Etymology
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epi- 

before vowels reduced to ep-, before aspirated vowels eph-, word-forming element meaning "on, upon, above," also "in addition to; toward, among," from Greek epi "upon, at, close upon (in space or time), on the occasion of, in addition," also "after," from PIE *epi, *opi "near, at, against" (source also of Sanskrit api "also, besides;" Avestan aipi "also, to, toward;" Armenian ev "also, and;" Latin ob "toward, against, in the way of;" Oscan op, Greek opi- "behind;" Hittite appizzis "younger;" Lithuanian ap- "about, near;" Old Church Slavonic ob "on"). A productive prefix in Greek; also used in modern scientific compounds (such as epicenter).

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litho- 
before vowels, lith-, word-forming element meaning "stone, rock;" from Greek lithos "stone, a precious stone, marble; a piece on a game board," a word of unknown origin.
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supra- 
word-forming element meaning "above, over, beyond, before," from Latin supra "above, over, before, beyond, on the upper side," in supera (parte), literally "on the upper (side)," from old fem. ablative singular of superus (adj.) "above," related to super "above, over" (from PIE root *uper "over"). In English interchangeable with, but somewhat more technical than, super-. Rare as a prefix in Latin, more common in Medieval Latin, in English chiefly scientific or technical.
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onto- 

word-forming element meaning "a being, individual; being, existence," from stem of Greek on (genitive ontos) "being," neuter present participle of einai "to be" (from PIE root *es- "to be").

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ultra- 

word-forming element meaning "beyond" (ultraviolet) or "extremely" (ultramodern), from Latin ultra- from ultra (adv. and prep.) "beyond, on the other side, on the farther side, past, over, across," from PIE *ol-tero-, suffixed form of root *al- "beyond." In common use from early 19c., it appears to have arisen from French political designations. As its own word, a noun meaning "extremist" of various stripes, it is first recorded 1817, from French ultra, shortening of ultra-royaliste "extreme royalist."

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macro- 

word-forming element meaning "long, abnormally large, on a large scale," taken into English via French and Medieval Latin from Greek makros "long, large," from PIE root *mak- "long, thin."

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be- 

word-forming element of verbs and nouns from verbs, with a wide range of meaning: "about, around; thoroughly, completely; to make, cause, seem; to provide with; at, on, to, for;" from Old English be- "about, around, on all sides" (the unstressed form of bi "by;" see by (prep.)). The form has remained by- in stressed positions and in some more modern formations (bylaw, bygones, bystander).

The Old English prefix also was used to make transitive verbs and as a privative prefix (as in behead). The sense "on all sides, all about" naturally grew to include intensive uses (as in bespatter "spatter about," therefore "spatter very much," besprinkle, etc.). Be- also can be causative, or have just about any sense required. The prefix was productive 16c.-17c. in forming useful words, many of which have not survived, such as bethwack "to thrash soundly" (1550s) and betongue "to assail in speech, to scold" (1630s).

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retro- 

word-forming element of Latin origin meaning "backwards; behind," from Latin retro (prep.) "backward, back, behind," usually in reference to place or position, rarely of time, "formerly, in the past," probably originally the ablative form of *reteros, based on re- "back" (see re-).

L. retro stands to re- as intro, "in, within"; to in, "in," and as citro, "hither," stands to cis, "on this side." [Klein]

Common in combinations in post-classical Latin (the classical equivalent was post-). Active in English as a word-forming element from mid-20c.

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lopho- 
before vowels loph-, word-forming element used in science from 19c. and meaning "crest," from Greek lophos "neck of draught animals and men; crest of a helmet, crest of a hill, ridge," also "tuft on the head of birds, crest of feathers, cockscomb," a word of uncertain origin.
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ambi- 
word-forming element meaning "both, on both sides," from Latin ambi- "around, round about" (before vowels amb-, also sometimes reduced to am-, an-), from PIE root *ambhi- "around," which is probably an ablative plural (*ant-bhi "from both sides") of *ant- "front, forehead."
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