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In subsequent trials, fish were sampled as above, but at seven and 14 dpe (Trial 2) and at 28 and 43 dpe (Trial 3).
Furthermore, a bootstrap analysis with 100 pseudo-replicates was performed under the CAT+Γ4 model, a chain per dataset was run for the same length and sampled as above, the "burn-in" was fixed to 1,000 cycles.
Then, randomly generated observations from that normal distribution were sampled as above.
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From those who agreed, the same data and samples as above were obtained.
In addition, ΔCtendo was calculated by using endogenous control Ct values for the same calibrator sample as above, and subtracting subsequent endo Ct values from that calibrator [55].
The same samples as above were sequenced using commercial kits and protocols provided by Life Technologies, Carlsbad, USA.
We clustered the samples as above and compared these clusters to the class labels predicted by the decision tree model with Cohen's kappa statistic [ 24, 25].
Blood was sampled as described above.
Afterwards root canals were treated using PDT and sampled as described above.
The same blood samples as above were analyzed by flow cytometry and indirect ELISA.
For histology and fluorescence imaging analysis, 12-µm-thick sections were prepared from the same OCT embedded frozen sample as above.
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