> Example of Question:
> - What is the role of PrnP in mad cow disease?

First thing is do not directly query questions. Manually formulate queries:
remove 'what' 'is' 'the' 'of' '?' etc.

For example i would convert this question into:

"mad cow"^5 "cow disease"^3 "mad cow disease"^15 "role PrnP"~5^2 "role mad cow 
disease"~45 mad^0.1 role^0.5 cow disease PrnP^10

> I am running in 11.638 documents and the result is 10410
> docs for this question (lowwwwww precision)

Use OR default operator, collect and evaluate top 1000 documents only.

And instead of Porter you can try KStem.
http://ciir.cs.umass.edu/cgi-bin/downloads/downloads.cgi

Try different length normalization described here. Also their Lucene query 
example (SpanNear) can inspire you.  
http://trec.nist.gov/pubs/trec16/papers/ibm-haifa.mq.final.pdf


      

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