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The sizes of cell nuclei (n > 600 from at least three mouse lungs in each genotype group) were evaluated by quantifying their average areas under 630X magnification using Fiji imaging software (1.48q).
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Autophagic activity was evaluated by quantifying the average number of GFP LC3 punctae per cell.
NFAT and GR translocation was quantified by calculating the Manders coefficient using the JaCOP plugin (Bolte & Cordelieres, 2006) for ImageJ, and colocalization of phagosomal markers was assessed by quantifying the average pixel intensity around single conidia using ImageJ.
Δψm was measured by quantifying the average fluorescence intensity of BA stained with the combination of MTG and TMRE before and after stimulation, as previously described in detail (Wikstrom et al, 2007).
Next, we tested for differences between alleles in the rate of cell-to-cell movement by quantifying the average effective radius of expanding foci at increasing hpi, and comparing these dynamics across hosts.
Silvering and reflectance in the skin is one of the most prominent morphological changes that occur in smolts and was measured by quantifying the average white pixel intensity of a defined region on the left lateral side of the body in 2057 fish.
We examined the effects of beads in the posterior and distal zones by quantifying the average change in tissue growth rate and deformation anisotropy in the region within 200 µm from the center of the bead implanted in each zone (see also supplementary material Fig. S3).
These procedures provided us with a conventional view of spatial genetic structure within each species by quantifying average structure patterns across our geographical region of interest [30].
To identify which spacing parameters define the optimal predictor, we varied both spacings simultaneously, and quantified their predictability by averaging the expression change of their 30 highest ranking genes.
One way of judging the efficiency of the filters is to compare the quality of the computed SACFs by quantifying the noise by average normalized χ values with respect to the model functions.
Elicitation was proposed by quantifying design attributes into Weighted Average Importance Index (WAII) and Consistency Index (CI).
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