Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma

In this study we have identified key genes that are critical in development of astrocytic tumors. Meta-analysis of microarray studies which compared normal tissue to astrocytoma revealed a set of 646 differentially expressed genes in the majority of astrocytoma. Reverse engineering of these 646 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I–IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. All of these genes were up-regulated, except MPP2 (down regulated). These 10 genes were able to predict tumor status with 96–100% confidence when using logistic regression, cross validation, and the support vector machine analysis. Markov genes interact with NFkβ, ERK, MAPK, VEGF, growth hormone and collagen to produce a network whose top biological functions are cancer, neurological disease, and cellular movement. Three of the 10 genes - EGFR, COL4A1, and CDK4, in particular, seemed to be potential ‘hubs of activity’. Modified expression of these 10 Markov Blanket genes increases lifetime risk of developing glioblastoma compared to the normal population. The glioblastoma risk estimates were dramatically increased with joint effects of 4 or more than 4 Markov Blanket genes. Joint interaction effects of 4, 5, 6, 7, 8, 9 or 10 Markov Blanket genes produced 9, 13, 20.9, 26.7, 52.8, 53.2, 78.1 or 85.9%, respectively, increase in lifetime risk of developing glioblastoma compared to normal population. In summary, it appears that modified expression of several ‘key genes’ may be required for the development of glioblastoma. Further studies are needed to validate these ‘key genes’ as useful tools for early detection and novel therapeutic options for these tumors.

Empirical aspects of a mixed method approach to economic network analysis

We discuss the interactions among the various phases of network research design in the context of our current work using Mixed Methods and SNA on networks and rural economic development. We claim that there are very intricate inter-dependencies among the various phases of network research design - from theory and formulation of research questions right through to modes of analysis and interpretation. Through examples drawn from our work we illustrate how choices about methods for Sampling and Data Collection are influenced by these interdependencies.

Structural and agentic analysis of supply-chains: a social network analysis approach

This research adds to a body of work exploring the role of Social Network Analysis (SNA) in the study of both relational and structural characteristics of supply chain networks. Two contrasting network cases (food enterprises and digital-based enterprises) are chosen in order to elicit structural differences in business networks subject to divergences in local embeddedness and the relative materiality of the goods and services produced. Our analysis and findings draw out differences in network structure as evidenced by metrics of network centralization and cohesion, the presence of components and other sub-groupings, and the position of central actors. We relate these structural features both to the nature of the networks and to the (qualitative) experiences of the actors themselves. We find, in particular, the role of customers as co-creators of knowledge (for the Food network), the central role of infrastructure and services (for the Digital network), the importance of ICT as a source of codified knowledge inputs, along with the continuing importance of geographical proximity for the development and transfer of tacit knowledge and for incremental learning.

Forces of agglomeration and dispersal in rural business networks: a social network analysis

Two concepts in rural economic development policy have been the focus of much research and policy action: the identification and support of clusters or networks of firms and the availability and adoption by rural businesses of Information and Communication Technologies (ICT). From a theoretical viewpoint these policies are based on two contrasting models, with clustering seen as a process of economic agglomeration, and ICT-mediated communication as a means of facilitating economic dispersion. The study’s conceptual framework is based on four interrelated elements: location, interaction, knowledge, and advantage, together with the concept of networks which is employed as an operationally and theoretically unifying concept. The research questions are developed in four successive categories: Policy, Theory, Networks, and Method. The questions are approached using a study of two contrasting groups of rural small businesses in West Cork, Ireland: (a) Speciality Foods, and (b) firms in Digital Products and Services. The study combines Social Network Analysis (SNA) with Qualitative Thematic Analysis, using data collected from semi-structured interviews with 58 owners or managers of these businesses. Data comprise relational network data on the firms’ connections to suppliers, customers, allies and competitors, together with linked qualitative data on how the firms established connections, and how tacit and codified knowledge was sourced and utilised. The research finds that the key characteristics identified in the cluster literature are evident in the sample of Speciality Food businesses, in relation to flows of tacit knowledge, social embedding, and the development of forms of social capital. In particular the research identified the presence of two distinct forms of collective social capital in this network, termed “community” and “reputation”. By contrast the sample of Digital Products and Services businesses does not have the form of a cluster, but matches more closely to dispersive models, or “chain” structures. Much of the economic and social structure of this set of firms is best explained in terms of “project organisation”, and by the operation of an individual rather than collective form of “reputation”. The rural setting in which these firms are located has resulted in their being service-centric, and consequently they rely on ICT-mediated communication in order to exchange tacit knowledge “at a distance”. It is this factor, rather than inputs of codified knowledge, that most strongly influences their operation and their need for availability and adoption of high quality communication technologies. Thus the findings have applicability in relation to theory in Economic Geography and to policy and practice in Rural Development. In addition the research contributes to methodological questions in SNA, and to methodological questions about the combination or mixing of quantitative and qualitative methods.

Measuring the Diversity and the Integration of Film Production in Mercosur: A Social Network Analysis

Based on an original and comprehensive database of all feature fiction films produced in Mercosur between 2004 and 2012, the paper analyses whether the Mercosur film industry has evolved towards an integrated and culturally more diverse market. It provides a summary of policy opportunities in terms of integration and diversity, emphasizing the limiter role played by regional policies. It then shows that although the Mercosur film industry remains rather disintegrated, it tends to become more integrated and culturally more diverse. From a methodological point of view, the combination of Social Network Analysis and the Stirling Model opens up interesting research tracks to analyse creative industries in terms of their market integration and their cultural diversity.

Acoustic telemetry and network analysis reveal the space use of multiple reef predators and enhance marine protected area design

Marine protected areas (MPAs) are commonly employed to protect ecosystems from threats like overfishing. Ideally, MPA design should incorporate movement data from multiple target species to ensure sufficient habitat is protected. We used long-term acoustic telemetry and network analysis to determine the fine-scale space use of five shark and one turtle species at a remote atoll in the Seychelles, Indian Ocean, and evaluate the efficacy of a proposed MPA. Results revealed strong, species-specific habitat use in both sharks and turtles, with corresponding variation in MPA use. Defining the MPA's boundary from the edge of the reef flat at low tide instead of the beach at high tide (the current best in Seychelles) significantly increased the MPA's coverage of predator movements by an average of 34%. Informed by these results, the larger MPA was adopted by the Seychelles government, demonstrating how telemetry data can improve shark spatial conservation by affecting policy directly.

Acoustic telemetry and network analysis reveal the space use of multiple reef predators and enhance marine protected area design

Marine protected areas (MPAs) are commonly employed to protect ecosystems from threats like overfishing. Ideally, MPA design should incorporate movement data from multiple target species to ensure sufficient habitat is protected. We used long-term acoustic telemetry and network analysis to determine the fine-scale space use of five shark and one turtle species at a remote atoll in the Seychelles, Indian Ocean, and evaluate the efficacy of a proposed MPA. Results revealed strong, species-specific habitat use in both sharks and turtles, with corresponding variation in MPA use. Defining the MPA's boundary from the edge of the reef flat at low tide instead of the beach at high tide (the current best in Seychelles) significantly increased the MPA's coverage of predator movements by an average of 34%. Informed by these results, the larger MPA was adopted by the Seychelles government, demonstrating how telemetry data can improve shark spatial conservation by affecting policy directly.

Use of social network analysis to identify the coopetition in a Commercial Cluster Plan

The cluster provides a greater commercial relationship between the companies that comprise it. This encourages companies to adopt competitive structures that allow solving problems that would hardly alone (Lubeck et. Al., 2011). With that this paper aims to describe the coopetition between companies operating on a commercial cluster planned, from the point of view of retailers, taking as a basis the theoretical models proposed by Bengtsson and Kock (1999) and Leon (2005) and operationalized by means of Social Network Analysis (SNA). Data collection consisted of two phases, the first exploratory aspect to identify the actors, and the second was characterized as descriptive as it aims to describe the coopetition among the enterprises. As a result we identified the companies that cooperate and compete simultaneously (coopetition), firms that only compete, companies just cooperate and businesses that do not compete and do not cooperate (coexistence).

Power relations and good governance: a social network analysis of the evolution of the integrity in public office act in the Commonwealth of Dominica

La Banque mondiale propose la bonne gouvernance comme la stratégie visant à corriger les maux de la mauvaise gouvernance et de faciliter le développement dans les pays en développement (Carayannis, Pirzadeh, Popescu & 2012; & Hilyard Wilks 1998; Leftwich 1993; Banque mondiale, 1989). Dans cette perspective, la réforme institutionnelle et une arène de la politique publique plus inclusive sont deux stratégies critiques qui visent à établir la bonne gouvernance, selon la Banque et d’autres institutions de Bretton Woods. Le problème, c’est que beaucoup de ces pays en voie de développement ne possèdent pas l’architecture institutionnelle préalable à ces nouvelles mesures. Cette thèse étudie et explique comment un état en voie de développement, le Commonwealth de la Dominique, s’est lancé dans un projet de loi visant l’intégrité dans la fonction publique. Cette loi, la Loi sur l’intégrité dans la fonction publique (IPO) a été adoptée en 2003 et mis en œuvre en 2008. Cette thèse analyse les relations de pouvoir entre les acteurs dominants autour de évolution de la loi et donc, elle emploie une combinaison de technique de l’analyse des réseaux sociaux et de la recherche qualitative pour répondre à la question principale: Pourquoi l’État a-t-il développé et mis en œuvre la conception actuelle de la IPO (2003)? Cette question est d’autant plus significative quand nous considérons que contrairement à la recherche existante sur le sujet, l’IPO dominiquaise diverge considérablement dans la structure du l’IPO type idéal. Nous affirmons que les acteurs "rationnels," conscients de leur position structurelle dans un réseau d’acteurs, ont utilisé leurs ressources de pouvoir pour façonner l’institution afin qu’elle serve leurs intérêts et ceux et leurs alliés. De plus, nous émettons l’hypothèse que: d’abord, le choix d’une agence spécialisée contre la corruption et la conception ultérieure de cette institution reflètent les préférences des acteurs dominants qui ont participé à la création de ladite institution et la seconde, notre hypothèse rivale, les caractéristiques des modèles alternatifs d’institutions de l’intégrité publique sont celles des acteurs non dominants. Nos résultats sont mitigés. Le jeu de pouvoir a été limité à un petit groupe d’acteurs dominants qui ont cherché à utiliser la création de la loi pour assurer leur légitimité et la survie politique. Sans surprise, aucun acteur n’a avancé un modèle alternatif. Nous avons conclu donc que la loi est la conséquence d’un jeu de pouvoir partisan. Cette recherche répond à la pénurie de recherche sur la conception des institutions de l’intégrité publique, qui semblent privilégier en grande partie un biais organisationnel et structurel. De plus, en étudiant le sujet du point de vue des relations de pouvoir (le pouvoir, lui-même, vu sous l’angle actanciel et structurel), la thèse apporte de la rigueur conceptuelle, méthodologique, et analytique au discours sur la création de ces institutions par l’étude de leur genèse des perspectives tant actancielles que structurelles. En outre, les résultats renforcent notre capacité de prédire quand et avec quelle intensité un acteur déploierait ses ressources de pouvoir.

Using social network analysis to identify key stakeholders in agricultural biodiversity governance and related land-use decisions at regional and local level

In 2013 the European Commission launched its new green infrastructure strategy to make another attempt to stop and possibly reverse the loss of biodiversity until 2020, by connecting habitats in the wider landscape. This means that conservation would go beyond current practices to include landscapes that are dominated by conventional agriculture, where biodiversity conservation plays a minor role at best. The green infrastructure strategy aims at bottom-up rather than top-down implementation, and suggests including local and regional stakeholders. Therefore, it is important to know which stakeholders influence land-use decisions concerning green infrastructure at the local and regional level. The research presented in this paper served to select stakeholders in preparation for a participatory scenario development process to analyze consequences of different implementation options of the European green infrastructure strategy. We used a mix of qualitative and quantitative social network analysis (SNA) methods to combine actors’ attributes, especially concerning their perceived influence, with structural and relational measures. Further, our analysis provides information on institutional backgrounds and governance settings for green infrastructure and agricultural policy. The investigation started with key informant interviews at the regional level in administrative units responsible for relevant policies and procedures such as regional planners, representatives of federal ministries, and continued at the local level with farmers and other members of the community. The analysis revealed the importance of information flows and regulations but also of social pressure, considerably influencing biodiversity governance with respect to green infrastructure and biodiversity.

The mosaic of habitats of the Seine estuary: Insights from food-web modelling and network analysis

Ecological network analysis was applied in the Seine estuary ecosystem, northern France, integrating ecological data from the years 1996 to 2002. The Ecopath with Ecosim (EwE) approach was used to model the trophic flows in 6 spatial compartments leading to 6 distinct EwE models: the navigation channel and the two channel flanks in the estuary proper, and 3 marine habitats in the eastern Seine Bay. Each model included 12 consumer groups, 2 primary producers, and one detritus group. Ecological network analysis was performed, including a set of indices, keystoneness, and trophic spectrum analysis to describe the contribution of the 6 habitats to the Seine estuary ecosystem functioning. Results showed that the two habitats with a functioning most related to a stressed state were the northern and central navigation channels, where building works and constant maritime traffic are considered major anthropogenic stressors. The strong top-down control highlighted in the other 4 habitats was not present in the central channel, showing instead (i) a change in keystone roles in the ecosystem towards sediment-based, lower trophic levels, and (ii) a higher system omnivory. The southern channel evidenced the highest system activity (total system throughput), the higher trophic specialisation (low system omnivory), and the lowest indication of stress (low cycling and relative redundancy). Marine habitats showed higher fish biomass proportions and higher transfer efficiencies per trophic levels than the estuarine habitats, with a transition area between the two that presented intermediate ecosystem structure. The modelling of separate habitats permitted disclosing each one's response to the different pressures, based on their a priori knowledge. Network indices, although non-monotonously, responded to these differences and seem a promising operational tool to define the ecological status of transitional water ecosystems.

Credible Commitments and Post-Conflict Refugee Return: A Statistical and Network Analysis

I examine determinants of refugee return after conflicts. I argue that institutional constraints placed on the executive provide a credible commitment that signals to refugees that the conditions required for durable return will be created. This results in increased return flows for refugees. Further, when credible commitments are stronger in the country of origin than in the country of asylum, the level of return increases. Finally, I find that specific commitments made to refugees in the peace agreement do not lead to increased return because they are not credible without institutional constraints. Using data on returnees that has only recently been made available, along with network analysis and an original coding of the provisions in refugee agreements, statistical results are found to support this theory. An examination of cases in Djibouti, Sierra Leone, and Liberia provides additional support for this argument.