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The formed haplotype blocks were analyzed by using the PLINK software, with the sliding window approach, regression models, and controlling for age and sex.
The amplitudes of raw MEPs recorded during baseline blocks were analyzed by means of a mixed-model ANOVA, with Muscle (FDI and ADM), TMS Intensity (120% and 140% of rMT) and Session (PRE and POST) as within-subjects factors, and with Experiment (arm forwards, EXP1, and arm backwards, EXP2) as a between-subjects factor.
Tissue cores (3 mm diameter; 0.8 to 1.7 mg) punched from the formalin-fixed, paraffin embedded tissue blocks were analyzed by mass spectrometry (MS) [ 26].
Paraffin-embedded tumor blocks were analyzed by immunohistochemistry for DCC and p53 proteins expression using a standard avidin-biotynilated peroxidase complex (ABC) staining method [ 15].
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The significance of each haplotype within the defined blocks was analyzed by PLINK software [ 25] (http://pngu.mgh.harvard.edu/~purcell/plink/).edu/~purcell/plink/
To improve the reliability of the classification, the other missing parameters (number of floors and position in the block) were analyzed by assigning both the minimum and the maximum score admitted in the Bernardini et al. (2008) method.
The parsimony tree file for each 4gamete block was analyzed by the program TreeScan [27], which identifies the edges in the tree and, for each edge, the alleles that belong to the two clades defined by the edge.
This was repeated for each of the three blocks and the sample for each block was analyzed by the Cornell Nutrition Analysis Laboratory (Ithaca, NY).
Percent infected data from the two blocks were analyzed together because their grand means differed by only 1%.
A total of three blocks were analyzed.
For 198 cases one paraffin block was analyzed, while for 34 cases 2 paraffin blocks were analyzed and for 3 cases 3 paraffin blocks were analyzed.
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