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When should I use italics in scientific writing?

I noticed that proper nouns, such as names of theorems or techniques are often set in italics in scientific writing but not always. Are there rules about it, for example each proper noun should be set ...
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Using the Minto Pyramid

Using the Minto Pyramid, should I order the paragraphs of my paper by going through the rows of the pyramid like this? Thesis > Why > How > Where > A > B > C > D > E Or should I start at the top ...