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The result of the methods is compared at the end of the manuscript using a numerical example.
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In the current manuscript, using a combination of bioinformatic predictions and manual adjustments, it was estimated that approximately 6% of these repetitive sequences are TEs, and 12 new families were found.
In this manuscript, using a murine model of OIR, we also demonstrate that suppression of apelin expression significantly inhibits pathological angiogenesis without reduction of both VEGF mRNA and its protein expression (Supplemental Figure S10).
Therefore, as an example, we repeated all the analyses described in this manuscript using a two-sample (parametric) t-test (although we could be far from certain that its distributional assumptions were satisfied) instead of the Wilcoxon test.
The following is an excerpt of the changes made to different parts of the manuscript: "Using a higher-level analysis (mixed-model ANOVA) with between-subjects factor "PROTOCOL" we directly contrasted the effects from Experiment 1 and Experiment 2 for each of the analyses conducted.
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The second part of the manuscript uses a simulated example to illustrate the different sampling procedures.
The Inamori, et al. 2013 manuscript used a disaccharide for establishing rates due to the low activity observed for monosaccharide as a substrate consistent with our findings.
This manuscript used a dataset that was freely available from online sources (http://ghdx.healthmetricsandevaluation.org/record/nicaragua-reproductive-health-survey-2006-2007).
The original manuscript used a previously published formula from Hajdin et al. RNA (2010) for estimating the p-value of a 3D RNA structure prediction but calculated these p-values using the incorrect mean RMSD values.
Reviewer #2: This manuscript uses a combination of bioinformatics and three-dimensional structures to discover a "missing" enzyme in an alternate pathway to isopentenyl pyrophosphate (IPP) in the mevalonate pathway.
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