Topological Motif Library.

Topological Motif Library.</p

Extended-fingerprint Jaccard similarity between biological RNAs.

<p>Upper triangle. Sequence identity. Lower triangle. Extended-fingerprint Jaccard Similarity of all the curated RNA structures (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0164726#pone.0164726.s008" target="_blank">S3 Fig</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0164726#pone.0164726.s010" target="_blank">S5</a> Table for IDs). Sequence identity is shown in color, ranging from 0 (blue) to 1 (red) at steps of 0.1. A neighbor-joining dendrogram calculated according to the extended-fingerprint Jaccard similarity is shown on the right side of the heat map. </p

XIOS graph stem-stem relationships.

<p>Edges show the relationship between two stems, and may be one of four types: X (mutually exclusive), I (included or nested), O (overlapping or pseudoknotted), or S (serial or adjacent). </p

Subgraph random sampling pseudocode.

<p>Subgraph random sampling pseudocode.</p

Scaling of sampling with graph size.

<p>Fingerprints for 151 RNA graphs in the curated set were determined multiple times (10 times per RNA graph) by random sampling. Numbers above the dots indicate the number of different graphs with the same size (vertex number); each dot represents the average number of iterations needed to determine the complete fingerprint for this specific size group, with bars showing the maximum and minimum iterations as well.</p

Classification performance of similarity functions.

<p>Pairwise similarities were calculated, using the indicated similarity functions, for all RNAs in the curated dataset and ranked from high to low. A pair of RNAs from the same curated family is considered a positive match; otherwise they are considered to be a negative match. In all panels, the dashed line indicates the simple fingerprint, and the solid line the extended fingerprint. The AUC for the simple and extended fingerprints, respectively, are indicated in parentheses, below. (A) Intersection Similarity (AUC simple, 0.759; extended, 0.746), (B) Cosine Similarity (0.867; 0.753), (C) Dice Similarity (0.821; 0.864), (D) Hamming Similarity (0.789; 0.834), and (E) Jaccard Similarity (0.870; 0.952). (F) Classification after random removal of vertices from RNA graphs. All RNAs (except for tRNA and 5S rRNA which are too small for 70% stem removal) are included. The five lines show ROC curves with differing fractions of stems removed (AUC in parentheses): (0) no stem removal (AUC = 0.909), (1) 10% stem removal (0.844), (2) 30% stem removal (0.810), (3) 50% stem removal (0.691), and (4) 70% stem removal (0.605).</p

RNA fingerprint similarity functions.

<p>X and Y are fingerprints of the two structures being compared.</p

Example of an RNA fingerprint.

<p>All 3-vertex motifs (corners) in a 6-vertex RNA graph (center) are shown. The thick solid lines represent RNA chain, the thin solid lines represent base pairs, and the dotted lines represent RNA sequences whose connectivity is not completely specified. </p

Parent-Child relationships.

<p>The parent graph is a 4-stem motif; two different child graphs are created by adding one stem to the parent graph.</p

Selecting Doped Er³⁺/Ho³⁺/Tm³⁺ in the Perovskite-Like Material Cs₃YF₆: Yb³⁺ to Achieve Ultrasensitive Luminescence Intensity Ratio Temperature Sensing

Luminescence intensity ratio (LIR) thermometry based on distinct up-conversion luminescence centers was established in Cs-based fluorides. By contrasting the nonthermally coupled luminescence intensity of Er3+/Ho3+/Tm3+, it is possible to determine which kind of up-conversion emission ion is more suited for the perovskite-like Cs3YF6 material. The best option is Er-doped Cs3YF6 samples with a relative sensitivity (Sr) of 0.96% K–1, according to a comparison of the LIR fitting findings. However, the extremely high absolute sensitivity (Sa) in Cs3YF6: Yb, Tm suggests that Sa is not trustworthy in the LIR temperature evaluation system according to the temperature resolution δT. This work provides recommendations for the LIR temperature sensing design for comparable Cs-based fluorides while minimizing time and expense