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Burkhard Rost › Comments

Ruchira S. Datta
Thanks so much for the coverage today!
I happily join in this shoulder clapping reverence to your group's important contribution to the success of this meeting. What else could ISCB do to support your efforts? - Burkhard Rost
How about some form of travel award, or registration discount? It might be conditioned on some minimum microblogging metric (carefully designed to avoid perverse incentives). - Ruchira S. Datta
Roland Krause
Is there interest in a Birds of Feather session tomorrow regarding (micro) blogging?
... or simpy a joint luncheon? - Roland Krause
joint luncheon sounds good. - Mickey Kosloff
mentioned this before but might have been lost: if ISCB has to do something to support this crucial activity: let us know! - Burkhard Rost
OK, then let's meet for lunch tomorrow. Please spread the word. It'll be easiest if we meet at 12:50 at the hallway leading to the ballrooms on the 3rd floor. Burkhard: Thanks for the support, we'll get back to you. - Roland Krause
@Burkhard: most people that sat next to me had no idea about this room or about FF, despite the prominent slide and the links from the ISMB webpage. Perhaps if you show a screenshot before a keynote, awareness will increase? - Mickey Kosloff
Afraid the horrible wireless connection made (live) blogging nearly impossible for many sessions. Was going to cover the late breaking research session today from 201, but no luck. - Oliver Hofmann
Must have missed you. Got there a couple of minutes late and didn't see anyone. - Mickey Kosloff from iPod
Hmm, let's try to meet at the reception. It'll be a search in 2D space so we should find each other in finite time. I will be in room 302 for the remainder of the afternoon. - Roland Krause
What about another projector projecting the feed, in talks by some daring presenters? - Barb Bryant
I won't be able to make the reception. My 3 ideas are: separate (secure) wireless for bloggers. Incentives (e.g. Priority for plos-cb postcard publications). Wider campaign to recruit micro bloggers before ismb. - Mickey Kosloff from iPod
1. projection of the feed: don't get the reason. 2. wireless 4 blog: good idea, 3. plos-cb postcard slot: will talk to phil/plos, 4. other incentives: what you want? - Burkhard Rost
Reason for wireless4blog is most likely due to low speed here - arne
It's not a bandwidth problem, I had throughputs on the MB/s. More likely, many of our computers have problems in this mixed settings with "smart" handling of receiver power etc. In Vienna, I had a clever tech guy that helped to disentangle these issues with my network card. What we (all) would really need is some sort of true hacker with proper equipment but I have no good idea how to recruit such a person. - Roland Krause
Can bottleneck be between local server and ISP ? - Mickey Kosloff from iPod
ISMB
Keynote: Steven Brenner - Ultraconserved nonsense: gene regulation by splicing & RNA surveillance
ISMB2010 just kicked off - Venkata P. Satagopam
Prof Søren Brunak introducing Steven Brenner, ISCB overton prize winner - Venkata P. Satagopam
Brenner contributed to many fields in bioinformations, starting in structureal biology ober RNA to metagenomics. - Roland Krause
A short biography, summarizing Soren Brunaks kind introduction http://compbio.berkeley.edu/people... - Roland Krause
The morphology of steves paper: http://www.improbable.com/airchiv... - Shannon McWeeney
Intro: The ultraconservative (as seen from Berkely) and nonsense (as found in Through the Looking Glass - Roland Krause
The jabberwocky poem does have meanings and is elegantly crafted. - Roland Krause
Generally, nonsens in biology is bad. - Roland Krause
Nonsense is generally bad, even in a codon - Venkata P. Satagopam
Truncated proteins might interfere with physiological function (dominant negative). The cell removes such transcripts through nonsense-mediated decay (NMD). - Roland Krause
Good example for NMD: Sox10 - Roland Krause
Mutations early in the gene leads to less severe phenotypes than later ones - Roland Krause
NMD is an mRNA surveillance system - Venkata P. Satagopam
NMD important to development of the immunesystem and cleans up other transcriptional errors. - Roland Krause
We do not know how NMD works outside the mammals. - Roland Krause
The mechanism involves the splicing machinery. If a stop is found wwithin 50nt upstream of the exon junction complex, it is removed.. - Roland Krause
50 nucleotide rule - translated normally or degraded by NMD - Venkata P. Satagopam
brilliant nytimes article title - surviving on low number of genes - Shannon McWeeney
splicing can introduce PTC - premature termination codon - Venkata P. Satagopam
AS as mechanism to introduce PTCs - can lead to unproductive splicing - Shannon McWeeney
these isoforms often have PTC - Venkata P. Satagopam
Humans have fewer genes but better genes, due to AS. - John Greene from fftogo
Are PTC splice forms funcitonal? - Venkata P. Satagopam
Many PTC mRNAs are noise - Venkata P. Satagopam
analgous mechanism to shrinter: http://www.geeky-gadgets.com/cool-ga... - Shannon McWeeney
Humans have fewer genes but better genes, due to AS. - John Greene from fftogo
Alt splicing can yield isoforms differentially subjected to NMD - Venkata P. Satagopam
SR protein - 11 in human which are serine and arginine rich - Venkata P. Satagopam
SR proteins have premature stop codons. - Roland Krause
SR genes has mRNAs with premature termination codons - Venkata P. Satagopam
AS of PTC isoforms is mechanism for autoregulation of proteins - Ted Laderas
NMD has a large effect on isoform abundance - Venkata P. Satagopam
NMD has impact on isoform abundance - example of NMD clearing the major isoform - Shannon McWeeney
minor isoforms are only shared 25% of time - modrek and lee 2003 - Shannon McWeeney
Not just anecdotal stories, splice patterns are conserved in mouse, implying functional significance. - Roland Krause
(Unpulbished work) - Roland Krause
All the SR proteins are talking to each other - Venkata P. Satagopam
SR proteins 'compensate' for each other via coupling via AS and NMD - Ted Laderas
SR genes have ultraconversed elements .. Bejerano et al 2004 Science 304: 1321 - Venkata P. Satagopam
Most ultraconserved regions are in intergenic regions, the regions in SR within genes. - Roland Krause
question of why conserved - not protein coding, no obvious significant RNA secondary structure - Shannon McWeeney
No proteins are produced from these genes. - Roland Krause
The reason why SR sequences are highly conserved - most of the seq are not protein coding, - Venkata P. Satagopam
no repetitive elements - Venkata P. Satagopam
why conserved part 2 - no overrepresentation of binding / regulatory elements - Shannon McWeeney
No simple explanations e.g. from miRNA binding etc. - Roland Krause
no similarity elsewhere in genome except retropseudogenes - Venkata P. Satagopam
analysis on origin of unproductive splicing - Shannon McWeeney
No sequence similarity between the conserved elements. Seems to have been introduced mutliple times. - Roland Krause
mouse and human SRp55 conserved but changing - Venkata P. Satagopam
working on chordate SR proteins - Venkata P. Satagopam
here intron and exon structure is more informative - Venkata P. Satagopam
at this point - he has requested no further blogging - unpublished work - Shannon McWeeney
no blog slides may be over - Burkhard Rost
# Looks like interesting work. - Roland Krause
wonderful talk - Shannon McWeeney
Tells a (hard to blog) story about the successful treatment of collaborator with novel treatment based on genotyping. - Roland Krause
Wow - what a conclusion! Fantatic talk... - John Greene from fftogo
# Certainly great work. The talk was nice too, and he only bitched at other reseachers in person once, another step up. - Roland Krause
"Ultraconversed elements in SR genes ONLY show similarity to retropseudogenes" - what does this mean? Any takers? - Saravanamuttu Gnaneshan
Ruchira S. Datta
I'm here and will be attending the BioPathways SIG. I figured there should be some place to say non-talk-specific things like "I've arrived!", so here it is. - Ruchira S. Datta
Will be switching between DAM, BOSC and the BioPathways. Once I've figured out which talk is when ;) - Oliver Hofmann
Uhoh. I sense a lack of places to recharge notebooks. This is going to be fun during the session breaks.. - Oliver Hofmann
I forsee a problem with the SIG posts in FF - only one heading, and many, many speakers.... Hopefully will be OK for people following. - Allyson Lister
The projectionist kindly suggested I power up in the projection cubicle during the coffee break. - Ruchira S. Datta
Network is slowing down to a crawl for me. - Oliver Hofmann
Sitting at home, following the conference. Great job folks! My only wish is that there was some place where the speakers would upload their presentations. - Lars Juhl Jensen
Help! Anyone got a UK plug adaptor with them I could borrow for an hour or so? Will happily exchange laptop charge for beer/coffee. - Cass Johnston
Oliver, I've been having that problem too. There were some times when I had posted a comment and wanted to post another one, but the first hadn't finished posting, so I had to wait for the post to finish, hold my comment in my head, and also pay attention to what the speaker was currently saying... - Ruchira S. Datta
Talked to the organizers. They are aware of the problem, IT is looking into increasing bandwidth. Yay. - Oliver Hofmann
@Oliver well done! Perhaps we could ask someone to look into more power extension leads? :) - Allyson Lister
Anyone up for a FF lunch / dinner / drink at some point during ISMB? - Oliver Hofmann
Sounds good. I'm about to go orienteering, though, so will be out of reach this evening... - Ruchira S. Datta
Monday and Tuesday are the only "free" nights, with poster sessions going from 5:45 to 8:30 pm. Shall we just set Monday night for the FF meet-up? When would people want to leave the conference at the earliest? 8 pm? - Michael Kuhn
Monday's going to be busy meeting everyone; I'd probably try and stick around 'till 8pm. Meet at the registration booth close to the entrance at 8:15? Can decide on a venue depending on our numbers and whether people are willing to travel to the city center. - Oliver Hofmann
I think I would prefer 8:40. I have a poster. I haven't figured out yet whether it's Monday or Tuesday, but others might have posters too? Last year, at least, I was explaining my poster to people pretty much constantly until the poster session closed. - Ruchira S. Datta
Monday or Tuesday is good for me - either way, and any time is fine. It's a good idea! - Allyson Lister
8:45 on Monday then, same place (registration area)? Do we have any locals with suggestions? - Oliver Hofmann
ok - see you all in registration at 8:45 monday :) - Allyson Lister
If everyone has already seen Gamla Stan by that time, we could go to Södermalm--plenty of good restaurants. I'm staying there. - Ruchira S. Datta
@Ruchira: works for me as long as we have a guide to get us there :) - Oliver Hofmann
@Allyson There are lots of power extensions along the windows just inside the T hall. Let me know if those are still too full and I'll see what I can do about getting more. - Dave Messina
@Oliver The conference organizers have bought high-speed internet. Anyone can go to the registration desk for a free login. Spread the word! - Dave Messina
@Dave, yep, got mine this morning. World of a difference. - Oliver Hofmann
@Dave, any chance of getting extension cords to the other conference rooms? Starved for outlets at K21 :) - Oliver Hofmann
I'll be arriving today, would it be worth to pack a extension cords with multiple sockets? - Roland Krause
@Roland: This is always a good idea. Problem is that some rooms only have power on the stage and in the projection booth. - Michael Kuhn
Organizers also have extra extension cords for emergencies, but even the main conference room has no outlets. Best to recharge during the breaks, but that means leaving the notebook unattended... - Oliver Hofmann
photos from ISMB/ECCB, please put on flickr under tag "ismbeccb2009" - Burkhard Rost
The projectionist here just unplugged my power cord from their outlet and said none of us will be allowed to use their outlet; we'll need to use the outlets in Hall C. He said the organizers did not pay for extra outlets, so we will still have this power problem. - Ruchira S. Datta
Well, at least I'll be able to sit closer to the front where I can see better. - Ruchira S. Datta
Even the "free" network is considerably faster and more responsive today. Well… we'll see what happens when the first coffee break hits. - Johann Visagie
@Ruchira: Ouch. That's not going to help. We can get extension cords and use them in the smaller meeting rooms though. - Oliver Hofmann
@Johann agreed - I also think the network is faster today - Allyson Lister
I love the fierce, ofttimes violent competition for the limited resource that is power outlets during coffee break! - Johann Visagie
It seems a simple #ismb is the twitter hashtag of choice. Also note Burkhard's suggestion above to use "ismbeccb2009" as Flickr tag. (Hey! Flickr tags can has spaces! ;) - Johann Visagie
@Johann: Bring your own socket multiplier and you are loved by everyone ;-) - Oliver Hofmann
Any chance of leaving / recharging our desktops at the registration desk during the breaks? Would rather not leave mine in a conference room unattended. - Oliver Hofmann
Lonely FFer near the registration desk is looking for some chatting... anyone? - Egon Willighagen
Sure, I'll wander by momentarily. - Ruchira S. Datta
I'm sitting on the ground in front of the registration desk, waering a black t-shirt... - Egon Willighagen
Any poster presenters here on FriendFeed? Maybe you can start a new post in the ISMB/ECCB room and attach your poster PDF? - Egon Willighagen
Great idea, Egon! Not being at the conference, I would very much appreciate being able to see some of the posters on FF. - Lars Juhl Jensen
Lars, are you in Stockholm? - Egon Willighagen
What about special sessions, I do not see them here. - Diego M. Riaño-Pachón
I'm having a special FF sessions outside, but I am the only participant :) (after a nice meet up with Ruchira earlier) - Egon Willighagen
@Egon - shame - I was offline for lunch. At least I assume it was lunch you said that. FF doesn't put up the time each comment was made - so add times please if you're talking about meetups! Hopefully see most of you this evening after the poster session anyway :) - Allyson Lister
P.S. The network seems to have slowed down again. Anyone else notice, or is it just me? - Allyson Lister
@Dave thanks for the power extension cable - except for the main victoria hall (as we discussed) it's really helped a lot :) - Allyson Lister
@Allysin, I'm still around... in front of E.A.T. now.... - Egon Willighagen
@Egon - ah, but I'm in a talk! :) - Allyson Lister
@Egon, no I decided not to go this year - Lars Juhl Jensen
@Allyson: As half of the conference is probably sharing the username / password for the closed network I am not surprised it is slowing down :) - Oliver Hofmann
Maybe it is because I am happily uploading Jmol 11.7.45 to SourceForge ? :) - Egon Willighagen
@Allyson Glad to help! - Dave Messina
@Oliver Hopefully it's that rather than someone downloading Genbank. :) Still plenty of FREE logins for the closed wifi are available at the registration desk for anyone who wants one. - Dave Messina
Fun to see how quickly many of us have found a workaround for the 'Oops'... :) - Egon Willighagen
Is there a place for posting jobs/student positions available to ISMB attendees? (i.e. http://tinyurl.com/brinkma...) I'm not at the ISMB this year, so am definitely checking out FF and related resources and thank you all for your posts! - Fiona Brinkman
Does anyone know how to 'filter out' all group:ismbeccb2009 messages in my main feed? So that I can just open the ISMB/ECCB 2009 group in a separate window? - Egon Willighagen
Thanks to everyone - organizers, reviewers, presenters, friends, bloggers etc etc etc : I must away, but had loads of fun! :) - Allyson Lister
@Allyson, safe travels. @all, see you in Boston. Feel free to PM/mail me for tips where to stay, eat or party in the city. - Oliver Hofmann
nice meeting you, Allyson, and have a safe trip! - Ruchira S. Datta
I am leaving too, was nice meeting you all and have a good trip back. - Roland Krause
Conference finally closed. - Peter Menzel
i'm now at the Stockholm airport en route to Cambridge for another conference (!) http://www.functionalgenomics.org.uk/section... It was fun meeting some of you and microblogging together. Hope we'll see each other around at future conferences. Next year in Boston! - Ruchira S. Datta
@Egon: if you go to the ismbeccb09 room and click the "(edit)" link to the right of "Lists" then you can deselect it from your Home feed. - Lars Juhl Jensen
A top-ten of talks (well, not really - just the top ten of my ISMB posts based on number of hits). What was everyone interested in enough to click through to my blog? Find out: http://themindwobbles.wordpress.com/2009... - Allyson Lister
Shirley Wu
ISMB 2008 = highest profit/participant, as mentioned proudly by the chairman. He assures it's not because of the food, that they are actually spending quite a bit on the food. Maybe it's being delivered to the wrong place.
What I heard is that the number of paper submissions was down by 30%. - pn
can anyone tell me why the espresso machine at the convention center breaks down every moment precisely when i need it most? - Shannon McWeeney
Paulo: So is the amount of free t-shirts. Conincidence ? ;) - Daniel Jurczak
we paid $435/head for food and coffee, the conference center+AV+MCC related costs amounted to another about $180/head. you do the math how much of your money went into food. totally with you on your surprise, but it is actually the same for most places in the world we went to; some were much worse than toronto, others much better (e.g. vienna). - espresso machine: another one of those things: i for one need good espresso: you guys have no clue what the MCC would have charged for 'second cup' quality .. - Burkhard Rost
In Detroit there was no included food and in some days there was almost no place close to the GM Centre with good food (if you call Detroit's greektown a place that you can get decent food ...) and the registration price was adequate. Why include food in the registration when some people cannot afford it? Like me, unsupported post-doc living in Toronto. No way I am shelling 775 (700 reg + annual fee) plus whatever the BOSC costed and eat moderately bad food. - pn
The ISMB is a community effort and the organizers thereby responsible to the community to organize a financially viable meeting. I am glad that Burkhard is as bold as to discuss this issues in public. Organizing a conference is a multi-optimization problem that should have higher weights on scientific content, adequate conference rooms and WLAN (in that order) than food quality, which were met at this years' ISMB for sure. - Roland Krause
Some conferences do not provide lunch at all (e.g. the genetics congress in Berlin in July), but for Stockholm, this is probably not an option (fair ground). - Roland Krause
IMO, good conferences do make a profit, always tough for scientific ones. But the logistics and experience better be worth it then. - Deepak Singh
no lunch is what i have been proposing since years; will become stronger on this! for Stockholm: too late (and yes too difficult); for Boston 2010: we already signed the contract including food, however, we will try our best to get out of it; for 2011 in vienna: difficult - upside: that's perceived as "good food" - Burkhard Rost
profit: half of the ISCB annual budget originates from the ISMB profit, we need $180K from ISMB to survive; we now run ISMB at an incredibly ambitious low budget saving wherever we can, this is one reason why Toronto will create high profit/participant - mostly due to the fact that we cut on organizing costs. still the major issue remains that we pay for the facilities that could welcome 1000 more participants and with every new participant we would profit more. put differently: we have to grow or to shrink - Burkhard Rost
Was that "paper submissions down by 30%" true? $550 - 900 per person. 1000 attendee. Let's say... 30% on foods: $300 X 1000 = $300,000 for lunch and matrix party. Foods must be delivered to the wrong place. - Kuan-Ting Lin
see our paper in PLoS CB on ISMB 2008 about numbers, although the following may not be in there: vienna proceedings submission=492, toronto: 292; ok; NOW please realize that this has absolutely NOTHING to do with costs! One issue: we had over 180 talks at ISMB 2008; 48 were from proceedings=less than 1/3. now the money: food/head was over $400 NOT 30%!!! there were over 1400 participants and the food was way more than 2* your estimate; matrix party was cheap! food & rent for Liberty Grand was a lot. - Burkhard Rost
Hey folks, ISCB almost died from less profitable meetings in Brazil and Australia...give Burkhard a break. I like his openness. Yes, the food could have been better (the box lunches at the Member's meeting during lunchtime were really good!), but I didn't see enough affordable restaurants on Front Street or near the CN Tower to handle us all. I do agree that when possible, letting us... more... - John Greene
In Vienna (that is if it is again at the Vienna International Center) it is not that easy to get to food. I mean there is nothing in the immediate vicinity. Additionally as Burkhard already mentioned the food there was actually quite fine. Anyway, i appreciate the openness of the discussion here. - Daniel Jurczak
Roland Krause
ISMB 2008 report by the organizers (PLoS Computational Biology) - http://www.ploscompbiol.org/article...
Aye. - Roland Krause
note the date: was written BEFORE ISMB, i for one am not good enough to devine "reviews" - we invite you guys to write reports about the meeting and send them to BJ to coordinate where they will go - Burkhard Rost
Pedro Beltrao
"ISCB is looking for a few aspiring reporters, who also happen to be attending ISMB 2008 in Toronto. (...)This year we are also seeking a select corps of students and Jr. Scientists to take on the role of writing about the vast scientific content of the conference and the personal experience of participating in this large, international bioinformatics event. Submissions will be reviewed for posting to the ISMB website, and will be considered for publication in the designated ISCB pages of PLoS Computational Biology, the Society's official journal, as a single author report or as part of a larger report compiled from the contributions of multiple authors." - Pedro Beltrao from Bookmarklet
Hmm, shouldn't we (the ususal suspects) grab the bull by horns and write a decent conference report, compiled from multiple sources? - Roland Krause
folks: another one of those: spent a lot of energy in vain hoping to get something similar to what you guys pulled off: totally impressed!!! Thanks. write it up, we'll put it onto our journal pages if we'd find it ok. other than that: we'll like a blog at a central place in stockholm and will link to this one as soon as steven leard is back from his deserved break. burkhard - Burkhard Rost
Hi Burkhard , I am glad you find this experiment interesting. It ended up being a useful way not only to gather notes about the conference but to set up events on the fly. It would be great to have something like this set up from the beginning at the next ISMB. - Pedro Beltrao
Just add my voice to the fact that I think this was really impressive grass roots reporting. I felt like I was actually at two meetings at the same time, one where I was physically present, and one where I was just a fly on the wall. Great example of what can be done (with enough people and the right tools) - Cameron Neylon
again: have tried to find you guys before; now that i found you i will do whatever i can to support this for future ISMBs; let me give you another impression: i saw the blog for the first time during the wed morning keynote, after the keynote i stood up and thanked Lars & Neil (those were the ones i had seen in the 20 secs i spent on this); at least 30 people walked up to me after that announcement and asked how to get at that blog! - Burkhard Rost
Thanks Burkhard! I think that it would be a great idea to improve the visibility of the live blogging from the official ISMB web site. However, it is also important that we don't try to formalize it too much as this would likely kill a grassroot effort like this. I find that FriendFeed worked remarkably well (much better than my personal attempts on Tumblr), so I suggest that we try to stick to that but somehow tie it in with the ISMB web site. - Lars Juhl Jensen
One possibility would be to set up an ISMB2009 room ahead of the conference and prefill it with one thread per presentation. These can then be used to comment on each talk. By making them ahead of time, we could link to the thread in an iframe on an official ISMB page with the speakers abstract. This would allow people to work in an almost unchanged manner, yet it would structure the comments slightly better and hook it up with the official web site. - Lars Juhl Jensen
Another wild idea: virtual poster sessions. Could we somehow get people to upload a high-resolution bitmap of their poster? These could then again be linked with a FriendFeed thread to allow commenting. Perhaps the posters could even go on Flickr and be fed directly into FriendFeed? - Lars Juhl Jensen
Roland & Neil, I'm also up for helping out on writing a conference report. Burkhard, where would the conference report be published - in PLoS Comp Biol or Bioinformatics? - Lars Juhl Jensen
Lars, we are in touch with BJ Morrison. There is a Googledoc with 5 minutes worth of scribbles by me but I wonder whether a fresh start - or sketch - wouldn't be advantageous. 2000 - 5000 words, I guess, the rest is up to us. Oh and yes, PLoS Comp Bio. - Roland Krause
Roland, excellent - can you email me an invitation to join the Googledoc? I can try to take a look at it later today. - Lars Juhl Jensen
neil: you did not see this because you had obviously left already; i saw your feed first on wed. morning; i stepped up after hannah's talk and announced it and was bombarded by questions: 'how to find that' for the rest of the day, literally at least 20 people approached me. Will anybody write for journals? - Burkhard Rost
Daniel Jurczak
Does anyone know, whether the live video feeds of each presentation they are streaming to the iMacs next to the Biomed Central stand are recorded in any way ?
Went to the information desk and asked. People there were surprised to hear that there even is a videocast. So even though, from a technical point of view, everything is in place, there is no recording. - Daniel Jurczak
ISMB sent me a fax to sign to allow them to record my talk and to make derivatives such as videos that would enhance a publication. My talk is for the PLoS track so I assumed that it was for them to record the talks to add to SciVee. - Pedro Beltrao
1) glad you liked it; was my idea and a hell of work; 2) no recording because (i) everyone else felt this is too low quality, (ii) actually, not that simple to record what is streamed is it? - Burkhard Rost
Pedro Beltrao
some pictures from ISMB2008 (sorry for the duplication) - Pedro Beltrao
want to put up a web site with many photos from ISMB 2008: anyone to help? - Burkhard Rost
Shirley Wu
We're putting together a conference report but would like to include the more "human" side of things. If you have funny stories, anecdotes, speaker quotes, reflections, or would like to contribute, just encapsulate it in 1 para or less and we'll fit in as many as we can. Paste here or link to it.
great: let ISCB know, we'll link to it! - Burkhard Rost
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