85 research outputs found

    Detailed network statistics for aggregates generated from a select set of eight rod architectures.

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    <p>(A) Graphs showing distributions of node degree, betweenness and cluster coefficients for nodes generated from networks associated with the eight rod architectures leading to aggregates with the highest average node degree (domain architectures 25–32 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002406#pcbi-1002406-g003" target="_blank">Figure 3</a>). (B) Heatmaps showing the frequency of nodes (as a percentage) with specific values of betweenness and node degree. Rod architectures are indicated to the left of each heatmap. Aggregates composed of a large fraction of nodes which are both of high node degree and high betweenness are expected to be more resistant to mechanical failure. Standard deviations are provided for ten replicates.</p

    Network analysis of aggregate stability.

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    <p>Based on potential cross-links formed by neighbouring cross-linking domains, a network of rod connectivity can be generated (A). In this network nodes indicate individual rods and edges represent potential cross-links. (B) Graphs showing graph theoretical properties of networks generated for 32 different rod architectures composed of different numbers and sizes of elastomeric (blue) and cross-linking (red) domains. Domain architectures are indicated at the bottom. The arrow indicates architecture 28 used to construct the network in (A). Error bars indicate standard deviations for ten replicates. (C) Magnified section of the network presented in (A) highlighting a node (green) which has a high value of betweenness and low node degree and may therefore represent a weak point within the aggregate.</p

    Quantitative effects of domain number on aggregate morphology and stability.

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    <p>(A) Graphs showing the impact of increasing the relative number of domains while keeping rod length constant (20 units). Two conformations were examined: conformation 1 refers to rods in which the number of elastomeric domains (blue) exceeds the number of cross-linking domains (red); conformation 2 refers to rods in which the number if cross-linking domains exceeds the number of elastomeric domains. (B) Graphs showing the impact of adding additional domains. Here three conformations were investigated: conformation 1 consists of rods composed of domains of length one unit; conformation 2 consists of rods composed of elastomeric domains of length 4 units and cross-linking domains of length 1 unit; and conformation 3 is an asymmetrical rod consisting of two sets of: a elastomeric domain of length five units and a cross-linking domain of length two, between which are increasing numbers of elastomeric domains of length four and a cross-linking domain of length one. Error bars indicate standard deviations for ten replicates.</p

    Phylogenetic profile of 74 gene families derived from 'promiscuous' sequences

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    <p><b>Copyright information:</b></p><p>Taken from "The global landscape of sequence diversity"</p><p>http://genomebiology.com/2007/8/11/R238</p><p>Genome Biology 2007;8(11):R238-R238.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2258180.</p><p></p> We identified 13,055 sequences from the complete genome datasets as possessing significant sequence similarity to each of the 198 complete genomes. Gene family assignments obtained from the COGENT database were used to group these promiscuous sequences into 74 gene families. Annotations associated with the gene families show the high incidence of tRNA synthetases (blue text) and ABC transporters (red text). Phylogenetic profiles of each gene family were constructed from the presence or absence of promiscuous sequences in each genome. Two dimensional hierarchical clustering was performed on the profiles using average linkage on the basis of their Spearman rank correlation coefficients. Colored boxes indicate: presence of a promiscuous sequence in the genome (yellow); presence of a non-promiscuous sequence in the genome (blue, shaded according to the number of genomes with which it shares a sequence similarity match - in cases of more than one family member in a genome, the member with the highest number of matches was used); or absence of any family member in the genome (black box). Although the first nine gene families (indicated by the orange bar) contain representatives from the majority of genomes, the remaining gene families demonstrate various levels of specificity. For example, an additional 17 families (light green bars) are common to at least 50% of the eukaryotic genomes while 25 families possessed promiscuous sequences from only a single genome (purple bar). This specificity has led to a clear grouping of genomes into the three domains of life (as indicated on the left of the figure) with the exceptions of (placed by itself outside the main group of eukaryotes) and , which has been grouped with two strains of and . Both species are members of the Apicomplexa, a group of related protist parasites and appear to lack representative sequences from several of the 17 gene families that help define the other eukaryotes as a single group

    Distribution of conservation of sequences from full and partial genomes and functional characterization

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    <p><b>Copyright information:</b></p><p>Taken from "The global landscape of sequence diversity"</p><p>http://genomebiology.com/2007/8/11/R238</p><p>Genome Biology 2007;8(11):R238-R238.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2258180.</p><p></p> The frequency of sequences from full and partial genomes with significant sequence similarity to other full or partial genomes. Most sequences are associated with only a limited number of genomes; however, two peaks on the respective graphs indicate that there is a large proportion of sequences from full and partial genomes that have similarity to sequences from 198 and 185 genomes and partial genomes, respectively. The number of partial genome sequences with specific BLAST annotations that are conserved across either 50-191 (b) or 100-191 (c) other partial genomes (see Materials and methods for more details)

    Taxonomic distribution and functional analysis of genes from fully sequenced genomes

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    <p><b>Copyright information:</b></p><p>Taken from "The global landscape of sequence diversity"</p><p>http://genomebiology.com/2007/8/11/R238</p><p>Genome Biology 2007;8(11):R238-R238.</p><p>Published online 8 Nov 2007</p><p>PMCID:PMC2258180.</p><p></p> On the basis of a raw BLAST score cutoff of 50, we determined the number of sequences with similarity of sequences derived from the three domains of life. The Venn diagram shows the proportion of sequences associated with each group. Numbers in grey boxes show the proportion of sequences specific to their parent domain; numbers in white boxes show the proportion of sequences that are shared with one or more members of the same domain. The numbers in the overlapping regions of the diagram show the proportion of sequences shared between the overlapping domains: yellow, archaeal sequences; blue, bacteria; red, eukaryotes. Pie charts showing the proportion of each functional category for three datasets of sequences: highly conserved sequences (with sequence similarity to every other complete genome dataset); semi-conserved sequences (with similarity to at least one species from each of the three domains of life); and sequences unique to a genome (possessing no similarity to any other genome dataset). Functional categories were assigned with reference to the KEGG database (see Materials and methods)

    Brands and Inhibition: A Go/No-Go Task Reveals the Power of Brand Influence

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    <div><p>Whether selecting a candy in a shop or picking a digital camera online, there are usually many options from which consumers may choose. With such abundance, consumers must use a variety of cognitive, emotional, and heuristic means to filter out and inhibit some of their responses. Here we use brand logos within a Go/No-Go task to probe inhibitory control during the presentation of familiar and unfamiliar logos. The results showed no differences in response times or in commission errors (CE) between familiar and unfamiliar logos. However, participants demonstrated a generally more cautious attitude of responding to the familiar brands: they were significantly slower and less accurate at responding to these brands in the Go trials. These findings suggest that inhibitory control can be exercised quite effectively for familiar brands, but that when such inhibition fails, the potent appetitive nature of brands is revealed.</p></div

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    Global metabolic network indicating taxonomic representation of metabolic activities within the cow rumen dataset. Global metabolic network indicating taxonomic representation of metabolic activities within the cow rumen dataset. Pie charts indicate the relative proportion of each taxon, size of pie chart indicates relative expression (see key). Indicated are specific metabolic pathways. (PDF 1162 kb

    Performance of participants for the different measures, and the different subjective-ratings.

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    <p>(a) GO trial accuracy. I.e. pressing the space bar when required to do so. (b) Percentage of commission errors. I.e. pressing the space bar when it was not required to do so. (c) Mean RT for GO trials, (d) Mean RT for commission errors. Error bars indicate standard error. * Denotes significance.</p
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