Etymology
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-cide 

word-forming element meaning "killer," from French -cide, from Latin -cida "cutter, killer, slayer," from -cidere, combining form of caedere "to strike down, chop, beat, hew, fell, slay," from Proto-Italic *kaid-o-, from PIE root *kae-id- "to strike." For Latin vowel change, see acquisition. The element also can represent "killing," from French -cide, from Latin -cidium "a cutting, a killing."

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a- (1)

prefix or inseparable particle, a relic of various Germanic and Latin elements.

In words derived from Old English, it commonly represents Old English an "on, in, into" (see on (prep.)), as in alive, above, asleep, aback, abroad, afoot, ashore, ahead, abed, aside, obsolete arank "in rank and file," etc., forming adjectives and adverbs from nouns, with the notion "in, at; engaged in." In this use it is identical to a (2).

It also can represent Middle English of (prep.) "off, from," as in anew, afresh, akin, abreast. Or it can be a reduced form of the Old English past participle prefix ge-, as in aware.

Or it can be the Old English intensive a-, originally ar- (cognate with German er- and probably implying originally "motion away from"), as in abide, arise, awake, ashamed, marking a verb as momentary, a single event. Such words sometimes were refashioned in early modern English as though the prefix were Latin (accursed, allay, affright are examples).

In words from Romanic languages, often it represents reduced forms of Latin ad "to, toward; for" (see ad-), or ab "from, away, off" (see ab-); both of which by about 7c. had been reduced to a in the ancestor of Old French. In a few cases it represents Latin ex.

[I]t naturally happened that all these a- prefixes were at length confusedly lumped together in idea, and the resultant a- looked upon as vaguely intensive, rhetorical, euphonic, or even archaic, and wholly otiose. [OED]
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super- 
word-forming element meaning "above, over, beyond," from Latin super (adverb and preposition) "above, over, on the top (of), beyond, besides, in addition to," from *(s)uper-, variant form of PIE root *uper "over." In English words from Old French, it appears as sur-. The primary sense seems to have shifted over time from usually meaning "beyond" to usually meaning "very much," which can be contradictory. E.g. supersexual, which is attested from 1895 as "transcending sexuality," from 1968 as "very sexual."
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over- 

word-forming element meaning variously "above; highest; across; higher in power or authority; too much; above normal; outer; beyond in time, too long," from Old English ofer (from PIE root *uper "over"). Over and its Germanic relations were widely used as prefixes, and sometimes could be used with negative force. This is rare in Modern English, but compare Gothic ufarmunnon "to forget," ufar-swaran "to swear falsely;" Old English ofercræft "fraud."

In some of its uses, moreover, over is a movable element, which can be prefixed at will to almost any verb or adjective of suitable sense, as freely as an adjective can be placed before a substantive or an adverb before an adjective. [OED]

Among the old words not now existing are Old English oferlufu (Middle English oferlufe), literally "over-love," hence "excessive or immoderate love." Over- in Middle English also could carry a sense of "too little, below normal," as in over-lyght "of too little weight" (c. 1400), overlitel "too small" (mid-14c.), overshort, etc.

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sch- 
this letter group can represent five distinct sounds in English; it first was used by Middle English writers to render Old English sc-, a sound now generally pronounced (and spelled) "-sh-." Sometimes it was miswritten for -ch-. It also was taken in from German (schnapps) and Yiddish (schlemiel). In words derived from classical languages, it represents Latin sch-, Greek skh-, but in some of these words the spelling is a restoration and the pronunciation does not follow it (as in schism).
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in- (2)
Origin and meaning of in-

element meaning "into, in, on, upon" (also im-, il-, ir- by assimilation of -n- with following consonant), from Latin in- "in," from PIE root *en "in."

In Old French (and hence in Middle English) this often became en-, which in English had a strong tendency to revert to Latin in-, but not always, which accounts for pairs such as enquire/inquire. There was a native form, which in West Saxon usually appeared as on- (as in Old English onliehtan "to enlighten"), and some of those verbs survived into Middle English (such as inwrite "to inscribe"), but all now seem to be extinct.

Not related to in- (1) "not," which also was a common prefix in Latin, causing confusion: to the Romans impressus could mean "pressed" or "unpressed;" inaudire meant "to hear," but inauditus meant "unheard of;" in Late Latin investigabilis could mean "that may be searched into" or "that cannot be searched into." Latin invocatus was "uncalled, uninvited," but invocare was "to call, appeal to."

The trouble has continued in English; the hesitation over what is meant by inflammable being a commonly cited example. Implume (1610s) meant "to feather," but implumed (c. 1600) meant "unfeathered." Impliable can mean "capable of being implied" (1865) or "inflexible" (1734). Impartible in 17c. could mean "incapable of being divided" or "capable of being imparted." Impassionate can be "free from passion" or it can mean "strongly stirred by passion." Inanimate (adj.) is "lifeless," but Donne uses inanimate (v.) to mean "infuse with life or vigor." Irruption is "a breaking in," but irruptible is "unbreakable."

In addition to improve "use to one's profit," Middle English also had a verb improve meaning "to disprove" (15c.). To inculpate is "to accuse," but inculpable means "not culpable, free from blame." Infestive has meant "troublesome, annoying" (1560s, from infest) and "not festive" (1620s). In Middle English inflexible could mean "incapable of being bent" or "capable of being swayed or moved." In 17c., informed could mean "current in information," formed, animated," or "unformed, formless" ("This was an awkward use" [OED]). Inhabited has meant "dwelt in" (1560s) and "uninhabited" (1610s); inhabitable likewise has been used on opposite senses, a confusion that goes back to Late Latin.

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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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