Innovative in silico approaches to address avian flu using grid technology

The recent years have seen the emergence of diseases which have spread very quickly all around the world either through human travels like SARS or animal migration like avian flu. Among the biggest challenges raised by infectious emerging diseases, one is related to the constant mutation of the viruses which turns them into continuously moving targets for drug and vaccine discovery. Another challenge is related to the early detection and surveillance of the diseases as new cases can appear just anywhere due to the globalization of exchanges and the circulation of people and animals around the earth, as recently demonstrated by the avian flu epidemics. For 3 years now, a collaboration of teams in Europe and Asia has been exploring some innovative in silico approaches to better tackle avian flu taking advantage of the very large computing resources available on international grid infrastructures. Grids were used to study the impact of mutations on the effectiveness of existing drugs against H5N1 and to find potentially new leads active on mutated strains. Grids allow also the integration of distributed data in a completely secured way. The paper presents how we are currently exploring how to integrate the existing data sources towards a global surveillance network for molecular epidemiology.Comment: 7 pages, submitted to Infectious Disorders - Drug Target

Coupling geometry on binary bipartite networks: hypotheses testing on pattern geometry and nestedness

Upon a matrix representation of a binary bipartite network, via the permutation invariance, a coupling geometry is computed to approximate the minimum energy macrostate of a network's system. Such a macrostate is supposed to constitute the intrinsic structures of the system, so that the coupling geometry should be taken as information contents, or even the nonparametric minimum sufficient statistics of the network data. Then pertinent null and alternative hypotheses, such as nestedness, are to be formulated according to the macrostate. That is, any efficient testing statistic needs to be a function of this coupling geometry. These conceptual architectures and mechanisms are by and large still missing in community ecology literature, and rendered misconceptions prevalent in this research area. Here the algorithmically computed coupling geometry is shown consisting of deterministic multiscale block patterns, which are framed by two marginal ultrametric trees on row and column axes, and stochastic uniform randomness within each block found on the finest scale. Functionally a series of increasingly larger ensembles of matrix mimicries is derived by conforming to the multiscale block configurations. Here matrix mimicking is meant to be subject to constraints of row and column sums sequences. Based on such a series of ensembles, a profile of distributions becomes a natural device for checking the validity of testing statistics or structural indexes. An energy based index is used for testing whether network data indeed contains structural geometry. A new version block-based nestedness index is also proposed. Its validity is checked and compared with the existing ones. A computing paradigm, called Data Mechanics, and its application on one real data network are illustrated throughout the developments and discussions in this paper

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Cortex, countercurrent context, and dimensional integration of lifetime memory

The correlation between relative neocortex size and longevity in mammals encourages a search for a cortical function specifically related to the life-span. A candidate in the domain of permanent and cumulative memory storage is proposed and explored in relation to basic aspects of cortical organization. The pattern of cortico-cortical connectivity between functionally specialized areas and the laminar organization of that connectivity converges on a globally coherent representational space in which contextual embedding of information emerges as an obligatory feature of cortical function. This brings a powerful mode of inductive knowledge within reach of mammalian adaptations, a mode which combines item specificity with classificatory generality. Its neural implementation is proposed to depend on an obligatory interaction between the oppositely directed feedforward and feedback currents of cortical activity, in countercurrent fashion. Direct interaction of the two streams along their cortex-wide local interface supports a scheme of "contextual capture" for information storage responsible for the lifelong cumulative growth of a uniquely cortical form of memory termed "personal history." This approach to cortical function helps elucidate key features of cortical organization as well as cognitive aspects of mammalian life history strategies

Novel Multidimensional Models of Opinion Dynamics in Social Networks

Unlike many complex networks studied in the literature, social networks rarely exhibit unanimous behavior, or consensus. This requires a development of mathematical models that are sufficiently simple to be examined and capture, at the same time, the complex behavior of real social groups, where opinions and actions related to them may form clusters of different size. One such model, proposed by Friedkin and Johnsen, extends the idea of conventional consensus algorithm (also referred to as the iterative opinion pooling) to take into account the actors' prejudices, caused by some exogenous factors and leading to disagreement in the final opinions. In this paper, we offer a novel multidimensional extension, describing the evolution of the agents' opinions on several topics. Unlike the existing models, these topics are interdependent, and hence the opinions being formed on these topics are also mutually dependent. We rigorous examine stability properties of the proposed model, in particular, convergence of the agents' opinions. Although our model assumes synchronous communication among the agents, we show that the same final opinions may be reached "on average" via asynchronous gossip-based protocols.Comment: Accepted by IEEE Transaction on Automatic Control (to be published in May 2017

Reasoning & Querying – State of the Art

Various query languages for Web and Semantic Web data, both for practical use and as an area of research in the scientific community, have emerged in recent years. At the same time, the broad adoption of the internet where keyword search is used in many applications, e.g. search engines, has familiarized casual users with using keyword queries to retrieve information on the internet. Unlike this easy-to-use querying, traditional query languages require knowledge of the language itself as well as of the data to be queried. Keyword-based query languages for XML and RDF bridge the gap between the two, aiming at enabling simple querying of semi-structured data, which is relevant e.g. in the context of the emerging Semantic Web. This article presents an overview of the field of keyword querying for XML and RDF

Media coverage of climate change mitigation in the spanish press

This article analyzes how the Spanish press covers the mitigation of climate change. We have used the search engine MyNews to study in El País and El Mundo, the newspapers with the largest circulation in Spain during the years 2016 and 2017, the news that includes the words "mitigacion" o "reducción de emisiones", y "cambio climatico” o “calentamiento global" in the most circulation newspapers in Spain in 2016 and 2017: El País and El Mundo. To explain how mitigation is covered by the Spanish press, we have used a series of categories and variables. As a result, we find an important difference between the urgency expressed by the scientific community and the reduced presence of this topic in the Spanish press