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I found a solution myself. With the following recipe - everything works very well.
title = u'Nature feed'
oldest_article = 7
max_articles_per_feed = 100
no_stylesheets = True
extra_css = '.heading { font: serif large }'
use_embedded_content = True
feeds = [(u'Nature', u'http://barf.jcowboy.org/nature.xml')]
I think this is a great way to aggregate PubMed data for a large number of scientific journals through barf.jcowboy.org and calibre for the kindle and other e-book readers.
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