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If you tell LaTeX the encoding of a certain file were latin1, but it is utf-8 in reality, you might encounter strange effects and errors. Even worse: changing encoding while writing... The encoding of a file is not stored in the file. It might be necessary to reencode your file, here is how to do that: How do I change the encoding of my files?

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You can tell LaTeX what character encoding you are using with for example \usepackage[utf8]{inputenc} or \usepackage[latin1]{inputenc} With Emacs+AUCTeX the editor will recognize that line as well, and change the file's character coding if necessary. With other editors you might not be so lucky. Other than that, it's not really stored in the LaTeX file ...

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Perhaps the reason is that you compile with bibtex, not biber. Bibtex doesn't understand utf8 — not even 8-bit encoding. Probably you should use biblatex — in which case the syntax for loading the database and a bibliography style should be (for the alphabetic style, for instance): \usepackage[backend=biber,style=alphabetic]{biblatex} ...

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