities.

Athletic injury care training in high school coaches

The purpose of this qualitative study was to understand the client and occupational therapist experiences of a mental health group. A secondary aim was to explore the extent to which this group seemed to have reflected a client-centred approach. The topic emerged from personal and professional issues related to the therapist as teacher and to inconsistencies in practice with the profession's client-centred philosophy. This philosophy, the study's frame of reference, was established in terms of themes related to the client-therapist relationship and to client values. Typical practice was illustrated through an extensive literature review. Structured didacticexperiential methods aiming toward skill development were predominant. The interpretive sciences and, to a lesser extent, the critical sciences directed the methodology. An ongoing support group at a community mental health clinic was selected as the focus of the study; the occupational therapist leader and three members became the key participants. A series of conversational interviews, the . core method of data collection, was supplemented by observation, document review, further interviews, and fieldnotes. Transcriptions of conversations were returned to participants for verification and for further reflection Analysis primarily consisted of coding and organizing data according to emerging themes. The participants' experiences of group, presented as narrative stories within a group session vignette, were also returned to participants. There was a common understanding of the group's structure and the importance of having "air time" within the group; however, differences in perceptions of such things as the importance of the group in members' lives were noted. All members valued the therapeutic aspects of group, the role of group as weekly activity and, to a lesser extent, the learning that came from group. The researcher's perspective provided a critique of the group experience from a client-centred perspective. Some areas of consistency with client-centred practice were noted (e.g., therapist attitudes); however the group seemed to function far from a client-centred ideal. Members held little authority in a -relationship dominated by the leaders, and leader agendas rather than member values controlled the session. Possible reasons for this discrepancy ranging from past health care encounters through to co-leader discord emerged. The actual and potential significance of this study was discussed according to many areas of implications: to OT practice, especially client-centred group practice, to theory development, to further areas of research and methodology considerations, to people involved in the group and to my personal growth and development.

Creativity and the working artist/teacher : the relationships

The purpose of this qualitative study was to understand the relationships between creativity and the working artist/teacher employed by an art college. The topic emerged from my job as an instructor at The Ontario College of Art which was used as the primary data resource and provided the highest caliber of professionals to chose from. Existent data were used to facilitate the study generated by the research of Cawelti, Rappaport, and Wood (1992). The data were generated by a group of 5 faculty members from The University of Northern Iowa, recognized for their expertise in the arts (a painter, a poet, a sculptor, a novelist, and a photographer). They were asked to respond to the following statement: "In as much detail as you like, list the things that you did, thought, or felt the last time you created an artistic product. II Cawelti, Rappaport, and Wood (1992) produced three models of the creative process, each building on the previous, with the resultant third,being in my opinion, an excellent illustration (text/visual) of the creative process. Model three (Appendix D) presented a "multi-dimensional view of the creative process: time, space, observatility, and consciousnessll (p. 90). Model three utilized a visual mapping device along the bottom of the page linked to text segments above. Both the visual and the text were interrelated so that they harmonized into a comprehensive "picture." The parti'cipants of this qualitative study were asked to consider model three from their professional perspective as artist/teachers. The interpretive sciences directed the methodology. The hermeneutic circle of continuous reflection from the whole to the part and back to the whole was an important aspect of the data analyses. Four members of the Foundation Department at The Ontario College of Art were the key participants. A series of conversational interviews was the primary source of data collection, this was augmented by observation, fie,ldnotes, and follow up telephone interviews. Transcripts of interviews were returned to participants for reflection and the telephone was used to discuss any additional -points raised. Analysis consisted of coding and organizing data according to emerging themes. These themes formed the basis for the narrative stories. The text of the narrative stories were given back to each participant for further comment. Revisions were made until both the researcher and the participants felt that the stories reflected reality. The resultant whole was critiqued from the researcher's perspective. The significance of this study was discussed as it pertains to the working artist/teacher and areas in need of further study are pointed out.

Molecular cloning restriction enzyme analysis, bovine adenovirus type 2 genome

Adenoviruses are non-enveloped icosahedral-shaped particles which possess a double-stranded DNA genome. Currently, nearly 100 serotypes of adenoviruses have been identified, 48 of which are of human origin. Bovine adenoviruses (BAVs), causing both mild respiratory and/or enteral diseases in cattle, have been reported in many countries all over the world. Currently, nine serotypes of SAVs have been isolated which have been placed into two subgroups based on a number of characteristics which include complement fixation tests as well as the ability to replicate in various cell lines. Bovine adenovirus type 2 (BAV2), belonging to subgroup I, is able to cause pneumonia as well as pneumonic-like symptoms in calves. In this study, the genome of BAV2 (strain No. 19) was subcloned into the plasmid vector pUC19. In total, 16 plasmids were constructed; three carry internal San fragments (spanning 3.1 to 65.2% ), and 10 carry internal Pstl fragments (spanning 4.9 to 97.4%), of the viral genome. Each of these plasmids was analyzed using twelve restriction endonucleases; BamHI, CiaI, EcoRl, HiOOlll, Kpnl, Noll, NS(N, Ps~, Pvul, Saj, Xbal, and Xhol. Terminal end fragments were also cloned and analyzed, sUbsequent to the removal of the 5' terminal protein, in the form of 2 BamHI B fragments, cloned in opposite orientations (spanning 0 to 18.1°k), and one Pstll fragment (spanning 97.4 to 1000/0). These cloned fragments, along with two other plasmids previously constructed carrying internal EcoRI fragments (spanning 20.6 to 90.5%), were then used to construct a detailed physical restriction map using the twelve restriction endonucleases, as well as to estimate the size of the genome for BAV2(32.5 Kbp). The DNA sequences of the early region 1 (E1) and hexon-associated gene (protein IX) have also been determined. The amino acid sequences of four open reading frames (ORFs) have been compared to those of the E1 proteins and protein IX from other Ads.

Native women, theory and research : contexts and contestations

In this thesis I outline a critical approach to interpreting the considerable academic literature on Aboriginal women in North America. I locate the scholarship concerning Native women within an understanding of three developments related to a philosophy of science: (I) paradigmatic shifts concerning the philosophy of science, (2) materialist-idealist debates and (3) transitions in feminist theory characterized by what is tenned the shift from second to third wave feminism. My exploration of emergent themes suggests that the elements indicated above provide overlapping frameworks within which most scholarship about Indigenous women is positioned. I illustrate my finding that employing critical discourse analysis and postcolonial feminism as both method and theory provides a useful approach in attending to intersecting experiences of 'race, class, and gender.' I view these intersecting experiences as central to the socio-political positioning of Indigenous women within contemporary feminist theorizing. I conclude my thesis by reflecting on the conceptual struggles I experienced in fonnulating and organizing the thesis and the significance of my underlying epistemological position and value-orientation as both a feminist and Native woman.

Disrupting heterosexual space? : the implementation of a campus Positive Space Campaign

Drawing on a growing literature on the interconnection of queer theory, sexuality and space, this thesis critically assesses the development, implementation and impact of a campus-based Positive Space Campaign aimed at raising the visibility and number of respectful, supportive, educational and welcoming spaces for lesbian, gay, bi, trans, two-spirited, queer and questioning (LGBTQ) students staff and faculty. The analysis, based on participatory action research (PAR), interrogates the extent to which the Positive Space Campaign challenges heteronormativity on campus. I contend that the Campaign, in its attempt to challenge dominant notions of sex, gender and sexuality, disrupts heterosexual space. Further, as I consider the meanings of 'queer', I consider the extent to which Positive Space Campaigns may be 'queering' space, by contributing to an 'imagined' campus space free of sexual and gender-based discrimination. The case study contributes to queer theory, the literature on sexuality and space, the literature on queer organizing in educational spaces and to broader queer organizing efforts in Canada.

Occupational therapist and client experiences of a mental health group

The purpose of this qualitative study was to understand the client and occupational therapist experiences of a mental health group. A secondary aim was to explore the extent to which this group seemed to have reflected a client-centred approach. The topic emerged from personal and professional issues related to the therapist as teacher and to inconsistencies in practice with the profession's client-centred philosophy. This philosophy, the study's frame of reference, was established in terms of themes related to the client-therapist relationship and to client values. Typical practice was illustrated through an extensive literature review. Structured didacticexperiential methods aiming toward skill development were predominant. The interpretive sciences and, to a lesser extent, the critical sciences directed the methodology. An ongoing support group at a community mental health clinic was selected as the focus of the study; the occupational therapist leader and three members became the key participants. A series of conversational interviews, the . core method of data collection, was supplemented by observation, document review, further interviews, and fieldnotes. Transcriptions of conversations were returned to participants for verification and for further reflection. Analysis primarily consisted of coding and organizing data according to emerging themes. The participants' experiences of group, presented as narrative stories within a group session vignette, were also returned to participants. There was a common understanding of the group's structure and the importance of having "air time" within the group; however, differences in perceptions of such things as the importance of the group in members' lives were noted. All members valued the therapeutic aspects of group, the role of group as weekly activity and, to a lesser extent, the learning that came from group. The researcher's perspective provided a critique of the group experience from a client-centred perspective. Some areas of consistency with client-centred practice were noted (e.g., therapist attitudes); however the group seemed to function far from a client-centred ideal. Members held little authority in a relationship dominated by the leaders, and leader agendas rather than member values controlled the session. Possible reasons for this discrepancy ranging from past health care encounters through to co-leader discord emerged. The actual and potential significance of this study was discussed according to many areas of implications: to OT practice, especially client-centred group practice, to theory development, to further areas of research and methodology considerations, to people involved in the group and to my personal growth and development.

The interpretation of environmental sustainability (ES) by the IOC/Olympic Games 1994-2008

The purpose of this qualitative multi-case study was to examine the interpretation of environmental sustainability (ES) within the Olympic 11 Movement. Two research questions guided the inquiry - first, how has the concept of ES been defined by the International Olympic Committee (lOC), and second, how has the concept of ES been defined and enacted by the Organizing Committees ofthe Olympic Games (OCOGs)? During the past two decades, the International Olympic Committee (lOC) established several policies and programs related to ES. Its actions reflect a broader trend of environmentalism within economic and social spheres around the world (Milton-Smith, 2002). Despite the numerous initiatives, the Olympic Games continue to cause significant environmental damage. Frey, et al. (2007) argued that the Olympic Movement contradicts the fundamental premises of ES because the Games are hosted in a two week time period, are situated in a confined area, and accumulate operating and infrastructure costs in the billions of dollars. Further, Etzion (2007) stated "there is positive and significant correlation between firm siz~ and environmental performance" (p. 642) and in the context of the Olympics the sizeimpact relation is striking. Since 1972, the year the UN launched its international environmental awareness efforts, the Summer Olympics grew to 201 nations (39% increase), 10,500 athletes (32% increase), 28 sports (30% increase), and 302 events (43% increase) (Johnson, 2004; Girginov & Parry, 2005; Upegui, 2008). The proliferation of Games activities counters the ES principles that exist within many of the IOC declarations, policies and programs.