What is "transcribed strand"
In my opinion they should mean the template strand, and they probably do. Perhaps if we had a link to the paper we could have examined the language more closely.

Here is a paper which uses the term in that sense:


  Mugal, CF et al. (2008) Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes. Molecular Biology and Evolution 26,131-142


In the abstract (which I have linked to) the authors make a clear reference to the transcribed strand in contrast to the coding strand (i.e. the strand of DNA with the same sequence as the RNA transcript):


  All three [mutational rates] considered are found to be on average higher on the coding strand and lower on the transcribed strand...


There are also definitions confirming this at this Wikipedia page.