Tissue-specific expression of histone H3 variants diversified after species separation

Additional file 3: Predicted CDS of human histone H3/H4 variants, contains Table S2, which lists the CDS locus information of the predicted human histone H3 and H4 variants in an Excel file

Acoustic wave scattering from random porous media

Acoustic wave scattering from random porous media is formulated from the Biot theory, which describes the acoustic interaction between a porous solid matrix and pore fluid. Equations of motion valid for heterogeneous, non-uniform porous materials are derived fast. The equations are simplified in the absence of the shear-wave. By applying a modal decoupling method to the simplified Biot\u27s equations of motion, coupled Helmholtz equations for compressional waves in inhomogeneous porous medium are derived. A first-order perturbation and the Born approximation are applied to the coupled Helmholtz equations in random porous media. Pressure reflection and transmission coefficients necessary for the model are derived as well. The state-of-the-art model applying the Biot theory to volume-scattering enables us to evaluate the effects of volume-scattering from Biot\u27s slow compressional wave. Numerical evaluations show that effects of the slow wave in the volume-scattering from the air-saturated sand are detectable.The model-data comparison of the back-scattering at a frequency of 5.5 kHz is made. The interface roughness-scattering model is extended to the poro-elastic medium. Unknown parameters are estimated using a non-linear optimization procedure based on the matched field processing and the adaptive simulated annealing. The model-data comparison shows that the interface roughness-scattering is dominant at lower grazing angles, while the volume-scattering is dominant at higher grazing angles at the sandy site. The frequency dependence of sound speeds is also discussed

MOESM4 of Tissue-specific expression of histone H3 variants diversified after species separation

Additional file 4: Predicted CDS of rat histone H3 variants, contains Table S3 for the rat H3 sequence prediction results as an Excel file, which is the same format as Table S2

MOESM5 of Tissue-specific expression of histone H3 variants diversified after species separation

Additional file 5: Similarity of amino acid and DNA sequence, contains Table S4, which shows amino acid and DNA sequence similarities between mouse H3 variant proteins/genes in Excel file

Establishment of preanalytical conditions for microRNA profile analysis of clinical plasma samples.

The relationship between the expression of microRNAs (miRNAs) in blood and a variety of diseases has been investigated. MiRNA-based liquid biopsy has attracted much attention, and cancer-specific miRNAs have been reported. However, the results of analyses of the expression of these miRNAs vary among studies. The reproduction of results regarding miRNA expression levels could be difficult if there are differences in the data acquisition process. Previous studies have shown that the anticoagulant type used during plasma preparation and sample storage conditions could contribute to differences in measured miRNA levels. Thus, the impact of these preanalytical conditions on comprehensive miRNA expression profiles was examined. First, the miRNA expression profiles of samples obtained from healthy volunteers were analyzed using next-generation sequencing. Based on an analysis of the library concentration, human genome identification rate, ratio of unique sequences and expression profiles, the optimal preanalytical conditions for obtaining highly reproducible miRNA expression profiles were established. The optimal preanalytical conditions were as follows: ethylenediaminetetraacetic acid (EDTA) as the anticoagulant, whole-blood storage at room temperature within 6 hours, and plasma storage at 4°C or -20°C within 30 days. Next, plasma samples were collected from 60 cancer patients (3 facilities × 20 patients/facility), and miRNA expression profiles were analyzed. There were no significant differences in measurements except in the expression of erythrocyte-derived hsa-miR-451a. However, the variation in hsa-miR-451a levels was smaller among facilities than among individuals. This finding suggests that samples obtained from the same facility could show significantly different degrees of hemolysis across individuals. We found that the standardization of anticoagulant use and storage conditions contributed to reducing the variation in sample quality across facilities. The findings from this study could be useful in developing protocols for collecting samples from multiple facilities for cancer screening tests