Etymology
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tom-tom (n.)
1690s, "drum" (originally used in India), from Hindi tam-tam, probably of imitative origin (compare Sinhalese tamat tama and Malay tong-tong). Related: Tom-toms.
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Moluccas 

island group of Indonesia, the Spice Islands, attested in French by 1520s as Moluques, from Malay Maluku "main (islands)," from molok "main, chief," perhaps so called for their central location in the archipelago.

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cootie (n.)

"body louse," 1917, British World War I slang, earlier in nautical use, said to be from Malay (Austronesian) kutu, the name of some parasitic, biting insect.

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junk (n.2)
"large, seagoing Chinese sailing ship," 1610s, from Portuguese junco, from Malay (Austronesian) jong "ship, large boat" (13c.), probably from Javanese djong. In English 16c. as giunche, iunco.
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lime (n.2)
"greenish-yellow citrus fruit," 1630s, probably via Spanish lima or Portuguese limão, said to be from Arabic lima "citrus fruit," from Persian limun, in reference to the Persian lime, which might be a hybrid of the "Key" lime and the lemon; the word is perhaps from or related to Sanskrit nimbu "lime."

The Key lime indigenous to India and the Malay archipelago (Arabs introduced it to the Levant, North Africa, Spain, and Persia in the Middle Ages); compare Malay (Austronesian) limaw "lime," also, generically, "citrus fruit," which might be the ultimate source. Yule and Burnell think the English got the word from the Portuguese in India. Lime-green as a color is from 1890.
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orangutan (n.)

also orang-utan, orang-outang, "anthropoid ape of the lowlands of Borneo and Sumatra," 1690s, from French orang-ou-tang and directly from Dutch orang-outang (1631), from Malay (Austronesian) orang utan, literally "man of the woods," from orang "man" + utan, hutan "forest, wilderness, the wild." It is possible that the word originally was used by town-dwellers on Java to describe savage forest tribes of the Sunda Islands and that Europeans misunderstood it to mean the ape. The name is not now applied in Malay to the animal, but there is evidence that it was used so in 17c. [OED]

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upas (n.)
legendary poisonous tree of Java, 1783, via Dutch, from Malay (Austronesian) upas "poison," in pohun upas "poison tree." As the name of an actual tree (Antiaris toxicaria) yielding poisonous sap, from 1814.
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launch (n.2)
"large boat carried on a warship," 1690s, from Portuguese lancha "barge, launch," apparently from Malay (Austronesian) lancharan, from lanchar "quick, agile;" if so, the English spelling has been influenced by launch (v.).
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amok (adv.)

in run amok a verbal phrase first recorded 1670s, from Malay (Austronesian) amuk "attacking furiously." Earlier the word was used as a noun or adjective meaning "a frenzied Malay," originally in the Portuguese form amouco or amuco.

There are some of them [Javanese] who ... go out into the streets, and kill as many persons as they meet. ... These are called Amuco. ["The Book of Duarte Barbosa: An Account of the Countries Bordering on the Indian Ocean and Their Inhabitants," c. 1516, English translation]

Compare amuck.

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kapok (n.)
also in early use capoc, "type of silky wool used for stuffing, etc.," 1735 in reference to the large tropical tree which produces it; 1750 of the fiber, from Malay (Austronesian) kapoq, name of the tree.
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