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SummarizeOverlaps was used to calculate counts of reads for each gene with the default mode of "Union".

We calculated counts of the number of synonymous mutations that resulted in changes from preferred to unpreferred codons (P2U), or unpreferred to preferred codons (U2P), using the optimal codons defined in our analysis of ∆RSCU and the outgroup E. paradoxa to infer the ancestral state [ 31].

PTEN expression, detected with the primary antibody anti-PTEN (clone 28H6, NeoMarkers, Fremont, CA 94539TS 106) was quantified by using a visual grading system based on the intensity of staining and the percentage of positive nuclei calculated counting of 1000 cells in 3 different optical fields at 40× magnification.

The transduction efficiency was calculated counting the number of green cells in 10 randomly selected fields, 24 hours after transduction.

The participation rate was calculated counting the number of patients present at the outpatient clinic and the respective inpatient units at the time of assessment.

For each of the three years, the (30 arc seconds) GPWv4 population count and nation identifier data were used to calculate the counts of Chinese and Indian population for each grid cell in Fig. 1.

To estimate the relative carriage rate of oral consortia in panDCs or PBMCs, we calculated total counts of the three species in relation to total numbers of DCs and PBMCs in PD patients.

The incidence of fatal overdose (fODDTES) was calculated using counts of drug-induced deaths in the Downtown Eastside published annually by the British Columbia Vital Statistics Agency [36]-[44] [36]-[44]

In addition, breast cancer incidence rates could be calculated using counts of the female membership.

Flipper use was calculated as counts of strokes and total time of the entire sequence using the same flipper.

At 24 h, the percentage of gastrulae was calculated from counts of normal/abnormal and arrested embryos (see Gilbert 2000).

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