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A
aa, ee, un, saa = yes (informal)
abayo = casual goodbye, kinda like "see ya"
abunai = dangerous, threatening; when shouted as a command it translates to "look out!"
aburi = fried tofu
ahou = moron
ai = love
aisatsu ni = to greet, say hello to
aishiteru = I love you (romantic love)
aisuru = love, sweetheart, beloved
akari = light
aku = evil, wicked, bad, etc.
aku soku zan = literally "kill evil instantly"
ane-ue = respectful word for "older sister"; you would use this to talk about your sister when she's not in your presence. If you were talking to her, you would use "onee-san"
ani-ue = respectful word for "older brother"; you would use this to talk about your brother when he's not in your presence. If you were talking to him, you would use "onii-san"
ano/sono/kono/dono/ = basically means "this" when referring to people. In order: "that over there", "that", "this", and "which one?"
ano hi = "this day"
ano hito = literally "that person"
ano toki = literally "that time"; often translates to "back there", "back then", etc.
anou = "well..."
ara/are = oh, or "huh?" ; "Ara" is used by women, "Are" by men.
are/sore/kore/dore = means "this" when referring to objects. Meanings are the same as listed above for "ano/sono/kono/dono"
arigatou gozaimasu = "thank you very much"; the more formal version is "domo arigatou gozaimasu"; the casual verion is "arigatou" (thanks, thank you)
arimasen/imasen = isn't ("arimashita" = was, were)
asagohan/hirugohan/bangohan = in order: breakfast/lunch/dinner/meal
ashita = tomorrow
asoko/soko/koko/doko = means "this" when referring to locations. In order: "there" (far away), "there", "here", "where?"; both "doko wa" and "koko wa" can translate as "where am I?" (literally "where is this place?")
atama = head
atarashii = new
atsui = hot (temperature or weather)

B
baka = idiot, fool, stupid, etc. (all-purpose insult)
bakaga = impossible
bakemono = monster
bento = a box lunch
betsu ni = a multi-purpose negative phrase, usually translated as "nothing" or "not really"
bishonen = beautiful boy
bishoujo = beautiful girl (sometimes translated as "pretty"; the word itself is a combination of "bi" = beautiful and "shoujo" = girl)
bouzu = kid (often used as an insult)
budo = a set of goals/morals for martial artists,  such as a philosophy that goes with your particular style, such as "protect the weak" or "revitalize people" or something of that sort.
bushido = the "warrior's code", or code of honor among samura.  One of the main rules of Bushido seems to be "death before dishonor"
busu = ugly girl (a pretty rude insult)

C 
chibi = little; can be a noun or adjective
chichi-oya = formal, respectful word for "father"; this is how you would refer to your father outside of his presence. If you were talking to him you would use "otou-san"
chikyuu = Earth (as in the planet)
chigau = different (can also be used as "no" as in "no, it's something different" or "that's wrong"). The verb form is "chigaimasu" ("to be different/wrong")
chiisai = small (as in "small in size"); I've also heard the variation "chisana", which may be the noun version, I'm not %100 sure on that.
chotto matte = "wait a minute!" ("matte" is the gerund from of "to wait" which is "matsu"); "chotto" = "for a short time". "chotto" actually has many different meanings, it varies according to context and I don't have a full understanding of this word yet.
clothing nouns: kimono, yukata (summer kimono), obi (sash), haori (coat), hanten (jacket), hakama (skirt pants), tabi (split-toed socks), gi (short men's kimono), zori (sandals for kimono), geta (wooden sandals), warajii (sandals with many woven straw straps for keeping it on your foot securely), manto (cloak)

D

da = as in "no da", a phrase used by Chichiri of Fushigi Yuugi. This is an example of a character using archaic Japanese; he ends almost everything he says with "no da". Chichiri says this to put more emphasis into his arguments and statements, it means something like "what I'm saying is true."
daga = however/but
daijoubu = don't worry, I'm okay, I'll be all right, etc. "daijouka" is "are you okay?"
daikon = large Japanese radish
daimyo = fuedal lord; these people were the next rank above samurai in Japan's fuedal era and were the major landowners.
daisho = traditional pair of swords carried by samurai, consisting of a katana (long sword) and wakizashi (short sword)
daisuki desu/da = I love you. This has more emphasis than "suki desu/da" which means "I love you/I like you" (this refers to boyfriend/girlfriend type love, not romantic marraige-type love. Important difference!). "daisuki" can also describe your favorite things.
dakara = so, therefore
damare = means "be quiet", often translates as "shut up!" or "silence!"
dame = this actually means "bad" or "it's no good" (the opposite of "ii", which means "good") but it's often used (and translated) as "no" (as in "don't do that!")
de gozaru = a "polite phrase" that can be added to the ends of sentences. Only Himura Kenshin of Rurouni Kenshin uses this. It's a very outdated, archaic form of the polite "de gozaimasu" and would almost be like someone walking up to you and saying stuff like "thou art" and other Shakespearan-era English. You know what it means, but you would never use it in regular converstion. Kenshin's just odd
desu = this has many complicated uses in speech, but basically it's a polite modifier, and is a more casual form of "de gozaimasu". See a grammar dictionary for how to properly translate "desu", I could never explain it properly
demo/datte = but
densetsu = legend, legendary
dewa = an interjection, has various meanings including "Then...","Well...","Now..." etc.
dim sum = pork buns (a Chinese dish)
do-iu koto da = "what do you mean?"
dojo = school (as in a maritial arts training hall)
doki doki = a phrase meaning "sometimes/from time to time"; it also describes a heartbeat
domo = This word has so many uses I couldn't possibly list them all. One common use is "thank you", functioning as the short version of the full (i.e. very formal) version of "thank you very much" ("domo arigatou gozaimasu")
doozo = here you go, here you are (giving someone something)
dou = how, in what way?; "dou da?" is "how about it?"
dou shite = why?/why not?/how come?; "doushita" can mean "what's wrong?"

 

eeto... = like saying "um..." or "erm...", that sort of thing
expletives: mou, che, chikuso, kuso, shimatta (all meaning damn, shit, crap, etc.)

F

fuku = uniform
fureru = "to touch"
furo = bath
futon = the thin, soft mattresses some Japanese sleep on (most people use Western beds nowadays). They are folded and stored in cabinets when not in use.
fushigi = mystery, wonder, mysterious, etc.

G

gaijin = refers to any foreigner
gakkou = highschool
gambatte ne! = "do your best!"
genki da = cheer up, be well, take care, etc. ("genki" literally means energy)
gochisousama! = said at the end of mealtimes, means "thank you for the meal/I'm finished"
gomen nasai = I'm sorry

H

ha = the cutting edge of a sword (just one of many meanings for "ha")
haha-oya = respectful word for "mother"; this is how you would refer to your mother outside of her presence. If you were talking to her you would use "okaa-san"
hai = yes
hajime = beginning, start, the first time, etc. The verb "to begin" is "hajimeru" (with the often-heard command form "hajimete")
hajimemashite = "I'm pleased to meet you (for the first time)"
hakubaikou = white plum (the scent and the flower)
han = half; examples are "hanbun" ("half of me" or "part of me") and "hanyou" ("half-demon")
hana = there are a few meanings for this, including "flower" and "nose"
hanase = imperative form of "to release", it often translates as "release me!" or "let me go!"; the dictionary form is "hanasu"
hanashi = as a noun it means "news, account, story", etc. The dictionary from of the verb "to talk" is "hanasu"; "hanasu also means "to release" (see above)
hane = spring (as in the season)
hayaku = means "faster"; also translates as "hurry up" or "quickly" when used as a command.
hen = weird or strange
hentai = literally "strange", though it's often used in such a way as to get the translation "pervert"
henshin = transform or change
hidari = left
hidoi = mean, cruel
hikari = light, energy (as in a glare, gleam, or ray)
hime = princess
himitsu = secret
hito = man, person
hitokiri = assassin; "hito" means "man" and "kire" is a form of the verb "to cut" ("kiru"), so "hitokiri" literally means "Man-Slicer" or "ManSlayer", hence why it's an appropriate job title for an assassin ;)
hitomi = to see, eye
hitotsu no = a part of something (a, one, etc.)
honorifics: the Japanese "honorific" has no English equivalent. They are a way of showing your status in relation to another person and so, depending on how they are used, they can be either respectful or insulting. In rank from highest respect to lowest they are: -sama, -san, -dono, -kun, -chan. They are used as suffixes attached to the ends of words. There has been some debate amongst myself and others about the exact usage of "-dono" as it occurs in anime and manga; it's an older honorific and seems to imply that the speaker is in the service of another person, but this isn't always true in context. As far we can tell its usuage is on a case-by-case basis.
honto = really ("honto desu ka" = "really?")
houshi = priest

I
 

ichiban = first, the best, favorite, etc.; "ichi" is "one" and when the Japanese count things they use different classifiers along with the number (kind of like the way we say "two pieces of bread" instead of "two breads"). "-ban" is used specifically for counting numerical order.
ie = house
ii = good, nice; "ii desu ka" means "is it okay?", the casual version is "ii ne/na"; the past tense of "ii" is "yokatta" (yup you grammar-seekers, it's an irregular. I hate irregulars :P)
iie, iya = no; the first is more formal, the second more relaxed and conversational
iinazuke = fiancee
ikari = fury
ikenai = "oh no!"
iku = the dictionary form of "to go"; often you hear it as "ikuzo" meaning "let's go!" This form isn't in my grammar book, so I'm guessing it's some sort of ultra-casual slang version of the verb, but I can't be sure about that.
ima = now
imouto = younger sister
inochi = life
inu = dog
irrashimase! = welcome! (used in restaurants to greet customers)
itachi = weasel
itadakimasu = said at the start of meals, means "let's eat!", "here's to good food", etc.
ite = ouch, ow
itte kimasu = "I'm taking off!" or "I'm leaving now!"; the "itte" part of this is the gerund form of the verb "to go" ("iku") but there is no conjugation with "kimasu" on the end of it, so I'm wondering if I'm not hearing the phrase correctly...
istu = when; "istu mo" means "always, constantly, forever", etc.

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J

ja ne/ja na = see you later/see you then
ja matta/mattana = casual "goodbye"
-ja nai/-nai = a suffix that gives an adjective a negative meaning. Japanese "adjectives" don't fully correspond to the English ones, you need to see a grammar book for a proper explanation of negative forms.
janken = the Japanese version of "rock, paper, scissors"; the phrase is "Janken, Janken, Pon!"
jibun = one's self, yourself/himself/herself
jikai = next time
jinchuu = Earthly justice (is also sometimes translated as "revenge")
jitsu wa = "actually..."
jou-chan = "little missy"
joudan janai ="this is no joke!" or "you've got to be kidding!", etc.
juunishi = Japanese version of the Chinese Zodiac (featured in the anime Fruits Basket)

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K

ka = a particle that indicates a question
kakkoii! = "cool!"
kami = some common meanings for this word are "spirit" ("Kami-sama" is God), "hair", and "paper"
kamiya = flower; this isn't the generic word for "flower" so I'm thinking it refers to a specific species, I have no idea which one though...
kanai = wife
kanji = perception, feeling. Also refers to the Chinese characters used in Japanese writing.
kanojo = girlfriend
kao = face
kaoru = scent
kare/kareshi = boyfriend
kawaii/kawaiku ne = cute/uncute (from Ranma 1/2)
kaze = wind
keisatsu = police
ken = sword; there are many words for sword according to their type (usually determined by length). Examples: wattou (long battle katana, usually greater than 30 inches in length), katana (generally 25-30 inches long), wakizashi (short sword), kodachi (short sword between a wakizashi and katana in length), tanto (long dagger), kunai (short throwing knives), sakabatou (a fictional reverse-bladed sword), zanbatou (giant sword used to cut down both horse and rider), bokken (wooden sword), and shinai (bamboo practice sword). The sheath or scabbard for a sword is called a "saya".
kenjutsu = swordsmanship
kenkaku = swordsman
kenshin = devotion, dedication; in Rurouni Kenshin it's written with the kanji reading "Heart of Sword"
keredo/kedo = though, although, but
ki/chi = the Asian concept of a life force or life spirit; it's mentioned a lot in martial arts anime. "Ken-ki" is used in Rurouni Kenshin in reference to swords, and in Inuyasha "youki" is used to describe demon energy. "Ki" also means "tree". "Chi" is closer to the Chinese pronuciation of the word.
kimochi = feeling, emotion, pleasure
ki o tsukete = The gerund (command) form of "be careful"; dictionary form is "ki o tsukeru"
kitsune = fox
kirei = pretty, lovely; unlike in English, the Japanese word for "pretty" can also be a noun, and so sometimes you hear it as an affectionate nickname for someone.
kizu = wound (physical cut)
kodomo = child
koekeishiya = successor
koishii, koibito = beloved, lover, sweetheart, etc.
koi = this words has a ton of meanings, including love, goldfish, and "come here!" (the imperative form of the verb "to come", which is "kuru")
kokoro = heart, mind, soul, etc.
konbanwa = good evening
koneko = kitten
konnichi wa = hello, good afternoon
korosu = "to kill"
kotaeru = "to answer"; you'll hear it in various forms in anime, often as a command: "answer me!"
koto wa = thing, what, affair/matter
kotowaru = "to decline" (to refuse do something, such as fight)
kowai = scared, fear, afraid
kumo = a couple meanings, including "spider" and "cloud"

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M

maa, maa = "now, now" ; a phrase used to placate someone
maa na = "I guess"
maboroshi = means "illusion", as in a dream or illusion constructed by someone; figuratively it means "mystic" or "mystical". In Escaflowne "Maboroshi no tsuki" means "The Mystic Moon."
machigainai = there's no mistake! (like when you recognize someone, or verify information)
mada = not yet, still
mamoru = "to protect"
masaka = "of course not!", "impossible", "it can't be!", "not really", etc.
massushiro = a phrase, means "clean and white"
mattaku = sheesh, yeesh, jeez, "oh for heaven's sake", etc. General expression of annoyance.
miko = priestess
minna = everyone
miru = "to see"
miso = Japanese soy-based soup
mizu = water
mochi = a Japanese dessert: rice dough (kinda marshmallow in texture) stuffed with ohagi (sweet bean paste)
moko-dono = from Ranma 1/2, means "son-in-law"
mon = family crest, often seen on formal kimono. In the Meji era a "mon" was also a form a currency that was worth less than a "sen". The mon, as far as I know, is no longer in use as money in Japan.
mononoke = vengeful spirit
mooto = increases the amount of something. An example is "hayaku, hayaku, mooto hayaku" (a phrase from a Spirited Away image song) which means "faster, faster and faster" but "mooto" doesn't mean "and"; it's simply increasing the amount of "hayaku"
mori = forest
moshi moshi = hello (on the phone)
mou ii = a phrase, means "no more" or "that's enough!"
mune = the dull edge of a Japanese sword. It also means "heart"
musume = daughter (in Rurouni Kenshin "itachi musume" = "weasel girl" or literally the daughter of a weasel. Obviously in this case it's being used as in insult)
muzukashii = difficult
myuun = the sound a cat makes, they also make a "nyaa nyaa" sound :)

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N

na ha = a very impolite and abbreviated way to ask someone their name. "O-namae wa" is standard-polite; if you wantto be even more formal you would use "O-namae wa nan to iimasu ka" or "O-namae wa nan to osshaimasu ka" (the latter is very polite ^^)
nakanai de = don't cry, the negative form of the verb "to cry" ("naku"). "nakanaide kudasai" = "please don't cry"
nan da/nan de = why, what. "nan da to" is an extreme version of "what", sort of like "WHAT?!"
nan de sute = "what did you say?"
nan = what; a common casual version of this is "nani"
nani yatten no = "what are you doing?"
nani-mo = nothing
naruhodo = I see (as in "I understand")
naze = why (an extreme why, as in "why did you do that?!")
ne = when put as a question, means "right?" (as in "correct"). This is just one of the many meanings of "ne"
neko = cat
nezumi/onezumi = mouse/rat
nigeru = "to run"
nihon, nippon/nihongo = Japan/Japanese (language)
nikuma = pork buns
ningen = human
nidoto = never (as in "I'll never do that again")
no = serves several purposes, often as a particle marking a possessive ("Akane no iinazuke" would be "Akane's fiancee" for instance)
numbers: ichi (one), ni (two), san (three), shi or yon (four), go (five), roku (six), shichi or nana (seven), hachi (eight), kyuu or ku (nine), juu (ten), etc.

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O

obasan = aunt
obaasan = grandmother. It's important to note that this word is very different from "obasan" above (which only has one "a" in romanji or a short "a" sound in speech). The "a" sound in "obaasan" is held twice as long.
obaba = great-grandmother, or a fairly rude way of saying "old woman"
obou = monk
oden = a mixed meat/vegetable stew
ohagi = sweet bean paste
oi = hey!
oishii = delicious, tasty
ojisan = uncle, or "mister" when used by a non-relative. The Japanese have the habit of sometimes referring to strangers or aquaintances with familial terms. This is one such example.
ojiisan = grandfather. Just as with "obasan" it's important to note the difference in spelling. You hold the "i" sound longer when you want to say "grandfather" as opposed to "uncle".
okaa = mother; in speech this word is almost always used with an honorific. "Okaa-sama" is very respectful, "Okaa-san" is general respect (this is the usual form you hear), "Okaa-chan" is informal and is sort of like saying "mommy".
okari nasai = welcome home
okashira = commander or boss
okonomiyaki = Japanese "pizza" (it's similar to a pancake with sauce and other toppings added. Yum ^_^)
ohayou gozaimasu = good morning (just "ohayou" is like "morning!")
ohisashiburi = "it's been a long time" or "long time no see!"
omoshiroi = interesting or amusing
onna = woman
onegai = please (the full version is "onegai-shimasu" when you're being really polite; if used like a command I've seen it translated as "I beg of you!")
onee = older sister (informal: onee-chan, polite: onee-san
oni = ogre or demon
onii = older brother (informal: onii-chan, polite: onii-san)
onigirii = rice ball
onsen = hot spring
ooji = prince
ookii = big
osuwari = the command form of "to sit" ; actually this is technically a dog command...
otaku = in Japan this words simply refers to a fan of anything, in America it's come to describe an fan of anime specifically.
otoko = man
otou = father; in speech, just as with "okaa", this word is almost always used with an honorific. "Otou-sama" is very respectful, "Otou-san" is general respect (this is the usual form you hear), "Otou-chan" is informal and is sort of like saying "daddy".
otouto = younger brother
otto = husband
ougi = succession technique for a sword or martial arts school, literally means "deep act"
owari = "the end", as in the end of a show or story. The verb "to end" is "owaru"
oyaji = "old man", as in your dad (often used as an insult in anime)
oyasumi nasai = good night

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P

paku = the sound a fish makes
pan = bread
particle: the Japanese "particle" refers to the short syllables (no, to, ni, mo, etc.) sprinked in Japanese sentences. The meaning and uses of particles are many and varied. They often serve as object and topic markers, identifying the subject of the sentence (first person pronouns are nearly always followed by a particle. Examples would be "watashi no", "sessha mo", etc.). They also serve a function similar to English preposition "filler" words such as: of, and, the, from, to, etc. To understand particles you need a Japanese grammar dictionary and/or a good textbook. Since I haven't taken a formal Japanese language class, I'm far from having a good understanding of how to use particles -_-;;
piyo = the sound a bird makes
pronouns: watakushi (formal "I"), watashi (standard "I"), atashi (young woman's "I"), ore (informal men's "I"), boku ("I" for kids or when you're being submissive), sessha ("this unworthy one"), washi (used by old people) anata (formal "you", or "beloved" if used between a married couple), kimi (standard "you"), omae (casual men's "you"), onushi ("you" used by old people), temee (rude version of "you"), kisama (really rude version of "you", as in "you bastard!")
Notes on pronoun use: generally used in pairs. The following info was generously provided by Jan Story, who's a lot more knowlegeable about Japanese than me:
Complementary I/you pairs by politeness level! There are a lot of ways of referring to oneself, depending on gender, age, social position, and relation to the person being addressed. Usually, a person who habitually uses a given first person pronoun will use a complementary second person pronoun to address others.
Ore/omae. Ore is the tough-guy way of saying I, and a guy who says ore usually addresses other (men) as omae. Omae *used* to be polite, it literally means something like honorable-one-in-front-of-me, but usage tends to drag down second (and sometimes first) person pronouns to lower and lower politeness levels. Anime characters who use it: Sanosuke, Yahiko, Battousai, Ranma, Ryouga -- tough guys in general.
Boku/kimi. Boku is the boy's I, used almost from the time a boy becomes aware that he is a boy, up until he decides he's a M-A-N and starts using ore. Kimi is the complementary you; most boku-users seem to use it. Boku-users in anime usually tend to be softer-spoken -- though why Tatewaki Kunou uses it is a mystery, since most of the rest are nice guys: Tenchi Masaki, Tonbo in Kiki's Delivery Service, Hakkai in Gensoumaden Saiyuuki.
Watashi/anata. Standard-polite, used by nearly all adults who don't talk tough.
Atashi/anta. This is a young girl's version of standard-polite and is a little more casual. Akane Tendou uses this.
Washi. I don't remember the complementary you for this; it's a form used by old people. Happousai, Cologne, and Genma use it (even though Genma's not that old).
Sessha/onushi. This unworthy one... and onushi means something like honored lord. Again, both are around 300 years out of date. And we all know who uses these!
Then there are two other words for you that I should mention. At least technically they mean you -- they're usually used as epithets: kisama and temee (that's the rough-masculine pronunciation, but it's the only one I ever see). In Japanese, most curses, epithets and insults are simply very rude ways of saying you.

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R

rei = soul
rounin = masterless samurai
rurouni = vagabond or wanderer (it's important to note that this word was made up by the creator of Rurouni Kenshin, combining "rounin" (masterless samurai) and "rurou" (vagabond). It doesn't actually exist in the Japanese language)
ryu = school or style (for example, a sword style such as "Hiten Misturugi Ryu").
ryuu = dragon

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S

sake = rice "wine" (it's brewed like a beer)
sakura = cherry blossom
samurai = Japan's ancient warrior class (one step above peasants), officially abolished at the start of the Meji era (1868)
sashimi = sliced raw fish
sasuga ha = "nothing less from", as when someone lives up to his/her reputation or does something cool that you expected
satsujinhan-nin = killer/murder; "satsujin" is a shorter version.
sayounara = farewell (as in "goodbye forever" or for a long time)
seiyuu = voice actor/actress
sen = a breakdown of Japanese currency, in today's money I believe 100 sen = 1 yen (not %100 sure though)
sensei = teacher; it's often used as a suffix after someone's name and indicates that they are very knowledgeble in a certain area (doctors, teachers, and writers often get a "-sensei" after their name). In America "sensei" has a more limited definition as a "martial arts instructor".
shishou = old term for "master" in the martial arts
senshi = soldier
sempai = upperclassmen/predecessor; essentially someone who has studied or been there before you
sepukku = ritual suicide
shakkin = debt (as in money)
shihondai = assistant master
shikari shite = generally translated as "hang in there! or "snap out of it!". "shikari shiro" is the informal male speech version. The literal "snap out of it" is "ii kagen ni shinasai/ii kagen ni shiro" (male speech); it kind of means "behave yourself!"
shikashi = however/but
shinda = "died"; this is the plain past tense of "shinu", which means "to die".
shinji = form of the verb "to believe" ("shinjiru"). You hear the verb in its various forms everywhere in anime, but I've only heard "shinji" as a name (from Evangelion). I'm not sure of its precise meaning in that form.
shinjitsu = truth
shinma = literally "gods" + "demons", used to describe the supernatural beings in Vampire Princess Miyu
shinpai = worry
Shinto/Shintoism = the native religion of Japan. Shintoism consists mainly of ancestor worship and the worship of various animal spirits. Shinto temples are distinguished by the large orange-red "Tori" gates placed outside the main temple (these are commonly seen in anime).
shitsure shimasu = lit. "please excuse what I am about to do". It's what you say when you enter someone else's house.
shogun = warlord
shoji = the sliding rice paper doors in Japanese houses
shounen = boy

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