22 research outputs found

    Calculation of a mov-vs-mov pattern.

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    <p>Patterns are calculated from each 1-vs-1 classifier; subsequently scaled and transformed into the source space; we then calculated the absolute value and averaged over patterns. Finally, we averaged over non-overlapping time segments. The same processing pipeline applies to the mov-vs-rest pattern.</p

    Classifier patterns.

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    <p>Shown are patterns between -0.4 s and 0.4 s relative to movement onset (<b>a</b>-<b>d</b>) and averaged over this time period (<b>e</b>-<b>h</b>). <b>a</b> and <b>e:</b> mov-vs-mov patterns during ME. <b>b</b> and <b>f:</b> mov-vs-rest patterns during ME. <b>c</b> and <b>g:</b> mov-vs-mov patterns during MI. <b>d</b> and <b>h:</b> mov-vs-rest patterns during MI. Only significant voxels are colored. Blue corresponds to zero, red to the maximum value.</p

    MI classification results for the single time point classification.

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    <p><b>a:</b> mov-vs-mov classification accuracies of all 15 subjects and the average (thick black line). Time point 0 s corresponds to the movement onset. <b>b:</b> mov-vs-rest classification accuracies. The horizontal solid line in a and b is the chance level; the horizontal dashed line is the significance level for the average. <b>c:</b> mov-vs-mov confusion matrix (occurrences sum to 100%). <b>d:</b> mov-vs-rest confusion matrix. Confusion matrices were calculated at the time point with the highest average classification accuracy (mov-vs-mov: -0.13 s; mov-vs-rest: 0.06 s).</p

    Classification accuracies for different window lengths.

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    <p>Time point 0 s corresponds to the movement onset. The horizontal solid lines are the chance level; the horizontal dashed lines are the significance levels. <b>a:</b> subject averaged ME mov-vs-mov classification accuracies. <b>b:</b> subject averaged ME mov-vs-rest classification accuracies. <b>c:</b> subject averaged MI mov-vs-mov classification accuracies. <b>d:</b> subject averaged MI mov-vs-rest classification accuracies.</p

    Maximum MI classification accuracies for the single time point classification.

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    <p>Maximum MI classification accuracies for the single time point classification.</p

    Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (<i>Shh, Ihh and Dhh</i>) in Vertebrates

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    <div><p>The Hedgehog (<i>Hh</i>) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one <i>Hh</i> gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – <i>Shh</i>; Indian hedgehog – <i>Ihh</i>; and Desert hedgehog – <i>Dhh</i>), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the <i>Hh</i> genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of <i>Hh</i>-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three <i>Hh</i> paralogs. We find suggestions that following the WGD events, vertebrate <i>Hh</i> paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the <i>Hh</i> orthologs. Our results provide new insights on the evolutionary history of the <i>Hh</i> gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.</p></div

    Structural features of the Hh proteins.

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    <p>The hedgehog proteins are composed by two main domains: the Hedge (N-terminal) and Hog (C-terminal) domains. The Hedge domain forms the HhN portion of the Hh proteins (together with the signaling sequence, SS) that is separated from the rest of protein by an auto-cleavage reaction preformed by the Hog domain <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Lee1" target="_blank">[4]</a>. The Hog domain forms the HhC portion of the Hh proteins and shares similarity with self-splicing Inteins on the Hint module <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Burglin2" target="_blank">[22]</a>. The auto-cleavage reaction occurs on a GCF (glycine-cysteine-phenylalanine) motif that forms the boundary between the two main parts of the Hh proteins, with the cysteine residue initiating a nucleophilic attack on the carbonyl carbon of the preceding residue, the glycine <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Beachy1" target="_blank">[5]</a>. The sterol-recognition region (SRR) forms the C-terminal region of the Hog domain and binds a cholesterol moiety that acts as an electron donor on a second nucleophilic attack that results in the cleavage of the bound between the glycine and cystein residues and in the attachment of the cholesterol moiety to the glycine residue <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Beachy1" target="_blank">[5]</a>. After auto-cleavage, the sterified HhN fragment is further palmitoylated on the cystein residue immediately after the SS region <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Chamoun1" target="_blank">[13]</a> and leaves the endoplasmic reticulum (ER) for later export <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074132#pone.0074132-Chen3" target="_blank">[11]</a>.</p

    Illustrative representation of the evolution of the LMBR1L–Dhh-RHEBL1-MLL2 linkage group evolution in vertebrates and their paralogs on the synteny of vertebrate <i>Shh</i> and <i>Ihh</i> genes.

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    <p>A dotted line between two genes is equivalent means these two genes are neighbors in this species but not in the reference species, where their orthologs are separated by one or more genes. The 3<sup>rd</sup> WGD duplication in the teleost lineage is not represented.</p
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