We showed unassembled original data, validating the conclusion.
We showed original data. Figures were correctly assembled (Potential aberration in figures pointed by this accuser can be explained by the limited ability of powerpoint operation).
Original data show identical error bars. But another issue arose through the investigation (see Corrections in our papers).
We showed the original image, which excluded the possibility of a copy and paste. However, a faint band in the IP IgG lane was partly erased by flaFening (see Corrections in our papers).
We showed original data. No image manipulation occurred.
We showed original data. All figures were correctly assembled. In graph e, the fold enrichment to the arm region (zfs) is shown (as described in the legend). Therefore, a set of zfs scores is always ‘1’.
We showed original data. Graphs were correctly assembled.
We showed original data. Graphs were correctly assembled.
We showed the original pictures. All pictures were similarly assembled from two parts in the same plate, so they are valid. Erroneously introduced different adjustment does not influence the conclusion.
The original data indicate that there are minus scores in the ChIP assays. The indicated error bars derive from scores near zero or minus. Graphs were correctly assembled.
We explain that the plates contain phloxin B so that the dead cells become darker. No image manipulation occurred.
We showed original graph, which we traced to produce the published version.
We showed original data in all these panels. No image manipulation occurred. The accentuated contrast, however, erased faint bands in the panels of Tubulin (Fig 3e), CAP-H (Fig 3g), Cdc13 (Fig 5a) and Ac-n (Fig S16) (see Corrections in our paper).
We showed original data. No image manipulation occurred.
These are artifacts arising from the PDF conversion. We showed the original data in Powerpoint file. No image aberration occurred.
We showed original data of all panels, including the right upper panel. Although the leZ two panels derive from the same sample, these were concatenated to assemble the published figure (see Corrections in our papers).
We showed original data in the Excel file. These errors were caused by a mis-calculation of the Excel file (see Corrections in our papers).
We showed original data. No image manipulation occurred.
(出典:Accusation(E).pdf 太字強調は当サイトによる)
“This is a totally groundless and false accusation by a faceless complainant,” Kadowaki told ScienceInsider in an email. “We have absolute confidence in all of our data,” he wrote. (University of Tokyo to investigate data manipulation charges against six prominent research groups. Science News ScienceInsider By Dennis Normile Sep. 20, 2016)
Fig. 1, If you open the paper PDF in Inkscape or Adobe Illustrator, and put aside some objects on the bar graphs, the hidden parts of the error bars come into sight. You can find similar inappropriate data presentation all over this paper, as Ordinary_researchers pointed out in the documents.
告発文書によれば、この論文の図4のバーグラフでは、なんとエラーバーの長さが複数のグラフに対して2種類しかないそうです。先ほどと同様に論文のPDFファイルをInkscapeで開きます。不自然な箇所の指摘は多数ありますが、とりあえず、Figure 4a i のグラフに絞ってみてみます。ここには9個の棒グラフおよびエラーバーがありますが、エラーバー以外を全て取り去り、「グループ解除」「グループ化」「整列」「配置」などを使って、エラーバーの高さがわかりやすいように整列させてみました(下図)。告発文書の指摘通り、9つのエラーバー(標準偏差)なのに、大きさが2種類しかありません。
Fig.4a i, When aligned, it becomes obvious that some error bars are identical to each other. You can find similar inappropriate data presentation in other graphs in this paper, as pointed out by Ordinary_researchers in the documents. Semba et al., 2016 Nat Commun Fig.4a iで用いられていた9つのエラーバーを整列させたところ、高さが2種類しかない
(Fig.3d, When aligned, it becomes obvious that the error bars in Fig.3d are identical. For more detailed information, see the Ordinary_researchers’ documents.)
The Impact Factor of journal J in the calendar year X is the number of citations received by J in X to any item published in J in (X-1) or (X-2), divided by the number of source items published in J in (X-1) or (X-2). (Measuring a journal’s impact. ELSEVIER)
World’s most influential journals for 2017 unveiled in the Journal Citation Reports from Clarivate Analytics (Clarivate Analytics News releases):”PHILADELPHIA, June 14, 2017 /PRNewswire/ — Clarivate Analytics today released the 2017 Journal Citation Reports (JCR), an annual update of the world’s most influential and comprehensive resource for information on highly cited, peer-reviewed publications and the source of Journal Impact Factor (JIF) scores. “
World’s most influential journals for 2017 unveiled in the Journal Citation Reports (tass.com June 14,2017 16:00 UTC+3) :”Clarivate Analytics today released the 2017 Journal Citation Reports (JCR), an annual update of the world’s most influential and comprehensive resource for information on highly cited, peer-reviewed publications and the source of Journal Impact Factor (JIF) scores.”
ACMG’s Genetics in Medicine Journal Receives Record High Impact Factor of 8.229 for 2016: GIM Now in Top 2.5% of All Indexed Journals (PR Newswire/American College of Medical Genetics and Genomics 15 Jun, 2017, 11:33 ET):”The American College of Medical Genetics and Genomics (ACMG) announced that the Thomson Reuters Impact Factor Journal Citation Reports has just increased the impact factor of the ACMG’s peer-reviewed medical genetics and genomics journal, Genetics in Medicine (GIM) to 8.229 for 2016, up from 7.710 in 2015. GIM is currently ranked 10 of 166 titles in the Genetics & Heredity category and is the top-ranked of genetic journal that has a primarily clinical focus.”
Clinical Chemistry Impact Factor Rises to 8, the Highest in the History of the Journal (Newswise/American Association for Clinical Chemistry (AACC) 15-Jun-2017 1:00 PM EDT):”AACC, a global scientific and medical professional organization dedicated to better health through laboratory medicine, is pleased to announce that the impact factor of its journal, Clinical Chemistry, has risen to 8.008 in the 2016 Thomson Reuters Journal Citation Reports. This impact factor places Clinical Chemistry in the top 2.6% of 12,062 ranked academic journals and speaks to the significant influence of the science it publishes on laboratory medicine and patient care.”
Celebrating a high performing new journal in quantum information (EurekAlert!/University of New South Wales Public Release: 15-Jun-2017):”UNSW Sydney is proud of the early publication performance, influence and reach of its Nature Partner Journal npj Quantum Information, from advancing discovery to affecting public discourse. At a time of the year when the Journal Citation ReportsTM are published, UNSW sees npj Quantum Information’s inaugural Impact Factor in the context of a variety of journal-based metrics that provide a richer view of the journal’s performance. For 2016, the range of performance metrics, which are made available on the journal website, include:2-year Impact Factor: 9.111 Immediacy Index: 1.560 Eigenfactor® score: 0.00060 Article Influence Score: 4.617″
都司さんは甲子園球場の近くの小学校に通っている頃は、常に1番の成績だった。灘中(神戸市)に進学すると、1学年150人ほどのうち、130番前後になった。「はじめて強烈な劣等感を持ちました。私の学力ではかなわない生徒ばかりだったのです」(“灘中→麻布高校→東大”で、抱き続けた劣等感 PRESIDENT Online 2016.1.5)
晴れて入学したその有名進学校で、しかし、私は大きな挫折を味わいます。数学オリンピックの金メダリスト・高校生クイズで優勝した人・両親が東大理科三類出身で異常に頭が切れるイケメン・東大病院の教授の子供……有名進学校は枚挙にいとまがないほどの天才集団でした。「地元じゃ負け知らず」の私も、そんな天才たちの前にはただの凡人。(競争社会を勝ち抜き続けてきた東大生の「将来やりたいことがない」という葛藤に満ちた就職活動 2018年9月20日(木) ONE CAREER)
When you’ve lived all the time as number one or number two (or even possibly number three) in high school science, and when you know that everybody who’s below average in the science courses where you came from is a complete idiot, and now you suddenly discover that you are below average – and half of you guys are – it’s a terrible blow, because you imagine that it means you’re as dumb as those guys used to be in high school, relatively. (The Quotable Feynman)
But there is also a certain disadvantage: because Caltech has such a good reputation, almost everybody who’s the first or second in his high school class applies here. There are lots of high schools, and all the very best men apply. Now, we have tried to figure out a system of selection,
with all kinds of tests, so that we get the best of the best. And so you guys have been very carefully picked out from all these schools to come here. But we’ re still working on it, because we’ve found a very serious problem: no matter how carefully we select the men, no matter how patiently we make the analysis, when they get here something happens: it always turns out that approximately half of them are below average!
Of course you laugh at this because it’s self-evident to the rational mind, but not to the emotional mind – the emotional mind can’t laugh at this. When you’ve lived all the time as number one or number two (or even possibly number three) in high school science, and when you know that everybody who’s below average in the science courses where you came from is a complete idiot, and now you suddenly discover that you are below average – and half of you guys are – it’s a terrible blow, because you imagine that it means you’re as dumb as those guys used to be in high school, relatively. That’s the great disadvantage of Caltech: that this psychological blow is so difficult to take. Of course, I’m not a psychologist; I’m imagining all this. I don’t know how it would really be, of course!
The question is what to do if you find you’re below average. There are two possibilities. (Feynman’s Tips on Physics: Reflections, Advice, Insights, Practice)
現役名人がコンピューターに負けた。将棋電王戦が、人間同士と違う部分。(Number Web 2017/04/08 茂野聡士):コンピューター将棋ソフトの中でも最強と言われる電王「PONANZA」と佐藤天彦名人の対局。現役のタイトルホルダー、それも順位戦を経て決まる名人がコンピューターと相まみえるということもあり、大きな注目が集まった一戦は71手で先手・PONANZAの勝利に終わった。
Ponanzaとは、山本一成が開発したコンピュータ将棋ソフトウェアである。2013年3月30日、第2回電王戦第2局で佐藤慎一四段と対戦して勝利し、現役のプロ棋士に公の場で勝った史上初の将棋ソフトとなった。Bonanzaへのリスペクトを表した名前だが、現在はBonanzaライブラリ不使用である。POnanza is Not bonANZA でPonanzaとのこと。(ponanza ニコニコ大百科)
Xenopus laevis stage series Digitized images and developmental data from Nieuwkoop and Faber (1994) Normal Table of Xenopus laevis (Daudin). Garland Publishing Inc, New York ISBN 0-8153-1896-0. (xenbase.org)
Nature Communications 7, Article number: 11635 (2016) doi:10.1038/ncomms11635 Published online:18 May 2016. HIF-1α-PDK1 axis-induced active glycolysis plays an essential role in macrophage migratory capacity. Hiroaki Semba, Norihiko Takeda, Takayuki Isagawa, Yuki Sugiura, Kurara Honda, Masaki Wake, Hidenobu Miyazawa, Yoshifumi Yamaguchi, Masayuki Miura, Dana M. R. Jenkins, Hyunsung Choi, Jung-whan Kim, Masataka Asagiri, Andrew S. Cowburn, Hajime Abe, Katsura Soma, Katsuhiro Koyama, Manami Katoh, Keimon Sayama, Nobuhito Goda, Randall S. Johnson, Ichiro Manabe, Ryozo Nagai & Issei Komuro 問題点:エラーバーの長さが2種類のみの図
International Heart Journal Vol. 57 (2016) No. 2 p. 198-203. http://doi.org/10.1536/ihj.15-332. Shorter Heart Failure Duration Is a Predictor of Left Ventricular Reverse Remodeling During Adaptive Servo-Ventilator Treatment in Patients With Advanced Heart Failure.Teruhiko Imamura1), Koichiro Kinugawa1), Daisuke Nitta1), Issei Komuro2) 1) Department of Therapeutic Strategy for Heart Failure, Graduate School of Medicine, The University of Tokyo 2) Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo. Released on J-STAGE 20160322 [Advance Publication] Released 20160311. 問題点:奇妙なまでに一致する平均値とSD PubPeer.comでの議論:https://pubpeer.com/publications/26973264
Scientific Reports5, Article number: 14453 (2015) doi:10.1038/srep14453. Published online: 25 September 2015. Angiotensin II receptor blockade promotes repair of skeletal muscle through down-regulation of aging-promoting C1q expression. Chizuru Yabumoto, Hiroshi Akazawa, Rie Yamamoto, Masamichi Yano, Yoko Kudo-Sakamoto, Tomokazu Sumida, Takehiro Kamo, Hiroki Yagi, Yu Shimizu, Akiko Saga-Kamo, Atsuhiko T. Naito, Toru Oka, Jong-Kook Lee, Jun-ichi Suzuki, Yasushi Sakata, Etsuko Uejima & Issei Komuro 問題点:Fig.7 完全に一致するエラーバーの長さ PubPeer.comでの議論:https://pubpeer.com/publications/26571361
Nature455, 251-255 (11 September 2008) | doi:10.1038/nature07217; Received 8 April 2008; Accepted 27 June 2008; Published online 17 August 2008. Heterochromatin links to centromeric protection by recruiting shugoshin. Yuya Yamagishi, Takeshi Sakuno, Mari Shimura & Yoshinori Watanabe 問題点:異なるSDを持つ同一データ;背景が均一なウェスタンブロット画像;背景が均一化された蛍光顕微鏡画像;グラフのデータは実在するのか?;切り貼りされ、縁の奇妙な酵母培養ディッシュ
Science 08 Oct 2010:Vol. 330, Issue 6001, pp. 239-243 DOI: 10.1126/science.1194498. Two Histone Marks Establish the Inner Centromere and Chromosome Bi-Orientation. Yuya Yamagishi, Takashi Honda, Yuji Tanno, Yoshinori Watanabe 問題点:数学的にあり得ないSD
Nature Cell Biology 12, 500 – 506 (2010) Published online: 11 April 2010 | doi:10.1038/ncb2052Shugoshin–PP2A counteracts casein-kinase-1-dependent cleavage of Rec8 by separase. Tadashi Ishiguro, Koichi Tanaka, Takeshi Sakuno & Yoshinori Watanabe 問題点:部分的に諧調を変更した培養ディッシュ;粗雑なグラフ PubPeer.comでの著者らの回答:https://pubpeer.com/publications/20383139
Nature 2011 Jun 1;474(7352):477-83. doi: 10.1038/nature10179. Condensin association with histone H2A shapes mitotic chromosomes. Kenji Tada,Hiroaki Susumu,Takeshi Sakuno & Yoshinori Watanabe 問題点:エラーバーが調節された可能性;ノイズが消失した背景;その他グラフについて
EMBO Reports 2011 Oct 28;12(11):1189-95. doi: 10.1038/embor.2011.188. Acetylation regulates monopolar attachment at multiple levels during meiosis I in fission yeast. Ayano Kagami, Takeshi Sakuno, Yuya Yamagishi, Tadashi Ishiguro, Tatsuya Tsukahara, Katsuhiko Shirahige, Koichi Tanaka, Yoshinori Watanabe 問題点:背景が均一なウェスタン画像
Unregistered Submission:( August 22nd, 2016 4:53pm UTC )
I’m not looking forward to a flood of posts suggesting that the error bars are too similar. In order to improve the quality of such posts, I suggest the following.
1) Try only to work with figures where the graphics exist in a vectorial format (pdf).
2) Open the figure in a vector graphics program (illustrator, inkscape,…)
3) Delete all the elements except those of interest (the error bars)
4) Save as postscript (uncompressed)
5) Examine the file as text
6) The precise coordinates (in pts) should be available
7) If several error bars are exactly the same, then you have something to write about.
(https://pubpeer.com/publications/26973264)
「学習時の記憶情報は前頭前皮質にもすでに存在したのです。この実験結果は、記憶が徐々に転送されるという従来の学説に反するものです。」と北村博士は述べた。(原文:“Already the prefrontal cortex contained the specific memory information,” Kitamura says. “This is contrary to the standard theory of memory consolidation, which says that you gradually transfer the memories. The memory is already there.”)(参考:MITニュース)
Neuroscientists identify brain circuit necessary for memory formation New findings challenge standard model of memory consolidation. ( MIT News April 6, 2017 Anne Trafton):”When we visit a friend or go to the beach, our brain stores a short-term memory of the experience in a part of the brain called the hippocampus. Those memories are later “consolidated” — that is, transferred to another part of the brain for longer-term storage.”
Ingredients for lasting memories (RIKEN April 7, 2017):”Published in Science magazine, the study proves the existence of long-lasting engram cells in the frontal part of the brain and shows how connections with other brain regions allow these cells to mature as new memories become permanent. “
Rules of memory ‘beautifully’ rewritten (BBC 7 April 2017 By James Gallagher):”The US and Japanese team found that the brain “doubles up” by simultaneously making two memories of events. One is for the here-and-now and the other for a lifetime, they found. It had been thought that all memories start as a short-term memory and are then slowly converted into a long-term one.”
データサイエンティストとは、どのような職業なのか? どうすればなれるのか? (ライフハッカー 2015.03.27 08:00 pm, How to Become a Data Scientist,Dann Albright原文/訳:コニャック):”データサイエンティストの仕事は、統計学、コンピュータサイエンス、データ分析を駆使して、膨大なデータを構造化しながら整理して、企業がデータを活用したアクションを起こすために必要な情報となるように、解析結果を導き出すというものです。… また、データサイエンティストは、発見した情報の意味を適切な表現で他人に伝える必要があります。… 要するに、データサイエンティストは、大量のデータを分析し、それらのデータを実行可能な事業戦略に変換するのが仕事です。””