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I recently presented a poster at an undergraduate research conference, and they are now soliciting write-ups for the conference proceedings. I was surprised at their formatting guidelines, specifically the requirement that all sub-headings be lower case. Ex.:

1. Main Heading
  1.1 this is a secondary heading
    1.1.2 this is a tertiary heading 

I have never seen this convention. I've always thought the preferred style for sub-headings is to either use the same capitalization format as for main headings, or capitalize the first letter of the first word.

I find this all-lower case format to be unprofessional-looking, and was wondering: is this a common convention, and if so, what is the underlying rationale?

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I have never in my academic life seen this convention: I have always seen lower-level sub-headings follow exactly the same convention as higher-level headings.

Do what they tell you to do (the world has lots of strange Official Requirements for Our Unique And Special Snowflake Publication Venue), but I wouldn't worry about it for anywhere else in life.

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The basic rule for all publications is to follow the guide-lines to the point. In this case it seems that the conference is expecting what used to be called "camera-ready" manuscripts, i.e. manuscripts that are "published" as is and not going through additional formatting by the conference organisation. With journals, the guidelines usually concern the formatting of a manuscript which later undergoes additional formatting before being published.

In any case, just follow the guidelines to the point. You would be surprised by how many fail to do so and you may even end up putting a smile on the recipients face.

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