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For the different gene feature models we excluded genes that lacked the gene feature in question and for the promoter models we excluded genes for which their entire 500 bp upstream region overlapped a neighbouring gene (promoters with partial overlap to other genes or promoters were truncated).
In the regression models we excluded all 126 patients from Hospital 309 for whom data on pre-existing comorbid conditions were not available and also other two, one and five patients from Hong Kong, Beijing and Taiwan respectively with unknown age, pre-existing comorbid conditions, onset date or admission date.
Because we focus on quantitative decision models, we excluded literature that strictly covers general management, marketing and service management issues, and does not discuss modeling aspects and decision support systems at all.
In the final models, we excluded cases reported through PAS when first-diagnosis status was unknown.
For all models, we excluded variables if the partial likelihood test P-value>0.05.
In these models, we excluded regions with limited structural stability (i.e. regions with high modelling errors: signal peptides and regions following LRRCT).
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For each dinucleotide w, we define the set M w as the set of all positions i such that a nucleosome starting at i would cover the subsequence w, and we define m w i as the number of appearances of w in the sequence covered by a nucleosome starting at i (as with our biophysical models, we exclude the leading and trailing 3 bases of the sequence each nucleosome covers).
Since no second-order interaction terms were found significant in preliminary estimates of the regression model, we excluded them.
From the model we excluded those women with adenosquamous, small cell, neuroendocrine, or undifferentiated carcinomas owing to small numbers.
In the final model, we excluded the variable foot care, which is part of self-management, and this improved the fit of model.
To reduce the number of variables in the final model, we excluded potential confounders that were associated with the outcome in univariate analysis with P > 0.2.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com