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

From Coherent Modes to Turbulence and Granulation of Trapped Gases

The process of exciting the gas of trapped bosons from an equilibrium initial state to strongly nonequilibrium states is described as a procedure of symmetry restoration caused by external perturbations. Initially, the trapped gas is cooled down to such low temperatures, when practically all atoms are in Bose-Einstein condensed state, which implies the broken global gauge symmetry. Excitations are realized either by imposing external alternating fields, modulating the trapping potential and shaking the cloud of trapped atoms, or it can be done by varying atomic interactions by means of Feshbach resonance techniques. Gradually increasing the amount of energy pumped into the system, which is realized either by strengthening the modulation amplitude or by increasing the excitation time, produces a series of nonequilibrium states, with the growing fraction of atoms for which the gauge symmetry is restored. In this way, the initial equilibrium system, with the broken gauge symmetry and all atoms condensed, can be excited to the state, where all atoms are in the normal state, with completely restored gauge symmetry. In this process, the system, starting from the regular superfluid state, passes through the states of vortex superfluid, turbulent superfluid, heterophase granular fluid, to the state of normal chaotic fluid in turbulent regime. Both theoretical and experimental studies are presented.Comment: Latex file, 25 pages, 4 figure

Mechanical, electrical and electro-mechanical properties of thermoplastic elastomer styrene–butadiene–styrene/multiwall carbon nanotubes composites

Composites of styrene-butadiene-styrene (SBS) block copolymer with multiwall carbon nanotubes (MWCNT) were processed by solution casting in order to investigate the influence of filler content, the different ratio of styrene/butadiene in the copolymer and the architecture of the SBS matrix on the electrical, mechanical and electro-mechanical properties of the composites. It was found that filler content and elastomer matrix architecture influence the percolation threshold and consequently the overall composite electrical conductivity. The mechanical properties are mainly affected by the styrene and filler content. Hopping between nearest fillers is proposed as the main mechanism for the composite conduction. The variation of the electrical resistivity is linear with the deformation. This fact, together with the gauge factor values in the range of 2 to 18, results in appropriate composites to be used as (large) deformation sensors.This work was funded by FEDER funds through the "Programa Operacional Factores de Competitividade – COMPETE" and by national funds by FCT - Fundação para a Ciência e a Tecnologia, through project references PTDC/CTM/69316/2006, PTDC/CTM/73465/2006, PTDC/CTM-NAN/112574/2009, and NANO/NMed- SD/0156/2007. PC, JS and VS also thank FCT for the SFRH/BD/64267/2009, SFRH/BD/60623/2009 and SFRH/BPD/63148/2009 grants, respectively. The authors also thank support from the COST Action MP1003 ”European Scientific Network for Artificial Muscles” and the COST action MP0902 “Composites of Inorganic Nanotubes and Polymers (COINAPO)

Toxicogenomic Analysis Suggests Chemical-Induced Sexual Dimorphism in the Expression of Metabolic Genes in Zebrafish Liver

10.1371/journal.pone.0051971PLoS ONE712

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

An analysis of waves underlying grid cell firing in the medial enthorinal cortex

Layer II stellate cells in the medial enthorinal cortex (MEC) express hyperpolarisation-activated cyclic-nucleotide-gated (HCN) channels that allow for rebound spiking via an I_h current in response to hyperpolarising synaptic input. A computational modelling study by Hasselmo [2013 Neuronal rebound spiking, resonance frequency and theta cycle skipping may contribute to grid cell firing in medial entorhinal cortex. Phil. Trans. R. Soc. B 369: 20120523] showed that an inhibitory network of such cells can support periodic travelling waves with a period that is controlled by the dynamics of the I_h current. Hasselmo has suggested that these waves can underlie the generation of grid cells, and that the known difference in I_h resonance frequency along the dorsal to ventral axis can explain the observed size and spacing between grid cell firing fields. Here we develop a biophysical spiking model within a framework that allows for analytical tractability. We combine the simplicity of integrate-and-fire neurons with a piecewise linear caricature of the gating dynamics for HCN channels to develop a spiking neural field model of MEC. Using techniques primarily drawn from the field of nonsmooth dynamical systems we show how to construct periodic travelling waves, and in particular the dispersion curve that determines how wave speed varies as a function of period. This exhibits a wide range of long wavelength solutions, reinforcing the idea that rebound spiking is a candidate mechanism for generating grid cell firing patterns. Importantly we develop a wave stability analysis to show how the maximum allowed period is controlled by the dynamical properties of the I_h current. Our theoretical work is validated by numerical simulations of the spiking model in both one and two dimensions

In silico design and biological evaluation of a dual specificity kinase inhibitor targeting cell cycle progression and angiogenesis

Methodology: We have utilized a rational in silico-based approach to demonstrate the design and study of a novel compound that acts as a dual inhibitor of vascular endothelial growth factor receptor 2 (VEGFR2) and cyclin-dependent kinase 1 (CDK1). This compound acts by simultaneously inhibiting pro-Angiogenic signal transduction and cell cycle progression in primary endothelial cells. JK-31 displays potent in vitro activity against recombinant VEGFR2 and CDK1/cyclin B proteins comparable to previously characterized inhibitors. Dual inhibition of the vascular endothelial growth factor A (VEGF-A)-mediated signaling response and CDK1-mediated mitotic entry elicits anti-Angiogenic activity both in an endothelial-fibroblast co-culture model and a murine ex vivo model of angiogenesis

Differential Actions of Chlorhexidine on the Cell Wall of Bacillus subtilis and Escherichia coli

Chlorhexidine is a chlorinated phenolic disinfectant used commonly in mouthwash for its action against bacteria. However, a comparative study of the action of chlorhexidine on the cell morphology of Gram-positive and Gram-negative bacteria is lacking. In this study, the actions of chlorhexidine on the cell morphology were identified with the aids of electron microscopy. After exposure to chlorhexidine, numerous spots of indentation on the cell wall were found in both Bacillus subtilis and Escherichia coli. The number of indentation spots increased with time of incubation and increasing chlorhexidine concentration. Interestingly, the dented spots found in B. subtilis appeared mainly at the hemispherical caps of the cells, while in E. coli the dented spots were found all over the cells. After being exposed to chlorhexidine for a prolonged period, leakage of cellular contents and subsequent ghost cells were observed, especially from B subtilis. By using 2-D gel/MS-MS analysis, five proteins related to purine nucleoside interconversion and metabolism were preferentially induced in the cell wall of E. coli, while three proteins related to stress response and four others in amino acid biosynthesis were up-regulated in the cell wall materials of B. subtilis. The localized morphological damages together with the biochemical and protein analysis of the chlorhexidine-treated cells suggest that chlorhexidine may act on the differentially distributed lipids in the cell membranes/wall of B. subtilis and E. coli