Signatures of currency vertices

Many real-world networks have broad degree distributions. For some systems, this means that the functional significance of the vertices is also broadly distributed, in other cases the vertices are equally significant, but in different ways. One example of the latter case is metabolic networks, where the high-degree vertices -- the currency metabolites -- supply the molecular groups to the low-degree metabolites, and the latter are responsible for the higher-order biological function, of vital importance to the organism. In this paper, we propose a generalization of currency metabolites to currency vertices. We investigate the network structural characteristics of such systems, both in model networks and in some empirical systems. In addition to metabolic networks, we find that a network of music collaborations and a network of e-mail exchange could be described by a division of the vertices into currency vertices and others.Comment: to appear in Journal of the Physical Society of Japa

Functional cartography of complex metabolic networks

High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enables us to extract and display information contained in complex networks. Specifically, we demonstrate that one can (i) find functional modules in complex networks, and (ii) classify nodes into universal roles according to their pattern of intra- and inter-module connections. The method thus yields a ``cartographic representation'' of complex networks. Metabolic networks are among the most challenging biological networks and, arguably, the ones with more potential for immediate applicability. We use our method to analyze the metabolic networks of twelve organisms from three different super-kingdoms. We find that, typically, 80% of the nodes are only connected to other nodes within their respective modules, and that nodes with different roles are affected by different evolutionary constraints and pressures. Remarkably, we find that low-degree metabolites that connect different modules are more conserved than hubs whose links are mostly within a single module.Comment: 17 pages, 4 figures. Go to http://amaral.northwestern.edu for the PDF file of the reprin

Visualisation of Bluetongue Virus in the Salivary Apparatus of Culicoides Biting Midges Highlights the Accessory Glands as a Primary Arboviral Infection Site.

BACKGROUND Arthropods transmit a wide range of pathogens of importance for the global health of humans, animals, and plants. One group of these arthropod vectors, Culicoides biting midges (Diptera: Ceratopogonidae), is the biological vector of several human and animal pathogens, including economically important livestock viruses like bluetongue virus (BTV). Like other arthropod-borne viruses (arboviruses), Culicoides-borne viruses must reach and replicate in the salivary apparatus, from where they can be transmitted to susceptible hosts through the saliva during subsequent blood feeding. Despite the importance of the salivary gland apparatus for pathogen transmission to susceptible animals from the bite of infected Culicoides, these structures have received relatively little attention, perhaps due to the small size and fragility of these vectors. RESULTS In this study, we developed techniques to visualize the infection of the salivary glands and other soft tissues with BTV, in some of the smallest known arbovirus vectors, Culicoides biting midges, using three-dimensional immunofluorescence confocal microscopy. We showed BTV infection of specific structures of the salivary gland apparatus of female Culicoides vectors following oral virus uptake, related visualisation of viral infection in the salivary apparatus to high viral RNA copies in the body, and demonstrated for the first time, that the accessory glands are a primary site for BTV replication within the salivary apparatus. CONCLUSIONS Our work has revealed a novel site of virus-vector interactions, and a novel role of the accessory glands of Culicoides in arbovirus amplification and transmission. Our approach would also be applicable to a wide range of arbovirus vector groups including sand flies (Diptera: Psychodidae), as well as provide a powerful tool to investigate arbovirus infection and dissemination, particularly where there are practical challenges in the visualization of small size and delicate tissues of arthropods

Network Landscape from a Brownian Particle's Perspective

Given a complex biological or social network, how many clusters should it be decomposed into? We define the distance $d_{i,j}$ from node $i$ to node $j$ as the average number of steps a Brownian particle takes to reach $j$ from $i$. Node $j$ is a global attractor of $i$ if $d_{i,j}\leq d_{i,k}$ for any $k$ of the graph; it is a local attractor of $i$, if $j\in E_i$ (the set of nearest-neighbors of $i$) and $d_{i,j}\leq d_{i,l}$ for any $l\in E_i$. Based on the intuition that each node should have a high probability to be in the same community as its global (local) attractor on the global (local) scale, we present a simple method to uncover a network's community structure. This method is applied to several real networks and some discussion on its possible extensions is made.Comment: 5 pages, 4 color-figures. REVTeX 4 format. To appear in PR

CLOCK 3111 T/C SNP Interacts with Emotional Eating Behavior for Weight-Loss in a Mediterranean Population

Objective: The goals of this research was (1) to analyze the role of emotional eating behavior on weight-loss progression during a 30-week weight-loss program in 1,272 individuals from a large Mediterranean population and (2) to test for interaction between CLOCK 3111 T/C SNP and emotional eating behavior on the effectiveness of the weight-loss program. Design and Methods: A total of 1,272 overweight and obese participants (BMI: 31±5 kg/m2), aged 20 to 65 years, attending outpatient weight-loss clinics were recruited for this analysis. Emotional eating behavior was assessed by the Emotional Eating Questionnaire (EEQ), a questionnaire validated for overweight and obese Spanish subjects. Anthropometric measures, dietary intake and weight-loss progression were assessed and analyzed throughout the 30-week program. Multivariate analysis and linear regression models were performed to test for gene-environment interaction. Results: Weight-loss progression during the 30-week program differed significantly according to the degree of emotional eating behavior. Participants classified as 'very emotional eaters' experienced more irregular (P = 0.007) weight-loss, with a lower rate of weight decline (−0.002 vs. −0.003, P = 11), lost significantly less weight than those C carriers with a low emotional score (<11) (P = 0.005). Conclusions: Emotional eating behavior associates with weight-loss pattern, progression and total weight-loss. Additionally, CLOCK 3111 T/C SNP interacts with emotional eating behavior to modulate total weight loss. These results suggest that the assessment of this locus and emotional eating behavior could improve the development of effective, long-tern weight-management interventions

Validation of a questionnaire on emotional eating for use in cases of obesity : the Emotional Eater Questionnaire (EEQ)

Introduction: Emotions have a powerful effect on our choice of food and eating habits. It has been found that in some people there is relationship between eating, emotions and the increased energy intake. This relationship should be measurable to better understand how food is used to deal with certain mood states and how these emotions affect the effectiveness of weight loss programs. Objective: To develop and analyze the psychometric characteristics of a questionnaire on emotional eating for obesity easy to apply in clinical practice. Subjects and methods: A ten-item questionnaire called Emotional-Eater-Questionnaire (EEQ) was developed and administered to a total of 354 subjects (body mass index, 31 ± 5), aged 39 ± 12, who were subjected to a weight-reduction program. The questionnaire was specifically designed for obesity. Analysis of the internal structure, internal consistency, test-retest reliability and convergent validity with Mindful-Eater-Questionnaire (MEQ) were conducted. Results: After principal components analysis, the questionnaire was classified in three different dimensions that explained 60% of the total variance: Disinhibition, Type-of-food and Guilt. Internal consistency showed that Cronbach's alpha was 0.773 for the "Dishinibition" subscale, 0.656 for the "Type of food" subscale and 0.612 for the "Guilt" subscale. The test-retest stability was r =0.70. The data showed that the percentage of agreement between the EEQ and the MEQ was around 70% with a Kappa index of 0.40; P < 0.0001. Conclusion: We have presented a new questionnaire, which classifies individuals as a function of the relation between food intake and emotions. Such information will permit personalised treatments to be designed by drawing up early strategies from the very beginning of treatment programmesIntroducción: Las emociones tienen un poderoso efecto sobre la elección de alimentos y los hábitos alimentarios. Existe una relación entre comer, emociones y el aumento del aporte calórico. Esta relación debería ser medible para comprender mejor cómo utilizamos los alimentos en determinados estados de ánimo y cómo las emociones afectan a la eficacia de los programas de pérdida de peso. Objetivo: Desarrollar y analizar las características psicométricas de un cuestionario para identificar la ingesta emocional en la obesidad de fácil aplicación en la práctica clínica. Material y métodos: Se ha desarrollado y administrado un cuestionario de diez ítems llamado Cuestionario-de-Comedor-Emocional (CCE) a un total de 354 sujetos (Índice de Masa Corporal: 31 ± 5), (Edad: 39 ± 12 años), pertenecientes a un programa de reducción de peso. Se llevó a cabo un análisis de la estructura interna del cuestionario, de la consistencia interna, la fiabilidad testretest y la validez convergente con el Mindful-Eater- Questionnaire (MEQ). Resultados: El análisis de componentes principales del cuestionario encontró tres dimensiones diferentes que explicaban el 60% de la varianza: desinhibición, tipo de alimento y culpa. La consistencia interna mostró que el alfa de Cronbach fue de 0,773 para la subescala "Desinhibición", 0,656 para "Tipo de alimentos" y 0,612 para "culpa". La estabilidad test-retest fue de r = 0,70. Los datos mostraron que el porcentaje de acuerdo entre el CCE y MEQ era del 70% con un índice Kappa de 0,40, P < 0,0001. Conclusión: Hemos presentado un nuevo cuestionario, que clasifica a los individuos en función de la relación entre la ingesta de alimentos y las emociones. Esta información permitirá el diseño de tratamientos personalizados desde el inicio para la obesida

Comparing community structure identification

We compare recent approaches to community structure identification in terms of sensitivity and computational cost. The recently proposed modularity measure is revisited and the performance of the methods as applied to ad hoc networks with known community structure, is compared. We find that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes. The work is intended as an introduction as well as a proposal for a standard benchmark test of community detection methods.Comment: 10 pages, 3 figures, 1 table. v2: condensed, updated version as appears in JSTA

Depositional and structural controls on a fault-related dolostone formation (Maestrat Basin, E Spain)

Fault-related dolomitisation is responsible for the development of numerous hydrocarbon reservoirs hosted in diagenetically-altered carbonates and is therefore critical to hydrocarbon exploration, subsurface storage (i.e. CO2), the formation of associated mineralisation (i.e. MVT-deposits) and for understanding the key controls on subsurface fluid flow. Multiple dolomitised outcrop analogues have been characterised in recent years, but uncertainty still remains as to the controls on dolomitisation in terms of dolostone geobody size and geometries, their distribution and how they impact reservoir quality. Late Tithonian shallow-marine carbonates at Serra Esparreguera in the Maestrat Basin (E. Spain) were partially dolomitised on the seismic scale, resulting in a spectrum of geobodies with varying degrees of spatial connectivity. Dolostone predominantly replaces Polpís Fm wackestones and packstones, and bioclastic grainstones of the Bovalar Fm. Dolostone geobodies transition through vertical stratigraphy from being massive and spatially extensive to localised stratabound bodies as textural heterogeneity increases. Irregular dolostone geometries occur in the Polpís Fm, which is texturally homogenous relative to the overlying Bovalar Fm, cross-cutting bedding in areas with high abundance of faults. Faults occur adjacent to dolostone and constrain its lateral extent across the outcrop. Dolomitisation fronts are typically sharp with morphologies affected by small-scale faults and bedding-parallel stylolites. Dolomitisation occurred under burial conditions and dolostones were later overprinted by phases of calcite and saddle dolomite cementation. The spatial distribution of dolostone is strongly influenced by the depositional heterogeneity and faults, while smaller structures (i.e. metre-scale fractures and stylolites) and bedding surfaces controlled the dolomitisation front geometry. Dolostone geobodies at Serra Esparreguera provide new insights into the structural, depositional and diagenetic controls on dolomitisation at a seismic scale, which can be used as a predictive guide to improve the understanding of carbonate reservoirs with complex paragenetic histories

Large-scale structural organization of social networks

The characterization of large-scale structural organization of social networks is an important interdisciplinary problem. We show, by using scaling analysis and numerical computation, that the following factors are relevant for models of social networks: the correlation between friendship ties among people and the position of their social groups, as well as the correlation between the positions of different social groups to which a person belongs.Comment: 5 pages, 3 figures, Revte

Structural efficiency of percolation landscapes in flow networks

Complex networks characterized by global transport processes rely on the presence of directed paths from input to output nodes and edges, which organize in characteristic linked components. The analysis of such network-spanning structures in the framework of percolation theory, and in particular the key role of edge interfaces bridging the communication between core and periphery, allow us to shed light on the structural properties of real and theoretical flow networks, and to define criteria and quantities to characterize their efficiency at the interplay between structure and functionality. In particular, it is possible to assess that an optimal flow network should look like a "hairy ball", so to minimize bottleneck effects and the sensitivity to failures. Moreover, the thorough analysis of two real networks, the Internet customer-provider set of relationships at the autonomous system level and the nervous system of the worm Caenorhabditis elegans --that have been shaped by very different dynamics and in very different time-scales--, reveals that whereas biological evolution has selected a structure close to the optimal layout, market competition does not necessarily tend toward the most customer efficient architecture.Comment: 8 pages, 5 figure