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To compare differences in microbiota members between time points we used a linear mixed model.
Because metabolite concentrations varied widely between time points, we averaged the concentrations of each metabolite across the two samples.
Despite marked differences between acids and between time points, we were nonetheless successful in identifying a pH-independent core transcriptional response to all four tested acids at all times.
Because four separate nonparametric ANOVAs were performed and we could potentially perform 12 post-hoc tests between time points, we applied the Bonferroni correction factor [ 20] and considered p = 0.003 (e.g. 0.05/16) as the threshold for significance.
By allowing the model to change based on the duration between time points we provide a dynamic relationship for the model: as the spacing between time points increases, the mean and variance of the feature space changes (e.g., the variance on the cell movement increases while the mean division angle decreases).
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To test for differences in mercury concentrations between specific time points, we used contrast analysis.
A large portion of the net decrease in fitness of each line was due to a single drop between adjacent time points (we hereafter refer to a pair of adjacent time points as a "step").
To compare the longitudinal changes in likelihood of becoming a GP between the three time points, we used one-way repeated-measures ANOVA.
To compare disease severity between individuals and time points, we estimated the disease phenotype using a blinded scoring system based on the observed redness, scaliness, and plaque size and density (see Materials and Methods for detailed description).
To understand the functions of DEGs in mice during acute and chronic T. gondii infection and to characterize the overlap between DEGs at these time points we performed GO term enrichment analyses.
For comparisons between groups at specific time points, we used the Wilcoxon rank-sum test for non-normally distributed continuous variables, t-test for normally-distributed continuous variables, and Chi-square or Fisher exact tests for categorical variables.
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