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Thanks all for your help. Problem solved.

Not sure what you mean by "It depends on how you actually do it". I use natbib.

This is my relevant preamble:

\documentclass[a4paper,12 pt]{report}%,aps,pra,nofootinbib


\usepackage{float,geometry,amsmath,amsfonts,booktabs,pdfsync,setspace,titlesec,}
\usepackage[pdftex]{graphicx}
\usepackage ...

I'm using the bibliography style IEEETR and at the end of each individual reference it puts the section that the reference appears in:

F. J. DiSalvo, “Thermoelectric Cooling and Power Generation,” Science, vol. 285,
no. 5428, pp. 703–706, 1999. 1.1

How do I remove this? Do I have to modify the ...

When I use \autoref{subsection} I get the output 'in Subsection x.y.z'. Is there a way of changing the formatting so that when I'm referencing a subsection, the output it 'in Section x.y.z' instead?