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## Complex networks: the key to systems biology

COSTA, Luciano da Fontoura; RODRIGUES, Francisco A.; CRISTINO, Alexandre S.
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
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Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. The key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.; FAPESP; CNPq

## The modularity of seed dispersal: differences in structure and robustness between bat- and bird-fruit networks

MELLO, Marco Aurelio Ribeiro; MARQUITTI, Flavia Maria Darcie; GUIMARAES JR., Paulo R.; KALKO, Elisabeth Klara Viktoria; JORDANO, Pedro; AGUIAR, Marcus Aloizio Martinez de
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.31524%
In networks of plant-animal mutualisms, different animal groups interact preferentially with different plants, thus forming distinct modules responsible for different parts of the service. However, what we currently know about seed dispersal networks is based only on birds. Therefore, we wished to fill this gap by studying bat-fruit networks and testing how they differ from bird-fruit networks. As dietary overlap of Neotropical bats and birds is low, they should form distinct mutualistic modules within local networks. Furthermore, since frugivory evolved only once among Neotropical bats, but several times independently among Neotropical birds, greater dietary overlap is expected among bats, and thus connectance and nestedness should be higher in bat-fruit networks. If bat-fruit networks have higher nestedness and connectance, they should be more robust to extinctions. We analyzed 1 mixed network of both bats and birds and 20 networks that consisted exclusively of either bats (11) or birds (9). As expected, the structure of the mixed network was both modular (M = 0.45) and nested (NODF = 0.31); one module contained only birds and two only bats. In 20 datasets with only one disperser group, bat-fruit networks (NODF = 0.53 +/- A 0.09...

## Efeito da amostragem nas propriedades topológicas de redes complexas; Sampling effect on the topological properties of complex networks

Boas, Paulino Ribeiro Villas
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Relevância na Pesquisa
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## Redes de empresas e o impacto regional: o caso de Santa Maria (RS); Company networks and regional impact: the case of santa maria (RS)

Tonin, Guerino Antonio
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Relevância na Pesquisa
36.296887%
A presente tese aborda o tema sobre o processo de formação, desenvolvimento e consolidação de redes entre Pequenas e Médias Empresas (PMEs) e sua contribuição para o desenvolvimento regional. Partindo da revisão analítica das teorias de redes interorganizacionais, de criação, desenvolvimento, consolidação e dos processos de gestão, buscou-se a compreensão da relevância estratégica das redes para o desenvolvimento regional. A partir de evidências teóricas, a questão da pesquisa confrontada foi compreender como ocorrem formação e desenvolvimento de redes interempresariais horizontais e sua contribuição para o desenvolvimento regional. A pesquisa estudou e qualificou os fatores subjacentes à formação e consolidação de redes horizontais de cooperação e sua contribuição para o desenvolvimento regional. No estágio de formação da rede, são analisados os fatores de motivação, escolha do grupo, papel da liderança e a confiança. No processo de desenvolvimento/consolidação, a análise dá-se na direção de fatores de gestão - preparação das empresas, coordenação, governança e escolha dos parceiros - e dos fatores sociais - liderança, capital social e confiança. A contribuição das redes para o desenvolvimento regional foca fatores econômicos e sociais. Para verificar a experiência da construção e consolidação das redes...

## The modularity of seed dispersal: differences in structure and robustness between bat- and bird-fruit networks

MELLO, Marco Aurelio Ribeiro; MARQUITTI, Flavia Maria Darcie; GUIMARAES JR., Paulo R.; KALKO, Elisabeth Klara Viktoria; JORDANO, Pedro; AGUIAR, Marcus Aloizio Martinez de
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.30702%
In networks of plant-animal mutualisms, different animal groups interact preferentially with different plants, thus forming distinct modules responsible for different parts of the service. However, what we currently know about seed dispersal networks is based only on birds. Therefore, we wished to fill this gap by studying bat-fruit networks and testing how they differ from bird-fruit networks. As dietary overlap of Neotropical bats and birds is low, they should form distinct mutualistic modules within local networks. Furthermore, since frugivory evolved only once among Neotropical bats, but several times independently among Neotropical birds, greater dietary overlap is expected among bats, and thus connectance and nestedness should be higher in bat-fruit networks. If bat-fruit networks have higher nestedness and connectance, they should be more robust to extinctions. We analyzed 1 mixed network of both bats and birds and 20 networks that consisted exclusively of either bats (11) or birds (9). As expected, the structure of the mixed network was both modular (M = 0.45) and nested (NODF = 0.31); one module contained only birds and two only bats. In 20 datasets with only one disperser group, bat-fruit networks (NODF = 0.53 +/- A 0.09...

## Broad band “Western Mediterranean” and ocean bottom “Fomar” seismological networks

Martin-Davila, J.; Pazos, A.; Buforn, E.; Udias, A.; Bezzeghoud, M.; Caldeira, B.; Rimi, A.; Harnafi, M.; Hanka, W.; Nadji, A.
Fonte: Broad band “Western Mediterranean” and ocean bottom “Fomar” seismological networks Publicador: Broad band “Western Mediterranean” and ocean bottom “Fomar” seismological networks
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
46.072427%
To study the seismicity associated to the Ibero-Maghrebian region, the Real Instituto y Observatorio de la Armada in San Fernando (ROA) has installed, since 1898, different types of seismological stations. At present two networks are in operation: Long Period station and Short Period net (ROA) and Western Mediterranean Broad Band (WM) net (in collaboration among several institutions). The installation of a network of ocean-bottom seismographs (FOMAR) is underway. The Ibero- Maghrebian region corresponds to the western part of the Eurasia-Africa plate boundary and is of great seismological and tectonic interest. It extends from 12oW to 3oE, comprising Southern Iberia and northern Africa, including the Gulf of Cadiz and Alboran Sea (figure 1). Seismicity is characterized by the occurrence of moderate and large magnitude earthquakes at shallow depth, intermediate depth earthquakes (30

## The effects of social networks on the health of older Australians.

Giles, Lynne Catherine
Relevância na Pesquisa
36.33483%
Background: Over the past three decades, social relationships have been shown to have important effects upon health. However, many different definitions and aspects of social relationships have been considered in the various studies, making comparison of findings difficult. Furthermore, the effects of social relationships upon different health outcomes have rarely been investigated within the same cohort of older people. In addition, there is a paucity of information concerning the effects of social relationships upon health of older Australians. Aim: This thesis aims to investigate the effects of the structural aspects of social relationships – that is, social networks – on health among older Australians. The three specific health outcomes considered in this thesis were disability, residential care use and death. The specific aims of the thesis were to: 1. Develop a measurement model of social networks. 2. Examine the effects of total and specific social networks upon disability. 3. Determine the effects of total and specific social networks upon use of residential care. 4. Investigate the effects of total and specific social networks upon survival. An additional aim was to determine if there were threshold effects of social networks on the three specific health outcomes. Methods: The study drew on six waves of data from 1477 participants in the Australian Longitudinal Study of Ageing. A range of statistical techniques...

## People Smuggling Networks in the Australian Context

Ngiam, Marie
Tipo: Relatório
Português
Relevância na Pesquisa
36.30702%
The Australian government has become increasingly frustrated at the inability to prevent people smugglers from transporting asylum seekers to Australia, despite increasing law enforcement measures. Yet research on people smuggling networks remain dispersed and fail to take into account recent developments on people smugglers and their activities. This report thus addresses a need to re-examine people smuggling networks that target Australia as the destination country. There are various conceptual frameworks used to examine transnational organised crime as well as people smuggling networks. However, only certain elements of each framework 'fit' the Australian context. This gives credence to the argument that people smuggling networks are constantly developing and stereotypes of smuggling networks are unhelpful. As such, this report draws from elements of these networks and applies them to empirical research on people smuggling activities. In addition these elements are applied to profiles that have been created of individual smugglers as well as information from media reports and government documents. Research on people smuggling networks have established that they are highly adaptable and resilient and this is further strengthened by the profiles of smugglers. These profiles also suggest that roles traditionally assigned to specific actors within these smuggling networks do not fit in the Australian context. People smuggling networks also show flexibility in the way they respond to law enforcement measures and routes used to enter into Australia. Nevertheless...

## Betazeta Networks S.A.

Betazeta Networks S. A.; Corp Santiago Innova; Mabel Guerrero A.
Fonte: Corporação de Fomento da Produção Publicador: Corporação de Fomento da Produção
Tipo: proyecto
Relevância na Pesquisa
46.072427%
El proyecto consiste en exportar el modelo de blogs desarrollado en español por la empresa, al portugués considerando en esta exportación uno de los sitios emblemáticos de Betazeta (FayerWayer) el cual reporta anualmente ingresos en Chile del orden de USD 135.000, entre agosto y diciembre 2008, con una proyección de USD 750.000 para el año 2009.El mercado portugués a nivel de América Latina, que controla más del 50% del presupuesto de gasto publicitario en Internet: Brasil (según PriceWaterhouseCoopers Global Entertainment and Media Outlook). Dado esto ser exitoso en Brasil capturando el primer año un 15% de los lectores de blogs, tiene un impacto multiplicativo en nuestra empresa comparativamente pensando en cualquier otro mercado destino lo cual trae aparejado la generación de muchas oportunidades para el desarrollo de nuestra empresa, a nivel Latino Americano. Actualmente el sitio de Fayerwayer en portugués se encuentra visible y dando sus primeros pasos en fase de crecimiento, contando con 5 blogueros brasileros y un editor en jefe chileno y puede ser consultado en www.fayerwayer.com.br .En el siguiente Analytics se puede ver el crecimiento real que, actualmente, lleva adelante Fayerwayer Brasil lo cual nos permite reforzar la tesis de crecer en este mercado con una estrategia expansiva. Las macro acciones que considera realizar el proyecto son fundamentalmente dos : Actividad Global Detalle Promocionar y comercializar FayerWayer Brasil...

## The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

Greenbury, Sam F.; Johnston, Iain G.; Smith, Matthew A.; Doye, Jonathan P. K.; Louis, Ard A.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
36.296887%
We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SFboth and SFout topologies. The functionality of the SFout topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SFout and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability...

## Cooperating epidemics of foodborne diseases with diverse trade networks

Min, Yong; Ge, Ying; Jin, Xiaogang; Chang, Jie
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
36.302231%
The frequent outbreak of severe foodborne diseases warns of a potential threat that the global trade networks could spread fatal pathogens. The global trade network is a typical overlay network, which compounds multiple standalone trade networks representing the transmission of a single product and connecting the same set of countries and territories through their own set of trade interactions. Although the epidemic dynamic implications of overlay networks have been debated in recent studies, some general answers for the overlay of multiple and diverse standalone networks remain elusive, especially the relationship between the heterogeneity and diversity of a set of standalone networks and the behavior of the overlay network. In this paper, we establish a general analysis framework for multiple overlay networks based on diversity theory. The framework could reveal the critical epidemic mechanisms beyond overlay processes. Applying the framework to global trade networks, we found that, although the distribution of connectivity of standalone trade networks was highly heterogeneous, epidemic behavior on overlay networks is more dependent on cooperation among standalone trade networks rather than on a few high-connectivity networks as the general property of complex systems with heterogeneous distribution. Moreover...

## Quantitative Function and Algorithm for Community Detection in Bipartite Networks

Li, Zhenping; Wang, Rui-Sheng; Zhang, Shihua; Zhang, Xiang-Sun
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.30702%
Community detection in complex networks is a topic of high interest in many fields. Bipartite networks are a special type of complex networks in which nodes are decomposed into two disjoint sets, and only nodes between the two sets can be connected. Bipartite networks represent diverse interaction patterns in many real-world systems, such as predator-prey networks, plant-pollinator networks, and drug-target networks. While community detection in unipartite networks has been extensively studied in the past decade, identification of modules or communities in bipartite networks is still in its early stage. Several quantitative functions proposed for evaluating the quality of bipartite network divisions are based on null models and have distinct resolution limits. In this paper, we propose a new quantitative function for community detection in bipartite networks, and demonstrate that this quantitative function is superior to the widely used Barber's bipartite modularity and other functions. Based on the new quantitative function, the bipartite network community detection problem is formulated into an integer programming model. Bipartite networks can be partitioned into reasonable overlapping communities by maximizing the quantitative function. We further develop a heuristic and adapted label propagation algorithm (BiLPA) to optimize the quantitative function in large-scale bipartite networks. BiLPA does not require any prior knowledge about the number of communities in the networks. We apply BiLPA to both artificial networks and real-world networks and demonstrate that this method can successfully identify the community structures of bipartite networks.; Comment: 18 pages...

## Cancer Networks: A general theoretical and computational framework for understanding cancer

Werner, Eric
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
36.290884%
We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms. Cancer networks are special cases of developmental control networks. Cancer results from transformations of normal developmental networks. Our theory generates a natural classification of all possible cancers based on their network architecture. Each cancer network has a unique topology and semantics and developmental dynamics that result in distinct clinical tumor phenotypes. We apply this new theory with a series of proof of concept cases for all the basic cancer types. These cases have been computationally modeled, their behavior simulated and mathematically described using a multicellular systems biology approach. There are fascinating correspondences between the dynamic developmental phenotype of computationally modeled {\em in silico} cancers and natural {\em in vivo} cancers. The theory lays the foundation for a new research paradigm for understanding and investigating cancer. The theory of cancer networks implies that new diagnostic methods and new treatments to cure cancer will become possible.; Comment: Key words: Cancer networks...

## Exactly scale-free scale-free networks

Zhang, Linjun; Small, Michael; Judd, Kevin
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.296887%
Many complex natural and physical systems exhibit patterns of interconnection that conform, approximately, to a network structure referred to as scale-free. Preferential attachment is one of many algorithms that have been introduced to model the growth and structure of scale-free networks. With so many different models of scale-free networks it is unclear what properties of scale-free networks are typical, and what properties are peculiarities of a particular growth or construction process. We propose a simple maximum entropy process which provides the best representation of what are typical properties of scale-free networks, and provides a standard against which real and algorithmically generated networks can be compared. As an example we consider preferential attachment and find that this particular growth model does not yield typical realizations of scale-free networks. In particular, the widely discussed "fragility" of scale-free networks is actually found to be due to the peculiar "hub-centric" structure of preferential attachment networks. We provide a method to generate or remove this latent hub-centric bias --- thereby demonstrating exactly which features of preferential attachment networks are atypical of the broader class of scale-free networks. We are also able to statistically demonstrate whether real networks are typical realizations of scale-free networks...

## Community Structures Are Definable in Networks: A Structural Theory of Networks

Li, Angsheng; Pan, Yicheng; Li, Jiankou
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.30702%
We found that neither randomness in the ER model nor the preferential attachment in the PA model is the mechanism of community structures of networks, that community structures are universal in real networks, that community structures are definable in networks, that communities are interpretable in networks, and that homophyly is the mechanism of community structures and a structural theory of networks. We proposed the notions of entropy- and conductance-community structures. It was shown that the two definitions of the entropy- and conductance-community structures and the notion of modularity proposed by physicists are all equivalent in defining community structures of networks, that neither randomness in the ER model nor preferential attachment in the PA model is the mechanism of community structures of networks, and that the existence of community structures is a universal phenomenon in real networks. This poses a fundamental question: What are the mechanisms of community structures of real networks? To answer this question, we proposed a homophyly model of networks. It was shown that networks of our model satisfy a series of new topological, probabilistic and combinatorial principles, including a fundamental principle, a community structure principle...

## Sandpile cascades on interacting tree-like networks

Brummitt, Charles D.; D'Souza, Raissa M.; Leicht, Elizabeth A.
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.290884%
The vulnerability of an isolated network to cascades is fundamentally affected by its interactions with other networks. Motivated by failures cascading among electrical grids, we study the Bak-Tang-Wiesenfeld sandpile model on two sparsely-coupled random regular graphs. By approximating avalanches (cascades) as a multi-type branching process and using a generalization of Lagrange's expansion to multiple variables, we calculate the distribution of avalanche sizes within each network. Due to coupling, large avalanches in the individual networks are mitigated--in contrast to the conclusion for a simpler model [36]. Yet when compared to uncoupled networks, interdependent networks more frequently suffer avalanches that are large in both networks. Thus sparse connections between networks stabilize them individually but destabilize them jointly, as coupling introduces reservoirs for extra load yet also inflicts new stresses. These results suggest that in practice, to greedily mitigate large avalanches in one network, add connections between networks; conversely, to mitigate avalanches that are large in both networks, remove connections between networks. We also show that when only one network receives load, the largest avalanches in the second network increase in size and in frequency...

## Fermionic Networks: Modeling Adaptive Complex Networks with Fermionic Gases

Javarone, Marco Alberto
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
36.290884%
We study the structure of Fermionic networks, i.e., a model of networks based on the behavior of fermionic gases, and we analyze dynamical processes over them. In this model, particle dynamics have been mapped to the domain of networks, hence a parameter representing the temperature controls the evolution of the system. In doing so, it is possible to generate adaptive networks, i.e., networks whose structure varies over time. As shown in previous works, networks generated by quantum statistics can undergo critical phenomena as phase transitions and, moreover, they can be considered as thermodynamic systems. In this study, we analyze Fermionic networks and opinion dynamics processes over them, framing this network model as a computational model useful to represent complex and adaptive systems. Results highlight that a strong relation holds between the gas temperature and the structure of the achieved networks. Notably, both the degree distribution and the assortativity vary as the temperature varies, hence we can state that fermionic networks behave as adaptive networks. On the other hand, it is worth to highlight that we did not find relation between outcomes of opinion dynamics processes and the gas temperature. Therefore, although the latter plays a fundamental role in gas dynamics...

## The shortest path to complex networks

Dorogovtsev, S. N.; Mendes, J. F. F.
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.302231%
1. The birth of network science. 2. What are random networks? 3. Adjacency matrix. 4. Degree distribution. 5. What are simple networks? Classical random graphs. 6. Birth of the giant component. 7. Topology of the Web. 8.Uncorrelated networks. 9. What are small worlds? 10. Real networks are mesoscopic objects. 11. What are complex networks? 12. The configuration model. 13. The absence of degree--degree correlations. 14.Networks with correlated degrees.15.Clustering. 16. What are small-world networks? 17. Small worlds' is not the same as small-world networks'. 18. Fat-tailed degree distributions. 19.Reasons for the fat-tailed degree distributions. 20. Preferential linking. 21. Condensation of edges. 22. Cut-offs of degree distributions. 23. Reasons for correlations in networks. 24. Classical random graphs cannot be used for comparison with real networks. 25. How to measure degree--degree correlations. 26. Assortative and disassortative mixing. 27. Disassortative mixing does not mean that vertices of high degrees rarely connect to each other. 28. Reciprocal links in directed nets. 29. Ultra-small-world effect. 30. Tree ansatz. 31.Ultraresilience against random failures. 32. When correlated nets are ultraresilient. 33. Vulnerability of complex networks. 34. The absence of an epidemic threshold. 35. Search based on local information. 36.Ultraresilience disappears in finite nets. 37.Critical behavior of cooperative models on networks. 38. Berezinskii-Kosterlitz-Thouless phase transitions in networks. 39.Cascading failures. 40.Cliques & communities. 41. Betweenness. 42.Extracting communities. 43. Optimal paths. 44.Distributions of the shortest-path length & of the loop's length are narrow. 45. Diffusion on networks. 46. What is modularity? 47.Hierarchical organization of networks. 48. Convincing modelling of real-world networks:Is it possible? 49. The small Web..; Comment: 25 pages...

## Location-Aware Protocols for Energy-Efficient Information Processing in Wireless Sensor Networks

Sabbineni, Harshavardhan
Tipo: Dissertação
Relevância na Pesquisa
36.311333%

Advances in the miniaturization of microelectromechanical components have led to battery powered and inexpensive sensor nodes, which can be networked in an ad hoc manner to perform distributed sensing and information processing. While sensor networks can be deployed in inhospitable terrain to provide continuous monitoring and processing capabilities for a wide range of applications, sensor nodes are severely resource-constrained; they typically run on batteries and have a small amount of memory. Therefore, energy-efficient and lightweight protocols are necessary for distributed information processing in these networks.

The data provided by a sensor node is often useful only in the context of the location of the data source. Thus, sensor networks rely on localization schemes to provide location information to sensor nodes. The premise of this thesis is that location-aware protocols, which are based on the assumption that sensor nodes can estimate their location, improve the efficiency of data gathering and resource utilization of wireless sensor networks. Location-awareness improves the energy-efficiency of the protocols needed for routing, transport, data dissemination and self-organization of sensor networks. Existing sensor network protocols typically do not use location information effectively...

## Cooperation and resource optimization in wireless networks

Guan, Yang
Fonte: University of Delaware Publicador: University of Delaware