A Generalized Approach to Complex Networks

This work describes how the formalization of complex network concepts in terms of discrete mathematics, especially mathematical morphology, allows a series of generalizations and important results ranging from new measurements of the network topology to new network growth models. First, the concepts of node degree and clustering coefficient are extended in order to characterize not only specific nodes, but any generic subnetwork. Second, the consideration of distance transform and rings are used to further extend those concepts in order to obtain a signature, instead of a single scalar measurement, ranging from the single node to whole graph scales. The enhanced discriminative potential of such extended measurements is illustrated with respect to the identification of correspondence between nodes in two complex networks, namely a protein-protein interaction network and a perturbed version of it. The use of other measurements derived from mathematical morphology are also suggested as a means to characterize complex networks connectivity in a more comprehensive fashion.Comment: 10 pages, 2 figur

Parametrizing positroid cells using bicolored tilings

Bicolored tilings are given by a collection of smooth curves in a disk with a coloring map on the tiles these curves form. Postnikov diagrams can be viewed as the image of certain bicolored tilings under the Scott map. We introduce a reduction technique on bicolored tilings, and show that a tiling maps to a Postnikov diagram if and only if it is reduced. We then use bicolored tilings to parametrise positroid cells in the Grassmannian, and use the reduction, along with another transform, to generate tilings associated to lower-dimensional positroids cells. We also show that the parametrisation of such a cell can be derived from the parametrisation of the higher-dimensional cell

Statistical Mechanics Characterization of Neuronal Mosaics

The spatial distribution of neuronal cells is an important requirement for achieving proper neuronal function in several parts of the nervous system of most animals. For instance, specific distribution of photoreceptors and related neuronal cells, particularly the ganglion cells, in mammal's retina is required in order to properly sample the projected scene. This work presents how two concepts from the areas of statistical mechanics and complex systems, namely the \emph{lacunarity} and the \emph{multiscale entropy} (i.e. the entropy calculated over progressively diffused representations of the cell mosaic), have allowed effective characterization of the spatial distribution of retinal cells.Comment: 3 pages, 1 figure, The following article has been submitted to Applied Physics Letters. If it is published, it will be found online at http://apl.aip.org

Energy management

Tese de mestrado integrado. Engenharia Electrotécnica e de Computadores (Energy). Faculdade de Engenharia. Universidade do Porto. 201

Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria

Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness - were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.PTDC/MAR-BIO/1547/2014; full PhD scholarship from the Erasmus Mundus Programme/SALAM EMA2 lot7/SALA1206422info:eu-repo/semantics/publishedVersio