Retraction Watch

Tracking retractions as a window into the scientific process

Weekend reads: Trying unsuccessfully to correct the scientific record; drug company funding and research

with 74 comments

booksThere were lots of pieces about scientific misconduct, publishing, and related issues posted around the web this week, so without further ado:

Written by Ivan Oransky

January 25th, 2014 at 9:54 am

Comments
  • Jaime A. Teixeira da Silva January 25, 2014 at 2:25 pm

    Frustration in dealing with errors in the plant (and allied sciences) science literature

    These are all important stories, but I would say that the one that relates most to plant scientists – except for the story on the Ronald lab – is in fact the story by Stefan Franzen. I wish to echo his frustration in my own attempts to show how the plant science literature is fraught with errors, but that there is currently little appetite to correct the literature for a few reasons. Many of my own colleagues and friends have been critical of me, even asking me “why” or “for what purpose”, and thus exposing oneself (and ones work and legacy) to critique is one of the greatest challenges that plant scientists face.

    a) Arrogance and fear among editors and editors-in-chief (EICs) who do not want to admit that their quality control (QC) – personal, professional or system-related – failed during the traditional peer review process. A corrigendum under their name would reflect poorly on their management and their legacy would be stained. Which editor wants to, frankly speaking, have a stain on their CV even long after they have left this earth?

    b) The failure to convince such editors and EICs that issuing an erratum (if the author brings forth the claim), a corrigendum (if the publisher recognizes that the error was theirs) is the morally and ethically correct thing to do. There seems to be a serious case of serial and wide-spread denial among plant scientists, or, even worse, a passive lack of will for change.

    c) The lack of desire by publishers to expose that their peer review systems have been fallible and weak, with inherent weaknesses, simply because perfection can only be achieved (if ever), where sample size tends towards infinity. And since most peer reviews in moderate to high IF journals in the plant sciences (IF = 1.0 to 3.5) rely on the “expert” opinion of usually not more than three individuals in a pool that probably contains several million, it is quite easy to understand how the system of traditional peer review is broken, imperfect, and open to abuse, errors and fraud. The current climate of retractions is trying to focus on the authors and scientists, while protecting their own backs and images, thus skirting deeper scrutiny of the current publishing model, which is fundamentally highly flawed.

    d) The real “crime” occurs when there are errors that have been pointed out by the academic community as factual, evidence-based information and critical analysis [1], but which the editors then fail to take into consideration, i.e., the active ignoring of the advice, the facts and the warning signals. Failure to act will be the ultimate down-fall of the reputation of an editor, of the fame of the journal, and the trust of a publisher. Unfortunately, however, if in fact an erratum, corrigendum, or retraction were to be issued for the level that I am personally observing in the plant sciences, then I am afraid that this could potentially wipe out an entire slice of the plant science literature, calling into question the validity of studies that referenced such flawed or erroneous studies. In some cases, the decision is made by the EIC, or by two or three editors. In other words, the fate of the correction of science lies in the hands of a tiny elite and dangerously powerful status quo. Such ego-centric decisions are fundamentally wrong, self-centered, and of course, fraught with bias. But this is one large reality that explains the resistance we are facing in the plant sciences.

    e) The fear by the community of the down-stream effects. No scientist wants their work to be remembered by an erratum, correction or in the worst case, retraction. But these three aspects need to form part of the quotidian landscape of science publishing. And retro-active analysis, and punishment – where merited – should be the mainstay of science moving forward. The equivalent of not assuming this position, no matter how unpalatable it is, is like using the internet thinking that one would be free of virus attacks, hacking, or spying. Naivety, ignorance, and inaction are making corrections to the plant science literature much more than just an uphill climb. In some cases, they are making corrections impossible. The human, intellectual and psychological firewall in place is massive.

    f) There is a lack of understanding of a basic principle that science is a constant conversation. A theory that was established 50 or 80 years ago, if valid at that time, should form part of the discussion even now. In some ways, I am very concerned about the aggressive wave of anti-science activists who are blindly looking at all problems, big and small, as being valid targets for retractions. Those that hate science will seek every means possible to retract anything related to science. Those that care about science want to see the issues resolved correctly, and fairly. Therefore, clear fraud should be punished with a retraction (and more), but “relatively minor” issues should face more lenient or rational punishment, such as an erratum or corrigendum. We are in a historical phase in science, I believe in which retractions seem to be as fashionable as the iPAD or Twitter, and everyone is trying to jump on the band-wagon, especially the skeptics and the critics who have now found a valid avenue to vent their frustrations. However, when we retract a piece of literature, in some ways, it is gone forever. So, we need to inculcate among our peers and editors, a new culture of change. If we can accept that errors are fundamental parts of – if not the essence of – science, then there is hope. And if we can accept that talking about errors, corrections and retractions as part of the everyday conversation [2], even in the literature, then this solidifies hope and breeds change.

    g) The lack of a solid support framework that involves an advice hub, a claims center, a counseling center, the acceptance of anonymity, and the decentralization of power. Although this may sound perfect, in fact it is extremely easy, and cheap, to achieve. This is because it only requires the consciousness of scientists, their time and their willingness to do what is right. Unfortunately, most scientists face that thing called reality! Long work hours and increasingly reduced pay and grants/funding, greater pressure for productivity, and increase scrutiny. Thus, there is little desire to offer their time, intellect and effort to conduct post-publication peer review (PPPR) [1] because it’s simply not convenient. From personal experience, I can say that PPPR is painful, time-consuming, exasperating, frustrating, and damaging (to others and to ourselves). The peer pool is already excessively squeezed, with few drops of additional effort and time to add to the need for precise scrutiny in PPPR. Thus, I believe that we have a real crisis in plant science in which the call for the need is not being met by the correct attitude of the base it is meant to be correcting (and assisting). The crisis is being further fueled by an aggressive attitude by retraction hard-liners that any error, small or large, is something that should be subjected to a retraction. I suspect that there is an underground agenda (but not yet reported on) that is using retractions, and the twisting of ethical values and guidelines, to achieve permanent damage to science, and to undermine its importance in society. This “underground” movement (hypothesis) would be counterproductive to the genuine efforts by real scientists, and real academics, who simply want to see unfairness in science and science publishing eliminated (or reduced as much as possible), and that recognize that one effective way of achieving this is through PPPR.

    The frustrations I feel about plant science relate not so much to the lack of retractions, but to the lack of acceptance that the literature has problems, and needs to be corrected. I was going to substantiate my claims with real examples, as I usually do, but I have decided to reduce them to two references only (to passive my critics who dislike my verbosity). When the time is right, more factual evidence will be released into the blogosphere. PubPeer and PubMed commons are useful tools, but when push comes to shove, the final message to our peers should be one of encouragement and active participation, and not one of fear.

    [1] http://www.frontiersin.org/Journal/10.3389/fpls.2013.00485/full
    [2] See a simple model for reporting publically on errors in the chrysanthemum literature, some of which merit retractions: http://retractionwatch.com/2014/01/07/journal-dumps-grain-paper-for-controversial-data/#comments

    • O Baptista March 30, 2014 at 10:33 pm

      Report of apparent data/paper duplication: Acta Horticulturae (International Society for Horticultural Science)

      Miguel, M.G., Duarte, F., Venâncio, F. and Tavares, R. 2002. CHEMICAL COMPOSITION OF THE ESSENTIAL OILS FROM THYMUS MASTICHINA OVER A DAY PERIOD. Acta Hort. (ISHS) 576:87-90
      http://www.actahort.org/books/576/576_15.htm
      http://wwwlib.teiep.gr/images/stories/acta/Acta%20576/576_15.pdf

      Miguel, M.G., Duarte, F., Venãncio, F. and Tavares, R. 2003. CHEMICAL COMPOSITION OF THE ESSENTIAL OILS FROM THYMUS MASTICHINA OVER A DAY PERIOD. Acta Hort. (ISHS) 597:75-78
      http://www.actahort.org/books/597/597_8.htm
      http://wwwlib.teiep.gr/images/stories/acta/Acta%20597/597_8.pdf

      • O Baptista April 18, 2014 at 3:01 pm

        An update. The 2003 copy has been retracted. The official e-mail follows (e-mails redacted):

        From: Jozef Van Assche
        Sent: 04/01/14 04:10 PM
        To:
        Subject: Miguel (UALG): duplication report

        Dear Sir,
        Dear Dr. Paulo Baptista,

        I have been informed about your complaint to the ISHS President, Prof. Antonio Monteiro, on a so called duplicate publication of the article entitled ‘Chemical Composition of the Essential Oils from Thymus mastichina over a Day Period’, by M.G. Miguel, F. Duarte, F. Venâncio and R. Tavares.

        I hereby wish to inform you that this happened outside of the will of the authors.

        The contributions of the International Conference on Medicinal and Aromatic Plants, Budapest, Hungary, 8-11 July, 2001, were published in two volumes of Acta Horticulturae, AH 576 Volume I and AH 597 Volume II. The first Volume was published soon after the meeting as Acta Horticulturae 576, the second batch of papers was published as Volume II as Acta Horticulturae 597 some time later, and containing additional contributions of the symposium.

        For one reason or another, the Editors did not noticed that the paper of Dr. M.G. Miguel et al, was published in 576, and they also included it in the batch for 597. All this just by accident. This is this a human failure were the same article was published twice in the set of proceedings on the same meeting.

        We hereby are pleased to inform you that the article has been retracted from AH 597, and that the original stands in AH 576.

        We wish to thank you for bringing this to our attention and remain.
        Faithfully

        Jozef

        Jozef Van Assche
        Executive Director

        International Society for Horticultural Science
        PO Box 500 – 3001 Leuven 1 – Belgium
        Phone: +32 16229427 Fax: +32 16229450

        Visit our website at http://www.ishs.org
        The ISHS, dating from 1864 and formally constituted in 1959, has more than 7000 members representing over 140 countries. It is the world’s leading independent organization of horticultural scientists. ISHS publishes Acta Horticulturae, Chronica Horticulturae, and Scripta Horticulturae.

  • Jeanette Garwood January 25, 2014 at 2:29 pm

    Hi,

    Thank you so much for all the brilliant posts you guys send out. I have a professional interest in bad behaviour, and Integrity officer status at my university, and Retraction Watch is so educative.

    Thank you so much for all your hard work :-)

    Jeanette (Oxford D.Phil 1991)

  • Nurse Dina January 26, 2014 at 1:23 am

    Stay on it guys. You are the only encouragement to me, a victim of plagiarism. Just when I think I can’t fight anymore, one of your posts will appear and keep me going.

    • Qui? February 7, 2014 at 8:46 am

      Report of apparent figure duplication: for EMBRAPA, SIVB, IVCDB, Acta Scientiarum, Authors, other parties

      Paper 1: Pinto de Carvalho ACP, Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Otoni WC. Produção de mudas micropropagadas de antúrio (Anthurium andraeanum) cv. Eidibel por embriogênese somática. Embrapa Circular Técnica (Fortaleza) 2012;41:1-14
      Paper 2: Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Pinto de Carvalho ACP, Jardim de Oliveira E, Otoni WC. Somatic embryogenesis in anthurium (Anthurium andraeanum cv. Eidibel) as affected by different explants. Acta Scientiarum Agronomy 2014;36:87-98.
      Paper 3: Pinheiro MVM, Martins FB, Ferreira da Cruz FC, Pinto de Carvalho ACP, Ventrella MC, Otoni WC. Maturation of Anthurium andraeanum cv. Eidibel somatic embryos from nodal segments. In Vitro Cellular & Developmental Biology – Plant 2013;49( 3):304-312.

      We wish to make an anonymous report of potential figure duplication.
      Fig 2B, C and E of paper 1 seem identical to Fig. 3A, B and K of paper 2.
      Fig. 3B seems identical to Fig. 4A in paper 2 (rotated 90°)
      Fig. 3A, B, C and D of paper 1 seem identical to Fig. 4B, C, D and G of paper 2, with B and D of the former being cropped and size/proportion manipulated.
      Fig. Fig 6B in paper 1 seems identical to 4I in paper 2.
      Fig. 5E, F, G, H, J in paper 1 seem identical to Fig. 5E, F, G, H, J in paper 3.

      Paper 1 was not reported in paper 2 or paper 3, even though paper 1 appears as open access online and even though it is a formal publication of Embrapa Agroindústria Tropical. Figure duplication would thus also possibly constitute copyright infringement.

      Figure duplication and manipulation is a serious academic offense that distorts the accuracy of the academic record and we call on the retraction of the 2014 paper from Acta Scientiarum and the 2013 paper from In Vitro Cellular & Developmental Biology – Plant. We call on the authors, editors and publishers to take responsible action.

      See sections 4.1, 4.2 and 4.3 of Springer 2013 Publication Ethics Manual for Editor and Authors:
      http://static.springer.com/sgw/documents/1393202/application/pdf/Publication_Ethics_Guide_for_Editors_from_Springer_27052013.pdf

      See clause 3 of Acta Scientiarum Agronomy:
      http://www.scielo.br/revistas/asagr/iinstruc.htm (“Author(s) should state that the manuscript, reporting original work, was not sent, in part or in whole, for publication to another scientific journal.”)

      AR Qui

      • Qui? February 18, 2014 at 12:29 pm

        Case 30

        Kalimuthu K, Prabakaran R (2013b) In vitro flowering from nodal explants of Ceropegia pusilla Wight and Arn. International Journal of Botany and Research 3(3), 35-42
        http://tjprc.org/journals.php?jtype=2&id=46 (no editor board)
        Kalimuthu K, Prabakaran R (2013c) In vitro and micropropagation for conservation of rare and threatened medicinal plant Ceropegia species – a review. International Journal of Biological Technology 4(2), 23-36
        http://www.gbtrp.com/journal/ijbt%20volume%20no%204(2).htm
        Kalimuthu K, Prabakaran R, Paulsamy S, Jeyaraman S (2014) Microtuberization of Ceropegia pusilla Wight and Arn. an endangered medicinal plant. European Journal of Medicinal Plants 4(1), 64-74
        http://www.sciencedomain.org/issue.php?iid=383&id=14
        Prabakaran R., Sasikala T., Kalimuthu K. (2013) Regeneration of shoots from callus of Ceropegia pusilla Wight and ARN. British Biotechnology Journal 3(3), 416-423
        http://www.sciencedomain.org/journal-home.php?id=11

        Apparent data duplication
        data in Table 2 of 2014 = data in Table 1 of Prabakharan et al. 2013
        data in Table 3 of 2014 = data in Table 4 of Prabakharan et al. 2013
        Notice how micromolar amounts are used by Prabakharan et al. 2013 and mg/l amounts in 2014

        Apparent figure duplication and manipulation
        1F of 2013b = 1E of 2013c = 1G of 2014
        1A of 2013c = 1A of Prabakharan et al. 2013
        1B of 2013c = 1B of Prabakharan et al. 2013
        1F of 2013c = 1F of Prabakharan et al. 2013
        1D of 2014 = 1C of 2013b
        1E of 2014 = 1C of 2013c
        1B of 2013b = 1D of Prabakharan et al. 2013 (tilted and twisted)

        Apparent plagiarism:
        2013 review copies the abstracts of most studies in the literature, and presents this as a review, listing the studies chronologically. Subsequently, this paper has already been retracted, 24 hours after we issued our report:
        IJBT Biotek Editor writes “Thank you for your advice. As the plagiarism is serious, we have retracted the article now on consulting with the consent editor and corresponding author. The retracted article link is given below for your reference.”
        http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29kalimuthu%20abs.htm
        http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29/ijbt150813104.pdf

        Apparent salami slicing and data/method duplication
        in vitro tuberization, shoot and flower induction already reported in 2013b (classical salami slice adding information to text in 2013b and data in tables in 2014 to feign originality; self-plagiarism exact text copied, see M&M section; values reported in molar amounts in 2013b and then in g/l amounts in 2014 to appear original, but are identical concentrations.

        • Qui? February 18, 2014 at 12:30 pm

          Case 31

          Kondamudi R, Murthy, K.S.R. 2011. Micropropagation of Ceropegia pusilla Wt. & Arn. – an endangered and rare medicinal Asclepiad. Journal of Tropical Medicinal Plants 12: 41-48
          http://tropmedplants.com/article.php?aid=464 (no editor board)
          Kondamudi R, Vijayalakshmi V, Murthy, K.S.R. (2010) Induction of morphogenetic callus and multiple shoot regeneration in Ceropegia pusilla Wight and Arn. Biotechnology, 9: 141-148
          http://scialert.net/qredirect.php?doi=biotech.2010.141.148&linkid=pdf (ANSI; no editor-in-chief; http://scialert.net/eboard.php?issn=1682-296x)
          Murthy KSR, Kondamudi R (2010) Effect of cytokinins and auxins on in vitro flowering of endangered Ceropegia spiralis Wight and C. pusilla Wight & Arn. Phytomorphology. 60: 32-37
          Murthy KSR, Kondamudi R, Vijayalakshmi V (2010a) Micropropagation of an endangered medicinal plant Ceropegia spiralis Wight. J Agric. Tech 6: 179-191
          Murthy KSR, Kondamudi R, Pullaiah T (2010b) High frequency somatic embryogenesis in Ceropegia spiralis Wight – an endemic and endangered medicinal plant. Indian J. Biotechnol. 9, 414-418
          http://nopr.niscair.res.in/bitstream/123456789/10441/1/IJBT%209%284%29%20414-418.pdf (NISCAIR; IF = 0.477)
          Murthy KSR, Kondamudi R (2011) Rapid shoot regeneration from thin cell layer explants of an endangered medicinal asclepiad Ceropegia spiralis L. Plant Tissue Cult. Biotech. 21(1): 63-73
          http://www.banglajol.info/index.php/PTCB/article/view/9564 (BAPTC&B)
          Murthy KSR, Kondamudi R, Karuppusamy S. (2012) Microtuberization of Ceropegia spiralis Wight and Ceropegia pusilla Wt. and Arn. African J. Plant Sci. 6: 321-327
          http://academicjournals.org/article/article1380125590_Murthy%20%20et%20al.pdf (Academic Journals)

          Apparent data duplication
          20 shoot-related data points in Table 2 of Kondamudi and Murthy 2011 are identical to data in Table 3 of Kondamudi et al. 2010
          Data in Table 2 of Murthy and Kondamudi 2010 identical to data in Table 3 of Kondamudi and Murthy 2011
          Table 2 data of Murthy et al. 2010a = Table 1 data of Murthy et al. 2011
          Table 4 data of Murthy et al. 2010a = Table 1 data of Murthy et al. 2012

          Apparent figure duplication and/or manipulation
          Fig 1D of Kondamudi et al. 2010 identical to Fig. 1F of Kondamudi and Murthy 2011
          Fig. 1B of Murthy and Kondamudi 2010 identical to Fig. 1E of Kondamudi and Murthy 2011
          Fig 1B of Murthy and Kondamudi 2011 = Fig. 1B of Murthy et al. 2010a = Fig. 1Ce of Murthy et al. 2012
          Fig 1A of Murthy and Kondamudi 2011 = Fig. 1Cb of Murthy et al. 2012
          Fig 1D of Murthy and Kondamudi 2011 = Fig. 1Cc of Murthy et al. 2012
          Fig. 1G of Murthy et al. 2010a rotated 90° = Fig. 1i of Murthy et al. 2010b
          Fig 1A of Murthy et al. 2010a = Fig. 1A of Murthy et al. 2012
          Fig. 1F of Murthy et al. 2012 = Fig. 1D of Kondamudi et al. 2010
          Fig. 1E of 2012 repeated twice (self-plagiarism)

          This would also directly influence the claims of originality in the review written by this group:
          Murthy, K.S.R., Kondamudi, R., Reddy, M.C., Karuppusamy, S., Pullaiah, T., 2012b. Check-list and conservation strategies of the genus Ceropegia in India. Int. J. Biodivers. Conserv. 4(8), 304-315 (Academic Journals)

          • Qui? March 3, 2014 at 5:56 pm

            We reported this case on February 11, 2014. By March 3, 2014, the 2012b paper had been retracted, but without any notice. The paper just vanished.

            Raad MK, Zanjani SB, Shoor M, Hamidoghli Y, Sayyad AR, Kharabian-Masouleh A, Kaviani B. Callus induction and organogenesis capacity from lamina and petiole explants of Anthurium andraeanum Linden (Casino and Antadra). Australian J Crop Sci 2012a;6(5):928-937. (Southern Cross Publishing Group, Australia, listed at http://scholarlyoa.com/publishers/)

            Raad MK, Zanjani SB, Sayyad AR, Maghsudi M, Kaviani B. Effect of cultivar, type and age of explants, light conditions and plant growth regulators on callus formation of anthurium. American-Eurasian J Agric Environ. Sci 2012b;12(6):706-712. (IDOSI Publications, Dubai, listed at http://scholarlyoa.com/publishers/)

            Fig. 1 data of 2012a is identical to “Callus weight” column of Table 1 (2012b)
            Fig. 2 of 2012a is identical to Fig. 1 of 2012b
            Fig. 3 data of 2012a is identical to “Days to callus induction” column of Table 1 (2012b)
            Table 1 data of 2012a is repeated in Fig. 2 and Fig. 3

            Neither paper acknowledged the existence of the other paper.

            We wish to deposit this case here as a public record.

          • Qui? March 3, 2014 at 5:59 pm

            We wish to report an apparent partial duplication.

            Javad Sharifi Rad, Majid Sharifi Rad, Abdolhossein Miri (2013) Regulation of the Expression of Nitrate Reductase genes in Leaves of Medical plant, Foeniculum vulgare by Different Nitrate Sources. International Journal of Agriculture and Crop Sciences 5 (24), 2911-2916
            http://ijagcs.com/wp-content/uploads/2013/09/2911-2916.pdf

            Javad Sharifi Rad, Majid Sharifi Rad (2013) Regulation of the Expression of Nitrate Reductase Genes in Leaves of Medical Plant, Foeniculum vulgare by Different Nitrate Sources. World Applied Sciences Journal 28 (9): 1311-1315
            http://www.idosi.org/wasj/wasj28(9)13/18.pdf

            Fig. 4 of IJCAS = Fig. 1 WASJ
            Fig. 1 WASJ = Fig. 2 WASJ = Fig. 3 WASJ = Fig. 4 WASJ

            This serves as a public record.

          • ABV Prasad March 3, 2014 at 6:04 pm

            I want to report a possible partial duplication.

            Sule WF, Okonko IO, Joseph TA, Ojezele MO, Nwanze JC, Alli JA, Adewale OG, Ojezele OJ (2010a) In vitro antifungal activity of Senna alata Linn. crude leaf extract. Research Journal of Biological Sciences 5 (3): 275-284 (Publisher: Medwell Journals)
            http://www.medwelljournals.com/fulltext/?doi=rjbsci.2010.275.284
            http://docsdrive.com/pdfs/medwelljournals/rjbsci/2010/275-284.pdf

            Sule WF, Okonko IO, Joseph TA, Ojezele MO, Nwanze JC, Alli JA, Adewale OG, Ojezele OJ (2010b) In-vitro antifungal activity of Senna Alata Linn. Crude leaf extract. Advances in Applied Science Research 1 (2): 14-26 (Publisher: Pelagia Research Library)
            http://www.pelagiaresearchlibrary.com/advances-in-applied-science/vol1-iss2/AdSSR-2010-1-2-14-26.pdf

            A third paper, 2011 published on the bark, has identical results (Tables 1, 3 and 4) as the 2010a and 2010b paper about leaves. Table 2 has similar data to the 2010a and 2010b papers:

            Sule W. F., Okonko I. O., Omo-Ogun S., Nwanze J. C., Ojezele M. O., Ojezele O. J., Alli J. A., Soyemi E. T., Olaonipekun T. O. (2011) Phytochemical properties and in-vitro antifungal activity of Senna alata Linn. crude stem bark extract. Journal of Medicinal Plants Research 5(2), 176-183 (Academic Journals)
            http://www.academicjournals.org/article/article1380554162_Sule%20et%20al.pdf

            All three publishers are listed on Jeffrey Beall’s http://www.scholarlyoa.com

          • T-bone steak March 27, 2014 at 1:29 am

            Mr. Prasad, I followed up on your lead. I contacted the editor boards of all three publishers and early in March, Pelagia Research Library retracted the Sule et al. 2010b paper. Not only does clicking the link above lead to an HTTP error, the journal issue web-page lists a gap: http://pelagiaresearchlibrary.com/advances-in-applied-science/vol1-iss2.html
            Unfortunately, this gap is not useful, or instructive about the problem, and the research community has no idea why the paper was retracted, so I indicated one clear case of a good, informative retraction notice, with a red stamp RETRACTED on the original PDF. I am not sure that they will take the trouble of making this change, but if they do, this would be a positive sign that we may start to be able to correct the literature, by placing pressure on authors and publishers simultaneously.

          • Bhavin July 24, 2014 at 10:09 am

            Dear Qyi?,
            Excellent detection, many of Murthy publications are from predatory journals

      • Qui? November 19, 2014 at 1:42 am
  • Nasraoui, Bouzid April 15, 2014 at 12:46 pm

    As the Editor-in-Chief of Tunisian Journal of Plant Protection (TJPP), I discover via a colleague of mine, that one scientific paper was published in 2009 at the same time in TJPP and in Journal of Biopesticides. The paper dealt with the “Efficiency of Spinetoram as a biopesticide to Onion Thrips (Thrips tabaci Lindeman) and Green Peach Aphid (Myzus persicae Sulzer) under laboratory and field conditions” with the first author “Mahmoud Farag Mahmoud”. Noting that is a case of a flagrante delicto of scientific honesty lack, TJPP withdraw from its website this paper simultaneously published in Tunisian Journal of Plant Protection 4 (2): 221-227 (2009) and Journal of Biopesticides, 2(2): 223- 227 (2009).

  • Science Society November 7, 2014 at 3:38 pm

    We wish to report a case of potential plagiarism.
    Thulasi Muneppa Sridhar, Chenna Reddy Aswath
    Department of Biotechnology, Indian Institute of Horticultural Research (IIHR), Bangalore, India
    Review on Medicinal Plants Propagation: A Comprehensive Study on Role of Natural Organic Extracts in Tissue Culture Medium
    American Journal of Plant Sciences, 5, 3073-3088. doi: 10.4236/ajps.2014.520324
    http://www.scirp.org/journal/PaperInformation.aspx?paperID=50185&

    The following sections are text that has been copied from the four sets of sources below, word for word, without attribution to the source, or without quotation marks, as follows:
    From [1], 707 words (or 10.9% of total)
    From [2], 373 words (or 5.7% of total)
    From [3], 960 words (or 14.8% of total)
    From [4], 192 words (or 3% of total) (including some self-plagiarism)

    [1] Molnár Z, Virág E, Ordog V (2011) Natural substances in tissue culture media of higher plants. Acta Biol Szeged 55:123–127.
    [2] George EF, Hall MA, Klerk G-J De (2007b) The components of plant Tissue culture media ll: organic additions, osmotic and pH effects, and support systems. In: George EF, Hall MA, Klerk G-J De (eds) Plant Propag. by Tissue Cult. Springer Netherlands, Dordrecht, pp 115–173 + George EF, Hall MA, Klerk G-J De (2007a) The components of plant tissue culture media I: macro- and micro-nutrient. In: George EF, Hall MA, Klerk G-J De (eds) Plant Propag. by Tissue Cult. Springer Netherlands, Dordrecht, pp 65–113
    [3] Yong JWH, Ge L, Ng YF, Tan SN (2009) The chemical composition and biological properties of coconut (Cocos nucifera L.) water. Molecules 14:5144–64. doi: 10.3390/molecules14125144
    [4] Other sources:
    Anonymous (2014) Plant Tissue Culture- Mavens Biotech Limited. http://www.mavensbiotech.com/Biotechnology/Plant Tissue Culture.html. Accessed 15 Oct 2014
    Lakshmi S, Benjamin J (2010) In vitro propagation of Hoya wightii ssp. palniensis KT Mathew, a highly vulnerable and endemic species of Western Ghats of Tamil Nadu, India. African J Biotechnol 9:620–627. doi: 10.5897/AJB09.846
    Mehta J, Kumar V, Syedy M, et al (2012) In vitro shoot regeneration of Bacopa monnieri ( L .) using cyanobacterial media- a novel approach and effect of phytoregulators on in vitro micropropagation. Asian J Plant Sci Res 2:699–706.
    Sivanesan I, Jeong BR (2007) Direct shoot regeneration from nodal explants of Sida cordifolia Linn. In Vitr Cell Dev Biol – Plant 43:436–441. doi: 10.1007/s11627-007-9090-1
    Sridhar TM, Aswath CR (2014) Influence of additives on enhanced in vitro shoot multiplication of Stevia rebaudiana (Bert.)—An important anti diabetic medicinal plant. Am J Plant Sci 05:192–199. doi: 10.4236/ajps.2014.51025
    Tanwer BS, Choudhary R, Vijayvergia R (2010) In-vivo and in-vitro comparative study of primary metabolites and antioxidant activity of Andrographis paniculata. J Chem Pharm Res 2:489–495.

    The publisher of American Journal of Plant Sciences, SCIRP, is listed on Jeffrey Beall’s list of “possible” predatory OA journals: http://scholarlyoa.com/publishers/

    Finally, this study received the following funding: “The authors are thankful to Department of Biotechnology for providing financial assistance in the form of DBT sponsored Post Doctoral Fellowship (Dr .T. M. Sridhar).”

  • Tehran November 8, 2014 at 12:27 pm

    A case of apparent duplicate papers:
    Salwee, Y., Nehvi, F.A. (2014) Effect of Plant Growth Regulators on Microcorm Formation in Saffron (Crocus sativus L.). International Journal of Current Microbiology and Applied Sciences Volume 3, Number 7, pp. 702-712
    ISSN: 2319-7706 http://www.ijcmas.com/Archives-20.php
    http://www.ijcmas.com/vol-3-7/Salwee%20Yasmin%20and%20F.A.Nehvi.pdf

    Salwee, Y., Nehvi, F.A. (2014) In Vitro Microcorm Formation in Saffron (Crocus sativus L.). Journal of Cell and Tissue Research Vol. 14(2), 4463-4470
    Received June 2014; No DOI
    ISSN: 0973-0028; E-ISSN: 0974-0910
    http://tcrjournals.com/tr_currentabstract.php?vid=57
    http://tcrjournals.com/uploads/7314136._Salvee.pdf

    Dr. Salwee Yasmin is at Baba Ghulam Shah Badshah University, Jammu and Kashmir, Rajouri, India, and Prof. Firdos Ahmad Nehvi is Senior Scientist, Saffron Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST) of Kashmir, India.

    There is a separate case of retraction caused by plagiarism by SKUAST researchers (Mushtaq Ahmad, Gul Zaffar, S.D. Mir, S.M. Razvi, M.A. Rather and M.R. Mir):
    http://scialert.net/abstract/?doi=rjmp.2011.630.649
    http://scialert.net/qredirect.php?doi=rjmp.2011.630.649&linkid=pdf
    The retraction notice states “Science Alert considers misappropriation of intellectual property and duplication of text from other authors or publications without clear and unambiguous attribution totally unacceptable. Plagiarism is a violation of copyright and a serious breach of scientific ethics. The Editors and Publisher have agreed to officially retract this article.”

  • Hyderabad November 9, 2014 at 3:22 pm

    I report a retraction of an onion study:
    J.I. Córcoles, J.F. Ortega, D. Hernández, M.A. Moreno
    Use of digital photography from unmanned aerial vehicles for estimation of leaf area index in onion (Allium cepa L.)
    European Journal of Agronomy, Volume 45, February 2013, Pages 96-104
    http://www.sciencedirect.com/science/article/pii/S116103011300124X
    http://ac.els-cdn.com/S1161030112001463/1-s2.0-S1161030112001463-main.pdf?_tid=fc3cc9c0-684d-11e4-ac8a-00000aab0f26&acdnat=1415564668_7549d27073690fbb43946bd637c897f3
    The notice writes: “This paper has been retracted because a near identical version of this paper was published in the Journal Biosystems Engineering: J.I. Córcoles, J.F. Ortega, D. Hernández, & M.A. Moreno (2013). Estimation of leaf area index in onion (Allium cepa L.) using an unmanned aerial vehicle. Biosystems Engineering. 115: 31–42; http://dx.doi.org/10.1016/j.biosystemseng.2013.02.002. This article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.”

  • Strelitzia Watch November 15, 2014 at 1:12 pm

    Title: Genus: Strelitzia
    Authors: Marcos Ribeiro da Silva Vieira, Giuseppina Pace Pereira Lima, Damiana Cleuma de Medeiros, Ângela Vacaro de Souza, Emídio Cantidio Almeida de Oliveira
    Journal of Horticulture and Forestry Vol. 4(11), pp. 178-180, November 2012
    DOI: 10.5897/JHF12.025
    http://www.academicjournals.org/article/article1379513573_Vieira%20et%20al.pdf

    There are two queries. First, the source of the photos in the four figures. Three of the photos / figures (2-4) are identical to images from the internet, without attribution to the source. To verify, simply add the Latin names of the three Strelitzia species into Google and Yahoo, click on images, and scroll down. Secondly, why does it require 5 individuals to write a 3-page review?

  • Vivek Kumar query November 17, 2014 at 1:08 am

    A case of potential partial (self-)plagiarism.

    Paper 1: Vivek Kumar (2014) Nanobiotechnology and its implementation in Agriculture. Journal of Advanced Botany and Zoology V1-I1.
    (research article on the PDF; editorial online) DOI 10.15297/JABZ.V1I1.02
    Received: December 28, 2013, Accepted: December 30, 2013, Published: January 3, 2014
    http://scienceq.org/archive.php?jname=abz&jid=abz0114462&tit=Nanobiotechnology and its implementation in Agriculture#.VGmFNJVxnIU
    http://scienceq.org/archive_user.php?jname=abz#.VGl9mpVxnIU (Publisher: ScienceQ*)

    Paper 2: Ram Prasad 1*, Vivek Kumar 1, Kumar Suranjit Prasad 2 (2014) Nanotechnology in sustainable agriculture: Present concerns and future aspects. African Journal of Biotechnology 13(6), 705-713 (review)
    DOI: 10.5897/AJBX2013.13554; Article Number – 1C0ABA342977
    1 Amity institute of Microbial Technology, Amity University Uttar Pradesh, Sector 125, Noida- 201303, UP, India
    2 Department of Environmental Biotechnology, Ashok & Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New Vallabh Vidyanagar, Anand-388121, Gujarat, India
    Received: 12 November 2013, Accepted: 16 January 2014; Published: 05 February 2014
    http://www.academicjournals.org/journal/AJB/article-abstract/1C0ABA342977
    http://www.academicjournals.org/journal/AJB/article-stat/1C0ABA342977 (total views: 603; downloaded: 2202)

    Problem/concern:
    The entire introduction of paper 2 (pp. 705-706) and parts of the conclusions (pp. 711-712) is identical, in most parts, word for word, to paper 1. Neither paper references the other, nor indicates the existence of the other.

    Paper 1 states “Vivek Kumar is working as Associate. Professor, Amity Institute of Microbial Technology, AMITY University, Noida, India. He did his Master’s and Doctoral degree in Microbiology. He has served as Microbiologist in Public Authority of Agricultural Affairs, Kuwait for 8 years. Guided many M.Sc/M.Tech students and guiding two doctoral degree students. Has published 51 research papers, 7 book chapters, 4 review articles and one book. He has delivered many research related lectures in conferences in India and abroad. He is recipient of “Young Scientist ward” in Agricultural Microbiology by Association of Microbiologists of India. His area of research interests are; plant-microbe-interactions, bioremediation, environmental microbiology and nanotechnology.”

    Dr. Kumar is on the board of editors at JABZ, the journal in which paper 1 was published:
    http://scienceq.org/editormenu.php?jname=abz#.VGmLl5VxnIU

    * Listed as predatory open access publishers on Jeffrey Beall’s blog. Both journals/publishers consider plagiarism to be a serious academic offense:
    http://www.academicjournals.org/publication_ethics
    http://scienceq.org/instruction_author.php#.VGmOqJVxnIU

  • Dendrobium concerns November 19, 2014 at 9:54 am

    Paper A (Springer)
    Padmaja Mohanty, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) Cryopreservation of pharmaceutically important orchid Dendrobium chrysanthum Wall. ex Lindl. using vitrification based method. Acta Physiologia Plantarum 35: 1373–1379
    Plant Biotechnology Laboratory, Centre for Advanced Studies in Botany North Eastern Hill University, Shillong, India
    http://www.nehu.ac.in/
    DOI 10.1007/s11738-012-1163-z
    http://link.springer.com/article/10.1007/s11738-012-1163-z
    No citations

    Paper B (Springer)
    Padmaja Mohanty, Pynbeitsyon Nongkling, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) Short-term storage of alginate-encapsulated protocorm-like bodies of Dendrobium nobile Lindl.: an endangered medicinal orchid from North-east India. 3 Biotech 3: 235–239
    DOI 10.1007/s13205-012-0090-4
    http://link.springer.com/article/10.1007/s13205-012-0090-4 (open access)
    No citations

    Paper C (Springer)
    Padmaja Mohanty 1, J. Das 2 (2013) Synthetic seed technology for short term conservation of medicinal orchid Dendrobium densiflorum Lindl. Ex Wall and assessment of genetic fidelity of regenerants. Plant Growth Regulation 70(3):297–303
    1. National Research Centre for Orchids, Pakyong, 737106, Sikkim, India (http://www.nrcorchids.nic.in/)
    2. Plant Bioresources Division, Institute of Bioresources and Sustainable Development (IBSD), Sikkim Centre, Tadong, 737102, Gangtok, India (http://www.ibsd.gov.in/currentResearch.htm)
    DOI 10.1007/s10725-013-9801-z
    Erratum: http://link.springer.com/article/10.1007/s10725-013-9831-6
    http://download.springer.com/static/pdf/652/art%253A10.1007%252Fs10725-013-9831-6.pdf?auth66=1416229592_ab8f79c7a260625e009a76ff46ab3d55&ext=.pdf states “Due to an institutional conflict on research program, the corresponding author of the article would like to remove the fig 1 from the original publication of the article.” (Published online: 6 June 2013)
    Retraction: http://link.springer.com/article/10.1007/s10725-013-9801-z states “This article has been retracted at the request of the Publisher due to a violation of Springer’s publishing integrity. The figure 1 of the article has been duplicated from different research papers and led to some serious scientific flaw in the article.”
    Retraction notice: http://link.springer.com/article/10.1007/s10725-013-9871-y
    http://download.springer.com/static/pdf/883/art%253A10.1007%252Fs10725-013-9871-y.pdf?auth66=1416229764_7b3d67ec9fdd98a8796cff5a05661142&ext=.pdf
    No citations

    Paper D (Springer)
    Padmaja Mohanty, Meera C. Das, Suman Kumaria, Pramod Tandon (2013) High-efficiency cryopreservation of the medicinal orchid Dendrobium nobile Lindl. Plant Cell Tissue and Organ Culture 109(2):297–305
    DOI 10.1007/s11240-011-0095-4
    http://link.springer.com/article/10.1007/s11240-011-0095-4
    No citations

    Six apparent figure duplications

    1) Fig 3D of Paper A is identical to Fig. 1B of Paper C
    False (unintended) conclusion: Dendrobium chrysanthum = Dendrobium densiflorum

    2) Fig. 3E of Paper B is identical to Fig 1A of Paper C
    Fig. 3B of Paper B is identical to Fig 1D of Paper C
    False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

    3) Fig. 3A of Paper B is identical to Fig 1C of Paper C
    False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

    4) Fig. 7G of Paper D is identical to Fig 3H of Paper B
    Fig. 7E of Paper D is identical to Fig 1E of Paper C
    False (unintended) conclusion: Dendrobium nobile = Dendrobium densiflorum

    Several figures have been duplicated across four manuscripts. This raises doubts about the correct plant material used in any of the in vitro experiments described in all four papers. Since several photos are duplicated and/or mixed up, there are also doubts about the validity of the interpretation of the data sets, and if they in fact refer to the plant that is being referred to in each title. The integrity of all four papers is thus in doubt, and a key question arises: which manuscript actually represents which Dendrobium species?

    Institutional profile (Tandon, Kumaria, Das):
    http://nehu.ac.in/Schools/Life%20Sciences/Botany/faculty.php
    Professional profiles:
    Pramod Tandon (Professor): http://nac.nic.in/members/pramod.php
    Suman Kumaria (Professor): http://www.researchgate.net/profile/Suman_Kumaria/publications?pubType=dataset
    Meera C. Das (Lecturer): http://www.researchgate.net/profile/Meera_Das/topics
    Padmaja Mohanty: not listed at NRCO: http://www.nrcorchids.nic.in/Personnel.html
    Pynbeitsyon Nongkling: after MSc (2008-2010) at NEHU, PhD candidate 2011-2012 (candidate no. 5):
    http://www.nehu.ac.in/Schools/Life%20Sciences/Botany/bot_151111.pdf (supervisor = H. Kayang)
    The institutional web-page of J. Das cannot be identified.

    There are now four PubPeer entries corresponding to Papers A to D:
    Paper A: https://pubpeer.com/publications/8448D8CF8D1F69936CDC1A35D9BBCC
    Paper B: https://pubpeer.com/publications/1CE3174266AF780AD6AB8EC0ABADE1
    Paper C: https://pubpeer.com/publications/1801EC08556E90F5026575FA1431B2
    Paper D: https://pubpeer.com/publications/C7D8632E7ED6D6F852A93D9A516A49

    • Meera C. Das November 20, 2014 at 4:32 am

      The following is my response to the commentary posts:

      Similar allegations were made earlier by the anonymous whistleblower to Springer Publications.

      I reproduce the decision of Springer:

      [Dear Dr. Das,

      I would like to inform you that the anonymous whistleblower has received the following response by my colleague Jacco Flipsen:

      “Following up to COPE standards, we have evaluated your retraction request related to duplication of figures. The case also has been evaluated by the Ethics group at Springer. We have come to the conclusion that the article in Plant Growth Regulation should not have been published because of figure duplication. This article will be retracted shortly; the authors have been informed. […]”

      So the article in Plant Growth Regulation will be retracted, all other papers are not affected.

      Kind regards
      Christina Eckey
      — 
Christina Eckey, PhD
      Springer
Senior Editor, Plant Sciences]

      I wish to put the matter straight. In fact I had complained to all the concerned Editors of Springer and officials of Institute of Bioresource Development (place of work of J. Das) and National Research Centre on Orchids (place of work of P. Mohanty) about the use of photographs from our earlier published work in the following publication:

      Paper C: Mohanty, P. and J. Das (2013)
      Plant Growth Regulation 70:297–303
      DOI 10.1007/s10725-013-9801-z

      Healthy criticism is always welcome, but a matter already decided by Springer needs no further clarification from my end. I will not engage in any form of correspondence in this matter henceforth.

      Meera C Das, Botany Department, North-Eastern Hill University, Shillong 793022, India

  • Dendrobium concerns November 19, 2014 at 10:09 am

    Concerns about Vyas et al. 2009, 2011 and 2012 Dendrobium papers

    2009 paper
    Vyas, S., Guha, S., Bhattacharya M, Usha Rao, I. 2009. Rapid regeneration of plants of Dendrobium lituiflorum Lindl. (Orchidaceae) by using banana extract. Scientia Horticulturae 121:32-37 (Elsevier)
    Department of Botany, University of Delhi, Delhi, 110007, India
    http://www.sciencedirect.com/science/article/pii/S0304423809000107
    DOI: 10.1016/j.scienta.2009.01.012

    2011 paper
    S. Vyas, P. Kapoor-Pandey, S.Guha, I. Usha Rao. 2011. Synchronous plantlet formation by using banana extract and in vitro hardening in orchid, Dendrobium lituiflorum Lindl. Journal of Ornamental and Horticultural Plants 1(3): 175-184
    http://webzoom.freewebs.com/jornamental/vol%203/Shivani2.pdf
    No DOI

    2012 paper
    Vyas, S., Kapai, V.Y., Kapoor, P., Guha, S., Usha Rao, I. 2012. In vitro plantlet regeneration from protocorms of Dendrobium lituiflorum Lindl. and Cymbidium bicolor Lindl. and their acclimatization: effect of salts, sucrose, and banana extract. Journal of Horticultural Science and Biotechnology 87(5): 485-492
    http://www.jhortscib.org/Vol87/87_5/15.htm
    No DOI

    Similarities (suggesting partial duplication and salami publication):
    a) same orchid: Dendrobium lituiflorum
    b) same plant material: seed-derived protocorms
    c) same parameters assessed: banana extract
    d) same medium: Knudson’s C
    e) same acclimatization protocol: 9:1 (cocopeat : perlite)
    f) same stats analyses.
    g) The 1st line of the 2012 R&D paper states: “The present study indicated that the natural additive, BE, promoted plantlet regeneration and subsequent growth.” This fact alone nullifies the originality of this manuscript since this fact was already proved in the 2009 and 2011 papers.

    Concerns:
    a) Fig. 3E of the 2011 paper appears to be a photo of the same plants photographed in Fig. 7H of the 2009 paper (2009 paper in oblique view, 2011 paper in top view).
    b) For best protocorm development, in the 2009 paper, the authors recommend 10% BE, in the 2011 paper, 20% BE and in the 2012 paper 10% or 20% BE. Given the fact that this is identical plant material, why are different optimal levels recommended? Which concentration should orchid scientists use, and average of 15% BE? In the 2009 paper, the authors stated “A significant increase (p < 0.05) in protocorms with developing leaves and rhizoids (stage 4) with higher percentages of BE up to 10% (v/v) BE in KC medium was observed (Figs 3 and 7A).” However, studying Fig 3 it is clear that there was no significant difference between the effects of BE at 2.5, 5 or 10% on the percentage of protocorms in stage 4. Moreover they stated, that “The higher concentrations [of BA] proved to be inhibitory”. However, studying Fig. 2 it is clear that BA had no effect on germination, either stimulatory or inhibitory, because no significant differences were presented between the treatments or even relative to the control. If the data has not been correctly interpreted, then how accurate are the subsequent claims made in the subsequent 2011 and 2012 papers?
    c) For best plantlet development, in the 2009 paper, the authors recommend 12.5% BE, in the 2011 paper, 20% BE and in the 2012 paper 20% BE. Which concentration should orchid scientists use, considering that it is identical plant material?
    d) In all three papers, the English is very poor and riddled with serious grammatical errors. This makes interpretation of the data a little difficult to understand.
    e) In the 2011 paper, Figures 1A and 1C indicate the exact same parameters with completely different data. This is a serious fault that casts doubt on the validity of the data set. The negative values on the Y-axis make absolutely no sense (just as the paper from 2012). Most likely Fig 1A was about root and shoot number. In the 2010 and 2011 papers, the authors reference the Vyas et al (2009) paper in the text several times, but no paper is listed under Vyas et al (2009) in the reference list. What study and paper exactly were the authors referring to? Is there a fourth, unknown paper? The authors use a confusing term in their 2011 paper “the root length was clubbed into two categories”: what does this mean?
    f) The data on root and shoot length and number has been stretched over 2-3 papers (i.e., possible salami publication).
    g) In all three papers, it is not indicated if percentage values were transformed prior to analyses. What version of SPSS was used?
    h) Why are the authors so different despite almost the same parameters having been studied? This shows why it is important for journals to indicate clearly the authors’ contributions. In particular, the authors Kapai and Bhattacharya. Why is one author indicated as Kapoor-Pandey in the 2011 paper but only as Kapoor in the 2012 paper? Are these in fact the same individual? If yes, then this confuses metrics and accurate referencing.
    i) Finally, in the conclusion of the 2009 paper, the authors state “conservation of biodiversity.” However, biodiversity is not an issue in this paper. Surely, the authors meant “germplasm conservation” since the in vitro protocol generates clonal material which is the antithesis of biodiversity?

    Although the three papers do describe additional analyses and some differences (e.g. testing BA in the 2009 paper, data on Luffa sponge and agar-agar in the 2011 paper, or some new additives and another orchid, Cymbidium bicolor, in the 2012 paper), the similarities between all three papers are substantial (abstract, introduction, M&M, and R&D sections) and the main findings have already been published in the 2009 paper and thus should not, in my opinion, have appeared in the 2011 or 2012 papers as “original data”, which it is not. It is redundant data. At minimum, the authors had the responsibility of declaring the 2009 paper in the 2011 references, and the 2011 paper in the 2012 references, but they did not. Why did the authors not indicate the existence of these previous papers?

  • Qui? November 19, 2014 at 2:32 pm

    An update on the following case, and insight into why the 2012b paper suddenly vanished from the IDOSI web-site. Note that even though Dr. Hamidoghli claims that he was not aware of both of these papers, that the 2012a paper continues intact, without any notice, or expression of concern.

    Raad MK, Zanjani SB, Shoor M, Hamidoghli Y, Sayyad AR, Kharabian-Masouleh A, Kaviani B. Callus induction and organogenesis capacity from lamina and petiole explants of Anthurium andraeanum Linden (Casino and Antadra). Australian J Crop Sci 2012a;6(5):928-937.

    Raad MK, Zanjani SB, Sayyad AR, Maghsudi M, Kaviani B. Effect of cultivar, type and age of explants, light conditions and plant growth regulators on callus formation of anthurium. American-Eurasian J Agric Environ. Sci 2012b;12(6):706-712.

    Dr. Y. Hamidoghli, Dept. of Horticulture, University of Guilan, Rasht, Iran, provided a formal explanation:
    “I shall thank you for your e-mail and notification, because I was not aware of the tow published articles. In 2011, Mr. Raad MK, Zanjani finished his Msc. thesis with me and Dr. M. Shoor as supervisors. According to your e-mail, Dr. Kavyani (I don,t know him) wrote! an article from this dissertation (in 2012) and added some other names as ”Authors” in the article. This article was published in AJCS. In the same year, he published another copy of this article, with some other names as authors, in American-Eurasian J Agric Environ. Sci Journal. Please be aware that all these publications were without my permission or awareness. Due to this plagiarism, I request the deletion of both articles from stated journals. Please include Dr. Kavyani and Dr. Ardashir Kharabian-Masouleh’s names in the black list so that this would not be repeated. Thank you for your cooperation sincerely Dr. Y. Hamidoghli”

  • Anthurium query November 19, 2014 at 3:50 pm

    Gantait S, Mandal N, Bhattacharyya S, Das PK. In vitro mass multiplication with pure genetic identity in Anthurium andraeanum Lind. Plant Tissue Culture and Biotechnology 2008;18(2):113-122. (Publisher: Bangladesh Association for Plant Tissue Culture and Biotechnology)
    Department of Biotechnology, Instrumentation and Environmental Science, B.C.K.V., Mohanpur, W.B.‐741252, India
    http://www.baptcb.org/ptc/Full_article/ptc18_2_03.pdf (open access)
    No DOI

    Saikat Gantait, Nirmal Mandal. Tissue culture of Anthurium andraeanum: a significant review and future prospective. International Journal of Botany 2010;6(3):207-219. (Publisher: Science Alert*)
    Institutional address: as above.
    http://scialert.net/fulltext/?doi=ijb.2010.207.219 (open access)
    DOI: 10.3923/ijb.2010.207.219

    Saikat Gantait, Uma Rani Sinniah. Morphology, flow cytometry and molecular assessment of ex-vitro grown micropropagated anthurium in comparison with seed germinated plants. African Journal of Biotechnology 2011;10(64):13991-13998. (Publisher: Academic Journals*)
    Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
    http://www.academicjournals.org/article/article1380884655_Gantait%20and%20Sinniah.pdf
    DOI: 10.5897/AJB11.1855 (valid DOI?)

    Saikat Gantait 1, Uma Rani Sinniah 1, Nirmal Mandal 2, Prakash Kanti Das 3. Direct induction of protocorm-like bodies from shoot tips, plantlet formation, and clonal fidelity analysis in Anthurium andreanum cv. CanCan. Plant Growth Regulation 2012;67(3):257-270. (Publisher: Springer Science + Business Media)
    1. Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
    2. Department of Biotechnology, Instrumentation and Environmental Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, WB, 741252, India
    3. Department of Genetics, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, WB, 741252, India
    http://link.springer.com/article/10.1007/s10725-012-9684-4
    DOI: 10.1007/s10725-012-9684-4

    In the 2012 paper, figure 3e of the acclimatized plants is identical to Fig. 1a of the 2011 paper

    Of concern is that the first five lanes of Fig. 1f of the 2010 paper are identical to the full gel indicated in Fig. 2A of the 2008 paper. The 2010 paper does not indicate whether it has used the same gel image from the 2008 paper. The first sample lane of the 2008 gel, labelled as P, refers to the mother plant. The first sample lane of the 2010 gel, labelled as C1, refers to a clone. The 2008 P lane appears to be identical to the C1 lane of the 2010 gel. It is evident that identical lanes cannot represent different samples.

    Authors and all journals were anonymously notified of these concerns in February, 2014.

    * Open access publishers considered to be “predatory” by Jeffrey Beall: http://scholarlyoa.com/publishers/

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/7D433CBB6E3CF846EF798FA747B0F0#fb16726

  • Ceropegia query November 19, 2014 at 11:40 pm

    Paper 1 (P-1)
    Publisher: Trans Stellar*
    Kalimuthu K, Prabakaran R (2013) In vitro flowering from nodal explants of Ceropegia pusilla Wight and Arn. International Journal of Botany and Research 3(3), 35-42
    Plant Tissue Culture Division, PG and Research, Department of Botany, Government Arts College (Autonomous), Coimbatore, Tamil Nadu, India
    http://tjprc.org/journals.php?jtype=2&id=46 (no editor board)
    http://tjprc.org/view-archives.php?year=2013_14_2&id=46&jtype=2&page=2
    No DOI (open access)
    No submission, acceptance or publication dates.
    Funding: “The authors extend their gratitude to the University Grants Commission (UGC File No 35-35/2008(SR) dt.19.03.2009), New Delhi of their financial assistance.”

    Paper 2 (P-2) (PDF watermarked “RETRACTED”)
    Publisher: Gyathri Publishers
    Kalimuthu K, Prabakaran R (2013) In vitro and micropropagation for conservation of rare and threatened medicinal plant Ceropegia species – a review. International Journal of Biological Technology 4(2), 23-36
    Institutional address as for P-1.
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204(2).htm (if links problematic, search from root menu: http://gbtrp.com/ijbt.htm)
    No DOI (open access)
    No funding statement.
    Published: 15, August, 2013. No submission or acceptance dates.

    Paper 3 (P-3)
    Publisher: ScienceDomain International*
    Kalimuthu K 1, Prabakaran R 1, Paulsamy S 2, Jeyaraman S 1 (2014) Microtuberization of Ceropegia pusilla Wight and Arn. an endangered medicinal plant. European Journal of Medicinal Plants 4(1), 64-74
    1 Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
    2 Department of Botany, Government Arts College (Autonomous), Salem-636007, India.
    http://www.sciencedomain.org/issue.php?iid=281&id=13?aid=729
    http://www.sciencedomain.org/abstract.php?id=13?aid=729&aid=2256
    DOI: 10.9734/EJMP/2014/5266 (open access)
    Funding: “The authors extend their gratitude to the University Grand Commission (UGC), New Delhi for their financial assistance.”
    Received 12th June 2013; Accepted 14th September 2013; Published 11th October 2013
    “Authors’ contributions: All the authors have cordially supported to the work and preparation of manuscript. Authors KK and RP have designed the entire study and protocols with interpretations of the results and prepared the first draft of the manuscript. Author SJ managed the analyses of the study and computational work respectively. Author SP guided in the entire research and documented the final draft of the manuscript. All the authors have read and approved the final manuscript.”

    Paper 4 (P-4) (PDF watermarked “UNDER INVESTIGATION”)
    Publisher: ScienceDomain International*
    Prabakaran R 1, Sasikala T 2, Kalimuthu K 1 (2013) Regeneration of shoots from callus of Ceropegia pusilla Wight and ARN. British Biotechnology Journal 3(3), 416-423
    1 Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
    2 Department of Botany, Government Arts College (Autonomous), Salem-636007, India.
    http://www.sciencedomain.org/issue.php?iid=217&id=11
    http://www.sciencedomain.org/abstract.php?iid=217&id=11&aid=1596
    DOI: 10.9734/BBJ/2013/4048 (open access)
    Funding: “The authors extend their gratitude to the University Grand Commission (UGC), New Delhi for their financial assistance.”
    Received 25th March 2013; Accepted 10th June 2013; Published 29th June 2013
    “Authors’ contributions: This work was carried out in collaboration between the three authors. Author KK designed the study, performed the statistical analysis, and made the final draft of the manuscript. Authors RP and TS managed the literature searches, carried out the study under the supervision of author KK and wrote the protocol. All authors read and approved the final manuscript.”

    Apparent data duplication
    data in Table 2 of P-3 = data in Table 1 of P-4
    data in Table 3 of P-3 = data in Table 4 of P-4
    Notice how micromolar amounts are used by P-4 and mg/l amounts in P-3

    Apparent figure duplication and manipulation
    1F of P-1 = 1E of P-2 = 1G of P-3
    1A of P-2 = 1A of P-4
    1B of P-2 = 1B of P-4
    1F of P-2 = 1F of P-4
    1D of P-3 = 1C of P-1
    1E of P-3 = 1C of P-2
    1B of P-1 = 1D of P-4 (tilted and twisted)

    Apparent plagiarism:
    2013 review (P-2) copies the abstracts of most studies in the literature, and presents this as a review, listing the studies chronologically. Subsequently, this paper has already been retracted, 24 hours after we issued our report:
    IJBT Biotek Editor writes “Thank you for your advice. As the plagiarism is serious, we have retracted the article now on consulting with the consent editor and corresponding author. The retracted article link is given below for your reference.”
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29kalimuthu%20abs.htm
    http://www.gbtrp.com/journal/ijbt%20volume%20no%204%282%29/ijbt150813104.pdf

    Apparent salami slicing and data/method duplication
    in vitro tuberization, shoot and flower induction already reported in P-1 (classical salami slice adding information to text in P-1 and data in tables in P-3 to feign originality; self-plagiarism exact text copied, see M&M section; values reported in molar amounts in P-1 and then in g/l amounts in P-3 to appear original, but are identical concentrations.

    Paper 5 (P-5) (PDF watermarked “UNDER INVESTIGATION”)
    Publisher: ScienceDomain International*
    Interestingly, another paper by the same authors, on the same plant, but on another aspect and in another journal by the same publisher, Sciencedomain.
    R. Prabakaran1, K. Kalimuthu1*, C. Vani2 and C. Brindha3 (2014) Angiogenesis and Antioxidant Activity of in vitro and in vivo Tuber of Ceropegia pusilla Wight and Arn. British Journal of Pharmaceutical Research 4(5), 608-616
    1Plant Tissue Culture Division, PG and Research Department of Botany, Government Arts College (Autonomous), Coimbatore-641018, India.
    2Department of Biotechnology, Karunya University, Coimbatore-641 114, India.
    3Department of Microbiology PSG College of Arts and Science Coimbatore-641 014, India.
    http://www.sciencedomain.org/issue.php?iid=383&id=14
    http://www.sciencedomain.org/abstract.php?iid=383&id=14&aid=3262
    DOI: 10.9734/BJPR/2014/7481
    Funding: None declared.
    Received 18th October 2013; Accepted 24th December 2013; Published 12th January 2014
    “Authors’ contributions: This work was carried out in collaboration between all authors. Authors RP and C.B conducted the plant extraction, antioxidant assays, performed the statistical analysis and wrote the manuscript. Author KK participated in designing the experimental details and interpreting the work and revising the paper. Author CV conducted the in vivo CAM assay and critically revised the paper. All authors read, edited and approved the final manuscript.”

    There are three PubPeer entries:
    P-3: https://pubpeer.com/publications/465647BF634B1332302F3A5FFF4382
    P-4: https://pubpeer.com/publications/0878DCF9FB46DF7AE12D59B6F730A4
    P-5: https://pubpeer.com/publications/937ED73ED01C18847EE9F4A9256E42

    * Publishers listed as “predatory” by Jeffrey Beall at http://scholarlyoa.com/publishers/

  • Das Eckey query November 20, 2014 at 7:17 am

    Dear Prof. Meera Das. You are kind and courageous to respond. It is healthy to have an open and frank discussion about your three papers. However, it appears as if there are about 150 errors and concerns with these three papers. How do you plan to address those errors? Also, can you or Christina Eckey kindly indicate who forms part of this “ethics group” at Springer that oversees such important decisions? Will Springer request you to address the approximately 150 comments, questions and concerns related to your three papers, and will a comprehensive erratum be published that addresses all the issues? Or will you and your co-authors voluntarily come forward to address the comments, and then request an erratum, or even an expression of concern?

    Does your statement “I will not engage in any form of correspondence in this matter henceforth” indicate that you are not prepared to respond to the concerns and queries and to correct the academic record? Do you feel that this would be the most responsible attitude towards the plant science community, especially orchidologists who would need to rely on accurate, clear and well-explained protocols to complete work on Dendrobium?

    Finally, your note was very curious. If we enter the name, Christina Eckey*, into the main scientific data-bases (Elsevier’s sciencedirect.com, Springer’s SpringerLink, Taylor and Francis Online, Wiley Online, PubMed, Walter deGryter), the data-bases turn up two very respectable papers from 2004** and 2005*** related to molecular phytopathology, when it appears as if Dr. Eckey appears to have obtained her PhD from Justus-Liebig-University. I am assuming that this experience in plant science is what allowed her to be given the position of Springer
Senior Editor, Plant Sciences. What experience has Dr. Eckey had in the past 8 years in plant science research that would then qualify her to make a scientifically validated judgment about orchid biotechnology? And what criteria are required to form part of the Springer “ethics group”? Perhaps Christina Eckey might like to come forward to explain these important issues since transparency underlies not only the peer review process, but also the decisions regarding retractions and errata. As equally as scientists are expected to trust the transparency of an editor board, so too, surely, should the scientific pool also request more transparency from Springer?

    * http://www.springer.com/biomed/contact?SGWID=0-1755214-0-0-0
    ** http://link.springer.com/article/10.1007/s11103-004-0275-2
    Christina Eckey, Michael Korell, Katja Leib, Dagmar Biedenkopf, Carin Jansen, Gregor Langen, Karl-Heinz Kogel Identification of powdery mildew-induced barley genes by cDNA-AFLP: functional assessment of an early expressed MAP kinase Plant Molecular Biology May 2004, Volume 55, Issue 1, pp 1-15
    *** http://www.sciencedirect.com/science/article/pii/S0168945204003814
    Carin Jansen, Michael Korell, Christina Eckey, Dagmar Biedenkopf, Karl-Heinz Kogel Identification and transcriptional analysis of powdery mildew-induced barley genes. Plant Science, Volume 168, Issue 2, February 2005, Pages 373-380
    Department of Phytopathology and Applied Zoology, Interdisciplinary Research Centre for Environmental Sciences, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany

  • Wheat query November 21, 2014 at 4:51 am

    C. L. Olliver, A. Grobler-Rabie, C. D. Boyd (1984) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: Nucleic Acids Methods in Molecular Biology Volume 2, pp 137-144
    Affiliation for all three authors: MRC Unit for Molecular and Cellular Cardiology, University of Stellenbosch Medical School, Tygerberg, South Africa
    Editor: John M. Walker
    DOI: 10.1385/0-89603-064-4:137
    Publisher and copyright holder: Humana Press
    http://link.springer.com/protocol/10.1385/0-89603-064-4%3A137

    Louise Olliver, Anne Grobler-Rabie, Charles D. Boyd (1998) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: RNA Isolation and Characterization Protocols Methods in Molecular Biology™ Volume 86, pp 229-233
    Ollivier and Grobler-Rabie: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
    No affiliation for Boyd.
    Editors: Ralph Rapley and David L. Manning
    DOI: 10.1385/0-89603-494-1:229
    Publisher and copyright holder: Humana Press
    http://link.springer.com/protocol/10.1385/0-89603-494-1%3A229

    An estimated 90-95% of the whole book chapter is identical. Only tiny fractions of the introduction (page 229, 1998 paper) and the notes (page 232, 1998 paper) are different. For the remainder, it is a word-by-word copy. The 1998 paper does not reference or acknowledge the 1984 chapter.

    When DOIs are entered into PubPeer, they reveal a “null” result, so unfortunately PubPeer entries cannot be created. Are these real or registered DOIs?

  • Wheat query 2 November 21, 2014 at 12:11 pm

    There is an update to the above post (Wheat query: 1984 and 1998 book chapters). Another two identical book chapters were discovered on the DOI/CrossRef web-site and have been analyzed. This comment complements the above one and also adds more details about the comparisons.

    C. L. Olliver, A. Grobler-Rabie, C. D. Boyd (1996) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: Basic DNA and RNA Protocols. Methods in Molecular Biology™ Volume 58, 1996, pp 485-490
    Ollivier and Grobler-Rabie: MRC Unit for Molecular and Cellular Cardiology, University of Stellenbosch Medical School, Tygerberg, South Africa
    Boyd: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
    Editor: Adrian J. Harwood
    DOI: 10.1385/0-89603-402-X:485
    Publisher and copyright holder: Humana Press
    http://link.springer.com/protocol/10.1385/0-89603-402-X%3A485

    Louise Olliver, Anne Grobler-Rabie, Charles D. Boyd (2000) In Vitro Translation of Messenger RNA in a Wheat Germ Extract Cell-Free System. In: The Nucleic Acid Protocols Handbook 2000, pp 891-894
    Ollivier, Grobler-Rabie, Boyd: University of Medicine and Dentistry of New Brunswick, New Brunswick, NJ
    Editor: Ralph Rapley
    DOI: 10.1385/1-59259-038-1:891
    Publisher and copyright holder: Humana Press
    http://link.springer.com/protocol/10.1385/1-59259-038-1%3A891

    The 1996, 1998 and 2000 chapters are 100% identical. The older chapters do not acknowledge the existence of any of the previously published chapters.

    An estimated 90-95% of the 1984 vs 1996/1998/2000 book chapters are identical. Only tiny fractions of the introduction (page 229, 1998 paper) and the notes (page 232, 1998 paper) are different. For the remainder, it is a word-by-word copy. The 1996/1998/2000 chapters do not reference or acknowledge each other, or the 1984 chapter.

    When the DOIs of the 1996/1998/2000 book chapters are entered into PubPeer, they reveal a “null” result, so unfortunately PubPeer entries cannot be created. However, a PubPeer entry was created for the 1984 chapter:
    https://pubpeer.com/publications/083EB54A0D6E64C345340CA4C8564D#fb16836

  • Plant tissue culture query November 21, 2014 at 9:21 pm

    P-1
    Trevor A. Thorpe History of Plant Tissue Culture. Plant Cell Culture Protocols Methods in Molecular Biology™ Volume 318, 2006, pp 9-32
    Editors: Victor M. Loyola-Vargas, Felipe Vázquez-Flota
    Publisher and Copyright Holder: Humana Press
    http://link.springer.com/protocol/10.1385/1-59259-959-1%3A009
    DOI: 10.1385/1-59259-959-1:009

    P-2
    Trevor A. Thorpe History of plant tissue culture. Molecular Biotechnology October 2007, Volume 37, Issue 2, pp 169-180 Date: 27 Jun 2007
    http://link.springer.com/article/10.1007/s12033-007-0031-3
    Publisher: Humana Press Inc.; Copyright Holder: not indicated.
    DOI: 10.1007/s12033-007-0031-3
    23 citations

    P-3
    Trevor Thorpe History of Plant Tissue Culture. Plant Cell Culture Protocols Methods in Molecular Biology Volume 877, 2012, pp 9-27 Date: 02 Apr 2012
    Editors: Víctor M. Loyola-Vargas, Neftalí Ochoa-Alejo
    Publisher: Humana Press; Copyright Holder: Springer Science+Business Media, LLC
    http://link.springer.com/protocol/10.1007/978-1-61779-818-4_2
    DOI: 10.1007/978-1-61779-818-4_2

    P-4
    Trevor A. Thorpe Chapter 1 – History of Plant Cell Culture. Plant Tissue Culture (Third Edition), 2013, Pages 1-22
    Publisher and Copyright Holder: Elsevier Inc.
    http://www.sciencedirect.com/science/article/pii/B9780124159204000013
    DOI: 10.1016/B978-0-12-415920-4.00001-3

    P-1, p. 11: “This current article is based on an earlier review by the author (24) (used with permission from Elsevier).”
    P-2, p. 170: “This current article is based on an earlier review by the author [24] (used with permission from Elsevier).”
    P-3, p. 10: “This current article is based on an earlier review by the author ( 24 ) (used with permission from Elsevier).”
    P-4: no statement indicating any permission or reference to any of the previous chapters.

    In P-1, P-2 and P-3, reference 24 is referring to the following 2000 book chapter (extremely difficult to access):
    Thorpe, T. A. (2000). History of plant cell culture. Chap. 1. In R. H. Smith (Ed.), Plant tissue culture: Techniques and Experiments (2nd ed., pp. 1–32). California: Academic Press

    The concern:
    Except for the very brief, approximately 1 page introduction in all 4 chapters, the remainder of the chapter is identical, in most parts (estimated at 90-95%) word-for-word identical. Even section titles and sub-sections are identical. The slight differences that exist most likely reflect edits that each editor requested as the chapters got updated along the way.

    The requests/queries:
    1) Can the term “based on” be equated with the copying word for word?
    2) The author is kindly requested to publicly provide a copy of the three copyright permissions for P-1, P-2 and P-3.
    3) The author is kindly requested to indicate if the content of P-4, which is almost identical to that of P1, P-2 and P-3, is also identical, or similar in parts, to the 2000 book chapter.
    4) The author is kindly requested to make available, a copy of the 2000 chapter, without breaking any copyright laws (perhaps Academic Press could be so kind as to make the copy available in open access at PubPeer, for the purpose of verification of this case).
    5) The author is kindly requested to explain why the list of papers on his professional web-site listed below is incomplete, and does not list these apparent partial chapter duplications.
    6) The editors are kindly requested to also join in the conversation and provide their perspectives.
    7) If a scientist would like to reference a/the chapter entitled “History of plant cell culture”, but the content of the latter 4 (P-1, P-2, P-3, P-4) is almost identical, which of the four copies does the author recommend be used in the citation?
    8) The last part of the four duplicated chapters, entitled “The present” is “interesting” because the chapters span from 2006-2013, yet they say the exact same thing, except for P-2 and P-4 which provide a one sentence and a few-sentences update. See excerpt below of P-1(2006) vs P-3 (2012).*

    Prof. Trevor A. Thorpe:
    Biological Sciences Department, University of Calgary, Calgary, AB, Canada, T2N 1N4
    http://www.bio.ucalgary.ca/contact/faculty/thorpe.html
    B.Sc. Agriculture (Pomology), University of Allahabad, India, 1961
    M.Sc. Horticultural Science, University of California, Riverside, USA, 1964
    Ph.D. Plant Science – Plant Physiology, University of California, Riverside, USA, 1968

    Abstracts

    P-1: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the beginning of the 20th century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogen-free plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology. The historical development of these in vitro technologies and their applications are the focus of this chapter.”

    P-2: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the begining of the 20th century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those that were already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogenfree plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology. The historical development of these in vitro technologies and their applications are the focus of this chapter.”

    P-3: “Plant tissue culture, or the aseptic culture of cells, tissues, organs, and their components under defined physical and chemical conditions in vitro, is an important tool in both basic and applied studies as well as in commercial application. It owes its origin to the ideas of the German scientist, Haberlandt, at the beginning of the twentieth century. The early studies led to root cultures, embryo cultures, and the first true callus/tissue cultures. The period between the 1940s and the 1960s was marked by the development of new techniques and the improvement of those that were already in use. It was the availability of these techniques that led to the application of tissue culture to five broad areas, namely, cell behavior (including cytology, nutrition, metabolism, morphogenesis, embryogenesis, and pathology), plant modification and improvement, pathogen-free plants and germplasm storage, clonal propagation, and product (mainly secondary metabolite) formation, starting in the mid-1960s. The 1990s saw continued expansion in the application of the in vitro technologies to an increasing number of plant species. Cell cultures have remained an important tool in the study of basic areas of plant biology and biochemistry and have assumed major significance in studies in molecular biology and agricultural biotechnology in the twenty-first century. The historical development of these in vitro technologies and their applications is the focus of this chapter.”

    * Excerpt from “The present”
    P-1, p. 20: “The current emphasis and importance of plant biotechnology can be gleamed from the last two International Congresses on Plant Tissue and Cell Culture and Biotechnology held in Israel in June 1998, and in the United States in June 2002. The theme of the Israeli Congress was Plant Biotechnology and In Vitro Biology in the 21st Century and the theme of the last Congress was Plant Biotechnology 2002 and Beyond. The proceedings for these two congresses (194, 195) were developed through a scientific program that focused on the most important developments, both basic and applied, in the areas of plant tissue culture and molecular biology and their impact on plant improvement and biotechnology. They clearly show where tissue culture is today and where it is heading (i.e., as an equal partner with molecular biology), as a tool in basic plant biology and in various areas of application. In fact, progress in applied plant biotechnology is fully matching and is without doubt stimulating fundamental scientific progress, which remains the best hope for achieving sustainable and environmentally stable agriculture (196). Indeed, the advancements made in the last 100 yr with in vitro technology have gone well beyond what Haberlandt and the other pioneers could have imagined.”

    P-3, p. 19-20: “The current emphasis and importance of plant biotechnology can be gleamed from the last three International Congresses on Plant Tissue and Cell Culture and Biotechnology held in Israel in June 1998, in the USA in June 2002, and in China in August 2006. The theme of the Israeli Congress was Plant Biotechnology and In Vitro Biology in the 21st Century ; the theme of the 2002 Congress was Plant Biotechnology 2002 and Beyond , while the theme of the 2006 Congress was Biotechnology and Sustainable Agriculture 2006 and Beyond. The proceedings for these three congresses ( 194– 196 ) were developed through scientific programs that focused on the most important developments, both basic and applied, in the areas of plant tissue culture and molecular biology and their impact on plant improvement and biotechnology. They clearly show where tissue culture is today and where it is heading (i.e., as an equal partner with molecular biology) as a tool in basic plant biology and in various areas of application. In fact, progress in applied plant biotechnology is fully matching and is without doubt stimulating fundamental scientific progress, which remains the best hope for achieving sustainable and environmentally stable agriculture ( 197 ) . Indeed, the advancements made in the last 100 years with in vitro technology have gone well beyond what Haberlandt and other pioneers could have imagined.”

    There are two PubPeer entries (the other two papers’ DOIs could not be linked to PubPeer):
    P-2: https://pubpeer.com/publications/5E8393A80298AD8B1FEA9210CC368D#fb16846
    P-4: https://pubpeer.com/publications/19294ED07445E31E5855FB46F8786E#fb16847 

  • Balanites query November 23, 2014 at 8:15 am

    Paper 1
    Siddique, I., Anis, M., 2009. Direct plant regeneration from nodal explants of Balanites aegyptiaca L. (Del.): a valuable medicinal tree. New Forests 37:53–62. doi:10.1007/s11056-008-9110-y (Springer Science + Business Media)
    http://link.springer.com/article/10.1007/s11056-008-9110-y
    20 citations

    Paper 2
    Anis, M., Varshney, A., Siddique, I. 2010. In vitro clonal propagation of Balanites aegyptiaca (L.) Del. Agroforestry Systems 78:151–158. DOI: 10.1007/s10457-009-9238-6 (Springer Science + Business Media)
    http://link.springer.com/article/10.1007/s10457-009-9238-6
    6 citations

    Paper 3
    Varshney A. 2012. PhD thesis (Studies on micropropagation and biochemical analysis in Balanites aegyptiaca Del)
    Open access (all thesis chapters): http://ir.inflibnet.ac.in:8080/jspui/handle/10603/11369
    (issued September, 2013)

    Paper 4
    Varshney, A., Anis, M., 2013a. Evaluation of clonal integrity in desert date tree (Balanites aegyptiaca Del.) by inter-simple sequence repeat marker assay. Acta Physiologiae Plantarum 35:2559–2565. DOI:10.1007/s11738-013-1292-z (Springer Science + Business Media)
    http://link.springer.com/article/10.1007/s11738-013-1292-z
    2 citations

    Paper 5
    Varshney, A., Anis, M., 2013b. Direct plantlet regeneration from segment of root of Balanites aegyptiaca Del. (L.)- A biofuel arid tree. International Journal of Pharma and Bio Sciences 4(2):987–999 (section biological science, paper No. 117).*
    http://www.ijpbs.net/archive-issue.php?issueid=22
    http://www.ijpbs.net/cms/php/upload/2343_pdf.pdf

    Paper 6
    Varshney, A., Anis, M., Aref, I.. M., 2013. Control of bioregulants on plant resurgence in vitro from mature seeds of Egyptian Myrobalan Tree (Balanites aegyptiaca Del.)- a plant affluent in saponins. International Journal of Pharmaceutical Sciences Review and Research 22:23–28. (Global Research Online**)
    http://globalresearchonline.net/journalcontents/v22-1/05.pdf

    Paper 7
    Varshney, A., Anis, M., 2014a. Synseed conception for short-term storage, germplasm exchange and potentialities of regeneration genetically stable plantlets of desert date tree (Balanites aegyptiaca Del.). Agroforestry Systems 88:321–329. DOI: 10.1007/s10457-014-9685-6 (Springer Science + Business Media)
    http://link.springer.com/article/10.1007/s10457-014-9685-6
    No citations

    Paper 8
    Varshney, A., Anis, M., 2014b. Trees: Propagation and Conservation: Biotechnological Approaches for Propagation of a Multipurpose Tree, Balanites aegyptiaca Del. Springer, New Delhi, India, p. 116. DOI:10.1007/978-81-322-1701-5 (Springer Science + Business Media)
    http://link.springer.com/book/10.1007/978-81-322-1701-5

    * Listed as “predatory open access publishers” by Jeffrey Beall: http://scholarlyoa.com/individual-journals/
    ** Listed as “predatory open access publishers” by Jeffrey Beall: http://scholarlyoa.com/publishers/

    The symbol = is used next to denote “identical to”.

    Fig. 2C (paper 5) = Fig. 1C (paper 6) = Fig. 1E (paper 4) = Fig. 4.18c (paper 8)
    Table 4 (paper 5) = Table 4 (paper 6) = Table 4.28 (paper 8)
    Problem: shoots are from root segments in the presence of 5 µM BA + 1 µM NAA (Fig. 2C), those from Fig. 1C are from seeds germinated in the presence of GA3, those in Fig. 1E are from nodal explants from mature trees in the presence of 12.5 µM BA + 1 µM NAA, while those in Fig. 4.18c are rooted shoots in the presence of 2 µM IBA.
    Issue 1: how is it possible for the exact same shoots to be derived from three completely different and distinct biological tissues and sources and in response to completely different plant growth regulators?
    Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in any of the other sources.
    Issue 3: Materials and method section. Paper 8 used 3-4 cm shoots while in paper 5, 4-5 cm shoots and in paper 6, shoots with expanded leaves are used (but no size specified).

    Fig. 1D (paper 6) = Fig. 1F (paper 4) = Fig. 4.20b (paper 8)
    Problem: plants are from seedlings (Fig. 1D), but those from Fig. 1F are from nodal segments. The source of plants in Fig. 4.20b is not specified, only the age (four-month-old plantlets).
    Issue 1: how is it possible for the exact same plants to be derived from at least two completely different and distinct biological tissues?
    Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in any of the other sources.

    Fig. 1C (paper 4) = Fig. 4.2a (paper 8)
    Problem: shoots from nodal explants derived from mature trees (Fig. 1C), but those from Fig. 4.2a are from cotyledonary nodes (i.e., from seed-derived shoots).
    Issue 1: how is it possible for the exact same shoots to be derived from two completely different and distinct biological tissues?
    Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

    Fig. 1B (paper 6) = Fig. 4.6a (paper 8)
    Problem: intact seedlings from seeds (Fig. 1B) are also shoots from seedling-derived nodal explants (Fig. 4.6a).
    Issue 1: how is it possible for the exact same plants to be derived from two completely different and distinct biological tissues?
    Issue 2: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

    Fig. 1A-D (paper 5) = Fig. 4.8a-d (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Fig. 2A (paper 5) = Fig. 4.9a (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Fig. 2B (paper 5) = Fig. 4.10a (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Fig. 1A (paper 6) = Fig. 4.12b (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Fig. 1B (paper 2) = Fig. 4.16a (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 2.

    Fig. 3B,C,D (paper 7) = Fig. 4.21b,c,d (paper 8)
    Issue: none of the text, figure legends, or acknowledgements acknowledges the existence of the same figure in each of the sources.

    Fig. 1E (paper 1) = Fig. 4.18b (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 1.

    Fig. 2D (paper 5) = Fig. 4.19b (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Fig. 1E (paper 5) = Fig. 4.22d (paper 8)
    Issue: none of the text, figure legends, or acknowledgements of paper 8 acknowledges the existence of the same figure in paper 5.

    Other queries and concerns about this set of 8 closely-linked papers:
    a) Why are the ISSR banding patterns in Fig. 2 of paper 4 so different from those in Fig. 4.27 (paper 8) when the exact same primers have been used? Admittedly, the samples may be different, but these are not clearly explained in paper 8.
    b) Why has paper 8 not referenced paper 4 and paper 6, even though paper 8 was published in 2014 while papers 4 and 6 were published in 2013?
    c) In Fig. 1E of paper 1, the figure legend states “in vitro rooted plantlet on MS + IBA (1.0 µM) + activated charcoal (0.5%)”. However, the use of activated charcoal at this concentration would clearly stain the medium black. There is thus clearly a problem with the description of the medium, or of the results. In the PhD thesis (paper 3), the description for the exact same figure states “In vitro rooted shoots cultured on half strength MS medium with 2.0 μM IBA after 4 weeks” (chapter 4, p. 71).
    d) In paper 4, the materials and method section clearly states that the medium is “half-strength MS medium supplemented with IBA (1 µM)” but in the figure 1E caption this is specified as “MS + IBA (1 µM)”. The same figure in paper 5 states that the rooting medium is “half strength MS medium with 2.0 µM IBA”. That indicates clearly a discrepancy between the media used, and thus an error in the methods reported.
    e) See materials and method section of paper 2. “Healthy, small twigs (3–4 cm) of B. aegyptiaca were collected from 20 years old healthy mature tree growing at Arid Forest Research Institute (AFRI) campus Jodhpur, India.” Distance from Jodhpur to Aligarh (authors’ institute) by air is 528 Km and by road 648 Km according to a trip website http://www.makemytrip.com/routeplanner/jodhpur-aligarh.html. It is surprising how only 3-4 cm small twigs can be preserved for long and over such a great distance, although how the material was preserved over this period is not explained. In this case, experience indicates that generally fresh samples of explants are used and experiments are performed in the early morning. However, it is possible to keep material on ice, but regeneration efficacy is poor in comparison with freshly collected plant material and the chance of contamination by endophytes is higher. Or, if a sample is collected from far away, 2 to 2.5 meter branch (for tree species) and 20 to 50 cm twig (for shrub) from same mother plant and placed in 200 mg/l IAA for 5 h, for rooting, then transplanted. Only mother plants that regenerate (after about 4 months) are used as the source of explants, not freshly collected material. Regrettably, none of these fine-scale but essential details are indicated in the materials and method section, which only mentions that the experiment is repeated in triplicate but the number of replicates are not mentioned anywhere in the text.
    f) Chapters 2 and 3 of the thesis (paper 3) are identical to chapters 2 and 3 of the book (paper 8), without attribution. The reference list at the end of both book chapters does not reference paper 3, the Varshney thesis. Paper 3, chapter 1 is approx. 90% identical to paper 8, chapter 1. Paper 3, chapter 2 is approx. 90% identical to paper 8, chapter 2. Vast tracts of text in the thesis (paper 3, chapter 2) as well as in paper 8, chapter 2 (estimated at about 30%) appear to be copied from George et al. (2007), without acknowledgement. Paper 3, chapter 3 is almost identical to paper 8, chapter 3, the same for chapter 4 and chapter 5.
    g) Plagiarism software was not used, and values represent rough estimates by crude line-by-line comparisons.

    Funding:
    a) Paper 1: “Authors gratefully acknowledge the University Grants Commission, New Delhi for financial assistance and the Department of Science and Technology, Govt. of India, New Delhi, for providing research support under DST-FIST Program.”
    b) Paper 2: “This research is supported by a Grant from the University Grants Commission (2006–2009), New Delhi. Authors gratefully acknowledge the Department of Science and Technology, Govt. of India, New Delhi for providing research support under DST-FIST (2005) Program.”
    c) Paper 3: “Financial support from UGC in the form of Project Fellow in a major research project on Balanites aegyptiaca (2007-2009) and Non-Net fellowship (2011-2012) is greatly acknowledged.”
    d) Paper 4: “Authors gratefully acknowledge the Department of Science and Technology, and the University Grant Commission, Govt. of India, New Delhi for providing research support under DST-FIST (2005) and UGC-SAP DRS-I (2009) Programs, respectively.”
    e) Paper 5: “Authors also gratefully acknowledge the Department of Science and Technology, Govt. of India, New Delhi for providing research support under DST- FIST (2005), UGC – SAP DRS-I (2009) Programs respectively.”
    f) Paper 6: “Authors gratefully acknowledge the Department of Science and Technology, and the University Grant Commission, Govt. of India, New Delhi for providing research support under DST-FIST (2005) and UGC-SAP DRS-I (2009) Programs, respectively.”
    g) Paper 7: “Research support from the Department of Science and Technology (Govt. of India) New Delhi under the DST-FIST (2011) and UGC-SAP (2009) Programmes are duly acknowledged.”
    h) Paper 8: “The research support and assistance rendered by the Department of Science and Technology and the University Grant Commission, Govt. of India, New Delhi, in the form of DST-FIST (2011–2016) and UGC-DRS-I (2009–2014) programs is duly acknowledged. The award of Young Scientist under DSTFAST TRACK scheme to Ankita Varshney is also gratefully acknowledged.”

    Mohammad Anis 1,2; Ankita Varshney 1; I. Siddique (not listed at 1); I. M. Aref 2.
    1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
    2. Department of Plant Production, College of Food & Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia

    1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
    http://www.amu.ac.in/dfacultylist.jsp?did=40
    2. College of Food & Agricultural Sciences, King Saud University
    http://ksu.edu.sa/Deanships/DeanshipofGraduateStudies/Pages/CollegeofFoodSciencesandAgriculture.aspx

    There are four PubPeer entries:
    Paper 1: https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
    Paper 2: https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878 
    Paper 4: https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879 
    Paper 7: https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880 

    Paper 8 DOI could not be read by PubPeer.

    • Balanites query December 3, 2014 at 3:45 pm

      Update.

      Dr. Ankita Varshney has responded to an anonymous request to comment on this case but does not understand the concept of anonymity. What the authors also do not appear to understand is that this is a public case that affects the entire plant science literature and all plant scientists, and may have wider consequences and repercussions on academic integrity in plant science journals. Rather than skirting the issue, surely it is best to address them publically at PubPeer as well as directly with the journals, journal editors and publishers? Public accountability for one’s research and publications is not a matter of negotiation, it is a matter of scientific responsibility.

      12/3/14 at 8:19 PM “Thanks for your mail dated 23 Nov. 2014. Sir, before reponding publically to queries and concerns about some of our publications at PubPeer, we would like to have your brief introduction. I have seen an unregistered submission at PubPeer for the same. I request you to please tell your designation and credentials to us. Looking for your reply. Thanking You. Dr. Ankita varshney. DST Young Scientist. Plant Biotechnology Lab. Dept. of Botany, AMU Aligarh.” And, one day earlier, 12/2/14 at 6:34 PM “We will shortly submit our clarification at PubPeer. Regards, Dr. Ankita Varshney.”

  • Ceropegia query November 25, 2014 at 5:00 pm

    “Original” research papers

    P-1
    Kondamudi R, Murthy, K.S.R. 2011. Micropropagation of Ceropegia pusilla Wt. & Arn. – an endangered and rare medicinal Asclepiad. Journal of Tropical Medicinal Plants 12: 41-48
    http://tropmedplants.com/article.php?aid=464 (no editor board)
    No DOI. (paid access)

    P-2
    Kondamudi R, Vijayalakshmi V, Murthy, K.S.R. (2010) Induction of morphogenetic callus and multiple shoot regeneration in Ceropegia pusilla Wight and Arn. Biotechnology 9(2): 141-148
    http://scialert.net/qredirect.php?doi=biotech.2010.141.148&linkid=pdf
    (Asian Network for Scientific Information, ANSI*; http://scialert.net/eboard.php?issn=1682-296x)
    DOI: 10.3923/biotech.2010.141.148 (open access)

    P-3
    Murthy KSR, Kondamudi R (2010) Effect of cytokinins and auxins on in vitro flowering of endangered Ceropegia spiralis Wight and C. pusilla Wight & Arn. Phytomorphology 60: 32-37.
    (Publisher: International Society of Plant Morphologists)
    No DOI. (paid access)

    P-4
    Murthy KSR, Kondamudi R, Vijayalakshmi V (2010a) Micropropagation of an endangered medicinal plant Ceropegia spiralis Wight. Journal of Agricultural Technology 6: 179-191.
    http://www.ijat-aatsea.com/past_v6_n1.html
    http://www.ijat-aatsea.com/pdf/Jan_v6_n1_10/19-55-IJAT2009_35R.pdf
    (Publisher: Association of Agricultural Technology in Southeast Asia (AATSEA))
    No DOI. (open access)

    P-5
    Murthy KSR, Kondamudi R, Pullaiah T (2010b) High frequency somatic embryogenesis in Ceropegia spiralis Wight – an endemic and endangered medicinal plant. Indian Journal of Biotechnology 9, 414-418.
    http://nopr.niscair.res.in/bitstream/123456789/10441/1/IJBT%209%284%29%20414-418.pdf
    (NISCAIR; IF = 0.477) (open access)

    P-6
    Murthy KSR, Kondamudi R (2011) Rapid shoot regeneration from thin cell layer explants of an endangered medicinal asclepiad Ceropegia spiralis L. Plant Tissue Culture and Biotechnology 21(1): 63-73.
    http://www.banglajol.info/index.php/PTCB/article/view/9564
    (Publisher: Bangladesh Association for Plant Tissue Culture and Biotechnology (BAPTC&B))
    (Banglajol: http://www.banglajol.info/index.php/index)
    DOI: 10.3329/ptcb.v21i1.9564 (open access)

    P-7
    Murthy KSR, Kondamudi R, Karuppusamy S (2012a) Microtuberization of Ceropegia spiralis Wight and Ceropegia pusilla Wt. and Arn. African Journal of Plant Science 6: 321-327.
    http://academicjournals.org/article/article1380125590_Murthy%20%20et%20al.pdf
    Total views: 221: downloaded: 345
    (Academic Journals*)
    DOI: 10.5897/AJPS12.107 (open access)

    P-8
    Murthy, K.S.R., Kondamudi, R., Reddy, M.C., Karuppusamy, S., Pullaiah, T., 2012b. Check-list and conservation strategies of the genus Ceropegia in India. International Journal of Biodiversity and Conservation 4(8), 304-315.
    http://www.academicjournals.org/article/article1380023122_Murthy%20et%20al.pdf
    Total views: 241: downloaded: 176
    (Academic Journals*)
    DOI: 10.5897/IJBC12.011 (open access)

    P-9
    KSR Murthy, MC Reddy, R Kondamudi (2013) Synthetic seeds – A novel approach for the conservation of endangered C. spiralis wt. and C. pusilla. Bangladesh Journal of Scientific and Industrial Research 48(1), 39-42. (Banglajol: http://www.banglajol.info/index.php/index)
    http://www.banglajol.info/index.php/BJSIR/article/view/15412
    No DOI. (open access)

    The symbol = denotes “identical to” in the following lists.

    Tables:
    20 shoot-related data points in Table 2 of P-1 are identical to data in Table 3 of P-2
    Table 2 data of P-3 = Table 3 data of P-1
    Table 2 data of P-4 = Table 1 data of P-6
    Table 4 data of P-4 = Table 1 data of P-7 (the latter does, however, include additional information and all negative results in treatments, but 19 identical data points, nonetheless)

    Figures:
    Fig. 1D of P-2 identical to Fig. 1F of P-1
    Fig. 1B of P-3 identical to Fig. 1E of P-1 (slightly rotated)
    Fig. 1B of P-6 = Fig. 1B of P-4 = Fig. 1Ce of P-7
    Fig. 1A of P-6 = Fig. 1Cb of P-7 (rotated ~90°)
    Fig. 1D of P-6 (slightly squashed) = Fig. 1Cc of P-7
    Fig. 1G of P-4 (rotated ~45° and tilted) = Fig. 1i of P-5
    Fig 1A of P-4 = Fig. 1A of P-7 (slightly rotated)
    Fig. 1F of P-7 (left test-tube removed) = Fig. 1D of P-2
    Fig. 1E of P-7 repeated twice (in Fig. 1E and Fig. 1C)

    These concerns would surely also directly influence the claims in the review written by this group in P-8. Moreover, several of these papers have been referenced in P-9.

    Affiliations:
    K Sri Rama Murthy, R Kondamudi, MC Reddy, V Vijayalakshmi: School of Conservation Biology and Plant Biotechnology, Department of Biotechnology, Montessori Mahila Kalasala, Vijayawada, 520 010, Andhra Pradesh, India.
    http://www.researchgate.net/profile/K_Sri_Rama_Murthy (Head of Department, Department of Biotechnology)
    http://www.minglebox.com/college/Montessori-Mahila-Kalasala-College-Vijayawada (actual web-site difficult to trace)
    S Karuppusamy: Department of Botany, the Madura College, Madurai, Tamil Nadu – 625 011, India.
    http://www.maduracollege.org/botany.php
    T Pullaiah: Departent of Botany, Sri Krishnadevaraya University, Anantapur 515 003, Andhra Pradesh, India
    http://www.htcampus.com/college/department-botanysri-krishnadevaraya-university/

    Financial assistance:
    P-1: “The authors extend their gratitude to the Council of Scientific and Industrial Research, New Delhi for financial assistance.”
    P-2: “The authors extend their gratitude to the Council of Scientific and Industrial Research, New Delhi of their financial assistance.”
    P-3: “The authors are thankful to the Council of Scientific and Industrial Research (CSIR), New Delhi, India for providing the financial assistance.”
    P-4: “The receipt of financial assistance from the Council of Scientific and Industrial Research (CSIR), New Delhi, is gratefully acknowledged.”
    P-5: “The financial assistance received from Council of Scientific and Industrial Research, New Delhi, is gratefully acknowledged.”
    P-6: “The authors thank the authority of The Council of Scientific and Industrial Research (CSIR), New Delhi for providing financial assistance to carry our the present work.”
    P-7: “The receipt of financial assistance from the Council of Scientific and Industrial Research (CSIR), New Delhi, is gratefully acknowledged.”
    P-8: “One of the authors (KSM) received financial support from the Council of Scientific and Industrial Research, New Delhi, for this study.”

    * Publisher listed as “predatory” by Jeffrey Beall at http://scholarlyoa.com/publishers/

    Even though the corresponding author, one other author, and all publishers (except for P-9) were anonymously notified of these problems on February 19, 2014, the entire literature listed above remains untouched, and uncorrected.

    There are four PubPeer entries for this case:
    P-2: https://pubpeer.com/publications/19CF7D9BE88DB147E132A284ECF9AC#fb17111
    P-6: https://pubpeer.com/publications/0955F74AA995CED3982A2EB55880F5#fb17110
    P-7: https://pubpeer.com/publications/5CC152B8CBCF256457B718A51F1399#fb17112
    P-8: https://pubpeer.com/publications/9D91F963C8EFFC96AB2C2D3710E556#fb17113

  • Cotton concerns November 26, 2014 at 3:14 am

    Cotton 1
    Eltayb Abdellatef, Mutasim M. Khalafalla (2008) Influence of growth regulators on callus induction from hypocotyls of medium staple cotton (Gossypium hirsutum L). cultivar Barac B -67. Journal of Soil and Nature 2(1): 17-22
    Commission for Biotechnology and Genetic Engineering, National Centre for Research, Khartoum, Sudan
    Publisher: Green Global Foundation (GGF) (formerly Green World Foundation (GWF)): http://ggfjournals.com/ *
    Accepted for publication: February 03, 2008. No submission or publication dates.
    http://ggfjournals.com/content/issue/jsn-v2-is1
    http://ggfjournals.com/content/papers/v2i117-22
    http://ggfjournals.com/assets/uploads/4.17-22_.pdf (open access)
    No DOI.

    Cotton 2
    Eltayb Abdellatef, Mutasim M. Khalafalla (2008) Ethylene inhibitors promote in vitro regeneration of medium staple cotton (Gossypium hirsutum L.) cultivar Barac B- 67. Advances in Natural and Applied Sciences 2(3): 178-184.
    Publisher: American Eurasian Network for Scientific Information (AENSI, Jordan) *
    No submission, acceptance or publication dates.
    PDF states: “This is a refereed journal and all articles are professionally screened and reviewed.”
    http://www.aensiweb.com/old/anas_sept-dec_2008.html
    http://www.aensiweb.com/old/anas/2008/178-184.pdf (open access)
    No DOI.

    Cotton 3
    Eltayb Abdellatef, Mutasim M. Khalafalla (2007) Adventitious shoot and plantlet formation in medium staple cotton cultivar (Gossypium hirsutum L. cv Barac [67] B). International Journal of Agriculture and Biology 9(6): 913-916.
    Publisher: Friends Science Publishers, Pakistan (http://www.fspublishers.org) *
    Received 31 May 2007; Accepted 06 August 2007. No publication date.
    http://www.fspublishers.org/Issue.php?categoryID=109
    http://www.fspublishers.org/published_papers/35232_..pdf (open access)
    No DOI.

    Fig 1C of Cotton 1 = Fig 1A of Cotton 2
    Fig. 1D of Cotton 2 = Fig. 1F of Cotton 3
    Table 1 data of Cotton 1 is identical to Table 1 data of Cotton 3.
    The protocols are almost identical, with only small tweaks.

    * Listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/).

    Authors and publishers were alerted anonymously to this case on 12 February 2014. No action has yet been taken.

    Funding:
    Cotton 1: “We gratefully acknowledge the financial support of the National Center for Research, Ministry of Science and Technology, Sudan.”
    Cotton 2: “We gratefully acknowledge the financial support of the National Center for Research, Ministry of Science and Technology, Sudan.”
    Cotton 3: “We thank National Center for Research, Ministry of Science and Technology, Sudan for financial support.”

    As there are no DOIs, the case cannot be linked to PubPeer.

  • Moringa concerns November 26, 2014 at 3:18 am

    Mutasim M. Khalafalla 1, Hussein M. Dafalla 1, A. Nassrallah 2, Khalid M. Aboul-Enein 3, Hany A. El-Shemy 2, Eltayb Abdellatef 1 (2011) Dedifferentiation of leaf explants and antileukemia activity of an ethanolic extract of cell cultures of Moringa oleifera. African Journal of Biotechnology 10(14), 2746-2750, 4 April, 2011 (Academic Journals*)
    1 Commission for Biotechnology and Genetic Engineering, P. O. Box 2404 Khartoum, Sudan.
    2 Faculty of Agriculture Research Park (FARP) and Department of Biochemistry, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt.
    3 Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt.
    http://www.academicjournals.org/journal/AJB/cited-by-article/E47D15925665
    http://www.academicjournals.org/article/article1380729752_Khalafalla%20et%20al.pdf (open access)
    http://www.ms.academicjournals.org/article/article1380729752_Khalafalla%20et%20al.pdf
    DOI: 10.5897/AJB10.2099
    Total views: 146; Downloaded: 199
    Accepted: 30 December 2010; Published: 04 April 2011; Submission date not indicated.

    Eltayb Abdellatef, Mutasim M. Khalafalla (2010) In vitro morphogenesis studies on Moringa olifera L. an important medicinal tree. International Journal of Microbiological Research 2010; 1(2): 85-89
    (Publisher: Medicobiological Research Publications)
    http://www.ijmedres.com/issue2.php
    http://www.ijmedres.com/article/013_In_vitro_morphogenesis_studies_on_Moringa_olifera_L_An_important_medicinal_tree_Eltayb_adbedllatef_Mutasim.pdf (this link now apparently dead)
    https://app.box.com/s/15e8gfaty3x58fom3jbv (open access)
    Received on: 09.08.2010; Revised on: 15.08.2010; Accepted on: 18.10.2010; Published: date not indicated.
    No DOI.

    5 data points in Table 1 data of the 2011 paper duplicate the same data in Table 2 of the 2010 paper.
    Fig. 1A in both papers is identical.
    The 2011 paper does not acknowledge the existence of the 2010 paper in its reference list, nor does it indicate that the table data or figure are identical.

    *AJB, listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/), claims to follow the COPE ethics (http://www.academicjournals.org/journal/AJB/publication-ethics), which would also automatically imply the implementation of the COPE guidelines for retractions in the case of duplications.

    Authors and publishers were alerted to this case on 12 February 2014. No action has yet been taken. Neither paper acknowledges any funding. Even though the AJB paper has a DOI, it cannot be read by PubPeer.

  • Anthurium retraction report November 26, 2014 at 4:20 am

    Jagan Mohan Reddy, A. K. Bopaiah (2012) Studies on the intiation of callusing and regeneration of plantlets in three different basal media with varied plant growth regulators for the micropropagation of Anthurium scherzeriaum using leaf and spathe as explants. African Journal of Biotechnology 11(23), 6259-6268. (the duplicate paper) (Publisher: Academic Journals, Nigeria*)
    Accepted: 27 January 2012. Published: 20 March 2012. Submission date not indicated.
    http://www.academicjournals.org/article/article1381128672_Reddy%20and%20Bopaiah.pdf
    DOI: 10.5897/AJB10.1292
    Total views: 259; Downloads: 109

    Jagan Mohan Reddy, A. K. Bopaiah, Abhilash M (2011) In vitro micropropagation of Anthurium digitatum, using leaf as explant. Asian Journal of Pharmaceutical and Health Sciences 1(2): 70-74 (the original paper)* (listed at http://scholarlyoa.com/individual-journals/)
    Received: 11 February, 2011; Accepted: 11 March, 2011; Available online: 11 May, 2011.
    http://ajphs.com/archives-sub/?id=45 (the paper was retracted and appears on the web-site as “null”):
    http://ajphs.com/archives-details/?post_id=582&cat_id=45 (small note reads: “article retracted due to plagiarism…”)

    *AJB, listed as a “predatory” open access publisher by Jeffrey Beall (http://scholarlyoa.com/publishers/), claims to follow the COPE ethics (http://www.academicjournals.org/journal/AJB/publication-ethics), which would also automatically imply the implementation of the COPE guidelines for retractions. AJB and the authors were alerted to this case on June 1, 2013, with a follow-up reminder on July 2, 2013. What is extremely odd about this case is why the earlier paper was retracted, and not the later paper. Does the fact that the remaining paper in AJB, with other concerns (see below), reflect something about peer review and editorial oversight in this journal, or by this publisher?

    Even though the one paper was retracted, there is no history of the problems that had been encountered that led to the retraction. This deposit at PubPeer aims to provide a listing of some of the problems.

    In the 2011 AJPHS paper, the authors describe an in vitro protocol for Anthurium digitatum.
    In the 2012 AJB paper, the authors describe an in vitro protocol for Anthurium scherzeriaum.

    Concerns about the papers:
    a) Fig 1 in AJPHS is identical to Fig. 9 in AJB. Naturally, the same figure cannot represent two different plant species. This immediately calls into question whether all other figures of both papers are valid and what photos truly represent A. digitatum and which truly represent A. sherzerianum.
    b) In the AJB paper, the wrong spelling is used throughout the entire manuscript for Anthurium scherzerianum: it is reported as Anthurium scherzeriaum. This plant does in fact not exist and thus invalidates the entire manuscript.
    c) The language of the AJPHS paper is barely English. It is full of grammatical errors that many statements leave open the possibility for multiple interpretations. Ambiguous language implies ambiguous data sets and unreliable data that cannot be used with confidence in the laboratory. The English of the AJB paper is also borderline.
    d) In all tables of AJB, 2,4-D is written in almost every possible way (at least 5 variations). Are we dealing with 5 different chemical compounds?
    e) Table 9, AJB paper. How can you represent a range of values for the parameters? No sample sizes are given, no statistical analyses exist. How can you have 3-4 roots, for example? Is it 3? Is it 4? Is it an average of 3.4?
    f) AJB paper. Figure 2 is identical to Fig. 3, only that Fig 3 is tilted about 30 degrees clockwise and the tone/hue/brightness have been manipulated to give it the impression of a different figure.
    g) AJB paper, Figure 8 legend. What is the difference between leaf lamina and leaf size? The figure legend makes no sense as the figure is uninformative.
    h) In the AJB paper, only 6 references are listed. Yet, the Anthurium in vitro literature had at least, until 2012, approximately 30-40 studies. Why was the literature so grossly under-represented? The exact same references were used for the AJPHS paper.
    i) The exact same experimental design and the exact same explants were used in both studies, except for the spathe in the AJB paper. The plants in vitro look remarkably similar, suggesting that in fact the exact same Anthurium species was used. It is impossible for a reader to verify the actual species and the actual cultivars.
    j) The Introduction of the AJB paper does not have a single reference. Yet, it makes many factual claims that are not supported by the literature. Thus, the AJB paper can be considered to be plagiaristic as it does not appropriately list the literature from which this information has arisen.
    k) The Introduction of the AJPHS paper is equally unscientific in nature. Not only does it not explore the wide literature on Anthurium in vitro, it makes unsupported statements as indicated at the end of the first paragraph regarding the locations of commercial production.
    l) In the AJPHS paper, the authors use non-standard scientific English. For example, what is transflasking? What is 6/6H2O2? These are transcendental errors.
    m) In the AJB paper, what is White’s medium? Why is there no reference for this medium? What is Nitsch’ (why the apostrophe?). What are medias?
    n) In the AJPHS paper, what are these “secretory products” mentioned in the Introduction?

    Requests to the authors on May 30, 2013 for a PDF file of another of their papers remained unanswered:
    Jaganmohan Reddy and A.K. Bopaiah
    Studies on the Potentiality of Inflorescence Spathe in the Formation of Callus and Regeneration of Plantlets in Ornamentally Important Anthurium andraeanum rubum in Vitro pp. 219-229
    http://www.ripublication.com/Volume/ijbbrv2n2.htm

    Affiliations:
    Jagan Mohan Reddy: Department of Biotechnology, Acharya Institute of Technology, Soladevanahally, Bangalore-560 090, Karnataka, India.
    http://www.acharya.ac.in/ait.php
    A. K. Bopaiah: Department of Botany, St. Joseph’s College, Bangalore-560 001, Karnataka, India.
    http://www.sjc.ac.in/dep_botany.html
    M. Abhilash: UST Global, Technopark, Trivandrum, India.
    http://www.ust-global.com/en/

    Neither paper acknowledges any funding.

    The authors published another very weak paper on this ornamental:
    http://ijiit.webs.com/documents/120104-03.pdf

    There is a PubPeer entry associated with this case:
    https://pubpeer.com/publications/2FA8EA21F3078386552B1B4A71C6C3#fb17166

  • Rare earth elements + plants report November 26, 2014 at 4:26 am

    In this case, none of the three DOIs of the three papers under discussion, published by Springer Science+Business Media, link to PubPeer.

    Concerns about statistical analyses (and thus conclusions) in three Biological Trace Element Research (BTER) papers by the same group of authors. An anonymous report was made to Springer, and the Editor-in-Chief, BTER, Prof. Gerhard N. Schrauzer, on 31 July, 2013. This resulted in an expression of concern, but the background concerns were not listed in detail by the Editor-in-Chief, by the journal, or by the publisher, which is as concerning as the three papers themselves because the readers cannot appreciate the actual problems. For this reason, it is important to detail the concerns at PubPeer and RW.

    Paper 1: http://link.springer.com/article/10.1385/BTER%3A89%3A3%3A277
    Biological Trace Element Research December 2002, Volume 89, Issue 3, pp 277-284
    Effects of lanthanum element on the rooting of loquat plantlet in vitro
    Weiping Song, Fashui Hong, Zhigang Wan
    All authors: Department of Biology, Life Sciences College, Suzhou University, Suzhou, People’s Republic of China
    DOI: 10.1385/BTER:89:3:277 (this DOI leads to a different paper on PubPeer)
    Publisher and copyright holder: Humana Press Inc.
    Citations: 2

    Paper 2: http://link.springer.com/article/10.1385/BTER%3A104%3A2%3A185
    Biological Trace Element Research 1-May-2005, Volume 104, Issue 2, pp 185-191
    Effect of La(III) on the growth and aging of root of loquat plantlet in vitro
    Hong Fashui, Song Weiping, Wan Zhigang, Yu Mingliang, Yu Jia, Liu Jiajia, Sheng Ye, Xi Qunhua
    Minglinang Yu: Agriculture Academy of Jiangsu Province, 210049, Nanjing, People’s Republic of China
    All other authors: Life Sciences College, Suzhou University, 215006, Suzhou, People’s Repubilic of China
    DOI: 10.1385/BTER:104:2:185 (this DOI leads to the same incorrect paper on PubPeer)
    Publisher and copyright holder: Humana Press Inc.
    Citations: 1

    Paper 3: http://link.springer.com/article/10.1385/BTER%3A95%3A3%3A259
    Biological Trace Element Research December 2003, Volume 95, Issue 3, pp 259-268
    Effects of cerium on nitrogen metabolism of peach plantlet in vitro
    Song Weiping 1, Hong Fashui 1, Wan Zhigang 1, Zhou Yuzhen 2, Gu Fugen 1, Xu Hongoing 1, Yu Mingliang 2, Chang Youhong 2, Zhao Mizhen 2, Su Jiale 2
    1. College of Life Sciences, Suzhou University, 215006, Suzhou, People’s Republic of China
    2. Agriculture Academy of Jiangsu Province, 210049, Nangjing, People’s Republic of China
    DOI: 10.1385/BTER:95:3:259 (this DOI leads to the same incorrect paper on PubPeer)
    Publisher and copyright holder: Humana Press Inc.
    Citations: 8

    Paper 1
    1. Statistical analyses not described.
    2. Experimental design, randomization and sampling not described.
    3. p. 278 “The relationship between La(NO3)3 concentration and the number of roots was studied. The results are shown in Table 1. The rate of rooting was 41–42% more than that of the control when the La(NO3)3 concentration in the rooting medium was 0.5–5.0 μmol/L, and is significantly different between concentration and control (p ≤ 0.05 level). The average number of roots was 1 to 2.3 times greater than that of the control, and 0.5–3.0 μmol/L concentration of La(NO3)3 was better than the others (p ≤ 0.05 level).” The second statement is false.
    4. p. 279. In Table 1, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable.
    5. p. 280. Why are no statistical analyses provided to show differences between treatments in Figures 1 and 2?
    6. In all analyses, sample sizes are not indicated.
    7. In all analyses, it is not indicated whether error bars are SE or SD.
    8. It appears as if the study was not repeated, i.e., a single trial. No indication of replicates, sample sizes per treatment or repetitions.

    Paper 2
    1. The exact cultivar or variety was not described. Such experiments are always genotype-dependent.
    2. Experimental design, randomization and sampling not described.
    3. p. 187 (Table 1) and p. 189 (Tables 2 and 3). In all three Tables, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable. It appears as if the authors simply assigned the letter a to the table’s upper-most value and then simply pasted ensuing letters of the alphabet for other values in the table going down the table.
    4. Table 1 describes the number of explants as being 50. However, a description of the cultures on p. 186 indicates that 50 bottles were cultured for each treatment, and that each bottle contained 4 shoots each. The sample size should therefore be 200 in Table 1. Is 50 correct, or is it 200?
    5. Why are the rooting results in Table 1 of Paper 1 so radically different from the results reported in Table 1 of paper 2? This is the exact same plant, the exact same concentrations of La(NO3)3. Therefore, strictly speaking, there should be little variation. However, the data indicates extremely different results. The results of both studies are thus questionable.
    6. p. 188. If the authors claim that statistical analyses were conducted, then where are the analyses for Fig. 1?
    7. Why are the POD results reported in Table 3 totally different to the analyses also already conducted in Fig. 3 of Paper 1? Why are the units different? Completely different results and analyses when the exact same parameter (POD) and plant material are used invalidate both data sets.

    Paper 3
    1. p. 260 “We tried to find the best rooting concentration of Ce3+ and also did some research on the relationship between root growth and nitrogen metabolism. We hope that it will supply the theoretical basis and be a technological guide for the application of REEs in a wood plant cultured in vitro.” Poor grammar, typical of all three papers, and highly unscientific description of the hypotheses being tested.
    2. Peach variety not defined.
    3. Murashige and Skoog medium is claimed to be used, but the 1962 reference for Murashige and Skoog (Physiologia Plantarum) is not provided.
    4. Choice of concentrations tested inappropriate. After 5 μmol/L CeCl3, the next concentration was 50. This is incorrect. It should be 10.
    5. The authors claim that plant growth was assessed after 15 days in vitro. 15 days for hardwood species is hardly enough time for even root initials to form, let alone assess in vitro plant growth. The observation period is thus too short and thus conclusions based on it are unreliable or unrealistic.
    6. Statistical analyses not described.
    7. Experimental design, randomization and sampling not described.
    8. p. 261. In Table 1, the letters apparently signifying statistical differences between treatments are completely incorrect. Thus, which treatments are truly significantly different is totally unclear. The conclusions based on these incorrect analyses are thus not reliable.
    9. p. 262. Figure 1 stats analyses unclear, in some cases, covered, and the control treatment is missing.
    10. Figures 2-8 lack statistical analyses, thus the data sets are unreliable and inconclusive. Without statistical analyses, the authors cannot claim that treatment X is better or worse than treatment Y (at least not with any level of confidence).

    These questionable (incomplete, incorrect, inaccurate) statistical analyses may nullify the validity of the data set and thus all conclusions drawn by these three papers.

    A collective expression of concern was published for the three papers on January 10, 2014, but the expression of concern is not linked to the top page of the three manuscripts on SpringerLink. Consequently, the readership that accesses any of these three papers is unaware of the expression of concern. Springer and Prof. Schrauzer have been alerted to this point. The expression of concern was published here:
    http://link.springer.com/article/10.1007/s12011-013-9881-7
    DOI: 10.1007/s12011-013-9881-7 (this DOI cannot be linked to PubPeer)
    (http://download.springer.com/static/pdf/283/art%253A10.1007%252Fs12011-013-9881-7.pdf?auth66=1416982954_e0113e14befce561566c2d968c987df7&ext=.pdf) (open access)

    Funding:
    Paper 1: “This work was funded by a Person of Ability Recommended Foundation of Suzhou University (XQ316011).”
    Paper 2: “This work was supported by the Natural Science Fund of Jiangsu Province (no. BK2002501).”
    Paper 3: “This work was funded by the Natural Science Foundation of Jiangsu Provice (BK2002501).”

    Of note, Prof. Gerhard N. Schrauzer is now Editor-in-Chief Emeritus:
    http://www.springer.com/life+sciences/biochemistry+%26+biophysics/journal/12011
    It appears as if Prof. Schrauzer was the EIC for at least two decades, or at least associated with BTER for such a long period, including the period in which these three papers were published.

    Incidentally, there is an erratum within the same journal, for one of Prof. Schrauzer’s papers:
    Original:
    http://link.springer.com/article/10.1007/s12011-010-8608-2
    http://download.springer.com/static/pdf/415/art%253A10.1007%252Fs12011-010-8608-2.pdf?auth66=1416983999_00ac1df5f365cdf52e3114aaa7df1372&ext=.pdf
    DOI: 10.1007/s12011-010-8608-2
    Erratum:
    http://link.springer.com/article/10.1007/s12011-010-8811-1
    http://download.springer.com/static/pdf/310/art%253A10.1007%252Fs12011-010-8811-1.pdf?auth66=1416983962_ce09c2764487133334a77ae6a1f1ad09&ext=.pdf

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/07BBFCFFAC98395499B34DE77D3BF8#fb17161

  • Dendrobium query November 27, 2014 at 1:49 am

    Yifeng Xu, Hao Yu, Prakash P. Kumar (2010) Characterization of floral organ identity genes of the orchid Dendrobium crumenatum. Asia Pacific Journal for Molecular Biology and Biotechnology 18 (1) : 185-187
    Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543
    http://www.msmbb.org.my/apjmbb/html181/181cont.htm
    http://www.msmbb.org.my/apjmbb/html181/181ar.pdf (open access)
    No DOI.

    Yifeng Xu, Lai Lai Teo, Jing Zhou, Prakash P. Kumar, Hao Yu (2006) Floral organ identity genes in the orchid Dendrobium crumenatum. The Plant Journal, 46: 54–68.
    1 Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Science Drive 4, 117543 Singapore, and 2 Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
    http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02669.x/full
    http://www.ncbi.nlm.nih.gov/pubmed/16553895
    http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02669.x/pdf (open access)
    DOI: 10.1111/j.1365-313X.2006.02669.x

    2010 paper, Fig. 1ABCD identical to 2006 paper, Fig. 6abcd. The 2010 paper references the 2006 paper, but does not explicitly indicate that these four photos are taken from the 2006 paper, i.e., no attribution to the source. Both papers are considered to be original research papers.

    Funding:
    2006: “This work was supported by Research Grants R-154-000-232-101 and R-154-000-125-112 and PhD scholarships (to YX, LLT and JZ) from the National University of Singapore, and the intramural research funds from Temasek Life Sciences Laboratory.”
    2010: “This work was supported by Research Grants from the National University of Singapore.”

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/1B16E05C482DF6EEF2AFD3C3F18715#fb17213

  • Ipomoea query November 27, 2014 at 1:40 pm

    Original Article
    Anwesha M. Bhaduri, M. H. Fulekar (2012) Assessment of arbuscular mycorrhizal fungi on the phytoremediation potential of Ipomoea aquatica on cadmium uptake. 3 Biotech 2:193–198
    Environmental Biotechnology Laboratory, Department of Life Sciences, University of Mumbai, Santacruz (E), Mumbai, 400098, India
    Received: 14 November 2011; Accepted: 24 January 2012; Published online: 16 February 2012
    Publisher: Springer-Verlag
    DOI: 10.1007/s13205-012-0046-8
    http://link.springer.com/article/10.1007/s13205-012-0046-8/fulltext.html
    http://link.springer.com/article/10.1007%2Fs13205-012-0046-8
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433885/
    http://download.springer.com/static/pdf/94/art%253A10.1007%252Fs13205-012-0046-8.pdf?auth66=1417058799_4d0d93bc31ab79d4a9770b7a88ac9c13&ext=.pdf (open access)

    Concerns:
    1) The statistical analysis section states: “Significant differences of measured parameters between AMF, non-AMF were determined by one way ANOVA at p < 0.05 and p < 0.1.” (p. 194) The exact test used to assess significant differences between means, or what software was used to conduct such tests, is not indicated anywhere in the manuscript.
    2) The text states, in many places*, that statistically significant differences were observed, referring constantly to the figures. However, not a single figure shows any statistical analyses, or any indication of what treatments are significantly to which others.
    3) In one case (2 below), claims of significance are made without a shred of data.
    4) In case 3 below, this indicates that a broad claim is made characterizing the trend as being the same across all four enzymes tested (SOD, GPX, CAT, APX), although it is absolutely unclear from the graphs exactly which Cd treatments are significantly different to which other Cd treatments (Fig. 3).
    5) Page 197: “The results in (Fig. 4) clearly show that soil microorganisms played a major role in combating toxic effect of Cd.” Does Fig. 4 really show this?
    6) There is thus little confidence about the analyses, and considerable lack of clarity about the interpretation of the data, since the reader has simply no way of verifying the veracity of the claims.

    * Some examples:
    1) “Growth parameters in terms of total biomass, and root and shoot length were significantly (p<0.05), (p<0.1) affected by Cd concentration in both the conditions. In broad-spectrum AMF association exhibited higher growth in terms of fresh biomass, and root and shoot length (Fig. 2a, b).” (p. 195) Fig. 2a and 2b, however, only show relative percentage data.
    2) “Phosphorous showed a significant (p<0.05) amount in AMF plants as compared to non-AMF.” and “Phosphorous and potassium were significantly (p<0.05) high in AMF in all concentration as compared to non-AMF. Moreover, nitrogen content in plants was significantly (p<0.1) higher in AMF as compared non-AMF.” appear within the same paragraph (p. 196) Problem is that not a single graph, figure or table contain any data about P, K or N concentrations. So, are the authors referring to unpublished data, or did they forget, perhaps, to submit the respective graphs, tables or data with the manuscript to support these large claims?
    3) “Although variations of plant enzymes expressed similar relations in both the conditions, AMF showed significantly (p<0.05) higher enzyme activity than non-AMF with increasing concentrations (Fig. 3).” (p. 197) Unfortunately, the statement is unclear. Are the authors referring to SOD, GPX, CAT, APX? And to which concentrations of Cd? And relative to what? Are comparisons being made across treatments, of between AMF vs non-AMF for each treatment?

    Request:
    The authors should kindly provide the original data sets for verification, and also request the publisher to publish an erratum, or online supplement that shows clearly, in each figure, the statistical analyses.

    Note:
    “3 Biotech is supported by King Abdulaziz City for Science and Technology (KACST) in Saudi Arabia and is currently evaluated by Thomson Reuters editors for coverage in Web of Science.”
    http://www.springer.com/chemistry/biotechnology/journal/13205

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/C7148CDEBC1130EEBD5419B3ABB46A#fb17214 

  • Prof. Deepak Pental November 28, 2014 at 4:35 pm

    BREAKING NEWS:
    Professor Deepak Pental, 63, a “respected” plant geneticist, and the former Delhi University vice chancellor [1], was arrested on two charges, and has been jailed, without bail [2], although there are conflicing stories about the bail. The charges are:
    a) plagiarising a fellow professor’s work;
    b) theft of cobalt from a laboratory.

    [1] http://en.wikipedia.org/wiki/Deepak_Pental
    [2] http://www.ndtv.com/article/india/ex-delhi-university-vice-chancellor-deepak-pental-sent-to-tihar-jail-on-plagiarism-complaint-625613

    He has some very good papers which now merit closer examination following the accusations by the other professor, especially considering that he is active “real time”:
    Journal of Plant Biochemistry and Biotechnology November 2014
    Date: 13 Nov 2014
    Effective restoration of male-sterile (barnase) lines requires overlapping and higher levels of barstar expression: A multi-generation field analysis in Brassica juncea
    Naveen C. Bisht, Arun Jagannath, Rehna Augustine, Pradeep K. Burma, Vibha Gupta, Akshay K. Pradhan, Deepak Pental
    http://link.springer.com/article/10.1007/s13562-014-0289-z

    For example, was the stolen cobalt or any other stolen chemicals used in this paper or in any other research he published? Surely, the use of stolen chemicals should be subject to at least an expression of concern if not a downright retraction? Springer should be alerted.

    This story provides a bit more insight:
    http://timesofindia.indiatimes.com/City/Delhi/Delhi-court-gave-ex-DU-vice-chancellor-bail-yet-he-landed-in-jail/articleshow/45290356.cms
    “In 2009, Saradhi had filed the private complaint before a Delhi court under various sections of IPC, including forgery, criminal conspiracy and criminal breach of trust. Saradhi, who now teaches in DU’s Environmental Studies Centre, alleged Pental had plagiarised his work on genetically-modified Indian mustard, with the help of Prasad, then a research scholar. Saradhi had alleged that Prasad worked under him on his PhD thesis and went on to conduct research under Pental and, in connivance with Pental, the scholar took the seed of codA transgenic Indian mustard developed by Saradhi’s team under India-Japan Cooperate Science Programme. Pental allegedly allowed Prasad to show this work, carried in his lab during 2001-04, and the data of submitted by Saradhi’s team to the science and technology department.”

    This now suggests that a detailed post-publication peer review of his entire published literaure on Indian mustard, and other BRassica species, for example [3], need to be extremely closely examined:
    http://www.biomedcentral.com/content/pdf/1471-2164-14-463.pdf

  • Vitex negundo concerns December 1, 2014 at 4:28 am

    Paper 1:
    Naseem Ahmad, Mohammad Anis. 2007. Rapid clonal multiplication of a woody tree, Vitex negundo L. through axillary shoots proliferation. Agroforestry Systems 71(3), 195–200.
    Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, UP, India
    http://link.springer.com/article/10.1007%2Fs10457-007-9078-1
    DOI: 10.1007/s10457-007-9078-1 (PubPeer cannot read this DOI)
    Publisher: Springer Netherlands
    27 citations

    Paper 2:
    Naseem Ahmad, S. A. Wali, Mohammad Anis. 2008. In vitro production of true-to-type plants of Vitex negundo from nodal explants. The Journal of Horticultural Science and Biotechnology 83(3): 313-317.
    Publisher: The Invicta Press
    http://www.jhortscib.org/Vol83/83_3/index.htm
    http://www.jhortscib.org/Vol83/83_3/4.htm
    No DOI.

    Paper 3:
    Naseem Ahmad (1), Mohammad Anis (1,2). 2011. An efficient in vitro process for recurrent production of cloned plants of Vitex negundo L. European Journal of Forest Research 130(2): 135–144.
    1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, UP, 202 002, India
    2. Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
    http://link.springer.com/article/10.1007%2Fs10342-010-0415-y
    DOI: 10.1007/s10342-010-0415-y
    Publisher: Springer-Verlag
    13 citations.

    Concern 1: data duplication

    Table I Ahmad et al. 2008 BA and Kin regeneration frequency data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1A (table vs figure representation). = 13 data points identical
    Table 1 Ahmad et al. 2008 BA and Kin number of shoots per explant data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1B (table vs figure representation). = 13 data points identical
    Table 1 Ahmad et al. 2008 BA and Kin mean shoot length data for all 5 concentrations (0.1, 0.5, 1.0, 2.0 µM) identical to data in Ahmad and Anis 2011 Fig 1C (table vs figure representation). = 13 data points identical
    Total = 39 identical data points

    Table II Ahmad et al. 2008 BAxNAA regeneration frequency data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2A percentage response (table vs figure representation, parameter name changed). = 4 data points identical
    Table II Ahmad et al. 2008 BAxNAA number of shoots per explant data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2B mean number of shoot (table vs figure representation, parameter name changed). = 4 data points identical
    Table II Ahmad et al. 2008 BAxNAA mean shoot length data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 2C (table vs figure representation). = 4 data points identical
    Total = 12 identical data points

    Table II Ahmad et al. 2008 KinxNAA regeneration frequency data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3A percentage response (table vs figure representation, parameter name changed). = 4 data points identical
    Table II Ahmad et al. 2008 KinxNAA number of shoots per explant data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3B mean number of shoot (table vs figure representation, parameter name changed). = 4 data points identical
    Table II Ahmad et al. 2008 KinxNAA mean shoot length data for all 4 molar ratios (5:0.1, 5:0.5, 5:1.0, 5:2.0, µM) identical to data in Ahmad and Anis 2011 Fig 3C (table vs figure representation). = 4 data points identical
    Total = 12 identical data points

    Table III data Ahmad et al. 2008 (IBA and NAA), 4 concentrations each + control data identical to Table 1 data of Ahmad and Anis 2011 for three parameters: % Rooting, number of shoots/root (and Mean number of roots), mean root length.
    Total = 27 identical data points

    Grand total of 90 identical data points in Ahmad et al. 2008 and Ahmad and Anis 2011.

    Concern 2:
    “Few attempts for direct in vitro regeneration of Vitex negundo have been made earlier (Sahoo and Chand 1998; Chandramu et al. 2003b; Rani and Nair 2006; Ahmad and Anis 2007a).” Comment made in Ahmad and Anis 2011 EJFR p 136. But this comment is extremely misleading because the basal protocol for the 2011 paper was based almost exclusively on an identical protocol published in 2007. No other mention of the 2007 paper occurs throughout the whole manuscript.

    Concern 3:
    How can 2 µM IBA form 4.6 roots/shoot in Ahmad et al. 2008 but 4.6 at 200 µM IBA in Ahmad and Anis 2007? In other words, a 10-fold difference in concentration of the exact same auxin gives the exact same root number? Given the fluctuations shown in the values of this growth parameter caused by other concentrations of this same auxin, this result is simply impossible.

    These concerns would immediately cause doubt about the claims made in paper 4:
    Naseem Ahmad 1, Md Imran Khan 1, Sarfaraz Ahmed 2, Saad Bin Javed 1, Mohammad Faisal 3, Mohammad Anis 1, Sumbul Rehman 4, Syed Mohammad Umair 4. 2013. Change in total phenolic content and antibacterial activity in regenerants of Vitex negundo L. Acta Physiologiae Plantarum 35(3): 791–800.
    1. Plant Biotechnology Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, 202 002, India
    2. Natural Product Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh, 202 002, India
    3. Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
    4. Department of Ilmul Advia, Faculty of Unani Medicine, Aligarh Muslim University, Aligarh, 202 002, India
    http://link.springer.com/article/10.1007/s11738-012-1120-x
    DOI: 10.1007/s11738-012-1120-x (PubPeer cannot read this DOI)
    Publisher: Springer-Verlag

    Funding
    Paper 1: “The award of a Senior Research Fellowship to N A by the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, is greatly acknowledged. Research support from The Department of Science and Technology (Govt. of India) New Delhi under the FIST-DST Programme, is also acknowledged.”
    Paper 2: “Financial assistance, in the form of a Senior Research Fellowship to N. A. from the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, is gratefully acknowledged. We also acknowledge the Department of Science & Technology, (Government of India), New Delhi for rendering assistance to the Department under DST-FIST Programme 2005.”
    Paper 3: “N. Ahmad is thankful to the Department of Science and Technology (DST), Govt. of India, New Delhi, for its award of a SERC Fast Track Young Scientist Scheme (SR/FT/LS-014/2009). The authors acknowledge the Department of Science and Technology (DST) and the University Grants Commission (UGC), Govt. of India, New Delhi, for rendering assistance to the Department under DST-FIST (2005) and UGC-DRS (2009) programmes, respectively.”
    Paper 4: “The award of DST, Young Scientist (SR/FT/LS-014/2009) Scheme to Naseem Ahmad by the Department of Science and Technology (DST), Government of India, New Delhi, is greatly acknowledged. Research support from the Department of Science and Technology (Govt. of India) New Delhi under the DST-FIST (2011) and UGC-SAP (2009) Programme, is also acknowledged.”

    Incidentally, Prof. Mohammad Anis has been the subject of another large query regarding Egyptian Myrobalan Tree (Balanites aegyptiaca Del.) with 4 PubPeer entries:
    https://pubpeer.com/publications/62D5875E85F2922AC08EACE9862FBB#fb16868
    https://pubpeer.com/publications/9323C402F8E2469B36B285C3DC26FE#fb16878 
    https://pubpeer.com/publications/8089001C1AFA6E8AA4B6D868D68E78#fb16879 
    https://pubpeer.com/publications/B3EF31732E35DA552F0D786E90C375#fb16880 

    The authors, who have been contacted, are kindly requested to address these issues publically and to correct the literature.

    This case has a PubPeer entry for paper 3:
    https://pubpeer.com/publications/228844D355BBACF479209E2D15459E#fb17547

    • Vitex negundo concerns December 1, 2014 at 1:51 pm

      Erratum: Concern 3 should read 100-fold instead of 10-fold.

      • Vitex negundo concerns December 3, 2014 at 3:36 pm

        Update. A formal response has been received from the authors and AMU.

        Naseem Ahmad has responded to an anonymous request to comment on this case but do not understand the concept of anonymity. What the authors also do not appear to understand is that this is a public case that affects the entire plant science literature and all plant scientists, and may have wider consequences and repercussions on academic integrity in plant science journals. Rather than skirting the issue, surely it is best to address them publically at PubPeer as well as directly with the journals, journal editors and publishers? Public accountability for one’s research and publications is not a matter of negotiation, it is a matter of scientific responsibility.

        12/3/14 at 6:02 PM “Thanks for your mail dated 30.11.2014 on the subject of “data duplication” in our papers of Vitex negundo. I appreciate your concern about the issue of “data duplication”. As you are working for a noble cause, therefore it should be in a proper way. Comments were raised by an unregistered person on the public platform. Therefore, I request you please register yourself properly on this blog with your correct name, designation, affiliation, email, contact numbers and most importantly your area of expertise as it is most important for understanding the findings of the research. I assure you that I will answer each of your queries one by one on any public platform, if you comply.”

  • Of mice and maize December 3, 2014 at 4:32 am

    A startling development in maize genomic research. The story just broke at PubPeer:
    https://pubpeer.com/publications/89407FFD3DC7905BA81AA548B3FD1B#fb17718
    How does one confuse a rat with corn? This is astonishing. If Diego at PubPeer has intel, he should share. Also, he should indicate exactly which GenBank entries are being removed. How will this affect papers that used, relied on, or referenced those incorrect sequences? The authors are strongly encouraged to explain how mice were confused with maize.

    • herr doktor bimler December 3, 2014 at 6:07 pm

      Obviously a misspelling. Someone confused a rat with a maze.

  • Parthenium hysterophorus queries December 5, 2014 at 2:20 am

    3 Biotech July 2011, Volume 1, Issue 1, pp 1-9,
    Open Access. Date: 27 Apr 2011
    Harmful and beneficial aspects of Parthenium hysterophorus: an update
    Seema Patel
    Department of Biotechnology, Lovely Professional University, Jalandhar, 144402, Punjab, India
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339593/
    http://link.springer.com/journal/13205/1/1/page/1
    http://link.springer.com/article/10.1007/s13205-011-0007-7
    http://download.springer.com/static/pdf/779/art%253A10.1007%252Fs13205-011-0007-7.pdf?auth66=1417733929_94de5d29a6f9c08fe755facddb75451b&ext=.pdf
    DOI: 10.1007/s13205-011-0007-7
    Publisher: Springer-Verlag

    Concerns about the source of images used in this review.

    Acknowledgements: “The author acknowledges the internet website http://www.wikipedia.org/ for providing with the figures.” If any of the key-words for these images are entered into Wikipedia, these images do not appear. What then is the source. Some web-trawling revealed the following (already back in July, 2013).

    NONE OF THESE FIGURES, EITHER IN THE TEXT, FIGURE LEGENDS OR ANYWHERE WITHIN THE MANUSCRIPT, INDICATE ANY OF THE SOURCES THAT MAY BE THE ORIGINAL SOURCES OF THE FIGURES.

    Figure 1A of Parthenium hysterophorus from http://www.ecoport.org ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    Figure 1B: The world map. From the Weed Science Society of Pakistan (www.wssp.org.pk) ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    The styles of the chemical structures in Figure 2 are very different, some stretched, some perfect, some blurred. It is thus likely that the source is different and that the author did not use software like ChemDraw to design each compound. What then is the source(s) of these compound images?

    Figure 3A: photo of Zygogramma bicolorata from http://www.texasento.net ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    Figure 3B: photo of Epiblema strenuana appears to be taken from the Moth Photographer’s Group of the Mississippi Entomological Museum at MSU (http://mothphotographersgroup.msstate.edu/species.php?hodges=3172), then squashed. The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    Figure 3C: photo of Listronotus setosipennis from old.padil.gov.au ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    Figure 3D: photo of Carmenta ithacae from http://www.discoverlife.org ? The photo does not appear in Wikipedia, unlike what Dr. Patel claims.

    Other concerns:
    a) The entire first paragraph of the Introduction lists many facts, but not supported by a single reference.
    b) Is it usual for a journal to only accept reviews if the authors are not apparent professionals or specialists in their fields of study? The name of Dr. Patel cannot be found in the reference list. Is Dr. Patel qualified to write a review on this noxious weed?
    c) The review itself fails to address the literature accurately, making this review incomplete. Why were other reviews not referenced, or mentioned, and why did the “peer” reviewers and editors not detect this issue, as well as the image concerns during peer review? A review by the Australian Government in 2001 (http://www.daff.qld.gov.au/documents/Biosecurity_EnvironmentalPests/IPA-Parthenium-Nsplan.pdf) is also not mentioned. A review by Javaid, A. and T. Anjum (2005). Parthenium hysterophorus L. – a noxious alien weed. Pak. J. Weed Sci. Res. 11: 1-6 was not mentioned. A review by Javaid, A., S. Shafique and S. Shafique. (2006). Parthenium weed – an emerging threat to plant biodiversity in Pakistan. Int. J. Biol. Biotech. 3(3): 619-622 was not mentioned. A paper by Javaid, A., T. Anjum and R. Bajwa (2005). Biological control of Parthenium II: Allelopathic effect of Desmostachya bipinnata on distribution and early seedling growth of Parthenium hysterophorus L. Int. J. Biol. Biotech. 2: 459-463 was not mentioned. A review by VR Paudel in 2009 http://nepjol.info/index.php/BOTOR/article/viewFile/2915/2954 is not mentioned. A review by Ramamoorthy, K.; Radhamani, S.; Amanullah, M. M.; Subbian, P. (Biology and integrated management of congress grass (Parthenium hysterophorus L.) – a review.) Green Farming 2009 Vol. 2 No. 10 pp. 702-706 is also not referenced or mentioned. An important study in 2010 by Shreshtha et al was not referenced: http://www.forestrynepal.org/images/publications/2010_Shrestha%20et%20al_Fortuitous%20biocontrol%20of%20Parthenium.pdf.

    There is a PubPeer entry for this paper:
    https://pubpeer.com/publications/28076B5AAF504B0E3720D9F53BB159#fb17924

  • Kailash C. Bansal query December 6, 2014 at 8:10 pm

    Transgenic or GM crops has seen a fair bit of scandal and controversy in India. One of those as-yet unclarified scandals involves Dr. Kailash C Bansal, who is a Professor listed on the Scientific Advisory Committee at the National Institute of Plant Genome Research (NIPGR) [1].

    However, he is listed on this 2014 paper on transgenic chickpea as being at the National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India [2, 3]:
    Maneesha S. Saxena, Deepak Bajaj, Alice Kujur, Shouvik Das, Saurabh Badoni, Vinod Kumar, Mohar Singh, Kailash C. Bansal, Akhilesh K. Tyagi, Swarup K. Parida (2014) Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea. PLoS ONE 9(9): e107484. DOI: 10.1371/journal.pone.0107484

    These facts in themselves might not be newsworthy or even strange to the untrained eye. However, given the fact that two news stories emerged in 2012 of concern [4, 5], claiming the following: “The scientist, Dr Kailash C. Bansal, was given the prestigious Rafi Ahmed Kidwai Award for “outstanding research” in transgenic crops for the year 2007-2008 on the basis of claims that he had “filed three patents for novel gene discovery”, including one on transgenic brinjal. In reality, no such patent application or patent existed when he was given the award on July 16, 2009. Documents obtained under RTI and investigation made by Mail Today show that no patent application had been filed for brinjal discovery in October 2008 when Bansal was nominated for the award or in July 2009 when he was presented the award. Bansal holds top positions in the research hierarchy of the Indian Council of Agriculture Research (ICAR). When he got the Kidwai award he was a professor at the National Research Centre on Plant Biotechnology (NRCPB) and presided over ICAR’s transgenic research programme involving about 20 institutes all over the country and five-year budget exceeding Rs.135 core. Top brass in ICAR have not only ignored the patent goof-up but has also rewarded Bansal by making him director of India’s plant gene bank, officially known as National Bureau of Plant Genetic Resources.”

    This then makes the listing in the PLOS ONE paper of great significance because apparently an unresolved and serious issue that led to his rise to the director of that institute, and which also allowed him to obtain a prestigious science prize, remains unresolved. Is this then not a serious conflict of interest that was not disclosed to PLOS ONE when the paper was published? This is somewhat odd, given the fact that the PLOS ONE paper states, under competing interests: “The authors have declared that no competing interests exist.”

    A very recent chapter on the topic of the controversy, transgenic brinjal (British for eggplant, or Solanum melongena L.), was published in a Springer Science + Business Medium book [6]:
    Chloroplast Biotechnology Methods in Molecular Biology Volume 1132, 2014, pp 305-316
    Date: 03 Feb 2014; DOI: 10.1007/978-1-62703-995-6_19
    Plastid Transformation in Eggplant
    Kailash C. Bansal, Ajay K. Singh
    In this paper, Dr. Bansal lists himself as being at the National Bureau of Plant Genetic Resources (ICAR), New Delhi, India.

    This is odd. Why does Dr. Bansal list two very different institutional addresses for two different papers published at almost the exact same time? There are three possibilities here:
    a) He works at both, but failed to disclose the second working position in both papers, which would constitute an important omission of information, or of a COI.
    b) He only works at one, but has used another address inappropriately.
    c) None of the above two.

    In that chapter, a reference to a 2010 paper [7] might lead to clues on the genetic brinjal the story is referring to:
    Singh A, Verma SS, Bansal KC (2010) Plastid transformation in eggplant (Solanum melongena L.). Transgenic Res 19:113–119:
    Strangely, there is no mention of a patent in either paper.
    At that time, Dr. Bansal was listed as being at the National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India.

    To complicate the case a notch further, the news paper stories [4, 5] state, referring to Dr. Bansal: “His boss in ICAR, Dr Swapan K. Datta, also echoed the same line, “ICAR has taken official response on this matter. Dr Bansal is still working within ICAR”. He did not reply when asked specifically what the official stand of the council was.”

    Dr. Datta, Dr. Bansal’s boss, is a member of the editor board of Taylor and Francis’ GM Crops and Food.

    Despite wide-spread calls for the resignation of Dr. Bansal [9], he appears to retain his position (as the head?) at NBPGR. That decision appears to have been heavily influenced by politics, as the article indicates: “Stressing on the need to introduce GM crops, the Centre has said it would not be able to meet the First Millennium Development Goal of cutting the proportion of hungry people by half with such technologies. A moratorium of 10 years would put the country 20 years back in scientific research, it added.”

    It would be important to get a full clarification of this case since there has been a burst of papers in 2014 with Dr. Bansal as co-author, thus any unresolved issues could have an influence on a wide range of individuals.

    [1] http://www.nipgr.res.in/about_us/committees.php#governing
    [2] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107484
    [3] http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0107484&representation=PDF
    Received May 1, 2014; Accepted August 11, 2014; Published September 15, 2014
    [4] http://indiatoday.intoday.in/story/genetically-modified-food-crops-researcher-kailash-c-bansal-grabbed-rafi-ahmed-kidwai-award-for-patent-claim/1/226654.html
    [5] http://www.dailymail.co.uk/indiahome/indianews/article-2224489/Top-GM-food-scientist-false-patent-claim.html
    [6] http://link.springer.com/protocol/10.1007/978-1-62703-995-6_19
    [7] http://link.springer.com/article/10.1007%2Fs11248-009-9290-z
    [8] http://indiatoday.intoday.in/story/association-of-scientists-activists-and-farmers-demand-removal-of-top-gm-researcher/1/228522.html

  • Cymbidium CryoLetters concern December 8, 2014 at 3:21 pm

    Concerns about this paper were linked on PubPeer to other papers of concern by Prof. Pramod Tandon, because this paper does not have a DOI:
    https://pubpeer.com/publications/8448D8CF8D1F69936CDC1A35D9BBCC
    https://pubpeer.com/publications/1CE3174266AF780AD6AB8EC0ABADE1
    https://pubpeer.com/publications/C7D8632E7ED6D6F852A93D9A516A49

    It should be noted that Prof. Tandon has still not come forward with a suitable public explanation for these concerns in his publications, and we would hope that he will address the concerns about his Dendrobium and Cymbidium papers. He is also called upon to release the original data-sets and statistical analyses that correspond to this Cymbidium paper.

    Gogoi K, Kumaria S, Tandon P (2012) A comparative study of vitrification and encapsulation-vitrification for cryopreservation of protocorms of Cymbidium eburneum L., a threatened and vulnerable orchid of India. CryoLetters 33:443–452.
    http://www.cryoletters.org/Abstracts/vol__33_6_2012.htm
    http://www.cryoletters.org/Abstracts/vol__33_6_2012.htm#443
    Plant Biotechnology Laboratory, Department of Botany, North-Eastern Hill University, Shillong 793 022, India.
    Funding: UPE–Biosciences programme, University Grants Commission, New Delhi, India

    There is concern about this manuscript published in CryoLetters in 2012. An anonymous report was made to the senior management of the company that publishes this journal, CryoLetters LLP, and approximately half a dozen editors of the editor board. That report was submitted on the 9th August, 2013. More than one year later, not a single note, erratum, expression of concern, or retraction appears which itself is of concern. These issues affect the plant science community and thus deserve to be discussed openly, in public, since the authors and the publisher, and its editors, are not forthcoming. PubPeer has thus been selected for this purpose.

    Concerns involve primarily incomplete experimental design, and incorrect of flawed statistical analyses:
    a) The first sentence of the Introduction makes factual claims but is not supported by any literature.
    b) Characterization of a plant should never be made in the title (i.e., the threatened and vulnerable status).
    c) “Due to loss of habitats and heavy anthropogenic pressure for commercial purposes, the species is on the verge of extinction. According to the Red Data Book of Plants of India, C. eburneum is regarded as vulnerable and hence this urgently calls for its conservation (25).” Verge of extinction and vulnerable are completely different concepts in conservation, and are very distant from each other in terms of how close a species is to extinction. Was the former claim made by the authors to exaggerate the status of the plant and maximize the chance of acceptance?
    d) “Ex situ conservation of endangered and threatened plants through in vitro cultured plants also requires high maintenance costs and there is a risk of somaclonal variation and genetic instability, due to continuous subculturing of the in vitro raised plantlets.” Claims are made but no literature support is provided.
    e) “Encapsulation-vitrification is a combination of both vitrification and encapsulation-dehydration methods. For encapsulation-vitrification, explants are encapsulated in alginate beads and then submitted to highly concentrated vitrification solutions. Encapsulation-vitrification combines advantages of these two techniques, the rapidity of implementation for vitrification and the ease of manipulation of explants for encapsulation.” Claims are made but no literature support is provided.
    f) Materials and Methods, Plant material: Why are protocorms used? Protocorms are seed-derived and thus are not clonal material. Therefore, the use of this tissue is inherently flawed in that variation caused by seed-derived material (i.e., protocorms) may also influence the response to treatments and thus the quantitative outcome of data. The idea material that should have been used would have been clonal protocorm-like bodies (PLBs) derived from protocorms. The use of clonal PLBs would have eliminated the inherent variation caused by the biological material.
    g) Materials and Methods, Plant material: “agar-gelled Murashige and Skoog medium”. The concentration of agar and the commercial source are not clearly indicated. How can this step be repeated?
    h) Materials and Methods, Plant material: “were used for cryopreservation experiments (Fig. 5 A-B).” Why is Figure 5 mentioned first in the text and not Figure 1?
    i) Materials and Methods, Plant material: The authors fail to describe the following about the plant material: a) the source of the seeds (commercial or wild) and if the protocorms are of the same size (size in fact not defined, only the age); b) if wild plants, the exact location from which plants were collected and permission from Indian authorities with license numbers to collect red-listed rare orchid plants from the wild; c) the growth conditions of the protocorms during asymbiotic seed germination are totally ignored, including temperature, light vs dark, relative humidity. Is the reader supposed to guess the conditions? How are other scientists supposed to repeat this protocol?
    j) Materials and Methods, Cryopreservation procedure: A) “12 h light/12 h dark photoperiod” is incorrect, it should be a 12-h photoperiod (the use of the words light and dark and photoperiod make the words light and dark redundant). Exact same problem in the next section of the M&M. B) “60 µmol m-2 s-1 light intensity” is incorrect. Light intensity would be in lux. µmol m-2 s-1 refers to photosynthetic photon flux density or PPFD. C) The city and country of the cryovials maker is not indicated. D) The authors fail to disclose the commercial source of any of their equipment and chemicals (which is an important aspect for these companies). E) Why is DMSO abbreviation defined if it is not used again? F) “different time periods (5 – 60 min)”. This information is useless. The exact time period tested should have been indicated. G) “different concentrations of sucrose (0.0 – 0.7 M)” . This information is useless. The exact sucrose concentrations tested should have been indicated.
    k) Materials and Methods, Protocorm survival and plant regeneration: A) “Petri plates”. The correct term is Petri dishes. The size, diameter and depth as well as the maker are not defined. B) “provided by cool fluorescent tubes”. The maker of the light bulbs, the strength of the bulbs in Watts, and the distance from cultures have all been omitted. These are all important aspects of tissue culture that can affect the effectiveness of the culture. C) “after 8 weeks in culture” unclear whether this is over and above the previous 6 weeks in culture, so in fact, 14 weeks after the beginning of culture. These ambiguities do not make this protocol repeatable.
    l) Materials and Methods, Statistical analyses: A) The randomness or design of the experiment were not indicated. B) “Statistical analysis was done by ANOVA at P<0.05 and the means compared using Tukey’s test” There are two serious inaccuracies and incorrect description of the statistics. ANOVA is not a statistical test. ANOVA is used merely to separate the means. Tukey’s test does not exist. It is Tukey’s multiple range test. Where is the reference for the test? C) “PC version Origin 7.0 Northampton, MA, USA).” Something sounds extremely wrong here. It sounds as if the authors are actually describing Windows version 2007, but have represented it incorrectly as if it were a statistical software. What is the name of the statistical software? Who is the manufacturer of this software? This information is absolutely unclear. If statistical analyses are described so incorrectly/inaccurately, what confidence is there that the analyses are actually accurate? The answer may lie in the next three points.
    m) Results: Fig 1. For Vit treatments, the stats analyses appear to be sound (i.e. highest value represented with a, lowest by b), but when we observe the E-V treatments, the statistical analyses are completely incorrect. The highest value is represented by c, the intermediate value by a, and the lowest value by c. The statistical analysis is completely wrong. Therefore, any conclusion made in the text based on these statistical analyses is by association debatable. The first incorrect claim comes in this statement “When using the vitrification technique, the lower sucrose concentrations (0.1 – 0.3 M) employed during preculture led to higher regeneration of non-cryopreserved protocorms, with an optimum of 60% for 0.2 M sucrose (Fig. 1). Higher sucrose concentrations (0.4 – 0.8 M) produced lower regeneration percentages, between 34 and 20%.” In fact, the 0.3 M sucrose treatment is significantly similar to 0.1 and 0.2 and also to 0.4-0.8. That is why it is represented by the letters ab. The comment made is incorrect and thus misleading. The next statement is even more serious: “By contrast, with the encapsulation-vitrification technique, higher sucrose concentrations (0.7 – 0.8 M) in the preculture medium gave higher regeneration, with an optimum of 70% for 0.7 M sucrose. Lower sucrose concentrations (0.1 – 0.5 M) produced lower regeneration, between 20 and 34%. Intermediate regeneration (54 %) was achieved after preculture with 0.6 M sucrose.” This entire conclusion is totally invalid since the statistical analyses are incorrect, the representation of the statistical analyses is incorrect, and thus any conclusions drawn from incorrect statistics are also automatically incorrect.
    n) Results: Fig 1. On the Y-axis, the parameter measured is regeneration. What exactly is regeneration? Is it callus formation? PLB production? Protocorm growth? Leaf formation? Plantlet growth? The term is so broad that it makes the parameter being measured totally redundant. The entire figure and what it actually teaches the reader is useless because “regeneration” is not defined.
    o) Results: Fig 2 and 4. The statistics representation and/or analyses of both vitrification and E-V are completely incorrect with exactly the same problems as listed in m) for the E-V statistics. Consequently, all text in the results related to this figure is invalid.
    p) Results: Fig 2, 3, 4. The same problem related to the term Regeneration (%) on the Y-axis as found for Fig. 1 exists (see n) above).
    q) Results: Fig 1, 2, 3 and 4 legends. “Means followed by the same letter are not significantly different according to Tukeys’s test”. In fact, an extremely important aspect has been omitted from this description: the fact that analyses were not conducted across treatments. Therefore, the correct way in which the figure legends should have read would have been: Means followed by the same letter within each treatment are not significantly different according to Tukey’s multiple range test. Within each treatment refers to vitrification and encapsulation-vitrification. Incidentally, it should be Tukey’s and not Tukeys’s.
    r) Discussion: this section was not analysed since it lost its value in the light of the incorrect statistical analyses of the Results section. However, several very important key orchid cryopreservation studies were omitted.
    s) Conclusions: “This is the first report for long-term conservation of protocorms of” This is a false statement. The M&M section clearly states the storage period “These cryocanes were rapidly dipped in a 35 1 narrow neck liquid nitrogen (LN) storage Dewar-flask and stored at -196°C for 1 h.” 1 hour is NOT long-term.

    These errors and oversight then also call into question the quality of the peer review at CryoLetters.

    Why has no erratum, expression of concern or retraction not appeared on the CryoLetters web-site to alert readers?

  • Welbaum and Tay query December 8, 2014 at 9:26 pm

    AH paper
    Mweetwa, A.M., Welbaum, G.E. and Tay, D. 2008. A PRELIMINARY INVESTIGATION ON THE EFFECT OF SEED PHYSIOLOGICAL STAGE, CONCENTRATION AND DURATION OF EXPOSURE TO CALCIUM HYPOCHLORITE ON IN VITRO GERMINABILITY AND SEEDLING DEVELOPMENT OF PHALAENOPSIS AMABILIS ORCHIDS. Acta Hort. (ISHS) 782:99-106.
    http://www.actahort.org/books/782/782_9.htm
    No DOI.
    Copyright holder: International Society for Horticultural Science
    No received, revised or publication dates.
    Financial support: J. Harper and the Mid-American Orchid Congress

    SH paper
    Scientia Horticulturae Volume 117, Issue 3, 23 July 2008, Pages 257–262
    Effects of development, temperature, and calcium hypochlorite treatment on in vitro germinability of Phalaenopsis seeds
    A.M. Mweetwa, Gregory E. Welbaum, David Tay
    Mweetwa, Welbaum: Department of Horticulture, Saunders Hall Virginia Tech, Blacksburg, VA 24061, USA
    Tay: USDA-ARS, Ornamental Plant Germplasm Center, 670 Tharp Street, The Ohio State University, Columbus, OH 43210, USA
    http://www.sciencedirect.com/science/article/pii/S0304423808001015
    DOI: 10.1016/j.scienta.2008.03.035
    Copyright holder: Elsevier Ltd.
    Received 17 August 2007; Received in revised form 21 March 2008; Accepted 27 March 2008
    Financial support: J. Harper and the Mid-American Orchid Congress

    The following is duplicated:
    A) Large tracts of text, for example the first few paragraphs of the introduction and most of the methodology, in both manuscripts.
    B) Table 1 of both papers is identical.
    C) Fig. 1 of both papers is identical.
    D) Fig. 2 of both papers is identical.
    E) Fig. 3 of AH is identical to Fig. 5 of SH.
    F) Fig. 4 of AH is identical to Fig. 6 of SH.
    G) Neither paper references the other nor indicates the existence of the other.

    There is a PubPeer entry associated with this case:
    https://pubpeer.com/publications/CA87E4627D35A037995FC65384B8E2#fb18138

  • ISHS query December 9, 2014 at 5:10 am

    Professor Pierre Debergh, University of Gent, Belgium
    https://biblio.ugent.be/person/801000185165
    Now deceased following communications with the University of Ghent since October 24, 2013.

    The author is thus not available for comment, nor can his co-authors be tracked. The academic responsibility for this paper thus should lie squarely on the shoulders of the International Society for Horticultural Science (ISHS).

    Hamidah et al. (1995, 1997a, 1997b). The Hamidah et al. (1997a) paper describes a protocol for the induction of somatic embryos from leaves of A. scherzerianum. The authors determine that 18 µM 2,4-dichlorophenoxyacetic acid and a high sucrose concentration (6%) are the ideal conditions. However, 6% is not tested in the protocol and in fact, the ideal carbohydrate concentration is not clear, although in Hamidah et al. (1997b), the authors claim it to be 2% sucrose + 4% fructose, which corresponds to medium B in Table 1 of Hamidah et al. (1997a). It is unclear why so many PGR combinations in Table 1 were only tested on medium A, and not medium B or C, and it is not clear why the authors made this statement on p. 190: “Medium A was used in the beginning; based on literature review and preliminary experiments (not presented)”. A search of the literature in fact reveals that the Hamidah et al. (1995) paper already reported the data of the 1997a paper. Thus, the 1997a paper is a partial data duplication of the 1995 paper. The 1997b paper has no data, no figures and reports the exact same conclusions about the results as the 1995 and 1997a papers, making it a duplicate and a redundant paper in the anthurium literature. The 1997b paper only has two pages, with absolutely no figures to prove somatic embryogenesis or secondary somatic embryogenesis, and no data or tables to prove absolutely any claims made in the text regarding somatic embryogenesis, secondary somatic embryogenesis or in vitro regeneration. In the 1997b paper, the authors claim to use media that are original, but which are not since the exact same parameters and ideal medium concentrations, related to basal medium, the level of 2,4-D and the very specific concentration of 4% sucrose and 2% glucose are not original ideas, the latter having already been devised by Kuehnle et al. (1992) while the ideal method was simultaneously reported in Hamidah et al. (1997a; PCTOC; M&M section + p. 193).

    References:

    Hamidah M, Abdul Karim AG, Debergh PC (1995) Somatic embryogenesis of Anthurium scherzerianum Schott. Med. Fac. Landbouw, Univ. Ghent 60/4a: 1671–1673

    Hamidah Musa (1), Abdul Ghani Abdul Karim (2), Pierre Debergh (1) (1997a) Somatic embryogenesis and plant regeneration in Anthurium scherzerianum. Plant Cell, Tissue and Organ Culture 48: 189–193.
    1. Dept. Plant Production – Horticulture, University Gent, Coupure Links 653, B9000, Gent, Belgium
    2. Dept. Botany, Faculty of life Sciences, National University of Malaysia, 43600, Bangi, Selangor, Malaysia
    Received 12 June 1995; accepted in revised form 14 March 1997.
    http://link.springer.com/article/10.1023%2FA%3A1005834131478
    DOI: 10.1023/A:1005834131478
    Publisher: Kluwer Academic Publishers
    Copyright holder: Springer Science + Business Medium

    Hamidah, M., Debergh, P., Ghani, A. and Karim, A. 1997b. CYCLIC SOMATIC EMBRYOGENESIS OF ANTHURIUM SCHERZERIANUM SCHOTT. Acta Hort. (ISHS) 447:123-124
    http://www.actahort.org/books/447/447_15.htm
    No DOI, and is thus linked to the 1997a paper by the authors on PubPeer.

    Kuehnle AR, Chen F & Sugii N (1992) Somatic embryogenesis and plant regeneration in Anthurium andraeanum hybrids. Plant Cell Rep. 11: 438–442

    The Acta Horticulturae instructions for authors (http://www.ishs.org/authors) clearly states that “Submission of a manuscript implies: that the work described has not been published before” and “Important elements of the publisher’s role in the scientific communication process are reviewing, recognition and consistent quality assurance.” Online http://www.ishs.org/publications, it is stated that “Acta Horticulturae (ISSN 0567-7572) is a peer reviewed series”. Finally, on the Q&A page, in response to the question “Is Acta Horticulturae a sound peer reviewed journal?” http://www.ishs.org/faq/acta-horticulturae-sound-peer-reviewed-journal, the ISHS states the following: “Acta Horticulturae exclusively contains research which has been presented at an ISHS symposium or at the ISHS Congress”. “Final contributions are submitted by the Editor(s) to the Editorial Board for scientific review.” “Each symposium has an Editorial Board. The Editorial Board includes the most eminent researchers in that particular field of research and this to guarantee a consistent quality of the scientific review process.” “Acta Horticulturae is a sound scientifically reviewed proceedings series.”

    The two editors of this volume of Acta Horticulturae (http://www.actahort.org/books/447/index.htm), Prof. Arie Altman, and Prof. Meira Ziv, the management of the ISHS, as well as the University of Gent have yet to correct the literature, even 14 months after a formal report.

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/773785209C305926E01A2F28265C3F#fb18158

  • Cymbidium stealth retraction December 10, 2014 at 12:22 pm

    The original
    Naruemol Kaewjampa, Kazuhiko Shimasaki, Syeda Jabun Nahar (June, 2012) Hyaluronic Acid Can be a New Plant Growth Regulator for Hybrid Cymbidium Micropropagation. Plant Tissue Culture and Biotechnology 22(1): 59-64
    The United Graduate School of Agriculutral Sciences, Ehime Unversity, 3‐5‐7 Tarumi, Matsuyama, Ehime, 790‐8556 Japan
    DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11261
    http://www.banglajol.info/index.php/PTCB/article/view/11261
    http://www.baptcb.org/ptc/Full_article/ptc22_1_07.pdf (open access)

    The duplicate
    Full Length Research Paper (was open access)
    Naremol Kaewjampa 1, Kazuhiko Shimasaki 2, Nahar Syeda Jabun 1 (2013) Hyaluronic acid can be an alternative plant growth regulator for hybrid Cymbidium micropropagation. African Journal of Agricultural Research Vol. 8(28), pp. 3731-3734
    1The United Graduate School of Agriculutral Sciences, Ehime Unversity, 3-5-7 Tarumi, Matsuyama, Ehime,
    790-8556 Japan.
    2Faculty of Agricuture, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502 Japan.
    DOI: 10.5897/AJAR12.564
    ISSN 1991-637X ©2013 Academic Journals*
    http://www.academicjournals.org/AJAR
    Accepted 24 July, 2013
    The original site where the paper existed:
    http://www.academicjournals.org/journal/AJAR/edition/26_July,_2013

    The duplicate paper was retracted, and not a trace can be found either on the publisher’s web-site, the journal web-site or on any Google or other internet search engines. In other words, a stealth retraction.

    *Incidentally, the duplicated paper was published by Academic Journals, a publisher listed on Beall’s list of predatory open access journals:
    http://scholarlyoa.com/publishers/

    This case has a PubPeer entry:
    https://pubpeer.com/publications/8F0B31D4CDD2BF8EFB531CB41536B7#fb18279

    The authors have another paper with concerns listed at PubPeer:
    https://pubpeer.com/publications/44D816438CDBCF351D11B405B824BE#fb17832

  • Anthurium query December 11, 2014 at 12:33 am

    Beyramizade and Azadi (2008) vs Beyramizade et al. (2008) (Iran and Japan).
    1) Duplicate figure (Fig. 1A of the latter paper the same as top right figure on page 184 of the former paper) and methodology (i.e., response of leaves to 2,4-D and BA, and callus and shoot regeneration potential). There is no statement that indicates that the same figure was used, or due attribution.
    2) Strangely, different results are presented despite the exact same cultivar and methodology. What does this suggest: an irreproducible protocol, or worse?
    3) In the latter study, authors claim somatic embryogenesis but show absolutely no proof of somatic embryos through scanning electron microscopy, cross sections showing leaf and root tissue connectivity, only some embryo-like structures, at best (Fig. 2B).
    4) “Leaf plate explants” used. What are these?
    5) No financial assistance was acknowledged in either paper.

    Beyramizade E, Azadi P. Effect of growth regulators on shoot formation of Anthurium andraeanum Lind. Pajouhesh & Sazandegi 2008;76:179-184. (in Farsi with English abstract)
    Department of Biotechnology, National Research Center of Ornamental Plants, Mahallat, Iran
    http://en.journals.sid.ir/ViewPaper.aspx?ID=119133

    Beyramizade E, Azadi P, Mii M. Optimization of factors affecting organogenesis and somatic embryogenesis of Anthurium andraeanum Lind. Tera. Propag Ornament Plant 2008;8:198-203.
    Masahiro Mii: Laboratory of Plant Cell Technology, Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo City, Chiba 271-8510, Japan
    http://www.journal-pop.org/2008_8_4_198-203.html
    http://journal-pop.org/References/Vol_8_4(198-203).pdf

    About Mii:
    http://www.researchgate.net/profile/Masahiro_Mii
    http://academic.research.microsoft.com/Author/27549444/masahiro-mii
    A legend of sorts: http://ajw.asahi.com/article/behind_news/social_affairs/AJ201203220005

    About Azadi:
    Azadi is the Director General of National Institute of Ornamental Plants (NIOP), Mahallat, Iran, and also the President of Iranian society for ornamental plants (ISOP) (www.isop.ir):
    http://www.isopcongress.ir/Files/CurriculumVitaeAzadi2014.pdf

    Azadi and Mii have been the topic of potential figure duplication at PubPeer (without any public responses, or correction of the literature):
    https://pubpeer.com/publications/B3161A9A5157B83F1A08506CD22966#fb16666
    https://pubpeer.com/publications/5740E043753A1CEC14D4494FD2EAA8#fb16667

    Listed at PubPeer, together with another query about the same authors:
    https://pubpeer.com/publications/5740E043753A1CEC14D4494FD2EAA8#fb18313

  • Clerodendrum indicum query December 11, 2014 at 12:40 am

    Anindita Mukherjee (a), Abhijit Bandyopadhyay (a), Sikha Dutta (a), Sukalyan Basu (b) (2013) Phytoaccumulation of iron by callus tissue of Clerodendrum indicum (L), Chemistry and Ecology, 29:6, 564-571.
    DOI: 10.1080/02757540.2013.779681
    a) Department of Botany, The University of Burdwan, Burdwan 713104, India
    b) Department of Chemistry, The University of Burdwan, Burdwan 713104, India
    Received 9 April 2012; final version received 21 February 2013
    http://www.tandfonline.com/doi/full/10.1080/02757540.2013.779681#.VIkozJVxnIU
    http://www.tandfonline.com/doi/pdf/10.1080/02757540.2013.779681 (open access)

    The authors, in their 2013 paper published in Chemistry and Ecology (Taylor and Francis), report on a methodology in sections 2-1 through to 2.3, on the callus induction of Clerodendrum indicum. However, that methodology is not original, and was already published, by the same group of authors, in 2012, as follows.

    Anindita Mukherjee, Sikha Dutta, Abhijit Bandyopadhyay (2012) Micropropagation of Clerodendrum indicum (L.)Kuntze: An Unexplored Medicinal Plant. International Journal of Pharma and Bio Sciences Oct; 3(4): (B) 659-668 (paper No. 74, open access)
    http://www.ijpbs.net/archive-issue.php?issueid=20 (click on Biological Science)
    No DOI.

    The authors fail to reference those important results and source of methodology from manuscript published in 2012. The text and the reference also fail to indicate the existence of this prior publication. This is a very important, and serious, omission.

    Could the authors, editors, and publisher kindly take the necessary steps to correct the literature so that this very important information is indicated (e.g., an erratum).

    Incidentally, the 2012 journal is listed as a “predatory” stand-alone journal by Jeffrey Beall:
    http://scholarlyoa.com/individual-journals/

    There is a PubPeer entry for this case:
    https://pubpeer.com/publications/9260619E6F61AA7D51ED7D0231C2BE#fb18324

  • Jaime A. Teixeira da Silva December 11, 2014 at 2:04 pm

    Given the clear extent of wide-ranging problems in the plant science literature, I wish to make a public call for ALL editors-in-chief (representing therefore the communal voice of ALL editors on that board) of all plant science journals, particularly those that carry an impact factor (and even those that do not carry one), especially from the main STM publishers, including Elsevier, Springer Science + Business Media (including BioMed Central), Wiley, Taylor and Francis (including the Routledge group), McMillan Publishers (including the Nature Publishing Group), Oxford University Press, and all publishers listed here (http://journalseek.net/publishers.htm), as well as all COPE-paying publishers, and ICMJE-enforcing publishers, to make a voluntary public commitment to editorial quality and editor ethics, as defined by the UNCC, and to post such a declaration publically on their web-pages.

    This will go a very long way to ensure editor accountability, openness in manuscript processing, transparency when there are publisher- and editor-related issues. It will ensure, ultimately, that editors are held up to the exact same standards that authors are held up to, in a fair, equal, unbiased and equally scrutinous way.

    https://editorethics.uncc.edu/editor-ethics-2-0-code/ (Dec 2014) (verbatim quotation)

    “Ethical Practices of Journal Editors: Voluntary Code of Conduct
    I __________as an Editor or Associate Editor of____________, already bound by the ethical standards of my respective journal(s), professional association(s), and discipline, affirm [as an individual and not on behalf of my journal(s) or sponsoring association] the importance of the following practices:
    Article I. Refraining from coercive citation practices, inappropriate citation inflation practices, and citation cartels (whereby editors link together and encourage authors to cite work published in the journals with whom they have partnered).
    In both public submission guidelines, and well as within the peer review process, authors will be encouraged to omit citations that are irrelevant to a paper’s main thesis. Specifically, I will refrain from encouraging authors to cite my journal, or those of my colleagues, unless the papers suggested are pertinent to specific issues raised within the context of the review. In other words, it should never be a requirement to cite papers from a particular journal unless the work is directly relevant and germane to the scientific conversation of the paper itself. I acknowledge that any blanket request to cite a particular journal, as well as the suggestion of citations without a clear explanation of how the additions address a specific gap in the paper, is coercive and unethical.
    I will monitor for, refrain from, and discourage the practice of citation cartels, reviewer/action editor self-serving citation advisement, and editorial regimes and partnerships. As for the latter, this could include serving as a guest editor (or having one of my associate editors serve in this capacity) of another journal with the intent of using it as a mechanism to cite articles from one’s principal journal.
    As an editor, I recognize that metrics such as impact factors are one of many imperfect methods of measuring the impact of published papers, and will not engage in efforts to game or influence these calculations (such as those listed above). I also recognize that, although all journals are entitled to aspire to certain acceptance rate levels and determine their own threshold for what is acceptable work to be published, journals should not artificially reduce the number of papers accepted so as to increase the probability of creating a more favorable impact factor.
    I will also consider the ethical implications of how editorial material is presented, and ensure that the use of editorials or the citations therein are in no way used to game citation counts or impact factor computations.
    Article II. Promotion of ethical research practices.
    In recognizing the global dialog regarding data fraud, research integrity, and implicit pressures on authors to manipulate findings, hide results, etc., I will, whenever possible and appropriate given the scope of my journal, encourage:
    1. data transparency including identifying potential conflicts of interest
    2. the citing of archival data sources properly, and for one-off data collections, revealing to action editors the full set of variables (if reasonable) and other papers emerging from the data sample under review (or for larger-scale investigations, involving publicly available, representative datasets, providing adequate context with which to assess the unique contribution of the reported study).
    3. the reporting (and publishing) of theoretically/methodologically relevant null results
    4. substantive and important replication efforts and the use of both (quality) inductive and deductive research.
    5. the refraining from opportunistic post-hoc hypothesizing under the guise of deductive research.
    6. compliance to journal policy, and discipline-specific ethical standards surrounding data sharing, data retention (to permit colleagues to verify results), and the reporting of results.
    7. careful monitoring for plagiarism, self-plagiarism, and the re-submission of papers rejected by previous editorial teams.
    Article III. Fairness to authors.
    I will encourage:
    1. the providing of clear feedback to authors about what is required to make a paper publishable.
    2. the keeping of commitments made in decision letters.
    3. the keeping of the revision process timely and/or not overly cumbersome or unduly prolonged.
    4. the holding of action editors and reviewers accountable to a high level of due diligence. I recognize that reviewers are expected to prepare high quality reviews that may require additional work beyond reading the manuscript, and that they should not review papers for which they are unqualified. I will monitor review quality and consider returning poor quality reviews, providing such reviewers feedback and/or flagging poor reviewers in the reviewer database. I also recognize that editors and reviewers have an obligation to justify, with relevant citations as appropriate, any recommendations for substantial change in the substantive focus or analytic methods of a paper.
    5. the timely dissemination of published work. I recognize the need to make authors’ published work publicly available as quickly as possible (e.g., through the immediate production of papers and posting on early view, online first, and other web-based listings of in press papers. These papers should be fully formatted and contain a permanent doi code.
    Article IV. The handling of investigations into potential errors and/or potential unethical research practices.
    I recognize that an investigation into alleged errors and/or unethical research practices is a very sensitive matter which involves the protection of the rights of multiple stakeholder groups, including but not limited to authors, accusers, reviewers, action editors, journals, and publishers. In instances where appeals or accusations require an investigation, I commit to handle such situations in a way that maximizes procedural justice and professionalism toward all involved. In many cases this may involve following a standard procedure for handling such issues, such as those put out by the Committee on Publication Ethics (COPE; who provides flowcharts for handling ethical problems and guidelines on retractions) or other governing bodies (American Psychological Association, Academy of Management, etc.). In other instances, it may involve following practices established by the journal publisher which are designed to uphold professional ethical standards.
    Article V. Communicating ethical standards.
    I commit to communicate these and other relevant ethical standards to associate editors, board members, and authors; and to convey these principles within appropriate public forums (e.g., editors’ panels at professional conferences). I will encourage reviewers and action editors to report to the Editor (or to the Editor Ethics Advisory Board) when they feel
    the articles herein have been violated. I will encourage action editors to similarly report occasions when reviewers are seen as engaging in unethical practices.
    Article VI. Dissemination of this code.
    I approve of this Code and its signatories being posted on a public Internet site.
    Affirming names are in ABC order by date of the affirmation.”

  • Avraham Albert Levy queries December 14, 2014 at 1:57 pm

    Concerns have been raised about some of the images in some of Prof. Levy’s manuscripts.
    Wheat, Nature Genetics:
    https://pubpeer.com/publications/021DF5B37988FD51AA82DF7EE91435#fb18719
    Arabidopsis, The Plant Journal:
    https://pubpeer.com/publications/34E373A96F6D20C3F21574831F8302#fb18713
    Tomato, Journal of Experimental Botany:
    https://pubpeer.com/publications/31CB6054868D8AAA6F60522F9EB61B#fb18711
    Prof. Levy is at the Weizmann Institute of Science in Israel:
    http://www.weizmann.ac.il/plants/levy/

  • Anthurium concerns December 14, 2014 at 5:38 pm

    There are at least another two dozen papers in the anthurium tissue culture literature with problems, errors and/or concerns. Analyses are made at PubPeer.

    Farsi M (1), Taghavizadeh Yazdi ME (2), Qasemiomran V (3). Micropropagation of Anthurium andraeanum cv. Terra. African Journal of Biotechnology 2012;11(68):13162-13166.
    1Ferdowsi University of Mashhad, Mashhad, I. R. Iran.
    2Department of Plant Sciences, Eram Biotechnology Research Center, Technical and Vocational Training Organization, Mashad, I. R. Iran
    3Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources University, Sari, Iran.
    http://www.ms.academicjournals.org/journal/AJB/article-abstract/F030B9532224
    http://www.ms.academicjournals.org/article/article1380816254_Farsi%20et%20al.pdf
    Total views: 227; PDF downloads: 146
    DOI: 10.5897/AJB12.893
    Publisher and copyright holder: Academic Journals (Nigeria), listed as “predatory” by Jeffrey Beall:
    http://scholarlyoa.com/publishers/
    PubPeer analysis:
    https://pubpeer.com/publications/5356319CAAB66A911B78574FF2711C#fb18264

    Islam SA, Dewan MMR, Mukul MHR, Hossen MA, Khatun F. In vitro regeneration of Anthurium andraeanum cv. Nitta. Bangladesh Journal of Agricultural Research 2010;35(2):217-226.
    1Scientific Officer, Bangladesh Rice Research Institute (BRRI), Gazipur-1701, Bangladesh (all except Khatun).
    2Department of Agricultural Extention Education, Bangladesh Agricultural University (BAU), Mymensingh-2202, Bangladesh (Khatun).
    http://www.banglajol.info/index.php/BJAR/issue/view/356
    http://www.banglajol.info/index.php/BJAR/article/view/5884
    http://www.banglajol.info/index.php/BJAR/article/viewFile/5884/4618
    DOI: 10.3329/bjar.v35i2.5884
    PubPeer analysis:
    https://pubpeer.com/publications/40F0D7CDEE1BE9C43B9008E7819877#fb18267

    Anindita Mukherjee (a), Abhijit Bandyopadhyay (a), Sikha Dutta (a), Sukalyan Basu (b) (2013) Phytoaccumulation of iron by callus tissue of Clerodendrum indicum (L), Chemistry and Ecology, 29:6, 564-571.
    DOI: 10.1080/02757540.2013.779681
    a) Department of Botany, The University of Burdwan, Burdwan 713104, India
    b) Department of Chemistry, The University of Burdwan, Burdwan 713104, India
    Received 9 April 2012; final version received 21 February 2013
    http://www.tandfonline.com/doi/full/10.1080/02757540.2013.779681#.VIkozJVxnIU
    http://www.tandfonline.com/doi/pdf/10.1080/02757540.2013.779681 (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/9260619E6F61AA7D51ED7D0231C2BE#fb18324

    Jahan MT, Islam MR, Khan R, Mamun ANK, Ahmed G, Hakim L. In vitro clonal propagation of anthurium (Anthurium andraeanum L.) using callus culture. Plant Tissue Culture and Biotechnology 2009;19(1):61-69.
    DOI: 10.3329/ptcb.v19i1.4961
    Plant Biotechnology and Genetic Engineering Division, Institute of Food and Radiation Biology (IFRB), Atomic Energy Research Establishment (AERE), Post‐DEPZ, Savar, Dhaka, Bangladesh
    No received, revised, accepted or published dates.
    http://www.banglajol.info/index.php/PTCB/article/view/4961+ruseli%20porno (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/40B0C68EA97A393602B9255C7C651D#fb18548

    Peiris SE (1), De Silva EDUD (2), Edussuriya M (3), Attanayake AMURK (1), Peiris BCN (1). CSUP technique: a low cost sterilization method using sodium hypochlorite to replace the use of expensive equipment in micropropagation. Journal of the National Science Foundation of Sri Lanka 2012;40(1):49-54.
    DOI: 10.4038/jnsfsr.v40i1.4168
    1 Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
    2 Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihinthale, Sri Lanka.
    3 Department of Chemistry, Faculty of Science, University of Ruhuna, Matara, Sri Lanka.
    Revised: 22 July 2011 ; Accepted: 16 September 2011
    http://www.sljol.info/index.php/JNSFSL/article/view/4168 (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/FE35CECA0454A5577B9693F5C4B009 

    Atak Ç, Çelik Ö. Micropropagation of Anthurium spp. In: Nabin Kumar Dhal, N.K., Sahu, S.C. (Eds.), Plant Science, Intech, Croatia 2012; pp 241-254.
    http://www.intechopen.com/books/plant-science/micropropagation-of-anthurium-spp- (open access)
    DOI: 10.5772/51426
    Atak Ç, Çelik Ö. Micropropagation of Anthurium andraeanum from leaf explants. Pakistan Journal of Botany 2009;41(3):1155-1161.
    Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Kultur University, Ataköy, Istanbul, Turkey
    http://pakbs.org/pjbot/PDFs/41(3)/PJB41(3)1155.pdf (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/D3F78C630ED61FAAD1083C8925D90D#fb18201

    Bejoy M, Sumitha VR, Anish NP. Foliar regeneration in Anthurium andraeanum Hort. cv. Agnihothri. Biotechnology (Pakistan) 2008;7(1):134-138.
    Commercial Tissue Culture Unit, Tropical Botanic Garden and Research Institute, Palode 695 562, Trivandrum, Kerala, India
    DOI: 10.3923/biotech.2008.134.138
    http://scialert.net/archivedetails.php?issn=1682-296x&issueno=26
    http://scialert.net/qredirect.php?doi=biotech.2008.134.138&linkid=pdf (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/62C91250EC6834E221A129EFE40F88#fb18205

    Farsi M (1), Taghavizadeh Yazdi ME (2), Qasemiomran V (3). Micropropagation of Anthurium andraeanum cv. Terra. African Journal of Biotechnology 2012;11(68):13162-13166.
    1Ferdowsi University of Mashhad, Mashhad, I. R. Iran.
    2Department of Plant Sciences, Eram Biotechnology Research Center, Technical and Vocational Training Organization, Mashad, I. R. Iran
    3Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources University, Sari, Iran.
    http://www.ms.academicjournals.org/journal/AJB/article-abstract/F030B9532224
    http://www.ms.academicjournals.org/article/article1380816254_Farsi%20et%20al.pdf
    Total views: 227; PDF downloads: 146
    DOI: 10.5897/AJB12.893
    Publisher and copyright holder: Academic Journals (Nigeria), listed as “predatory” by Jeffrey Beall:
    http://scholarlyoa.com/publishers/
    PubPeer analysis:
    https://pubpeer.com/publications/5356319CAAB66A911B78574FF2711C#fb18264

    Islam SA, Dewan MMR, Mukul MHR, Hossen MA, Khatun F. In vitro regeneration of Anthurium andraeanum cv. Nitta. Bangladesh Journal of Agricultural Research 2010;35(2):217-226.
    1Scientific Officer, Bangladesh Rice Research Institute (BRRI), Gazipur-1701, Bangladesh (all except Khatun).
    2Department of Agricultural Extention Education, Bangladesh Agricultural University (BAU), Mymensingh-2202, Bangladesh (Khatun).
    http://www.banglajol.info/index.php/BJAR/issue/view/356
    http://www.banglajol.info/index.php/BJAR/article/view/5884
    http://www.banglajol.info/index.php/BJAR/article/viewFile/5884/4618
    DOI: 10.3329/bjar.v35i2.5884
    PubPeer analysis:
    https://pubpeer.com/publications/40F0D7CDEE1BE9C43B9008E7819877#fb18267

    Jahan MT, Islam MR, Khan R, Mamun ANK, Ahmed G, Hakim L. In vitro clonal propagation of anthurium (Anthurium andraeanum L.) using callus culture. Plant Tissue Culture and Biotechnology 2009;19(1):61-69.
    DOI: 10.3329/ptcb.v19i1.4961
    Plant Biotechnology and Genetic Engineering Division, Institute of Food and Radiation Biology (IFRB), Atomic Energy Research Establishment (AERE), Post‐DEPZ, Savar, Dhaka, Bangladesh
    No received, revised, accepted or published dates.
    http://www.banglajol.info/index.php/PTCB/article/view/4961+ruseli%20porno (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/40B0C68EA97A393602B9255C7C651D#fb18548

    Peiris SE (1), De Silva EDUD (2), Edussuriya M (3), Attanayake AMURK (1), Peiris BCN (1). CSUP technique: a low cost sterilization method using sodium hypochlorite to replace the use of expensive equipment in micropropagation. Journal of the National Science Foundation of Sri Lanka 2012;40(1):49-54.
    DOI: 10.4038/jnsfsr.v40i1.4168
    1 Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
    2 Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihinthale, Sri Lanka.
    3 Department of Chemistry, Faculty of Science, University of Ruhuna, Matara, Sri Lanka.
    Revised: 22 July 2011 ; Accepted: 16 September 2011
    http://www.sljol.info/index.php/JNSFSL/article/view/4168 (open access)
    PubPeer analysis:
    https://pubpeer.com/publications/FE35CECA0454A5577B9693F5C4B009

  • Barnyard-grass + rice query December 15, 2014 at 2:38 am

    Hisashi Kato-Noguchi (2011) The chemical cross talk between rice and barnyardgrass. Plant Signaling & Behavior 6:3, 1207-1209
    Copyright: 2011 Landes Bioscience (now Taylor and Francis)
    Department of Applied Biological Science; Faculty of Agriculture; Kagawa University; Miki, Kagawa Japan
    DOI: 10.4161/psb.6.8.15869
    Submitted: 15 April 2011; Accepted: 15 April 2011
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260724/pdf/psb0608_1207.pdf (open access)

    It states:
    Addendum to: Kato-Noguchi H. Barnyard grass-induced rice allelopathy and momilactone B. Journal of Plant Physiology 2011; 168:1016-20; PMID: 21392842 (Elsevier)
    http://www.sciencedirect.com/science/article/pii/S0176161711000836
    DOI: 10.1016/j.jplph.2010.12.021

    Queries/concerns at PubPeer:
    PSB: https://pubpeer.com/publications/4DE0D4122B6A6A7217D911E531D61E#fb18749
    JPP: https://pubpeer.com/publications/9B92B05C287761C01069E76B078B99#fb18741

  • Pakistan Journal of Agricultural Sciences December 15, 2014 at 11:32 am

    There is one journal that is of concern to me: Pakistan Journal of Agricultural Sciences. It has an impact factor of 1.054, although the web-site advertises an incorrect (outdated) IF of 1.240. What is of concern is that in over 50 years of publishing history, and 51 volumes, not a single retraction appears, and only one single erratum (spelt incorrectly as “erratrum”), in the latest September, 2014 issue:
    http://www.pakjas.com.pk/papers/2339.pdf
    (and no small erratum, either)

    Translated: a near-perfect publishing track record. However, a broad glance and random picks will reveal several problems, making this journal an ideal pick for journal-based PPPR. Such an analysis would allow for scientists to better understand how journals obtain their IF, and if there is any correlation with paper qality.

    Site: http://www.pakjas.com.pk

  • Science Society November 17, 2014 at 12:51 pm

    Till date Professor Pramod Tandon has published 21 Research Papers on Dendrobium according to Google scholar data base.
    Are there problems in any of those papers?
    http://scholar.google.co.in/scholar?as_q=Dendrobium&as_epq=&as_oq=&as_eq=&as_occt=title&as_sauthors=%22Pramod+Tandon%22&as_publication=&as_ylo=&as_yhi=&btnG=&hl=en&as_sdt=0%2C5

    Professor Pramod Tandon is a Big Name in the Field of Plant Tissue Culture
    He received Padma Shri award in 2009 in the field of Science and Engineering. He has been nominated as member of the high-profile National Advisory Council (NAC) in June 2010
    http://en.wikipedia.org/wiki/Pramod_Tandon

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