When the word percent was first brought into English in the 1560s and until the 1900s, it was stylized per cent, which more closely matches the Latin phrase it was taken from, per centum. This meant "by the hundred", which makes a lot of sense even in the current context. Per, meaning "by" or "through", comes from the Proto-Indo-European root per, with a general definition of "before". Centum (also the root of English cent), through Proto-Italic kentom, derives from PIE kmtom, or "one hundred". The percent sign, %, traces back to the Italian practice of abbreviating por ciento to p. 100, then dropping the p., then moving the 1 into the middle of the number to get o/o and finally giving us our modern symbol. Usage of the word percent peaked in the 1980s and has been declining since.
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