The goal of this study is to determine the best substitution proportion of the SSOS for fine and coarse aggregates.
The adverse effects of HES may depend on the molecular weight and the degree of substitution (proportion of hydroxylethyl groups on glucose molecules) [ 13].
The alignment data are provided in Additional File 3. Protein maximum-likelihood analyses were performed using PhyML [ 62] with the WAG model of amino acids substitution, proportion of variable rates estimated from the data, and nine categories of substitution rates.
After binning these simulated data into the five allele frequency classes, we estimate basic evolutionary parameters including mean Grantham score of amino acid substitutions, proportion of non-synonymous SNPs, fraction of polymorphisms in 1st codon position, and shifts in codon preference.
Ten concrete mixtures were prepared, varying w/c ratio, admixtures content, recycled coarse aggregate substitution ratio and aggregates proportioning methods.
A heuristic search for a maximum-likelihood tree, under time reversible model of nucleotide substitution, with proportion of invariable sites and gamma rate distribution was made.
Parameters such as base frequencies, numbers of substitution types, proportion of invariable sites, and Gamma distribution shape were optimized using Modeltest3.7 [37] with the Akaike Information Criterion AICC).
The input trees were calculated using PHYML 3.0 [69] with a GTR substitution model, proportion of invariable sites and among site rate parameters estimated from the data.
The parameters of character state frequencies, substitution rates, proportion of invariable sites, and gamma shape were unlinked across the different partitions for all analyses.
We used the default options of PhyML_aLRT with the JTT matrix for amino acid substitutions, the proportion of invariable sites set to zero, and with only one category of substitution rate [ 28].
The uncorrected mean number of nucleotide substitutions (d) and proportion of nucleotide substitutions (p) were calculated for the coding regions (all positions and third codon positions) and the non-coding regions of all pairs of unique alleles [56] using MEGA.
