HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

The Influence of Attentional Focus on the Self-Efficacy-Performance Relationship in a Continuous Running Task

The self-efficacy-performance relationship in continuous sport tasks has been shown to be significantly reciprocal yet unequal with stronger influences in the performance-to-self-efficacy pathway rather than self-efficacy-to-performance pathway (e.g., LaForge-MacKenzie & Sullivan, 2014b). Bandura (2012) suggested that sociocognitive variables may influence this relationship. Attention as a sociocognitve factor may bias the processing of performance and self-efficacy information (Bandura, 1982, 1997; Bandura & Jourden, 1991). As confidence and attention are important aspects of peak running performance (Brewer, Van Raalte, Linder, & VanRaalte, 1991), the primary purpose of the present study was to examine the self-efficacy-performance relationship under three conditions of attentional focus. The secondary purpose was to examine self-efficacy and performance as separate constructs under the same conditions of attention. Participants ran continuously for one kilometer in one of three randomly assigned attentional focus conditions: internal-focus (n = 51), external-focus (n = 50), and control (n = 49). Self-efficacy was assessed using a one-item measure every 200 meters. Path analyses examining the primary objective revealed significant self-efficacy-to-performance pathways in all conditions: external-focus (p < .05, βs ranging from -.17 to -.32), internal-focus (p < .05, βs ranging from -.26 to -.36), and control (p < .05, βs ranging from -.29 to -.42). Significant reciprocal relationships were absent in all conditions. ANOVAs examining the secondary objectives found significantly faster performance in the control condition at the start (F (2, 147) = 3.86, p < .05) and end of the task (F (2, 147) = 3.56, p < .05). Self-efficacy was significantly higher in the internal-focus condition at the end of the task (Self-Efficacy 4 (F (2, 147) = 3.21, p < .05) and Self-Efficacy 5 (F (2, 147) = 4.74, p < .05). In contrast to previous within-trial research (e.g., LaForge-MacKenzie & Sullivan, 2014b) self-efficacy-to-performance effects were more significant and robust than performance-to-self-efficacy effects. These results provided support for Bandura’s (2012) suggestion that sociocognitive factors may have the ability to alter the causal structure of the self-efficacy-performance relationship, proposing complexities in the self-efficacy-performance relationship (Sitzmann &Yeo, 2013). Results were discussed from both theoretical and applied perspectives.

Drivers of Local Firms’ Focus on Internal R&D in Emerging Economies and Their International Performance

Grounded on the resource-based view of the firm, the study of this thesis investigates the effect of four internal and external factors – engineer intensity, location, affiliation with the government, government funding – on Chinese firms’ decision to either invest in internal R&D activities or external R&D and the effect of this decision on the firms’ international market success. In addition, the moderating role of the presence of foreign firms in China is examined. To understand these relationships, the thesis’ theorization focuses on the issue of how firms can combine optimally the two options – “internal R&D” and “external R&D”. In this regard I juxtapose internal R&D and external R&D and compare their advantages and disadvantages. To test my model, I apply panel data from the Annual Industrial Survey Database provided by the Chinese National Bureau of Statistics. My results show that three of the four investigated factors affect Chinese firms’ resource allocation decisions; and effective resource allocation decisions lead effectively to international market success, strengthened by the presence of foreign firms in China. Moreover the findings bear several theoretical and managerial contributions. First I propose the last dimension of the “VRIO framework” – “organization” – as an endogenous component of the VRIO framework, as my study investigated how firms can effectively combine resources to generate a competitive advantage in terms of international market success. Previous academic literature so far focused on examining whether internal and external R&D are complements or substitutes. My study fills a gap in the literature by investigating the determinants of the efficient combination of the two strategies and the outcome of the combination. One of the managerial implications is that Chinese firms can learn from foreign companies that are present in China.

Riffing on a Theme: Faculty Experiences With Service-Learning in a Food Security Research Network in Ontario

While service-learning is often said to be beneficial for all those involved—students, community members, higher education institutions, and faculty members—there are relatively few studies of the attraction to, and effect of, service-learning on faculty members. Existing studies have tended to use a survey design, and to be based in the United States. There is a lack of information on faculty experiences with service-learning in Ontario or Canada. This qualitative case study of faculty experiences with service-learning was framed through an Appreciative Inquiry social constructionist approach. The data were drawn from interviews with 18 faculty members who belong to a Food Security Research Network (FSRN) at a university in northern Ontario, reports submitted by the network, and personal observation of a selection of network-related events. This dissertation study revealed how involvement with service-learning created opportunities for faculty learning and growth. The focus on food security and a commitment to the sustainability of local food production was found to be an ongoing attraction to service-learning and a means to engage in and integrate research and teaching on matters of personal and professional importance to these faculty members. The dissertation concludes with a discussion of the FSRN’s model and the perceived value of a themed, transdisciplinary approach to service-learning. This study highlights promising practices for involving faculty in service-learning and, in keeping with an Appreciative Inquiry approach, depicts a view of faculty work at its best.

The Impact of Directed Mirror Focus and Technique Cues on Psychological, Cognitive and Emotional Exercise Correlates in an Introductory Weight Training Orientation

The purpose of the study was to investigate whether teaching inactive and low active women to use mirrors for form and technique purposes could lessen the negative impact of mirrors on self-presentational concerns, affect, and self-efficacy. Eligible women (N = 82) underwent a one-on-one weight training orientation with a personal trainer. Participants were randomized into one of four experimental groups, each unique in the type of feedback (general or technique-specific) and the degree of focus on the mirror for technique reinforcement. Questionnaires assessed study outcomes pre- and post-orientation. Results indicated groups did not significantly differ on any post-condition variables, when controlling for pre-condition values (all p’s >.05). All groups showed outcome improvements following the orientation. This suggests that during a complex task, a personal trainer who emphasizes form and technique can facilitate improvements to psychological outcomes in novice exercisers, independent of the presence of mirrors or directional cues provided.

What happens in the first 200 ms of word reading : ERP studies on visual word recognition with top-down and bottom-up approaches /

In this thesis, three main questions were addressed using event-related potentials (ERPs): (1) the timing of lexical semantic access, (2) the influence of "top-down" processes on visual word processing, and (3) the influence of "bottom-up" factors on visual word processing. The timing of lexical semantic access was investigated in two studies using different designs. In Study 1,14 participants completed two tasks: a standard lexical decision (LD) task which required a word/nonword decision to each target stimulus, and a semantically primed version (LS) of it using the same category of words (e.g., animal) within each block following which participants made a category judgment. In Study 2, another 12 participants performed a standard semantic priming task, where target stimulus words (e.g., nurse) could be either semantically related or unrelated to their primes (e.g., doctor, tree) but the order of presentation was randomized. We found evidence in both ERP studies that lexical semantic access might occur early within the first 200 ms (at about 170 ms for Study 1 and at about 160 ms for Study 2). Our results were consistent with more recent ERP and eye-tracking studies and are in contrast with the traditional research focus on the N400 component. "Top-down" processes, such as a person's expectation and strategic decisions, were possible in Study 1 because of the blocked design, but they were not for Study 2 with a randomized design. Comparing results from two studies, we found that visual word processing could be affected by a person's expectation and the effect occurred early at a sensory/perceptual stage: a semantic task effect in the PI component at about 100 ms in the ERP was found in Study 1 , but not in Study 2. Furthermore, we found that such "top-down" influence on visual word processing might be mediated through separate mechanisms depending on whether the stimulus was a word or a nonword. "Bottom-up" factors involve inherent characteristics of particular words, such as bigram frequency (the total frequency of two-letter combinations of a word), word frequency (the frequency of the written form of a word), and neighborhood density (the number of words that can be generated by changing one letter of an original word or nonword). A bigram frequency effect was found when comparing the results from Studies 1 and 2, but it was examined more closely in Study 3. Fourteen participants performed a similar standard lexical decision task but the words and nonwords were selected systematically to provide a greater range in the aforementioned factors. As a result, a total of 18 word conditions were created with 18 nonword conditions matched on neighborhood density and neighborhood frequency. Using multiple regression analyses, we foimd that the PI amplitude was significantly related to bigram frequency for both words and nonwords, consistent with results from Studies 1 and 2. In addition, word frequency and neighborhood frequency were also able to influence the PI amplitude separately for words and for nonwords and there appeared to be a spatial dissociation between the two effects: for words, the word frequency effect in PI was found at the left electrode site; for nonwords, the neighborhood frequency effect in PI was fovind at the right elecfrode site. The implications of otir findings are discussed.

Attention focus and balance control in young and older adults

This thesis investigated attention focus and balance control in eighteen healthy young adults and eighteen healthy older adults. All participants performed sixteen consecutive trials of a balance task which involved standing for 30-s on an unstable platform that could rotate only in the roll direction. There were no attention focus instructions provided on any of the sixteen trials. Following the completion of the initial and final attempt in the series, participants reported "where" their attention had been focused when performing the task. The results showed differences in balance between young and older adults and improvements in balance with practice in both young and older adults. However, there were no differences in attention focus strategies between young and older adults. Both age groups directed attention to multiple sources during the balance task. An equal focus on internal (i.e., feet, trunk, and other body parts) and external (i.e., the platform) sources with little focus on events not related to the task dominated on the first attempt of the balance task. Focus on internal sources was maintained and focus on events not related to the task increased at the expense of focus on external sources on the final attempt of the balance task. Following the series of sixteen trials to establish "natural" attention focus, participants performed three randomly presented trials, each with specific attention focus instructions (i.e., think about minimizing movements of the feet, the trunk, or the platform). The results showed that, in contrast to the literature, instructions to focus on an internal source, the trunk, actually augmented control of the task as reflected in reduced trunk sway whereas instructions to focus on an internal source, the feet, or an external source, the platform, did not benefit performance on the task. Thus, the distance fi-om the interaction point of the body with the external source is critical and may not depend on whether the source is internal or external. Thus, a global attention focus instruction may not be beneficial and the nature of the task should be considered when adopting attention focus instructions for young and older adults.

Understanding space, place and leisure of women over 85 living in the community

There is an increase in the number of older adults 85 and over, who are choosing to live alone within the community. Moreover, older adults who live alone are reportedly spending an extensive amount of time alone within the home environment. In an effort to provide additional support and resources to older adults living in the community, a compliment of services are being offered through public and private organizations. These in-home supports focus on the instrumental or functional tasks of daily living, such as personal and rehabilitative care, nourishment, maintenance and upkeep of the home, as well as volunteer social visitation. However leisure resources and programs are not included among these services. Consequently, this creates a gap in leisure provision among this segment of the population. Throughout the life course, an individual's identity, role and purpose are developed and sustained through instrumental work roles in the formal and informal sector, as well as through personally meaningful leisure pastimes and experiences. Although roles shift post retirement, participation in instrumental and expressive activities can provide opportunities through which older adults are able to fulfill their need for agency (individuality and autonomy) and affiliation (social relatedness). Therefore barriers that inhibit instrumental or leisure experiences can negatively impact older adults' quality of life. This study explored the leisure lifestyles of four older adults, all of whom were over 85, lived alone within the community and were oriented to person, time and place. It became apparent that participants ordered their lives around a routine that consisted of instrumental, expressive and socially integrated tasks and activities. Moreover participants purposely chose to remain at home because their home environment facilitated freedom, choice and independence. As a result all four participants viewed their independence within the home as a critical determinant to their overall quality of life. Challenges associated with the home environment, participants' personal capacities and relationships were negotiated on a daily basis. Failure to positively adapt to these challenges inhibited meaningful engagement and personal fulfillment. Traditionally, leisure service delivery has been offered within institutions and through various community based venues. As a result leisure provision has been focused on the needs of the frail elderly who reside in institutions or the well elderly who are able to access leisure amenities within the community. However the growing number of older adults electing to live alone is on the rise. As individuals age the home becomes the preferred context for leisure experiences. If older adults are choosing to live alone, then both their instrumental and leisure needs must be addressed. As a result, it is imperative that leisure professionals extend the scope of service delivery to include home centered older adults.

Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

Examining the inclusion experiences of students with intellectual disabilities : a study focusing on the transition from elementary to secondary school

Transitioning from elementary to secondary school is a major event in adolescents' lives and can be associated with academic, social, and emotional challenges (Shaffer, 2005; Sirsch, 2003). Considerably less research has focused on the transitional experiences of students with intellectual disabilities (lD) as they enter secondary school and the role of educational inclusion in this process (Noland, Cason, & Lincoln, 2007). Conceivably, students with ID who leave inclusive elementary schools, where they have been educated alongside their peers without ID, and who enter segregated secondary educational placements may experience unique social and emotional challenges (Farmer, Pearl, & Van Acker, 1996; Fryxell & Kennedy, 1995; Shaffer, 2005). This study examined the transitional experiences of 6 students with ID and the role of educational inclusion, with a focus on elementary to secondary school transitions from inclusive to segregated settings and vice versa. This study included the collection of multiple sources of data. Semi-structured interviews with 6 caregivers and students with ID were conducted. Students' Individual Education Transitional Plans were discussed in caregivers' interviews to determine how they shaped students' educational inclusion experiences (Ontario Ministry of Education & Training, 1999/2000/2004). Parts ofthe following questionnaires were "qualitized" (Tashakkori & Teddlie, 1998) and administered orally: "Youth Self-Report" (YSR; Achenbach, 2001 c) and "Child Behaviour Checklist Caregivers Form" (CBLC/6-18; Achenbach, 200la). The findings of this study contribute to the literature on educational inclusion by highlighting the positive/negative social and emotional impact of congruent and incongruent transitional experiences of students with ID and the role of educational inclusion.

Search engine advertising in web retailing : an efficiency analysis

This study examines the efficiency of search engine advertising strategies employed by firms. The research setting is the online retailing industry, which is characterized by extensive use of Web technologies and high competition for market share and profitability. For Internet retailers, search engines are increasingly serving as an information gateway for many decision-making tasks. In particular, Search engine advertising (SEA) has opened a new marketing channel for retailers to attract new customers and improve their performance. In addition to natural (organic) search marketing strategies, search engine advertisers compete for top advertisement slots provided by search brokers such as Google and Yahoo! through keyword auctions. The rationale being that greater visibility on a search engine during a keyword search will capture customers' interest in a business and its product or service offerings. Search engines account for most online activities today. Compared with the slow growth of traditional marketing channels, online search volumes continue to grow at a steady rate. According to the Search Engine Marketing Professional Organization, spending on search engine marketing by North American firms in 2008 was estimated at $13.5 billion. Despite the significant role SEA plays in Web retailing, scholarly research on the topic is limited. Prior studies in SEA have focused on search engine auction mechanism design. In contrast, research on the business value of SEA has been limited by the lack of empirical data on search advertising practices. Recent advances in search and retail technologies have created datarich environments that enable new research opportunities at the interface of marketing and information technology. This research uses extensive data from Web retailing and Google-based search advertising and evaluates Web retailers' use of resources, search advertising techniques, and other relevant factors that contribute to business performance across different metrics. The methods used include Data Envelopment Analysis (DEA), data mining, and multivariate statistics. This research contributes to empirical research by analyzing several Web retail firms in different industry sectors and product categories. One of the key findings is that the dynamics of sponsored search advertising vary between multi-channel and Web-only retailers. While the key performance metrics for multi-channel retailers include measures such as online sales, conversion rate (CR), c1ick-through-rate (CTR), and impressions, the key performance metrics for Web-only retailers focus on organic and sponsored ad ranks. These results provide a useful contribution to our organizational level understanding of search engine advertising strategies, both for multi-channel and Web-only retailers. These results also contribute to current knowledge in technology-driven marketing strategies and provide managers with a better understanding of sponsored search advertising and its impact on various performance metrics in Web retailing.

Adult Participants’ Experiences of a Sport Program Implementing the Easy-Play Model: Implications for an Active Lifestyle

The Easy-Play Model is a useful framework for facilitating sport among a diverse group of participants of different ages and ability levels. The model’s focus on de-emphasizing competitiveness in an effort to establish an optimally competitive environment has facilitated positive play experiences. This study investigated the experiences of players who have been a part of a weekly soccer program implementing the Easy-Play Model. In-depth interviews of 8 participants provided insight concerning the benefits and weaknesses of the approach and the notable experiences of the players. Results provided data confirming the model’s effectiveness in facilitating positive social interactions, safe play experiences where injury is generally a negligible concern, and productive opportunities to be physically active through sport. This study of the Easy-Play Model sets the foundation for future research which should further add to our understanding of productive ways to engage people in physical activity through sport.

Effects of Instruction on Walking and Turning Performance in Individuals with Parkinson's Disease

Parkinson’s disease (PD) is characterized by postural instability and gait impairment. Verbal instructions can reduce postural sway and improve gait performance in PD. For gait, this evidence is limited to unobstructed straight-path walking. As falls in PD often occur when turning, the purpose of this thesis was to determine if instructions can benefit turning performance in this population. Twelve individuals with PD performed two walking tasks (normal walking, walking with a 180 degree turn) under four instruction conditions (no instruction, take big steps, make larger trunk movements, focus on end and/or turn point). Task duration and trunk yaw and roll sway were calculated. In general, the results demonstrated that the instruction to take big steps improved performance for both tasks compared to providing no instruction or externally based instruction. These results suggest that instructions related to step amplitude may facilitate walking and turning performance in PD.

Effect of increased milk intake combined with endurance exercise training on body composition, blood-lipids and inflammatory markers in overweight young males

Consuming low-fat milk (LFM) after resistance training leads to improvements in body composition. Habitual aerobic exercise and dairy intake are relatively easy lifestyle modifications that could benefit a population at risk for becoming obese. Thus, the purpose of this study was to investigate combining increased LFM intake with endurance exercise on body composition, blood-lipid profile and metabolic markers. 40 young males were randomized into four groups: one ingesting 750mL LFM immediately post-exercise, the other 6hrs post-exercise; and two isocaloric carbohydrate groups ingesting at the two different times. Participants completed a 12 week endurance-training program (cycling 1 hour/day at ~60%VO2peak, 5 days/week). 23 participants completed the study. Increases in lean mass (p < 0.05), and decreases in anti-inflammatory marker adiponectin (p < 0.05) were seen in all groups. No other significant changes were observed. Future analyses should focus on longer duration exercise and include a larger sample.

Geographical Applications for Sound Walks

Geography has long been a predominantly visual discipline, but recent work in geography has sought to explore the multisensory, embodied, emotional and affective dimensions of people’s relations with places. One way to engage this type of exploration is through the use of sound walks: walks along a specified route accompanied by a soundtrack (on headphones or stationary speakers) that conveys information, enacts a story, produces an ambience or atmosphere, or illuminates certain aspects of the environment through which the listener is walking. This thesis aims to show how geographers can benefit from using sound walks as thinking tools, representational tools and teaching tools. Drawing on my own experiences producing sound walks, I first examine the ways that sound walk production processes help generate productive geographical thinking for those producing sound walks (Chapter Two). The various stages of producing a sound walk require different skill sets, pose different challenges, and require different sorts of environmental awareness, and therefore present novel opportunities for developing geographical insights about specific places or spatial relations. Second, I focus on four experientially-oriented aspects of sound walks – using multiple senses, walking, contingency, and moments of interaction – to argue that sound walks can be useful representational tools for geographers, whether those creating sound walks subscribe to a representational or non-representational theory of knowledge (Chapter Three). The value of sound walks as representational tools is in the experience of ‘doing’ them. That is, audiences discover for themselves through interaction what is being represented, rather than having it delivered to them. The experiential elements of ‘doing’ sound walks recommend them as potentially helpful representational tools for geographers. Third, by examining the work of a small sample of fourth year “Advanced Geography of Music” students, I develop the argument that sound walks can be effective tools for teaching students and for creating circumstances for students to learn independently (Chapter Four). Sound walks have potential to be effective pedagogical tools because they are commensurate with several key pedagogical schools of thought that emphasise the importance of requiring students to engage actively with their environment using a combination of senses. The thesis demonstrates that sound walks are a worthwhile resource for geographers to use theoretically, representationally and pedagogically in their work. The next step is for geographers to put them into practice and realize this potential.