Etymology
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den (n.2)

in good den, found in the early dramatists, a contraction of good e'en "good evening;" the phrase was short for God give you good den.

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den (n.1)

Old English denn "wild animal's lair, hollow place in the earth used by an animal for concealment, shelter, and security," from Proto-Germanic *danjan (source also of Middle Low German denne "lowland, wooded vale, den," Old English denu "valley," Old Frisian dene "down," Old High German tenni, German tenne "threshing floor," perhaps from a PIE word meaning "low ground").

Transferred to den-like places in human habitations in Middle English: "secret lurking place of thieves, place of retreat" (late 13c.); "apartment, private chamber" (late 14c.), but the modern use for "small room or lodging in which a man can seclude himself for work or leisure" [OED] is a modern development, originally colloquial, attested by 1771. By 1956, however, at least in U.S., the den had come to be a sort of family all-purpose room. In 19c. it also often had a bad sense, "a haunt, squalid place of retreat" (as in the set phrase den of iniquity for a brothel, etc.).

For, in truth, without a den or place of refuge, a man can achieve neither tranquility nor greatness. Jefferson wrote the Declaration of Independence in a quiet rooming house in Philadelphia. The soaring ideas that went into it evolved during hours of reading and contemplation in a secluded library. Had it been a study-TV-guest-family room, the United States might still be a colony. [The Kiplinger Magazine, September 1956]
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dene (n.1)

"small thickly wooded valley," from Old English denu "valley" (see den). Confused in Middle English with den. In Middle English down and dene meant "hill and dale."

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good den 
salutation, Elizabethan corruption of good e'en, itself a contraction of good even "good evening," which is attested from c. 1500, first as gud devon, showing a tendency toward misdivision. See good (adj.) + even (n.).
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hollow (n.)
"lowland, valley, basin," 1550s, probably a modern formation from hollow (adj.), which is from Old English holh (n.) "cave, den; internal cavity."
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cote (n.)

"a hut, a little house," Old English cote, fem. of cot (plural cotu) "small house, bedchamber, den;" see cottage. Applied to sheds for animals from early 15c.

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calaboose (n.)
"prison, a common jail or lock-up," 1792, Western and Southwestern American English, from Louisiana French calabouse, from Spanish calabozo "dungeon," probably from Vulgar Latin *calafodium, from pre-Roman *cala "protected place, den" + Latin fodere "to dig" (see fossil).
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Hague 
city in Netherlands, from Dutch Den Haag, short for 's Gravenhage, literally "the count's hedge" (i.e. the hedge-enclosed hunting grounds of the counts of Holland); see haw (n.). In French, it is La Haye.
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match-girl (n.)

"girl who sells matches," 1765, from match (n.1) + girl. The tragic story of "The Little Match-Girl" (Danish title Den lille pige med svovlstikkerne) by Andersen was published in 1845, translated into English by 1847.

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thalamus (n.)
plural thalami, 1753, "the receptacle of a flower," Modern Latin, from Latin thalamus "inner chamber, sleeping room" (hence, figuratively, "marriage, wedlock"), from Greek thalamos "inner chamber, bedroom," related to thalame "den, lair," tholos "vault, vaulted building." Used in English since 1756 of a part of the forebrain where a nerve appears to originate.
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