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I do not think what was described above qualifies in any useful way. So I think it would be more convincing if you provided an example or explained...
I do not think what was described above qualifies in any useful way. So I think it would be more convincing if you provided an example or explained...
In the opinion of many, yes. It is ok to disagree.
So there was - and still is. But is blogging on your own site self-promotion? My understanding of self-promotion is that this requires reaching out to those not already in the know (or who do know…
"is there or is there not evidence of PubPeer self-promotion during the STAP scandal?"There was a blog post: http://blog.pubpeer...
What is surprising is Dr. Hanna is an author in a new Nature paper, "Failure to replicate the STAP phenomenon" http://www.nature.com/nature/journal/v525/n7570/full/nature15513...
Jacob Hanna tweets that social media was irrelevant to the STAP discovery process. Also that PubPeer used this opportunity for self-promotion...
Demonstrations that STAP cells weren’t made have now been published by Nature in two BCA (brief communications arising) critiques.http://www...
In the recently published BCA in Nature (Konno et al E4 | NATURE | VOL 525 | 24 SEPTEMBER 2015), the authors demonstrate that intestine and pancreas tissue was GFP-negative from the host!
That's the key question indeed! What happened in those 8 months? Did the authors address reviewers' criticism? It doesn't seem likely looking at what was eventually published...
The big question is whether the referees ever saw and gave an opinion on the revised version of the manuscript. I know journals like Nature tend to review the impact more than the science, but to…
After carefully analyzing the partially "censored" Nature reviewer comments letter to Obokata in April 2013,http://news.sciencemag.org/sites/default/files/NATURE%20REVIEWS...
https://research.bwhanesthesia.org/research-groups/cterm/stap-cell-protocolAlbeit the paper has been retracted, Prof. Vacanti opened a revised protocol for generating STAP cells...
The Science piece about the retraction is quite interesting. The gel splice that was commented early on had been spotted by a referee at Science (who then rejected the MS)...
Madhusudana Girija Sanal | Mar 10 2014 18:33 ESTIt is a common observation that stressed cells, dying and dead cells start to become fluorescent...
Before a press conference on the final report of investigation committee about STAP papers, RIKEN replaced the interim report of the investigation released on 15 Mar with a new version which deleted…
Before a press conference on the final report of investigation committee about STAP papers, RIKEN replaced the interim report of the investigation released on 15 Mar with a new version which deleted…
There is newspaper coverage of the Riken panel's news conference regarding their "final report" e.g.http://www.japantimes.co.jp/news/2014/04/01/national/high-profile-stem-cell-papers-contain-fraudulent…
you are correct regarding that TCRB band. it should not be there according to their model. If ~20% of the cells become oct4-gfp+ and the starting cells are all rearranged at the TCR, then how do they…
His commentary is convoluted and not premised on much which would actually be helpful. The comments section of that blog allude to the faults.
It is worth linking to a detailed discussion of the FACS experimental design posted by Jun Seita on Paul Knoepfler's blog:http://www...
The second link in the above comment is broken. The correct one is as follows:http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit
RIKEN showed Raw Data of Fig.1i on Feb. 14 at the URL ofhttp://www.riken.jp/~/media/riken/pr/topics/2014/20130314_1/document-5.pdf PDF file (P9-P10) ...
Thanks for the tineye research. Just a couple questions to make sure of the misdemeanors:1. Are you sure the directionality of the plagiarism? That O took the photos from those sites, versus the…
Please check out the following HP address: http://stapcells.blogspot.jp/2014/02/nature-article.html Also, check out the following photo in which Nature 505 pp641-647 Fig...
> I am however not sure if they really are different experiments without the context.Sorry. I confirmed that they should indeed be from different experiments, since the one in this article is splenic…
Moreover, the Image of STAP cells-derived mesoderm (alpha-smooth muscle actin) in Fig.2d of this Nature article is similar to that of bone marrow-derived mesoderm in Fig...
The interim report of the Riken investigation is here:http://www.riken.jp/en/pr/press/2014/20140314_1/
RIKEN showed Raw Data of Fig.1i on Feb. 14 at the URL ofhttp://www.riken.jp/~/media/riken/pr/topics/2014/20130314_1/document-5.pdf PDF file (P9-P10) ...
"I am however not sure if they really are different experiments without the context. "This is the key point. If the thesis is about the same work, which is not totally impossible from 2011, it might…
I think the point here is that they are supposedly the results from different experiments. I am however not sure if they really are different experiments without the context...
The left figures (Nature 2014) are shots of STAP cells-derived mesoderm, and the right figures (Obokata Doctral Thesis 2011) are the bone marrow-derived mesoderm...
References lists in Chapter 2, 3, 4, 5 in Obokata's D.thesis http://stapcells.up.seesaa.net/image/References.pdfwere copied and pasted from other articles...
An anonymous researcher (probably one of the other researchers of bioinformatics in RIKEN?) claimed that the researcher analyzed the experimental data on NCBI (http://www...
The ensuing investigation revealed that Obokata plagiarized doctoral thesis.33 pages of Obokata’s doctoral dissertation introductory chapter, it was almost all copy and paste...
If I see Videos 1 and 2 supplemented in this paper without any assumptions, I will believe that these video images display phagocytosis of green particles by macrophages...
Obokata's Doctral Thesis 2011Backgroundhttp://stapcells.up.seesaa.net/image/Background.pdfReferenceshttp://stapcells...
Fig1c. At upper right panel at day 7, should see two populations because still a large number of cells w/o gfp.
These many problems in her doctoral thesis have been reported in http://stapcells.blogspot.com/2014/02/blog-post_2064.htmlThis thesis contain images of bone marrow-derived teratoma in Fig...
You can get the copy of her thesis from National Diet Library http://www.ndl.go.jp/en/index.htmlor read it at Waseda University...
It is quite difficult to verify that the right figures are actually from her thesis because it is not available online. The PubPeer rule says that the comments should be based on "publicly verifiable…
my understanding of pubpeer is that comment on a particular published papers is sent to the corresponding author of that paper. Did the corresponding author(s) of this particular Nature paper respond…
does it mean that the figures published in the doctoral thesis should not be published in a journal again? just curious to know. This paper has already reached 100 comments and there is still going on.
The same anonymous researcher added an explanation on the following figure (mentioned in the above comment):http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit
The same researcher showed (some of) the results of the analysis mentioned in the above comment.The researcher implied that the following figures indicate that both low-pH-treated CD45+ and STAP stem…
I read very interesting analysis by bioinformatics professional in RIKEN. Analyzing the input of ChIP-seq data published, both STAP and STAP stem cells had no TCR-alpha and beta rearrangements...
RIKEN RIKEN showed Raw Data of Fig.1i on Feb. 14 at the URL ofhttp://www.riken.jp/~/media/riken/pr/topics/2014/20130314_1/document-5...
Dr. Obokata offered to withdraw her doctor thesis against Waseda university. (Japanese article) http://sankei.jp.msn...
When I read the paper for the first time one of the things that struck me was the incredible perfect differentiation of pancreas and endoderm in their teratomas...
The video image of STAP cell generation displayed in RIKEN homepage suggests to me that two GFP+ cells are dead because of the following reasons...
H. Obokota et al.report ( a new method of) "conversion of somatic cells into pluripotency ". Although these papers describe interesting observations, the authors should know that it is not…
@ Unreg ( January 31st, 2014 7:50pm UTC )(This is a minor point)As you point out 1E60 cells were not grown. So how would you interpret "Cell number" in the axis label? The text and methods don't seem…
i understand that is what they are doing. as i said, its a bizarre and yes silly way of presenting the data. why not just do population doublings over the course of 120 days? i have never come across…
These are the images of different color channels. Compare red and green.http://imgur.com/rKM0xEO
STAP stem cell crowdsourcing flowing along nicely! http://wp.me/P1xWpk-4pP 3 reported attempts, all didn't work. Still early days, but nice to see people into openscience like this...
I would also love to hear from them.If this would be the case, Dr.Obokata and Prof.Vacanti would get similar results by using human fibroblasts and bone marrow cells...
It should be noted that the Oct4-GFP line used in this paper has been widely used in investigations of reprogramming and tracking developmental Oct4 processes, so perhaps that is the quickest…
At day2, Oct4-GFP positive cells should be only a small fraction of total cell population. Therefore the signal in green channel at day2 is likely to be background fluorescence...
The sentence for "Karyotype analysis" in methods section of this article is exactly similar to "Chromosome preparation" methods in other researchers' article, "In Vitro Cell Dev Biol Anim...
I cannot see the cell with high endogenous Oct4 and no reporter (red but no green). I guess you mean the middle cells which have low intensity, because I actually do not see any cell shown there…
"What does that mean? If you are making an accusation about the image could you please clearly state the problem and reasoning?"The post was deliberately limited to a statement of fact...
What does that mean? If you are making an accusation about the image could you please clearly state the problem and reasoning? For my image program I get the same image as you using "emboss" not "sharp…
This can explain intracellular difference in distribution (nuclear versus cytoplasmic), but can not explain difference between cells. Concern is that cells with high endo-Oct4 show little GFP signal...
I am pretty sure they are not supposed to match. The GOF18-EGFP construct is described as a EGFP reporter driven by Oct4 promoter/enhancer (a 18 kb Oct4 genomic fragment)...
Positions of GFP-positive cells and Oct4-immunopositive cells do not match in day7 culture. This can be seen clearly if you separate green and red channels from the original color panel.
I don't think their Oct4-GFP is a fusion protein to represent proper localization, instead simply it appears to be a reporter. The original plasmid is GOF18-EGFP...
Two regions in Extended Data Fig. 2g seem to display very little noise. This can be seen in this processed version, in which a 'sharpen' operation slightly increases the noise and equalises the…
They are similar but not the same, and to my knowledge that is not too strange. Suspicion is good to have, but we should not make uncertain accusations...
Yes. On my computer I see no red in the low pH panel and no green in the control panel.
If you zoom in you can see nuclear overlap from the pinkish red/blue in all of them. As is common, each have red in some cell overlaps, showing they are not overlapped and there is some cytoplasmic…
Correct me if I am wrong, but since they produced cloned mice derived from single clones of STAP stem cells, previously derived from T-cells (cd45), the cloned mice should present only one kind of…
Extended Figure 2aEndogenous Oct4 staining does not match with Oct4-GFP expression. It is acceptable that Oct4 staining increases from day2 to day7, but a complementary pattern is quite odd...
I'm not sure that this concern is valid. The control (bottom left of Fig. 3B) seems to have slightly more red and green background than is found around the labeled cells (bottom right), but both…
I have a feeling that there may be hints of what could be vertical splice marks around the second lane of Extended Data 2g, which would fit with this...
Extended Data Fig. 2g, lane 2 and lane 3 are too similar.http://imgur.com/uqvuu8HThis can happen? Any idea?
You mean this one, right?http://imgur.com/fgYBksl
I completely agree, I spotted this a few days ago. I was surprised at just how black the control image was, then I looked a little closer and was very surprised...
Just take a screenshot of the whole figure, open in Photoshop, and adjust the brightness way up. At some point you'll see that the control panel is all red, no green...
I can try, but upload where?
Thank you. It was disturbing seeing many interjections/links to this blog. From comments on pubpeer suggesting it was legitimate I found the blog had about 20 links to STAP posts which feature…
If you increase the brightness in Fig. 3B you will see that the control image on left is all red without any green and the acid-treated panel on the right is all green with no red...
There is skeptic data shown in Obokata et al. 2011, Nature Protocols too.http://www.nature.com/nprot/journal/v6/n7/fig_tab/nprot.2011.356_F5...
"These guys" share two of the authors on both papers and the rest come from the same research centers. That is quite far from independent replication.
That's not true. They say that these guys successfully reproduced it: https://pubpeer.com/publications/0E26C2D789BDBE5B4850A1D6E37948
I don't believe that this is a compression artefact; the pixelation would be visible.That somebody altered the contrast of a lane is less unlikely, but some of the lane (near the bottom) is no…
Nature News have a interesting piece on the affairhttp://www.nature.com/news/acid-bath-stem-cell-study-under-investigation-1.14738Of note is their own survey of stem-cell experts about their success…
Well it could also be an enhancement of the contrast for a single line with photoshop which was not enough visible. I did it once for the PhD of my girlfriend...
It will be nice to see replications in other labs but this seems to have been a case of images being mixed up when assembling the paper. Surely these results will be reproduced soon?Here is an…
I think unreg is going in a bit hard here. Yes, there's not much science in a poll, but I looked at the results anyway (stem cell people don't know what's happening either...
Could you explain what is the point of these polls? They seem a little silly. You're just wondering how people are "feeling" about the papers? I can't see how this aims to help the scientific…
http://imgur.com/mqkT7OK
"Such a high profile paper" doesn't demand high-profile figures without traces of compression artifacts?
Are you getting the original from a pdf of the article? If so the pdf compression itslef may have introduced segmentation compression based on vertical line segmentation that the authors had nothing…
Week 2 polling on STAP stem cells is now up on my blog and reflects more uncertainty: http://www.ipscell.com/2014/02/stap-stem-cells-week-2-poll-results-more-uncertainty/
I think it's much too tedious and unaesthetic to put in different scale bars for each picture... I mentioned the same problem above for Fig. 5d.
Is a scale bar in Fig. 2a correct? In my view, size of DAPI-positive nuclei is completely different among panells in Fig. 2a. However, they used only one scale bar for them...
There's something I find slightly odd about Extended Data Fig. 2g. Most of the rightmost (4th) lane seems to be darker than the immediately adjacent background...
Here's an English translation of a popular Japanese blog post: http://horikawad.hatenadiary.com/update: 2014.2.14"Regarding the previous entry that talked about a portion of the image that was…
Latest news from Knoepfler's crowd-sourced replication/extension effort is that 0/8 attempts have led anywhere so far.http://www...
A compilation of some of the image issueshttp://stapcell.blogspot.com/The Riken research institute probes 'irregularities' in images associated with STAP cell discovery...
The blogger who reported the "unclear" issues with the images linked above has left an apology (in Japanese) to the authors stating that these are indeed likely to be compression artifacts and he…