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I've defined the following command

\newcommand{\CI}{\textsc{Ci}~}

which produces a C with a small uppercase i. The only problem I have is that when I use this command in the \chapter or \section environment the i is lower case. How can I fix that?

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    Please help us to help you and add a minimal working example (MWE) that illustrates your problem. It will be much easier for us to reproduce your situation and find out what the issue is when we see compilable code, starting with \documentclass{...} and ending with \end{document}. – user31729 Aug 18 '14 at 15:06
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    The standard Computer Modern fonts don't have boldface small caps. If you add \usepackage[T1]{fontenc} you should get what you want. – egreg Aug 18 '14 at 15:09

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