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I don't know if this is an issue with the PDF or your viewer, but one hackish way to do it is the following:

sage: def new_preparse(*args, **kwds):
....:     return preparse(*args, **kwds).replace('`', "'")
....: 
sage: sage.misc.preparser.preparse = new_preparse

Then you can do things like:

sage: print `cat`
cat

Note that this just does a "blind" replacement so something like

sage: print '`'

won't work correctly.