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  • Ivan Shatsky2018 Jan 17 3:56 p.m. (2 hours ago)

    The review contains an extensive bibliography and in general could be useful for many readers, especially those who are taking their first steps in studying the molecular mechanisms of translation initiation in eukaryotes. The main and serious drawback of the article is an incomplete and distorted presentation of the current status of cellular IRES-elements. I already wrote in Pub Med critical notes on the article from the same lab (Xue S et al. 2015. Nature 517 (7532):33-38)devoted to the same problem but, unfortunately, I was not heard. This review,again,does not say anything about a severe controversy in this field, it does not even mention the fact that the vast majority, if not all,of the cellular IRESs proposed to date must be validated since they all havw been indentified using the method of bicistronic DNA constructs, a method extremely prone to almost unavoidable artifacts. Most of the works on individual cellular IRES quoted in the review belong to the period from the late 1990s to the end of the first decade of 2000s. In recent years, however, several articles have been published that point to uncertainties of our knowledge on cellular IRES, describe various pitfalls in the approaches used to identify them and suggest methods to avoid artifacts and obtain reliable information. The main requirement in these approaches is to use various RNA constructs, rather than bicistronic DNA, to transfect cells and assess the level of their expression. These approaches and stringent criteria to analyze experimental data were described in several of our papers (see, for instance, Andreev et al. 2009. Nucleic Acids Res. 37: 6135–6147; Shatsky et al. 2010. Mol.Cells 30: 285–293; Andreev et al. 2012. FEBS Lett. 586: 4139–4143; Terenin et al. 2017. Cell Mol Life Sci. 74: 1431–1455) and employed in our lab to verify IRESs in c-Myc, Apaf-1 and LINE-1 mRNAs. The authors of this NRMCB article probably found these papers not worthy of attention since they are not quoted. The only exception is reference 101 which represents the article with a detailed analysis of the status of cellular IRES by 2013. The analysis was performed by Richard Jackson, a widely known expert in eukaryotic translation (Jackson 2013. Cold Spring Harb.Perspect. Biol. 5: a011569–a011569.) Remarkably,although this reference is present in the text, nothing is said about the actual content and conclusions of Jackson's work. The authors note that “over 100 proposed IRES-containing mRNAs have been reported” but “after decades of work, few examples have been well characterized”. However, the authors do not express any surprise why the progress is that slow, why the methods which have been successfully used to validate viral IRESs are not employed or not applicable to characterize cellular IRESs? The authors also note that putative cellular IRESs have “few structural similarities to each other” and that “their mechanisms of action are largely unknown”. Again, the authors do not ask the question: why for many years now we have not seen positive data on the validation of cellular IRES? Maybe most of these mysterious structures are simply not IRESs, and we must look for alternative mechanisms? Meanwhile, scientific journals, including top ranking ones, go on publishing papers with novel unvalidated cellular IRESs, thereby only thickening the fog in this area In short, it seems to me that this section of the review is written in an overly optimistic manner. It is unlikely to be useful for professionals in the translation mechanisms and may be misleading for new generation of researchers who do not have a sufficient background in the field.

  • Amanda Capes-Davis2018 Jan 15 10:44 p.m. (yesterday) 2 of 2 people found this helpful

    This paper has problems with its authentication testing, resulting in at least three misidentified cell lines (HeLa) being used as models for liver cancer.

    The Materials and Methods of the paper state that "All cell lines were regularly authenticated by morphologic observation under microscopy". This is consistent with the policy of the journal, Cancer Research, which strongly encourages authentication testing of cell lines used in its publications.

    However, morphologic observation is not a suitable method for authentication testing. Changes in morphology can be subtle and difficult to interpret; cultures can be misidentified before observation begins. To investigate the latter possibility, I examined publicly available datasets of STR genotypes to see if the cell lines listed in the paper are known to be misidentified.

    Three of the cell lines used in this paper (Bel-7402, L-02, SMMC-7721) had STR genotypes published by Bian X, 2017 and Huang Y, 2017. All three "liver" cell lines correspond to HeLa and are therefore misidentified.

    HeLa and its three misidentified derivatives were used in the majority of figures (Figures 2, 3, 5, and 6). Although the phosphorylation data appear to be unaffected, the conclusions regarding liver cancer metastasis must be re-examined.

    What can we learn to improve the validity of our research publications?

    For authors and reviewers:

    For journal editors and funding bodies:

    • Encouragement of authentication testing is a step forward, but is insufficient to stop use of misidentified cell lines.
    • Mandatory testing using an accepted method is effective (Fusenig NE, 2017) and would have detected and avoided this problem prior to publication.
    • Policy on authentication testing requires oversight and ongoing review in light of such examples. This is important for NIH and other funding bodies who have recently implemented authentication of key resources as part of grant applications.
  • Erick H Turner2018 Jan 14 6:40 p.m. (2 days ago)

    We appreciate the authors' covering this important topic. However, the search method might have missed some relevant publications. It did cover this 2012 paper of ours...

    • Turner EH, Knoepflmacher D, Shapley L. Publication Bias in Antipsychotic Trials: An Analysis of Efficacy Comparing the Published Literature to the US Food and Drug Administration Database. PLoS Med 2012;9:e1001189. Available at https://doi.org/10.1371/journal.pmed.1001189

    ...but the following two papers of ours, which employed the same methodology, were not included:

  • Evgenia V Dueva2018 Jan 14 5:54 p.m. (3 days ago)

    In their article Bailbe et al. conclude, that “Subetta and release-active dilutions (RAD) of antibodies to β-subunit insulin receptor treatments are effective to significantly improve glucose homeostasis in GK/Par diabetic rats” and that “chronic oral administration of Subetta and RAD of Abs to β-InsR significantly attenuated fasting hyperglycemia and improved glucose homeostasis in GK/Par rats”. However, they fail to mention that Subetta is made from antibodies diluted beyond Avogadro’s limit (12 consecutive dilutions of 1:100, see Google patents US8535664) and thus contains no active molecules. The authors do not mention homeopathy in their article, but this clearly is a homeopathic drug.

    The results obtained by the authors are likely false positives (due to some technical artifact are human biases) considering the very low prior probability of a drug with no active molecules having any specific effect on human adipocytes. The authors have not attempted to use any randomization or blinding techniques to account for such possibilities. More over the data presented in the original paper does not support the abovementioned conclusion, as far as after correct statistical analysis antidiabetic effect of Subetta, can not be distinguished from the effect of water control.

    On the ethical side, the authors did not declare conflict of interests, though OOO "NPF "MATERIA MEDICA HOLDING" is a Russian Company that markets a number of drugs which contain active ingredients diluted beyond Avogadro’s limit, including Subetta. Three out of four authors work for this company. Furthermore, Oleg Epstein is CEO of the abovementioned Company.

  • Randi Pechacek2018 Jan 14 12:47 p.m. (3 days ago)

    David Coil referenced this paper in a blog on microBEnet praising the extent of the research conducted.

  • Mordecai P Blaustein2018 Jan 13 5:47 p.m. (4 days ago)edited

    Response to Dr. Füerstenwerth:

    The case for a ouabain-Na pump endocrine system has been laid out in [1] and my previous response to Dr. Fürstenwerth. All the original reports are cited so that readers can verify my statements.

    I must, however, refute Fürstenwerth’s false claim that I made an “unfounded accusation of data manipulation” by stating that Baecher et al. [2] “’edited’ their raw data”. Fürstenwerth apparently has not read Vogeser and Baecher’s Letter to the Editor [3] in which they admit that “In… Fig. 2 of our article ([2])… at a retention time (RT)… of… 5.0 min… the trace signal is broken… This inconsistency was introduced by editing the… (mass spectrum) raw data.” They show (Fig. 2, top, in [3]) that they originally (Fig. 2, top, in [2]) edited out an ion current peak at 4.99 min, and they present a second example (Fig. 1, top, in [3]) in which a similar peak is seen at that same RT (4.98 min) (see [4] Data Supplement). They do not mention the other 28 plasma samples they tested [2]; how many of them exhibited the same peak? Why didn’t they show/describe all their data? (The “broken” trace signal in Fig. 2 of [2] is very difficult to see on the original journal page. Dr. Hamlyn suspected that the spectrum was 'unusually flat'. When he enlarged the image he discovered the discontinuity.) We suggest [4] that the ion current peak at the 5.0 min RT, which has the same mass/charge ratio as ouabain, may correspond to the more polar of two ouabain isomers that have previously been described [5, 6]. Other flaws in the Baecher et al. study [2] are discussed elsewhere [1, 4, 7].

    References:

    [1] Blaustein MP, 2017

    [2] Baecher S, 2014

    [3] Vogeser M, 2015

    [4] Hamlyn JM, 2016

    [5] Jacobs BE, 2012

    [6] Hamlyn JM, 2014

    [7] Blaustein MP, 2015

  • Mordecai P Blaustein2018 Jan 12 00:16 a.m. (5 days ago)edited

    Response to Dr. Fürstenwerth

    I thank Dr. Fürstenwerth for his comments about my article. His exuberant advocacy for the clinical use of ouabain is refreshingly entertaining. As he states, however, his views are based largely on “applying common sense”; he appears to ignore the experimental method and actual data. (“Common sense” also led to such ideas as, “the earth is flat,” and “the sun revolves around the earth” – notions that landed in the trash bin of history.)

    1. Fürstenwerth correctly asserts that k-strophanthin is the predominant cardenolide extracted from Strophanthus kombé, but this plant produces a mixture of related steroids [1].

    2. He states that the “endogenous ouabain-Na+ pump endocrine system… is… wishful thinking.” Data from multiple laboratories, summarized in my article, demonstrate that an inactivating mutation of the mouse alpha-2 Na+ pump ouabain binding site, or infusion of anti-ouabain antibodies to immuno-neutralize endogenous ouabain (EO) in rats, induces a clear phenotype. This loss of EO-Na+ pump interaction is manifested by specific disturbances of (e.g.) behavior and learning, exercise endurance, fetal development and basal blood pressure. In my view, these data trump Fürstenwerth’s “common sense”.

    3. He claims that “There is no endogenous ouabain.” Has he read (or understood) the articles listed in Table 2A? Rather than relying on “common sense”, I prefer the mass spectra and NMR spectra published by such distinguished chemists/biochemists as Prof. Wilhelm Schoner [2], Prof. Tadashi Inagami [3], and Prof. Koji Nakanishi [4], a member of the National Academy of Sciences USA and one of the world’s leading natural product chemists. Moreover, the very detailed original mass spectroscopy report included all the original, rigorous purification data [5-7]. In contrast, the few investigators who were unable to detect EO (Table 2C) cut methodological corners (see text and [8]) and even “edited” their raw data [9,10] (and see [8]).

    4. Fürstenwerth claims that my review “neglects” the “beneficial” effects of ouabain and “does not discuss (the)... obvious contradictions” that “ouabain lowers blood pressure, (but also) produces hypertension”. His statement is not true. Table 3 shows that mutation (inactivation) of the alpha-2 Na+ pump ouabain binding site elevates basal blood pressure; this implies that EO is normally needed to help keep blood pressure low (i.e., ‘normal’). On the other hand, Yuan et al. [11] were just the first of numerous investigators to show that prolonged, high ouabain levels elevate blood pressure. Like all hormones, ouabain can be expected to have both beneficial and, if greatly elevated for a prolonged period, detrimental effects (see Fig. 4 and pages C14 and C16 of my article).

    5. I do not dispute Fürstenwerth’s assertion that the “decisive factor is the (ouabain) serum concentration”. But, in that case, given the aforementioned data, his opposition to my call for “solid information” about plasma EO/ouabain levels before and during ouabain therapy makes no sense. Drug treatment based simply on “common sense” must give way to effective therapeutic dosing that utilizes all the available scientific information to optimize treatment and patient safety.

    6. Finally, Fürstenwerth states that “production of Strophanthus glycosides is… restricted to collection of wild plants.” This is not true. The complete chemical synthesis of ouabain was achieved by Deslongchamps [12] and a more concise method has now been developed [13].

    In conclusion, as Withering wrote in 1785 [14], “After all, in spite of opinion, prejudice or error, Time will fix the real value upon this discovery, and determine whether I have imposed upon myself and others, or contributed to the benefit of science and mankind”.

    References:

    [1] Jacobs & Hoffman, J Biol Chem 69: 153-163, 1926.

    [2] Schneider R, 1998

    [3] Tamura M, 1994

    [4] Kawamura A, 1999

    [5] Hamlyn JM, 1991

    [6] Ludens JH, 1991

    [7] Mathews WR, 1991

    [8] Hamlyn JM, 2016

    [9] Baecher S, 2014

    [10] Vogeser M, 2015

    [11] Yuan CM, 1993

    [12] Reddy MS, 2009

    [13] Renata H, 2015

    [14] Withering, “An Account of the Foxglove and Some of its Medical Uses”, M. Swinney for G.G.J. and J. Robinson, Birmingham, 1785.

  • Randi Pechacek2018 Jan 13 12:57 p.m. (4 days ago)

    Kaisa Koskinen, first author of this paper, wrote a blog post on microBEnet explaining some background to the research.

  • Peter Rogan2018 Jan 12 2:39 p.m. (5 days ago)edited 1 of 1 people found this helpful

    Twenty one BRCA1 and BRCA2 mRNA splice site variants were analyzed by semi-quantitative RT-PCR, with commercial software that scores putative splice sites by ad hoc methods, and with bioinformatic models based on Adaboost and Random Forest, which are general machine learning approaches. The authors cited our review on interpretation of splicing mutations (Caminsky N, 2014), however the analytic approach described in that paper was not evaluated. As an update to our previous BRCA mutation study (Mucaki EJ, 2011), we carried out information theory-based splicing analysis of all potential splicing mutations listed in Supplemental Table S3. The splicing consequences of all variants were accurately predicted by information analysis. We also report results of exon definition-based mRNA splicing mutation analysis (Mucaki EJ, 2013), which infers relative abundance of wild type and mutated splice isoforms from total splicing information content of each prospective exon. Due to length limitations in PubMed Commons commenting system, detailed results for each variant are described in: https://doi.org/10.5281/zenodo.1146708

    Also, during our analysis, some inconsistencies in mutation designation or interpretation were noted in the paper: (1) The complex BRCA2 duplication described in this article (c.425+415_4780dup[insGATCGCAGTGA]) is sometimes referred to as "c.426-415_4780dup[insGATCGCAGTGA]" (e.g. the title of Figure 5, and Suppl. Table S3), which are not congruent mutations. The true mutation is likely the former, as the Figure 5 legend describes an mRNA splice form that includes 293nt of intron 4. If the duplication was c.426-415_4780dup[insGATCGCAGTGA], the intron inclusion would only be 205nt long. (2) We report an additional inconsistency in regards to Figure 5: The legend of Figure 5E describes a splice form where a truncated exon 11 junctions with the aforementioned 11nt insertion. However, the diagram and the electropherogram in Figure 5e shows exon 11 (ending at c.2398) sharing a junction with the beginning of exon 5. The latter is most likely the correct isoform, as an acceptor is not predicted at the junction between c.4780 and the 11nt insertion.

  • Stefan Tino Kulnik2018 Jan 12 07:22 a.m. (5 days ago) 1 of 1 people found this helpful

    Further to my comment from 13 October 2017:

    In June 2017, we approached Journal of Physiotherapy and submitted a commentary, in which we pointed out the error in this meta-analysis and that the authors’ conclusion with respect to the impact of respiratory muscle training on respiratory complications is therefore unfounded. Unfortunately our commentary was rejected, and so we were denied the opportunity of entering a scientific exchange with the authors within the pages of the journal.

    The journal did acknowledge the data extraction error we pointed out and promised a correction, but a correction has not been published to date.

    It may be regarded as rather unfortunate that this systematic review and meta-analysis (a study design that many colleagues in clinical practice will view as highest level evidence) presents a strong clinical message in favour of implementing respiratory muscle training for the prevention of respiratory complications, based on an erroneous meta-analysis.

    Burden of treatment and opportunity cost to stroke survivors should not be underestimated, and it is important to focus clinical resources on the most meaningful rehabilitation activities based on best evidence.

    For members of the research community and colleagues in clinical practice who may be interested, I have uploaded the content of our rejected commentary on my ResearchGate page https://tinyurl.com/yb3wxmkf. In this we also present a re-calculated meta-analysis using Peto odds ratio, which is a more appropriate and statistically more powerful model of meta-analysis when events are rare, to demonstrate that even with this statistically more powerful method the meta-analysis still fails to reach statistical significance of the overall effect.

  • Tony Buffington2018 Jan 11 09:53 a.m. (6 days ago)

    Of all the comorbidities, was endometriosis the ONLY problem associated with an increased risk for IC?

  • Prashant Sharma, MD, DM2018 Jan 11 01:24 a.m. (6 days ago)

    A full-text, read-only version of this article is available at http://rdcu.be/nxtG.

  • Jim Woodgett2018 Jan 10 7:02 p.m. (6 days ago) 2 of 2 people found this helpful

    This is a comprehensive and up to date review of small molecule inhibitor classes of GSK-3 and is to be commended for recognizing the two isoform distinctions in the introduction. Some sections still refer to GSK-3beta specific effects (e.g tau phosphorylation where GSK-3alpha is essentially equally happy to phosphorylate this microtubule -associated protein that is implicated in Alzheimer pathology). All of the inhibitors listed in the review block both isoforms.

  • Europe PMC in 2017.

    Levchenko M.Nucleic Acids Res. 2018.1 comment

    Christopher Southan2018 Jan 10 03:55 a.m. (7 days ago)edited 1 of 2 people found this helpful

    While the advances described for EPMC are impressive, it remains somewhat misleading to imply European Patent Office biotechnology abstracts as a current resource, since the feed ceased in 2012. Would be great if EPO could backfill these which would then uniquely facilitate // searching of patents and literature.

  • Andy Collings2018 Jan 09 08:06 a.m. 2 of 2 people found this helpful

    A subset of experimental results from this study were the focus of a replication attempt as part of the Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/). The experimental designs and protocols were reviewed and approved in a Registered Report (https://doi.org/10.7554/eLife.13620) and the results of the experiments were published in a Replication Study (https://doi.org/10.7554/eLife.29747).

  • Andy Collings2018 Jan 09 08:04 a.m. 2 of 2 people found this helpful

    A subset of experimental results from this study were the focus of a replication attempt as part of the Reproducibility Project: Cancer Biology (https://osf.io/e81xl/wiki/home/). The experimental designs and protocols were reviewed and approved in a Registered Report (https://doi.org/10.7554/eLife.04024) and the results of the experiments were published in a Replication Study (https://doi.org/10.7554/eLife.30274).

  • Alexander Kraev2018 Jan 08 12:36 p.m.

    Please note that this is a peculiar case of retraction, since while there are indeed problems with certain images, the authors stated the following in the retraction notice: "Nevertheless, although we feel that the scientific conclusions of the paper (that loss of NNT impairs insulin secretion and impairs glucose tolerance in C57BL/6J mice) still stand, given the conclusion of scientific misconduct against the first author, the authors think the most responsible course is to retract the paper." It is important to understand that nuance especially in view that thousands of publications state that they used "C57BL6" without making a crucial distinction between C57BL/6J and C57BL/6N.

  • Christopher Southan2018 Jan 08 11:07 a.m.edited

    This paper has been updated in 2017 as "Last rolls of the yoyo: Assessing the human canonical protein count" https://www.ncbi.nlm.nih.gov/pubmed/28529709

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Collaborating to bring journal clubs to PubMed Commons: A librarian’s perspective

July 5, 2017
Univ of Kansas Nursing-imgJournal clubs can be a great tool in graduate and medical education. They provide opportunities for students to practice important skills: literature searching, critical reading, scholarly debate, and in some cases, even writing. Julie Hartwell shares how a collaboration with faculty on PubMed Commons got started and its initial impact. See full blog post

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