Remember that the commands in LaTeX are just macros, they collect any text and expand it where needed.

What you need is a command in the preamble of your LyX document of this kind:

\degree{Master of Science\\ \vspace{\baselineskip} in\\ \vspace{\baselineskip} Nuclear Engineering}

As I said, commands containing a @ have only been made for internal class use, they are not in user space.

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