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CHAPTER 4 (LMER; lmer function in R) were used for multiple factor analysis accounting for random effects (Kuznetsova et al., 2016), followed by the Benjamini-Hochberg procedure for multiple comparison post-hoc p-value adjustments (Benjamini and Hochberg, 1995). Log transformations (log[x+1]) were performed when the data was heteroscedastic. Residual plots were used to inspect LMER model fitting. For data that failed to fit LMERs, a Cumulative Link Mixed Model was fitted, accommodating one random factor, with the Laplace approximation (CLMM; clmm2 function in R) (Christensen, 2015). CLMM required categorising scores into bins that best represented the data. Histograms of complete data sets (blind to groups) were inspected to determine natural breaks in the data to define each category. CLMM models were inspected by plotting the observed data against the model predicated values, and comparing a linear model made with these data, to a line with an intercept of zero and a slope of 1. Post-hoc comparisons were performed using a Wilcoxon rank sum test on raw scores where applicable. Both models accommodated up to 4 fixed factors (treatment, side, regions and time), and one (CLMM: animal identification) or two (LMER: animal identification nested within their respective families) random factors. Models of CSSs were confirmed against models of RSSs, which enable more factors and thereby improved model fitting and statistical power. P values less than 0.05 were considered as statistically significant. 4.4 Results 4.4.1 Red light reduces mechanical hypersensitivity Hypersensitivity was defined relative to normal animals (n = 7). To determine the range of cumulative sensitivity scores (CSSs) of uninjured animals, mechanical sensitivity in non-injured control animals was quantified (NIC; n=7; Figure 4.1a). The majority of animals had a mix of category I and category II responses except for one animal that demonstrated two category III responses at the contralateral Above-Level region. The NIC group resulted in a mean CSS of 2.75 and a standard deviation of 2.09 and consequently a hypersensitivity threshold of 6.92 (mean + 2×SD) was established. The Above-Level was more sensitive than the At-Level (p = 0.036, CLMM), while side differences failed to reach significance (p = 0.054). Mechanical sensitivity responses at 1-7 days post spinal cord injury in animals with a spinal cord injury (SCI, untreated) and spinal cord injury with 670 nm light treatment were then quantified (SCI+670, Figure 4.1b; see Figure 4.2 for n values). Compared to NICs, CSSs were significantly elevated in the SCI group (p = 0.009, CLMM), which was evident as early as day 1 (p = 0.0046, Wilcoxon rank sum test) and day 3 (p = 0.0099, Wilcoxon rank sum test), while there was no significant difference between the NIC and SCI+670 groups (p = 0.23) over the 7 day recovery period. Furthermore, the SCI+670 group displayed a significant reduction of CSSs compared to 84PDF Image | Effects of Red Light Treatment on Spinal Cord Injury
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