Etymology
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up- 
prefix with various senses, from Old English up (adv.), corresponding to similar prefixes in other Germanic languages.
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phyto- 
word-forming element meaning "plant," from Greek phyton "plant," literally "that which has grown," from phyein "to bring forth, make grow," from PIE root *bheue- "to be, exist, grow."
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phanero- 

before vowels phaner-, word-forming element meaning "visible, manifest," especially from 18c. in biology, from Greek phaneros "visible, manifest, evident, apparent," from phainein "bring to light, cause to appear, show," from PIE root *bha- (1) "to shine." Opposed to crypto-.

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ana- 

before vowels an-, word-forming element meaning: 1. "upward, up in place or time," 2. "back, backward, against," 3. "again, anew," from Greek ana (prep.) "up, on, upon; up to, toward; throughout; back, backwards; again, anew," from an extended form of PIE root *an- (1) "on, upon, above" (see on, which is the English cognate). In old medical prescriptions, ana by itself meant "an equal quantity of each."

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phylo- 

before vowels phyl-, modern word-forming element, mostly in the sciences, often meaning "phylum," from Greek phylon, phylē "a tribe," also a political subdivision in ancient Athens, from base of phyein "to bring forth, produce, make to grow," whence also physis "nature" (from PIE root *bheue- "to be, exist, grow").

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hypo- 
word-forming element meaning "under, beneath; less, less than" (in chemistry, indicating a lesser oxidation), from Greek hypo (prep. and adverb) "under, beneath; up from under; toward and under (i.e. into)," from PIE root *upo "under."
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hypso- 
word-forming element meaning "height," from Greek hypsos "height, top," from PIE *upso-, from root *upo "under," also "up from under," hence also "over" The Greek word is cognate with Sanskrit os "above, over," Old Church Slavonic vysoku "high."
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mixo- 

word-forming element of Greek origin meaning "mixed," from Greek mixo-, from mixis "a mixing, mingling, intercourse," from root of mignynai "to mix, mix up, mingle" (from PIE root *meik- "to mix"). As in mixolydian in reference to a half-Lydian mode in ancient Greek music.

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sub- 
word-forming element meaning "under, beneath; behind; from under; resulting from further division," from Latin preposition sub "under, below, beneath, at the foot of," also "close to, up to, towards;" of time, "within, during;" figuratively "subject to, in the power of;" also "a little, somewhat" (as in sub-horridus "somewhat rough"), from PIE *(s)up- (perhaps representing *ex-upo-), a variant form of the root *upo "under," also "up from under." The Latin word also was used as a prefix and in various combinations.

In Latin assimilated to following -c-, -f-, -g-, -p-, and often -r- and -m-. In Old French the prefix appears in the full Latin form only "in learned adoptions of old Latin compounds" [OED], and in popular use it was represented by sous-, sou-; as in French souvenir from Latin subvenire, souscrire (Old French souzescrire) from subscribere, etc.

The original meaning is now obscured in many words from Latin (suggest, suspect, subject, etc.). The prefix is active in Modern English, sometimes meaning "subordinate" (as in subcontractor); "inferior" (17c., as in subhuman); "smaller" (18c.); "a part or division of" (c. 1800, as in subcontinent).
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em- 
word-forming element meaning "put in or into, bring to a certain state," sometimes intensive, from French assimilation of en- "in, into" (see en- (1)) to following labial stop (-b-, -p-, and often -m-), or from the same development in later Latin in- (to im-). "This rule was not fully established in spelling before the 17th c." [OED], but it is likely the pronunciation shift was in Old French and Middle English and spelling was slow to conform. Also a living prefix in English used to form verbs from adjectives and nouns (embitter, embody). In words such as emancipate, emerge, emit, emotion the e- is a reduced form of Latin ex- (see ex-) before -m-.
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