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.

The self-management approach of health education in the treatment of chronic illnesses

Health education is essential to the successful treatment of individuals with chronic illnesses. Self-management is a philosophical model of health education that has been shown to be effective in teaching individuals with chronic arthritis to manage their illness as part of their daily lives. Despite the proven results of arthritis self-management programs, some limitations of this form of health education were apparent in the literature. The present study attempted to address the problems of the self-management approach of health education such as reasons for lack of participation in programs and poor course outcomes. In addition, the study served to investigate the relationship between course outcomes and participation in programs with the theory upon which arthritis self-management programs are based, known as self-efficacy theory. Through a combination of qualitative and quantitative methodologies, data collection, and analysis, a deeper understanding of the self-management phenomenon in the treatment of chronic arthritic conditions was established. Findings of the study confirm findings of previous studies that suggest that arthritis self-management programs result in enhanced levels of self-efficacy and are effective in teaching individuals with arthritis to self-manage their health and health care. Findings of the study suggest that there are many factors that determine the choice of participants to participate in programs and the outcomes for the individuals who do choose to participate in programs. Some of the major determinants of enrollment and outcomes of programs include: the participant's personality, beliefs, attitudes and abilities, and the degree of emotional acceptance of the illness. Other determinants of course enrollment and outcomes included class size and length of time, timing of participation, and ongoing support after the program. The results of the study are consistent with the self-management literature and confirm the relationship between the underlying philosophies of adult education and Freire's model of education and self-management.

Creating a Space for Self-Transformation: Factors of Success for Adult Literacy Learners with Specific Learning Difficulties

A significant number of adults in adult literacy programs in Ontario have specific learning difficulties. This study sought to examine the holistic factors that contributed to these learners achieving their goals. Through a case study design, the data revealed that a combination of specific learning methods and strategies, along with particular characteristics of the instructor, participant, and class, and the evidence of self-transformation all seemed to contribute to the participant's success in the program. Instructor-directed teaching and cooperative learning were the main learning methods used in the class. General learning strategies employed were the use of core curriculum and authentic documents, and using phonics, repetition, assistive resources, and using activities that appealed to various learning styles. The instructor had a history of both professional development in the area of learning disabilities as well as experience working with learners who had specific learning difficulties. There also seemed to be a goodness of fit between the participant and the instructor. Several characteristics of the participant seemed to aid in his success: his positive self-esteem, self-advocacy skills, self-determination, self-awareness, and the fact that he enjoyed learning. The size (3-5 people) and type of class (small group) also seemed to have an impact. Finally, evidence that the participant went through a self-transformation seemed to contribute to a positive learner identity. These results have implications for practice, theory, and further research in adult education.

Hyperspectral Mineral Identification using SVM and SOM

Remote sensing techniques involving hyperspectral imagery have applications in a number of sciences that study some aspects of the surface of the planet. The analysis of hyperspectral images is complex because of the large amount of information involved and the noise within that data. Investigating images with regard to identify minerals, rocks, vegetation and other materials is an application of hyperspectral remote sensing in the earth sciences. This thesis evaluates the performance of two classification and clustering techniques on hyperspectral images for mineral identification. Support Vector Machines (SVM) and Self-Organizing Maps (SOM) are applied as classification and clustering techniques, respectively. Principal Component Analysis (PCA) is used to prepare the data to be analyzed. The purpose of using PCA is to reduce the amount of data that needs to be processed by identifying the most important components within the data. A well-studied dataset from Cuprite, Nevada and a dataset of more complex data from Baffin Island were used to assess the performance of these techniques. The main goal of this research study is to evaluate the advantage of training a classifier based on a small amount of data compared to an unsupervised method. Determining the effect of feature extraction on the accuracy of the clustering and classification method is another goal of this research. This thesis concludes that using PCA increases the learning accuracy, and especially so in classification. SVM classifies Cuprite data with a high precision and the SOM challenges SVM on datasets with high level of noise (like Baffin Island).

The role of self-presentation in adolescent health risk behaviours

Self-presentation has been identified as playing a key role in the perfonnance of various potentially hazardous health behaviours such as substance abuse, eating disorders and reckless behaviours (Leary, Tchividjian, & Kraxberger, 1994; Martin & Leary, 2001; Martin, Leary, & O'Brien, 2001). The present study investigated the role of selfpresentation on adolescent health-risk behaviours. Specifically, this study examined the prevalence of adolescent identified health-risk behaviours rooted in self-presentational motives in youths aged 13-18 years. The current study also identified the specific images associated with these behaviours desired by youth, and the targets of these behaviours. Also, the relationship between these behaviours, and several trait measures (social physique anxiety, public-self consciousness, fear of negative evaluations, selfpresentational efficacy) of self-presentation were examined. Finally, the gender differences in health risk behaviours and self-presentational concerns were examined. Participants in the present study were 96 adolescent students, 34 male and 62 female, recruited from various private schools across Southern Ontario. Students ranged in age from 13 to 18 years for both males (M age = 15.81 years, SD = 1.49) and females (M age = 14.89 years, SD = 1.17) and ranged from grades 8 through 13. Results of the current study suggested that Canadian adolescents between the ages of 13 and 18 years participated in health risk behaviours for self-presentational purposes. Drinking alcohol, skipping school, and performing stunts and dares were identified as the most common health risk behaviours performed for self-presentational purposes by both males and females. Appearing fun and cool were the most commonly reported desired images while appearing brave and mature were the least reported. The most desired target group cited was same sex friends, followed by other sex friends. Trait measures of self-presentational concerns identified females as being higher in public self-consciousness, and social physique anxiety than males. Males were found to be higher in self-presentational efficacy than females. The total number of health risk behaviours was predicted by selfpresentational efficacy and social physique anxiety for males, and social physique anxiety for females. Findings of the current study suggest that Canadian adolescents' health risk behaviours are rooted, in part, in self-presentational motives. Thus far, an educational approach to health interventions has been favoured and/or adopted by teachers, health promoters, and educators (Jessor, 1992). Implications of the current study suggest that although educational interventions are beneficial in presenting the associated risks with certain activities and/or behaviours, one reason this type of approach may be ineffective in changing adolescent behaviour over the long run is that it does not address the strong and prominent influences of interpersonal motives on health damaging behaviour. It is evident that social acceptance and public image are of importance to adolescents, and the desire to make the "right" impression and to achieve peer approval and acceptance often override health and safety concerns (Jessor, 1992). Thus, a self-presentational approach focusing on changing the images associated with the behaviours may be more successful at deterring adolescent health risk behaviours.

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.

Aerobic exercise in adolescence : self-efficacy and stage of change

The purpose of this cross-sectional exploratory study was to examine the relationships among self-efficacy, stage of change, and exercise behaviour in a sample of younger (Grade 9) and older (Grade 12) adolescents. A secondary objective of this study was to apply the transtheoretical model of Stage of Change, as a measure of intention to change, in order to discover the applicability of the model to an adolescent cohort in relation to exercise behaviour. This five-stage model is a self-report measure of an individual's readiness to adopt a new behaviour (e.g., regular exercise). The transtheoretical model incorporates Bandura's self-efficacy factor, which is purported to be a predictive measure of exercise behaviour and a covariant of stage. Exercise behaviour was measured with the Physical Activity Scale, and the University of Rhode Island Change Assessment Scale (URleA) was used to measure the stage of change and self-efficacy variables. The results of this study indicated significant differences between younger and older adolescents, and between males and females in their exercise behaviour. No significant differences were found for grade and gender on stage of change as measured by either a single-item question or a continuous measure of stage. Although grade and gender subgroups were not significantly different in their self-efficacy, significant interaction was found in the grade*gender variable.

Co-operative education and the development of self-esteem, an internal locus of control and work habits

This study compared approximately 50 grade 12 students studying In th~ co-operative education mode with approximately 50 grade 12 students studying in a traditional English course. Measures of self-esteem, locus of control and work habits were compared before and at the conclusion of one semester's involvement in the different programs. Using Coopersmith's Self-Esteem Inventory, the students who had chosen to study in the co-operative education mode scored significantly higher than the students in the traditional course. At the end of the semester, the co-operative education students' scores remained significantly higher than the English students'. Although the test showed no sjgnifi~ant changes in self-esteem. anecdotal reports indicated that co-operative education students had increased self-esteem over the semester. No significant differences in locus of control were observed between the two groups at any time. Significant differences in work habits were observed. While both groups had the same number of absences and the same marks before taking these courses, students who were involved in co-operative education had significantly fewer absences and significantly higher marks than the students studying in the traditional course. Anecdotal reports also indicated an improv~ment in work habits for students who had been involved in co-operative education. Recommendations of the study are for further research to determine more exactly how self-esteem and work habits develop in co-operative education students. Also. students. parents, teachers. and administrators need to be made aware of the success of this program.

Evaluation of self-esteem before and after preceptorship experience for student nurses

seventy-eight diploma nursing students participated (from a class of 112 students) in completing the Coopersmith Self-Esteem Inventory administered by mailed questionnaire before and at the end of the preceptorship. Also a rating form was completed by 70 preceptors to determine how the observed level of self-confidence compared to self-reported self-esteem at the end of the preceptorship program. As well, four preceptors and five preceptees completed weekly diaries and six preceptors and six preceptees participated in weekly phone interviews with the investigator. Overall, self-esteem went up after the preceptorship. A comparison was made between the pretest and posttest using the t-test (dependent paired samples). Significant difference (p=.05) was demonstrated. Self-confidence ratings by preceptors were inaccurate as they had no relation to the self-reported self-esteem level of students. The diaries and interviews of preceptors and preceptees were a rich source of data as well.

The convergence of psychopathy, self-rated vulnerability, and other-rated vulnerability

Previous research has found that victims of crime tend to exhibit asynchronous movement (e.g. Grayson & Stein, 1981), and the fact that victims display different body language suggests that they may be sending inadvertent signals to their own vulnerability (e.g. Murzynski & Degelman, 1996). Body language has also be en linked with s e l f identification as a victim (Wheeler et aI., 2009), and self-identification has be en found to act as a proxy for more severe victimization (Baumer, 2002) and greater fear of crime (Greenberg & Beach, 2004). The first prediction in the present study, then, was that self-perceived vulnerability would be correlated with body language, while number of previous victimizations mayor may not show the same relationship. Findings from the present study indicate that self-perceived vulnerability exhibits a positive correlation with the body language cues that approaches significance r (10) = .45,p =.07, one-tailed. Different types of victimization, however, were not significantly correlated with these cues. A second goal of the study was to examine the relationship between psychopathic traits and accuracy in judgments of vulnerability. Seventy male participants rated the vulnerability of 12 female targets filmed walking down a hallway who had provided selfratings of vulnerability. Individuals scoring higher on Factor 2 and total psychopathy were significantly less discrepant from target self-rat~ngs of vulnerability, r (64) = - .39,p < .001; r (64) = - .29,p >.01, respectively. The final purpose of this study was to determine which body language cues were mos t salient to raters when making judgments of vulnerability. Participants rated the apparent vulnerability of a target in 7 video clips portraying each body language cue in isolation and a natural walk. Results of repeated measures analyses indicate that the videos rated as most vulnerable to victimization were those displaying low energy and l a ck of synchrony, followed by wide stride, short stride, and stiffknees, while the video displaying ne ck stiffness did not receive significantly different ratings from the mode l ' s natural walk. Replication with a larger sample size is necessary to increase confidence in findings and implications.