15,883 research outputs found

    Mammalian Brain As a Network of Networks

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    Acknowledgements AZ, SG and AL acknowledge support from the Russian Science Foundation (16-12-00077). Authors thank T. Kuznetsova for Fig. 6.Peer reviewedPublisher PD

    A multidimensional perspective on microbial interactions

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    Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.R01 GM121950 - NIGMS NIH HHSPublished versio

    A Similarity Based Approach for Chemical Category Classification

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    This report aims to describe the main outcomes of an IHCP Exploratory Research Project carried out during 2005 by the European Chemicals Bureau (Computational Toxicology Action). The original aim of this project was to develop a computational method to facilitate the classification of chemicals into similarity-based chemical categories, which would be both useful for building (Q)SAR models (research application) and for defining chemical category proposals (regulatory application).JRC.I-Institute for Health and Consumer Protection (Ispra

    Leveraging Citation Networks to Visualize Scholarly Influence Over Time

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    Assessing the influence of a scholar's work is an important task for funding organizations, academic departments, and researchers. Common methods, such as measures of citation counts, can ignore much of the nuance and multidimensionality of scholarly influence. We present an approach for generating dynamic visualizations of scholars' careers. This approach uses an animated node-link diagram showing the citation network accumulated around the researcher over the course of the career in concert with key indicators, highlighting influence both within and across fields. We developed our design in collaboration with one funding organization---the Pew Biomedical Scholars program---but the methods are generalizable to visualizations of scholarly influence. We applied the design method to the Microsoft Academic Graph, which includes more than 120 million publications. We validate our abstractions throughout the process through collaboration with the Pew Biomedical Scholars program officers and summative evaluations with their scholars

    Regulation of tomato fruit ripening

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    Fruit ripening is a sophisticatedly orchestrated developmental process, unique to plants, that results in major physiological and metabolic changes, ultimately leading to fruit decay and seed dispersal. Because of their strong impact on fruit nutritional and sensory qualities, the ripeningassociated changes have been a matter of sustained investigation aiming at unravelling the molecular and genetic basis of fruit ripening. Tomato rapidly emerged as the model of choice for fleshy fruit research and a wealth of genetic resources and genomics tools have been developed, providing new entries into the regulatory mechanisms involved in the triggering and coordination of the ripening process. Some of the key components participating in the control of tomato fruit ripening have been uncovered, but our knowledge of the network of signalling pathways engaged in this complex developmental process remains fragmentary. This review highlights the main advances and emphasizes issues still to be addressed using the rapidly developing ‘omics’ approaches
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