Diante da abundância de informações e de compartilhamentos em sites de redes sociais e da proliferação de convites para o uso desses sites na Educação, esta tese propõe a pesquisa das estruturas relacionais que emergem das interações sociais em grupos no site de rede social Facebook. O objetivo geral é compreender como as interações sociais em rede e nas redes podem contribuir para uma Educação em Rede a partir da análise dos padrões de interação social em grupos no site Facebook. Analisamos dois casos distintos de redes sociais organizadas como parte de processos pedagógicos. Os recursos curtir, comentar e curtir comentários são os tipos de interação social em rede que deram origem aos grafos analisados. As temáticas das postagens e os tipos de suportes tecnológicos são identificados na análise dos padrões de interação social em rede e nas redes, nas quais destacamos a participação, o engajamento e o sentimento de pertencimento dos atores. A Análise de Redes Sociais é o método utilizado para compreender as dinâmicas das interações. O Modelo de Análise da Comunicação Assíncrona é adotado na análise de conteúdo das postagens e dos comentários dessas postagens com vistas a destacar as temáticas compartilhadas e discutidas. Nas redes sociais em foco, as pessoas se organizam e interagem, prioritariamente, com o professor ou com os atores sociais que assumem as funções de professor. Considerando que os recursos tecnológicos disponíveis permitem fluxo de informações de diferentes fontes, o que observamos é que o professor é a pessoa fundamental para articular as aprendizagens nas redes sociais. A configuração da sala de aula analógica se transfere para os comportamentos e às expectativas do que deve acontecer na sala de aula em redes sociais. Essa dinâmica fornece subsídios para propor orientações à formação de professores e diretrizes para a realização de Educação em Rede. A difusão das informações e a circulação de atores-ponte na rede contribuem para que haja presença social. A presença social é uma peça fundamental para a presença cognitiva. O uso de sites de redes sociais na educação tem valor pedagógico desde que haja presença social endereçada ao ensino. É necessário que um ator ou alguns atores ajam de modo a garantir relações de ensino e aprendizagem. / Faced with the abundance of information and shares on social networking sites and invitations proliferation to the use of these sites in education, this thesis proposes the research of relational structures that emerge from social interactions in groups on the Facebook social networking site. The overall goal is to understand how social interactions network and the networks can contribute to an Education Network based on the analysis of patterns of social interaction in groups on Facebook site. We analyzed two different cases of social networks organized as part of pedagogical processes. Resources Like, Comment and Like Comments are the types of social interaction network that gave rise to the analyzed graphs. The thematic of posts and the types of technological support are identified in the analysis of patterns of social interaction in the network and the networks in which we highlight the participation, engagement and sense of belonging of the actors. The Social Network Analysis is the method used to understand the dynamics of interactions. The Asynchronous Communications Analysis Model is adopted in the content analysis of posts and comments of these posts with a view to highlight the shared and discussed themes. In social networks in focus, people are organized and interact primarily with the teacher or with the social actors who assume the teacher functions. Whereas the available technological resources enable flow of information from different sources, which we observe is that the teacher is the key person to articulate learning in social networks. The configuration of the analog classroom is transferred to the behaviors and expectations of what should happen in the classroom in social networks. This dynamic provides subsidies to propose guidelines for teacher training and guidelines for conducting Education Network. The dissemination of information and the circulation of actors bridge on the network contribute to social presence there. Social presence is a key part of cognitive presence. The use of social networking sites in education has educational value as long as there is social presence addressed to education. It is necessary for an actor or some actors to act in order to ensure teaching and learning relations. / Frente a la abundancia de información y acciones en las redes sociales y la proliferación de las invitaciones a la utilización de estos sitios en la educación, esta tesis propone la investigación de las estructuras relacionales que surgen de las interacciones sociales en grupos en la red social Facebook. El objetivo general es entender cómo las interacciones de la red social y las redes puede contribuir a una red de educación basado en el análisis de los patrones de interacción social en grupos en Facebook. Se analizaron dos casos diferentes de redes sociales organizados en el marco de los procesos pedagógicos. Recursos Me gusta, Comentar y Me Gusta el Comentario son los tipos de red de interacción social que dieron origen a los gráficos analizados. La temática de los puestos y los tipos de apoyo tecnológico son identificados en el análisis de los patrones de interacción social en la red y las redes en las que podemos destacar la participación, el compromiso y el sentido de pertenencia de los actores. El análisis de redes sociales es el método utilizado para entender la dinámica de las interacciones. El Modelo de Análisis de Comunicaciones asíncronas se adopta en el análisis del contenido de los mensajes y los comentarios de estos mensajes con el fin de poner de relieve los temas compartidos y discutidos. En las redes sociales en el enfoque, las personas se organizan e interactúan principalmente con el profesor o con los actores sociales que asumen las funciones de los maestros. Considerando que los recursos tecnológicos disponibles permiten el flujo de información de diferentes fuentes, que observamos es que el maestro es la persona clave para articular el aprendizaje en las redes sociales. La configuración del clase analógica se transfiere a los comportamientos y expectativas de lo que debería ocurrir en el aula en las redes sociales. Esta dinámica proporciona subsidios a proponer directrices para la formación del profesorado y directrices para la realización de la Red de Educación. La difusión de la información y la circulación de los actores puente en la red contribuyen a la presencia social allí. La presencia social es una parte clave de la presencia cognitiva. El uso de las redes sociales en la educación tiene un valor educativo, siempre y cuando no hay presencia social dirigida a la educación. Es necesario que un actor o algunos actores para actuar con el fin de garantizar las relaciones de enseñanza y aprendizaje.

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We are currently faced with the global challenge of conserving biological diversity while also increasing food production to meet the demands of a growing human population. Land-use change, primarily resulting from conversion to production land, is currently the leading cause of biodiversity loss. This occurs through habitat loss, fragmentation of remaining natural habitats, and resulting edge effects. Land-sparing and land-sharing approaches have been discussed as alternative ways to engineer landscapes to mitigate biodiversity loss while meeting production objectives. However, these represent extremes on a continuum of real-world landscapes, and it will be important to understand the mechanisms by which adjacent land use affects natural remnant ecosystems in order to make local land-management decisions that achieve conservation, as well as production, objectives. This thesis investigates the impact of juxtaposing production and natural forest on the community-wide interactions between lepidopteran herbivores and their parasitoids, as mediated by parasitoid spillover between habitats. The first and overarching objective was to determine whether herbivore productivity drives asymmetrical spillover of predators and parasitoids, primarily from managed to natural habitats, and whether this spillover alters trophic interactions in the recipient habitat. The study of trophic interactions at a community level requires understanding of both direct and indirect interactions. However, community-level indirect interactions are generally difficult to predict and measure, and these have therefore remained understudied. Apparent competition is an indirect interaction mechanism thought to be very important in structuring host-parasitoid assemblages. However, this is known primarily from studies of single species pairs, and its community-wide impacts are less clear. Therefore, my second objective was to determine whether apparent competition could be predicted for all species pairs within an herbivore assemblage, based on a measure of parasitoid overlap. My third objective was to determine whether certain host or parasitoid species traits can predict the involvement of those species in apparent competition. My key findings were that there is a net spillover of generalist predators and parasitoids from plantation to native forest, and that for generalists, this depends on herbivore abundance in the plantation forest. Herbivore populations across the edge were linked by shared parasitoids in apparent competition. Consequently, an experimental reduction of herbivore density in the plantation forest changed parasitism rates in the natural forest, as predicted based on parasitoid overlap. Finally, several host and parasitoid traits were identified that can predict the degree to which host or parasitoid species will be involved in apparent competition, a finding which may have extensive application in biological control, as well as in predicting spillover edge effects. Overall, this work suggests that asymmetrical spillover between production and natural habitats occurs in relation to productivity differences, with greater movement of predators and parasitoids in the managed-to-natural forest direction. The degree to which this affected species interactions has implications for landscape design to achieve conservation objectives in production landscapes.

<p>Protein malfunction can cause human diseases, which makes the protein a target in the process of drug discovery. In-depth knowledge of how protein functions can widely contribute to the understanding of the mechanism of these diseases. Protein functions are determined by protein structures and their dynamic properties. Protein dynamics refers to the constant physical movement of atoms in a protein, which may result in the transition between different conformational states of the protein. These conformational transitions are critically important for the proteins to function. Understanding protein dynamics can help to understand and interfere with the conformational states and transitions, and thus with the function of the protein. If we can understand the mechanism of conformational transition of protein, we can design molecules to regulate this process and regulate the protein functions for new drug discovery. Protein Dynamics can be simulated by Molecular Dynamics (MD) Simulations.</p> <p>The MD simulation data generated are spatial-temporal and therefore very high dimensional. To analyze the data, distinguishing various atomic interactions within a protein by interpreting their 3D coordinate values plays a significant role. Since the data is humongous, the essential step is to find ways to interpret the data by generating more efficient algorithms to reduce the dimensionality and developing user-friendly visualization tools to find patterns and trends, which are not usually attainable by traditional methods of data process. The typical allosteric long-range nature of the interactions that lead to large conformational transition, pin-pointing the underlying forces and pathways responsible for the global conformational transition at atomic level is very challenging. To address the problems, Various analytical techniques are performed on the simulation data to better understand the mechanism of protein dynamics at atomic level by developing a new program called Probing Long-distance interactions by Tapping into Paired-Distances (PLITIP), which contains a set of new tools based on analysis of paired distances to remove the interference of the translation and rotation of the protein itself and therefore can capture the absolute changes within the protein.</p> <p>Firstly, we developed a tool called Decomposition of Paired Distances (DPD). This tool generates a distance matrix of all paired residues from our simulation data. This paired distance matrix therefore is not subjected to the interference of the translation or rotation of the protein and can capture the absolute changes within the protein. This matrix is then decomposed by DPD</p> <p>using Principal Component Analysis (PCA) to reduce dimensionality and to capture the largest structural variation. To showcase how DPD works, two protein systems, HIV-1 protease and 14-3-3 σ, that both have tremendous structural changes and conformational transitions as displayed by their MD simulation trajectories. The largest structural variation and conformational transition were captured by the first principal component in both cases. In addition, structural clustering and ranking of representative frames by their PC1 values revealed the long-distance nature of the conformational transition and locked the key candidate regions that might be responsible for the large conformational transitions.</p> <p>Secondly, to facilitate further analysis of identification of the long-distance path, a tool called Pearson Coefficient Spiral (PCP) that generates and visualizes Pearson Coefficient to measure the linear correlation between any two sets of residue pairs is developed. PCP allows users to fix one residue pair and examine the correlation of its change with other residue pairs.</p> <p>Thirdly, a set of visualization tools that generate paired atomic distances for the shortlisted candidate residue and captured significant interactions among them were developed. The first tool is the Residue Interaction Network Graph for Paired Atomic Distances (NG-PAD), which not only generates paired atomic distances for the shortlisted candidate residues, but also display significant interactions by a Network Graph for convenient visualization. Second, the Chord Diagram for Interaction Mapping (CD-IP) was developed to map the interactions to protein secondary structural elements and to further narrow down important interactions. Third, a Distance Plotting for Direct Comparison (DP-DC), which plots any two paired distances at user’s choice, either at residue or atomic level, to facilitate identification of similar or opposite pattern change of distances along the simulation time. All the above tools of PLITIP enabled us to identify critical residues contributing to the large conformational transitions in both HIV-1 protease and 14-3-3σ proteins.</p> <p>Beside the above major project, a side project of developing tools to study protein pseudo-symmetry is also reported. It has been proposed that symmetry provides protein stability, opportunities for allosteric regulation, and even functionality. This tool helps us to answer the questions of why there is a deviation from perfect symmetry in protein and how to quantify it.</p>