On 2014 Apr 24, B Hidalgo commented:

Thanks for your comment. Yes, predictors/risk factors, etc. Hope this helps.

On 2015 May 21, Viswanath Reddy Belum commented:

This most likely falls in the spectrum of nasal vestibulitis: http://www.ncbi.nlm.nih.gov/pubmed/25876156

On 2014 Mar 05, Christopher Southan commented:

A full-text version can be found at: http://figshare.com/articles/Challenges_and_recommendations_for_obtaining_chemical_structures_of_industry_provided_repurposing_candidates/978680

The link below is to a March 2014 version of molecular structures and patent mappings for 58 structures from the 77 code names, but note many of these still do not have a name match in PubChem. http://figshare.com/articles/NCats_Compounds_with_identifications/92850

On 2016 Jan 31, Christopher Southan commented:

Aspects described are relevant to the Jan 2016 BIA-10-2474 clinical trial disaster where the structure was initialy blinded http://cdsouthan.blogspot.se/2016/01/the-unfortunate-case-of-bia-10-2474.html

On 2014 Jan 21, Ellen M Goudsmit commented:

This paper describes some of the political issues that have undermined the study of CFS and its subsets during the past ten years. I too have felt the pressure to promote one intervention rather than another, or to support the use of criteria which were clearly flawed. However, the non-scientific influences that have distorted the view of fatigue syndromes are various and often rather surprising. For example, a number of highly regarded journals have for years refused to publish any article which challenges the CBT model of CFS [1]. The last time that the BMJ published a report alluding to a pathological cause was in 1995 (Lane, cited in 1). Alternative views are relegated to the correspondence page. And the one journal that deals with fatigue has just rejected a paper describing criteria which in the past, have shown to select a homogeneous group. The latest issue (2014, 2, 1,) includes two studies that recommend the formulation of new criteria focusing on core symptoms but when these were offered, the editor decided the subject was contentious. We can identify problems but not try and resolve them. Ergo, we are using different terms for different symptom complexes. ME/CFS could refer to CFS or to ME or a hybrid. Is it any surprise that patients and doctors are confused?

Perhaps it is useful to recall that fatigue is a symptom and not an illness. However, the Oxford criteria for CFS used in the PACE trial require only the presence of fatigue to some degree, at sometime, during six months. A number of referees seem to miss that point. Fatigue is a symptom of many illnesses, and of chronic stress. Five minutes on PubMed would lead one to the conclusion that CBT might well help tiredness but there's no evidence to support its value to deal with dizziness and muscle weakness. If trials only measure fatigue and sleep, and define recovery in terms of a lower score on one or two measures and report that a person feels better, it's easy to argue that it's effective. It's not effective for the majority. It helps with tiredness but as any clinician will admit, there's more to CFS than fatigue.

There's a lack of balance in scientific publications and some serious spin re CBT and GET, which patients and independent scientists are well aware of. But this journal, like others, doesn't invite commentaries from people who aren't enthusiastic about the CBT protocol as evaluated in RCTs. Readers therefore don't get a range of opinions. It helps no one and undermines the scientific process. Most of all, it's very, very sad.

[1] Goudsmit, E and Stouten, B. Chronic fatigue syndrome: editorial bias in the British Medical Journal. Journal of Chronic Fatigue Syndrome, 2004, 12, 4, 47-59.<br> http://freespace.virgin.net/david.axford/JCFS.pdf

On 2014 Jul 05, David Keller commented:

An important factual error in this paper was corrected by JAMA on their website, as of 7/10/2014. A copy of this paper which is posted on the PubMed Central website was corrected, as of 7/31/2014.

For readers of the paper edition of JAMA, here is the incorrect statement, from the end of paragraph #5 of this paper's "Comment" section (1):

"In addition, the Supplementation en Vitamines et Mineraux Antioxydants (SU.VI.MAX) primary prevention trial (2) of 13,017 participants randomized to a low-dose combination of vitamin C, vitamin E, beta carotene, selenium, and zinc found no overall effect on total cancer, but there was a significant interaction with sex with a reduction in risk of total cancer in women only...."

The above sentence should read "...a reduction in risk of total cancer in men only". To confirm this, I copied the following sentences from the Conclusions section of the abstract of the above-cited Su.Vi.Max study:

"Conclusions After 7.5 years, low-dose antioxidant supplementation lowered total cancer incidence and all-cause mortality in men but not in women. Supplementation may be effective in men only because of their lower baseline status of certain antioxidants, especially of beta carotene."

I wish to thank PubMed Central and JAMA for correcting this important error on their websites.

References

1: Gaziano JM, Sesso HD, Christen WG, Bubes V, Smith JP, MacFadyen J, Schvartz M, Manson JE, Glynn RJ, Buring JE. Multivitamins in the prevention of cancer in men: the Physicians' Health Study II randomized controlled trial. JAMA. 2012 Nov 14;308(18):1871-80. PubMed PMID: 23162860; PubMed Central PMCID: PMC3517179.

Below is the link to the JAMA website page which contains the corrected version:

http://jama.jamanetwork.com/article.aspx?articleid=1380451

Below is the link to the PubMed Central version, which has been corrected, as of 7/31/2014:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517179/

2: Hercberg S, Galan P, Preziosi P, Bertrais S, Mennen L, Malvy D, Roussel AM, Favier A, Briançon S. The SU.VI.MAX Study: a randomized, placebo-controlled trial of the health effects of antioxidant vitamins and minerals. Arch Intern Med. 2004 Nov 22;164(21):2335-42. Erratum in: Arch Intern Med. 2005 Feb 14;165(3):286. PubMed PMID: 15557412.

On 2016 Jan 30, Gary Goldman commented:

The Goldman and King review did not contain an exhaustive summary of varicella vaccine trends. The editor, Dr. Gregory Poland, while not allowing a 500-word rebuttal response letter from Goldman and King, suggested that their material "may be suitable for other peer-reviewed journals."

In response to Myers' Vaccination to prevent varicella, additional statistically significant trends and supporting documentation derived from annual summary reports to the CDC were published by a different journal editor in Vaccination to prevent varicella: Goldman and King's response to Myers' interpretation of Varicella Active Surveillance Project data. Goldman GS, King PG. Hum Exp Toxicol. 2014 Aug;33(8):886-93. doi: 10.1177/0960327113512340. Epub 2013 Nov 25. Goldman GS, 2014

On 2014 Aug 13, Amanda Capes-Davis commented:

Much of the work done here is performed using the KB cell line. Please be aware that KB is not an appropriate model for oral squamous cell carcinoma. KB cells are cross-contaminated with HeLa, from cervical adenocarcinoma. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2017 Dec 12, Peter Rogan commented:

Regarding GABRQ:c.306G>C: Whereas none of the splicing analysis programs tested predict outcomes shown in the mini-gene construct shown in Figure 2A, information theory-based exon definition analyses using ASSEDA (Mucaki EJ, 2013) was completely concordant. A novel band 116nt longer than the product expected from the wild type exon is observed. The mutation reduces the strength of the natural donor splice site of exon 3 from 9.5 -> 4.5 bits (32 fold). The pre-existing intronic cryptic site 116 nt downstream (8.6 bits) is 17 fold stronger than the mutated splice site. ASSEDA indicates that the total exon information (Ri,total) of wildtype exon is reduced (19.8 -> 14.8 bits) and the corresponding strength of the gap-surprisal adjusted cryptic exon significantly exceeds this (17.7 bits). The wildtype exon is predicted to be ~5-6 fold more abundant than the cryptic exon BEFORE mutation, and the cryptic exon is predicted to be ~8 fold more abundant AFTER mutation.

On 2014 Jan 08, Brett Snodgrass commented:

Dear Authors,

Thank you for the excellent report.

Please provide your kind consideration to the distinction between the vessels of Wearn and the Thebesian veins.

http://bit.ly/JTWearn

http://bit.ly/Thebesius

Morphological and Functional Alterations of the Coronary Circulation. Harvey Lecture, 1940 - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933738

http://www.ncbi.nlm.nih.gov/pubmed/22704295

For examples of Thebesian veins, please see:

1. http://www.ncbi.nlm.nih.gov/pubmed/18703466

2. http://www.ncbi.nlm.nih.gov/pubmed/23428022

3. http://bit.ly/Thebesius

4. http://bit.ly/ThebesianByPratt

For additional commentary, please see

https://twitter.com/BrettSnodgrass1/status/418890181509263360

https://twitter.com/BrettSnodgrass1/status/406332234073792512

https://twitter.com/BrettSnodgrass1/status/417945453498335232

Comments and feedback are welcome.

Thank you very much.

On 2015 Dec 11, Mark Johnston commented:

An interactive protocol from this article is freely available at protocols.io.

On 2014 Aug 12, Miguel Lopez-Lazaro commented:

In this article, my team assessed the in vitro cancer therapeutic potential of the compounds using a colorectal cancer cell line (HT29). We observed that several compounds improved the cytotoxic potency of the anticancer drug 5-fluorouracil; the IC50 value of the five most cytotoxic compounds was between 0.36 and 1.48 micromolar, and the IC50 value of 5-Fluroracil was 4.32 micromolar. Because our compounds killed cancer cells at lower concentrations that those of this commonly used anticancer drug, we discussed that they could have therapeutic potential.

More recently, we assessed the cytotoxic potency of these five compounds against lung cancer cells (A549) and lung nonmalignant cells (MRC5). Their IC50 values were between 0.96 and 4.31 micromolar in the cancer cell line and between 1.24 and 3.11 micromolar in the nonmalignant cell line. Some of the compounds were in fact more cytotoxic against the nonmalignant cell line.

Considering these new results, I think that the potential of these compounds for the treatment of colorectal cancer and lung cancer is low. I also think that my experimental design was unable to reveal their cancer therapeutic potential. To properly assess therapeutic potential using in vitro experiments one should use the most suitable experimental conditions to answer the following question:

Can my compounds improve the ability of the standard drugs to kill cancer cells without significantly affecting nonmalignant cells from a variety of appropriate tissues? (1)

Unfortunately, we did not address this question in our article.

Dr. Lopez-Lazaro

(1) Lopez-Lazaro, M. Experimental Cancer Pharmacology for Researchers: At What Concentration Should my Drug Kill Cancer Cells so that it has Potential for Cancer Therapy? 2014, ASIN: B00MMO25NM http://www.amazon.com/Experimental-Cancer-Pharmacology-Researchers-Concentration-ebook/dp/B00MMO25NM/ref=sr_1_1?ie=UTF8&qid=1407829198&sr=8-1&keywords="at+what+concentrations+should"

On 2014 Mar 09, Gyanshankar Mishra commented:

We have also done a study on Tuberculosis management In India: Mishra G, Mulani J. Tuberculosis Prescription Practices In Private And Public Sector In India. NJIRM. 2013; 4(2): 71-78. Available online at http://www.scopemed.org/?mno=36915

Our other study highlights the fact of how drug resistant TB is created under programmatic management of TB in India: Gyanshankar Mishra, S V Ghorpade, Jasmin Mulani (2014) XDR-TB: An outcome of programmatic management of TB in India. Indian Journal of Medical Ethics 11: 1. 47-52 Jan-Mar.Available online at http://216.12.194.36/~ijmein/index.php/ijme/article/download/932/2179

Full text article Available online at http://www.ijme.in/index.php/ijme/article/view/932

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2013 Dec 23, Gregory Francis commented:

A longer version of the following text was submitted to JPSP as a comment. The editor agreed with three reviewers who felt that even if the analysis was valid, it was not useful to publish such a critique.

Based on six experiments, Wiltermuth and Gino (2012), henceforth WG, concluded that separating rewards into categories increased people’s motivation to complete reward-earning tasks. An analysis of the reported findings suggests that the experiments do not properly support the conclusion.

The primary variable for experiments 3, 4, and 5 was analyzed with a two-sample t-test, and post-hoc power was estimated with standard calculations. The analyses of the primary variable for experiments 1, 2, and 6 involved a logistic regression analysis, and the post-hoc power for each analysis was estimated with 10,000 simulated data sets that were drawn from populations having parameters matching the sample statistics from the experiments. The simulated data sets were then analyzed in the same way as the original experiments and the proportion of times they reported statistical significance was computed as an estimate of power. For experiment 6, the conclusion of a successful experimental outcome involved two different comparisons being statistically significant, and this requirement was also imposed on the estimate of experimental power. In every case, power was measured as the probability of rejecting the null hypothesis in the direction consistent with the findings reported in WG.

When re-computing the p-values for the data presented in the paper, experiments 2, 3, and 4 produced p-values slightly above the standard significance criterion (.0546, .0516, .0544). The deviations are large enough that they cannot be due to rounding of the reported sample proportions or t-statistics. It appears that WG rounded down some p-values to .05 and then indicated statistical significance. In practice, this means that for these experiments WG used a significance criterion of .055 rather than the typical .05. Experimental power increases with the p-criterion, so the value .055 was used to estimate power, as this properly reflects the criterion used by WG.

Since most of the experiments just barely rejected the null hypothesis, the post hoc power values tend to be close to one half. For the six experiments, the estimated power values are: .618, .507, .509, .499, .677, .561, respectively. Since each experiment is independent, the expected number of experiments that would reject the null hypothesis is the sum of the power values, which is 3.37. The probability that six experiments like these would all reject the null hypothesis is the product of the power values, which is .030. This probability is so low (an often used criterion is .1) that it renders the reported experimental results “too good to be true.”

The analysis does not specify how such unusual results could have been produced, but there are three broad possibilities. First, the reported experiments might be a subset of a larger experiment set that included unreported null results. Second, the reported experiments may have been subject to a verification bias that utilized improper sampling methods. Third, the reported statistical analyses may have been one of several different methods (e.g., using different criteria to indicate significance) that were used to find one that produced statistically significant results. All of these approaches misrepresent the properties of the populations or the experimental outcomes. Thus, readers should be skeptical about the theoretical conclusions derived from the data reported in WG.

R code for the simulated experiments is available at http://www1.psych.purdue.edu/~gfrancis/Publications/WiltermuthGino/

On 2015 Jun 12, Bill Cayley commented:

A great example of "Less-is-more" medicine: https://lessismoreebm.wordpress.com/about/less-is-more-database/

On 2013 Jun 22, Martin Fenner commented:

This editorial provides a good overview of the important open questions in the treatment of Hodgkin lymphoma:

• Is radiation therapy needed and if so, who should receive it?
• Is there a role for midcycle PET scanning in treatment planning and if so, what is it?
• What about escalated BEACOPP?
• Is there any prospect for new effective therapies that might actually be an improvement over ABVD?

This editorial accompanies the report Gordon LI, 2013 of a randomized phase III trial showing no improvement of the response rate with Stanford V chemotherapy compared to standard ABVD. This report comfirms the results of an earlier phase III trial Hoskin PJ, 2009, clearly demonstrating that Stanford V is no improvement over ABVD, and that ABVD remains the standard of care.

The discussion of the role of escalated BEACOPP in advanced Hodgkin lymphoma is of particular importance, because it is the standard of care for patients up to 60 years old in Germany, but not in the US and other countries. The author follows the logic of the study Viviani et al. Viviani S, 2011 that showed higher progression-free survival for BEACOPP vs. ABVD, but similar overall survival because of salvage high-dose chemotherapy. The paper by Viviani et al. has been critizised in three comments published in the same journal (see link from PubMed page), for example because progression free survival at 5 years was the primary endpoint and no power calculation was made for the secondary endpoint overall survival.

It is positive to see a discussion of important studies on journal pages (and to make the comments available to readers without a journal subscription), but we are in the unfortunate situation that standard treatment practices for patients with advanced Hodgkin lymphoma vary between countries. If the scientific community can't agree on a standard treatment strategy (the first randomized phase III trial with BEACOPP was published in 1998 Diehl V, 1998), then the different options should at least be clearly stated in treatment guidelines, editorials, and in particular in discussions with patients about to undergo treatment.

On 2014 Apr 03, Naresh Kasoju commented:

Link to the article full text: http://onlinelibrary.wiley.com/doi/10.1002/adhm.201200097/abstract

On 2015 Dec 02, Christopher Southan commented:

Queries (Dec 2015) return the quote "Due to technical difficulties, this service has been disabled for online analysis" So is this transient or permenant?

On 2016 Apr 20, Lydia Maniatis commented:

The authors of this study have constructed an experimental setup that has generated data that are “consistent with a stochastic process that degrades memory for each individual item and plays out independently across them.” On the basis of this, they conclude that “visual working memory is stochastic both at the level of a memory's content and at the level of its quality.”

A few objections to this assertion are in order. I want to preface them by noting that it has long been understood that it is always possible to generate data “consistent” with any point of view: “A nice adaptation of conditions will make almost any hypothesis agree with the phenomena” (J. Black (1803, Lectures on the Elements of Chemistry, quoted by Popper in Popper Selections, Miller, Ed, 1985). In order for “consistency” to carry weight, investigators must have really tried to look for “inconsistency” or falsification, wherever it seems most likely to be found.

As it happens, there is a preponderance of evidence that memory in general and visual memory in particular is not stochastic either in its content or its quality. With respect to visual memory, the organizing principles that influence the percept itself also influence the memory of those percepts, as is shown, for example, by Goldmeier (1981, The Memory Trace, its Formation and its Fate). Other investigators who have shown that memory changes are not random include Bartlett and Loftus.

If the authors want to challenge the legitimacy of the view that “degradation” and random change is not the proper account of memory, then they should do it. It would be fine if they validly challenged the results of studies that falsify their position. They could, for example, claim the methods of the falsifying experiments were flawed. What is not OK, however, is for scientists to ignore contradictory evidence, and set up experiments that produces “consistency” with their preferred view.

Significantly, the task used by Fougnie, Suchow and Alvarez' (2012) involves a structure-less feature – color - thus ensuring that the known effects on memory of structural principles will not interfere with their preferred outcome. As they note in their introduction, this is a task that is commonly used for such studies. Unfortunately, as here, many studies today rationalize their methodological choices not on theoretical grounds, but on the grounds that they are widespread, popular, common, even "traditional" (!). As here, a method may have become normalised for the wrong reason, i.e. because it doesn't complicate the perpetuation of preferred paradigms uncritically accepted.

In my discussion above I have not distinguished between “working memory” and other types of memory. The authors, while using the term “working memory” have not provided a working definition, i.e. a description of how they circumscribe the term and distinguish it from other types of memory. Once they do this, they might try and check the literature for examples that falsify their account, and construct experiments that, on the basis of what has already demonstrated, make a credible effort to falsify it, rather than simply to “confirm” it.

On 2014 Jan 08, Brett Snodgrass commented:

Dear Authors,

Thank you for the excellent article. Please provide your kind consideration to the vascular nomenclature and the distinction between the Thebesian veins and the vessels of Wearn.

The text highlights at the following website may illustrate the difference.

https://twitter.com/BrettSnodgrass1/status/417888788346462209

Comments and suggestions are welcome.

Thank you kindly.

On 2013 Jul 17, Jessie Tenenbaum commented:

A nice paper that raises some important points. I wonder about the composition of the readership of BB- seems like it's preaching to the choir in informatics- many known points. I wonder what % of readers are more on the biology side of things?

For that matter, for scientific literature more generally- in the pubmed era, where fewer journals are being read as bound paper versons, how do people come upon papers they decide to read? Scanning TOCs (how I came upon this one), references from other papers, pubmed searches for keywords or authors... Of those 3, only the middle option- bibliography from another paper- would seem likely to bring this paper to the attention of a non-informaticist.

On 2016 Jun 03, Ian Fingerman commented:

The Epigenomics database, a public repository that was developed to archive genome-wide maps of DNA and histone modifications, will be retired on June 1, 2016.

All epigenomics data are available in our GEO resource. If you are specifically interested in the NIH Roadmap Epigenomics Project, we will maintain a page for this project's data.

On 2017 Sep 29, Daniel Vaulot commented:

The PR2 database is now available on figshare: https://figshare.com/articles/PR2_rRNA_gene_database/3803709

You can also follow the different updates via research gate: https://www.researchgate.net/project/Protist-Ribosomal-Reference-database-PR2

On 2013 Dec 23, Yannick Pouliot commented:

It would be nice if the gene expression data described in this paper were deposited into GEO...

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2014 Feb 23, ossama mansour commented:

it is an interesting topic in endovascular treatment of aneurysms. where actually we do not have such evidence based medicine regarding the optimum option for treatment of such aneurysm . we need to design a RCT for studying such notion.

On 2013 Oct 28, Steven Salzberg commented:

I heard a rumor very recently that the contamination problem, discussed cogently after the first Neanderthal papers (see http://www.ncbi.nlm.nih.gov/pubmed/17937503), has arisen again, and that the authors are now aware of the very real likelihood that modern human DNA is contaminating these samples. If true, this would invalidate the analysis of FOXP2 and the multiple other papers about this genome. What do the authors have to say?

On 2013 Dec 09, Gregory Francis commented:

I submitted the following text to J. Neuroscience a few months ago. The editor evaluated the critique but decided against publishing it.

Zhou, Zhang, Chen, Wang, and Chen (2012) reported experimental findings that perfectly matched their theory that olfaction influences early visual perception. Calculations of experimental power suggest that such perfection is contrary to the uncertainty that exists from random sampling.

Three results showed significant nostril-specific effects of odor on vision: experiments 1 (two results) and 2 had powers of 0.501, 0.513, and 0.529, respectively. Experiment 3 showed a significant effect of odor on visual perception (power 0.547) but, consistent with the theory, no nostril-specific effect.

Seventeen null results also provided evidence for the theory by ruling out alternative explanations. If the theory is valid, the true effects are similar to what was reported, and the null findings are accurate, then the probability of an entire set of findings being perfectly aligned with the theory is the product of the power values times the probability of the null findings: 0.075 x (0.95)¹⁷ = 0.031.

One hundred thousand simulated replications, using the observed significant statistics as population parameters, checked the possibility of a chance pattern. Applying the same power analysis, only two of the simulated experiment sets produced a probability below the observed 0.075. On average, a simulated experiment set produced 2.1 significant findings out of four experiments.

The too perfect data undermine the theoretical interpretation. Perhaps experiments were run improperly, the analysis was done improperly, or publication bias filtered out inconsistent experimental findings. Seemingly trivial choices in experimental design or analysis can bias findings that depend on complex patterns of experimental outcomes.

On 2014 Dec 17, Sean Ekins commented:

Slides http://www.slideshare.net/ekinssean/cheminformatics-workflows-using-mobile-apps-for-drug-discovery

On 2014 Dec 17, Sean Ekins commented:

A link to the app https://itunes.apple.com/us/app/oddt/id517000016?mt=8

On 2014 Dec 17, Sean Ekins commented:

Some slides on the app http://www.slideshare.net/ekinssean/why-you-need-this-app-slides

On 2014 Dec 17, Sean Ekins commented:

The story behind the app in slides http://www.slideshare.net/ekinssean/oddt-open-drug-discovery-teams-for-collaboration

On 2016 Sep 12, Morten Oksvold commented:

Please note that this article has been retracted and should therefore not be cited.

On 2015 Apr 08, Jason Stajich commented:

The genome sequence accession is AMRR00000000 but not linked to this pubmed record or vice-versa.

On 2014 Dec 01, Cosmin Saveanu commented:

Affinity purification of pre-60S complexes associated with tagged Ssf1, Rix1, Arx1 and Lsg1 (alias Kre35) coupled with quantitative mass spectrometry were used to obtain a picture of pre-60S dynamics in yeast. Overexpression of a dominant negative form of Drg1, as well as deletion of BUD20 were also used to perturb 60S assembly and test the changes in levels of various pre-60S factors.

The quantitations presented in this paper correlate well with our published results that were based on affinity purification of Rlp24, Nog1 and Mak11 associated particles under various mutant conditions and quantitative mass-spectrometry based on stable isotope labeling (Lebreton A, 2008).

The major caveat of these methods is the uncertainity in the faith of blocked pre-60S particle that accumulate under mutant conditions - are these "dead-end" or real intermediates in the pathway ?

On 2014 Jan 17, Amanda Capes-Davis commented:

What's in a name? A great deal, when it comes to cell lines. KB, one of the tumor cell lines used in this paper, is cross-contaminated and is actually HeLa. It is not a nasopharyngeal epidermoid cell line. For a database of cross-contaminated or otherwise misidentified cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2014 Jun 30, Torsten Seemann commented:

For those who not have access to the paywalled article, the web portal is accessible at http://www.proteomebrowser.org/

On 2014 Apr 10, Alexander Klabnik commented:

I recomend

On 2013 Nov 01, Stephen Turner commented:

RNA-seq enables transcript-level resolution of gene expression, but there is no appropriate methodology for simultaneously accounting for biological variability across replicates and uncertainty in mapping fragments to isoforms. Figure 1 in this paper illustrates the problem with existing approaches, which only count the number of fragments originating from either the entire gene or constitutive exons only. The method presented here addresses both of these problems simultaneously by modeling variability in the number of fragments generated by each transcript across biological replicates. Compared to existing methods, the procedure described here has equivalent sensitivity with a much lower false-positive rate when there is substantial isoform-level variability in gene expression between conditions. The manuscript also addresses and points out weaknesses in several undocumented 'alternative' workflows that are highly discussed in the field, where transcript counts from tools like Cufflinks and RSEM (RNA-Seq by expectation maximization) are used in downstream negative-binomial-based differential expression analyses.

On 2014 Aug 13, Frederic Y. Bois commented:

important advances in parameter estimation

On 2015 Jan 08, James Tsung commented:

Link to video accompanying article: http://youtu.be/R60PgPKQNeU

On 2015 Feb 25, James Tsung commented:

Link to lung ultrasound pneumonia videos - pitfalls to avoid: https://youtu.be/NwykDDXCSP4?list=PLHg2xyua_KjtgcSGdb5dfnN1DVMej5-B-

On 2015 Nov 13, University of Kansas School of Nursing Journal Club commented:

Reviewer (Team 11): April Urie, Caitlin Colston, Elizabeth Diaz, Bethany Macchi, Lauren Meyers, Madison Steele, & Huntre Graham (Senior Nursing Students - Class of 2016)

Background Introduction:

The purpose of this study is to investigate the perceptions of new graduate nurses on the influence of authentic leadership and empowerment on the quality of interprofessional collaboration in healthcare work environments (Laschinger & Smith, 2013). Many work environments have little to no interprofessional collaboration, especially new graduate nurses in feeling comfortable with being contributing members. Our team chose this article because we feel that through this study researchers will be able to define what best exemplifies authentic leadership and empowerment and how these two aspects influence interprofessional collaboration through healthcare practice as seen appearing in the lens of new graduate nurses. The article states that, in a previous study lack of communication and collaboration between healthcare team members showed to have dramatic effects and is responsible for approximately 70% of adverse events (Laschinger & Smith, 2013, p. 24). The study presents substantial text and statistics displaying the validity of authentic leadership, empowerment, and interprofessional collaboration within healthcare settings.

Methods:

Our group used CINAHL database engine to find opportune related articles. We searched “(Authentic AND Transformational) Leadership” and “Meaningful Recognition”. After sifting through the vast amount of articles we found that this article portrayed many key aspects relating to authentic and transformational leadership, creating a motivational climate, meaningful recognition, and staffing considerations. A correlational survey design and a secondary analysis from a larger longitudinal study of newly graduated nurses were used (Laschinger & Smith, 2013, p. 26). “The original sample was obtained from College of Nurses of Ontario registry list (n = 342). The 2nd wave of the study (2010) contained several items to capture new graduate nurses’ experiences of interprofessional collaboration on their units. 194 of new graduates form the 2nd wave constituted the sample” (Laschinger & Smith, 2013, p. 26). The method to collect data initially was mailed surveys and then reminder letters were sent out at 3 and 6 weeks after. The instrument that was used in this study consists of The Authentic Leadership Questionnaire to measure new graduates’ perspectives of their current leader’s leadership behaviors. The data was then plotted in Supplemental Digital Context 1 (Table) to measure psychometrics. A researcher- constructed Interprofessional Collaboration Scale was also used based on previous research identifying important characteristics of interprofessional collaboration (IPC) in health care setting (Laschinger & Smith, 2013). To analyze the data “The Statistical Package for Social Sciences” was used (Laschinger & Smith, 2013). The target population of this study is new graduate nurses and the impacts on interprofessional collaboration in the workplace if authentic leadership and empowerment is being used. This is important in healthcare settings in order to maximize patient care, outcomes, safety, success, decrease burnout, and the provide the opportunity for advancement and acknowledgement in healthcare environments. Laschinger & Smith (2013) suggests because authentic leaders are inclined toward values such as empathy, respect, trust and human connection they are more likely to create environments that empower employees to work with colleagues to accomplish their work in meaningful ways.

Findings:

Key findings and outcome of this study overall include, new graduates perceiving their leaders to display a moderate amount of authentic leadership where relational transparency was highest and self-awareness was lowest (Laschinger & Smith, 2013, p. 28). Overall perceptions of IPC on work units were high and personal beliefs that interprofessional teamwork improves patient care rated highest (Laschinger & Smith, 2013, p.28). However, what rated lowest by new graduates was the fact that healthcare professionals on their unit understood each other’s role in providing holistic patient care (Laschinger & Smith, 2013). When testing the hypothesis it was found that higher levels of supervisor authentic leadership and structural empowerment were significantly associated with a higher perceived quality of interprofessional collaboration (Laschinger & Smith, 2013, p. 28). This study has shown that new graduates views of the quality of interprofessional collaboration on their units were related to authentic leadership and structural empowerment. “In addition, new graduates perceptions’ of their manager’s authentic leadership behaviors and their own structural empowerment were significantly related to their feelings that their knowledge was respected by other health professionals, that health professionals on the team understood their roles in providing care, and that other healthcare professionals believed that IPC improves patient care” (Laschinger & Smith, 2013, p. 27). The article also spoke of the possibility of new graduates being exposed to interprofessional collaboration before graduating which would also reflect in today’s interactions and within the survey, for example, Team STEPPS. To compare and contrast how this study would be different if done in different parts of the U.S. We would make the assumption that the results would be approximately the same but could vary depending on what college is surveyed. For instance, University of Kansas has had the opportunity to have interprofessional collaboration before graduating nursing school while others have not. If this study was completed outside the US we could see how the results would be different because healthcare settings vary around the world. The cross-sectional, exploratory nature of the design limited their ability to draw strong casual inferences (Laschinger & Smith, 2013). The only other limitations include the possibility of bias from the responders and a low response rate due to mailing out the surveys (Laschinger & Smith, 2013, p. 28).

Implications:

This article is important to nursing and nursing practice because it depicts the differences in authentic leadership and structural empowerment in healthcare work environments. While also displaying how this type of leadership can affect interprofessional collaboration whilst influencing less fragmented patient care and positive outcomes. This aids persons’ of charge in knowing the perceptions of new graduates in authenticity and empowerment and how to improve these perceptions and the work environment. “Authentic Leaders are well positioned to ensure that new graduates are integrated into interprofessional teams and are seen as valued contributors in the delivery of care” (Laschinger & Smith, 2013, p. 28). In nursing it is crucial to have this collaboration and for all healthcare caregivers to be in congruence with each other when treating patients. This not only improves the work environment setting but this also improves the care being given. When working in a microsystem it is important to remember that a team is meant to work together, provide each member with the specialty knowledge that the other individual has, and to ultimately treat the patient with the best care possible.

References

Laschinger, H. S., & Smith, L. M. (2013). The Influence of Authentic Leadership and Empowerment on New-Graduate Nurses' Perceptions of Interprofessional Collaboration. Journal Of Nursing Administration, 43(1), 24-29 6p. doi:10.1097/NNA.0b013e318278606-

On 2014 Jan 08, Brett Snodgrass commented:

Dear Authors,

Thank you for the excellent article.

Is it possible that three of the connections are consistent with the normal connections reported by Wearn in 1933? http://bit.ly/JTWearn

Wearn identified the vessels of Wearn connecting to both atria and both ventricles. The above report by Sohrabi et al. document a connection between the LAD and LA, and two VCACs connecting to the LV. Wearn reported coronary-cameral connections to each of the four heart chambers and noted that they are were distinct from those described by Thebesius.

For further references please visit the following link. https://twitter.com/BrettSnodgrass1/status/418780318682738689

Comments, disagreements, concerns, and feedback are encouraged in the interest of accuracy and clarity.

Thank you kindly.

On 2016 Aug 25, Eran Elhaik commented:

Follow up studies on this topic are available at: * http://gbe.oxfordjournals.org/content/early/2016/03/03/gbe.evw046.full.pdf+html * http://journal.frontiersin.org/article/10.3389/fgene.2016.00141/full

On 2014 Jun 02, Claudio Gil Araújo commented:

For those interested in knowing more about the sitting-rising test (SRT), please access the Youtube link https://www.youtube.com/watch?v=MCQ2WA2T2oA

On 2013 Jun 29, Rahul Bakshi commented:

The association of 'delayed parasite clearance' in response to artemisinin with a general mechanism like DNA repair suggests that Cambodian parasites of interest may simply be 'fitter'in terms of dealing with the DNA damage that accompanies any drug-induced death pathway. This gives rise to a couple of questions: 1) Would these parasites demonstrate delayed clearance when challenged with other drug classes? 2)Why is the parasite population structure in Cambodia still so heterogenous? One would (perhaps naively) expect the fitter population to take over. Is there a cost associated with these SNPs in other stages of the lifecycle? 3)Would the parasite population structure in Cambodia change if artemisinin pressure was withdrawn? Thoughts, anyone?

On 2014 Jan 01, Qian Liu commented:

This is an official government file for Chinese oncologists. It would be updated in 2014.

On 2014 Mar 18, Gwinyai Masukume commented:

Nejad and colleagues present a case of a man with alcohol withdrawal delirium and multifactorial delirium. This patient had thrombocytopenia and part of his work-up included testing for antibodies against heparin-platelet factor 4 complexes to elucidate the cause of the thrombocytopenia - the test was negative (1). Thrombocytopenia in early alcohol withdrawal is associated with development of delirium tremens or seizures (2). In patients who develop severe alcohol withdrawal syndrome (like the one presented) thrombocytopenia is more frequent (2).

Additionally, from the provided laboratory data, this patient has a De Ritis (aspartate aminotransferase/alanine aminotransferase) ratio greater than 2. His albumin/globulin ratio of less than 1.6 is low. Given his history of alcoholism, a De Ritis ratio greater then 2, and a decreased albumin/globulin ratio a diagnosis of alcoholic liver disease is made (3,4). Liver disease is briefly mentioned in the article; however it is important to highlight the role of laboratory data in diagnosing alcoholic liver disease.

References

(1) Nejad SH, Schaefer PW, Bajwa EK, Smith FA. Case records of the Massachusetts General Hospital. Case 39-2012. A 55-year-old man with alcoholism, recurrent seizures, and agitation. N Engl J Med 2012, 367(25):2428-34.

(2) Berggren U, Fahlke C, Berglund KJ, Blennow K, Zetterberg H, Balldin J. Thrombocytopenia in early alcohol withdrawal is associatedwith development of delirium tremens or seizures. Alcohol Alcohol 2009, 44(4):382-6. Berggren U, 2009

(3) Majhi S, Baral N, Lamsal M, Mehta KD. De Ritis ratio as diagnostic marker of alcoholic liver disease. Nepal Med Coll J 2006, 8(1):40-2. Majhi S, 2006

(4) Das SK, Vasudevan DM. Biochemical diagnosis of alcoholism. Indian J Clin Biochem 2005, 20(1):35-42. Das SK, 2005

On 2014 May 26, Ivan Oransky commented:

This paper has been retracted: http://retractionwatch.com/2014/05/23/sampling-error-flawed-analysis-and-miscalculation-trigger-molecular-cell-retraction/

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 2013 Dec 11, Gary Ward commented:

This paper presents a clever new way to generate gene knockouts in T. gondii, using a conditional dimerizable Cre recombinase (DiCre) system. Because the knockouts are experimentally induced with rapamycin, even essential genes can be disrupted for phenotypic characterization. In a first application of the technique, the authors show that two genes encoding proteins previously believed to be essential for parasite invasion, myosin A and the secreted adhesin MIC2, are in fact dispensable. In the case of the myoA knockout parasites, it would be interesting to see whether or not another parasite myosin is upregulated or now associates with the myosin motor complex (e.g., as assessed by a GAP45 IP) in the absence of myosin A.

In contrast, parasites could not tolerate disruption of act1 (actin). Evidence is presented to suggest that the actin knockouts remain capable of invasion and the authors suggest that the most important defect is instead in apicoplast segregation. Have the authors attempted to isolate and maintain an act1 knockout clone in the presence of isopentenyl pyrophosphate (IPP)? Blood-stage Plasmodium falciparum can survive independently of the apicoplast as long as this isoprenoid precursor is provided (Yeh et al. PLOS Biol [2011] 9(8): e1001138). It would be interesting to look at the T. gondii act1 knockout’s ability (or perhaps inability) to glide and invade under similar conditions.

The picture that emerges from these ground-breaking studies is that myosin A, MIC2 and actin are involved in host cell invasion, as the current model would posit, but that there is another previously unrecognized way for the parasites to invade independent of these proteins.

Posted by Gary Ward on behalf of the University of Vermont Toxoplasma Journal Club (UVM ToxoJC); members include Jenna Foderaro, Anne Kelsen, Shruthi Krishnamurthy, Jacqueline Leung, Pramod Rompikuntal, Luke Tilley & Gary Ward

On 2016 Jan 21, Sebastian Lourido commented:

The conditional dimerizable Cre recombinase (DiCre) has been a powerful technique for conditional genome engineering in Toxoplasma, as first established in this article, and elaborated later (see Pieperhoff, et al. 2015. PLoS One). It has worked well in our hands for a variety of applications. Recently, we discovered that the reporter construct used in this study was cloned down stream and in frame of a Ty-tag (EVHTNQDPLD), such that the KillerRed expressed prior to recombination contains and N-terminal Ty-tag. This observation does not affect any of the experiments presented in the article. However, it might be important to note for future investigators planning further manipulations of the existing DiCre strains or reporter constructs.

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 NCT88597077. We believe the correct ID, which we have found by hand searching, is NCT00597077.

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 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 NCT0000473. We believe the correct ID, which we have found by hand searching, is NCT00004732.

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

* 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 Feb 03, Ivan Oransky commented:

The first author of this retracted paper has published a rebuttal of this retraction, 25 years later: http://retractionwatch.com/2015/02/03/25-years-aids-fraud-comes-back-swinging/

On 2016 Apr 19, Lydia Maniatis commented:

I would like to pose a few questions to the authors of this paper.

First, with respect to the meaning of the term “feature”

In paragraph 1, the authors state that: “Identifying a letter requires two steps of visual processing: the observer first detects the letter's features and then combines them to recognize the letter (Pelli, Burns, Farrell & Moore-Page, 2006).”

The insertion of the reference to Pelli et al (2006) seems to imply that this assertion has been corroborated by those authors, but it turns out that in fact, the study in question does not even clarify what it means by the term “features” nor does it employ “features” as independent variables.

Specifically, Pelli et al, (2006) define features “as an image, or image component...” So they have merely equated “feature” with “image” or “part of an image.” (That this is pretty useless is confirmed by them when they say that “Rather than start with a given list of features (e.g., Gibson, 1969), we left the features unspecified).” Substituting “image” for "feature" in Suchow and Pelli's (2013) title results in the somewhat nonsensical “Learning to detect and combine images (or parts of images) of an object.”

In their second paragraph Suchow and Pelli (2013) decide to tackle the question themselves, asking “However, what is a feature?” They “narrowly define features as discrete components of an image that are detected independently of each other (Pelli et al 2006).” (It's not clear what the significance of the Pelli et al (2006) reference is here, given the vagueness described above.) The term “component” is wholly uninformative – and there is no indication of which “components of an image” tend to be “detected independently of each other.” So the authors don't seem to have answered their own question. There is nothing in their definition of the term "feature" to help the reader understand what they mean by it. Claims built on terms without an intelligible working definition are not testable in principle, and therefore are not scientific.

In fact, the authors admit they don't know what they mean by the term “feature:” “To separate the [arbitrarily hypothesized] steps, we need to know the letters features; they are uncertain for traditional letters, so we use Gabor letters instead.” So now “feature” is equivalent to "Gabor". The title should read: “Learning to detect and combine the Gabors of an object.”

The authors “suppose that our Gabors are features, detected independently (Watson (1979) Robson, Graham (1981).” So we're not even stating on principle that our Gabors are features, merely "supposing" that they are. Neither of the two references provided to support this “supposing” seem to refer to features.

On what rationale are Gabors to be referred to as “features” rather than as “objects”?

It seems as though the authors just want something they can label a “feature” without worrying what they mean by it. They state that the “juxtaposition of n Gabors creates an n-feature letter” but this claim is not supported by the two citations they provide; one deals with peripheral vision and the other uses structures made from Gabors and calls them features but offers no definitions or rationale.

So I would ask the authors a. What is the basis for your claim, quoted above, that “Identifying a letter requires two steps of visual processing...” b. How do you (or do you) distinguish a “feature” from an image or an arbitrary part of an image, or from an “object”? c. What do you mean when you say that an (undefined) feature is “detected independently”?

With respect to the phrase “learning to detect.”

In normal circumstances, we don't need to learn to see the world around us. In your experiments, you're making it so difficult that people have to guess, and practice discerning particular forms when they are very faint or lack the homogeneous surface structure that our visual system relies on to segregate figure from ground. Even if it is possible to learn to harness expectation to achieve better quasi-guesses, why do you consider these difficult and unnatural conditions conducive to learning about the normal functioning of our visual system?

Is the 75% cut-off point used to define contrast threshold derived from studies of the visual system? On what basis is it chosen? If it is arbitrary, then how can calculations based on it illuminate visual function?

With respect to the use of “Gabors”

You say that: “Gabors are fairly well matched to the receptive fields of simple cells in the primary visual cortex” though you offer no references to support this statement. Do you mean to imply that different figures, e.g. drawings of puppies, might be poorly-matched to V1 receptive fields? Would this impair our perception of them? Given that V1 neurons are presumably involved in all of our visual percepts, on what basis do you infer a “well-matched” vs “poorly-matched” dichotomy? Are you aware of Teller's (1984) arguments that the notion that particular stimuli tap into particular neurons or groups of neurons is highly problematic on logical and empirical grounds?

On 2016 Apr 19, Lydia Maniatis commented:

You refer to “detection” and “identification.” In vision science, people often refer to “perception.” Where does perception come in, in your scheme? It would seem that identification of any percept presupposes perceiving it in the first place. In addition, we are capable of seeing things that we cannot “identify.” A random blob, for instance. Given that you refer (however invalidly) to the primary visual areas (V1), it would seem that you are interested in the way percepts arise, i.e. perception. Perceiving an object obviously doesn't correspond to detection, which you describe, in effect, as perceiving any inhomogeneity in the surface on which the stimulus is presented, and again, identification is post-perception. So where in your model does object perception come in?

Relatedly, your equations are founded on terms for contrast, but it seems inappropriate to model identification or recognition on contrast, since this is a post-perception act of comparison. You might say, in response, that your viewing conditions are so poor that observers need to guess, but what does guessing have to do with basic visual processes? And since the reliability of their guesses depends on an arbitrary selection of “letters” and their in particular their frequencies, of what relevance is such reliability to understanding perception?

Finally, are you aware that the perceptual emergence of parts of a stimulus are contingent on its structure? This was ascertained in experiments performed by Gottschaldt (1929) (in Ellis, A Source Book of Gestalt Psychology) using line drawings (and you state that you consider lines - “bars” - to be “features.”) He showed that for particular figures, the order of emergence of parts with increasing illumination (analogous to increasing contrast here), was repeatable and structure-dependent. You take for granted that all of the parts of your individual Gabors are “detected” (or identified, I'm not sure which) simultaneously, but if this is the case it is because of their structure, which you don't consider.

On 2016 Apr 19, Lydia Maniatis commented:

The authors state that "the conclusions of this paper do not depend on our claim that Gabor "letters" are letters; it is enough that they are objects." This seems to imply some kind of generality of the conclusions, extending to "objects" generally. But later they seem unsure if the method can be extended beyond collections of Gabor patches: "It may be possible to extend our approach beyond Gabor letters to other stimuli, such as words, faces and scenes, whose features are unknown. If one assumes the separability found here, then it may be easy to factor out the efficiency of detecting."

If the "features" of these other entities are unknown, then what is to be separated, and how? How might the "features" come to be known?

What is clear is that the authors have not considered and do not seem obliged to consider whether in principle (and on the basis of what principle), their specific experimental conditions and results have any generality - i.e. theoretical significance for perception - at all. In this case, they have simply collected some data and crunched the numbers in some arbitrary (because theoretically ambiguous) fashion. Yet this is supposed to be a top journal, whose editors, one might assume would take such factors into consideration.

The fact is that the whole conversation is moot because perception demonstrably does not and cannot consist of an arbitrarily asserted "two-step process of feature detection and combination" even if the authors could explain what they mean by "feature."

On 2016 Apr 19, Lydia Maniatis commented:

I don't think it is ever explained why "noise" is added to the stimuli.

On 2014 Nov 17, Raphael Levy commented:

The evidence behind the structure and special properties of “striped” nanoparticles has been challenged by Cesbron Y, 2012. The publication in 2012 of Cesbron Y, 2012 took three years and has been followed by post-publication peer review of the various existing and new stripy articles on my blog, PubPeer, etc.

A detailed analysis of this body of work is published today in PloS One by Stirling et al; from the abstract: “through a combination of an exhaustive re-analysis of the original data with new experimental measurements of a simple control sample comprising entirely unfunctionalised particles, we conclusively show that all of the STM evidence for striped nanoparticles published to date can instead be explained by a combination of well-known instrumental artefacts, strong observer bias, and/or improper data acquisition/analysis protocols.”

On 2013 Oct 28, Mick Watson commented:

We have now published the software behind many of the analyses in this paper:

Watson M, Schnettler E, Kohl A. (2013) viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. Bioinformatics. 29(15):1902-3

http://www.ncbi.nlm.nih.gov/pubmed/23709497

The website for the software is here: http://www.ark-genomics.org/bioinformatics/virome

On 2014 Aug 10, Raha Pazoki commented:

"GPRC6A in Myocardial Infarction"

The article by Rossol and co-workers demonstrated the role of GPRC6A in activation of inflammatory response in the necrotic area. This topic could be interesting in cardiovascular genetics specifically in understanding the mechanisms involved in cardioprotection during myocardial infarction (MI).

Depending on the size of infarction, tissue injury and necrosis of cardiomyocytes occurs during MI. GPRC6A may activate inflammatory response in the infarct area and may have a function in cardioprotectivity and healing of the damaged tissue. Experimental investigations are necessary to give insight on this topic.

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2014 Apr 13, Tom Kindlon commented:

When one looks at all the transfers (i.e. unemployment, etc.) the differences between the groups effectively disappear:

The abstract only gives the percentages who received disability pension. However, there are other transfers and most people in both groups got transfers.

"Transfer payments were divided into five categories: 1: disability pension; 2: flexible work (jobs created for persons with limited working capacity); 3: sickness benefit; 4: unemployed; and 5: self-supporting. Which of these five categories each patient fit into was determined at two time points: a 12-week period immediately before baseline and a 12-week period 15 months after baseline. We chose a 12-week period over a one-week period to obtain an estimate as precise as possible of the transfer payments received during the two time periods.

"We used the transfer payment categories proposed by Hjollund et al. [18] and Carstensen [19]. Carstensen [19] grouped sickness benefit and vocational rehabilitation as temporary health-related benefits, whereas flexible work and disability pension were grouped as permanent health-related benefits."

"Flexible work and disability pension are permanent health-related benefits"

Here are the results (I haven't tried to calculate the percentages but the sample sizes in both groups are virtually the same so one can see the similarities by inspection).

Mindfulness therapy (n=59):

Baseline: Self-support: 19 Unemployed: 6 Sickness benefit: 21 Flexible work: 9 Disability pension: 4

Follow-up: Self-support: 17 Unemployed: 9 Sickness benefit: 2 Flexible work: 16 Disability pension: 15

"Enhanced treatment as usual"

Baseline: Self-support: 17 Unemployed: 6 Sickness benefit: 23 Flexible work: 7 Disability pension: 7

Follow-up: Self-support: 13 Unemployed: 4 Sickness benefit: 3 Flexible work: 13 Disability pension: 27

So if one just looks at self-support, the only one that doesn't involve transfers, there is little difference (as well as there being a (small) deterioration in both groups):

Mindfulness therapy (n=59): Baseline: 19 Follow-up: 17

"Enhanced treatment as usual" (n=60) Baseline: 17 Follow-up: 13

On 2014 Apr 13, Tom Kindlon commented:

There are quite big differences between the two groups in terms of changes in healthcare costs:

In the abstract have collapsed the healthcare costs from the two groups, one of which is "enhanced treatment as usual" which would usually be seen as more like a control group.

Mindfulness therapy: One year prior to baseline: $4643 Baseline and one year ahead: $3937

"Enhanced treatment as usual" One year prior to baseline: $5996 Baseline and one year ahead: $3355

Also, the baseline figures may not be average figures for a typical year: this figure was in the year in the lead up to be referred to the clinic so these were likely in the period when the patients, and indeed health professionals, were looking for answers to do with their health problems.

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 NCT700732472. We believe the correct ID, which we have found by hand searching, is NCT00732472.

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 10, Martine Crasnier-Mednansky commented:

According to Bledig SA, 1996, deletion of FruR (Cra) resulted in an appreciable increase of pykF-encoded pyruvate kinase synthesis on gluconeogenic carbon sources as compared to glycolytic carbon sources (casamino-acids were added to the culture medium to allow gluconeogenic growth). In addition, overexpressed FruR repressed the transcription of the pykF gene significantly on gluconeogenic carbon sources but not on glycolytic carbon sources. Thus the FruR (Cra) effect on pykF transcription significantly takes place under conditions of gluconeogenic growth. Therefore using pykF as a reporter gene for analyzing, under glycolytic growth conditions, a transcriptional regulation by FBP/Cra appears inappropriate. In addition, the concentration of FBP is dependent on the concentration of PEP because phosphofructokinase is subject to allosteric control by PEP Blangy D, 1968. Therefore decreasing pyruvate kinase synthesis below physiological level also decreases the FBP concentration which is in conflict with the present data (see Fig. S1 and Fig. 2B).

As shown in Fig. 1C, concentrations of FBP controlling the glycolytic flux are below 1 mM. This concentration range has been reported to be insufficient for FBP to displace FruR from its operator sites. In addition, cAMP-dependent carbon catabolite repression was reported by Nanchen A, 2008 to be the dominant control mechanism of metabolic fluxes under glucose limitation condition (used in Fig. 1B, black squares).

On 2017 Oct 05, ROBERT HURST commented:

Unfortunately, KU-7 is not bladder cancer but is, instead, HeLa cells. PMC3805942

On 2015 Apr 02, Marcus Munafò commented:

Flegal and colleagues suggest that being overweight may decrease risk of all-cause mortality, and being slightly obese confers no increased risk compared to being of normal weight [1]. We think these conclusions are misleading and may give a detrimental public health message, particularly given the publicity they attracted.

Despite the authors’ suggestion that there is “little support for the suggestion that smoking and pre-existing illness are important causes of bias”, these factors are not consistently controlled for within the contributing studies [1]. It has been demonstrated in two large prospective studies that the increased risk of death from being overweight or obese can be masked when smoking is not adequately controlled for, and when sufficient initial years of follow up are not excluded [2]. Smoking is associated with both lower body mass index (BMI) and increased risk of death, while underlying illness can lower BMI prior to death. Furthermore, it is widely appreciated that conventional statistical approaches to “control” for such factors are inadequate. Support for a positive causal effect of BMI on mortality comes from studies less subject to the biases associated with BMI measured in later life because they used BMI in adolescence or offspring BMI as the exposure [3, 4]. These measures are suitable proxies since they are strongly associated with an individual’s BMI in middle age but are not substantially affected by reverse causality and are less confounded by smoking. Higher BMI in adolescence was associated with greater risk of all-cause mortality in middle age in a study of over 200,000 individuals [3]. Stronger inferred associations were observed with offspring BMI and all-cause and cardiovascular mortality than with own BMI, suggesting that positive associations of BMI and mortality may in fact be underestimated in conventional observational studies [4]. In addition, this study demonstrated that the commonly observed inverse association between BMI and death from respiratory and other diseases may also be due to such biases.

Given the importance of the public health messages regarding “healthy” weight, we feel that further research is needed in this area using innovative research methods to overcome potential biases; further conventional observational studies will simply recapitulate the biases inherent in all such investigations. One such approach would be Mendelian randomisation, using obesity-related genetic variants, such as those in FTO. Mendelian randomisation methods, when applied correctly, are free from confounding by environmental factors and are not affected by reverse causality [5].

Marcus Munafò, Amy Taylor and George Davey Smith

1. Flegal, K.M., et al., Association of all-cause mortality with overweight and obesity using standard body mass index categories: a systematic review and meta-analysis. JAMA, 2013. 309(1): p. 71-82.
2. Lawlor, D.A., et al., Reverse causality and confounding and the associations of overweight and obesity with mortality. Obesity (Silver Spring), 2006. 14(12): p. 2294-304.
3. Bjorge, T., et al., Body mass index in adolescence in relation to cause-specific mortality: a follow-up of 230,000 Norwegian adolescents. Am J Epidemiol, 2008. 168(1): p. 30-7.
4. Davey Smith, G., et al., The association between BMI and mortality using offspring BMI as an indicator of own BMI: large intergenerational mortality study. BMJ, 2009. 339: p. b5043.
5. Davey Smith, G. and S. Ebrahim, 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease? Int J Epidemiol, 2003. 32(1): p. 1-22.

On 2015 Apr 18, John Spitzer commented:

The article in JAMA by Flegal et al is a summary of the literature. It includes 97 articles with 2.88 million individuals and more than 270,000 deaths. The conclusions described as "misleading" by Munafò et al (below) are simply a summary of the results that arise from the data and the statistical methods. Munafò et al do not present any specific criticisms of the methods of the Flegal et al article nor do they assert that the summary of the literature is incorrect. The single study by Lawlor, described by Munafò et al as "large," based its results on 5,337 never-smoking participants, and it was one of the articles included in the review by Flegal et al. The majority of those articles do not show smoking and pre-existing illness as important causes of bias. Opinions about "detrimental" public health messages arising from scientific findings should be distinguished from scientific criticisms of those findings. In a commentary on reactions to the Flegal et al article the editors of Nature stated: "It is risky to oversimplify science for the sake of a clear public-health message." http://www.ncbi.nlm.nih.gov/pubmed/23936910

On 2015 Apr 25, Arnaud Chiolero MD PhD commented:

Probably the best and more exhaustive review addressing the issue of overweight and mortality. Many health scientists have difficulties to accept the idea that a BMI in the overweight category is not associated with a higher mortality. To move beyond this controversy, studies assessing the effect of interventions to reduce BMI will be needed (see e.g. Chiolero Epidemiology 2015). Meanwhile, it seems difficult to deny these observations.

On 2014 Apr 30, Jason Stajich commented:

Unfortunately the web server URL referenced in this manuscript is no long available (as of April 2014).

On 2014 May 31, Torsten Seemann commented:

There is now a HTTP redirect to the new version: http://cge.cbs.dtu.dk/services/snpTree-1.1/

On 2016 Apr 06, Lydia Maniatis commented:

The authors' approach has serious problems, similar to those discussed by Teller (1984), as commented on by me here: https://pubpeer.com/publications/23283693

On 2014 Dec 15, Chinmoy Saha commented:

I think there is a printing mistake in the abstract (line 3). Wrong: 13 to 8% in K562 cells? Right: 3 to 8% in K562 cells?

On 2013 Jun 17, John Overington commented:

Reviews and discusses two important concepts - firstly - ligand-based clustering of biological receptors on the basis of ensembles of ligands that bind to them, and then the development of an organisational framework based on these similarities; and secondly - the concept of a time domain in biological signalling and response to a given small molecule ligand - reflecting the limited repertoire of small molecule ligands and the response systems with radically different time constants.

On 2014 Feb 14, Daniel J Simons commented:

I just wrote a post-publication review of this paper on my blog: http://blog.dansimons.com/2014/02/hi-bar-10-questions-about-inattentional.html

If the method proves robust, this approach could have large theoretical and practical implications for our understanding of attention sets in inattentional blindness. I do have some concerns about how robust this effect is. And, as my blog post highlights, I have a number of questions about the methods and analyses. It would be great if the authors could provide additional information here or as supplemental material for their paper.

On 2016 Apr 09, Arnaud Chiolero MD PhD commented:

An easy-to-read review to better understand what brings modern approach of causal inference in epidemiology and public health.

On 2013 Nov 15, Gaétan Kerdelhué commented:

Two later studies confirmed a high recall of Google Scholar but argued it could not be used in realistic settings for systematic reviews. See Giustini D, 2013 and Boeker M, 2013.

On 2013 Dec 27, Wichor Bramer commented:

More recently another article was published that revisited the conclusions from Gehanno: Bramer WM, 2013.

In this article we conclude that, though the coverage of Google Scholar is near 100%, the retrieval is far from that. Because Google Scholar is only able to show the first 1000 hits, we investigated whether the authors of 21 reviews that used google scholar would have identified every included reference if they had used only google scholar.

Only 72% of all references would have been found, which is almost equal to the recall of PubMed (68%).

Therefor Google Scholar should not be used alone in searching for Systematic Reviews.

Not even with improved precision, because the factual precision (the number of hits found in the first 1000, divided by 1000) is not as problematic as when precision is calculated based on the (estimated) total number of hits, which very often is exeptionally high when searching Google Scholar.

On 2014 Mar 28, Farhad Shokraneh commented:

I think the conclusion of the paper is not supported by the data. This study just shows that "If you KNOW that a paper ALREADY exist, you can find it in Google Scholar". So the authors have NOT used Google Scholar for searching for systematic review but just for re-finding the list of the papers have ALREADY found by other resources and included in the systematic reviews. The conclusion could be right just when the authors use GS for systematic searching and finding the relevant studies among search results. Also, the next time I think 'Google' gives the same coverage!

On 2014 Mar 31, M Felix Freshwater commented:

The AMSTAR standard http://amstar.ca/Amstar_Checklist.php is 2 electronic sources. According to the Cochrane Handbook http://handbook.cochrane.org/ 6.2.1.3 Database overlap

Of the 4,800 journals indexed in EMBASE, 1,800 are not indexed in MEDLINE. Similarly, of the 5,200 journals indexed in MEDLINE, 1,800 are not indexed in EMBASE. o www.info.embase.com/embase_suite/about/brochures/embase_fs.pdf

On 2014 May 21, Francesc Roig commented:

From my point of view, according to the methodology of the study of Gehanno et col, and according to the results presented, they cannot affirm that "If the authors of the 29 systematic reviews had used only GS, no reference would have been missed". The only conclusion we could maintain would be something like "all references in the 29 systematic reviews selected were accessible through GS", but not that these references would be retrieved in a search with the objective to conduct the systematic reviews. As far as the study doesn’t compare search results in both engines (as other studies posted here actually do), it seems clear that you cannot maintain that results would be the same and then, you cannot maintain that using GS for the systematic reviews would produce the same results.

On 2014 May 27, Chris Hafner-Eaton commented:

This study should be viewed as one "data pull" of 29 systematic reviews. In order to support the conclusions, the study must be replicated many times. It will be through repeated true positives (the sensitivity) with minimal false positives/maximizing the specificity or true negatives that we will come closER (although never declarative) to saying that Google Scholar "could be use alone for systematic reviews." As others have noted, PubMed doesn't capture all and yet it is entirely possible to pick up too much erroneous material--particularly in the grey literature and for certain review topics such as Comparative Effectiveness Reserach. However, one must always weigh the costs of being wrong versus being late with the results!

On 2013 Nov 09, Jonathan Moore commented:

Very nice job to the team who made this. The prospects for integration of automated learning and literature-based curation of ontologies are great, and it looks like a useful tool for discovery - I'd like to try it in discovery mode with some other species with 'thin' ontology annotations.

One thing I wondered about is the need for the hierarchical tree imposed at step one, and its effects on the final result. I wonder whether the tree-like requirement leads to the possibility of falling into a local optimum final graph, ending up with more of the initial tree-like structure than the data really suggest, rather than finding the optimum final graph from the true shape of the input data. The computational requirements for learning an arbitrary graph at step one seem daunting though.

Maybe this could be part of the reason for the better match to GO for cellular components, which maybe tend to be more inherently hierarchical in comparison to molecular functions or biological processes.

On 2013 Nov 02, Matt Nolan commented:

Code for simulations in this study is available at: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=150031

On 2013 Oct 25, Stephen Turner commented:

Two of the most common questions at the beginning of an RNA-seq experiments are "how many reads do I need?" and "how many replicates do I need?". This paper describes a web application for designing RNA-seq applications that calculates an appropriate sample size and read depth to satisfy user-defined criteria such as cost, maximum number of reads or replicates attainable, etc. The power and sample size estimations are based on a t-test that the authors claim performs no worse than the negative binomial models implemented by popular RNA-seq methods, such as DESeq {1}, when there are three or more replicates present. Empirical distributions are taken from either (1) pilot data that the user can upload; or (2) built-in publicly available data. The authors find that there is substantial heterogeneity between experiments (technical variation is larger than biological variation in many cases), and that power and sample size estimation will be more accurate when the user provides their own pilot data.

On 2015 Aug 27, Zhicheng Lin commented:

The evidence that unconscious response inhibition emerges when subliminal stimuli are mixed with supraliminal stimuli (mixed session), but disappears when they are presented alone (single session) is unwarranted because the two types of session differ in a critical aspect: level of awareness (Lin and Murray, 2014). Indeed, when the level of awareness is comparable between sessions, there is no difference in unconscious response inhibition between the mixed and single sessions (Lin and Murray, 2015).

Refs: Lin, Z., Murray, S. O. (2014). Priming of awareness or how not to measure visual awareness. Journal of Vision, 14(1), 1–17. Lin, Z., Murray, S. O. (2015). Automaticity of unconscious response inhibition: Comment on Chiu and Aron (2014). Journal of Experimental Psychology: General, 144(1), 244–254.

Direct links to the refs: http://jov.arvojournals.org/article.aspx?articleid=2295565 http://psycnet.apa.org/journals/xge/144/1/244

On 2014 Dec 05, Dina Danso-Abeam commented:

The discussion part of this article mentions 3 proposed modes of inheritance for Olmsted syndrome (OS). However, via exome sequencing, it is now known that the X-linked inheritance form of the disease has MBTPS2 (Membrane-bound transcription factor protease, site 2) as the pathogenic gene. The autosomal dominant form of OS has TRPV3 (transient receptor potential cation channel, subfamily V, member 3) as the pathogenic gene Lin Z, 2012. Recent study from Wang et al, actually challenges the existence of the X-linked form to be a true OS instead of being a severe form of IFAP (Itchyosis follicularis, alopecia, and photophobia) syndrome Wang HJ, 2014.

References:

1. Lin, Z. et al. Exome sequencing reveals mutations in TRPV3 as a cause of Olmsted syndrome. American journal of human genetics 90, 558-564 (2012).

2. Wang, H.J. et al. Recurrent splice-site mutation in MBTPS2 underlying IFAP syndrome with Olmsted syndrome-like features in a Chinese patient. Clinical and experimental dermatology 39, 158-161 (2014).

On 2014 Nov 08, Ivan Oransky commented:

This paper is being retracted: http://www.retractionwatch.com/2014/11/04/kidney-journal-to-retract-stem-cell-paper-for-duplicated-and-doctored-images/

On 2013 Jul 01, lu tian commented:

The authors have made the timely call for moving beyond the traditional statistical analysis plan that “within the tried and true comfort zone for clinical acceptance and regulatory approval” in the setting of survival analysis with re-current events. In this case, the “comfort zone” is the so-called time to the first event analysis which is not only often underpowered but also completely fails to characterize the treatment effect beyond the first event. The true difficulty to go beyond the “comfort” zone is in summarizing the whole patient experiences during or after the treatment in an objective clinically meaningful way. For example, how to weigh the relative importance of non-fatal events compared with death? This is a difficult task and probably we will never be able to come up with a perfect consensus.

However, the authors convincingly conveyed the message that albeit those difficulties, clinicians and statisticians need to be bold to go beyond the simple “time to the first event analysis” to address the clinical meaningful question which is to understand the treatment effects on entire disease burden characterized by both non-fatal and fatal events in this case. The initial solution may not be perfect but at least we should answer the right question.

On 2017 Feb 17, Donald Forsdyke commented:

EPONYMS: "DM" FOR GENIC AND "WCB" FOR CHROMOSOMAL SPECIATION THEORIES

The remarkable observations made in this outstanding paper have been well supported by subsequent studies (e.g. Moehring 2011; Forsdyke 2016). However, encompassing both genic and non-genic incompatibilities under the Dobzhansky-Muller rubric is regrettable. As described elsewhere (Forsdyke 2011), while William Bateson's term "epistasis" is used to describe interactions between genes, he himself espoused a non-genic "chromosomal" model for the initiation of the divergence of one species into two species. Thus, Bhattacharyya et al. (2013) correctly employ the eponymous acronym "DM" rather than the widely employed "BDM."

Yet, they write that "several pieces of indirect evidence are in favor of D-M incompatibilities based on non-genic sequence divergence." This implies that Dobzhansky and Muller had non-genic viewpoints (which they did not). For those who like eponymous acronyms, some new form, relating to the history of the chromosomal viewpoint, would seem appropriate.

Clear articulations of the chromosomal viewpoint trace back to the Danish "father of yeast genetics" Ojvind Winge, and were elaborated in the 1920s by Crowther and Bateson. Thus, it would seem appropriate that, while retaining "DM incompatibilities" for appropriate genic speciation theories, we introduce "WCB incompatibilities" for appropriate chromosomal theories. For further background please see Bateson Webpage.

Bhattacharyya T, Gregorova S, Mihola O, Anger M, Sebestova J, Denny P, et al., (2013) Mechanistic basis of infertility of mouse intersubspecific hybrids. Proc Nat Acad Sci USA 110: E468–E477.Bhattacharyya T, 2013

Forsdyke DR (2011) The B in BDM. William Bateson did not advocate a genic speciation theory. Heredity 106: 202.Forsdyke DR, 2011

Forsdyke DR (2016) Evolutionary Bioinformatics, 3rd edn. Springer: New York.

Forsdyke DR (2017) Speciation: Goldschmidt's chromosomal heresy, once supported by Gould and Dawkins, is again reinstated. Biol Theor (in press) doi: 10.1007/s13752-016-0257-z

Moehring AJ (2011). Heterozygosity and its unexpected correlations with hybrid sterility. Evolution 65: 2621–2630.Moehring AJ, 2011

On 2014 Aug 09, Michael Cianfrocco commented:

To view the UCSF Chimera session associated with this paper, you can download the .zip Chimera session from figshare

If you use this Chimera session, please cite figshare!

On 2014 Jan 13, Brett Snodgrass commented:

Grant described the vessels of Wearn in 1926.

In 1929 Grant and Viko assessed hearts for the presence of the vessels of Wearn, but noted they were identified. The reason for this negative study is not entirely clear. It may be explained that some of the vessels of Wearn are greater than 10um but less than 40 um. 40um was the smallest lumen diameter of a vessel which the specific dye would enter.

Vessels of Wearn identified by Grant in 1926:

1. https://twitter.com/BrettSnodgrass1/status/420281076070637568

For additional commentary and reference to Grant's 1929 study, please see:

1. http://bit.ly/1929Grant

2. http://scholar.google.com/scholar?cluster=5189678684113164458&hl=en&as_sdt=0,26&sciodt=0,26

3. https://twitter.com/BrettSnodgrass1/status/410929217170206721

4. http://bit.ly/ThebesianVeins

5. http://bit.ly/vasaThebesii

Comments and suggestions are welcome. If this comment is not helpful, please consider adding a comment about how it may be improved.

Thank you kindly.

On 2014 Nov 25, Harri Hemila commented:

The paper has been commented on at the BMJ pages, see: http://www.bmj.com/content/346/bmj.f10/rr/629228.

On 2014 Oct 07, Murat Tunc commented:

Interesting study.

On 2013 Oct 31, John Cannell commented:

The authors reported that immune system dysregulation is common in autism spectrum disorder (ASD”. Vitamin D deficiency produces very similar immune dysregulation.

Prietl B, 2013

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< PMID:23359064>

< PMID:20427238>

Thus the vitamin D theory of ASD (vitamin D deficiency being the environmental risk factor for this highly heritable disorder) is consistent with the authors work. Three recent studies, using community controls, have found 25(OH)D levels are significantly lower in children with ASD. Two of the studies below (Mostafa et al and Gong et al) also found ASD severity, as rated on standard ASD rating scales, is inversely correlated with 25(OH)D levels. Mostafa et al found an R value of -.86 for the association of serum 25(OH)D with ASD severity.

Gong ZL, Luo CM, Wang L, Shen L, Wei F, Tong RJ, Liu Y. Serum 25-hydroxyvitamin D levels in Chinese children with autism spectrum disorders. Neuroreport. 2013 Oct 1. Gong ZL, 2014

Meguid NA, Hashish AF, Anwar M, Sidhom G. Reduced serum levels of 25-hydroxy and 1,25-dihydroxy vitamin D in Egyptian children with autism. J Altern Complement Med. 2010 Jun;16(6):641-5. Meguid NA, 2010

Mostafa GA, Al-Ayadhi LY.Reduced serum concentrations of 25-hydroxy vitamin D in children with autism: relation to autoimmunity. J Neuroinflammation. 2012 Aug 17;9:201. Mostafa GA, 2012

There is a plethora of basic science explaining why low gestational or early childhood 25(OH)D levels would adversely effect brain development.

Eyles DW, Feron F, Cui X, Kesby JP, Harms LH, Ko P, McGrath JJ, Burne TH. Developmental vitamin D deficiency causes abnormal brain development. Psychoneuroendocrinology. 2009 Dec;34 Suppl 1:S247-57. doi: 10.1016/j.psyneuen.2009.04.015. Epub . Review. Eyles DW, 2009

DeLuca GC, Kimball SM, Kolasinski J, Ramagopalan SV, Ebers GC. Review: the role of vitamin D in nervous system health and disease. Neuropathol Appl Neurobiol. 2013 Aug;39(5):458-84. doi: 10.1111/nan.12020. DeLuca GC, 2013

Eyles DW, Burne TH, McGrath JJ. Vitamin D, effects on brain development, adult brain function and the links between low levels of vitamin D and neuropsychiatric disease. Front Neuroendocrinol. 2013 Jan;34(1):47-64. doi: 10.1016/j.yfrne.2012.07.001. Epub 2012 Jul 11. Review. Eyles DW, 2013

Furthermore, the vitamin D theory of autism explains most of the epidemiological facts of ASD.

Cannell JJ. On the aetiology of autism. Acta Paediatr. 2010 Aug;99(8):1128-30. Cannell JJ, 2010

Cannell JJ. Autism and vitamin D. Med Hypotheses. 2008;70(4):750-9. Cannell JJ, 2008

70% of American toddlers do not take the American Pediatric Association's recommended vitamin D supplement of 400 IU/day and few toddlers or pregnant women get any sunshine due to the sun scare. As vitamin D fortified milk consumption and sun exposure has declined, so have toddlers and pregnant women’s vitamin D levels. The dramatic increase in the incidence of ASD occurred during the same time vitamin D levels were falling in toddlers and pregnant women.

Cannell JJ. Autism, will vitamin D treat core symptoms? Medical Hypotheses. 2013 Aug;81(2):195-8. Cannell JJ, 2013

Some autism researchers seem cognizant of the entire body of autism research. For example, a group of well-known European ASD researchers, including Professor Christopher Gillberg of the Gillberg Neuropsychiatric Institute, have recently called for the need for “urgent research” into the vitamin D deficiency theory of ASD.

Kočovská E, Fernell E, Billstedt E, Minnis H, Gillberg C. Vitamin D and autism: clinical review. Res Dev Disabil. 2012 Sep-Oct;33(5):1541-50. doi: 10.1016/j.ridd.2012.02.015. Epub 2012 Apr 21.Kočovská E, 2012

Until all autism researchers become cognizant of the wider body of scientific research, we will continue to wonder how to prevent - and perhaps even treat - this modern day plague.

John J Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org

On 2013 Oct 31, John Cannell commented:

The authors stated that markers of oxidative stress are present in autism spectrum disorder (ASD). I wonder if the authors are aware that the genes for the antioxidants superoxide dismutase and thioredoxin reductase are directly up-regulated by the secosteroid 1,25 di-hydroxy vitamin D3 (calcitriol). I believe both genes also harbor a vitamin D response element.

Peehl DM, Shinghal R, Nonn L, Seto E, Krishnan AV, Brooks JD, Feldman D. Molecular activity of 1,25‐dihydroxyvitamin D3 in primary cultures of human prostatic epithelial cells revealed by cDNA microarray analysis. J. Steroid Biochem Mol. Biol 2004;92:131–141. PMID:15555907>

Calcitriol also directly up-regulates glutathione reductase and increases glutathione levels.

Jain SK, et alo. Vitamin D upregulates glutamate cysteine ligase and glutathione reductase, and GSH formation, and decreases ROS and MCP-1 and IL-8 secretion in high-glucose exposed U937 monocytes. Biochem Biophys Res Commun. 2013 Jul 19;437(1):7-11. doi: 10.1016/j.bbrc.2013.06.004. Jain SK, 2013

Also, supplemental vitamin D significantly reduces oxidative stress in humans.

Nikooyeh B, et al. Daily intake of vitamin D- or calcium-vitamin D-fortified Persian yogurt drink (doogh) attenuates diabetes-induced oxidative stress: evidence for antioxidative properties of vitamin D.J Hum Nutr Diet. 2013 Jul 5. doi: 10.1111/jhn.12142. Nikooyeh B, 2014

Asemi Z, et al. Vitamin D supplementation affects serum high-sensitivity C-reactive protein, insulin resistance, and biomarkers of oxidative stress in pregnant women. J Nutr. 2013 Sep;143(9):1432-8. doi: 10.3945/jn.113.177550. Asemi Z, 2013

Thus the vitamin D theory of ASD (vitamin D deficiency being the environmental risk factor for this highly heritable disorder) is consistent with the authors work. Three recent studies, using community controls, have found 25(OH)D levels are significantly lower in children with ASD. Two of the studies below (Mostafa et al and Gong et al) also found ASD severity, as rated on standard ASD rating scales, is inversely correlated with 25(OH)D levels. Mostafa et al found an R value of -.86 for the association of serum 25(OH)D with ASD severity.

Gong ZL, Luo CM, Wang L, Shen L, Wei F, Tong RJ, Liu Y. Serum 25-hydroxyvitamin D levels in Chinese children with autism spectrum disorders. Neuroreport. 2013 Oct 1. Gong ZL, 2014

Meguid NA, Hashish AF, Anwar M, Sidhom G. Reduced serum levels of 25-hydroxy and 1,25-dihydroxy vitamin D in Egyptian children with autism. J Altern Complement Med. 2010 Jun;16(6):641-5. Meguid NA, 2010

Mostafa GA, Al-Ayadhi LY.Reduced serum concentrations of 25-hydroxy vitamin D in children with autism: relation to autoimmunity. J Neuroinflammation. 2012 Aug 17;9:201. Mostafa GA, 2012

There is a plethora of basic science explaining why low gestational or early childhood 25(OH)D levels would adversely effect brain development.

Eyles DW, Feron F, Cui X, Kesby JP, Harms LH, Ko P, McGrath JJ, Burne TH. Developmental vitamin D deficiency causes abnormal brain development. Psychoneuroendocrinology. 2009 Dec;34 Suppl 1:S247-57. doi: 10.1016/j.psyneuen.2009.04.015. Epub . Review. Eyles DW, 2009

DeLuca GC, Kimball SM, Kolasinski J, Ramagopalan SV, Ebers GC. Review: the role of vitamin D in nervous system health and disease. Neuropathol Appl Neurobiol. 2013 Aug;39(5):458-84. doi: 10.1111/nan.12020. DeLuca GC, 2013

Eyles DW, Burne TH, McGrath JJ. Vitamin D, effects on brain development, adult brain function and the links between low levels of vitamin D and neuropsychiatric disease. Front Neuroendocrinol. 2013 Jan;34(1):47-64. doi: 10.1016/j.yfrne.2012.07.001. Epub 2012 Jul 11. Review. Eyles DW, 2013

Furthermore, the vitamin D theory of autism explains most of the epidemiological facts of ASD.

Cannell JJ. On the aetiology of autism. Acta Paediatr. 2010 Aug;99(8):1128-30. Cannell JJ, 2010

Cannell JJ. Autism and vitamin D. Med Hypotheses. 2008;70(4):750-9. Cannell JJ, 2008

70% of American toddlers do not take

On 2015 May 04, Peter Rogan commented:

The Logic and Formulation of Exon Definition for Splice and Splicing Regulatory Sites with Negative Information Content. PK Rogan, EJ Mucaki

Update on: Mucaki EJ, 2013 and the Automated Splice Site and Exon Definition Analysis server (ASSEDA).

In Mucaki EJ, 2013, we described a method of predicting the overall strength of an exon by calculating its total information content (Ri,total) from the sum of the Ri values of its donor and acceptor splice sites, adjusted for their gap surprisal (the self-information of the distance between the two sites). Differences between ΔRi,total values are predictive of the relative abundance of these exons in distinct processed mRNAs.

Splice sites altered by mutations that prevent stable interaction with splicesomes are said to be abolished. Information theory predicts abolition of binding below their minimum binding affinity, Ri,minimum, which is empirically derived. This value is slightly above zero bits, the theoretical minimum for binding at equilibrium (ΔG = 0; Schneider TD, 1997). Sites with Ri < 0 are not bound, forming stable interactions would be endergonic (ΔG > 0). This raises the question, when predicting the change in exon strength (ΔRi,total) due to a mutation that inactivates binding, whether mutant sites with varying degrees of negative information content are energetically distinguishable from one another.

The computation of Ri,total contains the sum of the the Ri values of component binding sites, irrespective of their initial or final strengths. Thus, a mutated site with Ri << 0 would result in greater ΔRi,total compared to a site with Ri ~ 0. To assess whether the degree of unfavorable binding should be applied to the exon definition calculation, or if values below 0 bits should be computed similarly to a binding site at equilibrium (Ri ~ 0), we reevaluated experimentally validated natural and regulatory splicing mutations in our paper with both approaches. Ri,total was calculated for 10 variants from Supplementary Table 2, both including and excluding the negative information (ie. Ri < 0 vs. Ri = 0) of inactivated splice sites. Mutation #2 of Supplementary Table 2 [ADA:g.43249658G>A] abolishes a natural donor site, from 8.8 to -9.9 bits. In applying the full decrease in strength (ΔRi,total: -18.7 bits), the natural exon strength decreases from 21.0 to 2.3 bits. When the negative information content is set to zero bits, the change is significantly smaller (21.0 -> 12.2 bits; ΔRi,total = -8.8 bits). When a weak natural splice site is abolished, the difference as expressed as ΔRi,total can be quite small (Mutation #9; -14.8 vs -3.1 bits). In the case of Mutation #38, the reduction in ΔRi,total leads to a partially discordant prediction where the abolished natural exon is weaker than the experimentally confirmed activated cryptic exon. Results for this mutation were concordant with the published version when the negative bit value of the mutated natural site was included in the calculation.

The impact of mutations in splicing regulatory (SR) factors can also be predicted on ASSEDA, where the Ri of the SR binding site is added to the R_i,total, as well as a secondary gap surprisal value for the particular SR protein. These sites can also be abolished. But when a SR protein binding site is no longer active, should the SR gap surprisal still be applied, or is the SR gap surprisal no longer applicable?

We tested mutations from Mucaki EJ, 2013 (Supplementary Table 4), which abolish the splicing enhancer SF2/ASF with and without the SR protein gap surprisal when Ri of the SR site is < 0 bits. The removal of the gap surprisal term for Mutation #2 of Supplementary Table 4 leads to a discordant prediction, where the ΔRi is less than the SR gap surprisal at that distance and therefore the ΔRi,total is positive. As experimental evidence shows an increase in skipping, it is a discordant prediction. Therefore, the gap surprisal is still applied in the computation of both initial and final Ri,total values when the SR protein of interest is abolished as the site is naturally present and therefore expected for binding. Conversely, when we apply the gap surprisal to the initial Ri,total for a splicing factor that is being created, we are essentially applying a penalty for a site that does not normally exist. Therefore, we no longer apply the SR gap surprisal value to the initial Ri,total in these cases.

The revised Ri,total values of SR binding site mutations slightly differ from those reported in Mucaki EJ, 2013 (Supplementary Table 4). This is because the gap surprisal distributions were recomputed for the following factors: SF2/ASF, SC35 and SRp40, with updated versions of these models based on CLIP Seq data (Blin K, 2015, Khorshid M, 2011). This resulted in small changes to the distributions for SF2/ASF and SC35, however changes for SRp40 were significant, and now more closely resembles the other gap surprisal functions. The updated graphs of distance vs. gap surprisal are available at: http://splice.uwo.ca/gapsurprisals.html. While this should not significantly affect ΔRi,total values, it may affect the initial and final Ri,total values.

On 2014 May 06, Madhusudana Girija Sanal commented:

Dr. Norman is picturing the great progress in education as a result of the information distribution revolution as if it is an ‘unavoidable evil’! Probably, many of his generation expresses high inertia, still consider, 'physical' universities, libraries, books, lecture halls etc. very much essential! I understand their nostalgia! You know what this means for humanity? Rich countries such as USA hold only a small fraction of the world’s population. Through virtual universities more and more people across the world, irrespective of rich and poor, would be able to attend the best schools and courses. They would be able to take the same exams and get ranked along with the most privileged, rich or intelligent. This would be great! This is 'new' justice! (Although I believe “Justice is ‘man made’ or artificial”). All we want is better tools to evaluate human intellectual qualities, online. I do not think face to face lectures will be better than online recorded, interactive lectures, may be multidimensional (3D-4D-5D) lectures by several professors of the learner’s choice. Lectures will be ranked and paid by based on their quality by student communities and not by bureaucrats or by administrators and politicians. This system is great especially when I consider the advantages! On demand, personalized lectures would be "ready-made" for commonly observed (student) personality traits -say there are 100 personality subtypes and intellectual levels! Custom lectures are available for them all because there are much more people to teach online-lectures need not be real time. You can learn from a "personality" who matches your rare personality, perhaps, one who lived 10 years back. His lectures had to wait for ten years for a student like you! Is not this a very exciting possibility? However, I do agree that face to face lectures can be more individualized and beneficial (for the rich, because they only have money to ‘buy’ good teachers!) Nevertheless, I do not think there is a huge benefit for extreme personalization except for exceptional children who are extremely out-of-the-box in a positive or negative way. It may be, however, noted that overall poor but brilliant students have a better opportunity to come out and stand before the world. This global free learning system will benefit specially those brilliant minds in less privileged countries. Do Dr. Norman has any evidence to support his statements in the editorial? I do not know what Dr. Norman will write if tomorrow we find a new technology which allows direct transmission of knowledge to brains! Then what will happen? Think! Everyone will have equal opportunity to accumulate the same amount of information if he or she wants. Now who will win this game? Those who have money? Probably not! Those fractions of the society who are blessed with right genome, epigenome and the best neural connections!

On 2014 May 09, Chandan Kumar commented:

Is there a middle ground between Dystopia and Utopia?! May be the real, organic world, with or without the internet driven education system. Methinks, as well as the brick and mortar business has survived, nay thrived in an internet world, so the academic community has and will- if for no other reason, than that Education is Big Business!

On 2013 Nov 01, Casey M Bergman commented:

In reviewing the location of P-element insertions in the human genome reported in Table 1 of Majumdar S, 2013, we noticed that the sequences of the P-element target site duplications reported in the paper did not correspond to the sequences observed in the GRCh37/hg19 version of the human genome sequence available at the UCSC Genome Browser.

To resolve this discrepancy, we obtained the original data and methods used to generate the genomic coordinates reported in Table 1 from the authors. Sequence data for integration events catalyzed by the P-element transposase or THAP9 that were mapped from both the 5’ and 3’ end of the P-element insertions are as follows (target site duplication shown in capitals, posted with permission of the authors):

Drosophila P-element Transposase

ctacaaggatgccaagggctgtttcttcagcatggtggGTGGCCATatgtaagcaggtgtgcacacatgtgggcacatgtgctgcat cttgaatgagagctgtgattgttagtgatgtccaggtatgtGTCTGCCAtctcagagtgaccctgagaaaggcattcatttggaagctt tgtttcctgactttgctgtGTGTTCGAtcgtctgttttcaaagtgggatcattagttatgaaggaagatttttcatgaa tttctttccttgtctctgagacgccactttctcctggctctccttctttccgtcggTCTGCCTTttgctctccttttctggttccgtctcacca cgagccactggtggggctcctgccacctccacactgGTCGGCCTcggccacctccacgcctcagggatggggcgcgcgtgccc tctcagtagataatgaggatcactgcagatggcatgatatttagcagactacGGATCTCGagcagtcatccaggatctcaacagtgg

Human THAP9

gtggcgtgatcccagctcactgcaaccTCGGCCTGctcggcttaagtgatcctttcacctcagcttctcaagtagctgggactacag ccctgtccctgtgagtgatgttcccttgttgttccaGTCTCTCTtctctggtcaggaaggtaccactcaatccagggctttctcctggttt gaacttccccagtgagggcctGTGTCTGCattcaggagtgagagtttccccaggagaggagactgaaaagacctgggaaggcaa ccactggactccagcctgggcgacagagcgaTACGTCTCataaaaataaataaataaaacagaaacttaacacaattaaatgactg ataaagaggaatttgtttctccacaccacaaggcctttGTGCGAAGgtgactgtgtgtgtcaacgtcagacagtccctctttctgggag ttaaatgaggttgttagggtggtccatcattcaacatgactgcGGTCGTCCtaacgacaggaaatttgggccccagagacagacac

Using these data, we were able to reproduce the majority of the authors’ results in Table 1 using the default settings of the BLAST service at NCBI for the GRCh37/hg19 version of the human genome in September 2013. However, the same sequence data yielded different coordinates when mapped to either the UCSC Genome Browser (using default BLAT settings) or the Ensembl Genome Browser (using default BLAST settings), with consistent genomic coordinates being reported by both UCSC and Ensembl.

Based on empirical observation and through correspondence with Dr. Deanna Church at NCBI, we learned that results for the organism BLAST service at NCBI prior to mid-September 2013 defaulted to local (scaffold) not global chromosome ("top level") coordinates. Thus, the coordinates of the P-element insertions reported in Table 1 of Majumdar S, 2013 do not accurately reflect the exact location of integration on global chromosomal coordinates.

Based on our re-analysis, the chromosomal location of target site duplications for P-element insertions in the human genome are as follows (GRCh37/hg19, 0-based coordinates):

chrom start end strand

chr17 5024087 5024095 +

chr20 16619371 16619379 +

chr21 17382446 17382454 +

chr11 122102746 122102754 +

chr3 61550440 61550448 +

chr9 25178151 25178159 +

chr14 87818626 87818634 +

chr11 72875900 72875908 +

chr11 79446804 79446812 -

chr15 55619023 55619031 +

chrX 17150535 17150543 +

chr11 11291642 11291650 +

As a consequence of this interchange, NCBI have now updated the default behavior of their organism BLAST service to report global (scaffold) chromosome coordinates, as reported in the 17 Oct 2013 BLASTFeed update.

We thank the authors for making their raw data available and Deanna Church and others at NCBI to help resolve this issue, and thank the authors and Deanna Church for reviewing this comment before posting.

Sincerely,

Casey Bergman

Raquel Linheiro

On 2016 Aug 23, Ben Goldacre commented:

One of the trials in this article 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 NCT003766090. We believe the correct ID, which we have found by hand searching, is NCT00376090.

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 2013 Oct 23, Andrew R Kniss commented:

Although this paper provides necessary toxicity data on some common pesticides, the extension of that data to causing global amphibian decline is quite a leap (pun intended). Toxicity alone does not equal risk, and this paper (and many they cite) provide little information on the exposure aspect of risk. The authors also fail to provide context about other risks amphibians may face in the absence of pesticide use. If pesticides are removed, pests would still need to be controlled in agricultural fields. Those other pest management practices may be equally likely to harm amphibians. More information about the proper context for this study here.

On 2014 May 27, Irving I. Gottesman commented:

Scholars interested in a deep understanding of the complex etiology of ASD can find no better starting point than the perspective provided by Stein, Parikshak, & Geschwind and the citations they invoke to support their data-informed views.Uninformed pontifications in our field of inquiry are all too common. No one said it should be easy. Their perspective can be generalized to other complex psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, and even suicide.

On 2016 Feb 05, Kristina Hanspers commented: