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In general, equations in variables should be in italic, while subscripts should not. Subscripts that are themselves variables should be italic. However, all greek symbols should never be in italic irrespective of whether they are variables or subscripts. This convention is largely due to a lack of a universally available italic symbol font.
In this template, whatever FrameMaker thinks is a variable is formatted in italic. In some cases manual adjustment is necessary to reformat non-variables back to roman, using the predefined Roman character tag.
Thanks to Eric Eisenhandler for help and clarification of this issue.
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