2015-07-06.log

--- Log opened Mon Jul 06 00:00:02 2015
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jrayhawkhttps://www.flickr.com/photos/kylemcdonald/19266856649/sizes/o/02:46
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kanzure.title https://news.ycombinator.com/item?id=983633603:27
yoleauxHacking Team hacked, attackers claim 400GB in dumped data | Hacker News03:27
kanzure"Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces" http://www.bakerlab.org/system/files/Gonen_2DArrays_Baker2015.pdf03:44
kanzure"We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design ...03:44
kanzure... proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering."03:45
kanzure"Accurate design of co-assembling multi-component protein nanomaterials" http://www.bakerlab.org/system/files/King_Nature2014A.pdf03:47
kanzurefigure 4 "Electron micrographs of designed two-component protein03:47
kanzurenanomaterials."03:47
kanzureno wait, figure 5 is better03:47
kanzure"Automating human intuition for protein design" http://www.bakerlab.org/system/files/Niv%C3%B3n_prot24463_13M.pdf03:51
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kanzurea more general review of de novo protein design (open access) http://www.sciencedirect.com/science/article/pii/S0959440X1500069X03:54
kanzurea grammar for protein backbone structure using "protein blocks" http://onlinelibrary.wiley.com/doi/10.1002/pro.2581/pdf03:55
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kanzureeudoxia: same request goes for you (regarding listmaking of useful molecular machines)05:52
eudoxiahmm05:54
eudoxiaMNT style machines or just anything useful?05:54
kanzureanything useful05:59
kanzurenot necessarily molecular nanoprobe stuff05:59
eudoxiaright, also proteins and shit06:00
kanzurewell, protein-equivalent machines could count, but let's skip proteins themselves here06:02
kanzurehaving a molecular differential gear is nice, but only if you have other components to make use of it. meanwhile there are probably simple molecular machines that are useful in isolation.06:02
eudoxiasort of like what the parts library of NE was meant to become06:04
kanzurehuh?06:05
kanzurethe parts library was full of differential gears06:06
eudoxia.title http://crnano.org/interview.freitas.htm06:06
yoleauxNanotechnology: Robert Freitas Interview06:06
eudoxia>We’d expect the library of designed machine systems to rapidly expand from the current 1-2 dozen items (including mostly just a few bearings, gears, and joints) into the hundreds or thousands in just a few years.06:06
eudoxiaoh bobbie06:06
kanzureso you're saying the only simple molecular machines you are aware of are the ones listed here? https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib06:07
eudoxianot really, there's also a nanotube linear motor and this rack and pinion system that's not there06:08
eudoxiathen there's all sorts of bespoke binding sites people have designed over the years06:09
eudoxiawait a sec who did this https://github.com/kanzure/nanoengineer/tree/874e4c9f8a9190f093625b267f9767e19f82e6c4/cad/partlib/schafmeister06:09
justanotheruserkanzure: do you have a list started?06:10
justanotheruserAll I know of are drexlers designs06:10
kanzurewell the files in nanoengineer.git are a list beyond just drexler's designs06:11
kanzurehere are some protein things that are interesting, if that's what you're asking about http://diyhpl.us/wiki/dna/projects/#proteins06:11
justanotheruseryes, that is interesting06:12
justanotheruserwasn't aware of all the designs that come with nanoengineer06:12
* justanotheruser bookmarks06:13
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kanzurei'm surprised at the lack of responses- i was expecting obvious things like antennae arrays, rod arrays (for sensors or even dna separation), polymerase clamps, springs, spheres or beads, machine tools...06:26
eudoxiaregarding springs06:27
eudoxiadrexler mentioned in the design of rod logic that you'd need springs to bring the rods back into place06:27
eudoxianot knowing if there were small spring molecules like that, i imagined the way it would work would be something like06:27
eudoxiaa rotor with a cam would push the rods back into place, and travel perpendicular to a stack of identical rod-logical circuits06:27
eudoxiabut there are probably small linear spring molecules, no?06:28
kanzurehere is a more chemistry-oriented review of molecular machines http://www.researchgate.net/profile/Alberto_Credi/publication/12237218_Artificial_Molecular_Machines/links/0a85e531aec5618f45000000.pdf06:28
kanzurei don't think that small-scale rod logic is likely to work for a while-- you need lots of other machinery to make use of it06:30
eudoxiacertainly, just asking cause it came to mind06:30
justanotheruserhttp://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.100208606:32
justanotheruser.title06:32
yoleauxPLOS Biology: Open Labware: 3-D Printing Your Own Lab Equipment06:33
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kanzuresteganography framework https://github.com/bramcohen/DissidentX07:20
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CaptHindsightkanzure: the Agilent inkjet may be used for more than oligo probe hybridization, they are just focusing on that with their NextGen07:31
CaptHindsightHP makes lots of printheads that they don't resell07:32
kanzureit's not the inkjet which limits it; it's the lack of sample recovery07:33
CaptHindsightit looks like they have made some just for printing oligos07:33
CaptHindsightwhat's stopping/preventing the sample recovery?07:34
CaptHindsightit's a stack of oligos in wells07:34
kanzuresee pm07:34
kanzurewells are problematic because the only way to recover dna from wells (in this scenario) is pipetting, and if you have 2 million pores/wells then uh.. well.. pipetting will take forever.07:35
CaptHindsightdrop the bottom out07:36
kanzureto where? you need to keep the samples separated.07:36
CaptHindsightyou have to start connecting them somewhere07:37
kanzurenow would be an okay time for a phone call if you're up for it07:37
archelshmm, these guys coded their spiking neural network in Julia. I wonder why07:44
archels447 SLOC, pretty tight07:44
archelsno parallelism though07:44
archels                                if spiked[cc] #spike occurred07:46
archels                                        spiked[cc] = true;07:46
archels# make **REALLY REALLY** sure that this variable is set to true07:46
kanzureCaptHindsight: good talking with you capt'n08:24
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kanzurewin 508:39
kanzureeijroeqjrqi whoops08:39
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kanzurehttps://np.reddit.com/r/IAmA/comments/38jawf/im_the_president_of_the_liberland_settlement/crw1d0f?context=1009:06
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nmz787_i1kanzure: so what does CaptHindsight want to improve on specifically, just cost to manufacture a POSAM clone?10:36
nmz787_i1if that's the case, then I think replicating the POSAM chemicals list would be the best idea10:37
nmz787_i1and send me an email for the items that are no longer available with direct replacements... and we can search for a substitute10:38
nmz787_i1kanzure: a more interesting question to me is, who here would want to help with a micro/nano device?10:38
kanzurewhy bother with micro or nano if you can get enough scale without it? inkjet printing can do picoliter droplets.10:39
nmz787_i1yeah but eww10:39
nmz787_i1you want to do offsite sequencing10:39
kanzureelaborate?10:39
nmz787_i1how gross10:39
kanzureyes, i want to do offsite sequencing for now10:39
kanzurev2 can include other components10:39
nmz787_i1you need sequencing after every 1 to 10 or 50 additions10:39
kanzureputting all work upfront is not good.... likewise, putting everything off until later is also bad.10:40
nmz787_i1tdt plus nanopore would be more interesting10:40
kanzurei thought that required a mutated/not-yet-existing version of tdt10:40
nmz787_i1na10:40
nmz787_i1just some wires to sense the nanopore for when a nucleotide passes through10:41
nmz787_i1impedanceometry or whatever10:41
kanzurei'm not sure why you think that is easier than working with off-the-shelf inkjet heads?10:41
nmz787_i1because I have access to a FIB and silicon and gas-injection... I don't have inkjets, know their interfaces aren't stable for offlabel use10:42
kanzurefib is not the hard part when confining an enzyme in a nanopore10:45
nmz787_i1you don't want the enzyme in the nanopore though10:47
nmz787_i1the nanopore is just to limit diffusion and tunnel molecules past your molecule-counter electrodes10:47
nmz787_i1so you can know when to turn off the nucleotide pump10:47
nmz787_i1but anyway, yeah I'd say just replicate the POSAM chem list, and shoot me an email if there are items with questions or supply problems10:48
kanzureone thing you might be able to convince me about is single-molecule emulsions10:49
nmz787_i1the HO on water looks like the HO on the 2' site on the nucleotide rings, that's why it lowers efficiency... so anything with a similar HO can have that effect10:50
nmz787_i1(just FYI)10:50
nmz787_i1https://en.wikipedia.org/wiki/Directionality_(molecular_biology)10:50
nmz787_i1err10:50
nmz787_i1the 3'10:50
nmz787_i1https://en.wikipedia.org/wiki/Nucleotide10:51
nmz787_i1(the first link shows the hidden polymer form)10:51
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kanzure.title http://www.sciencemag.org/content/333/6042/613.short10:55
kanzure"A Single Molecule of Water Encapsulated in Fullerene C60"10:56
yoleauxA Single Molecule of Water Encapsulated in Fullerene C6010:56
kanzurehttps://scholar.google.com/scholar?hl=en&q=%22organic+cage%22+&btnG=&as_sdt=1%2C44&as_sdtp=10:57
kanzureor nanopipette stuff.. hm.11:00
kanzurehuh i'm surprised that single-molecule emulsions are not a thing11:07
archelssuperkuh: the website is down :(11:08
archelsthis should be fun  https://www.youtube.com/watch?v=7u8mheM2Hrg11:17
archels.title11:17
yoleauxRESPONSE TO ROBOT DUEL CHALLENGE. - YouTube11:17
nmz787_i1I think I'd basically just need some help with CAD models and idea putting-together... then I could convert them to FIB files or mask files, do the micro/nano work... then maybe send that off to someone with a machine shop to make the macro to micro manifold, hookup the pumps and chemicals. Before that the sensing board would need to be built or a good analog frontend (amplifier) would need purchased11:17
kanzurewhich cad models?11:18
CaptHindsightnmz787: what do you want to fabricate? the manifold?11:19
nmz787_i1I'd do the actual micro and nano device (on-chip peristaltic pumps, some mixing areas, a nanopore for each nucleotide, a chamber for tdt, a nano-lattice/pore-matrix to retain tdt so waste can flow, some purification areas)11:20
superkuhUh oh. Something didn't come back up from the lightning strike.11:21
nmz787_i1the manifold I'm guessing will look something like this http://www.ifitjams.com/images/f4-11.jpg11:21
superkuhOh, no, just another IP change.11:21
CaptHindsighta zero insertion force socket11:22
nmz787_i1the microchip just compresses onto the steel manifold, with some rubber or teflon between11:22
nmz787_i1I think that is LGA11:22
nmz787_i1so not quite ZIF11:22
CaptHindsightnmz787: LGA PGA11:22
nmz787_i1since there's no insertion11:22
CaptHindsightyeah just the pores11:22
CaptHindsightinlets11:23
CaptHindsightCAD models are no problem11:26
CaptHindsightkanzure: you have to decide which way you want to go11:27
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nmz787_i1I would prefer BRL-CAD personally11:28
CaptHindsightnmz787: heh, well you can spend the time converting from Step or Iges11:28
nmz787_i1that seems like the only approach that is reliable11:29
nmz787_i1nah i'd just use my python interface ;)11:29
nmz787_i1To make the CAD automated for the FIB, I ultimated neem a .BMP type file11:30
nmz787_i1need*11:30
nmz787_i1but if the device is a one-off, I can do it by hand11:30
nmz787_i1but we still need to layout the components, break/fan them out to the macro manifold, and design the manifold11:31
CaptHindsightI have all the design tools. I just don't bother with all the open source almost CAD tools11:33
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CaptHindsightheh, how does a single molecule qualify as in emulsion?11:39
CaptHindsightin/an11:39
nmz787_i1the cage would be the emulsifier11:39
CaptHindsightkidding11:39
archelssuperkuh: excellent11:39
CaptHindsightlow cost DIY FIB11:40
CaptHindsighta handy tool of the nano machine shop11:41
nmz787_i1yeah it would work as a mass-spec too, if reversed11:41
nmz787_i1err, maybe the DIY SEM would be a better candidate11:42
CaptHindsightwhat tools to build first? that was the discussion11:42
nmz787_i1but the DIY DUAL-BEAM would definitely be reversible for mass-spec11:42
CaptHindsightwell both, but where do we start11:42
CaptHindsightbuild tools to build tools11:42
CaptHindsight3-axis inkjet is pretty simple11:43
CaptHindsightalso DLP micro printer11:44
CaptHindsightthere are lots of old SEM's around11:44
CaptHindsightthe electronics could all be modular, motion control, imaging etc can all be done on a PC11:45
kanzurethere really is no substitute at the moment for solidworks, really11:45
kanzurebrlcad has iges/step support, so just do it in solidworks then export to step/iges11:45
CaptHindsightthere are not really any open analog boards for drivers and sensors11:46
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CaptHindsightNX, Catia, Creo, SW we run em all11:46
CaptHindsightbrl is coming along11:47
nmz787_i1BRL seemed to have better support for wide dynamic range in CAD models (they claim molecular to planetary scales)11:47
CaptHindsightit's all the automated plug-ins and tools in the CAD package that save you so much time11:48
CaptHindsightmost on the surface act about the same11:49
nmz787_i1BRL doesn't have great support for harder to define curves, at least in terms of defining them with math/equations11:49
CaptHindsightextrude, cut, rotate, chamfer etc11:49
CaptHindsightit's when you need to blend from one surface to another or hold some inner diameter on a contorted tube or similar is when the extra features come in handy11:50
CaptHindsightor generate a pattern of holes etc11:50
CaptHindsightbut that's not holding us back11:51
CaptHindsightthat's just a preference for tools11:51
CaptHindsightand how much time you have11:52
nmz787_i1I just need a BMP file11:52
nmz787_i1:P11:52
CaptHindsightyeah11:52
nmz787_i1256-bit greyscale and single-layer per BMP11:53
kanzureCaptHindsight: i'm a big fan of keeping it simple. nanopore stuff is fun, worth doing, but i still think keeping things simple can lead to good results.11:55
CaptHindsightkanzure: we have to start somewhere11:55
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CaptHindsightbuild a tool at a time, in a few years there will be a whole sub-micron CNC shop11:56
kanzureoh regarding the emulsion question earlier: the idea was to use an emulsion where the contents of the emulsion is a single molecule11:58
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kanzurethe actual emulsifier could be many multiple molecules11:58
CaptHindsightkanzure: whats the solvent or vehicle it's suspended in?12:00
nmz787_i1CaptHindsight: IMO the nanopore stuff is immensely less complicated from a success standpoint... no one is going to care if you make POSAM cheaper, because the reagents are so relatively unavailable, short shelf life, low value output (it creates stuff that was available mail-order 30 years ago)12:01
kanzureno idea, i was just looking around for papers to see if the emulsion idea exists elsewhere, doesn't matter12:01
CaptHindsightI'm translating from Bio to coating, ink, paint chemistry terminology12:01
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kanzurenmz787_i1: whether "no one is going to care if you make POSAM cheaper" does not modulate whether "the nanopore stuff is immensely less complicated from a success standpoint"...12:02
kanzureshort shelf life is probably because of contamination12:02
kanzurebeing available by mail-order is irrelevant12:02
nmz787_i1nope, that's why I included the chemistry point(s)12:02
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nmz787_i1tdt is all water-based, can be achieved with a few home-brew enzymes and purified molecules12:03
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CaptHindsightnmz787: https://en.wikipedia.org/wiki/Terminal_deoxynucleotidyl_transferase  making sure we are talking about this12:12
kanzureyes12:12
kanzureterrible diagram of tdt, it's essentially a donut12:13
kanzurebut the diagram fails to express this12:14
CaptHindsightsquished donut12:17
kanzurea less delicious donut12:18
CaptHindsighthttp://www.ebay.com/itm/Cambridge-Stereoscan-250-MK2-Scanning-Electron-Microscope-SEM-/400758845514  $800 as-is12:25
kanzureworking?12:25
CaptHindsightlooks like "untested" we have no clue how to either12:25
CaptHindsightI usually spot one or two for a few $K that are in working condition12:28
nmz787_i1e-ink remote control on Sony's home-grown crowdfunding site https://first-flight.sony.com/pj/2/HUIS%20REMOTE%20CONTROLLER12:31
CaptHindsighthttp://www.ebay.com/itm/Zeiss-Electron-Microscope-EM-109-/181783812468  $3500 was working12:32
drethelinnice12:32
CaptHindsightand another: This instrument was pulled from service many years ago and its operational status is not known, thus we are listing it as "for parts or not working" because we cannot guarantee its proper operation.  http://www.ebay.com/itm/JEOL-JSM-35C-Scanning-Electron-Microscope-with-Spectrum-Analysis-/33148205137312:33
CaptHindsight$250012:33
CaptHindsightwith Spectrum Analysis12:33
CaptHindsighthttp://www.ebay.com/itm/JEOL-T330A-Electron-Microscope-working/331599003517  $2500 working12:35
CaptHindsightwith video of it working  https://www.youtube.com/watch?v=FVpqDrAeKLU12:35
CaptHindsighthttps://www.youtube.com/watch?v=gejSPGIcWPo12:36
nmz787_i1the T330A looks pretty much like the scope I have (T200)... I think I might even have some schematics for the T330A too12:37
CaptHindsightI should try to find surplus gun, chamber, detector assemblies12:40
nmz787_i1https://www.tedpella.com/calibration_html/SEM_Calibration.htm12:40
nmz787_i1I think that JSM-35C was on craigslist for a while12:41
nmz787_i1oh, maybe not12:42
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kanzure.tell eleitl http://www.metzdowd.com/pipermail/cryptography/2015-July/025971.html12:58
yoleauxkanzure: I'll pass your message to eleitl.12:58
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kanzureapparently firefly synchronization is a thing http://www.eecs.harvard.edu/ssr/projects/sync/13:52
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kanzure"Some viruses that infect Archaea have complex structures that are unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.[80]"13:59
kanzure[80]  Prangishvili D, Forterre P, Garrett RA. Viruses of the Archaea: a unifying view. Nature Reviews Microbiology. 2006;4(11):837–48. doi:10.1038/nrmicro1527. PMID 17041631.13:59
kanzurehttp://www.nature.com/nrmicro/journal/v4/n11/full/nrmicro1527.html13:59
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kanzurehttp://www.researchgate.net/profile/Patrick_Forterre/publication/6753226_Viruses_of_the_Archaea_a_unifying_view/links/53f5c8700cf2888a7491e75e.pdf13:59
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nmz787_i.title http://hplusmagazine.com/2015/02/15/biology-technology-darpa-back-game-big-vision-h/15:20
yoleauxBiology is Technology - DARPA is Back in the Game With A Big Vision and It Is H+ - h+ Mediah+ Media15:20
nmz787_i'Most lenses are, by definition, curved. After all, they are named for their resemblance to lentils, and a glass lens made flat is just a window with no special powers.'15:26
nmz787_i/me had no idea of the relation to lentils15:26
nmz787_i=-O15:26
kanzure"Well known Silicon Valley venture capitalist, rocketeer, transhumanist, and super guy Steve Jurvetson was spotted “high fiving” a DARPA funded telepresence robot developed at Johns Hopkins APL at the reception."15:27
kanzure(jurvetson is the J and draper is the D in DFJ)15:27
kanzure(draper is the one with the kid that is desperate to fund someone building an iron man exoskeleton)15:28
kanzuredidn't know that these were the organ-on-a-chip people http://emulatebio.com/15:28
nmz787_i.title http://keyssa.com/technology/15:36
yoleauxOur Technology - Keyssa15:36
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nmz787_i.title http://www.voxel8.co/15:45
yoleauxVoxel8: 3D Electronics Printing15:45
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kanzure.title https://news.ycombinator.com/item?id=984120918:08
yoleauxAntibody wipeout relieves symptoms of chronic fatigue syndrome | Hacker News18:08
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kanzure.wik treponema pallidum18:22
yoleaux"Treponema pallidum is a spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws. The treponemes have a cytoplasmic and an outer membrane. Using light microscopy, treponemes are only visible using dark field illumination. They are gram negative, but some regard them too thin to be gram stained." — https://en.wikipedia.org/wiki/Treponema_pallidum18:22
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kanzureoh cool we have the genome of neurosyphilis18:23
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drethelingreat, now we can synthesize it!18:29
kanzurethere are easier ways to get neurosyphilis18:30
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kanzure"The metalloprotease Mpr1 has been demonstrated to be critical in blood-brain barrier penetration.[16]"18:40
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ryankarasonnmz787: ha! @ lentils.. nor did i..19:25
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kanzurehm20:09
kanzurewhatever happened to the brain preservation prize results. did that happen? or was it just a hit-and-run thing.20:10
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kanzurehrm.21:06
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