On 2015 Aug 10, NephJC - Nephrology Journal Club commented:

This study was discussed on July 28 and 29th 2015 in the open online nephrology journal club, #NephJC, on twitter .

Introductory explanatory comments, written by Matt Sparks, are available at the NephJC.

There was a very lively discussion, which included about 50 participants, enriched by the active engagement by two of the authors, Ben Humphreys and Rafael Kramann, and was complete with many citations to related research articles.

A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website.

The highlights of the tweetchat discussion were:

• The study does help establish that Gli1+ perivascular ('pericytes') MSC-like cells are the source of ~70% of myofibroblasts after organ injury, and are key players in the subsequent fibrosis.

• Successful/effective targeting of this pathway leads to less fibrosis in preservation of heart function after transverse aortic banding (a heart failure model), however substantial hurdles still exist in terms of delivering a potential therapeutic intervention to lessen fibrosis but ensuring the protective effects of fibrosis are not inhibited.

• The authors' did remarkable work in leveraging elegant techniques such as lineage tracing, multiple organ injury models, parabiosis and diphtheria toxin/Gli1 knockout.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.

On 2017 Jul 14, Randi Pechacek commented:

Amy Pruden, co-author of this paper, wrote an entertaining blog post on microBEnet providing background.

On 2016 Jul 01, Nicholas J L Brown commented:

Our reanalysis of the data from the article by Vedhara et al. (2015) showed that their results are fragile and ambiguous and depend on (a) the inclusion or exclusion of two study participants missing values for one of the control variables and (b) the accumulation of statistical suppression effects in the regression analyses. See 10.1016/j.paid.2015.11.055.

On 2014 Dec 23, GEANNCARLO LUGO commented:

This is a timely review article addressing the role of the STAT3-dependen signaling pathway in Tuberculosis. I find it easy to read, well structured, and quite helpful in summarizing everything that is known about these factor in the context of TB.

On 2016 Aug 05, Zvi Herzig commented:

Adding to Bates' comments below, here are some specific misrepresentations of the primary evidence by the Pisinger and Døssing review, relating to almost every major issue in e-cigarette toxicology (not an exhaustive list):

• “Some studies found high maximum concentrations of total TSNA”, citing studies showing TSNAs 100-200 times below cigarette smoke levels [1-3].
• “Exposure to formaldehyde was comparable with smoking", referring to a study calculating formaldehyde levels nine times below that from tobacco smoke [1].
• “Propylene glycol has been found to exacerbate and/or induce multiple allergic symptoms in children”, citing a study stating that "apparently… outcomes were not driven by propylene glycol” [4].
• “Values below the threshold limit don't necessarily protect against the health effect of 200–300 daily inhalations over decades”, referring to safety limits calculated for 8 hours exposures “day after day, over a working lifetime” [5].
• “These metals appear on the U.S. Food and Drug Administration's 'Harmful and Potentially Harmful Chemicals' list”, referring to metals detected below levels acceptable to the FDA for chronic inhalation [6-8].

[1] Goniewicz ML, Knysak J, Gawron M et al. Levels of selected carcinogens and toxicants in vapour from electronic cigarettes. Tob Control 2014

[2] Kim HJ, Shin HS. Determination of tobacco-specific nitrosamines in replacement liquids of electronic cigarettes by liquid chromatography-tandem mass spectrometry. J Chromatogr A 2013

[3] Farsalinos KE, Romagna G, Voudris V. Authors miss the opportunity to discuss important public health implications. J Chromatogr A 2013

[4] Choi H, Schmidbauer N, Spengler J et al. Sources of propylene glycol and glycol ethers in air at home. Int J Environ Res Public Health 2010

[5] ACGIH. Chemical Substances Introduction. acgih.org 2016. http://www.acgih.org/tlv-bei-guidelines/tlv-chemical-substances-introduction

[6] Siegel M. Metals in Electronic Cigarette Vapor are Below USP Standards for Metals in Inhalation Medications. The Rest of the Story: Tobacco News Analysis and Commentary. 2013.http://tobaccoanalysis.blogspot.com/2013/04/metals-in-electronic-cigarette-vapor.html .

[7] Farsalinos K. Metals and nanoparticles in e-cigarettes. 2013.http://www.ecigarette-research.com/web/index.php/2013-04-07-09-50-07/2013/89-metals-and-nanoparticles-i n-e-cigarettes-commentary.

[8] Farsalinos K, Voudris V, Poulas K. Are Metals Emitted from Electronic Cigarettes a Reason for Health Concern? A Risk-Assessment Analysis of Currently Available Literature. International Journal of Environmental Research and Public Health 2015

On 2016 Aug 05, Zvi Herzig commented:

None

On 2016 Aug 16, Clive Bates commented:

Note: The focus on conflicts of interests (COI) received criticism both for exaggeration and for the tacit assumption that a COI declaration somehow invalidates the scientific merit of the work. See Kosmider L, 2016 Ideology versus evidence: Investigating the claim that the literature on e-cigarettes is undermined by material conflict of interest and the reply from the authors Pisinger C, 2016 Reading the conflict of interest statement is as important as reading the result section: Response to the letter by Dr. Kosmider.

COI declaration is not intended as a form of self-invalidation, but for transparency. It is absurd to assert that it is as important as the substance of the work itself. COI tends to focus on conflicts arising from commercial interests, but many researchers in this field have undisclosed conflicts relating to funders, regulators, employers' prior policy positions, and their long-held beliefs. If these authors want to investigate COI (not the ostensible purpose of this work), then they should do it rigorously, and with a broader view of COI.

On 2016 Aug 05, Clive Bates commented:

Despite the title, the review does not address the "health effects of electronic cigarettes". Or perhaps to the extent that it does, it does not find anything negative to report. This may explain the diversionary conclusion, which resorts to an argument about competing interests rather than a critique of actual scientific findings [see note appended below].

It does, however, attempt to summarise various proxies for health effects but does this very poorly. Throughout the substance of the article, it fails to internalise the most basic concept in toxicology:

"the dose makes the poison" (attributed to Paracelsus, 1538).

The assessment of e-cigarette science by the Royal College of Physicians (London), Nicotine without smoke: tobacco harm reduction, 28 April 2016 included this review but passed over it in the following terms:

Recent reviews of the health effects of toxins inhaled during normal use of e-cigarettes have expressed concerns over potential adverse effects based on the presence of these contaminants, but not their levels, which are generally the more important determinant of toxicity.

The danger of a review that approaches toxicology in this way is that plays into public fears inspired by chemical names and may deter smokers, who are at well-established serious risk from high exposures to harmful agents, from switching to the much safer vapour products. In doing so, the careless framing of scientific findings can cause actual harm.

In addition, such work provides a citable source for irresponsible activism, and so can entrench misunderstanding in regulatory bureaucracies like the WHO, FDA and European Commission - further amplifying the harm through ill-conceived regulation.

For any future work, these authors or others should carefully distinguish between the following:

• The detection of the presence of a hazardous agent in vapour, recognising a de minimis level for which there is no material concern - see Burstyn I, 2014 for an approach that adopts occupational exposures as a frame of reference.

• Human exposure to a hazardous agent that may or may not present a risk to health recognising that magnitude of exposure and materiality matter. For an insight into how to approach this, see Farsalinos KE, 2014. These authors provide a good example in Table 3, showing e-cigarette nitrosamine exposure to be about 1,000 times lower than in cigarette smoke and comparable to the residual levels found in regulated medicinal NRT.

• Observed damage to cells found in vitro following exposure to vapour that may have no bearing on human exposure or risk. See criticism of the extreme misinterpretation of one cell study finding in PubMed Commons on Yu V, 2016. This study provides a good example of what not to do.

• Observed impacts in animal studies, which are rarely a reliable proxy for human experience - see discussion by the Laura and John Arnold Foundation of the weakness of animal studies: Why journalists should stop publishing mouse studies

• The illusion of risks induced by operating vaping equipment in a way that no human user will ever experience other than momentarily. The Jensen RP, 2015 study on 'hidden formaldehyde' is a case in point and has been severely and appropriately criticised (Bates CD, 2015) for running equipment too hot and in 'dry puff' conditions, and then sensationalising the findings as if they showed a cancer risk, and suggesting these may be greater than for smoking.

• Observed changes to the human body that are not necessarily an indication of harm to health. Nicotine and coffee both create changes to the cardiovascular system, but neither is a direct cause of material harm - see PubMed Commons review of Carnevale R, 2016.

• Signs of immediate health gains when e-cigarettes are used as an alternative to smoking - for examples see Polosa R, 2015 and Polosa R, 2014 for examples of 'harm reversal' in chronic respiratory patients.

Finally, given that almost all e-cigarette users are former or current smokers, then any attempt to provide useful information on e-cigarette risk should always use cigarette smoking and related risk as a point of reference, not only the risks compared to complete abstinence. To avoid this comparison is to miss the value of harm reduction as a strategy in tobacco control. There are many examples of this failure - to take just four:

• Allen JG, 2016 raised the alarm about an additive, diacetyl, but failed to point out that, as one critic put it, "average diacetyl exposure from vaping is 750 times lower than from smoking".

• Yu V, 2016 despite concluding that "e-cigarette vapor, both with and without nicotine, is cytotoxic to epithelial cell lines and is a DNA strand break-inducing agent", the study showed that cells exposed to the e-cigarette vapour medium were still alive after 8 weeks but all were dead in the tobacco smoke extract within 24 hours. This important comparison was buried in the paper, not mentioned in the abstract, and not included in the authors' publicity statements about the study.

• Schweitzer KS, 2015 attempted to show that nicotine causes "dose-dependent loss of lung endothelial barrier function, which is associated with oxidative stress and brisk inflammation". But this study has been criticised for using nicotine exposures 500-50,000 times higher than nicotine concentrations in the blood of typical smokers or vapers: Cell studies on e-cigarettes: don’t waste your time reading (at least most of) them

• Paley GL, 2016 concluded that e-cigarette battery fires and explosions were a "significant public health risk", based on six reported incidents. The authors asserted this without noting that in 2011 there were 90,000 smoking-material fires in the U.S. resulting in an estimated 540 civilian deaths, 1,640 civilian injuries and $621 million in direct property damage. To the extent vaping replaces smoking it will reduce this toll and result in a significant public health win.

On 2015 Jan 25, Reuben Strayer commented:

If anyone wants the full (not truncated) version of the manuscript, contact me at the email address above.

On 2017 Jul 09, Jeffrey Ross-Ibarra commented:

In our manuscript exploring the population genetics of local adaptation (Tiffin and Ross-Ibarra 2014) we included a discussion about the potential uses of reduced representation data (e.g. RAD-seq, GBS). To provide a sense of the probability of using reduced representation data to identify targets of selection, we included a figure showing the probability of having a SNP included in a region of the genome in which diversity had been severely reduced due to a recent selective sweep. Unfortunately this figure is not correct; an error in the code inadvertently used centimorgans as morgans, causing the recombination rate to be off by a factor of 100.

To correct this we have generated a new figure (see http://rpubs.com/rossibarra/257207; raw code is available at https://gist.github.com/rossibarra/be44cc3b3796f45840d942ad11c01ba1) that corrects this error and presents a more realistic model. Our previous model assumed SNPs were distributed evenly across the genome and the presence of a single SNP near a sweep was sufficient for detection. Instead, here we explicitly model sequence “tags” coming from RAD-seq or GBS, and incorporate information about the variation in diversity expected among tags in neutral regions of the genome. The figure clearly shows that with dense marker coverage and strong selection, the probability of detecting reductions in diversity due to recent selective sweeps from new beneficial mutations can be relatively high. We emphasize, however, that the purpose of the figure is solely to develop an intuition of the likelihood of detecting a recent selective sweep. The many simplifying assumptions made in generating the figure (no recent demographic change, both sequence tags and recombination occur uniformly along the genome, selection is on a novel beneficial mutation with additive effect that has recently swept to fixation), as well as the specific mutation rates, sample size, sequence length, and recombination rates assumed will all affect the actual probability of a tag being included in a selective sweep. Moreover, this figure does not touch on many other relevant issue such as multiple testing, complex demography, background selection, or other modes of positive selection (e.g. from standing variation, balancing selection, or selection on polygenic traits).

We have submitted a correction to the journal.

We thank Eric Johnson for drawing our attention to the error, and Eric Johnson, Kathleen Lotterhos, and Graham Coop for kindly reviewing previous versions of the code and assumptions we have used in generating this new figure.

On 2014 Dec 03, Paolo Tieri commented:

This article is one of the "Multi-omic Data Integration" Research Topic in Frontiers, which focuses on data integration approaches and methods of any type and extent, their application in understanding the pathogenesis of specific diseases or in identifying candidate biomarkers, in order to exploit the full benefit of multi-omic datasets and their intrinsic information content. For more information about multi-omic data integration check http://journal.frontiersin.org/ResearchTopic/2280

On 2015 Mar 17, Alan Taylor commented:

This confirms work done to determine causes of OA in elderly patients. Aromatase deficiency is a key contributor to OA. Not only is it responsible for the final step in the synthesis of estrogen from androstendione but also converts testosterone to estrogen in males. The estrogen acts on two E receptors in female bone cells/ in males there is one androgen receptor and one estrogen receptor. These are a essential for bone health and maintenance. In the genome wide study under expression of CYP19 gene that codes for aromatase was evident in most cases. Severe OA in a male has been successfully treated for 15 years using a low dose of transdermal estrogen. This effect has been shown to be reversible It takes 6 to 8 weeks for the treatment to reverse the OA. Discontinuation causes OA to redevelop after 6-8 weeks. Recommencement again reverses the OA to give no symptoms whatsoever. Aromatase inhibitors will obviously prevent the two E receptors in the osteocytes from working. In males testosterone deficiency also will prevent the aromatase from catalysing the formation of estrogen.

On 2015 Apr 12, James Tsung commented:

Video of Right Ventricular Puncture During Pericardiocentesis for Cardiac Tamponade: https://youtu.be/WflPJCDl34I

On 2014 Dec 15, Sean Ekins commented:

Also added in my roundup of 2014 papers http://www.collabchem.com/2014/12/15/a-year-in-publications-2014/

On 2014 Dec 04, Sean Ekins commented:

Here is a link to a discussion of how this came to be published in DDT and not a stem cell journal http://www.collabchem.com/2014/12/04/chemical-probes-and-parallel-database-worlds-who-wants-to-know-more-publishing-fun/

On 2015 Feb 05, G Gasim commented:

Dear Dr.Yousif congratulations for the great efforts

do you have an explanation for the variation in genotypes between monoinfected Sudanese patients and those coinfected with HIV?

On 2015 Apr 26, Geriatric Medicine Journal Club commented:

This is a systematic review of non-pharmacologic interventions for orthostatic hypotension including exercise, FES, compression, physical countermaneuvers, head of bed up, water intake, and meal strategies. This article was critically appraised at the April 2015 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full discussion can be found at: http://gerimedjc.blogspot.com/2015/04/april-2015-gerimedjc.html?spref=tw An interesting finding was that an acute bout of exercise may exacerbate orthostatic hypotension in short term. This review did not cover interventions like salt intake.

On 2014 Dec 17, Sean Ekins commented:

Some slides on earlier work are here http://www.slideshare.net/ekinssean/applying-computational-models-for-transporters-to-predict-toxicity

On 2015 Feb 09, David Keller commented:

Dr. Lee,

Your arguments against prescribing ezetimibe at this time are very persuasive, especially with regard to the cost of preventing cardiovascular events with this drug, even if the recent reports of such efficacy are eventually verified. This kind of perspective from a cardiovascular scientist is most beneficial to general internists like me.

Your comments regarding rosiglitazone form a sort of inverse analogy to ezetimibe; if physicians who prescribed rosiglitazone are not to be condemned for "guessing wrong" in advance of the data proving that drug was harmful, then physicians who prescribed ezetimibe should not be congratulated for "guessing right" if this drug is proven to be beneficial. Good point.

However, I chose never to prescribe rosiglitazone, even before its harmful outcomes were known. My decision was not due to luck or clairvoyance, but to the simple fact that rosiglitazone raises LDL cholesterol, and a very similar alternative drug (pioglitazone) exists which lowers LDL cholesterol instead. Knowing that every point of LDL increase in a diabetic is correlated with increased cardiovascular risk, I thought it would be folly to choose an agent which worsened LDL, even if it was only a surrogate marker.

So, all of these examples get back to the question of the strength of LDL-lowering as a surrogate marker for reduction of cardiovascular events. The example of rosiglitazone versus pioglitazone seems to strengthen LDL as a valid surrogate marker for events. It appears that the new data for ezetimibe will also do so, if it confirms that this weak LDL-lowering drug also weakly improves cardiovascular event rates. Of course, ezetimibe still may not be worth its cost, as you point out, and that appears to be the bottom line, at least until ezetimibe is available as a cheap generic medication.

On 2015 Feb 03, Todd Lee commented:

Dr. Keller,

You do make a very interesting point about hindsight.

It is a fact that billions of dollars have been spent in North America on a drug that, to date, does not have any high quality published evidence of efficacy in terms of clinical endpoints. This drug was thus used on the basis of theoretical arguments and a belief that lower LDL means lower events. The findings of IMPROVE-IT may suggest that some patients that have received this drug all of this time did derive benefit. However, based on the effect size in the trial and the patients enrolled, this may be the minority -- and at a considerable health care cost for each benefit.

I'm really not sure what to infer about physicians who believed in the drug all this time. Are they to be commended for being correct?

I'm not certain that money could not have been used for greater benefit with another intervention -- that is a question for health care economists; however, at $1,000,000 per event prevented (earlier post) it seems likely there may have been a more cost effective option.

Let me contrast that with another example as I believe the case for ezetimibe and LDL is analogous to what people believed about hemoglobin A1c and the complications of diabetes. ROSIGLITAZONE was an extremely popular drug in 2006 -- to the tune of US prescriptions exceeding 2 billion dollars. This was because people inferred that lower A1c meant improved outcomes. Later, after the landmark paper showed that ROSIGLITAZONE might have been associated with increased cardiovascular risks, the sales plummeted to less than 15 million dollars in 2012. Thousands of lawsuits were settled and billion dollar fines were paid (for ROSIGLITAZONE and issues around other drugs) by the manufacturer. Furthermore, that drug was withdrawn from numerous European markets.

I'm not sure what to infer about all of the physicians who believed in that drug. Are they all to be condemned? The answer is no. Physicians do the best they can for their patients within the limits of current medical knowledge. They had no a priori way of knowing that this intervention may actually harm patients more than help them.

That said, it is not an accident that both agents were billion dollar winners for their prospective companies and that they were heavily marketed.

Our group incidentally received a marketing pamphlet on ezetimibe in the mail today extolling the IMPROVE-IT trial. The jist of it: the lipid hypothesis is reaffirmed and ezetimibe has been proven effective in patients at risk of coronary artery disease. Does it matter that the paper hasn't been peer reviewed or put in the context of all of the negative papers before it? Not at all. That wouldn't be very good marketing.

On 2015 Jan 24, David Keller commented:

Thank you, Dr. Lee, for that thorough, informative and excellent reply to my comment. For many years, I avoided prescribing ezetimibe (either alone or with a statin) due to the lack of data documenting improved outcomes. Prior to IMPROVE-IT, I would not have questioned the need for your study, and I would have been curious to learn why other clinicians were prescribing ezetimibe despite its interesting ability to improve lipids but not outcomes. Other non-statins which improve lipids - such as niacin, fibrates and bile acid sequestrants - had been able to demonstrate improved cardiovascular outcomes, at least in certain populations or under certain circumstances. The reports of improved outcomes from IMPROVE-IT seemed to reaffirm the importance of lowering LDL and to remove the major obstacle which had prevented me from adding ezetimibe when patients failed to achieve their LDL goal on a tolerable dose of statin. Based on the reservations you have expressed regarding IMPROVE-IT, I will hold back from prescribing it until the questions you raised are answered.

For the sake of discussion, assume that cardiovascular outcome benefits of ezetimibe are eventually proved to your satisfaction. How, then, would that affect the utility of your investigation of why physicians were prescribing a drug which lacked outcome data, if their patients were thereby benefiting from lower event rates? These physicians may have prescribed ezetimibe based on their anecdotal experience with the drug, their knowledge of lipid physiology and pharmacology, or other factors, making them guilty of nothing more than being ahead of the randomized trial data, correctly predicting the outcome benefits of ezetimibe, and benefiting their patients with better outcomes sooner than more conservative physicians like me. Should we be trying to "correct" that kind of "mistake"?

On 2015 Jan 24, Todd Lee commented:

As stated in our paper, we need the data from IMPROVE-IT to better inform us on the use of ezetimibe. However, rather than relying on a conference presentation and press releases we will also need to await the peer-reviewed and sponsor-independent analysis of the IMPROVE-IT trial to judge the quality of the results and evaluate their impact on general practice. Given interim analysis was performed (and the study was subsequently re-sized) any multiple comparisons performed will require expert statistical review.

Furthermore, given no other positive studies exist, it may be prudent to perform an independent individual patient data analysis of all similar studies to better refine or confirm the estimate of effect prior to making any final conclusions from one trial.

The net conclusion of this study, if the presented data is taken at face value, is a number needed to treat (NNT) of 50 over 7 years for the composite outcome. Overall mortality was not reduced. At generic Canadian prices it would cost approximately $58,765 to prevent 1 event over 7 years (Ontario formulary price as of January 2015). However, at US brand name prices of approximately $8.50 per day (Lexicomp 2015) the cost of preventing one composite outcome would be more than $1,000,000.

It is also important to note that IMPROVE-IT was a secondary prevention study (acute event within 10 days) and not primary prevention. In primary prevention, the NNT is likely much higher and the corresponding costs per event prevented would increase proportionately and likely be substantial even at generic prices. In our cohort 6/17 (35%) were receiving ezetimibe for primary prevention.

Whether the drug lowers event rates in the absence of a statin remains unproven and cannot be inferred from this study. Nonetheless, it will be interesting to see the effects on monotherapy uptake given the publicity around this study and also when IMPROVE-IT is ultimately published.

The impact of this study on the uptake of other drugs approved on the basis of LDL as a surrogate marker is also not to be underestimated. The issue of treating to specific LDL targets is currently being debated amongst experts after recent changes to the guidelines. It would be somewhat naive to think that there isn't a substantial market pressure behind bringing back targets to be measured and obtained through additional medications.

On 2015 Jan 23, David Keller commented:

Recent evidence of ezetimibe outcome benefits undermines the premise of this study

The underlying premise of this study of ezetimibe prescribing patterns is that there is “a lack of evidence supporting its efficacy” in reducing adverse cardiovascular outcomes, despite its demonstrated efficacy in improving lipids and other surrogate endpoints (1).

In the recently reported “IMPROVE-IT” study, patients taking ezetimibe plus simvastatin experienced significantly fewer major cardiovascular events (as measured by a composite of cardiovascular death, non-fatal myocardial infarction, non-fatal stroke, rehospitalization for unstable angina or coronary revascularization occurring at least 30 days after randomization) than patients treated with simvastatin alone (2).

Now that there is evidence that ezetimibe improves cardiovascular outcomes, the question of why clinicians prescribed it inappropriately in the past seems moot. Perhaps their clinical experiences using ezetimibe convinced them that evidence of beneficial outcomes would emerge over time. If ezetimibe was improving outcomes all along, then studies based on the premise that it should not have been used seem less relevant.

References:

1: McDonald EG, Saleh RR, Lee TC. Ezetimibe use remains common amongst medical inpatients. Am J Med. 2014 Oct 19. pii: S0002-9343(14)00917-6. doi: 10.1016/j.amjmed.2014.10.016. [Epub ahead of print] PubMed PMID: 25448168.

2: Kohno T. Report of the American Heart Association (AHA) Scientific Sessions 2014, Chicago. Circ J. 2014 Dec 15. [Epub ahead of print] PubMed PMID: 25502168.

On 2017 May 21, Misha Koksharov commented:

This paper provides interesting insights on the role of the 471–481 and 487–495 flexible regions in P. pyralis luciferase and on their utility in improving its thermostability.

For those interested to investigate this topic further, I suggest to look also at the substitution D475P. As can be seen in the alignments below, this substitution occurs naturally in Luciola and in many other beetle luciferases:

D476: http://forumbgz.ru/user/upload/file33577.gif

D489: http://forumbgz.ru/user/upload/file33578.gif

Moreover, in the available structures of L. cruciata luciferase the region 471–481 is not flexible - in contrast to P. pyralis enzyme - so I expect that this mutation should work (where the mutations D476P (Yu H, 2015) and D476N (Amini-Bayat Z, 2012) were inefficient). Interestingly, the successful substitution H489P also naturally occurs in many pH-insensitive luciferases (as shown in the alignments above).

On 2015 May 26, Paul Brookes commented:

Portions of Figure 4 and Figure 5 from this paper appear more similar than would be expected by chance, when compared to portions of Figure 3 and Figure 8, from Zhao ZQ, 2012 Br J Pharmacol. 167, 1550-1562, PMID: 22823335

Relevant information is available in the following two images... http://imgur.com/0DI1G78 http://imgur.com/u47Fdr8

Usual disclaimers apply - i.e. go look for yourself at the originals and decide if they're similar, don't take my word for it, no implications about motives or underlying causes of this apparent similarity should be taken from this comment.

That being said, the lead author has had two papers retracted for similar matters... http://retractionwatch.com/2015/05/26/heart-repair-study-retraction-marks-second-for-mercer-unviersity-researcher/

On 2016 Aug 24, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT097115. We believe the correct ID, which we have found by hand searching, is NCT01857388.

This comment is being posted as part of the OpenTrials.net project^[1] , an open database threading together all publicly accessible documents and data on each trial, globally. In the course of creating the database, and matching documents and data sources about trials from different locations, we have identified various anomalies in datasets such as PubMed, and in published papers. Alongside documenting the prevalence of problems, we are also attempting to correct these errors and anomalies wherever possible, by feeding back to the originators. We have corrected this data in the OpenTrials.net database; we hope that this trial’s text and metadata can also be corrected at source, in PubMed and in the accompanying paper.

Many thanks,

Jessica Fleminger, Ben Goldacre*

[1] Goldacre, B., Gray, J., 2016. OpenTrials: towards a collaborative open database of all available information on all clinical trials. Trials 17. doi:10.1186/s13063-016-1290-8 PMID: 27056367

* Dr Ben Goldacre BA MA MSc MBBS MRCPsych<br> Senior Clinical Research Fellow<br> ben.goldacre@phc.ox.ac.uk<br> www.ebmDataLab.net<br> Centre for Evidence Based Medicine<br> Department of Primary Care Health Sciences<br> University of Oxford<br> Radcliffe Observatory Quarter<br> Woodstock Road<br> Oxford OX2 6GG

On 2015 Jul 24, Md. Shahidul Islam commented:

The 2015 Islet Society Meeting took place in Sydney during 19-21 July, 2015. This meeting, organised by Anand Hardikar was also of high scientific quality. The 2016 Islet Society meeting will be in Istanbul (15-17 July, 2016). The organizer of 2016 meeting is Erdal Karaoz

On 2015 Mar 05, Anders Prior commented:

High effect sizes and immortal person-time

In a paper published in Medicine, Wang et al. presented this cohort study of 47,225 stroke patients.¹ (Wang JY, 2014) They concluded that the 30-day mortality after stroke was significantly reduced if treatment with antipsychotic drugs was initiated before or after the stroke.

The reported effect sizes were very large; the mortality rate in stroke patients decreased by 73% in those who received antipsychotic treatment before the stroke and by 87% in those who received antipsychotic treatment shortly after the stroke. Effects of this size are rarely seen in such studies.

The study was based on a nested case-control design. Included cases were stroke patients who died within 30 days after having a stroke, while controls (matched on age, gender and stroke date) were stroke patients who survived at least 30 days after their stroke. The main exposure was antipsychotic drugs given at any time within 30 days after the stroke date. Multivariate logistic regression was used to calculate odds ratios of mortality.

We are concerned that the results may be substantially biased because the definition of the antipsychotic user group conditions on the future; in order to receive the antipsychotic treatment and become a member of the antipsychotic user group, study participants need to survive until the drug is prescribed. In other words, study participants in the antipsychotic user group are ‘immortal’ until the day of treatment (immortal person-time).² The authors do not describe any analytical measures taken to counteract this conditioning. If they have not taken this into account, this would pose a very serious problem as also described numerous times in the epidemiological literature.³ (Hanley JA, 2014) Immortal time bias will generate an illusion of treatment effectiveness and is frequently found in observational studies that compare with non-users.⁴ (Suissa S, 2007)

In general, suspicion for immortal time bias should be raised when exposure groups are assigned with no regard to exposure time in a longitudinal study. Furthermore, the reported effect sizes are surprisingly high, especially when considering the fragility of the population in question. This group consists of stroke patients with complications; they may suffer from e.g. post-stroke delirium and may need antipsychotic treatment. They would most likely have more adverse outcomes, not the opposite.^5,6 (Shi Q, 2012, Prior A, 2014)

Dr. Anders Prior, MD

Research Unit for General Practice and Section for General Medical Practice, Department of Public Health, Aarhus University, Denmark

Dr. Thomas Munk Laursen, PhD

National Centre for Register-based Research, Department of Economics and Business, Aarhus University, Denmark

Prof. Mogens Vestergaard, PhD

Research Unit for General Practice and Section for General Medical Practice, Department of Public Health, Aarhus University, Denmark

References

1 Wang JY, Wang CY, Tan CH, Chao TT, Huang YS, Lee CC. Effect of different antipsychotic drugs on short-term mortality in stroke patients. Medicine (Baltimore). 2014;93(25):e170.

2 Rothman KJ, Greenland S, Lash TL. Modern Epidemiology. 3rd ed. Philadelphia, PA: Lippincott Williams & Wilkins; 2008.

3 Hanley JA, Foster BJ. Avoiding blunders involving 'immortal time'. Int J Epidemiol. 2014;43(3):949-961.

4 Suissa S. Immortal time bias in observational studies of drug effects. Pharmacoepidemiol Drug Saf. 2007;16(3):241-249.

5 Shi Q, Presutti R, Selchen D, Saposnik G. Delirium in acute stroke: A systematic review and meta-analysis. Stroke. 2012;43(3):645-649.

6 Prior A, Laursen TM, Larsen KK, et al. Post-stroke mortality, stroke severity, and preadmission antipsychotic medicine use--a population-based cohort study. PLoS One. 2014;9(1):e84103.

On 2015 Jan 12, Larry Parnell commented:

This paper was my selection for Paper of the Week for 1-5 Dec 2014.

This is highly important work and the conclusions drawn are valuable and applicable to many areas of genetic research into complex phenotypes. It is great to see scientists of this stature adding important insight into the role of GxEs, especially in terms of influence on gene expression.

I don't feel that the relationship described in this paper for ADIPOQ is so meaningful as the variant described is not in high LD in most populations with the ADIPOQ variants that support known GxE interactions for cardiometabolic phenotypes. See http://www.biodatamining.org/content/7/1/21 Nonetheless, there is also in the BioData Mining article a list of GxEs described for UCP2, which does have evidence in this report above.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0093283. We believe the correct ID, which we have found by hand searching, is NCT00932893.

This comment is being posted as part of the OpenTrials.net project^[1] , an open database threading together all publicly accessible documents and data on each trial, globally. In the course of creating the database, and matching documents and data sources about trials from different locations, we have identified various anomalies in datasets such as PubMed, and in published papers. Alongside documenting the prevalence of problems, we are also attempting to correct these errors and anomalies wherever possible, by feeding back to the originators. We have corrected this data in the OpenTrials.net database; we hope that this trial’s text and metadata can also be corrected at source, in PubMed and in the accompanying paper.

Many thanks,

Jessica Fleminger, Ben Goldacre*

[1] Goldacre, B., Gray, J., 2016. OpenTrials: towards a collaborative open database of all available information on all clinical trials. Trials 17. doi:10.1186/s13063-016-1290-8 PMID: 27056367

* Dr Ben Goldacre BA MA MSc MBBS MRCPsych<br> Senior Clinical Research Fellow<br> ben.goldacre@phc.ox.ac.uk<br> www.ebmDataLab.net<br> Centre for Evidence Based Medicine<br> Department of Primary Care Health Sciences<br> University of Oxford<br> Radcliffe Observatory Quarter<br> Woodstock Road<br> Oxford OX2 6GG

On 2015 Jan 07, Mohammad Salman commented:

I'm surprised by the findings of this paper since several authors have reported antiinflammatory effects of Thymoquinone and inhibition of COX-2 and PGE2 via Thymoquinone. See:

1: Kundu JK, Liu L, Shin JW, Surh YJ. Thymoquinone inhibits phorbol ester-induced activation of NF-κB and expression of COX-2, and induces expression of cytoprotective enzymes in mouse skin in vivo. Biochem Biophys Res Commun. 2013 Sep 6;438(4):721-7. doi: 10.1016/j.bbrc.2013.07.110. Epub 2013 Aug 1. PubMed PMID: 23911786.

2: Al Wafai RJ. Nigella sativa and thymoquinone suppress cyclooxygenase-2 and oxidative stress in pancreatic tissue of streptozotocin-induced diabetic rats. Pancreas. 2013 Jul;42(5):841-9. doi: 10.1097/MPA.0b013e318279ac1c. PubMed PMID: 23429494.

3: El Mezayen R, El Gazzar M, Nicolls MR, Marecki JC, Dreskin SC, Nomiyama H. Effect of thymoquinone on cyclooxygenase expression and prostaglandin production in a mouse model of allergic airway inflammation. Immunol Lett. 2006 Jul 15;106(1):72-81. Epub 2006 May 22. PubMed PMID: 16762422.

4: Marsik P, Kokoska L, Landa P, Nepovim A, Soudek P, Vanek T. In vitro inhibitory effects of thymol and quinones of Nigella sativa seeds on cyclooxygenase-1- and -2-catalyzed prostaglandin E2 biosyntheses. Planta Med. 2005 Aug;71(8):739-42. PubMed PMID: 16142638.

On 2014 Dec 06, Yannis Karamanos commented:

This was not a "happy" idea to use ENGase for endoglucanase... This abreviation is in use, for many years, for endo-N-acetyl glucosaminidase

On 2015 Aug 17, Anders von Heijne commented:

It is so interesting to compare the workings of our different healthcare systems. The type of order/referral for overread of outside radiological stuies described in this paper have been used in swedish radiology for at least as long as I have been in practice - ie at least for three decades. In addition to the obvious advantages described by the authors, the clinican that places the overread order can add relevant facts and queries in the new order. One easy way of documenting the outside report is to add it as a DICOM image to the study and save it in the PACS, rather than transfering it between different RIS.

On 2016 Feb 18, Kristina Hanspers commented:

The pathway in figure 2 is available in the "Open Access Publication" collection at WikiPathways: http://www.wikipathways.org/index.php/Pathway:WP3297. This pathway can be downloaded for use in network analysis tools such as Cytoscape and PathVisio.

On 2015 Oct 22, Horacio Rivera commented:

A de novo inv dup(1) turns out to be a rea(1)dup q chromosome I remark that the de novo mosaic 1q32→qter duplication onto 1pter (concomitant with a normal clone) described by Levy et al. [2015] is not an inverted duplication because direct and inverted duplications are officially defined as “a gain of a chromosomal segment observed at the original chromosome location” [Shaffer et al., 2013], not to mention that the orientation of the extra segment was indeed a direct one. It is significant that in their discussion, Lévy et al. [2015] refer to three other similar chromosome-1 rearrangements entailing an 1q duplication (although none with interstitial telomeric repeats) and visualize them as “recombinants” from an hypothetical pericentric inversion. In this regard, a compilation of 104 recombinant-like chromosomes of de novo or sporadic occurrence [Rivera et al., 2013] lists 11 other comparable chromosome-1 composites entailing dup q/del p but without an interstitial telomere. To avoid a nonsensical “der vs rec” controversy, we have designated such rearranged chromosomes with the official term rea coupled with the lengthy description of the novel composite [Rivera et al., 2013]. In that paper, we pointed out that “this formula makes no causal assumptions, unambiguously describes the rearranged chromosome, allows for a meiotic or mitotic origin, and is consistent with the involvement of 1 or 2 homologs”. Moreover, the term rea had already been used for this purpose [Thomas et al., 2006] and properly describes a rearranged unbalanced chromosome mimicking a recombinant ensued from a pericentric inversion as it is epitomized by the rea(1)(qter→q32::pter→qter) here alluded to. It goes without saying that inv dup is also improperly used to designate mirror structures such as isodicentrics and neocentric isofragments [e.g., Warburton et al., 2000]. Although Lévy et al. [2015] recognized that “[T]he recurrent nature of all these similar recombinants, including our dup(1q), suggests an identical mechanism of formation”, they failed to identify it. According to D’Angelo et al. [2009], who analyzed in fine detail two dup q/del p and two other comparable chromosome-1 rearrangements, the DNA repair mechanism of non-homologous end joining (NHEJ) appears to be “the pathway in the formation of these de novo nonreciprocal translocations, because of the lack of evidence to support a homology-based recombination mechanism”. Yet, the location in unique, non-repetitive DNA sequences of all the breakpoints in the four chromosome-1 rearrangements above mentioned [D’Angelo et al., 2009] may call into question the NHEJ mechanism for rearranged chromosomes with an interstitial telomere alike to the exceptional rea(1) documented by Lévy et al. [2015]. Because Lévy et al. [2015] also omitted some relevant references on other rearrangements with interstitial telomeres, I reiterate here the academic and moral duty that authors, reviewers, editors, and readers have to improve the current citation practices [Rivera, 2014]. Finally, I stress that seven months ago a Letter to the Editor with these comments was judged unacceptable by the concerned journal because “the conclusions of Dr. Levy's paper are really not about terminology and nomenclature”. REFERENCES D’Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. 2009. Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. Hum Genet 125:551-563. Lévy J, Receveur A, Jedraszak G, Chantot-Bastaraud S, Renaldo F, Gondry J, Andrieux J, Copin H, Siffroi J-P, Portnoï M-F. 2015. Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements. Am J Med Genet Part A 167A:428-433. Rivera H. Commentary: peer review and incomplete reference lists. 2014. Account Res 21:138-141. Rivera H, Domínguez MG, Vásquez-Velásquez AI, Lurie IW. 2013. De novo dup p/del q or dup q/del p rearranged chromosomes: review of 104 cases of a distinct chromosomal mutation. Cytogenet Genome Res 141: 58-63. Shaffer LG, McGowan-Jordan J, Schmid M. 2013. ISCN 2013: an international system for human cytogenetic nomenclature (2013), Basel, S Karger. p. 69. Thomas NS, Durkie M, Van Zyl B, Sanford R, Potts G, Youings S, Dennis N, Jacobs P. 2006. Parental and chromosomal origin of unbalanced de novo structural chromosome abnormalities in man. Hum Genet 119: 444-450. Warburton PE, Dolled M, Mahmood R, Alonso A, Li S, Naritomi K, Tohma T, Nagai T, Hasegawa T, Ohashi H, Govaerts LC, Eussen BH, Van Hemel JO, Lozzio C, Schwartz S, Dowhanick-Morrissette JJ, Spinner NB, Rivera H, Crolla JA, Yu C, Warburton D. 2000. Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere. Am J Hum Genet 66:1794-1806.

On 2015 Jan 26, Vojtech Huser commented:

This is a report on a clinical trial and it is mentioned in the abstract (NCT02231866). Ideally, the identifier would be within the PubMed [SI] field. This results in this result article not displaying as linked on ClinicalTrials.gov

On 2014 Nov 27, Jürgen Hänggi commented:

Dear community

this new study shows that a recently published "apparent" sex effect in the form of "increased interhemispheric connectivity in women and increased intrahemispheric connectivity in men" (see http://www.ncbi.nlm.nih.gov/pubmed/24297904) is driven by brain size and not by sex per se.

On 2015 Sep 03, Lydia Maniatis commented:

It seems generally to be the case that when a darkish-looking surface grows in area, it appears to lighten. There is no doubt that this occurs, and also no doubt that the effect is subject to a large degree of variability between experiments and between individuals. Boyaci et al (2014) report, as their main finding, that the effect occurs in the context of "computer-rendered scenes" (their stimuli) as well as in the context of "real scenes" (referring to the rarefied laboratory set-up of Radonjic and Gilchrist (2014)).

As a way of describing experimental conditions - whose results, moreover, were subjected to technical analyses to determine which datasets fit a linear model, a quadratic model, a one-phase model, a two-phase model, and used to form hypotheses about the neurophysiological underpinnings of performance and to judge conceptual models - the crude distinction between "computer-rendered" and "real" seems rather insufficient. Indeed, when it comes anything more specific than the general consistency with the "larger gets lighter" effect, all bets are off. Noting that their results were different from those of Radonjic and Gilchrist (2014), the authors speculate simply that: "The disagreement between our studies is likely to be because of differences between the stimuli." More specifically: "Whereas their stimuli (Radonji砦 Gilchrist, 2014) were real and as simple as possible, ours were computer generated and relatively more complex." Like the unqualifed "real" vs "computer-generated" distinction, the "simple vs complex" distinction is too vague for the purpose. Very subtle and neurophysically complex perceptual operations can be triggered by geometrically simple stimuli. Surely, mathematical modelling and theoretical/neurophysiological extrapolations should follow, not precede, qualitative understanding of a phenomenon and the effects of conditions. Otherwise, such speculation is strictly ad hoc.

The "area rule" as originally proposed said more than that the darker of two areas will lighten with area. It said that this lightening of the darker area will "anchor" cause the appearance of the lighter area such that it brightens and eventually becomes luminous. The proposal was made in order to rationalize the luminosity observed in the disc in classic disc/annulus experiments, without having to ascribe a role to figure-ground organization. The predicted changes in the lightness of the lighter area qua area apparently haven't been corroborated and are no longer referred to or tested for. As an isolated phenomenon not affecting surrounding surfaces, it's hard to see the theoretical importance of a highly-variable and condition-sensitive tendency toward lightening of relatively darker surface with increases in area, or the value of making fussy models of this tendency, tailored to particular stimuli.

I would also like to take issue with the choice of references the authors chose to support their opening assertion that "The lightness of a surface depends not only on its luminance but also on its geometry and the context within which it is viewed (Boyaci, Doerschner, Snyder, & Maloney, 2006; Gilchrist, 2006; Kingdom, 2011; Maloney, Boyaci, & Doerschner, 2005; Maloney, Gerhard, Boyaci, & Doerschner, 2010)." The case for this was made in classic literature and experiments well before 2006. The assertion is so fundamental and uncontroversial that references are not even necessary.

On 2015 Nov 04, Lydia Maniatis commented:

Continuation of "area rule" story: Avoiding acknowledging the role of figure-ground in contrast effects also allowed advocates of "anchoring theory" to claim that "the debate seems to revolve around layer models and framework models" (Gilchrist, 2015), frameworks being adjacent "like countries on a map." Figure-ground structure means layers, and so would complicate this presentation.

On 2015 Sep 20, Lydia Maniatis commented:

In line with the earlier point about avoiding figure/ground issues, the "multi-sector" stimuli used here are of the sort used by Gestalt psychologists to demonstrate and study figure-ground effects (e.g. the role of sector color, size, orientation; bistability). But such effects and their potential lightness consequences are not acknowledged.

On 2015 Sep 17, Lydia Maniatis commented:

"Simple" vs "complex" stimulus is not a meaningful distinction, because there is no objective criterion for making it. Geometric simplicity may or may not produce complexity in the percept, of different kinds.

Which is more simple: a. the three pacmen of a Kanizsa triangle, that produce subjective contours/ contrast/amodal completion; b. the simultaneous contrast effect that produces contrast and amodal completion? c. the de Valois checkerboard that produces assimilation; d. a random array of variously shaped, overlapping white, grey, black shapes? e. the checkerboard used here, which produces transparency/inhomogenous illumination effects; f.a black shape that produces the impression of two overlapping black shapes; g. etc.

The authors offer their own “clear distinction” of simple vs complex. Not only is this proposed distinction unclear, it lacks theoretical content. The authors subsequently seem to ignore it, and use the terms in a loose and undefined way. The proposed distinction, attributed to “anchoring theory” is: “A simple image is one in which all the surfaces lie within a single illumination level (a single framework) whereas complex images contain multiple adjacent fields of illumination (multiple frameworks).” This distinction is theoretically hollow, because it references actual (actual level of illumination) and not perceived (perceived illumination) image features. By this definition, a photograph of sunlight and shadow should count as a single framework, provided it is being viewed under a homogeneous illumination. Even if we take the authors' distinction to refer to perceived illumination (which begs the question the “frameworks” argument is supposed to answer, i.e. how do we parse the scene into separate illumination “frameworks”), they don't stick to it. A little later, for example, we are told that the stimuli of Boyaci et al (2014) “are still fairly simple, [but] qualify [] as complex as they consist of more than one framework” (the distinction is invoked to explain discrepancies between those authors findings and the findings of R and G (2014). But Boyaci et al's stimuli are neither under inhomogeneous illumination nor are they designed to create such an impression. So the definition of “framework,” which wasn't explanatory to begin with, has shifted in the space of a few paragraphs, from “framework of illumination” to something else (what?). We are similarly told that “a dozen previous experiments...used images that qualify as complex images;” but many (perhaps all) of these studies did not involve inhomogeneous illumination, real or perceived.

On 2015 Sep 17, Lydia Maniatis commented:

A short, instructive history of the “area rule”

The “area rule” was born in an attempt to deny the role of figure-ground structure in lightness. This is its original sin, and has led to interesting distortions in theory and practice.

Classic disc-annulus experiments, which demonstrated the dependence of lightness on luminance ratios, also showed an asymmetrical influence of disc and annulus. The annulus would always look white, and push a lighter disc towards luminosity. In other words, raising the luminance of the annulus would lighten the disc, but not vice versa. The disc appeared to lie on top of an amodally-completed larger disc, so an easy provisional conclusion would be to assign different influences to figure and ground in mediating lightness perception of a surface (the same asymmetry applies to figure-ground contrast in general).

Gilchrist et al (1999) did not like this solution because it interfered with their preferred theoretical assumption that the highest luminance in a (vaguely-defined) “framework” would be white. Clearly, in the very simple, disc-annulus situation, the highest luminance was not necessarily white. Instead of acknowledging a role for figure-ground, Gilchrist et al (1999) created a new rule, stating that if the darker area was more than 50% larger than the smaller, then it would lighten, and progressively push the smaller, lighter area toward luminosity. They presented a speculative function, reprinted in Gilchrist and Radonjic (2009), that has never been corroborated, despite a number of attempts.

The Gilchrist group's own results constantly cried out for a figure-ground explanation. Tellingly, they were forced to modify their area claim to include “amodally-completed” area – thus in effect making the area rule indistinguishable from a figure-ground claim. Later, Economou et al (2007) acknowledged a similar, figure-ground-related asymmetry in the simultaneous contrast display. The team acknowledged the asymmetry but did not explore it further.

Preserving the highest-luminance-white rule was not the only or even most important incentive for rejecting a possible figure-ground role. Another fundamental claim of Gilchrist et al (1999) was that the classic simultaneous contrast demonstration is due to a process which, at a certain stage, treats each square and its interior as a separate “framework” and evaluates its contents based on the ratio principle and highest-luminance rule. The idea that the lightness of the targets is actually mediated by local luminance contrast between the apparent figure and its background was not compatible with this assumption. However, it is easy to show (Maniatis, 2015), by adding surfaces within each putative “framework” that border contrast between figure and ground, not the ratios with all surfaces contained in the background square, mediates this effect.

The commitment to avoiding acknowledging a role for figure-ground explains, I believe, the preference manifested by investigators with these theoretical commitments for stimuli which either did not produce figure-ground effects, or in which the contrast effects would average out. Specifically, they adopted the use of checkerboards or Mondrians, and random or semi-random selection of luminances. Such stimuli and choices muddy rather than clarify the role of structure in lightness. Thus, proponents of a “Gestalt” theory, were, paradoxically forced by their commitments to prefer stimuli in which image structuring could be ignored.

There was a second reason that this “Gestalt” theory needed to avoid confronting the role of structure in lightness, and this was that it did not/could not address the fact that we sometimes perceive surfaces as lying beneath transparent layers with their own lightness. As in the case of figure-ground/amodal completion effects, such layers arise when contours showing good continuation intersect, with the added proviso that the luminance structure is compatible with such a solution. Checkerboards, lacking such cues, avoid such effects.

Well, actually, they don't. They often produce multiple such effects, as well as luminosity. This latter result arose in Radonjic et al (2011). It was awkward and they tried to explain it away by selectively attributing inconvenient results to presentation on an “emissive” screen. Allred et al (2012) tentatively acknowledged, after much highly technical wrestling with very low-resolution data, the self-evident yet apparently unplanned-for fact that checkerboards do produce differential lightness impressions. So restricting the class of allowable stimuli (rationalized on the basis that they were “simple” and that results would carry over to more “complex” situations – a view codified in the oft-repeated “applicability assumption”) in order to avoid confronting figure-ground and transparency effects has nevertheless led researchers back to these same, unavoidable issues.

It is interesting that the checks on a checkerboard can coalesce into transparent overlays/underlying surfaces despite the absence of apparent overlap. It is surely not unrelated to the fact that checkerboards produce assimilation rather than contrast when we replace a black or white check with a grey one (the de Valois and de Valois checkerboard contrast demonstration). It would be worth analyzing.

On 2015 Aug 12, Lydia Maniatis commented:

This article is a bit misleading. The authors seem to be claiming to have corroborated the area rule, at least for the case where the darker area fills more than half the visual field.

As defined and illustrated by Gilchrist et al (1999) and Gilchrist and Radonjic (2009), the area rule predicts the onset of luminosity when the darker area exceeds half the display. But this prediction has never been corroborated, even for far, far larger darker area coverage, nor has the description of the rule changed. In addition, lightening of the darker are has never been shown to start until the latter covers far more than 50% of total area. So the claim that this study has corroborated the "area rule" needs to be qualified by the introduction of a new description of the area rule.

On 2013 Oct 25, DAVID SANDERS commented:

From the abstract of Ueda T, 1989

"Two proteins stimulating the GTPase activity of the smg-21 GTP-binding protein (smg p21) having the same effector domain as the ras proteins (ras p21s) are partially purified from the cytosol fraction of human platelets. These proteins, designated as smg p21 GTPase activating protein (GAP) 1 and 2, do not stimulate the GTPase activity of c-Ha-ras p21. smg p21 GAP1 and 2 are separated from c-Ha-ras p21 GAP by column chromatographies. The activity of smg p21 GAP1 and 2 is killed by tryptic digestion or heat boiling. The Mr values of smg p21 GAP1 and 2 are similar and are estimated to be 2.5-3.5 x 10(5) by gel filtration analysis. These results indicate that there are two GAPs for smg p21 in addition to a GAP for c-Ha-ras p21 in human platelets."

On 2014 Dec 10, Alberto Zambrano commented:

Dear Ilya, The Ab used was initially described by Dr. Sonenberg (Mol Cell Biol. 1998 Jan;18(1):334-42, A novel functional human eukaryotic translation initiation factor 4G.) and was kindly donated by Dr. Cesar de Haro (CBM, Madrid, Spain) There you can see that the size of the recombinant form of EIF4G2 (His-tagged) (Figure 3) recognized by the Ab is a little bit lower than 206 KDa. You can also see another prominent band higher than 117KDa, recognized by the Ab. In a another article from the same author (J Neurosci. 2012 Apr 18;32(16):5620-30. doi: 10.1523/JNEUROSCI.0030-12.2012. Regulation of neuronal mRNA translation by CaM-kinase I phosphorylation of eIF4GII) the same Ab was also used but, unfortunately the protein markers were not indicated. In our blots, the Ab reactivity shows either a prominent, discrete band or a doublet at size indicated. We don't observe any other significant reactivity in the full blots. In addition, those bands were sensitive to specific specific siRNA downregulation (figure 5). We don't have a clue about the origin of such differential electroforetic mobility differencies, described in the original paper or in ours (in MEFs, with respect to the predicted size but with the evidences we had, we assumed that protein identity.

On 2014 Dec 01, Ilya M Terenin commented:

Ghm... Guys, why your eIF4G2 is heavier than 150 kDa on blots? The protein is ~100 kDa.

On 2014 Dec 03, Rafael Najmanovich commented:

We predicted back in 2012 (Chartier M, 2012) as part of a large scale analysis of rare codon cluster that such clusters may play a role in the molecular recognition of the nascent protein for intracellular targeting and membrane insertion. It is unfortunate that the authors were not aware of our publication.

On 2015 Jan 03, William Grant commented:

Here are some papers not included in this review showing benefits of vitamin D testing. Peiris AN, Bailey BA, Grant WB, Mascitelli L. Vitamin D testing. Lancet 2012 May 5;379:1699-1701.

Der T, Bailey BA, Youssef D, Manning T, Grant WB, Peiris AN.,Vitamin D and prostate cancer survival in veterans. Military Med. 2014;179 (1) :81–84.

Peiris AN, Bailey BA, Manning T. Relationship of vitamin D monitoring and status to bladder cancer survival in veterans. South Med J. 2013 Feb;106(2):126-30.

Bailey BA, Manning T, Peiris AN. Vitamin D testing patterns among six Veterans Medical Centers in the Southeastern United States: links with medical costs. Mil Med. 2012 Jan;177(1):70-6.

Of course some may have been published after your literature search was completed. However, they do support the benefits of vitamin D testing among hospital patients.

Also, this paper is supportive in that it found that patients in the ICU with very low 25OHD concentrations benefited from vitamin D supplementation. Amrein K, Schnedl C, Holl A, Riedl R, Christopher KB, Pachler C, Urbanic Purkart T, Waltensdorfer A, Münch A, Warnkross H, Stojakovic T, Bisping E, Toller W, Smolle KH, Berghold A, Pieber TR, Dobnig H. Effect of High-Dose Vitamin D3 on Hospital Length of Stay in Critically Ill Patients With Vitamin D Deficiency: The VITdAL-ICU Randomized Clinical Trial. JAMA. 2014 Oct 15;312(15):1520-30.

One of the impediments to acceptance of vitamin D seems to be the lack of supportive trials. The trials have not supported the ecological and observational studies largely because the trials have not been properly designed. Too often, people with normal to high 25OHD concentrations are enrolled and given a small amount of vitamin D. The proper way to conduct such trials was outlined recently in this paper: Heaney RP. Guidelines for optimizing design and analysis of clinical studies of nutrient effects. Nutr Rev. 2014 Jan;72(1):48-54.

Disclosure I receive funding from Bio-Tech Pharmacal (Fayetteville, AR) and Medi-Sun Engineering, LLC (Highland Park, IL).

On 2014 Nov 25, Robert Eibl commented:

Sounds like a very good step forward in understanding these cells.

On 2015 Jan 12, Larry Parnell commented:

This paper was my selection for Paper of the Week for 10-14 Nov 2014.

On 2015 Mar 22, Sean Ekins commented:

And here is a post on the letter from editor http://www.collabchem.com/2015/03/22/what-warrants-an-erratum-and-why-the-old-publishing-model-must-change/

On 2015 Mar 22, Sean Ekins commented:

Here is the letter CAS sent to J Med Chem Editor (which was forwarded to me) regarding this paper http://figshare.com/articles/jm_2014_011308_CAS_report_of_error_2_pdf/1348274 alerting us to 20 document records for one patent which were not visible to us when the analysis was done in 2014.

On 2015 Feb 11, Christopher Southan commented:

None

On 2014 Dec 17, Sean Ekins commented:

Here are some slides on this work http://www.slideshare.net/ekinssean/medicinal-chemistry-due-diligence-computational-predictions-of-an-experts-evaluation-of-the-nih-chemical-probes

On 2014 Dec 17, Sean Ekins commented:

Here is a link to a post discussing this paper and also link to in the pipeline mention https://www.collaborativedrug.com/buzz/2014/12/16/beware-researchers-challenges-navigating-commercial-and-public-databases/

On 2014 Dec 15, Sean Ekins commented:

Also added in my summary of 2014 papers http://www.collabchem.com/2014/12/15/a-year-in-publications-2014/

On 2014 Dec 04, Sean Ekins commented:

Here is a link to a discussion of the peer review of this paper and it includes all reviewer comments http://www.collabchem.com/2014/12/04/chemical-probes-and-parallel-database-worlds-who-wants-to-know-more-publishing-fun/

On 2014 Dec 02, Nadia Litterman commented:

Here is a link to the related paper on using maching learning to model an expert's evaluations and due diligence: http://www.ncbi.nlm.nih.gov/pubmed/25244007

On 2014 Nov 29, Christopher Southan commented:

Comparative statistics updated and live links added at http://cdsouthan.blogspot.se/2014/11/pmid-25415348-back-story-on-bioactivity.html

On 2014 Nov 28, Paolo Tieri commented:

This article is one of the "Multi-omic Data Integration" Research Topic in Frontiers, which focuses on data integration approaches and methods of any type and extent, their application in understanding the pathogenesis of specific diseases or in identifying candidate biomarkers, in order to exploit the full benefit of multi-omic datasets and their intrinsic information content. For more information about multi-omic data integration check http://journal.frontiersin.org/ResearchTopic/2280

On 2015 Jan 29, Christopher Southan commented:

Please make the separate molecular classes (the numbers of which are specified in the abstact) available for download. This should have been a condition for publication. I cant even open the CFAM seed file.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0160325. We believe the correct ID, which we have found by hand searching, is NCT01603251.

This comment is being posted as part of the OpenTrials.net project^[1] , an open database threading together all publicly accessible documents and data on each trial, globally. In the course of creating the database, and matching documents and data sources about trials from different locations, we have identified various anomalies in datasets such as PubMed, and in published papers. Alongside documenting the prevalence of problems, we are also attempting to correct these errors and anomalies wherever possible, by feeding back to the originators. We have corrected this data in the OpenTrials.net database; we hope that this trial’s text and metadata can also be corrected at source, in PubMed and in the accompanying paper.

Many thanks,

Jessica Fleminger, Ben Goldacre*

[1] Goldacre, B., Gray, J., 2016. OpenTrials: towards a collaborative open database of all available information on all clinical trials. Trials 17. doi:10.1186/s13063-016-1290-8 PMID: 27056367

* Dr Ben Goldacre BA MA MSc MBBS MRCPsych<br> Senior Clinical Research Fellow<br> ben.goldacre@phc.ox.ac.uk<br> www.ebmDataLab.net<br> Centre for Evidence Based Medicine<br> Department of Primary Care Health Sciences<br> University of Oxford<br> Radcliffe Observatory Quarter<br> Woodstock Road<br> Oxford OX2 6GG

On 2015 Apr 06, Jeffrey Ross-Ibarra commented:

Muñoz-Fuentes et al. offer an interesting look at the relationship between domestication and recombination rate in animals. A quick correction worth mentioning: while they cite my 2004 paper on recombination and domestication in plants (PMID: 14767840) several times, it's done somewhat out of context. They quote me as saying

'"recombination rate is likely of little importance" in relation to plant domestication (Ross-Ibarra 2004)'

whereas the actual quote from my paper clearly referred specifically to preadaptation:

"Other hypothesized genetic preadaptations, such as polyploidy (Hilu 1993), have been shown to be unimportant in determining the successful domestication of plant species, and the present analysis suggests that recombination rate is likewise of little importance."

and the abstract is fairly unambiguous:

"The results support the hypothesis that domestication selects for an increase in recombination..."

On 2014 Nov 30, Hilda Bastian commented:

Thanks for the helpful and informative reply, Tetyana.

While modeling can take account of some known variables, it can't overcome the limitations of measures based on these traditional theories. Other mechanisms that could explain the results remain. There are assumptions used to explain the results of these data simulations (such as that hiring and firing exposes people to conflict and hostility, but pay decisions do not) that remain open to question.

The results do not exclude the possibility that the women did not have enough authority in comparison with the men with whom they were compared, or other associated (in)tangible benefits that the men could take for granted with the "hire/fire/influence pay" status. Having equal status may indeed have brought similar benefits. Adequate markers for a particular status attainment for the original in-group from whom the measures were derived, may lack the power to discriminate unequal status for others. If so, then like is not necessarily being compared with like. It wasn't possible to "take all other job characteristics into account," because they weren't measured.

Using unreported modifications of measurement tools for the key outcome makes it difficult for others to be able to assess the validity of the data and its interpretation. It would be helpful if that were done within the larger project, and linked here. Depression implies an adverse mental health condition (both in the community and clinically), and the study's conclusions refer to health benefits, not happiness. The CESD has cut-offs for symptomatology that has no clinical relevance.

While there's no doubt that workplace circumstances for women and other traditional "out groups" must change, I don't believe on the basis of this data that people should believe that workplace authority over others per se makes women depressed. But the data are enormously valuable, and this work is indeed an important contribution to addressing an important social issue. Thank you for that, as well as the additional information in your reply.

On 2014 Nov 30, Tetyana Pudrovska commented:

Dear Hilda, thank you for your thoughtful and insightful comments and for engaging in this dialogue. It was a pleasure to ponder over the points you made and to consider our methodology, data, and findings from another perspective. Below are some of my thoughts.

1. The measure of depression does not have a clear clinical relevance. Different terms are used interchangeably. Each item is coded 0 or 1.

The most widely used term for the CES-D scale is depressive symptoms. We also use depression because it is a very general term that doesn’t refer to a clinical diagnosis. Depression is not a disease in the DSM, “major depressive disorder” is.

The CES-D items (like almost all other measures of self-reported physical and mental health) are highly skewed because most people report no depressive symptoms. Hence, the dichotomization of each item. We conducted a variety of sensitivity analyses using different coding approaches for the outcome, such as averaging all items and taking a natural log to reduce the positive skew, and the findings were remarkably similar.

The issue of using continuous scales vs binary diagnoses has received a lot of attention in sociology of mental health. Both approaches have strengths and weaknesses. Our findings hold in a variety of alternative models when we use a binary measure with a cutoff at the 75th percentile or at 10+ symptoms.

Sociologists typically prefer continuous scales because they are better for capturing the stressful consequences of social inequality. Unlike clinicians, sociologists are interested in the full spectrum of mental health, not only its negative extremes. To uncover the effects of social structures and social relationships on individual mental health, we need a continuum from mild to very severe that enables us to compare social groups on this scale. Binary diagnoses can obscure important differences because people who have, for example, 5 symptoms are in the same category as people who have no symptoms.

Because the effects documented in our study are large in magnitude and statistically significant after adjustment for many factors that are traditionally used to explain women’s higher depression, our findings provide important insights into the psychological consequences of social arrangements.

Ultimately, clinical relevance is not consistent with the brunt of our argument. One of the major implications of our study is that a higher level of depression among women in authority positions is not a clinical issue that can be addressed by diagnosing and treating specific individuals. It’s a social issue that should be addressed at the macro-level of society and the meso-level of organizations.

2. The observed differences in depression may reflect not the effect of job authority itself but the effects of many other job characteristics that differ between men and women with job authority.

The workplace situation is certainly not equal between men and women in authority positions. It is well-documented that in the same occupations and at the same levels of human capital characteristics, women have lower earnings, lower autonomy, and lower levels of many other desirable workplace characteristics than men.

Yet, the gender difference in depression documented in our study is not due to the differences in other job characteristics between men and women. Our models control for all these variables, and the effects of job authority are observed after we take all other job characteristics into account.

In addition to multiple regression, we use counterfactual approach to improve causal inference. It’s also called a “quasi-experimental” design because it simulates random assignment in an experiment. Our approach matches people with job authority (the “treatment” group) and people without job authority (the “control” group) in 1993 on many characteristics, including baseline depression, education, occupation, earnings, weekly hours, job characteristics and job satisfaction, marriage, parenthood, and early-life characteristics, especially parents’ socioeconomic resources. By matching people, we make the two groups as similar as possible with the exception of job authority and then see how depression changes over time based on people’s authority status in 1993.

It is also important that we conduct not only between-gender comparisons but also within-gender comparisons. Women with job authority have more depressive symptoms compared to women without job authority. In contrast, men with job authority have lower depression than men without job authority. What’s striking is that women with job authority in our study are socially advantaged in terms of most socioeconomic characteristics that are strong predictors of positive mental health. These women have more education, higher income, more prestigious occupations, and higher levels of job satisfaction and job autonomy than women without job authority. By all traditional models of socioeconomic status and health women with job authority should fare better than lower-status women. Yet we find the opposite.

3. Absence of direct measures of interpersonal stress, harassment, and prejudice.

Ideally we’d certainly like to have all possible measures of interpersonal stress and discrimination. But such a data set simply does not exist. The Wisconsin Longitudinal Study (WLS) that we use is currently among the best for our purposes. We are doing more work with other data sets, including the National Longitudinal Surveys, but all data have their advantages and limitations. So we are launching our own data collection. The current study, by documenting these patterns and providing a theoretically and empirically grounded interpretation, makes an important contribution and one of the first steps to address an important social issue.

The WLS has very rich array of measures of job characteristics. We include all variables that are considered main stressors in traditional theories of work stress. Yet, the effect of job authority persists net of these traditional explanations, which bolsters the indirect evidence for the mechanisms we propose.

The WLS started in 1957 and is still ongoing. We have information about our participants’ employment histories for the last 55 years. Job authority (but not depression) was measured for the first time in 1975 when our participants were 36 years old. We used this earlier measure of job authority in related articles that are all components of a larger project.

On 2014 Nov 29, Hilda Bastian commented:

This paper uses the terms "depressive symptoms" and "depression" interchangeably. However, the relationship between the screening questions asked and the "clinical" condition of depression is unclear. A modified form of an unspecified version of the CESD screening tool was used. It included an unspecified 10 of the 16 CESD questions, applied only for the last week. In a further variation to the CESD, answers were scored with only a dichotomous outcome.

The cut-off for determining "depression" was also not explained and the "clinical" relevance of the measure (and associated increase) is unclear. If there has been a validation of an association between the scores used here and depression, it was not referred to in the paper. More details on this would be helpful to people interested in interpreting the results of this study.

The workplace situation was not equal between the men and women bracketed in the same job authority categories in this sample. The women worked fewer hours per week, earned less than the men of the same age, and were supervised more often. It's women's job authority with less pay and less freedom than men's job authority that is being compared. That would also be a function of the gender inequality the authors identify as a clear problem here. But it raises a question about the level of emphasis given to the psychological impact of having supervisory authority, and, therefore, to know what to do about it.

The range of workplace factors addressed by this study include the traditional ones related to autonomy. Those questions don't address the kinds of gender-related issues the authors point to in the literature as constituting psychological workplace adversity for women in management: such as endemic social exclusion by peers and supervisors, frequent slights from all directions, being judged more frequently as socially disruptive, unequal opportunity and status attainment, and harassment. More sensitive tools (and relevant data from before the age of 54) would have been needed to unpack what made that generation of women unhappier than the men. The underlying point these authors show, though - that psychological aspects of the workplace experience have serious bearing on women's happiness - is a critical one.

The full text of this article is available here.

On 2015 May 31, Shin Lin commented:

This response discusses the manuscript submitted by Gilad and Mizrahi-Man at F1000Reseach, as well as our two responses at that journal. For details, we encourage interested individuals to read those various pieces.

The batch effect that Gilad and Mizrahi-Man present as confounders of our findings are not the result of experimental protocols. Our sequencing libraries were largely prepared in one sitting by the same person, and we used matched primer indices/barcodes to minimize variation as observed in 't Hoen PA, 2013. The potential batch effect to which Gilad and Mizrahi-Man are referring is from sequencing on different lanes/flow cells/sequencing machines. In our experience, these effects are small (also found in 't Hoen PA, 2013), and we did not observe any such effects in the original published data. However, to further settle the issue, we reconstructed the sequencing libraries under a different multiplexing scheme to address their concerns, and we found the same clustering pattern as originally presented by Lin et al. Thus, we emphatically disagree with the conclusion from Gilad and Mizrahi-Man that our conclusions are “not warranted,” but rather, we argue that objective normalization procedures allow the discovery of the clustering of transcriptomes by species.

Gilad and Mizrahi-Man found clustering by tissue after normalization, because in their attempt to account for lane/flow cell/sequencing machine effect, they normalized away the species effect. In that set of experiments, tissues of the same species were multiplexed on the same sequencing lane; accounting for primer indices would not have been possible otherwise. That normalization of the data by each species separately causes clustering by tissue was known to authors of Lin S, 2014, as this observation was presented in the Mouse ENCODE main paper Yue F, 2014.

Gilad and Mizrahi-Man's work focused on one particular dataset in Lin S, 2014. However, that paper contains a principal component analysis (PCA) on data from multiple sources: Stanford (human, mouse), Salk (human), HBM (human), LICR (mouse), and CSHL (mouse). There are undoubtedly many technical differences between the various sources. Yet, the clustering by species was seen in higher order principal components (PCs) (see Figure 1A Lin S, 2014); clustering by tissues, in lower components (Figure 1B in Lin S, 2014) or by normalizing species separately (Extended Data Fig. 1C of Yue F, 2014). The same behavior is seen in the Stanford-only data—both in Lin S, 2014, which minimizes primer index effect (Figure 1C & 1D) and now the newly generated results that account for lane effect. The latter are consistent with our earlier observation that experimental batch did not drive the species-specific clustering.

As for the latest criticisms concerning sample collection, these are issues outside the scope of the manuscript by Gilad and Mizrahi-Man. We state that our procurement practices are consistent with what other investigators have done and continue to do. When we limit our analyses to the small number of tissues examined by recent studies showing tissue specific-clustering (i.e. those with a large number of tissue-specific genes), we also find tissue specific clustering (see Figure 1F in Lin S, 2014). Thus, there are no inherent biases in our data which account for species-specific clustering. Rather, it is our complete dataset with many additional tissue types which results in the different clustering pattern. This evaluation of a broad tissue set is the critical difference which led to our finding of species-specific clustering. Indeed, when we examine the broad dataset of mouse and human CAGE expression data from the Riken Fantom 5 project (FANTOM Consortium and the RIKEN PMI and CLST (DGT)., 2014), we confirm species-specific clustering.

Finally, as stated in the F1000 comment, we reiterate our enthusiasm of the mouse as a vital model system for experimental research, because of its many similarities to humans, which we show in our PNAS paper. However, an appreciation of the differences which exist between human and mouse will allow investigators to better interpret the disparities which are encountered when applying findings in the mouse model to humans.

***New data mentioned herein is available for download at the Mouse ENCODE website.

Shin Lin^1,2 , Yiing Lin³ , Michael A. Beer⁴ , Thomas R. Gingeras⁵ , Joseph R. Ecker^6,7 , Michael Snyder¹

¹ Department of Genetics, Stanford University, 300 Pasteur Drive, M-344 Stanford, California 94305; ² Division of Cardiovascular Medicine, Stanford University, Falk Building, 870 Quarry Road Stanford, California 94304; ³ Department of Surgery, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8109, St. Louis, Missouri 63110; ⁴ McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205; ⁵ Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742;⁶ Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; and ⁷ Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037.

Acknowledgement: We thank the other members of the Mouse ENCODE consortium in formulating this response.

On 2015 May 26, Steven Salzberg commented:

Serious technical questions have been raised about the main conclusion of this paper. Specifically, Yoav Gilad and Orna Mizrahi-Man described how the human and mouse samples were processed separately in several ways, any of which could lead to a significant "batch effect." They published some of their findings in F1000 Research, at http://f1000research.com/articles/4-121/v1. They showed that after removing the batch effects, the finding that human and mouse genes cluster separately completely disappeared. In the discussion of that paper on the F1000 site, further sources of batch effects were identified. Thus it appears that the main finding of this paper cannot be supported by the data, because the samples from human and mouse were handled and processed in distinct ways, confounding the batch effect and any possible biological effect.

On 2015 Jan 24, Wichor Bramer commented:

I think this article is a rathor open door article, in that its conclusions can be drawn beforehand, wihout executing the experiments. If you consider PICOS as PICO + S, surely then of course PICO will retrieve more relevant articles and PICOS sarches will be more specific. The searches used for testing PICOS were the exact searches for PICO, with an added element of S, which in this case was very basic (two or three tersm), compared to the exhaustive translation of the other elements (more than 10 terms). PICO, PICOS and SPIDER should not be used in the creation of search strategies. Not every element in those methods is necessary in a search query. Including specific outcomes and controls can introduce bias in the search results. For a good thorough systematic review, only P and I are used, and when necessary combined with a sensitive filter on study design, that consists of more than three terms and is verified (when possible). PICO, PICOS ad SPIDER can be useful in the process of evaluating the retrieved full text references for inclusion, but should not direct the search strategy.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT00696414. We believe the correct ID, which we have found by hand searching, is NCT00696514.

This comment is being posted as part of the OpenTrials.net project^[1] , an open database threading together all publicly accessible documents and data on each trial, globally. In the course of creating the database, and matching documents and data sources about trials from different locations, we have identified various anomalies in datasets such as PubMed, and in published papers. Alongside documenting the prevalence of problems, we are also attempting to correct these errors and anomalies wherever possible, by feeding back to the originators. We have corrected this data in the OpenTrials.net database; we hope that this trial’s text and metadata can also be corrected at source, in PubMed and in the accompanying paper.

Many thanks,

Jessica Fleminger, Ben Goldacre*

[1] Goldacre, B., Gray, J., 2016. OpenTrials: towards a collaborative open database of all available information on all clinical trials. Trials 17. doi:10.1186/s13063-016-1290-8 PMID: 27056367

* Dr Ben Goldacre BA MA MSc MBBS MRCPsych<br> Senior Clinical Research Fellow<br> ben.goldacre@phc.ox.ac.uk<br> www.ebmDataLab.net<br> Centre for Evidence Based Medicine<br> Department of Primary Care Health Sciences<br> University of Oxford<br> Radcliffe Observatory Quarter<br> Woodstock Road<br> Oxford OX2 6GG

On 2015 Oct 03, Torsten Seemann commented:

The source code is available at https://github.com/broadinstitute/pilon/wiki

On 2016 Sep 14, Peter Hajek commented:

There exists a simple test of whether the 'gateway effect' applies to humans. Over the past 60 years, the prevalence of smoking among young men in the US and UK declined about 4-fold. If nicotine use leads to increased use of cocaine and other drugs, the use of other drugs should decline as well. There is no sign of that.

On 2017 Jul 07, Wei Wang commented:

Several other problems have been reported: https://pubpeer.com/publications/DAA39CA8966C9B4DAB38EDAA343B4C

On 2014 Dec 15, Ivan Shatsky commented:

General comment: The phenomenon studied in this paper is very exciting. I read the article with a great interest. Unfortunately, I regret to say that the underlying mechanism remained uncovered. Although I agree that the authors identified some curious structures within the 5’UTRs of HOXA mRNAs which might be implicated in the regulation of these mRNAs by RPL38, I did not find sufficient evidence for existence of IRES-elements in these mRNAs. As in numerous other similar investigations, to identify IRES-elements the authors employed the method of DNA bicistronic constructs, the approach that had been repeatedly shown to be associated with almost unavoidable artifacts (see Jackson Cold Spring Harb Perspect Biol. 2013 Feb 1;5(2); Lemp et al. Nucleic Acids Res. 2012 Aug;40(15):7280-90.). And I suspect this paper is not free of those artifacts either (see below). Several crucial control experiments necessary to support or to exclude the IRES-mediated mechanism have been recently described (for references see Shatsky et al. Mol Cells. 2010 Oct; 30(4):285-93). One of them, for instance, is the ratio of translational activities for m7G capped versus uncapped (A-capped) monocistronic constructs. This value estimates contribution of the cap to the translational potential of a 5’UTR under selected conditions. If this contribution is very high (as is the case of cap-dependent mRNAs) one may exclude the presence of a true IRES. I think that this and other obligatory controls are feasible to perform with cells C3H10T1/2 used in this paper but they were not done.

Some specific points:

1. The authors regard the cap-independent and IRES-dependent modes of translation initiation as synonymous mechanisms and support this notion with reference 21. I should stress that not all specialists in eukaryotic translation would share this opinion since nobody has ever shown that a 5’end dependent translation initiation cannot be regulated by specific structures within the respective 5' UTR. The opposite has recently been demonstrated (Terenin et al. Nucleic Acids Res. 2013 Feb 1;41(3):1807-16.)
2. When listing examples of cellular IRESs identified to date (second paragraph), the authors mention c-myc, Apaf-1, XIAP. To the best of my knowledge, these cellular IRESs have been disproved (Andreev et al. Nucleic Acids Res. 2009 Oct;37(18):6135-47; Bert et al. RNA. 2006 Jun;12(6):1074-83; Baranick et al. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4733-8; van Eden et al. RNA. 2004 Apr;10(4):720-30); Lemp et al. Nucleic Acids Res. 2012 Aug;40(15):7280-90. )
3. “Extended data Figure 1a” raises a great concern: the HCV IRES should not be used as a normalizing construct for testing bicistronic DNAs since the HCV IRES has been reported to harbor a cryptic promoter (Dumas, E. et al. 2003 Nucleic Acids Res. 31 (4): 1275-1281) and hence may produce capped monocistronic mRNAs . By the way, among viral IRESs characterized to date the HCV IRES is regarded as one of the weakest.
4. The control test with Rluc shRNA (Extended data Figure 1 b,c) strongly suggests that some significant amount of monocistronic (and therefore capped) Fluc mRNAs is present in transfected cells since the residual Fluc activity after RNA interference is too high. This may also be the case for the control bicistronic mRNA containing the HCV IRES (see point 3). Otherwise, the pictures 1b and 1c must be similar. At least, in the analogous test performed in our lab, the Rluc and Fluc activities fall down to the similar background levels (Fig. 2D in Dmitriev et al. Mol Cell Biol. 2007 Jul;27(13):4685-97).
5. The authors suggest that the IRES elements are mostly confined within ~300 nts proximal to the start codon. As a support to this conclusion, they note that some of HOXA mRNAs possess a 5’ UTR of that size. If so, why the activity of HOXA9 construct 944-1266 is much lower than that for the full length 5’UTR (Fig. 1d)?<br>
6. “Extended Figure 1d”. This control is useless. It only shows that the bicistronic mRNA of the expected size is present in transfected cells but unable to show the presence of monocistronic mRNAs starting within the intercistronic region. The corresponding bands won’t be seen.
7. On the base of pull-down experiments the authors claim that 80S ribosomes are specifically formed on their IRES-elements. The problem is that they use 10mM of magnesium in these expts, i.e. the concentration at which the assembly of translation initiation complexes in mammalian systems should not occur.
8. The mode of action of TIE element looks absolutely puzzling. It is even difficult to imagine any mechanism for its operation. My question: is it specific to these particular cells?

On 2015 Jan 12, Larry Parnell commented:

This paper was my selection for Paper of the Week for 15-19 Dec 2014.

On 2015 Feb 06, Ryan Radecki commented:

Post-publication commentary: "Social Media in Medicine – Useless!"

Or, might it be how you use it that matters?

This is a brief report from the journal Circulation, regarding a self-assessment of their social media strategy. The editors of the journal performed a prospective, block-randomization of published articles to either social media promotion on Facebook and Twitter, or no promotion, and compared 30-day website page views for each article. 121 articles were randomized to social media and 122 to control, and were generally evenly balanced between article types.

And, the answer – unfortunately, for their 3-person associate editor team – is: no difference....

http://www.emlitofnote.com/2014/11/social-media-in-medicine-useless.html

On 2015 Nov 25, S A Ostroumov commented:

This article is exploring new links between issues of ecology (trophic web, trophic chains) and medicine (malaria control). It is very interesting.

On 2014 Dec 30, Kausik Datta commented:

To add to Hilda Bastian's informative comment, the press release mentions the misleading statement not only in the title, but also in the first paragraph - stating definitively: "The study, published Nov. 17 by Proceedings of the National Academy of Sciences, shows that triclosan causes liver fibrosis and cancer in laboratory mice through molecular mechanisms that are also relevant in humans." (Emphasis mine.)

This is, at best, irresponsible journalism (and at worst, a terrible disservice to people living with cancer). What seems particularly galling is the fact that this sacrifice of scientific accuracy at the altar of needless sensationalism in the press release was perpetrated by none other than the University (UCSD) at which the work was done. This brings to mind once again the age-old tussle in science communication, between science and journalism.

At the same time, the authors cannot deflect the blame completely, especially since the lead author, quoted in the Press Release, didn't seem to emphasize at all the dosage effect of Triclosan administration and exposure route - which is rather odd, given that the Triclosan was either fed to the mice or injected directly into their peritoneal cavity at a high enough amount, none of which would apply to humans.

I hope the authors pay heed to the most germane points raised by Hilda about the further inclusion of the data; I'd be most interested in the actual experimental outcomes.

On 2014 Nov 21, Hilda Bastian commented:

The title and abstract of this article focuses on the positive finding in tumor promotion, without emphasizing that the findings were negative on causation, in a way that is clearly accessible for non-specialist readers. This is of particular importance, as a university press release issued for this study was headed with this misleading statement: "The dirty side of soap: Triclosan, a common antimicrobial in personal hygiene products, causes liver fibrosis and cancer in mice." This encouraged unwarranted alarm in the community (which I discuss further in this blog post).

A 2010 inventory of animal and clinical studies of triclosan safety (Rodricks JV, 2010) found that oncogenicity studies to that point had not found cancer-related increases in any species, except for liver cancer in mice. Without pre-registration of studies on this question, we are unaware of what the outcomes have been for all oncogenicity studies on this substance, and thus whether there is publication bias.

Further areas of uncertainty relate to the experiments here. The article does not report sufficient data and methodological information to enable adequate assessment of the level of uncertainty associated with the experiments (see the NIH's Proposed Principles and Guidelines for Reporting Preclinical Research). It would be helpful if the authors took the opportunity to include key data here, specifically:

• how the sample size was determined;
• the inclusion/exclusion criteria;
• exact data on the experiments' results (including confidence intervals);
• whether or not allocation of mice to the groups was random, and if so, details of the method of randomization (including whether or not there was blinding);
• whether there was blinding in outcome assessment.

On 2014 Nov 20, Neven Patrick commented:

Looks like estrogen removal reduced the proliferation significantly and probably the tumor has high ER mRNA score and very sensitive to estrogen deprivation. My thought is to regard this tumor as luminal A. Also important would be to check the probability of the class assignment by PAM50. Some cases surely will have lower probability than others and this case might be one of those. Because I presume single case PAM50 algorithm based on distance from centroid of model cases of intrinsic subtype will be forcing the class assignment for the cases which in the clustering would be gray zone cases. Does Prosigna report provide such QC measure? Soon Paik

Truly fascinating (and not so simple) questions! To my knowledge this has not been studied, and I agree that removal of estrogen could potentially alter the proliferative rate of the tumor (and proliferation is a dominant aspect of most MGS to date). For this patient I would base treatment on the higher risk result. Kathy Albain

If one measures Ki67 on the core it will be higher because pt is on E but if you measure it again 2 wks later on the surgical specimen it will be lower and won't agree with that done on the core. I would be surprised if that is not true. C.Kent Osborne

Just saw a patient with an ER+ cancer, ki67 30% on core biopsy. Stopped HRT. Had surgery for T2N0 IDC and oncotype 14. Oncologist recommended chemo due to Ki67. Repeated ki67 on surgical sample and it was less than 5%. There is clearly an education opportunity here. Presumably the lower ki67 after stopping HRT is predicative of outcome and impact of hormone therapy. Interesting.<br> Hope S. Rugo

On 2015 Feb 18, Christophe Dessimoz commented:

Note that this article was published as open access and is thus freely available from the publisher's website.

On 2015 Jan 05, NephJC - Nephrology Journal Club commented:

This study was discussed on Dec 2nd 2014 in the open online nephrology journal club, #NephJC, on twitter (along with a related article).

Introductory comments, written by Eoin O'Sullivan, are available at the NephJC website and cross-posted at the Renal Fellow Network blog.

The discussion was quite intense, with more than 50 participants, including nephrologists, emergency medicine physicians, fellows and residents as also two of the authors, Bhupinder Singh and Edgar Lerma.

A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website.

The highlights of the tweetchat were:

• There is considerable interest in a drug such as ZS-9, given the incidence of hyperkalemia, both acute and chronic, sometimes resulting in the need to stop ACE-inhibitors and ARBs in CKD patients.

• There was considerable discussion about the choice of placebo (as against sodium polystyrene sultanate, or diuretics and/or low potassium diet) as a comparator; the authors provided insight that this was mainly to comply with FDA requirements.

• Though the results of the trial show that ZS-9 as studied was effective in lowering potassium levels, more information about the differential incidence of edema as also the details of diuretic use in both groups was sought.

Overall, though there is considerable enthusiasm about the availability of new agents for management of hyperkalemia, considerations of safety, cost and data from more studies will determine how widely this drug will be used once licensed.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.

On 2016 Apr 20, Jennifer S Walsh commented:

It wasn't possible to get perfect matching for all the factors, so it was done in order of: gender, age, height, postcode and smoking. Because smoking was the lowest priority, there were a few pairs who were matched on the other factors but not on smoking. The number of smokers was low overall, and we don't think the imperfect matches for smoking had any influence on the study results.

On 2016 Apr 15, Jose M. Moran commented:

There is an issue that needs to be addressed. Controls were recruited to be individually matched to an obese participant by sex, age (±3 years), height (±5 cm), postcode and smoking status (current smoker or nonsmoker). If controls were matched 1:1 by the smoking status, how it is possible that the percentage of current smokers differs between normal and obese subjects across all the age groups (except in men aged 25-45 years n=6)?

On 2016 Oct 03, Morten Oksvold commented:

Please note that after an investigation at the University of Cologne, six articles where T. Wenz figures as first or senior author were found to contain questionable data due to scientific misconduct. This article is one of these six articles.

The conclusion from the report was ready June 28, 2016, please see the link (in German):

http://www.portal.uni-koeln.de/9015.html?&tx_news_pi1[news]=4335&tx_news_pi1[controller]=News&tx_news_pi1[action]=detail&cHash=1deb8399d7f796d65ca9f6ae4764a1ce

On 2014 Dec 04, David Keller commented:

Cause and effect cannot be distinguished in the observed associations

Dopamine levels are reduced in the brains of patients with Parkinson's disease (PD). Dopamine inhibits the secretion of prolactin, and prolactin, in turn, reduces the activity of the steroid sex hormones (estrogen, testosterone, etc.) Thus, untreated PD patients should have low brain dopamine levels, high prolactin levels and thus low sex steroid hormone levels. These hormone actions are well-documented in physiology texts.

The next clinical scenario to consider is the effect of treating PD with levodopa, which is metabolized to dopamine in the brain. Clearly, brain dopamine levels will rise, driving down prolactin levels, which, in turn, allows an increase in sex steroid levels, ameliorating, to a variable degree, the hypogonadism caused by untreated PD.

To what degree does the dose of levodopa, taken in amounts sufficient to control the movement disorder symptoms of PD, also treat the hypogonadism caused by PD? This question is not addressed in the abstract.

The authors conclude that lower sex steroid levels and higher prolactin levels "may result in a bigger susceptibility to the disease in men." This observational study cannot possibly prove the cause-and-effect mechanism implied in that statement. The observed associations are explained equally well by the opposite conclusion: that PD causes men to have lower dopamine levels, higher prolactin levels and consequently lower sex steroid levels (hypogonadism), in other words, that hypogonadism is an effect of PD, not a cause. It would require a randomized, controlled interventional study in which hypogonadal PD patients were repleted with administered exogenous sex steroids to prove that hypogonadism is a cause, rather than just an effect, of PD.

On 2015 Jan 12, Larry Parnell commented:

This paper was my selection for Paper of the Week for 17-21 Nov 2014.

On 2014 Dec 19, Scott Federhen commented:

I am Scott Federhen, author of this article, and would like to report some aspects of our genomes from type that were discovered too late to include in the manuscript. A visual inspection of our k-mer tree revealed two genomes from type for Bacillus subtilis subsp. spizizenii that are placed quite distantly from each other.

The average nucleotide identity (ANI) statistics from the alignments of the type genomes from the relevant subspecies of Bacillus subtilis are as follows:

96.7997 CP002905 ADGS01 89.7316 94.8698 – spizizenii vs. spizizenii

94.6427 CP002905 AMXN01 89.4248 86.6265 – spizizenii vs. inaquosorum

93.2854 CP002905 AL009126 88.7053 88.4756 – spizizenii vs. subtilis

89.7% of CP002905 aligns with 94.9% of ADGS01, and the parts that align share 96.8% average nucleotide identity. These two genomes a likely to be from the same species, but probably not from the same subspecies - and certainly not from co-identical strains.

To examine this problem systematically, we looked for all of the cases where we had more then one genome from type from the same species (or subspecies) and sorted them by pairwise ANI. These were usually from different culture collections and often sequenced in different labs. 274 pairwise combinations break down like this:

4 pairs of genomes < 90% identical.

5 pairs of genomes 96% - 99% identical.

8 pairs of genomes 99% - 99.9% identical.

112 pairs of genomes 99.9% - 99.99% identical.

135 pairs of genomes 99.99% - 99.999% identical.

10 pairs of genomes > 99.999% identical

This is a wide range for genomes from strains that are supposed to be co-identical. The four most diverse pairs are likely to be from different species. The problem could lie in many places - the annotation in the sequence entries, a strain mixup in the sequencing lab, or a contamination, misannotation or misidentification in the culture collection. We are working with submitters and culture collections to resolve the most egregious discrepancies and improve the reliability of our subset of genomes and sequences from type. At some point the community is going to have to come to a consensus as to what constitutes identity between co-identical strains.

We look forward to the day when every described species of prokaryote has a complete genome sequence, and a genome is included with every new species description. At that point it would be useful for each culture collection holding strains from type to sequence at least a low-coverage genome to verify the identity of the strain.

On 2017 Jul 13, Randi Pechacek commented:

Sean Gibbons, first author of this paper, provided some background information on microBEnet.

On 2015 Feb 26, Harri Hemila commented:

Missing contradictory findings and other problems in Curtis AJ, 2014

Curtis AJ, 2014 state in their abstract that “The evidence from pooled analysis of 18 randomised controlled trials undertaken in apparently healthy people shows no effect of vitamin E supplementation at a dose of 23-800 IU/day on all-cause mortality.” This conclusion was based on the pooling of results from 18 RCTs that obtained RR = 1.01 (95% CI: 0.97 to 1.05).

In their calculation of the average effect of vitamin E from the 18 studies, Curtis (2014) assume that there exists an overall uniform effect for all of those 18 RCTs, which can be estimated by pooling their findings. However, a subgroup analysis of the ATBC Study (1994) refutes the notion that the effect of vitamin E is uniform for all people. The combination of age and dietary vitamin C in the subgroup analysis modified the effect of vitamin E, which provides very strong evidence of heterogeneity over 6 subgroups (P = 0.0005) Hemilä H, 2009. Such heterogeneity refutes the assumption of a uniform effect in pooling the findings of the 18 RCTs by Curtis (2014).

Curtis AJ, 2014 also state “Subgroup analyses by ... duration of exposure ... showed no association with all-cause mortality.” However, the effect of time should not be analyzed by comparing RCTs at the study level, some of the RCTs being long in duration while the others being short in duration. In the ATBC Study, harm from vitamin E in the young participants was seen after 3.3 years of supplementation. Longer vitamin E supplementation increased mortality by 38% (17% to 63%), whereas vitamin E had no effect on mortality over the earlier period, see Hemilä H, 2009. This finding of a time-dependent effect modification refutes the claim that the duration of vitamin E supplementation does not modify the effects of the vitamin with regard to all-cause mortality. Comparing RCTs on vitamin E by the mean durations of the RCTs, ie study-level analysis, cannot capture changes in the vitamin E effect after lag periods. Instead the analysis of time-dependent effect modification requires individual-level analysis.

Ecological fallacy occurs when mean data about a group is used to impute identical values for all individuals of the group. Thus, the assumption by Curtis AJ, 2014 that the calculated average effect of vitamin E on mortality for the 18 RCTs (ie RR = 1.01) is valid for all participants in these 18 studies, or for other individuals in the community, is an example of ecological fallacy. The conclusion by Curtis AJ, 2014 that “duration of exposure ... showed no association with all-cause mortality” is another example of ecological fallacy.

We do not know how far the heterogeneity of the ATBC Study can be generalized. The participants in that study were middle-aged males, who were aged 50-69 years at the start of the trial in the 1980s, which indicates that they were born before WW-II. In addition, all were smokers and lived in Finland. We do not know if similar effect modification occurs in other populations. Nevertheless, the heterogeneity found in this particular cohort refutes the notion that there might be a universal vitamin E effect on mortality that would be valid for all groups of people. Highly significant heterogeneity was also found in the effect of vitamin E on pneumonia incidence in Hemilä H, 2011 and on the incidence of the common cold in Hemilä H, 2006. Thus the evidence of heterogeneity of the vitamin E effect is not restricted to overall mortality but exists to other outcomes as well.

Furthermore, in the Table 1 of Curtis AJ, 2014 it is stated that the “study quality” of the ATBC Study (1994) was “medium”. As a justification for this classification, in Appendix 2 (“quality of included studies”) Curtis AJ, 2014 inserted question marks next to “blinding of personnel” and “blinding of participants” and a cross (to indicate high risk of bias) to “blinding of outcome assessment”.

The ATBC Study (1994), Alpha-Tocopherol, Beta Carotene Cancer Prevention Study Group., 1994, reported that “Participants and all study staff involved in the ascertainment of end points and the assignment of final diagnoses remained blinded to the participants' treatment assignments throughout the trial” (p. 1030). The same report also stated that “Deaths (n=3570) were identified from the National Death Registry, a branch of Statistics Finland” (p. 1030), which clearly indicates that the deaths in the ATBC study were recorded by an organization that had nothing to do with the administration of the tablets. Thus, the claims by Curtis (2014) about the blinding of participants and personnel in their Appendix 2 are inconsistent with the ATBC Study (1994) report.

Transparency in systematic reviews is important, so that the reader is correctly informed what the basis for the quality assessments is. Curtis AJ, 2014 do not give any explanations about why they dismiss the descriptions about blinding in the ATBC Study (1994) report. Therefore the readers are misled about the quality of the study that has the greatest weight in Fig. 2 of Curtis (2014).

Finally, the ATBC Study (1994) is wrongly cited in Curtis AJ, 2014. They write Virtamo (1998) in Fig. 2 ,Virtamo (2006) in Appendix 2, and Virtamo (2003) in the reference section. All of these three years are wrong. The ATBC Study was actually published in 1994, with the PubMed record Alpha-Tocopherol, Beta Carotene Cancer Prevention Study Group., 1994 (the correct year and reference). Virtamo (2003), which is listed in the reference section, does exist but it is a post-intervention follow-up report of the trial and not the correct reference for the main results of the ATBC Study (1994).

On 2017 Jan 09, Kausik Datta commented:

I came to this paper after reading about Dr. Hadiyah-Nicole Green on Social Media. Much plaudits to Dr. Green and her team. The principle - conversion of near Infra Red light to thermal energy by Gold nanorods - is exciting and full of possibilities, and the proof-of-concept is well-demonstrated both in vitro and in vivo. The question that I had about the AuNR-only group in Figure 2D is answered in the discussion, although I'd have loved to see confirmation of the visible light PTE hypothesis: because if visible light is able to show similar effects on AuNRs, it might make their therapeutic spectrum broader - but bring in problems of specificity as well. In cancer therapeutics, specificity/focus of treatment is an important issue in respect of preserving good cells and destroying rogue, tumorous ones. Ideally, visible or any other light should have minimal effect, while NIR should have maximal on rousing the AuNRs, so to speak.

Also in that respect, while intratumoral delivery of AuNRs takes care of stationary tumors, perhaps an antibody/ligand-based mechanism in conjunction with AuNRs may in future be able to target metastatic tumors as well? This is excellent work that I shall be much interested to follow. (I note that this paper is from 2014. Perhaps Dr. Green would be kind enough to provide a status update?)

On 2015 Mar 03, Dita Gratzinger commented:

We congratulate the authors on a comprehensive overview of this very complex and evolving field of research. Many of the crucial studies represent in vitro and mouse model research; we are characterizing the state of the intact bone marrow stroma in myelodysplastic syndromes. The authors state that

"Multiple data have shown that osteoprogenitors—MSPCs—exhibit normal morphology and frequency in the bone marrow of MDS patients, as well as undisturbed osteoblastic, adipocytic and chondrocytic differentiation potential in vitro."

We have recently published data, not available at the time this review was written, regarding the architecture and extent of the CD271+ mesenchymal stromal cell compartment in intact human bone marrow core biopsies Johnson RC, 2014, and in fact demonstrate an increase in the density of this compartment in higher grade MDS as compared to lower grade MDS and marrow from similarly aged cytopenic patients. We also found an association of high CD271+ mesenchymal stromal cell density with shorter overall survival among patients with MDS, independent of IPSS-R and history of transfusion. We acknowledge that it is not clear whether functionally described osteoprogenitors correspond to all or a subset of CD271+ mesenchymal stromal cells; however, as cited in your review, we have previously shown Flores-Figueroa E, 2012 that CD271+ mesenchymal stromal cells express CXCL12 and arborize extensively within marrow, in association with marrow vasculature, and are intimately associated with the majority of CD34+ hematopoietic stem/progenitor cells in intact human marrow, and are thus good candidates to represent a key functional component of the human bone marrow hematopoietic progenitor/stem cell niche.

On 2014 Nov 14, Hilda Bastian commented:

Very useful data on an important issue, given the high proportion of the population using contact lenses (Swanson MW, 2012). On the issue of the level of individual risk, readers might find a review of large-scale epidemiological studies helpful (Stapleton F, 2013).

The authors stress the importance of good lens hygiene to reduce the risk of infection. That's a critical issue, and people may well over-estimate the adequacy of their own lens care (Bui TH, 2010). Given the increased risk of extended wear (rising from 2-4 per 10,000 for daily use to about 20 for extended wear Stapleton F, 2013), users being better informed about reduced wear as a way of lessening risks may also help (covered along with social and historical aspects in this blog post.)

On 2014 Nov 24, Alexis Clapin commented:

Congratulation for your important work. In table 1, you state that the first approache to addressing attrition bias is intend-to treat analysis. Intend to treat analysis includes all data but when a clinical trial suffers from attrition bias, patients followed up for a longer duration are favouring one of the compared product. For a lot of outcome criteria, a longer duration means a more important impact on the criteria. Consequently, the intend to treat analysis is a biased evaluation of the difference between groups. An example of the impact of attrition bias on the intend-to-treat analysis is given in this article http://www.ncbi.nlm.nih.gov/pubmed/23662092. Without complete data, the best way to evaluate attrition bias is the comparison of intend-to-treat analysis and per-protocol analysis. If the per-protocol analysis provides us with a "better" result than intend-to-treat analysis, it means that patients followed up for the longer duration are favouring one of the compared product. This comparison should be done for all truncated trials. Unfortunately, it is not the case and a lot of clinical trials are truncated ; almost all based on survival analysis. To conclude, if intend-to-treat analysis is the only performed analysis, it is a good way to mask an attrition bias.

For french readers : a more complete evaluation of the advantages of performing both analysis : http://www.etudes-et-biais.com/per-protocole-ou-intention-de-traiter-les-deux-svp/

On 2014 Dec 31, Dennis Eckmeier commented:

We deposited an earlier version of the manuscript on the free pre-print repository bioRXiv: http://biorxiv.org/content/early/2014/08/12/002550

On 2013 Oct 25, DAVID SANDERS commented:

From abstract from Kikuchi A, 1989

"In this paper, two proteins stimulating the GTPase activity of smg p21 are partially purified from bovine brain cytosol. These proteins, designated as smg p21 GTPase-activating protein (GAP) 1 and 2, are separated from a c-ras p21 GAP described previously by column chromatographies. smg p21 GAP1 and -2 stimulate the GTPase activity of only smg p21 but not that of c-Ha-ras p21 or the rho and smg-25A GTP-binding proteins. The Mr values of smg p21 GAP1 and -2 are estimated to be 250-400 x 10(3) and 80-100 x 10(3) by gel filtration and sucrose density gradient ultracentrifugation, respectively. The activity of smg p21 GAP1 and -2 is killed by tryptic digestion or heat boiling. These results indicate that bovine brain contains two smg p21 GAPs in addition to c-ras p21 GAP.

On 2014 Nov 24, Guillaume Filion commented:

This article is one of the "CISCOM meta-analyses", which are very similar papers written by different authors. For more information about the CISCOM meta-analyses, check the blog post "A flurry of copycast on PubMed" at the following link http://blog.thegrandlocus.com/2014/10/a-flurry-of-copycats-on-pubmed

On 2017 Apr 05, Misha Koksharov commented:

None

On 2017 Apr 04, Misha Koksharov commented:

Great! Thank you! Apparently, in your field people normally don't describe the mutagenesis part much (in contrast to protein engineering field per se) and focus on characterization of the final version as I see from various papers.

On 2017 Mar 30, Yi Shen commented:

Thanks Misha for your interest in our work! We are happy to provide further detailed information regarding the experimental procedures. Please email me at yshen3@ualberta.ca.

On 2017 Mar 20, Misha Koksharov commented:

The developed FPs are nice. However, the experimental details (and intermediate results) of mutagenesis procedures are very limited and insufficient. It's impossible to understand what exactly you were doing at this part of the study.

On 2015 Nov 25, Uday Yanamandra commented:

Author name Uday Y should read as Yanamandra U

On 2015 Jul 23, thomas samaras commented:

Over 80 diverse populations show that weight increases as the cube of height increase. For example, the publication Advancedata, US Department of health, education, and welfare, Nov 19, 1976, Table 7 provided data for 18-24 year olds which allowed the following calculations.

Males: 1971 vs. 1960: (69.7"/68.7")cubed x 158 lb = 165 lb (predicted by cubed law) Actual weight given for taller cohort = 165 lb

For females, the results were 130 lb predicted and 132 lb actual.

Another publication, Secular growth and its harmful ramifications, 2002, confirmed the height cubed law (not height squared or BMI law)for five populations (Table 1):

Harvard male entrants (1958 vs. 1930) Wellesley female entrants (1958 vs. 1930) Malina's child data (1958 vs. 1934) Swedish males (n= 488,732) (1971 vs. 1960) US population (18-74 years)(1971 vs. 1960)

A number of more recent studies provide data that support the Ponderal Index or height cubed law.

On 2015 Mar 11, IRWIN FEINBERG commented:

Crawley et al 1 state that there have been few longitudinal studies of sleep/wake timing across adolescence. They fail to take note of our findings in a ten-year longitudinal study of 93 subjects aged 6-18 years. Sleep EEG was recorded twice yearly on habitual school-night schedules in subjects aged 6-18 years. In addition, weekend recordings with extended time in bed and a follow-up night, were obtained from subjects 9-18 years. Results published thus far could have added perspective to the findings of Cowley et al. In addition to defining the trajectories of NREM delta and theta EEG power 2, 3, their within-night dynamics 4, and their relations to puberty 5 and daytime sleepiness 6, we documented changes in NREM and REM bed schedules and sleep durations 7 that bear directly on the findings of Crowley et al. Our study demonstrated that school-night time in bed decreased by 13 min/year between ages 9-18 yrs (p<0.0001). From an average bedtime of 9:15 PM at age 9 yrs, bedtimes advanced by 13 min/year (p<0.0001), whereas rise times did not change (p=0.11). Sleep latency did not change (p=0.70), but sleep efficiency increased over this age range (p<0.0001). The net result was that total sleep time (TST) decreased by 10 min/yr from 515 min at age 9 to xx min at age 18 (p<0.0001). This TST reduction was not produced by shorter REM and NREM durations, as would be expected if it was the result of sleep deprivation due to restricted time in bed. Instead, TST declined because of a selective reduction of NREM sleep, which declined by 12 min/yr (p<0.0001). REM sleep durations actually increased significantly by 2 min/yr (p<0.0001). This pattern of change cannot be attributed to a phase advance. We interpret it, along with the massive decline in slow wave EEG power, as a manifestation of brain maturation driven by synaptic elimination. In our model, synaptic elimination during adolescence decreases the intensity of waking brain activity (shown also by declining cerebral metabolic rate 8) which decreases the need for NREM dependent recuperation of plastic neuronal systems.

1. Crowley SJ, Van Reen E, LeBourgeois MK, et al. A longitudinal assessment of sleep timing, circadian phase, and phase angle of entrainment across human adolescence. PLoS One 2014;9:e112199.
2. Campbell IG, Feinberg I. Longitudinal trajectories of non-rapid eye movement delta and theta EEG as indicators of adolescent brain maturation. Proc Natl Acad Sci U S A 2009;106:5177-80.
3. Feinberg I, Campbell IG. Longitudinal sleep EEG trajectories indicate complex patterns of adolescent brain maturation. Am J Physiol Regul Integr Comp Physiol 2013;304:R296-303.
4. Campbell IG, Darchia N, Higgins LM, et al. Adolescent changes in homeostatic regulation of EEG activity in the delta and theta frequency bands during non-rapid eye movement sleep. Sleep 2011;34:83-91.
5. Campbell IG, Grimm KJ, de Bie E, Feinberg I. Sex, puberty, and the timing of sleep EEG measured adolescent brain maturation. Proc Natl Acad Sci U S A 2012;109:5740-3.
6. Campbell IG, Higgins LM, Trinidad JM, Richardson P, Feinberg I. The increase in longitudinally measured sleepiness across adolescence is related to the maturational decline in low-frequency EEG power. Sleep 2007;30:1677-87.
7. Feinberg I, Davis NM, de Bie E, Grimm KJ, Campbell IG. The maturational trajectories of NREM and REM sleep durations differ across adolescence on both school-night and extended sleep. Am J Physiol Regul Integr Comp Physiol 2012;302:R533-R40.
8. Chugani HT, Phelps ME, Mazziotta JC. Positron emission tomography study of human brain functional development. Ann Neurol 1987;22:487-97.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0150177. We believe the correct ID, which we have found by hand searching, is NCT01501773.

This comment is being posted as part of the OpenTrials.net project^[1] , an open database threading together all publicly accessible documents and data on each trial, globally. In the course of creating the database, and matching documents and data sources about trials from different locations, we have identified various anomalies in datasets such as PubMed, and in published papers. Alongside documenting the prevalence of problems, we are also attempting to correct these errors and anomalies wherever possible, by feeding back to the originators. We have corrected this data in the OpenTrials.net database; we hope that this trial’s text and metadata can also be corrected at source, in PubMed and in the accompanying paper.

Many thanks,

Jessica Fleminger, Ben Goldacre*

[1] Goldacre, B., Gray, J., 2016. OpenTrials: towards a collaborative open database of all available information on all clinical trials. Trials 17. doi:10.1186/s13063-016-1290-8 PMID: 27056367

* Dr Ben Goldacre BA MA MSc MBBS MRCPsych<br> Senior Clinical Research Fellow<br> ben.goldacre@phc.ox.ac.uk<br> www.ebmDataLab.net<br> Centre for Evidence Based Medicine<br> Department of Primary Care Health Sciences<br> University of Oxford<br> Radcliffe Observatory Quarter<br> Woodstock Road<br> Oxford OX2 6GG

On 2015 Jan 02, Meenakshisundaram Ananthanarayanan commented:

I would like to clarify that the title of our paper is misleading since what we are describing in this study is the post-transcriptional regulation of type 3 InsP3R3 by miR-506 at the mRNA level and not at the protein level.

On 2015 Feb 10, Pieter-Jan Volders commented:

At the time of submission, we were unaware of a specific RefSeq lncRNA subset. As a result, we initially used the NR_* records larger than 200 nucleotides. When dr. Kim D. Pruitt contacted us regarding this issue, we repeated the analysis for the suggested RefSeq subset. This subset contains 4774 transcripts and was obtained through the UCSC table browser. As expected, the percentage of transcripts passing the PhyloCSF cutoff has decreased from 48% to 14% of the RefSeq subset. The online manuscript was updated and the current Figure 3 (online as of January 15, 2015) represents these new results. Additionally, LNCipedia.org was updated as well, and the RefSeq records that do not represent lncRNAs were removed from the database version 3.1.

It is worth noting that we could not find any information on the keyword that was used in the query suggested by dr. Kimm D. Pruit (biomolncrnalncrna), neither on the RefSeq website, nor in the cited manuscript. It is unclear to us how many researchers are aware of this and we would like to suggest to RefSeq to indicate this subset on their website as it is of great value to the lncRNA research community.

On 2014 Dec 03, Kim D Pruitt commented:

The RefSeq results that are presented in Figure 3 do not accurately reflect the high quality of the RefSeq lncRNA dataset.

The article does not describe how this dataset was defined but the authors kindly provided this information as well as a file listing all of the RefSeq accessions and PhyloCSF results. The authors’ definition of RefSeq lncRNA was too simple as it was primarily based on the RefSeq accession prefix (‘NR_’). However, this accession prefix is used by the RefSeq project for several types of noncoding transcripts (PMID:18927115). Roughly 50% of the RefSeq dataset analyzed represent transcribed pseudogenes or noncoding transcripts for protein-coding genes.

On 2016 Feb 05, Kristina Hanspers commented:

Figure 8 is available as a pathway in the "Open Access Publication" Collection at WikiPathways: http://wikipathways.org/index.php/Pathway:WP2886. This pathway can be used for data visualization and network analysis in tools like Cytoscape and PathVisio.

On 2015 Sep 08, CREBP Journal Club commented:

This study gives an excellent insight into GPs’ experiences of two contrasting interventions – training in communication skills (including use of a patient booklet) and the use of a point of care test (CRP). We found it encouraging that the clinicians reported gaining new knowledge from the interventions. Information, such as expected duration of illness and the benefits and harms of antibiotic treatment of acute respiratory infections should preferably be part of any intervention aimed at either GPs or patients. Both interventions achieved important reductions in antibiotic prescribing for acute respiratory infections – and combining the interventions was associated with an even greater reduction(1). The group discussed if future interventions should be multi-faceted. Anthierens et al. found that the GPs reported that the two interventions were complementary and often used for different situations, i.e. the CRP test when there was uncertainty about the severity of the infection, and the communication skills/booklet when an explanation was required. However, it was mentioned that in some countries, such as Australia, the CRP test is still not routinely used as a point of care test in general practice. The group found the information in the booklet very useful. However, the sections about “Helping your immune system fight infection” and “How you can care for your cough” were debated. E.g. a Cochrane Review on Echinacea products did not find any benefits for treating colds(2) and also in the booklet it is stated that the advice on fluids, rest and stress is based on evidence about how the immune system works. Preferably, information used in interventions to enhance the quality of antibiotic prescribing for acute respiratory infections should be based on solid evidence about the group of patients being examined – i.e. in this case patients with acute respiratory infections. In addition, high quality, primary care-based studies are needed to further explore alternatives such as probiotics, zinc and vitamin C and to develop and test new non-antibiotic treatments. See CREBP Journal Club for more information.

References: (1) Little P, Stuart B, Francis N, et al. Effects of internet-based training on antibiotic prescribing rates for acute respiratory-tract infections: a multinational, cluster, randomised, factorial, controlled trial. Lancet 2013; 382(9899): 1175-82. (2) Karsch-Volk M, Barrett B, Kiefer D, Bauer R, Ardjomand-Woelkart K, Linde K. Echinacea for preventing and treating the common cold. The Cochrane database of systematic reviews 2014; 2: Cd000530.

On 2015 Feb 27, Geriatric Medicine Journal Club commented:

This clinical trial of of Problem Adaptation Therapy (PATH) was critically appraised at the January 2015 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). A transcript of the discussion can be found here: http://gerimedjc.blogspot.com/2015/01/gerimedjc-january-30-2015.html?spref=tw Highlights include the question of how feasible it is to deliver this type intervention in our current health care climate.

On 2015 Jan 05, NephJC - Nephrology Journal Club commented:

This trial was discussed on Dec 16th and Dec 18th (in the first transatlantic version) in the open online nephrology journal club, #NephJC, on twitter. Introductory explanatory comments, written by Rheumatologist, Dr Paul Sufka, are available at the NephJC website, and Dr Sufka’s blog. It had more than 50 participants, including nephrologists, rheumatologists and nephrology and rheumatology fellows. Transcripts and curated (i.e. Storified) versions of the tweetchats are available from the NephJC website.

The salient highlights of the discussion included:

• The authors and the funding agency (the French Ministry of Health) should be commended for performing this trial to find better ways of minimizing relapses in ANCA associated vasculitis.

• There was significant discussion around the Azathioprine dose chosen (tapered down to levels below that used in the CYCAZAREM trial in later part of this trial); as also the finding of early separation between arms, suggesting some patients in the control arm were azathioprine non-responders.

• The Rituximab dosing strategy seemed quite astute, and was quite successful in reducing relapses without an increase in adverse events. The discussants looked forward to publication of more data from this trial, especially on B cell populations and ANCA titres, that could shed more light for a deeper understanding of the results.

Overall, there was significant enthusiasm for using Rituximab in this setting, though the results of more trials, especially RITAZAREM and MAINRITSAN-2 are now keenly awaited.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.

On 2014 Nov 12, KEVIN BLACK commented:

I think the effects of levodopa itself on brain activity may be of interest when interpreting the effects of levodopa on movement-related brain activity. Examples from my colleagues include the 4 following articles: PubMed Central IDs PMC21757 and PMC1738560, doi: 10.1038/sj.npp.1300632, and doi: 10.1006/exnr.2000.7522 .

On 2014 Nov 19, David Keller commented:

A landmark paper with important implications for melanoma patients

The results obtained by combining high-dose ipilimumab (10 mg/kg) with GM-CSF (sargramostim) are remarkable. The combination increased median overall survival by 4.8 months compared with high-dose ipilimumab alone, an increase of over 37%, and the combination also reduced the rate of serious adverse events significantly compared with high-dose ipilimumab monotherapy. Patients with advanced melanoma and poor response to existing treatments will want to discuss these results with their oncologists, particularly since GM-CSF is currently available in the U.S.

Since GM-CSF is already approved for other indications, there will be great pressure on oncologists to prescribe ipilimumab in combination with GM-CSF on the basis of this study, particularly for patients whose tumor burden worsens despite approved therapy. Questions which will be encountered include:

1) Would the pairing of GM-CSF with the approved dose of ipilimumab (3 mg/kg) have similar benefits, despite the fact that the ipilimumab dose used in the study was more than 3 times larger than the approved dose?

2) Given the reduction in toxicity of the combination compared with ipilimumab monotherapy, can the approved dose of ipilimumab be safely tripled to 10 mg/kg if used in combination with GM-CSF?

3) Is there any reason to believe that PD-1 checkpoint inhibitors, such as pembrolizumab, given in combination with GM-CSF, would not afford similar improvements in survival and adverse events?

Patients with advanced melanoma who do not respond to currently approved treatments have little to lose. There is no reason to force these patients to wait for the results of confirmatory studies which they may have little hope of surviving to see published. Those that can be accommodated into clinical trials should be encouraged to participate, while the others should be offered the option of adding GM-CSF to their checkpoint inhibitor, if the latter fails to control their disease.

On 2014 Nov 05, Dan Laks commented:

These data support earlier findings that chronic Hg exposure results in depletion of LH:

http://www.ncbi.nlm.nih.gov/pubmed/19914008 http://www.ncbi.nlm.nih.gov/pubmed/19697139

On 2015 May 04, Christopher Southan commented:

This paper is an good target mapping example, see http://cdsouthan.blogspot.se/2015/05/antimalarial-dot-joining-for-mmv008138.html for database mapping of compounds and forward pointer to http://www.ncbi.nlm.nih.gov/pubmed/25754494