2009-04-23.log

--- Day changed Thu Apr 23 2009
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bkeronom nom nom00:48
wrldpchttp://www.jewelinfo4u.com/Diamond_Mines.aspx?Mines00:51
fenni wonder if this feeling like i'm slowly dying is the normal feeling like i'm dying or due to a bad mango i ate01:20
katsmeow-afkfood poisoning can definitely make you feel death01:27
ybitkanzure, why not instead of creating a mailing list, just setup an rss feed of new papers you add to the collection?01:42
ybitalso of note: lxml01:44
ybithttp://www.ibm.com/developerworks/xml/library/x-hiperfparse/01:44
ybit..or maybe just setup a page to view the git log for biotech toolkit?01:49
ybiti guess the mailing list could work since it allows for feedback01:50
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kanzure"standard disclaimer: welcome to bryan's brain. he probably doesn't know it, but he's already beginning to neglect you. if you want to keep up, you will need to yell at him extensively for the IRC channels, RSS feeds, emails, etc., to keep up with him."07:56
kanzure:/07:56
kanzurewhy isn't there an automatic feedback mechanism built into RSS07:57
* kanzure hunts down aaron swartz07:57
facefacekanzure: you heard of DAS?07:58
facefaceDistributed annotation system07:58
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kanzureok, I've added RSS back to heybryan.org08:06
kanzureenjoy.08:06
pingfacethere is also a protocol called 'das writeback' for commenting on a das annotation08:08
UtopiahGHMLpingface: probably a bit different but ShiftSpace http://www.shiftspace.org/ is interesting 08:10
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pingfaceUtopiahGHML: right08:22
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kanzurehaha, I like how sonoluminescence has like 1% efficiency of mechanical energy into light11:11
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kanzurehttp://heybryan.org/books/papers/%20In%20situ%20DNA%20synthesis%20on%20glass%20substrate%20for%20microarray%20fabrication%20using%20self-focusing%20acoustic%20transducer.pdf12:40
kanzureDNA synthesis microfluidic device using piezos12:40
kanzureusing only four piezos12:42
kanzurehrm12:42
kanzureheh they mechanically rotate the entire device around so that they can manually do the washing / deblocking steps for phosphoramidite synthesis12:46
kanzuredroplets are continuously ejected for a minute each? hrm.12:48
xp_prgkanzure I so enjoy microfluidics, I can't wait to see something practical to use for bio tech experiments at the diybio level12:52
kanzureI think the first thing that might come is DNA synthesis, or possibly PCR12:52
kanzureI'm looking at this design and it doesn't make much sense12:53
kanzurethe idea is to use resevoires of nucleotides and to them cause droplets to move out of them and into a synthesis chamber12:53
kanzurebut then why are all of these microchannels intersecting each other. hrm.12:53
xp_prgdo you feel there are any practical microfluidic type usage at the diybio level yet?12:54
kanzureoh. it's for producing *only* 3x3 DNA probes haha12:54
kanzureyes, of course12:54
kanzurePCR, dna synthesis, dna sequencing, etc. etc.12:54
xp_prgit would be amazing to know those in detail, I would begin to use them for diybio-sf12:54
kanzurehttp://heybryan.org/books/papers/microfluidics/12:55
kanzurestart reading :)12:55
xp_prgok12:55
kanzurehere's an easy design for PCR: http://heybryan.org/books/papers/microfluidics/gkm389%20Miniaturized%20PCR%20chips%20for%20nucleic%20acid%20amplification%20and%20analysislatest%20advances%20and%20future%20trends.pdf12:56
kanzureit's a spiral, and at the four corners of the plate you put heating/cooling elements12:56
kanzurehrm13:27
kanzure"to have an idea of who you are.. ask me for a microlfuidics device that would useful for you adn i will make itwork and send it to you for free (and so you can see what i do).. i will only do the microfluidics working device (no electrical connections or computer interface). you can use any designing software that you wish..ok?"13:27
kanzurewonder what would be the best way to recover high density oligonucleotide arrays synthesized on a microfluidics chip13:52
kanzureespecially if it's not an open-air system13:52
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genehackercan you get him to tell us the smalllest feature size we can get?13:57
genehackerkanzure13:57
genehackerI'd like to know the smallest feature size that diybio guy will give us13:57
kanzureokay13:57
kanzure20 microns13:57
genehackerthat sounds pretty damn big13:58
genehackerI have preexisting designs for a logic gates13:58
genehackerI found a patent for a fluidic credit card reader and a couple fluidic registers13:59
kanzureyou don't have any designs already on your hard drive for anything relatively complete?13:59
genehackerwe can copy the circuit diagram and downsize it13:59
genehackerthe closest thing I have to relatively complete  is a fluidic amplifier silhouete14:00
kanzurewhat does it amplify?14:00
genehackersound14:00
kanzureokay14:01
kanzuresounds good to me14:01
genehackerhttp://www.dself.dsl.pipex.com/MUSEUM/COMMS/fluidicgramophone/fluidgram.htm14:01
genehackerit's in gif14:01
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genehackerhey you said you designed microcontroller right?14:03
kanzurethat's true.14:05
genehackerthis one has dimensions14:05
kanzurewhat?14:05
genehackerhttp://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=49401014:05
kanzureblah..14:05
genehackerhere's an actual design14:05
kanzureI just sent the fluidic amplifier design14:05
genehackercool14:06
genehackerso how does your microcontroller work?14:06
kanzureone thing I designed a long time ago was a simple 4 bit microprocessor14:06
kanzureso it had some basic arithmetic logic units for add, subtract, multiply, etc.,14:07
kanzureand then some logic elements to recognize instructions, read from the instruction buffer memory, etc.14:07
kanzurevery very basic14:07
genehackerhow many logic gates did it use?14:08
kanzureI don't know if I ever generated the final schematics, I was mostly just programming in Verilog or something14:10
xp_prgkanzure I suggested the simple pcr on diybio and they are open but feel it could be too difficult can you help explain why it is easy/possible?14:10
xp_prgwith microfluidics14:10
kanzurewhy do they feel it would be too difficult?14:10
genehackerwhat does programming in verilog look like?14:10
xp_prgcons: we have to figure out how to design the fluidic circuit, the heater/cooler, what materials to use, how to clean between samples, how to actually build it, and finally, how to integrate a visualiser so we can still do qPCR14:10
xp_prgI am down for doing this, but is it really going to be possible with our means?14:10
genehackerwe're talking about making a microfluidic graphing calculator14:11
genehackersomeone's offering to make any microfluidic device for us for free14:11
xp_prgwow cool!14:12
xp_prgwho is this person?14:12
genehackersomeone from diybio14:12
xp_prgwell who?14:12
xp_prgwhere are they located?14:12
genehackerthe only caveat is that we can't use electrical devices14:12
genehackerno idea who14:14
genehackerNanoscience technology is their post name14:14
xp_prgoh I did see that post14:14
xp_prgkanzure please respond to the thermocycler diybio thread14:16
kanzurexp_prg: with what14:16
xp_prgwith an argument addressing the concern with a microfluidic pcr approach14:16
kanzureat this point I think it would be better to go with the more traditional design because people already know how that works14:17
kanzureI'm more interested in working on a DNA synthesizer or something14:17
kanzurewhich might actually be simpler14:17
genehackerdamn good point14:17
kanzuregenehacker: so I think I can design a DNA synthesizer14:17
kanzurebut14:17
kanzurewhat I don't know how to do is get it so that all of the samples are easily accessible14:18
kanzureconsider for instance if there was a 2-plate sandwich DNA synthesizer14:18
kanzuremade out of microfluidic channels and such14:18
kanzurehow would samples be recovered14:18
kanzureone idea is to use a straw with emulsions so that you literally drain the DNA into the straw, and then cap it with oil or something on either side14:20
kanzureand then you number the slots in the straw14:20
kanzureand then you poke a hole when you want to drain it or something :p14:20
genehackercut copy paste14:20
kanzure?14:20
genehackerIE integrate a PCR step14:20
kanzurecut what?14:20
kanzureso wait14:20
kanzurewhat about for synthesizing multiple strands at once14:20
kanzurenot just synthesizing the same strand a million times 14:21
kanzureI guess doing the same sequence a million times would be fine14:21
kanzurethen you could mix it together14:21
kanzurebut where do you send it14:21
genehackerjust copy the final combined product over and over again14:21
genehackerhttp://www.youtube.com/watch?v=JvDZh8hmR84&feature=related14:21
kanzurewhere do you put it?14:21
genehackersharpie microfluidic based DNA sequencer14:21
genehackerer... droplet based14:21
genehackerwell I have to go, lets figure out some way we can design microfluidic circuits14:22
genehackersomething like verilog14:23
kanzuresure14:23
kanzurebut I still need to know where to *put* the products14:23
kanzuregenehacker: if you work for campbell over the summer we could get that verilog thingy working actually14:26
kanzureok guess we could do a drill-through screw-on-cap container drain dealy14:28
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kanzurehrm I think I've designed a non-reprogrammable (or non-programmable) DNA synthesizer15:02
kanzureit only synthesizes the specific sequence it was made to synthesize15:02
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kanzureso, I need to figure out how to properly do scheduling of droplet movements15:41
kanzurejust do rapid switching between interrupts? erm. so there's something like 500 elements that move the droplets15:42
kanzureeach one can be addressed individually15:42
kanzurewhen one is switched on (adjacent to the last one), the droplet moves towards the one that is switched on15:42
kanzureI mean, will I be shot for not writing a proper task manager?15:43
fenni've got quite a dependency tree built up before i can get a driver's license (before mine expires next week)16:02
kanzureeh?16:02
kanzurethings to do?16:02
fennthings i didnt know i had to do16:02
kanzureok, now stand on your head16:03
kanzureor else16:03
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fenni don't think it's all going to happen16:03
kanzure"Bryan, I realized I'm not quite clear on the title of your role at DIYbio. Co-founder, contributor, guru?"16:04
fennthis was the crayon sketch thingy i was trying to remember http://www.dgp.toronto.edu/~shbae/ilovesketch.htm16:09
kanzure"enormous prick"16:25
kanzureaw :(16:25
fennis that a compliment?16:28
kanzureI don't think so16:28
kanzurethey didn't say that16:29
kanzureI'm just expecting something un-nice16:29
fenni'm getting lots of spam email lately, mostly penis enlargement and related stuffs16:38
kanzurehttp://bioweathermap.org/ released16:50
kanzureok, some diagrams of schemes for DNA synthesis with droplets17:04
kanzurehttp://heybryan.org/~bbishop/docs/DNAsynthesizer/17:04
kanzurefear my mad diagramming skills.17:28
fenni think i'm going to give up on life and go back to my parent's house17:37
kanzure-depressed?17:37
fenni don't know.. 17:38
fennyesterday i wanted to go to the shop and work on stuff but i had to lay down.. for like 8 hours17:39
kanzure-weren't you feeling sick?17:39
fennit was just sort of more intense version of the usual17:40
fennanyway, i guess i don't have whatever it takes to keep my shit together17:40
kanzure-somebody yell at you?17:40
fennthere's no way i'm going to get all this stuff to fix my car17:40
kanzure-you mean, a license?17:41
fenni have to buy a new tail light and brake cylinder, install them, insurance17:41
fennneed ^^ and social security card to get a license, my license expires on may 2nd17:42
fennoh i also have to register the title and pay a 'new resident tax' which is $9017:42
kanzure-resident tax??17:42
fennand steve doesn't have money to pay me for another couple weeks17:42
fennso anyway, without a car i'm just a drag on les17:43
fennthat's the logic at least17:43
fenni've been struggling to keep up for about a year though17:43
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kanzure-KEEP WHAT UP?17:43
kanzure-erm, caps lock17:43
kanzure-so what happened to the idea of selling the car and getting something else?17:44
fennwas that an idea i had?17:44
kanzure-when you were thinking of coming down17:44
fennthere was some guy who left a note on the door a couple weeks ago expressing interest in buying the car17:45
kanzure-did you have a sign on it?17:45
fennno17:45
kanzure-is that usual behavior of people?17:45
fennbut i really like that car and don't expect to find another17:45
kanzure-to put notes on things expressing interest in buying it?17:45
fenni guess CRX's are popular with mexicans17:45
fennit's been sitting in les' driveway and i don't go places very often, so it's possible he thought it wasn't being driven at all17:46
kanzure-is les paying you anything?17:47
fenni did some metalworking stuff for a couple days and he mumbled something about 'maybe i'll give you a couple months rent at the shop'17:47
fennbut i haven't brought it up17:47
kanzure-other than that though?17:48
fennno17:48
fennhe is letting me stay in his house rent free though17:48
kanzure-worst case scenario you can get a job with my mom but the gas will kill you17:48
kanzure-she's out in Kyle, Tx17:49
kanzure-well, her shop is actually in Lockhart, Tx17:50
kanzure-alternatively you could make some rounds with me here at the labs if you want, 17:51
kanzure-there's a way to make this work.17:51
fenndo you really think they'd hire me at one of the labs?17:51
fennalso there's more to this than just money17:52
kanzure-yes17:52
* fenn goes to fill out a return to manufacturer authorization form for his body17:54
kanzure-if the not-getting-your-shit-together is just a matter of money, then that's solved17:54
fennone hypothesis for why i don't have a good steady job already is that i'm "addicted to the internet"17:55
kanzure-according to who?17:55
fennbut i don't think this is correct because i did an experiment17:55
kanzure-oh?17:55
fennaccording to me, based on sensationalist media about the dangers of technology17:56
kanzure-is it possible that you just haven't found an interesting job17:56
fennabout a year ago (?) i moved into my friend rob's house.. rob lives way out in the country with dialup.. basically impossible to use the net, so i didnt17:56
kanzure-er, what did you do ?17:56
fennabsolutely nothing17:57
kanzure-sounds boring17:57
fenni stared at the ceiling17:57
fennand my sleep phase was still off17:57
fennoh, and i worked on my car because it needed a new water pump17:57
kanzure-so again, is it possible that you just haven't found an interesting job [that pays]17:58
fennthat was when i realized i was basically stuck there without my car, and i'd have to drive anywhere to do anything or see any people (rob travels a lot), so i moved back into the old house17:58
fenneven though i have a pile of projects i haven't gotten around to doing them18:00
kanzure-do you have the resources to make them happen?18:00
fennso it'd be hard to find a more interesting job18:00
fenni have all the pieces necessary, yes18:01
kanzure-wait, really?18:01
fennwell, sort of.. i still need to con les out of his laser printer so i can etch circuit boards, but that doesn't stop me from doing the layout or whatever18:01
kanzure-for what?18:01
fennthe cnc motor drivers18:02
kanzure-oh. pcb boards for them.18:02
fennwhich i've been talking about since 200518:02
kanzure-sometimes thinking is hard for me. it's like squeezing out a thought or something.18:02
kanzure-tools sometimes make it easier or something18:02
kanzure-but it's always even more easy if somebody threw up a script to do it or something18:02
fenni can write my own script18:02
kanzure-well, script as in .. erm ..18:03
kanzure-not for the shell.18:03
kanzure-but for doing things18:03
fenntodo list, with bullet points18:03
kanzure-just because it's on a list doesn't mean you'll get it done18:03
kanzure-or that I'll get it done for that matter18:03
fennexactly18:03
kanzure-so here's a theory18:03
kanzure-with a limited set of bullets on a page18:03
fenni can make a detailed list but i won't do it18:03
kanzure-some percentage of them will get done by at least one of us18:03
kanzure-is it possible to make it so that we both do the other things that we won't do18:04
kanzure-heh'18:04
kanzure-or would that just make some sort of tri-combination of terribleness18:04
fennyes it's possible but there's interpretation issues18:04
fennmuch easier to do something you understand than to explain it to someone else18:04
kanzure-well, if you understand it, then you should be able to explain it (supposedly)18:04
kanzure-that's sometimes where I get worked up. recursing through the tree of explanations18:05
kanzure-or bush of explanations18:05
kanzure-gee, you know what would be useful here ..18:05
fennskdb wouldn't be useful here18:05
kanzure-why's that?18:06
fennexcept for maybe letting me know a month ago i had to do all this crap to get my driver's license 18:06
kanzure-oh. btw. there's a renew-your-license-over-the-web dealy here in texas18:06
fennnot for out of state license18:07
fenndid you know they take your thumbprints?18:07
kanzure-yes18:08
kanzure-so when I turned 18, I started ranting around asking for a 'guidebook to stuff that the state needs to tell you now that you're 18"18:13
kanzure-but nobody keeps that sort of documentation18:14
kanzure-anyway, keep me in the loop. I think you're more useful here than there.18:15
fennwell my idea was to go there and have them spend lots of money for me to go to various doctors, then i'll be fixed, and capable of actually doing stuff18:24
kanzure-do you have healthcare insurance?18:25
fenni don't actually have much faith in doctors but it might be something simple18:25
fennno, i don't have health insurance18:25
kanzure-ah, well then.18:25
fenndad was supposed to be setting that up but i guess he never finished18:25
kanzure-do you have to go there for them to get you health care?18:25
kanzure-you should probably poke him about that before you physically move18:25
kanzure-and if you want you can always try what they're forcing down my throat these days. it seems to do, something18:26
fennwhat's that, adderall?18:26
kanzure-yes. 5 mg, 10 mg, and 30 mg. and I'm also on prozac now, but I don't know what it's doing and wouldn't recommend it.18:27
fennwhy are you on prozac?18:27
kanzure-the doctor thinks I'm depressed18:27
kanzure-and honestly it's because mom says dad thought I was depressed18:27
kanzure-(she said that to the doctor)18:27
fennder... woah18:28
kanzure-yeah ..18:28
kanzure-he also thinks I have OCD, but that's not as bad as thinking I'm depressed18:28
kanzure-he's actually a bright guy. just don't agree about the depression stuff.18:28
kanzure-besides, it's one of those medications that takes a while to build up into the system18:29
kanzure-adderall will be working in 15 to 30 minutes.18:29
kanzure-um. so any ideas on making an oligonucleotide array but out of 2D channels for microfluidics operations?18:47
kanzure-without intersecting lines18:47
kanzure-I guess with electrowetting you don't need to have channel walls18:48
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DrTreadFYI I'm showing off the MakerBot kit @ the robot group tonite. 18:59
fennwhere's that?19:00
DrTreadsouth mopac19:00
kanzure-wah.19:00
kanzure-are you going to come and get me?19:00
DrTreadHeritage at Gaines Ranch retirement home19:01
fennah good, i think i'll go19:01
DrTreadyes. for reals?19:01
kanzure-I would appreciate a ride :)19:01
DrTreadwhere u @?19:01
kanzure-24th and Guadalupe.19:01
kanzure-http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=2323+San+Antonio+St,+Austin,+TX+78705&sll=37.0625,-95.677068&sspn=14.70541,65.302734&ie=UTF8&ll=30.297425,-97.742443&spn=0.007781,0.031886&t=h&z=15&iwloc=r019:02
kanzure-aren't you north of austin?19:02
DrTreadok. I'm leaving here in 10 min19:02
kanzure-do you have my number?19:02
DrTreadeast south east19:02
kanzure-oh19:02
DrTreadI think so. 19:02
kanzure-if I'm out of your way then don't bother19:02
kanzure-thought you were north19:03
DrTreadbut I want to get you! *pouts*19:03
kanzure-okay19:03
kanzure-fenn: will you be there?19:04
fennyep19:05
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kanzure-soo it looks like we just need algorithms for moving droplets over surfaces in some optimal way19:11
kanzure-and then some way to make more droplets from a resevoire19:11
DrTreadkanzure on my iPhone now. plz resend coordinates. 19:11
kanzure-pyrosequencing19:11
kanzure-erm19:11
kanzure-http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=2323+San+Antonio+St,+Austin,+TX+78705&sll=37.0625,-95.677068&sspn=14.70541,65.302734&ie=UTF8&ll=30.297425,-97.742443&spn=0.007781,0.031886&t=h&z=15&iwloc=r019:12
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DrTread_crap. as soon as I walk out of wifi range, the map disappears. email coordinates, plz19:14
kanzure-um, one moment19:14
kanzure-basically search for "The Castilian"19:14
kanzure-it's at 24th and San Antonio or 24th and Guadalupe (the main intersection)19:15
* fenn departs19:17
kanzure-http://cgi3.ebay.com/ws/eBayISAPI.dll?ViewUserPage&userid=dna_for_charity19:17
kanzure-bidding starts at $68k for whole genome sequencing by Knome19:18
kanzure-includes private dinner with Church19:18
kanzure-should I take out a loan and bid $100k?19:18
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bkeroSure19:34
kanzure?19:36
kanzurewill you give me the $100k?19:36
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kanzureDrTread__: have you left?19:37
kanzuregenehacker: want to see a makerbot tonight?19:37
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kanzureDrTread: have you left?19:37
DrTreadI'm in Austin now19:38
DrTreadeta 7:5119:38
genehackerMAKERBOT WHERE?19:42
genehackerAUUUUAUAGUCUACUACUCAUGAAGGUGCUAUGGAA19:42
genehackertranslate to protein19:42
kanzuregenehacker: where are you?19:42
genehackerin my dorm19:43
genehackerwhere are you?19:43
kanzureif you come to my dorm maybe you can hitch a ride with me19:43
kanzurewithin the next five minutes19:43
genehackerhow long will it take?19:43
kanzurepossibly until 1119:43
genehackerwhere are we going?19:43
kanzureI'm going to the robot group meeting19:43
kanzureDrTread is picking me up19:43
genehackerhmmmm...19:43
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genehackerchoices choices19:43
kanzureat least stop by and say hello19:43
genehackerdo you think they'd let me work on stuff there?19:43
genehackerlike my homework19:44
genehacker?19:44
genehackerah screw it19:44
genehackerI'm going 19:44
kanzureyeah sure19:44
genehackerI don't have that much19:44
genehackerAUUUUAUAGUCUACUACUCAUGAAGGUGCUAUGGAA19:44
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katsmeow-afktitanium nanotubes contaminated with potassium split water to hydrogen with 1/3 the electricity as uncontaminated : http://www.eurekalert.org/pub_releases/2009-04/nios-doa042309.php21:06
katsmeow-afkhow to punch nanoholes in cell membranes : The paper is called "Amyloid-beta-induced ion flux in artificial lipid bilayers and neuronal cells: Resolving a controversy."21:17
ybitw00t rss feeds :P21:27
ybithttp://www.darpa.mil/dso/programs.htm#m23:41
ybit"Mathematical Time Reversal "23:41
kanzurewell now.23:49
* kanzure gawks at tool list23:49
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kanzuregenehacker: hey23:52
kanzurethe interview will be published Monday23:52
genehackerwhat will?23:52
kanzurethe interview with singularity hub about diybio23:52
genehackerhmmm23:53

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