Data are presented as mean ± standard error of the mean (SEM), and a significance level of 0.05 was used for all analyses. All measurements (superoxide, MRI thickness, and 1/T1) were evaluated for a normal distribution by using residuals from the model used to test for differences, with no extreme departures from normality observed for any of the measurements. We used a linear mixed model for analyzing all outcome measurements. Type 3 tests in SAS (SAS Institute, Cary, NC, USA) were used to test fixed effects by using the Kenward-Roger method to calculate degrees of freedom.
Preliminary examination of the MRI profile data suggested that (1) superior and inferior sides of the retina exhibited distinctly different profiles in saline and MB Pde6brd10 mice, and (2) male Pde6brd10 mice appeared more responsive to MB than female Pde6brd10 mice. Thus, we included both side and sex in the analyses of the MRI profile data. We used a linear mixed model with cubic splines to model and compare mouse-specific MRI profiles. We included the fixed effects of “group” (wt, Pde6brd10 with saline, Pde6brd10 with MB), side, sex, MRI depth included as a cubic spline, and interactions among these effects. The number of “windows” with a relationship between 1/T1 and MRI depth (i.e., “knots”) was initially evaluated separately for each group (each “strain”/side/sex combination), and the Akaike information criteria (AIC) and Schwarz Bayesian information criteria (BIC) were used to identify the model with the fewest knots needed to model all groups. We also evaluated the number of knots in the potential full model that included all interactions. Based on this initial analysis, we used 5 knots for P23 mice and 7 knots for P30 mice in all remaining analyses. Random coefficients for the intercept and the depth-specific coefficients (cubic spline coefficients) were included in the model, based on comparing models with different sets of random coefficients by using AIC and BIC. For P23 mice, the 4-way interaction of group × sex × side × depth (all depth coefficients included) was marginally significant (P = 0.0712) based on a likelihood ratio test. Given the lower power expected for such a higher-order interaction, we decided to continue with a model that included the 4-way interaction. This 4-way interaction represents the differences in the 1/T1 MRI profiles among the specific combinations of group, sex, and side. For P30 mice, the 4-way interaction of group × sex × side × depth (all depth coefficients included) was not significant (P = 0.1969) based on a likelihood ratio test. All 3-way interactions were significant (P < 0.05), leading us to choose a final model with no 4-way interaction, but instead, all 3-way interactions. Mean differences between groups along depth were evaluated using contrasts based on the final model.
Superoxide was measured in 3 batches with 3 replicates per batch for each mouse, leading us to include random effects for mouse within group and batch within mouse and group. We included the fixed effects of strain and sex, along with the strain × sex interaction. Our preliminary analyses suggested that the variability differed among the strain × sex combinations. We included different residual and batch variances for male Pde6brd10 mice, based on evaluating potential heterogeneous variances by using the likelihood ratio test. Sex differences within strain, and strain differences within sex were examined using contrasts based on the final model.
Thickness was compared among postnatal day, strain (B6 vs. Pde6brd10), sex, and side (inferior vs. posterior) by using a linear mixed model that included a random intercept due to mouse nested within strain, day, and sex.