15 research outputs found

    Intestinal microbiota diversity in healthy young children and adults estimated by Simpson reciprocal index (1/D) and Shannon index.

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    <p>The whiskers show the highest and lowest value after excluding outliers (dots). The outliers are defined as more than 3/2 times of upper quartile or less than 3/2 times of lower quartile. Boxplot shows 25<sup>th</sup> and 75<sup>th</sup> percentile, with a line at median. The subjects are divided into two groups Adults (>21Y) and Children (<4Y) (A, C) or four groups‘<2Y’, ‘2-3Y’, ‘3-4Y’ and Adults (>21Y) (B, D). A) Simpson index of diversity shows a significant difference between adults and children (p = 0.007), B) Simpson index of diversity shows significant differences between ‘<2Y’and ‘3-4Y’ age groups and adults (*p = 0.006, **p = 0.002 respectively). C) Shannon index of diversity shows significant difference between adults and children (p = 0.001), D) Shannon index of diversity shows significant difference between ‘<2Y’, ‘3-4Y’ and adults, (*p = 0.003, **p = 0.001 respectively). Significant difference is also observed between ‘2-3Y’and ‘3-4Y’ age groups (***p = 0.043).</p

    Principal component analysis (PCA) (A) and redundancy analysis (RDA) (B) of fecal samples from healthy young children and adults at the phylum-like level.

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    <p>Log transformed data were used for analysis. In PCA, The first two principal components capture 21% (PCA1) and 16% (PCA2) of variance respectively. RDA plot shows the result from supervised PCA, where group assignment of subjects (adults or children) was used as a dependent variable. In RDA, first and second ordination axes are plotted, explaining 13% and 20% of the variance. Separation between children and adults is significant (p = 0.0002, permutation test).</p

    DNA-graphene interactions during translocation through nanogaps

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    <div><p>We study how double-stranded DNA translocates through graphene nanogaps. Nanogaps are fabricated with a novel capillary-force induced graphene nanogap formation technique. DNA translocation signatures for nanogaps are qualitatively different from those obtained with circular nanopores, owing to the distinct shape of the gaps discussed here. Translocation time and conductance values vary by ∼ 100%, which we suggest are caused by local gap width variations. We also observe exponentially relaxing current traces. We suggest that slow relaxation of the graphene membrane following DNA translocation may be responsible. We conclude that DNA-graphene interactions are important, and need to be considered for graphene-nanogap based devices. This work further opens up new avenues for direct read of single molecule activitities, and possibly sequencing.</p></div

    Comparison of bacterial groups showing significant differences in fecal samples from adults and healthy young children.<sup>*</sup>

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    *<p>Table includes groups at the genus-like level that constitute 0.01% or more of the total signal (total microbiota) in both adults and</p><p>young children, and show significant difference between the study groups.</p>A<p>Relative contribution of genus-like phylogenetic group is the average of relative abundances of the subjects in adults or children groups. </p>B<p>Ratio of the average relative abundance for each genus-like phylogenetic group. A – adults and C – children.</p>C<p>Adjusted p values from two sample t-test followed with the correction by Benjamini-Hochberg false discovery rate correction (p<0.05 significant).</p

    Principal component analysis (PCA) (A) and redundancy analysis (RDA) (B) of fecal samples from healthy young children and adults at the genus-like level.

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    <p>Log transformed data were used for analysis. In PCA, the first two principal components capture 33% (PCA1) and 11% (PCA2) of variance respectively. RDA plot shows the result from supervised PCA, where group assignment of subjects (adults or children) was used as a dependent variable. In RDA, first and second ordination axes are plotted, explaing 13% and 64% of the variance. Separation between children and adults is significant (p = 0.003, permutation test).</p

    Event detection and classification.

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    <p>(A) Raw current traces are recorded as described without DNA (black) and with DNA (red, blue). Eventual determination of rectangular and exponential events are indicated by blue square and red triangle, respectively. A dip in the control experiment (×) is discarded as a possible event as described in the text. (B) Narrow-band noise is removed from the traces and eventual event position is indicated. (C) Events are fitted with rectangular (blue) or exponential (red) traces depending on which fits better statistically.</p

    Recorded translocation of dsDNA through graphene nanogap with resistance of ∼ 36 MΩ.

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    <p>(A) Typical rectangular (blue, top) and exponential (red, bottom) translocation event. (B) Analysis of rectangular (blue squares) and exponential translocation events (red triangles, pointing up for Δ<i>G</i> > 0 and down for Δ<i>G</i> < 0). The solid lines are fits of the data to Δ<i>G</i> ∝ 1/<i>τ</i>. The error bars indicate the range of geometrical standard deviation.</p

    Effect of local nanogap geometry on translocation events, showing gaps and associated event data.

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    <p>(A) Illustration of continuously changing gap width over the length of the gap. As DNA translocates through the gap, its passage is characterized by the gap width at its point of traversal. (B) DNA passes through the upper gap, causing a rectangular conductance change. (C) DNA passes through the middle gap more slowly due to the narrower gap diameter. (D) DNA forces the edges of the lower gap to bend outward, which then relax to their equilibrium position once it has passed, causing an exponential decay event.</p
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