Let p be the fraction of sites occupied by a species which will be called its abundance.
A larger fraction of sites, perhaps as great as 15%, show at least some evidence for similar biases of smaller amplitude.
The small fraction of sites that show methylation-dependent binding in vivo are in turn characterized by highly variable CTCF occupancy across cell types.
In our work, we use the Lee model to create a two dimensional discrete dynamical system in variables for calcium concentration in the presynaptic area and the fraction of sites that are ready to release neurotransmitter into the synaptic cleft.
Hence, we present a simple, modified metapopulation model, which combines 'internal colonisation' with 'rescue effect', so that it can be used for identifying the environmental factors that determine the fraction of sites occupied by a given metapopulation.
The enhanced rates are most likely due to the ability of adsorbed oxygen to prevent carbon nucleation and/or scavenge carbon enabling the reforming reaction to turnover on a larger fraction of sites.
If we define m = ∑ j m j (2.4). to be the average molar density of all three species, that is, of the glass, then f j = m j m (2.5). is the fraction of sites in the glass occupied by species j.
As before, the specific effective reaction rate of species j is denoted F j, and the species is present in a fraction of sites f j in the crystal (that is, f j = number of j molecules divided by M ( N + 1 ) ).
To test for mutational saturation in these alignments we constructed NJ trees considering all substitution sites and then solely the unsaturated fraction of sites using ASATURA [16].
For the Tph1 alignment, the JTT matrix was employed and cut off values of 850 and 2348 were respectively used prior to tree reconstruction to consider all residues in the alignment and only the unsaturated fraction of sites.
The models permit detecting episodes of positive selection acting on a fraction of sites ("site" models) or on particular phylogenetic lineages ("branch" models), as well as a combination of both ("branch-site" models).
