$newfile =~ s/\b([A-Z]{2,})\b/\\emph{lc($1)}/ge;
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Unless you happen to have a function called emph, that's not going to work. If you want to use /e, write it as:

$newfile =~ s/\b([A-Z]{2,})\b/'\emph{' . lc ($1) . '}'/eg;
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But I would go for the \L method.

Abigail