The maps of proportions of sheep sampled were also used to display the locations of abattoirs used for sampling, so they were presented as regular land area based maps.
In the context of H3Africa studies, the expectation is that it would ultimately be beneficial to create cell lines for (selected) samples so that samples will not be limited for future research and additional resources will not be needed for renewed sample collection but this is not currently economically and technologically feasible.
Therefore, based on the reviewers' comments, we have worked to improve colormap and colorbar labeling to make reading these maps more intuitive: a) Only in Figure 1 do we show data in the colormaps for individual samples so that the reader has a feel for the within-group variability.
The FLIC and AIC perform well for small samples, while the FLIC and BIC are better for large samples, so we prefer to rely on the FLIC (Pilla and Charnigo, Consistent estimation and model selection in semiparametric mixtures, submitted).
Much shorter times are necessary for oriented samples, so that strain-induced crystallization occurs in a few hours.
The percentage lysis of human erythrocytes was below 5.0% for all samples, so it can be expected that the extract and fractions have a no cytotoxity [29, 30].
The exposure protocols were organized so that to (1) minimize waiting of aliquoted cells for EP exposure to less than 10 min (on a few occasions, up to 20 min), (2) ensure the same treatment conditions for parallel samples, so that the only variable would be the EP exposure regimen, and (3) carefully randomize all EP treatments, including "sham" exposures.
Briefly, keeping the number of patients fixed in each of the three groups, we randomly permutated group status for the samples (so that they were re-assigned to different groups) and re-calculated the number of enriched CNVs in both disease groups relative to Ctrl.
Dilutions with glacial acetic acid were necessary for some samples so that the absorbance was <1.0.
At 3 weeks after papain injection, however, the disruption extended into the annulus for all samples so treated.
