Prioritizing MCDC test cases by spectral analysis of Boolean functions

Test case prioritization aims at scheduling test cases in an order that improves some performance goal. One performance goal is a measure of how quickly faults are detected. Such prioritization can be performed by exploiting the Fault Exposing Potential (FEP) parameters associated to the test cases. FEP is usually approximated by mutation analysis under certain fault assumptions. Although this technique is effective, it could be relatively expensive compared to the other prioritization techniques. This study proposes a cost-effective FEP approximation for prioritizing Modified Condition Decision Coverage (MCDC) test cases. A strict negative correlation between the FEP of a MCDC test case and the influence value of the associated input condition allows to order the test cases easily without the need of an extensive mutation analysis. The method is entirely based on mathematics and it provides useful insight into how spectral analysis of Boolean functions can benefit software testing

Additional file 1: of Identification of SMCHD1 domains for nuclear localization, homo-dimerization, and protein cleavage

Sequences of the primers for constructions. (XLSX 23 kb

Additional file 2: of Identification of SMCHD1 domains for nuclear localization, homo-dimerization, and protein cleavage

Sequences of the primers for RT-qPCR. (XLSX 46 kb

<i>Mest</i> and miR-335 are coordinately expressed in skeletal muscle during postnatal development and regeneration.

<p>(A) qRT-PCRs for <i>Mest</i> mRNA and miR-335 were performed with TA muscles of P0, 6 weeks, and 12 weeks old WT mice (n = 3 per time point). (B) qRT-PCRs for <i>Mest</i> mRNA and miR-335 were performed with TA muscles of 3 months old WT (n = 4) and <i>DMD–null</i> mice (n = 7). (C) qRT-PCRs for <i>Mest</i> mRNA and miR-335 were performed with TA muscles from day 0 to day 10 after CTX injection (n = 3 per time point). (D) A schematic diagram of the Mest and miR-335 genomic region on chromosome 6 in mouse. (E) qRT-PCR for miR-335 was performed in TA muscles of WT and <i>Mest</i>^<i>+/-</i> mice (n = 3 per genotype). Expression of <i>Mest</i> and that of miR-335 are normalized to <i>Gapdh</i> and snoRNA-202, respectively. Error bars indicate the s.e.m. *<i>P</i> < 0.05, **<i>P</i> < 0.01, ***<i>P</i> < 0.001 compared with P0 (A), WT (B and E), and day 0 (C).</p

Mest is required for body and skeletal muscle growth.

<p>(A) Representative images of 4 weeks old mice in individual genotypes. (B and C) Body weights of male littermate WT (n = 3–22), <i>Mest</i>^<i>+/-</i> (n = 6–15), <i>DMD-null</i> (n = 4–25), and <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> mice (n = 4–22) from 1 to 12 (11–13) weeks old. (D) Body weights of WT (n = 15) and <i>miR-335</i>^<i>+/Neo</i> (n = 12) mice at 6 weeks. (E) Body weights of WT (n = 8–15) and <i>miR-335</i>^<i>+/-</i> mice (n = 15–18) from 1 to 6 weeks old. (F) TA muscle weights of male littermate WT (n = 13), <i>Mest</i>^<i>+/-</i> (n = 6), <i>DMD-null</i> (n = 18), and <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> mice (n = 11) at 6 weeks old. (G) TA/Body weights of male littermate WT, <i>Mest</i>^<i>+/-</i>, <i>DMD-null</i>, and <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> mice at 6 weeks old. (H) TA muscle weights of male littermate WT (n = 3), <i>Mest</i>^<i>+/-</i> (n = 6), <i>DMD-null</i> (n = 4), and <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> mice (n = 4) at 11–13 weeks old. (I) TA/Body weights of male littermate WT, <i>Mest</i>^<i>+/-</i>, <i>DMD-null</i>, and <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> mice at 11–13 weeks old. (J and K) The numbers and average cross section areas of TA muscle fibers of male littermate WT (n = 7) and <i>Mest</i>^<i>+/-</i> mice (n = 4) at 6 weeks. Error bars indicate the s.e.m. *<i>P</i> < 0.05, ***<i>P</i> < 0.001. NS = Not significant.</p

Mest is required for skeletal muscle growth during regeneration.

<p>(A) H&E staining of TA muscles under normal condition (top panel) and 14 days after CTX-induced injury (middle and bottom panels). Bottom panel shows the extended images of a part of middle panel. (B) Average cross section areas of TA muscles in WT (n = 3), <i>Mest</i>^<i>+/-</i> (n = 4) and <i>miR-335</i>^<i>+/Neo</i> mice (n = 6) under normal condition and WT (n = 7), <i>Mest</i>^<i>+/-</i> (n = 4) and <i>miR-335</i>^<i>+/Neo</i> mice (n = 6) 14 days after CTX injury. (C) H&E staining of TA muscles of <i>DMD-null</i>, <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> and <i>miR-335</i>^<i>+/Neo</i><i>; DMD-null</i> mice at 11–13 weeks old. (D) Average cross section areas of TA muscles in <i>DMD-null</i> (n = 8), <i>Mest</i>^<i>+/-</i><i>; DMD-null</i> (n = 4) and <i>miR-335</i>^<i>+/Neo</i><i>; DMD-null</i> mice (n = 4) at 11–13 weeks old. Error bars indicate the s.e.m. ^<i>#</i><i>P</i> = 0.0549 compared with WT mice. Scale bar: 100 μm.</p

Generation of miR-335 deficient mice.

<p>(A) Design of constructs used for generation of miR-335 deficient mice. The miR-335 genomic locus was replaced by a floxed neomycin-resistance cassette (loxP-Neo-loxP) to obtain <i>miR-335</i>^<i>+/Neo</i> mice. <i>miR-335</i>^<i>+/-</i> mice (+/-) were generated by crossing male <i>miR-335</i>^<i>+/Neo</i> mice with female CAG-<i>cre</i> transgenic mice. (B) Southern blot analysis of WT and G418 resistant ES clones with 5’ and 3’ probes. †: Non-specific band. (C and D) PCR analysis for targeted allele with genomic DNA in tails of WT (+/+), <i>miR-335</i>^<i>+/Neo</i> (+/Neo), and <i>miR-335</i>^<i>+/-</i> mice (+/-). In (C), an insertion and a deletion of a floxed neomycin-resistance cassette in genomic DNA of <i>miR-335</i>^<i>+/Neo</i> (+/Neo) and <i>miR-335</i>^<i>+/-</i> mice (+/-), respectively, were detected with PCRs amplified with primers shown in Fig 2A (Orange and Green arrows). In (D), a PCR analysis to distinguish alleles for WT (+/+), <i>miR-335</i>^<i>+/-</i> (+/-), and <i>miR-335</i>^<i>-/-</i> mice (-/-) was shown. The WT allele-specific (280 bp) and the mutant allele-specific (306 bp) bands were amplified with the primers shown in Fig 2A (Green arrow). (E, F and G) qRT-PCR for miR-335 was performed in TA muscles isolated from WT, <i>miR-335</i>^<i>+/Neo</i>, and <i>miR-335</i>^<i>+/-</i> or <i>miR-335</i>^<i>-/+</i> mice (n = 3 per genotype). (H and I) qRT-PCR for <i>Mest</i> mRNA was performed in TA muscles of WT, <i>miR-335</i>^<i>+/-</i>, and <i>miR-335</i>^<i>+/Neo</i> mice (n = 3 per genotype). Expression of <i>Mest</i> mRNA and that of miR-335 are normalized to <i>Gapdh</i> and snoRNA-202, respectively. Error bars indicate the s.e.m. *<i>P</i> < 0.05, **<i>P</i> < 0.01, ***<i>P</i> < 0.001.</p

Mest but Not MiR-335 Affects Skeletal Muscle Growth and Regeneration

<div><p>When skeletal muscle fibers are injured, they regenerate and grow until their sizes are adjusted to surrounding muscle fibers and other relevant organs. In this study, we examined whether <i>Mest</i>, one of paternally expressed imprinted genes that regulates body size during development, and miR-335 located in the second intron of the <i>Mest</i> gene play roles in muscle regeneration. We generated miR-335-deficient mice, and found that miR-335 is a paternally expressed imprinted microRNA. Although both <i>Mest</i> and miR-335 are highly expressed during muscle development and regeneration, only <i>Mest^+/-</i> (maternal/paternal) mice show retardation of body growth. In addition to reduced body weight in <i>Mest^+/-; DMD-null</i> mice, decreased muscle growth was observed in <i>Mest^+/-</i> mice during cardiotoxin-induced regeneration, suggesting roles of Mest in muscle regeneration. Moreover, expressions of <i>H19</i> and <i>Igf2r</i>, maternally expressed imprinted genes were affected in tibialis anterior muscle of <i>Mest^+/-; DMD-null</i> mice compared to <i>DMD-null</i> mice. Thus, Mest likely mediates muscle regeneration through regulation of imprinted gene networks in skeletal muscle.</p></div

Additional file 3: Table S2. of BET bromodomain inhibitors and agonists of the beta-2 adrenergic receptor identified in screens for compounds that inhibit DUX4 expression in FSHD muscle cells

Collection of compounds that target epigenetic modifier proteins. (XLSX 33 kb

Additional file 1 of Simultaneous measurement of the size and methylation of chromosome 4qA-D4Z4 repeats in facioscapulohumeral muscular dystrophy by long-read sequencing

Additional file 1: Fig. S1. Characteristic sequences detected by nCATS. Sequences of representative (A) 4qA- and (B) 10q-derived reads obtained from the indicated samples. The XapI/non-XapI and BlnI/non-BlnI sites in the most distal D4Z4 RU are shown. In Samples 8, 14, and 15, the XapI, XapI and non-BlnI, and non-XapI sites, respectively, in the second most distal D4Z4 RU are shown, due to the difficulty in identifying restriction sites. Table S1. Lengths of reads derived from the 4qA locus in each patient. Table S2. Lengths of reads derived from the 10q locus in each patient. Table S3. Methylation rates across all D4Z4 RUs at the 4qA and 10q loci