Bioinformatic analysis for exploring relationships between genes and gene products

To carry out their specific roles in the cell, genes and gene products often work together in groups, forming many relationships among themselves and with other molecules. Such relationships include physical protein-protein interaction relationships, regulatory relationships, metabolic relationships, genetic relationships, and much more. With advances in science and technology, some high throughput technologies have been developed to simultaneously detect tens of thousands of pairwise protein-protein interactions and protein-DNA interactions. However, the data generated by high throughput methods are prone to noise. Furthermore, the technology itself has its limitations, and cannot detect all kinds of relationships between genes and their products. Thus there is a pressing need to investigate all kinds of relationships and their roles in a living system using bioinformatic approaches, and is a central challenge in Computational Biology and Systems Biology. This dissertation focuses on exploring relationships between genes and gene products using bioinformatic approaches. Specifically, we consider problems related to regulatory relationships, protein-protein interactions, and semantic relationships between genes. A regulatory element is an important pattern or "signal", often located in the promoter of a gene, which is used in the process of turning a gene "on" or "off". Predicting regulatory elements is a key step in exploring the regulatory relationships between genes and gene products. In this dissertation, we consider the problem of improving the prediction of regulatory elements by using comparative genomics data. With regard to protein-protein interactions, we have developed bioinformatics techniques to estimate support for the data on these interactions. While protein-protein interactions and regulatory relationships can be detected by high throughput biological techniques, there is another type of relationship called semantic relationship that cannot be detected by a single technique, but can be inferred using multiple sources of biological data. The contributions of this thesis involved the development and application of a set of bioinformatic approaches that address the challenges mentioned above. These included (i) an EM-based algorithm that improves the prediction of regulatory elements using comparative genomics data, (ii) an approach for estimating the support of protein-protein interaction data, with application to functional annotation of genes, (iii) a novel method for inferring functional network of genes, and (iv) techniques for clustering genes using multi-source data.

Conflict and Consonance: Implementing an Evidence-Based Middle School Science Curriculum

This study is to investigate the middle school teachers’ concerns and perspectives during the implementation of an evidence-based curriculum that supports the development of both content knowledge and scientific practices. Two themes emerge from data analysis: consonance and conflict.

Mapping Transnational Crime in El Salvador: New Trends and Lessons from Colombia

Since El Salvador’s civil war formally ended in 1992 the small Central American nation has undergone profound social changes and significant reforms. However, few changes have been as important or as devastating as the nation’s emergence as a central hub in the transnational criminal “pipeline” or series of recombinant, overlapping chains of routes and actors that illicit organizations use to traffic in drugs, money weapons, human being, endangered animals and other products. The erasing of the once-clear ideological lines that drove the civil war and the ability of erstwhile enemies to join forces in criminal enterprises in the post-war period is an enduring and dangerous characteristic of El Salvador’s transnational criminal evolution. Trained, elite cadres from both sides, with few legitimate job opportunities, found their skills were marketable in the growing criminal structures. The groups moved from kidnapping and extortion to providing protection services to transnational criminal organizations to becoming integral parts of the organizations themselves. The demand for specialized military and transportation services in El Salvador have exploded as the Mexican DTOs consolidate their hold on the cocaine market and their relationships with the transportista networks, which is still in flux. The value of their services has risen dramatically also because of the fact that multiple Mexican DTOs, at war with each other in Mexico and seeking to physically control the geographic space of the lucrative pipeline routes in from Guatemala to Panama, are eager to increase their military capabilities and intelligence gathering capacities. The emergence of multiple non-state armed groups, often with significant ties to the formal political structure (state) through webs of judicial, legislative and administrative corruption, has some striking parallels to Colombia in the 1980s, where multiple types of violence ultimately challenged the sovereignty of state and left a lasting legacy of embedded corruption within the nation’s political structure. Organized crime in El Salvador is now transnational in nature and more integrated into stronger, more versatile global networks such as the Mexican DTOs. It is a hybrid of both local crime – with gangs vying for control off specific geographic space so they can extract payment for the safe passage of illicit products – and transnational groups that need to use that space to successfully move their products. These symbiotic relationships are both complex and generally transient in nature but growing more consolidated and dangerous.

Travel Marketing: Industry Relationships and Benefits

In the discussion - Travel Marketing: Industry Relationships and Benefits - by Andrew Vladimir, Visiting Assistant Professor, School of Hospitality Management at Florida International University, the author initially states: “A symbiotic relationship exists among the various segments of the travel and tourism industry. The author has solicited the thinking of 37experts and leaders in the field in a book dealing with these relationships and how they can be developed to benefit the industry. This article provides some salient points from those contributors.” This article could be considered a primer on networking for the hospitality industry. It has everything to do with marketing and the relationships between varied systems in the field of travel and tourism. Vladimir points to instances of success and failure in marketing for the industry at large. And there are points of view from thirty-seven contributing sources here. “Miami Beach remains a fitting example of a leisure product that has been unable to get its act together,” Vladimir shares a view. “There are some first class hotels, a few good restaurants, alluring beaches, and a splendid convention center, but there is no synergism between them, no real affinity, and so while visitors admire the Fontainebleau Hilton and enjoy the food at Joe's Stone Crabs, the reputation of Miami Beach as a resort remains sullied,” the author makes a point. In describing cohesiveness between exclusive systems, Vladimir says, “If each system can get a better understanding of the inner workings of neighboring related systems, each will ultimately be more successful in achieving its goals.” The article is suggesting that exclusive systems aren’t really exclusive at all; or at least they shouldn’t be. In a word – competition – drives the market, and in order for a property to stay afloat, aggressive marketing integrated with all attendant resources is crucial. “Tisch [Preston Robert Tisch, currently – at the time of this writing - the Postmaster General of the United States and formerly president of Lowe’s Hotels and the New York Visitors and Convention Bureau], in talking about the need for aggressive marketing says: “Never...ever...take anything for granted. Never...not for a moment...think that any product or any place will survive strictly on its own merits.” Vladimir not only sources several knowledgeable representatives in the field of hospitality and tourism, but he also links elements as disparate as real estate, car rental, cruise and airlines, travel agencies and traveler profiles to illustrate his points on marketing integration. In closing, Vladimir quotes the Honorable Donna Tuttle, Undersecretary of Commerce for Travel and Tourism, “Uniting the components of this industry in an effective marketing coalition that can compete on an equal footing with often publicly-owned foreign tourism conglomerates and multi-national consortia must be a high priority as the United States struggles to maintain and expand its share of a rapidly changing global market.”

Relationships: Food Safety and Organizational Behavior

A growing body of literature explores the relationship between organizational behavior and food safety in restaurants, but most findings are based on two participant observation studies which, while rick with insights, limit the generalizability of the results. This study attempts to overcome this limitation by surveying a sample of student-cooks enrolled in three South Florida culinary schools. Results indicate that restaurant managers must realize that the practice of food safety involves more than microbiology and HACCF!

Romantic Relationships and Adjustment in Early Adulthood: The Role of Cross-sex Experience in the Context of Social Norms and Support

Attachment and interpersonal theory suggest a sequential pattern of relationships beginning in the earliest stage of development and progressing to social and eventually romantic relationships. Theoretically, cross-sex experiences have an important role in the progression of interpersonal relationships. Despite the prevalence of these theories about the nature of romantic relationship development, the linkage of cross-sex experience (CSE) to romantic relationships has not been established. Indeed, it is an intuitive assumption, especially within Western society and these theories do not consider socio-cultural factors that may influence CSE and relationship satisfaction. This study addresses the varying contextual factors that may contribute to relationship satisfaction and adjustment, aside from CSE, and is divided into two parts. Study 1, addresses CSE, relationship satisfaction, and adjustment in a unique population, ultra-Orthodox Jews. Among this population, social or romantic CSE is limited and sexes are effectively segregated. Study 2, expanded the study to a larger sample of U.S. college students, to assess the linkage of CSE to romantic relationship satisfaction in a more typical Western population. It included social norm and support variables to address the contextual nature of relationship development and satisfaction. Results demonstrated clear differences in the relation between CSE and relationship satisfaction in the two samples. In the first sample CSE was unrelated to relationship satisfaction; nevertheless, relationship satisfaction was associated with adjustment as it is for more typical populations with greater CSE. These results suggested the importance of specifying how social norms and social support relate to CSE, relationship satisfaction and adjustment. The results from the second sample were consistent with the theoretical framework upon which the social/romantic literature is based. CSE was directly connected to relationship satisfaction. As anticipated, CSE, relationship satisfaction, and adjustment also varied as a function of social norms and support. These findings further validate the influence of socio-cultural factors on relationship satisfaction and adjustment. This study contributes to the romantic relationship literature and broadens our understanding of the complex nature of interpersonal and romantic relationships.

Social Decision-Making in Bonobos and Chimpanzees

Humans are natural politicians. We obsessively collect social information that is both observable (e.g., about third-party relationships) and unobservable (e.g., about others’ psychological states), and we strategically employ that information to manage our cooperative and competitive relationships. To what extent are these abilities unique to our species, and how did they evolve? The present dissertation seeks to contribute to these two questions. To do so, I take a comparative perspective, investigating social decision-making in humans’ closest living relatives, bonobos and chimpanzees. In Chapter 1, I review existing literature on theory of mind—or the ability to understand others’ psychological states—in these species. I also present a theoretical framework to guide further investigation of social cognition in bonobos and chimpanzees based on hypotheses about the proximate and ultimate origins of their species differences. In Chapter 2, I experimentally investigate differences in the prosocial behavior of bonobos and chimpanzees, revealing species-specific prosocial motivations that appear to be less flexible than those exhibited by humans. In Chapter 3, I explore through decision-making experiments bonobos’ ability to evaluate others based on their prosocial or antisocial behavior during third-party interactions. Bonobos do track the interactions of third-parties and evaluate actors based on these interactions. However, they do not exhibit the human preference for those who are prosocial towards others, instead consistently favoring an antisocial individual. The motivation to prefer those who demonstrate a prosocial disposition may be a unique feature of human psychology that contributes to our ultra-cooperative nature. In Chapter 4, I investigate the adaptive value of social cognition in wild primates. I show that the recruitment behavior of wild chimpanzees at Gombe National Park, Tanzania is consistent with the use of third-party knowledge, and that those who appear to use third-party knowledge receive immediate proximate benefits. They escape further aggression from their opponents. These findings directly support the social intelligence hypothesis that social cognition has evolved in response to the demands of competing with one’s own group-mates. Thus, the studies presented here help to better characterize the features of social decision-making that are unique to humans, and how these abilities evolved.

Essays on State-Building and Sectarian Violence

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This dissertation seeks to explain the role of governmental and non-governmental actors in increasing/reducing the emergence of intergroup conflict after war, when group differences have been a salient aspect of group mobilization. This question emerges from several interrelated branches of scholarship on self-enforcing institutions and power-sharing arrangements, group fragmentation and demographic change, collective mobilization for collectively-targeted violence, and conflict termination and the post-conflict quality of peace. This question is investigated through quantitative analyses performed at the sub-national, national, and cross-national level on the effect of elite competition on the likelihood of violence committed on the basis of group difference after war. These quantitative analyses are each accompanied by qualitative, case study analyses drawn from the American Reconstruction South, Iraq, and Cote d'Ivoire that illustrate and clarify the mechanisms evaluated through quantitative analysis.

Shared findings suggest the correlation of reduced political competition with the increased likelihood of violence committed on the basis of group difference. Separate findings shed light on how covariates related to control over rent extraction and armed forces, decentralization, and citizenship can lead to a reduction in violence. However, these same quantitative analyses and case study analysis suggest that the control of the state can be perceived as a threat after the end of conflict. Further, together these findings suggest the political nature of violence committed on the basis of group difference as opposed to ethnic identity or resource scarcity alone.

Together, these combined analyses shed light on how and why political identities are formed and mobilized for the purpose of committing political violence after war. In this sense, they shed light on the factors that constrain post-conflict violence in deeply divided societies, and contribute to relevant academic, policy, and normative questions.

Rwanda's Miracle: From Genocide and Poverty to Peace and Economic Prosperity

The purpose of this thesis was to examine how liberalization and the introduction of pro-poor policies can be successful in post-conflict countries using the Rwanda coffee market as a case study. My research supports the notion that economic development, political stability and peace can be a result of liberalization when policies that are pro-poor and focus on the largest sector of the population are created. The study examines why and how Rwanda chose to liberalize their economy in the way they did by focusing on the intentions of the actors and the effects their actions have had on the coffee market and country as a whole. The findings suggest that Rwanda’s coffee market liberalization has been successful and has contributed to stability and economic development in Rwanda. The conclusion indicates that pro-poor liberalization policies with the assistance from a variety of actors and institutions can lead developing countries on the path to development in ways the international community has not seen before.

Addressing conflict and tolerance through the curriculum

Political, religious and national divisions in Northern Ireland go back many hundreds of years so it is not surprising that the lack of a common national narrative has made the teaching of history in schools difficult. The fact that schools have largely been organized on a denominational basis has added to the challenge. When political violence broke out in the late 1960s many looked to schools to contribute to the promotion of reconciliation and the way history had been taught received significant critical attention. This chapter will outline the evolving nature of the history curriculum and review evidence on the impact of this curriculum on the historical understanding of students and young people. In addition, the chapter will briefly consider other ways in which students engage with historical issues through the teaching of citizenship, and wider family and community influences. Whereas the teaching of history in the past either was largely absent or often took on a partisan character, the development of a statutory curriculum in the 1990s helped promote a more dispassionate, skills-based approach which emphasized critical engagement with evidence and a multiperspectivity. While this represented a significant improvement on what had gone before, evaluation of the impact of this approach has highlighted the need for a consideration of the emotional impact of historical understanding and the need better to connect the lessons of history to contemporary society.

Team Member’s Centrality, Cohesion, Conflict, and Performance in Multi-University Geographically Distributed Project Teams

This study examined team processes and outcomes among 12 multi-university distributed project teams from 11 universities during its early and late development stages over a 14-month project period. A longitudinal model of team interaction is presented and tested at the individual level to consider the extent to which both formal and informal network connections—measured as degree centrality—relate to changes in team members’ individual perceptions of cohesion and conflict in their teams, and their individual performance as a team member over time. The study showed a negative network centrality-cohesion relationship with significant temporal patterns, indicating that as team members perceive less degree centrality in distributed project teams, they report more team cohesion during the last four months of the project. We also found that changes in team cohesion from the first three months (i.e., early development stage) to the last four months (i.e., late development stage) of the project relate positively to changes in team member performance. Although degree centrality did not relate significantly to changes in team conflict over time, a strong inverse relationship was found between changes in team conflict and cohesion, suggesting that team conflict emphasizes a different but related aspect of how individuals view their experience with the team process. Changes in team conflict, however, did not relate to changes in team member performance. Ultimately, we showed that individuals, who are less central in the network and report higher levels of team cohesion, performed better in distributed teams over time.

Exploring social representations of adapting to climate change using topic modeling and Bayesian networks

When something unfamiliar emerges or when something familiar does something unexpected people need to make sense of what is emerging or going on in order to act. Social representations theory suggests how individuals and society make sense of the unfamiliar and hence how the resultant social representations (SRs) cognitively, emotionally, and actively orient people and enable communication. SRs are social constructions that emerge through individual and collective engagement with media and with everyday conversations among people. Recent developments in text analysis techniques, and in particular topic modeling, provide a potentially powerful analytical method to examine the structure and content of SRs using large samples of narrative or text. In this paper I describe the methods and results of applying topic modeling to 660 micronarratives collected from Australian academics / researchers, government employees, and members of the public in 2010-2011. The narrative fragments focused on adaptation to climate change (CC) and hence provide an example of Australian society making sense of an emerging and conflict ridden phenomena. The results of the topic modeling reflect elements of SRs of adaptation to CC that are consistent with findings in the literature as well as being reasonably robust predictors of classes of action in response to CC. Bayesian Network (BN) modeling was used to identify relationships among the topics (SR elements) and in particular to identify relationships among topics, sentiment, and action. Finally the resulting model and topic modeling results are used to highlight differences in the salience of SR elements among social groups. The approach of linking topic modeling and BN modeling offers a new and encouraging approach to analysis for ongoing research on SRs.

Assessing the impacts of community participation policy and practice in Scotland and England

Background: Community participation has become an integral part of many areas of public policy over the last two decades. For a variety of reasons, ranging from concerns about social cohesion and unrest to perceived failings in public services, governments in the UK and elsewhere have turned to communities as both a site of intervention and a potential solution. In contemporary policy, the shift to community is exemplified by the UK Government’s Big Society/Localism agenda and the Scottish Government’s emphasis on Community Empowerment. Through such policies, communities have been increasingly encouraged to help themselves in various ways, to work with public agencies in reshaping services, and to become more engaged in the democratic process. These developments have led some theorists to argue that responsibilities are being shifted from the state onto communities, representing a new form of 'government through community' (Rose, 1996; Imrie and Raco, 2003). Despite this policy development, there is surprisingly little evidence which demonstrates the outcomes of the different forms of community participation. This study attempts to address this gap in two ways. Firstly, it explores the ways in which community participation policy in Scotland and England are playing out in practice. And secondly, it assesses the outcomes of different forms of community participation taking place within these broad policy contexts. Methodology: The study employs an innovative combination of the two main theory-based evaluation methodologies, Theories of Change (ToC) and Realist Evaluation (RE), building on ideas generated by earlier applications of each approach (Blamey and Mackenzie, 2007). ToC methodology is used to analyse the national policy frameworks and the general approach of community organisations in six case studies, three in Scotland and three in England. The local evidence from the community organisations’ theories of change is then used to analyse and critique the assumptions which underlie the Localism and Community Empowerment policies. Alongside this, across the six case studies, a RE approach is utilised to examine the specific mechanisms which operate to deliver outcomes from community participation processes, and to explore the contextual factors which influence their operation. Given the innovative methodological approach, the study also engages in some focused reflection on the practicality and usefulness of combining ToC and RE approaches. Findings: The case studies provide significant evidence of the outcomes that community organisations can deliver through directly providing services or facilities, and through influencing public services. Important contextual factors in both countries include particular strengths within communities and positive relationships with at least part of the local state, although this often exists in parallel with elements of conflict. Notably this evidence suggests that the idea of responsibilisation needs to be examined in a more nuanced fashion, incorporating issues of risk and power, as well the active agency of communities and the local state. Thus communities may sometimes willingly take on responsibility in return for power, although this may also engender significant risk, with the balance between these three elements being significantly mediated by local government. The evidence also highlights the impacts of austerity on community participation, with cuts to local government budgets in particular increasing the degree of risk and responsibility for communities and reducing opportunities for power. Furthermore, the case studies demonstrate the importance of inequalities within and between communities, operating through a socio-economic gradient in community capacity. This has the potential to make community participation policy regressive as more affluent communities are more able to take advantage of additional powers and local authorities have less resource to support the capacity of more disadvantaged communities. For Localism in particular, the findings suggest that some of the ‘new community rights’ may provide opportunities for communities to gain power and generate positive social outcomes. However, the English case studies also highlight the substantial risks involved and the extent to which such opportunities are being undermined by austerity. The case studies suggest that cuts to local government budgets have the potential to undermine some aspects of Localism almost entirely, and that the very limited interest in inequalities means that Localism may be both ‘empowering the powerful’ (Hastings and Matthews, 2014) and further disempowering the powerless. For Community Empowerment, the study demonstrates the ways in which community organisations can gain power and deliver positive social outcomes within the broad policy framework. However, whilst Community Empowerment is ostensibly less regressive, there are still significant challenges to be addressed. In particular, the case studies highlight significant constraints on the notion that communities can ‘choose their own level of empowerment’, and the assumption of partnership working between communities and the local state needs to take into account the evidence of very mixed relationships in practice. Most importantly, whilst austerity has had more limited impacts on local government in Scotland so far, the projected cuts in this area may leave Community Empowerment vulnerable to the dangers of regressive impact highlighted for Localism. Methodologically, the study shows that ToC and RE can be practically applied together and that there may be significant benefits of the combination. ToC offers a productive framework for policy analysis and combining this with data derived from local ToCs provides a powerful lens through which to examine and critique the aims and assumptions of national policy. ToC models also provide a useful framework within which to identify specific causal mechanisms, using RE methodology and, again, the data from local ToC work can enable significant learning about ‘what works for whom in what circumstances’ (Pawson and Tilley, 1997).

KEY COMPONENTS OF TEAMWORK AND THE SERVICE (TO) YOU (A) (A) DOMESTIC (A) AND EXTERNAL (A)

The article examines a range of components for the customer service from the point of view of marketing.It start with the explanation of several features that are required for a company to crystallize teamwork that finally, after all, will be provided by the success or failure of that company.These features are named: engagement, cooperation, companionship, communication, motivation and leadership.Subsequently, this article presents a section which explores human relationships and conflict management within organizations, with emphasis on attitudes, skills and personality types that present human beings as part of its essence.Finally, this text includes a section that highlights concepts related to customer service and sales techniques that exist today.

The effects of the quality of social relationships and emotion regulation ability on the happiness of introvert individuals

Previous research has shown that extraverts are happier than introverts and, although happy introverts exist, it is unclear under what conditions they can achieve happiness. The aim of the present study is to analyze the quality of social relationships and emotion regulation ability as a possible factor for happiness in introvert individuals. 1006 adults (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability and happiness. Results shows that introverts have significantly lower happiness, quality of life, quality of social relationship and emotion regulation ability scores than extraverts. Besides, those individuals with high quality social relationships or high emotion regulation ability were happier. Introverts were happier when they had high scores for quality of social relationships and emotion regulation ability, however the effect size was small. These results suggest that emotion regulation and social relationships are important to understand the relationships between introversion and happiness.