Over time, having adpated from the MS WORD/HTML formats I have learned to work fine with PDF, and in fact, almost all the articles our Journal does are now PDF simply because its almost a universal accepted format.   I've also found it uses up less space in general in most cases.   However, there are aspects of it's format I've yet to learn, especially in the area of graphics.   But I actually don't fault PDF in general for this since I've seen excellent done articles under this format with great graphics.

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