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I need to write a short abstract for research paper in Japanese, I used the desu/masu-kei, but thought about changing it to the formal writing style de aru form.

I get that である is used after nouns and adjectives and also verbs followed by の, however I have several sentences where I use "~たいと思っています" and "~したいのです”. Is it appropriate to use である after volitional that is ~たいのである? And will ~たいと思っています just turn into a simple ~たいと思っている or must I change it into ~たいと思っているのである?

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So-called である form isn't what you should put である in the end of every sentence. である only replace copula だ/です (and its conjugations), and other endings just remain as plain form. So when you change your style into である form from です form, you'll do:

したいです → したい
したいと思っています → したいと思ってい
したいのです → したいのである

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