On 2014 Dec 17, Sean Ekins commented:

An earlier post on this http://www.collabchem.com/2014/02/20/tb-mobile-version-2-0/ and here it is on app store for free https://itunes.apple.com/us/app/tb-mobile/id567461644?mt=8

On 2014 Dec 15, Sean Ekins commented:

Also added to our list of 2014 papers http://www.collabchem.com/2014/12/15/a-year-in-publications-2014/

On 2014 Dec 02, Sean Ekins commented:

TB Mobile 2 mentioned here http://www.collabchem.com/2014/11/04/app-exposure/

On 2015 May 21, Christopher Southan commented:

See a structural comparison of PDB ligands from different sources including this one http://cdsouthan.blogspot.se/2015/05/will-real-pdb-ligands-please-stand-up.html

On 2014 Oct 12, George Ntoumenopoulos commented:

I completely concur with these authors. In addition the potential impact of ventilatory and patient positioning strategy on the movement of airway secretions also deserves attention. Our recent case report (Physiother Res Int. 2014 Jun;19(2):126-8. doi: 10.1002/pri.1563. Epub 2013 Aug 17. Justification for chest physiotherapy during ultra-protective lung ventilation and extra-corporeal membrane oxygenation: a case study.Cork G1, Barrett N, Ntoumenopoulos G.) highlights the potential failings of current recommendations for secretion clearance. The ultra protective ventilator settings combined with head of bed upright positioning may predispose to secretion retention and warrants further investigation.

On 2016 Apr 02, Daniel Tsin commented:

I will like to mention that : Historically Dr. D.O. Ott performed a ventroscopy appendectomy during vaginal hysterectomy on April 26, 1906 and was published in 1908 : Ott D.O. (1908). Results achieved by the use of direct illumination of the abdominal cavity, colon and urinary bladder during operations and for examination. Russky Vrach 43: 3-11.

Besides our team performed transvaginal appendectomies under the name of Culdolaparoscopy without hysterectomy : Tsin DA, Colombero LT, Mahmood D, Padouvas J, Manolas P.Operative culdolaparoscopy: a new approach combining operative culdoscopy and minilaparoscopy.J Am Assoc Gynecol Laparosc. 2001 Aug;8(3):438-41 .

https://www.ncbi.nlm.nih.gov/pubmed/11509789?dopt=Abstract

On 2014 Oct 30, Christopher Southan commented:

It would be valuable to submit these 326K as a new PubChem source (https://pubchem.ncbi.nlm.nih.gov/)

On 2016 Aug 08, Christopher Southan commented:

Seems a shame if the 10yr momentum has stalled. Any prospect of updating from the declared 2013 statistics?

On 2014 Oct 31, R Y Seedat commented:

Thank you for the positive comments regarding the study.

Lesotho is a different country, with different demographics and burden of disease and a different healthcare system with differences in accessibility, availability of services and referral protocols. It would thus not make sense to combine the data.

I don't think that the calculation of confidence intervals would be a valid statistical test since the study was not based on a population samples but on entire populations. While the incidences calculated are an underestimate, the calculation of confidence intervals would not assist in determining the degree to which the incidence is underestimated.

On 2014 Oct 29, Farrel Buchinsky commented:

Nicely done study and well reported. I have seen several incidence reports but almost always from North America, or Denmark (or another developed country) and never from anywhere in Africa. The best-done North American studies show incidence of about 1 per 100000 or below (around 0.2-1). As the author states, The data described in the Free State and Lesotho is probably an underestimate since pediatric hoarseness (sans dyspnea or stridor) may not be diagnosed amongst those with less access to health care.

• If all the cases from Lesotho are referred to Bloemfontein why not combine the statistics?<br>
• Also, one could provide 95% confidence intervals (Poisson model probably) around the best estimates and see where the estimates from other reports fall within that range.

On 2014 Oct 20, Attila Csordas commented:

associated datasets available via PRIDE/ProteomeXchange: http://www.ebi.ac.uk/pride/archive/simpleSearch?q=PXD001042+PXD001390&submit=Search

On 2014 Oct 21, Bertie Gottgens commented:

One point worth making may be that the studies reported here were presumably done under pathogen-free conditions, and in the absence of predators or any other environmental stresses. "Normal" hemaopoiesis in the real world may therefore have to call on blood production from the traditional 'transplantation HSCs' more often than is suggested here.

On 2016 Jun 14, Christopher Uhde commented:

This study was commented on as the principle subject of two Correspondence articles in Development:

Transcriptional interpretation of Shh morphogen signaling: computational modeling validates empirically established models. Uhde CW, Ericson J. Development. 2016 May 15;143(10):1638-40. doi: 10.1242/dev.120972. No abstract available. PMID: 27190032

and

Mathematical models help explain experimental data. Response to 'Transcriptional interpretation of Shh morphogen signaling: computational modeling validates empirically established models'. Cohen M, Page KM, Perez-Carrasco R, Barnes CP, Briscoe J. Development. 2016 May 15;143(10):1640-3. doi: 10.1242/dev.138461. No abstract available. PMID: 27190033

On 2014 Oct 14, Jonathan Eisen commented:

I would like to point out that I and multiple coauthors published a paper on pooling mitochondrial genomes and shotgun sequencing them for biodiversity analysis in 2000. I believe our paper should have been cited and discussed in this paper. See A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Pollock DD, Eisen JA, Doggett NA, Cummings MP. Mol Biol Evol. 2000 Dec;17(12):1776-88..

Abstract is pasted below:

Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.

On 2014 Dec 02, Helen E Benson commented:

The IUPHAR/BPS Guide to PHARMACOLOGY contains curated information on ENaC and ASICs.

On 2015 Mar 27, KLAUS KAESTNER commented:

Dear Dr. Tarlow We are well aware of the fact that a CreER is required for genetic lineage tracing. We tried many times to derive a Foxl1-CreER line. Unfortunately, none of our six founders showed any expression. We will keep trying!

In the case of Foxl1 expression in the liver, there is an additional difficulty to consider. There are no Foxl1 expressing cell in the healthy, uninjured liver. Thus, even a Foxl1-CreER does not help, as it will not label any cell! The Foxl1 promoter becomes activated only AFTER specific types of liver injury.

Note that additional evidence for the bi-lineage potential of Foxl1-Cre marked cells comes from the fact that one can establish clones of cells from a SINGLE Foxl1-Cre/RosaYFP labelled cell, and these can be expanded indefinitely. Thus, these cells are clonogenic. In vitro, these cells can be differentiated towards both the cholangiocyte and hepatocyte lineage.

Note also that we acknowledge the limitations of our current model in the discussion of this paper. Klaus Kaestner

On 2014 Dec 23, Branden David Tarlow commented:

It's unclear why this group has not replicated their results with the Foxl1-Cre with a CreERT2 allele since the original 2009 publication. I agree with a recent review that stated "Experiments using non-inducible Cre lines do not constitute bona fide lineage tracing tools..." (see Lemaigre Hepatology 2014; doi: 10.1002/hep.27659)

On 2015 Dec 30, Vatsalya Vatsalya commented:

SOCIAL SECURITY Fact Sheet: For persons born in 1938 or later, their Social Security benefit may be affected by a provision that raises the age at which full Social Security benefits are payable.

The age for collecting full Social Security retirement benefits will gradually increase from 65 to 67 over a 22-year period beginning in 2000 for those retiring at 62.

Web-link: https://www.ssa.gov/pressoffice/IncRetAge.html

On 2014 Oct 08, Elizabeth Moylan commented:

Thank you for raising this, we are investigating in accordance with COPE guidelines (http://publicationethics.org/).

Elizabeth Moylan, Biology Editor, BioMed Central.

On 2014 Oct 08, Neil Saunders commented:

A substantial fraction of the text in this article has been copied verbatim from an earlier article which it cites. This can be demonstrated by entering the article URLs - http://genomebiology.com/2010/11/3/r25 and http://www.biodatamining.org/content/7/1/15 - into this online tool. Also, the first 10 or so references are identical and in the same order.

Discussion at this Twitter thread includes images which make the similarity very apparent.

On 2015 Jan 29, CREBP Journal Club commented:

This is a very informative and interesting paper, which highlights the utilities and caveats in the use of multiple-indication reviews. The coherent methodology of this article is admirable and we acknowledge that there is a lack of coherent terminology. The term “multiple-indication review” is unambiguous and should be used in future studies. We agree that producers of systematic reviews should consider using this kind of reviews instead of, or in addition to, reviews focusing on a single indication. Important information that we cannot get with traditional methods (single-indication reviews) can be achieved if this methodology is followed. For example, multiple-indication reviews are very useful in the fight against antibiotic resistance. Providing Health Care Professionals and patients with comprehensive information about the risk of adverse effects and the benefit-harm trade-off may reduce their desire for use of antibiotics. Chen et al identified three uses of multiple-indication reviews. However, we propose that the use of this kind of review can be broadly categorised as either:

● To get a better estimate of the effectiveness or harms e.g., 'What are the adverse effects of amoxicillin?' (P* I C H1, H2, …)

● To examine heterogeneity across indications or interventions e.g., 'When are prophylactic antibiotics effective?' (P1, P2, P3, … I C O1), or 'What is the optimum timing of prophylactic antibiotics before any surgery?' (P* I1 I2 I3, … C O1)

(PICO notation: P* = any disease; P1 P2 P3 = set of disease, I1 I2 I3 = set of interventions, C = comparison, O1 = outcome, H = harm)

When undertaking a multiple-indication review much attention has to be paid to the methodologically caveats such as ‘overlapping’ of included reviews; the extra level of complexity (potential heterogeneity in the contributing systematic reviews, in addition to heterogeneity in the primary trials); potential confounders (e.g. methodological quality of included studies and reviews) and risk of bias (e.g. different duration or dose of tested treatment or different control groups). Some of these methodological challenges can be dealt with in the designing of the review and some should be taken into account in the analytical approach. ‘Overlapping’ can be circumvented if only the data from the originals trials are included in the multiple-indication review. However, if the multiple-indication review is based on results from systematic reviews one need to take account of the potential ‘overlapping’ of included studies and we would be very interested in software routines to conduct these reviews - especially in a 2-step frequentist approach. See CREBP Journal Club for more information

On 2014 Dec 08, George Parris commented:

Between 2004 and 2009 I developed a hypothesis for the origin of HIV-1M based on the idea that anti-malarial drugs may have steered the evolution of HIV-1 along a unique trajectory Parris GE, 2004 Parris GE, 2007 Parris GE, 2007. My model deviates substantially from the widely accepted zoonosis model advocated by Sharp and Hahn (2008, 2011). Now, Faria et al. have independently proposed a model of HIV spread based on a detailed conventional analysis of the evolution of the HIV-1M sequence, which is consistent with my model:

Clearly the transfer of SIV to humans in SE Cameroon (about 1876 according to recent analysis Wertheim JO, 2009) substantially predates the MRCA of HIV-1M (1920s). Thus, the original SIV infection in humans lingered for as much as 50 years (1876-1926) and mutated without producing a pandemic while evolving into the HIV-1 clade. Through the 1920s many persons from SE Cameroon with HIV-1 likely visited Leopoldville (Kinshasa) via the Sangha River (see the reports of Louise Pearce concerning African sleeping sickness dating from 1921). The MRCA of HIV-1M subsequently arose in Leopoldville as a result of some unique mutations (not shared with HIV-1O or other HIV-1 groups). The date of this unique transformation has been the subject of several studies and according to Faria et al. (page 60) if subtypes B and C (which obviously evolved later) are eliminated from the dataset, the molecular clock is more appropriately calibrated and the date of the MRCA of HIV-1M settles at 1926. They point out that neither population growth nor genital ulcer disease can explain the "starburst" pattern of divergence of the numerous HIV-1M lines (i.e., few subtypes in the period 1926-1950 followed by many subtypes and sublines in the 1950s and beyond). Finally, they conclude that their findings are consistent with "iatrogenic interventions in Kinshasa...were critical for the emergence of group M." In my papers I describe a specific (well-documented) iatrogenic event in early 1927 in Leopoldville/Kinshasa, which involved a child associated by name and disease (she had sleeping sickness) with SE Cameroon and the Sangha River. It is documented that after being treated with a powerful anti-malarial (pamaquine that affects the white blood cells) she and two other young girls were tested for malaria (blood drawn by syringe) at the same place and same day in sequence.

The substantial delay in the spread of HIV-1M from Leopoldville (from 1927-1937)clarified by Faria et al. is consistent with the virus being in the bodies of children (under 10-years old in 1927). Had the virus been in the adult population (1926-onward) it undoubtedly would have spread geographically much earlier via rail and boat; moreover as a result of commercial sex workers and screening for sleeping sickness (e.g., by Jamot in Cameroon), there would have been many more unique subtypes generated in the period 1926-1940.

It is incredible to me that in spite of the fact that anti-malaria drugs (e.g., chloroquine) are known to affect the replication of HIV (see papers by Savarino A starting in 2001 Savarino A, 2001) that this effect has been universally ignored in analysis of the evolution of HIV. Chloroquine became a daily fact of life in the Congo Basin in the late 1950s, just when the starburst is observed. Moreover, suppression of HIV by chloroquine can explain why HIV was first detected in the US in the 1980s (where chloroquine was not being widely used).

On 2014 Dec 11, Ibrahim Masoodi commented:

This interesting case brings to the fore the multiple complications of SLE, a clinical scenario due to the generation of multiple autoantibodies directed towards the pancreas and the hemopoietic system. Acute vasculitis with its varied clinical presentation is often the commonest cause of abdominal pain in SLE, but acute pancreatitis and acute autoimmune hemolytic anemia, with its consequences, should be kept in mind in a given case of SLE. Further, this case emphasizes the need for close follow-up and proper health education in an SLE patient in order to circumvent any complication.

On 2015 Feb 24, Jonathan S Hausmann commented:

We read with great interest this article by Lukens JR, 2014 on the role of diet in the development of inflammatory bone disease in Pstpip2^cmo mice. They report that mice fed a low-fat diet had elevated levels of pro-IL-1B and developed inflammatory bone disease, a disease which resembles the human autoinflammatory disease chronic multifocal osteomyelitis. However, mice fed a high-fat diet had lower pro-IL-1B levels and did not develop osteomyelitis, despite their genetic predisposition.

The authors conclude that the different outcomes are due to differences in the composition of the diets. However, the diets differed in more than fat content—notably in gluten content. The low fat diet, LabDiet 5013 has wheat as a main ingredient, whereas the high-fat diet, Research Diets Incorporated D12107 contains no wheat and is gluten-free.

Pro-inflammatory effects of gluten have previously been demonstrated in mice. Non-obese diabetic (NOD) mice fed a standard wheat-containing diet had increased levels of inflammatory cytokines, as compared to those maintained on a gluten-free diet during gestation and early life (Hansen CH, 2014). Furthermore, those on gluten-free diets showed changes in the microbiome which conferred protection against the development of diabetes despite their genetic susceptibility.

In patients with familial Mediterranean fever (FMF), another autoinflammatory disease, attempts to modulate the frequency and severity of attacks based on the fat content of the diet have been largely unsuccessful (SOHAR E, 1962). It is now known that the microbiome of patients with FMF differs from that of healthy controls (Ktsoyan ZA, 2013). What has yet to be determined is how diet affects this altered microbiome, and whether a gluten-free diet can promote an anti-inflammatory microbiome and modulate the clinical course of FMF and other autoinflammatory diseases.

The question whether fat or gluten were responsible for the observed changes does not change the remarkable findings by Lukens JR, 2014 that diet can change the expression of this genetic autoinflammatory disease in mice by modulating the microbiome. However, when considering these results in developing possible treatments, it will be important to clearly determine the ingredients that changed the microbiome for the better.

On 2016 Feb 24, Lily Chu commented:

Above link is broken. See here for new link:

http://iacfsme.org/ME-CFS-Primer-Education/Bulletins/2009/Severe-ME-CFS-in-Adults-A-report-from-the-CH-(1).aspx

On 2014 Oct 21, Lily Chu commented:

The results of this study confirm those of an earlier study by Pheby et al. in 2009. That study also noted two onset peaks, one from ages 11-20 and another from 31-40.

Pheby's article can be accessed online here: http://www.iacfsme.org/BULLETINWINTER200910/Winter0910PhebySneddonHeinrichCHROMEReport/tabid/413/Default.aspx

On 2015 May 02, Arthur Yin Fan commented:

The original trial by Hinman's has many methodology flaws, please read the comments under the original trial report.

On 2014 Nov 08, Qin-hong Zhang commented:

None

On 2014 Oct 04, Ryan Radecki commented:

Post-publication commentary:

"ARISE, and Cast Off the Shackles of EGDT"

The sound you hear is a sigh of relief from Emergency Physicians and intensivists regarding the outcomes of the Australasian Resuscitation in Sepsis Evaluation (ARISE).

As ProCESS suggested, and as many have suspected all along, it seemed the critical intervention from Early Goal-Directed Therapy was the early part – and less the SCO2 monitoring and active management of physiologic parameters using dobutamine and blood transfusion. Now, we have a second study, in addition to ProCESS, supporting the same general conclusions....

http://www.emlitofnote.com/2014/10/arise-and-cast-off-shackles-of-egdt.html

On 2016 Jun 07, Arthur Yin Fan commented:

Acupuncture is Effective for Chronic Knee Pain: A Reanalysis of the Australian Acupuncture Trial. Altern Ther Health Med. 2016 Mar;22(3):32-6. Yin Fan A, Zhou K, Gu S, Ming Li Y. Abstract Context • In the October 2014 issue of the Journal of the American Medical Association (JAMA), Hinman et al published the results of an Australian clinical trial on acupuncture in a paper entitled "Acupuncture for Chronic Knee Pain: A Randomized Clinical Trial" (JAMA report), in which they concluded that neither acupuncture nor laser acupuncture had any greater effects than sham laser acupuncture for pain or function for patients aged 50 y and older with moderate-to-severe knee pain. That study has been criticized extensively by international scholars for its validity because serious methodological flaws existed throughout the study's design, implementation, and conclusions. Objective • The current study intended to re-examine the prior study's conclusions about the efficacy of acupuncture for chronic knee pain. Design • The current research team performed a reanalysis of relevant data from the JAMA report. Intervention • The original study included 4 groups: (1) an acupuncture group, which received needle acupuncture, inferred by the current authors to have been set up to be a positive control in the original study; (2) a laser acupuncture group, which received laser acupuncture; (3) a sham laser acupuncture group, which received sham laser acupuncture and acted as the negative controls for the laser acupuncture intervention; and (4) a control group, which received conventional care but no acupuncture or laser treatments. The study lasted 12 wk. Outcome Measures • The measures included evaluations in the following areas: (1) poststudy modifications-an evaluation of the consistency of the JAMA report with the study's intentions as identified for a grant that was originally approved and funded by the Australian National Health and Medical Research Council (NHMRC) in 2009, as indicated in the study's trial registration, and as compared with the published protocols and to the study's originally stated objectives; (2) high heterogeneity-an assessment of the heterogeneity among the 4 groups for the overall outcome related to pain; (3) ineffectiveness of laser acupuncture-an analysis of laser acupuncture's efficacy for chronic knee pain as stated in the JAMA report, using effect size (ES); (4) effectiveness of acupuncture-a reanalysis of acupuncture's efficacy for chronic knee pain in comparison with the original analysis in the JAMA report, using ES; and (5) acupuncture after data adjustment-a new analysis of acupuncture's efficacy for chronic knee pain using data from the original study that was discussed in the JAMA report, using ES, with an estimation after data adjustment and elimination of the dilution effect of the Zelen design. Results • Contrary to a general impression that acupuncture was the focus, laser acupuncture was the primary intervention tested in the actual study, "Laser Acupuncture in Patients With Chronic Knee Pain: A Randomized, Placebo Controlled Trial." The study discussed in the JAMA report was neither a truly randomized, controlled trial (RCT) for acupuncture nor was it an appropriately designed, randomized study in general. High heterogeneity was found among its groups in the evaluation of overall pain in patients. Both the ES of 0.60 that had been set by Hinman et al for the minimal clinically important difference (MCID) and the resulting interpretation of results in the JAMA report were not appropriate. Using the original study's criteria of efficacy, the reanalysis has confirmed that the laser acupuncture was not effective, whereas the acupuncture was found to be moderately effective for chronic knee pain (P < .05) for both overall pain and function at 12 wk, with an ES of 0.58, or after the adjustment of the data, with an ES of 0.67. Conclusions • The JAMA study was neither a conventional RCT nor an appropriately randomized trial, and its results are probably invalid. The ES of 0.60 for the MCID that was used in the JAMA study and the resulting explanation were not appropriate. Even with an ES of 0.60 for the MCID, acupuncture remained effective after data adjustment. Consequently, compared with conventional care, acupuncture treatment was found to be moderately effective for chronic knee pain in patients aged 50 y and older. PMID: 27228270 [PubMed - in process]

On 2015 May 30, Arthur Yin Fan commented:

The sample size calculation is inaccurate in this study. http://www.jcimjournal.com/articles/publishArticles/pdf/S2095-4964(15)60184-4.pdf

It should be 773, instead of 282. Hinman described she considered the factors of multiple groups' comparison, intra-therapies,however, she did not.

See the step by step sample size calculation detail in: The methodology flaws in Hinman’s acupuncture clinical trial, Part III: Sample size calculation. http://www.jcimjournal.com/articles/publishArticles/pdf/S2095-4964(15)60184-4.pdf

On 2015 May 29, Hongjian He commented:

One our main criticisms of this publication was that there was no detailed reporting of number of needles used per treatment, acupuncture sites targeted per treatment, and specific treatment duration and electric stimulation for each patient. Dr. Hinman responded by stating:

"Dr. He suggests lack of acupuncture standardization, treatment infrequency, and no electrical stimulation may explain our findings. However, when comparing acupuncture with sham treatment, a meta-analysis1 found no evidence that needle number or placement; use of electrical stimulation; or number, frequency, or duration of treatments influence acupuncture outcomes"

We looked at the article Dr. Hinman cited (MacPherson et al., PLoS 2013) and she did not do a good job of reading it. They showed that number of needles used per treatment was statistically significantly correlated with effect size. The electrical stimulation had a significantly stronger effect. She incorrectly summarized the study results. Therefore, Dr. Hinman’s statement that needle numbers, length of treatment and electric stimulation have no effect on acupuncture outcomes is incorrect. We still await a sufficient explanation for why these specifics were not reported in her study.

On 2016 Apr 09, Leigh Jackson commented:

Wit et al. conducted a pragmatic trial whose design had glaring weaknesses.

There was no sham control. There was no blinding. Control was usual care inviting negative bias. The non-randomized self-selecting cohort invited positive bias. Consort was not followed. Patients had individualised treatment creating a chaotic heterogeneity of data.

Wit et al. to Hinman et al. is as chalk to cheese. The difference in their results might be due to low dosage levels in Hinman et al. It might be due to high levels of bias in Wit et al.

On 2015 Apr 27, Qin-hong Zhang commented:

Acupuncture treatment for chronic knee pain: study by Hinman et al underestimates acupuncture efficacy

http://aim.bmj.com/content/33/2/170.full.pdf+html

Dr Hinman and colleagues [1] completed a Zelen-design clinical trial for acupuncture for chronic knee pain patients and concluded that neither laser nor needle acupuncture conferred benefit over sham for pain or function in patients older than 50 years with moderate or severe chronic knee pain. We disagree with authors because they failed to use the most effective acupuncture regimen in their trial.

We consider that their treatment regimen is inferior for the following reasons. First, the dosage of acupuncture is far from adequate. The protocol specified the acupuncture intervention as a twenty minute treatment once or twice weekly for 12 weeks, with 8 to 12 sessions in total permitted [1]. Treatment compliance was not reported. Even with an assumption of full compliance, the study participants received only 0.67 to 1.0 session weekly with a total 160 to 240 minutes in 12 weeks. This was below the treatment regimen in the trial by Witt, et al. [2], in which participants received 12 sessions of 30 min duration, administered over 8 weeks, i.e., average 1.5 sessions weekly, and 360 minutes in total for only 8 weeks. It is worthwhile to point out that Witt, et al. had opposite conclusions. Second, the study protocol did not require deqi (a renowned acupuncture sensation), which is profoundly regarded as a prerequisite of a preferable acupuncture treatment efficacy [3]. Third, the paper did not follow the CONSORT statement of acupuncture [4] that requires details of needling, such as needle manipulation, depth of needle insertion, and points selected unilateral, bilateral or both. Fourth, the dose of laser acupuncture was 0.2J per acupuncture point, which was considered too low to achieve a clinical effect [5]. Previous study suggested that the minimum dose should probably be 0.5 J/point [5] . Thus it is difficult to evaluate if effective treatment regimen was compared against the Sham.

Because the efficacy of acupuncture therapy depends on the dose and deqi of acupuncture intervention, it is premature to us to reach the conclusion that acupuncture is not effective to treatment osteoarthritis pain of the knee.

REFERENCES

1. Hinman RS, McCrory P, Pirotta M, et al. Acupuncture for Chronic Knee Pain A Randomized Clinical Trial. JAMA. 2014;312(13):1313-1322.

2. Witt C, Brinkhaus B, Jena S, et al. Acupuncture in patients with osteoarthritis of the knee: a randomised trial. Lancet. 2005;366(9480):136-143.

3. Shi GX, Yang XM, Liu CZ, et al. Factors contributing to therapeutic effects evaluated in acupuncture clinical trials. Trials. 2012; 13:42.

4. MacPherson H, Altman DG, Hammerschlag R, et al; STRICTA Revision Group. Revised STandards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA): extending the CONSORT statement. PLoS Med. 2010;7(6):e1000261.

5. Baxter GD. Laser acupuncture: effectiveness depends upon dosage. Acupunct Med. 2009;27(3): 92.

On 2015 Apr 16, Arthur Yin Fan commented:

The methodology flaws in Hinman’s acupuncture clinical trial, Part II: Zelen design and effectiveness dilutions: http://www.jcimjournal.com/articles/publishArticles/pdf/S2095-4964(15)60172-8.pdf

Hinman and colleagues concluded that “in patients older than 50 years with moderate or severe chronic knee pain, neither laser nor needle acupuncture conferred benefit over sham for pain or function. Our findings do not support acupuncture for these patients.” As pointed out in my former article (The methodology flaws in Hinman’s acupuncture clinical trial, Part I: Design and results interpretation. J Integr Med. 2015; 13(2): 65–68.), there were serious flaws in the trial design and statistics, as well as in the interpretation of the results. In here I address problems in the Zelen design used by them -Using Zelen design in this study does cause biases.

1 High drop-out rate:

The drop-out rates were 2.82% (2/71) in the control group; 22.86% (16/70) in the acupuncture group; 18.31% (13/71) in the laser acupuncture group; and 22.86% (16/70) for the sham laser acupuncture group. According to the acceptable standards for an RCT, dropout rates less than 10% are acceptable, drop-out rates between 10% and 20% mean that the resulting data quality is poor, and drop-out rates of more than 20% mean that the data quality is considered very poor and should not be used in analysis. In this trial analysis, the data quality in the acupuncture and sham laser acupuncture groups are very poor as the drop-out rates are over 20%; the authors should not have directly used them in any statistical analysis, unless they had re-adjusted and re-balanced the sample among the groups during the study. As outlined by the National Institutes of Health, if there is a differential drop-out rate of 15% or higher between study arms, such as between the control group and the treatment group in this clinical trial, then there is a very high potential for bias. This is a flaw that can decrease the quality of the study results.

2 The effectiveness in intervention groups was diluted by various factors

The dilution rates should then be 21.87% in the laser acupuncture group, 13.80% in the sham laser acupuncture group, and 31.27% in the acupuncture group (the dilution rate calculations were shown in Tables 1–3). The dilution rate was very significant in the acupuncture group, which causes the effectiveness to be undervalued in the acupuncture group, by almost 1/3.

The effective significance was masked by limited sample size due to the Zelen design of this study.

3.The sample size calculation in this study is questionable.Too small.

4 Conclusion

The effectiveness of the acupuncture group was diluted 31.27%, and its drop-out rate was 22.86%, much higher than that of the other groups in Hinman’s clinical trial, which constitutes major flaws in how this study is analyzed and interpreted[8]. Based on the bias of Zelen design used in the study, and incorrect sample size calculation, the conclusions drawn from this study are of poor quality, inaccurate, and invalid.

http://www.jcimjournal.com/articles/publishArticles/pdf/S2095-4964(15)60172-8.pdf

On 2015 Apr 11, Arthur Yin Fan commented:

The sham laser acupuncture is not a valid negative control for acupuncture

I agree acupuncture should have a real sham control in a vigorous RCT; however, in Hinman's acupuncture RCT, the sham laser acupuncture is only fit to the laser acupuncture, not to real acupuncture. Because Acupuncture and Sham laser acupuncture, these two interventions do not have comparability in both characteristics and form (i.e., not matched). Furthermore, there was no blinding method performed between these two groups-both the patients and the administrators who performed the interventions knew the difference between the groups, such as needling acupuncture and sham laser acupuncture.

On 2015 Apr 11, Arthur Yin Fan commented:

There is a crucial mistake in interpreting the Hypothesis testing - What means? if P>0.05.

Hinman said :"in......chronic knee pain, neither laser nor needle acupuncture conferred benefit over sham for pain or function (Dr. Fan notes: Her statement was based on P>0.05). Our findings do not support acupuncture for these patients”

From the perspective of hypothesis testing in Statistics, if acupuncture has better results and with significant difference over the primary control (no-treatment group), p<0.05, we can conclude that “acupuncture is effective”- no matter what the result get from the comparing to the secondary control, such as “sham laser acupuncture”, but Hinman intentionally does not report this effectiveness in her conclusion; if acupuncture has better results over “laser acupuncture” and “sham laser acupuncture”, without significant in statistics, p>0.05, we can conclude that “acupuncture is better than the laser acupuncture, and sham laser acupuncture, but need more studies to confirm”. We can’t conclude that “acupuncture is not effective” because that there are no significant difference in statistics between acupuncture and “laser acupuncture”, or between acupuncture and “sham acupuncture” does not mean there is no difference between these treatments clinically. Hinman et al mis-interprets the results and violates the basic principle of Statistics.

On 2015 Apr 11, Arthur Yin Fan commented:

Hinman's acupuncture RCT has too many methodology flaws and misleading

As an independent researcher and practitioner in Acupuncture and Chinese medicine for thirty years, I strongly disagrees with Hinman's conclusion, as there were serious flaws in the trial design, the statistical analysis of the data and in the interpretation of the results of this study. I published a commentary recently [Fan A. The methodology flaws in Hinman’s acupuncture clinical trial, Part I: Design and results interpretation. J Integr Med. 2015; 13(2): 65–68.] http://www.jcimjournal.com/articles/publishArticles/pdf/S2095-4964(15)60170-4.pdf

The major concerns are:

(1)There is a major mistake in the primary testing factor in this RCT: the laser acupuncture should be the primary testing factor, not the needle acupuncture;

(2)The interpretation of the results was misleading;

(3)The “under-dosed” acupuncture treatments diluted the potential real effectiveness of acupuncture;

(4)Laser acupuncture and acupuncture would be effective in Hinman’s RCT, if the statistics were re-analyzed after re-adjusting the data.

(5)It is improper to test two different testing factors in one RCT with so small sample size;

(6)Laser acupuncture is not one kind of acupuncture, the author intentionally mixes it with acupuncture;

(7)Acupuncture did have significant effectiveness (p<0.05 in week 12), compared to the control (this is a primary control). However, the author intentionally does not interpreter this important result into the conclusion, instead, she concludes acupuncture is not effective and says her findings do not support acupuncture for patients.

I feel the author, somehow, intentionally misleads readers by testing acupuncture as a major intervention in this RCT-There was no significance between the positive control and the naïve control (i.e., acupuncture and control groups). Therefore, we can only conclude that the positive control, acupuncture was under-dosed or the study was otherwise flawed. That the positive control shows significance is a basic sign of the success of a clinical trial. From this perspective, Hinman’s trial was a failed clinical trial for laser acupuncture. As it would be unethical to publish an astonishing article, with a group of almost scrapped data and confusing logic, that misleads the readers, including the general public, medical society and policy makers, the researchers should have re-adjusted or re-designed their study instead of publishing it.

On 2015 Jun 14, Arthur Yin Fan commented:

Meridians could be tested by physics method, they are low electric resistance lines.

On 2015 Jun 11, David Keller commented:

It is no longer accurate to label evidence-based science as "Western"

The scientific method is the most powerful tool ever developed for the advancement of humanity, and science has, in turn, been advanced by humans from all cultural backgrounds.

Ancient societies all developed superstition-based pseudo-sciences, which are incapable of predicting natural phenomena or truly understanding them. Astrology was a vain attempt to rationalize the movements of the planets, utterly useless until it was replaced by the science of astronomy. Similarly, alchemy led nowhere until it was transmuted by the scientific method into chemistry. Homeopathy is based on false concepts involving dilution, and yields "medicines" which are nearly pure placebo. Chiropractic medicine, in addition to being based on disproved concepts, can be downright dangerous. PubMed has documented many cases of carotid and vertebral artery dissections caused by chiropractic neck manipulations (search on "artery dissection chiropractor").

The National Institutes of Health were founded to advance the scientific method in pursuing solutions to the health problems which plague mankind. Superstition-based folk remedies should be investigated when there is a chance that ancient peoples may have stumbled on a real medicine - such as aspirin from willow bark or digitalis from the foxglove plant. The active ingredient should be isolated, synthesized, tested and meta-analyzed until it is thoroughly understood, using the scientific method.

Where in the human body can we find anatomical evidence of a meridian, or "chee"? Acupuncture is based on complex and detailed theories, but theories must be tested and proved in the material world, in a reproducible fashion. If acupuncture is incapable of demonstrating significant pain relief in a carefully conducted clinical study, perhaps its adherents should reexamine their beliefs rather than invoking ever more arcane and obscure objections to the study design.

On 2015 May 30, Arthur Yin Fan commented:

Western medicine more focuses on structure, and Eastern medicine more on function. So, when explaining a specific issue, for example, a disc hernia induced lower back pain, even sciatica, western medicine will say the nerve gets pinched, however, eastern medicine will says the Bladder meridian Qi stagnant. Both are correct. Just because using different perspective, and using different language.

What is the meridian? just a functional manifestation of the never. Nerve is the structure, the meridian is the function.

Quite simple.

On 2014 Nov 13, David Keller commented:

Should medical doctors recommend acupuncture to patients with chronic knee pain?

Here is a brief description of acupuncture: "In traditional Chinese medicine, certain body systems, called meridians, are thought to regulate body function through the normal flow of energy [this energy is spelled "qi" but pronounced "chee"] from one part to another. Disturbances in this flow are thought to cause disease. Acupressure and acupuncture techniques are believed by practitioners of traditional Chinese medicine to cure disease by restoring this flow."(1) Without physiological or anatomical evidence of the existence of meridians or qi, acupuncture should be viewed as similar to chiropractic or homeopathic therapies, which lack scientifically credible theoretical mechanisms of action. This study found no significant clinical benefit of acupuncture for chronic knee pain. Therefore, I will not begin referring patients with chronic knee pain for acupuncture. I would like to see this study repeated for chronic pain syndromes of other body regions. If the null result is confirmed in all such regions, acupuncture will have to be classified as an expensive and complex placebo. Funding for research on debunked alternative therapies should be diverted to investigators conducting basic or clinical research of a more scientific nature.

Reference

1: Wang W and Wu S. Treating Pain With Acupuncture. JAMA 2014;312(13):1365.

On 2014 Nov 07, Qin-hong Zhang commented:

None

On 2016 Apr 03, Leigh Jackson commented:

Laser acupuncture provides a means for double blinding. This is a useful methodology for acupuncture trials where double blinding has always been the weakest link.

On 2015 May 30, Arthur Yin Fan commented:

This study used a wrong sham for acupuncture, so the conclusion is not reliable.

On 2014 Oct 08, David Keller commented:

Acupuncture trials have difficulty addressing the placebo effect and blinding

Acupuncture has been challenging to test in a true double-blinded and placebo-controlled fashion. Skilled practitioners of acupuncture have invested years in their training and licensing, and may unintentionally transmit signals of their own strong belief in its purported beneficial effects, augmenting the placebo effect. Simply poking needles into a patient at randomly chosen points could have a strong placebo effect if done with an air of compassion and clinical authority.

It has been argued that sham acupuncture performed as placebo therapy in clinical trials may accidentally stimulate a true acupuncture point, and thereby reduce the apparent benefit of acupuncture in the intervention subjects compared to controls. The use of sham laser acupuncture seems to address that objection.

The arguments and criticisms of acupuncture trials will continue. More good evidence, such as the findings of this study, will be required before we can conclude that acupuncture is of no more benefit for relieving pain than placebo. Better understanding of the biological basis of pain is needed, to develop new and truly effective analgesic therapies.

On 2014 Oct 13, David Keller commented:

Will mapping of all neural circuits increase understanding of the brain in meaningful ways?

The Human Brain Mapping Initiative (HBMI) is a government-mandated research program with the goal of systematically mapping the neural circuitry of the entire human brain. Will this large-scale fiat-funded project result in commensurate advances in neuroscience, or will it divert scarce funds away from smaller, innovative research projects with the potential for breakthroughs in diverse realms? Are we trading away the prospect of new fundamental discoveries, in order to accumulate terabytes of minimally meaningful mapping data in a routine and mechanistic fashion? The brain circuit mapping study by Fox et al provides interesting and relevant findings, much to the credit of the overall Brain Initiative.

The Human Brain Mapping Initiative recalls prior large-scale government-mandated projects, such as the effort to put a man on the moon, and the Human Genome Sequencing Project. The moon shots consumed funding which could have driven great progress in more crucial areas of discovery than lunar geology and micro-gravity ant farming. And, while the Genome Project did yield important information quickly, it has been criticized for amassing huge amounts of expensive data before they were needed, when the same information would have accumulated naturally over the years during the course of other investigations, and at less expense. Supporters have replied that the Genome Project itself drove down the cost of DNA mapping, due to the large market for sequencing equipment it created and funded. Similar arguments can probably be made both to attack and to defend the Brain Mapping Project. Only time, and further results, will settle these questions.

On 2015 Sep 17, Ghassan El-Baalbaki commented:

authors of this comment are: Loose, T.^1,3 , Ashrah, L.^1, Romero, M.^1, Bégin, J.¹ and El-Baalbaki, G.^1,2 Affiliations, Université du Québec À Montréal^1, McGill University^2, Université de Nantes³ .

In this study, the authors examine the efficacy of Acceptance and Commitment Therapy (ACT) in treating partner aggression. After entering into communication with the first author, she confirmed that this study corresponds to her doctoral thesis (Zarling, 2013). We read her thesis in order to gain further knowledge about the published study, and we found two important aspects of the work that need to be brought into light: 1) we find it difficult to conclude that partner aggression was specifically reduced, because of threats to internal validity. 2) There seems to be inaccuracies in their statistical calculations.

The primary objective was to demonstrate that ACT reduces intimate partner aggression better than the placebo control group. The authors strongly suggest that ACT was indeed able to do so. However, several points call this statement into question.

First of all, it is worth noting that partner aggression is never specifically assessed. One may think that the Conflict Tactics Scales-2-Physical Assault Scale (CTS-2) did assess this construct (Straus, Hamby, Boney-McCoy & Sugarman, 1996), but when taking into account the exact content of the administered questionnaire that was figured in her thesis, it can be seen that the instructions were modified in order to include aggression towards “people we care about” (Zarling, 2013, p.132) instead of specifically towards a partner. This modification is not mentioned in the published article. Hence, participants could have hypothetically committed aggressive acts exclusively towards a non-partner, such as a child or a friend. It is thus hard to conclude that aggressive behavior, specifically among couples, decreased as a result of therapy.

Furthermore, after modifying the instructions, one of the items even became incoherent. More specifically, when taking into the modified instructions of the questionnaire, the item stated “When upset or in a disagreement with someone you care about … have you became angry enough to frighten your partner?” (italics added)(Zarling, 2013, p. 132). It seems that this question was destined to ask if the participant became angry enough to frighten someone that they « care about » and not their « partner ». For example, if the participants were (or became) single, they could have interpreted this question as if they were angry enough to frighten someone that is not necessarily their partner. It is unclear how the authors wanted the participants to interpret this item. The way that the construct of partner aggression was assessed calls into question the internal validity of the study.

It remains questionable why the authors neglected to assess attrition of couples during the study. Over the course of the study, it is possible that aggressive behavior decreased more in the ACT group as a result of more couples breaking up in this treatment condition than in the placebo control group. Even if the authors carried out both completer analysis and intent to treat analysis and the results did not differ on measured variables, the attrition of couples was not measured. Hence, it is impossible to know if the groups differed on partner attrition. It remains possible that participants continued to aggress former partners, but again this cannot be asserted simply because it was not measured. Assessing partner attrition would have helped neutralize a pertinent threat to internal validity. Hence, internal validity was limited by not taking into account partner attrition.

Lastly, it is worth bringing up that the first author and two other investigators co-led all administered interventions (p. 201). Even if the authors state this in their article, after looking at the detailed explanation of the recruitment process of investigators, this choice does not seem to be justified. It seems that the first author was able to recruit investigators at no extra cost and it is questionable as to why she did not recruit three instead of two, thus avoiding a potential threat to internal validity. The explanation provided in her thesis, but not the article, also states that all the manipulation checks were carried out by the first author and supervised by the second and third authors (Zarling, 2013, p.61). Because of the implication of the authors in the experimental procedure, the results are potentially attributable to the experimenter expectancy effect. This is another threat to internal validity that evokes the tendency for researchers to unintentionally bias the results of their investigations in accord with their hypotheses. In taking into account the previously stated points, it seems difficult to conclude that this study shows that ACT specifically reduces partner aggression better than a placebo control group.

On another note, the statistical validity of the study can be questioned:

Throughout the results section of the paper (pp. 205–207), the authors report many beta values (β) for intercepts and slopes. If these are indeed beta values, they should vary between approximately 1 and -1 (Cohen, Cohen, West & Aiken, 2002). However in many cases, reported values are outside of this range. For example the authors state “The ACT participants also reported significantly less psychological aggression, β = 2.05, SE = 0.71, t(97) = 8.33, p < .001, and physical aggression, β = 2.21, SE = 0.65, t(97) = 8.19, p < .001, at the 6-month follow-up assessment” (p. 8). This leads us to think that the authors are actually reporting non-standardized coefficients (B) because B values can vary outside of this range. However, if this is the case, then the t values reported become incoherent. t values should equal B/(2SE) (we retained the value of 2 after rounding up from 1.96 which corresponds to 95% of a normal distribution (Christensen, 1986)), but reported t values do not correspond to this calculation. For example, let’s take another look at the previous citation and assume that it actually refers to B values. According to our calculations, t = B/(2SE) = 2.05/(2*0.71)=1.44, but the authors report that t = 8.33, p < .001. More simply stated,if the authors are indeed reporting β values, then many of the β values seem to be impossible (outside of the ± 1 range), but if they are reporting B values, the t values seem to be impossible according to our calculations. We were wondering how these seemingly paradoxical results could be explained.

In conclusion, even if this research topic is of great interest, two main points should to be taken into account. First of all, it is hard to state that ACT is an effective treatment to reduce partner aggression because 1) partner aggression was never specifically assessed 2) partner attrition was not measured 3) of potential bias due to the experimenter expectancy effect. Secondly, it is hard to draw conclusions from the statistics figured in the study because 1) if β values were indeed being reported, then they lie outside of the ± 1 range and 2) if B values were actually reported, then the t values become incoherent.

References

Christensen, H. B. (1986). La statistique: démarche pédagogique programmée. Boucherville: Gaëtan Morin.

Cohen, J., Cohen P., West, S. G. et Aiken, L. S. (2002). Applied multiple regression/correlation analysis for the behavioral sciences. New York: Routledge.

Straus, M. A., Hamby, S. L., Boney-McCoy, S., & Sugarman, D. B. (1996). The revised conflict tactics scales (CTS2): Development and preliminary psychometric data. Journal of Family Issues, 17, 283–316.

Zarling, A. (2013). A preliminary trial of ACT skills training for aggressive behavior. University of Iowa.

On 2014 Oct 02, David Keller commented:

Quicker-and-sicker discharges inevitably result in increased hospital re-admissions

Medicare and many private insurers pay hospitals a fixed amount to treat a given diagnosis, regardless of length of stay, which creates a financial incentive to discharge patients as soon as possible. Targets for shorter lengths of stay are set by hospital managements and are incorporated into the performance reviews of employed hospitalist physicians. With hospitalists pushing the envelope to get patients discharged quicker, an increase in the number of "bounce-back" re-admissions is inevitable, due to inadequate treatment, recrudescence of illness, or the lack of resources or support needed to complete recovery at home. To discourage premature discharges, financial penalties for "bounce-back" re-admissions were created by Medicare and other payers. Of course, these penalties are also incorporated into the performance reviews of employed physicians, and create a disincentive to readmit patients who were recently discharged. But, if the patient presents for treatment at a different hospital, the readmission penalty applies against the first hospital to treat and discharge the patient, not the second hospital. Thus, recently-discharged patients who are still too sick to complete their recovery at home may find it easier to be readmitted at a new hospital for inpatient treatment, where they will be evaluated by physicians who do not have a disincentive to re-admit them. Switching hospitals can make it easier for a still-sick patient to get re-hospitalized, but it also results in discontinuities of care and resulting inefficiencies, because records need to be transferred, new doctors need to learn about the patient, etc. This all just demonstrates that for every action to reduce costs by penalizing providers, there are unintended consequences which can harm patients.

On 2014 Oct 12, Amanda Capes-Davis commented:

Cell lines derived from ductal carcinoma in situ are certainly needed. Many thanks to the authors for including an STR profile for ETCC001 as part of their work. Did the authors test the other derivatives that were transfected with hTERT? It would be worthwhile testing all derivatives, just to confirm that they come from the same donor.

On 2014 Oct 18, stephane burtey commented:

It is interesting to remind that pioglitazone the drug use in the experiments is associated with an increased risk of bladder cancer (http://onlinelibrary.wiley.com/doi/10.1111/bcp.12306/abstract;jsessionid=0BF19A6B1135280E0C6DAAB5F9A2BF21.f02t03) and was withdrawn in France for this reason. It could be very interesting that the authors discuss this strange fact. Why imagine to use a drug known to cause be associated with an increase risk of cancer to treat cancer?

On 2016 Apr 15, Amanda Capes-Davis commented:

This article has now been retracted. See http://www.ncbi.nlm.nih.gov/pubmed/26909548 for the retraction notice and further comment.

On 2014 Oct 15, Amanda Capes-Davis commented:

KB is not an OSCC cell line - KB cells are actually HeLa, from cervical adenocarcinoma. Cross-contamination of KB was discovered by Stanley Gartler back in 1967. Unfortunately, KB is still widely used as a model for oral cancer. Cross-contaminated cell lines are extensively used in the scientific literature, with many scientists not aware of this important problem.

A list of cross-contaminated or otherwise misidentified cell lines can be found at http://iclac.org/databases/cross-contaminations/.

On 2015 Aug 01, James C Coyne commented:

Discussion of recovery patterns and schizophrenia will be facilitated when these authors finally published the overdue results of Klingberg, S., Wittorf, A., Meisner, C., Wölwer, W., Wiedemann, G., Herrlich, J., ... & Buchkremer, G. (2010). Cognitive behavioural therapy versus supportive therapy for persistent positive symptoms in psychotic disorders: The POSITIVE Study, a multicenter, prospective, single-blind, randomised controlled clinical trial. Trials, 11(1), 123. <pubmed/21190574>. This represents the largest clinical trial of cognitive behavior therapy for psychosis ever undertaken.

On 2016 Jun 03, Ewen Gallagher commented:

This work analyses the MEKK1 (encoded by Map3k1) PHD motif genetically and by protein array substrate screening. Shows an important role for the MEKK1 PHD motif in TGF-β cytokine signaling and demonstrates how PHD ubiquitination can influence TAK1 signal transduction. Shows genetically by knockin mutation (Map3k1^mPHD allele) that MEKK1 is important for stem cell MAPK signaling, differentiation and tumorigenesis. Reports phenotypes of Map3k1^mPHD/+ mice. A review is also published for this work (1). Other recent works looking at MEKK1 activation by cytokines and hyperosmotic stress (2-3). A short review is available relating to this work (4).

Related work. (1). Suddason T, Gallagher E. A RING to rule them all? Insights into the Map3k1 PHD motif provide a new mechanistic understanding into the diverse roles of Map3k1. Cell Death Differ 2015. (2). Matsuzawa A, Tseng PH, Vallabhapurapu S, Luo JL, Zhang W, Wang H, Vignali DA, Gallagher E, Karin M. Essential cytoplasmic translocation of a cytokine receptor-assembled signaling complex. Science 2008; 321:663-8. (3). Steed E, Elbediwy A, Vacca B, Dupasquier S, Hemkemeyer SA, Suddason T, Costa AC, Beaudry JB, Zihni C, Gallagher E, et al. MarvelD3 couples tight junctions to the MEKK1-JNK pathway to regulate cell behavior and survival. The Journal of cell biology 2014; 204:821-38. (4). Gallagher E, Suddason T. The PHD motif of Map3k1 activates cytokine-dependent MAPK signaling. Molecular & cellular oncology 2015; 2:e980659.

On 2014 Oct 30, jizhao li commented:

说的太好了……

On 2014 Dec 18, DAVID ALLISON commented:

Regression to the mean is a concept that does not seem to be known by or intuitive to many scientists. This paper by Love-Osborne et al. provides an example of that. Specifically, the authors state “For the power calculation, we estimated that 50% of the participants in the IG [intervention group] would either decrease or maintain their BMI z-score and that only 25% of the participants in the CG [control group] would.” Yet, given that the subjects studied were “adolescents with BMI ≥ 85%” (i.e., above the 85 percentile) and who had baseline BMI z-scores nearly two standard deviations above the mean, by regression to the mean alone, we would expect subjects’ BMI z-scores to decrease on average and that more than 50% of subjects would have decreased BMI z-scores even without any intervention. Despite this, the randomization makes their study internally valid, but by not considering regression to the mean, the authors’ power analysis makes little sense.

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 NCT0172340. We believe the correct ID, which we have found by hand searching, is NCT01723540.

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 2014 Nov 02, Swapnil Hiremath commented:

This is a nice, and elegant study which reiterates the potential effects of the av fistula creation on cardiac remodeling. However, given the survival benefit with AVF (as compared to central venous catheters) these results should be interpreted with caution. Another confounding factor perhaps not considered in this study is the effect of worsening kidney function over time: over the 6 months of study, the kidney function of some of these patients would have worsened, and in some cases accompanied by salt and water retention - or worsening hypertension. It would have been helpful to present these details (and/or control for them). Indeed, the absence of controls (i.e. patients who may not have had an AVF created) is a significant limitation. Lastly, the authors do not cite previous work from our group which used echocardiograms (and not CMR), with slightly greater numbers and longer follow up.

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13627?shared_access_token=OGukLfM9EO6BSbpYbheoadRgN0jAjWel9jnR3ZoTv0POe1AjZIjLc5wjJjbVg-oyGpATNrRnQKoh2HCdCbDq3ScttggR2ffObRhAcKOQqFmeNbxcyhQhV9cnIGvcWscowE8WBpEwLn8yLPTwcMk1pAPpPVU1URXBQexR6luuQyXuMlYtL-u3mbvl2p6xYf6kWrrtHAus6cv4wV3XiQlwCG3cyjeioZt0V7k016U-9H0=

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13626?shared_access_token=HaZErFLTH6h7DrSUISFs8dRgN0jAjWel9jnR3ZoTv0PyCKvPcK02JGt8W9YRMh9IMnLVVjLgmkCHPhw7WEJrggju5olGZO8Tm0uNFvYzNxd1N2CfpF7ssvEBhBZO8WpxzumGiWbLqbdhZONDjC2wVkfMnbrngnEmWH7GiP00Yej2TWPGZ9VCn2_GNJ_aE8vbAgW2IDpQdfM3S1ZbC5p-6ZhnmK8k65sgCnnxuy9Ib18=

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13739?shared_access_token=x_CWqj2uJMQqrIflaK4W8dRgN0jAjWel9jnR3ZoTv0MxPVycR7YKwxiZdLjoUHR1ylhdkOlirUBCvBqIN0_qmTGPDGrluCn9iFYbXDFs99XlOrwzeF0HGhEA7c1xxjgIh8iDscoODx9O225w8aTuAuqWaKRUWTLWTxCD_J71UgSBAflAcgP75Zc8NtcNgjakOGo-Ryv3oRzwqCSsacykKHnLwm_ag25ibtteOwZ9uSE=

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13779?shared_access_token=58QUkQGSW2kxj81ABkPlddRgN0jAjWel9jnR3ZoTv0NOMV7FTSmr9qzCHkM8CKJUxI-F4eTGI7qNpcgdsNi1mmTxK7QmWuCz3pdTcpRgLFFwA0VYsJlLA8ffGb5TE6AvWafFwjrhOokzF-urd6339w-7BWPYmJh_Jwd98E6UOy180Pesaa2xJw1WxqtQslAVGvomZDx4RIGBREnZztELN055N5zguUSkbcAGolas4TE=

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13785?shared_access_token=XT_aqsYxAOSPspMsyKm-ltRgN0jAjWel9jnR3ZoTv0PXhmbkoukZsLZyJBntb3pJUi7-VGvpNfy1gyz_miEMNrh0S0EogQ7MbPgYzh5mEjXLXhvar5QIjy03cCclAKYSH-x0WnjUq3vteuX8HSVPDFQuFteI8taJw2BBFEi9priv3IGVgIrcvYTxSsIWe9GLU-PI6RpHSl0kfRhY7cvEuI4UQUaBCU9F602mlPgLY5A=

On 2015 Jan 05, Peter Gøtzsche commented:

Antidepressant drugs should not be used in old people

Warren D. Taylor mentioned that people with late-onset depression are at higher risk for subsequent dementia.1 However, none of the references he provided lend support to the idea that it is the disease that causes the dementia. It is more likely that it is the antidepressant drugs that cause the dementia, e.g. benzodiazepines double the risk for dementia.2

Taylor also noted that depressed older adults are at increased risk for suicide and he recommends SSRIs. However, it has never been shown in reliable studies that SSRIs protect against suicide, but it has been shown that they cause suicide.3 Further, as Taylor noted, SSRI cause falls, which is detrimental in old people, as 20-25% die when they get a hip fracture. A meticulous cohort study of depressed people over 65 years of age, in which the patients were their own controls, showed that for every 28 people treated for 1 year with an SSRI, there was one additional death, compared to no treatment. A further reason why antidepressants should not be used in old people is that their effect on the depression is doubtful.4

1. Taylor WD. Depression in the elderly N Engl J Med 2014;371:1228-36.

2. Billioti de Gage S, Moride Y, Ducruet T, et al. Benzodiazepine use and risk of Alzheimer's disease: case-control study. BMJ 2014;349:g5205.

3. Gunnell D, Saperia J, Ashby D. Selective serotonin reuptake inhibitors (SSRIs) and suicide in adults: meta-analysis of drug company data from placebo controlled, randomised controlled trials submitted to the MHRA’s safety review. BMJ 2005;330:385.

4. Gøtzsche PC. Why I think antidepressants cause more harm than good. Lancet Psychiatry 2014;1:104-6.

On 2014 Nov 19, Peter Gøtzsche commented:

Antidepressant drugs should not be used in old people

Warren D. Taylor mentioned that people with late-onset depression are at higher risk for subsequent dementia.1 However, none of the references he provided lend support to the idea that it is the disease that causes the dementia. It is more likely that it is the antidepressant drugs that cause the dementia, e.g. benzodiazepines can cause dementia.2

Taylor also noted that depressed older adults are at increased risk for suicide and he recommends SSRIs. However, it has never been shown in reliable studies that SSRIs protect against suicide, in fact they cause suicide.3 Further, as Taylor noted, SSRI cause falls, which is detrimental in old people, as many die when they get a hip fracture. A meticulous cohort study of depressed people over 65 years of age, in which the patients were their own controls, showed that for every 28 people treated for 1 year with an SSRI, there was one additional death, compared to no treatment. Antidepressants should not be used in old people, also because their effect on the depression is doubtful.4

1. Taylor WD. Depression in the elderly N Engl J Med 2014;371:1228-36.

2. Billioti de Gage S, Moride Y, Ducruet T, et al. Benzodiazepine use and risk of Alzheimer's disease: case-control study. BMJ 2014;349:g5205.

3. Gunnell D, Saperia J, Ashby D. Selective serotonin reuptake inhibitors (SSRIs) and suicide in adults: meta-analysis of drug company data from placebo controlled, randomised controlled trials submitted to the MHRA’s safety review. BMJ 2005;330:385.

4. Gøtzsche PC. Why I think antidepressants cause more harm than good. Lancet Psychiatry 2014;1:104-6

On 2015 Feb 09, Andrey Petrenko commented:

Dr. Junfeng Zhang and colleagues have demonstrated that postoperative deterioration of rat cognitive performance in the Barnes maze could be prevented by amantadine. Amantadine also increased GDNF production in hippocampus and pretreatment with anti-GDNF antibody could abolish cognitive improvement attained by this drug. Since both amantadine and GDNF also inhibited interleukin 1β production, the authors concluded that the observed beneficial effect of amantadine on cognition is essentially an anti-neuroinflammatory effect mediated through GDNF. These are novel and interesting findings suggesting possible therapeutic potential of amantadine in treating postoperative cognitive dysfunction in humans. While we do not doubt the overall authors’ conclusion, we believe that there may be another mechanism underlying the reported cognition-preserving effect of amantadine. It is based on the fact that amantadine is a noncompetitive NMDA receptor antagonist (Blanpied TA, 1997; Blanpied TA, 2005) that may have analgesic properties. Although Dr. Zhang and colleagues believe that by performing learning and memory tests one week after surgery they have avoided the influence of pain on their results, this might not be the case. Actual pain levels in operated animals were not assessed in this study, and it is possible that rats given amantadine could have experienced significantly less pain compared to those operated but not receiving the drug. Such a possibility is further supported by the regimen of amantadine administration chosen by the authors, which was similar to preventive analgesia (first dose of analgesic being administered before surgery) often employed to alleviate postoperative pain. In elderly patients postoperative pain can confound performance on cognitive tests (Heyer EJ, 2000) and also predicts decline in their mental status (Duggleby W, 1994). In aged rats postoperative pain impairs cognitive function and preventive administration of analgesics (including those with no anti-inflammatory effect) can prevent this cognitive decline　(Chi H, 2013; Kawano T, 2014). The extent of postoperative cognitive decline positively correlates with the level of expression of the NMDA receptor GluN2 subunits in rat hippocampus (Chi H, 2013), further supporting the notion that the NMDA receptor inhibiting properties of amantadine should have not be discarded when interpreting the results of the study in question. In adult spinal nerve ligated rats preventive administration of memantine (a derivate of amantadine and also a noncompetitive NMDA receptor antagonist) inhibits the phosphorylation of the NMDA receptor GluN2 subunits in the spinal cord and hippocampus, causes antinociception and, as a consequence, preserves their cognitive function (Morel V, 2013).<br> Finally, several reports indicate the involvement of NMDA receptors in brain expression of neurotrophic factors (including GDNF) (Al-Amin H, 2011; Ranju V, 2015) and in the mechanisms of neuroinflammation (Liu CH, 2011; Yan J, 2014) with documented beneficial effects of NMDA receptor antagonists. Thus, there is a possibility that the NMDA receptor-inhibiting properties of amantadine could also have contributed to its beneficial effect on neuroinflammation observed by Dr. Zhang and colleagues.

On 2014 Sep 30, Ryan Radecki commented:

Post-publication commentary:

"The 2014 AHA NSTE-ACS Guidelines"

One of the best things about Emergency Medicine is the preponderance of guidelines imposed upon our management of patients by non-Emergency Medicine clinicians. One of the most glorious offenders is the American Heart Association, dictating our care of Stroke and Acute Coronary Syndrome.

But, actually, this most recent update – despite the continued absence of Emergency Medicine from the Writing Committee – contains some interesting subtle shifts. Out of its 150-odd pages of content and evidence, most of the Emergency Medicine-relevant content is in Section 3: Initial Evaluation and Management. Many of the guidelines are not controversial – send patients with suspected ACS to the Emergency Department, give aspirin, obtain an ECG, etc....

http://www.emlitofnote.com/2014/09/the-2014-aha-nste-acs-guidelines.html

On 2015 Dec 11, Mark Johnston commented:

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

On 2016 Aug 30, Ben Goldacre commented:

This trial has the wrong trial registry link associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID in the link provided is NCT0102727. We believe the correct link, as found elsewhere in the text, is NCT01027273.

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 2014 Oct 16, Jongpil Kim commented:

To Whom It May Concern:

We have reviewed the concerns regarding some of the images presented in our study brought up by Paul Brookes on PubMed and Derek Lowe on his blog. In the wake of numerous controversial studies in the stem cell field, we appreciate the scrutiny of our results as skepticism plays a critical role in the progression of scientific research.

We have addressed all of the concerns raised on the internet regarding duplication of images and cropping of western blots and detail these responses separately.

First, regarding the similar radial contrast patterns in Figure 1C and 2D when black images are overexposed, we now provide high magnification versions of these images showing that while the radial contrast is similar between images (as would be expected when taking images from an essentially blank field on the same microscope with the same detector), there are clear differences observable upon higher magnification, demonstrating that these blank images were acquired independently.

Also, we have now provided all of the original western blots to the Journal that can be published in an erratum if the Journal deems this necessary. There were no sign of splicing or cropping of these original western data in Figure 4C, and we cut out the unnecessary part of images for the display on the limited area of paper in Figure 4F.

Finally, with regard to the image duplication of the brightfield micrograph of proliferating fibroblasts in Figure 2b: Yes, these are the same image, because this is the Time 0 timepoint of the experiment, prior to induction of EMF and factor infection. This began as a single culture at Time 0, after which half of the culture was exposed to EMF and the other half (control) was not (all in the presence of the Yamanaka factors). It is unclear to us why this is a concern for Paul Brookes, as he asserts this image was used to ‘represent different conditions’, however at Time 0, prior to the induction of EMF, these are in fact the same condition.

We are more than happy to provide all original images and discussion regarding these points in an erratum to the manuscript if the Journal deems it to be necessary.

On another note, we would like to point out significant errors made by Paul Brookes and Derek Lowe in their respective blogs in their interpretation of our study. Brookes states “in the wake of the STAP stem cell controversy, a paper claiming that iPSCs can be made using magnetic fields deserves special scrutiny”, and Lowe states “Yep, this paper says that stem cells can be produced from ordinary somatic cells by exposure to electromagnetic fields”. To us this suggests that neither Brookes nor Lowe actually read our manuscript, and rather just began altering contrast of images in the paper to find what they perceive as discrepancies.

Nowhere in our manuscript do we claim “iPSCs can be made using magnetic fields”. This would be highly suspect indeed. Rather, we demonstrate that in the context of highly reproducible and well-established reprogramming to pluripotency with the Yamanaka factors (Oct4, Sox2, Klf4, and cMyc/or Oct4 alone), EMF influences the efficiency of this process. Such a result is, to us, not surprising given that EMF has long been noted to have effects on biological system(Adey 1993, Del Vecchio et al. 2009, Juutilainen 2005)(There are a thousand of papers for biological effects of EMF on Pubmed) and given that numerous other environmental parameters are well-known to influence reprogramming by the Yamanaka factors, including Oxygen tension (Yoshida et al. 2009), the presence of Vitamin C (Esteban et al. 2010), among countless other examples.

For individuals such as Brookes and Lowe to immediately discount the validity of the findings without actually attempting to reproduce the central experimental finding is not only non-scientific, but borders on slanderous. We suggest that these individuals take their skepticism to the laboratory bench so that something productive can result from the time they invest prior to their criticizing the work of others.

“Often those that criticize others reveal what he himself lacks.” ― Shannon L. Alder

http://i.imgur.com/XgKBX47.jpg?1

http://i.imgur.com/gvZdZAQ.jpg

http://i.imgur.com/ljqPnxU.jpg

http://i.imgur.com/dEB1aoX.jpg

JP Kim

JONGPIL KIM, Ph.D. Assistant Professor Dept of Biomedical Engineering Dongguk University Seoul, Korea Tel: 82-02-2260-3371 Fax: 82-02-2260-8726 Email: jpkim153@dongguk.edu, jk2316@gmail.com

On 2014 Oct 14, Paul Brookes commented:

Cross-posted from PubPeer (https://pubpeer.com/publications/A730F960943331E553B54335FE8877)

This paper came up on Derek Lowe's "In the Pipeline" blog... http://pipeline.corante.com/archives/2014/10/14/electromagnetic_production_of_stem_cells_really.php

In the wake of the STAP stem cell controversy, a paper claiming that iPSCs can be made using magnetic fields deserves special scrutiny. Not surprisingly, there are a few problems with this paper...

Figure 2B - image re-use to represent different conditions http://i.imgur.com/Tu0kA52.jpg

Figures 4C & 4F - undisclosed splicing together of blots revealed at high contrast http://i.imgur.com/YREpQeF.jpg

Figures 1C & 4D - background fluo' images in some controls are "more similar than would be anticipated by pure coincidence" http://i.imgur.com/VKfgNIx.jpg http://i.imgur.com/2FfvvpH.jpg

There is another minor issue regarding the phase contrast images that are provided for numerous fluorescence images, including in the supplemental data. In short, it does not seem feasible that the fluorescent images shown could have originated from the cells shown in the phase contrast image. This probably means they just used different cells for the phase and the fluo' imaging, but this was not clearly stated anywhere, and is certainly not standard practice.

On 2016 Feb 03, Jahan Khalili commented:

Mutations that result in cancer-specific peptides with enhanced HLA affinity based on anchor residue preferences was first published in 2012. See "In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census", Results section "Mutation-mediated alteration in HLA-binding affinity" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518500/

On 2014 Oct 14, Xiang Hu commented:

Liang Cao and Xiang Hu are listed as Co-corresponding author

On 2014 Nov 21, Swapnil Hiremath commented:

This study was discussed on Nov 4th 2014 in the open online nephrology journal club, #NephJC, on twitter. Introductory explanatory comments, written by Dr Susan Steigerwalt, are available at the NephJC website. It was an interesting discussion, which served partly to explain the experiments to the non-scientists in the chat, and partly to critique the study itself. It had more than 20 participants, including nephrologists, physiologists, basic scientists and nephrology fellows. A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website. The highlights of the tweetchat were:

• The investigators have been pursuing this research area (the immune systems and hypertension) over many years, and report here exhaustive and meticulous experiments, including multiple animal models and human data.

• This group identified a novel connection between the production of isoketals (or isolevuglandins) in dendritic cells leading to isoketal-modified proteins which in turn activate T cells and promote hypertension.

• Though these findings were greeted with a lot of interest, the results do need to be independently replicated; additionally, the exact biological mechanisms, including the mechanism of T cell activation and resultant alteration in either vascular function or sodium homeostasis, need to be elucidated further. However, these results could lead to novel therapies exploiting the immune system for therapeutic benefit in hypertension and resultant end organ damage.

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

On 2014 Dec 17, Sean Ekins commented:

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

On 2014 Dec 17, Sean Ekins commented:

Another link to a post where we mention this paper https://www.collaborativedrug.com/buzz/2014/12/16/beware-researchers-challenges-navigating-commercial-and-public-databases/

On 2014 Dec 15, Sean Ekins commented:

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

On 2014 Dec 04, Sean Ekins commented:

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

On 2014 Dec 02, Nadia Litterman commented:

For a description of the process of gathering information on the probes, and a discussion of navigating between public and private data: http://www.ncbi.nlm.nih.gov/pubmed/25415348

On 2014 Dec 02, Nadia Litterman commented:

The NIH Probe structures, associated bioactivity data, and expert evaluations can be found here: https://www.collaborativedrug.com/pages/public_access

On 2014 Dec 02, Sean Ekins commented:

This article was mentioned here http://www.collabchem.com/2014/10/07/the-most-expensive-data-set-i-have-modeled-dont-blink-over-500m/

On 2015 Feb 06, Ryan Radecki commented:

Post-publication commentary: "Just Poop, It Doesn’t Matter How"

Hepatic encephalopathy, a consequence of bacterial overgrowth and impaired ammonia metabolism, contributes to (as these authors say) nearly $2B in healthcare costs due to hospitalization in the United States alone. Typical, goal-oriented, modern therapy? Lactulose, a non-digestible sugar, resulting in increased bowel movement frequency.

These authors, appropriately, challenge established dogma – noting, perhaps, there are more effective strategies for clearing the bowels....

http://www.emlitofnote.com/2014/12/just-poop-it-doesnt-matter-how.html

On 2015 Feb 27, Geriatric Medicine Journal Club commented:

This is study looks at the effect of using the STOPP/START criteria in the chronic geriatric facility setting and was discussed at the December 2014 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full discussion can be found at: http://gerimedjc.blogspot.com/2014/12/gerimedjc-december-19-2014.html?spref=tw One point of discussion was whether 20 minutes was a reasonable time frame for the intervention given the outcomes.

On 2016 Sep 12, Cicely Saunders Institute Journal Club commented:

The Cicely Saunders Institute journal club discussed this paper on Wednesday 7th September 2016.

We felt this is an important study that is opening the ‘black box’ of an intervention based on the habit formation model. The title itself stimulated discussion and reflection on the challenges of reducing sedentary behaviour.

We enjoyed discussing the development of the habit–based intervention for older adults and the protocol for the randomised controlled trial. The paper is presented as a study protocol, yet the first few pages actually describe the developmental stage of the intervention. We felt the development phase warranted being presented more fully in a separate paper. Questions arose in our discussion related to the nature of the adverse health consequences associated with sedentary behaviour and physical inactivity.

We commented on the pros and cons of publishing a protocol for a feasibility trial, including the need to publish amendments one year later. It was not clear how the behaviour change techniques utilised in the usual care fact sheet differed from those in the intervention booklet. Whilst we acknowledged there may be practical reasons for not presenting both the booklet and the control fact sheet in the protocol paper, we agreed that it would have been interesting to be able to see and compare these two documents.

We noted the authors acknowledgement of the difficulty of attributing a behaviour change effect to the habit formation elements in the booklet. We also discussed the possible contextual factors that might contribute to any effect and were interested in how the long term impact of habit-based interventions could be evaluated.

Commentary by Joanne Bayly and Roxana Vanderstay

On 2014 Sep 23, Samir Ounzain commented:

Very nice editorial distilling the main points from our recent study and highlighting some very interesting concepts for future consideration. I would just like to briefly address a couple of the main points.

Hofmann and Boon rightly point out ''it would be interesting to see if exogenous overexpression of one of these transcripts could have increased the mRNA levels of their putative target genes or whether genomic context is the main determininant for enhancer activity of lncRNAs''

This is a fascinating point that we are indeed trying to address,, and one that could have implications for future potential cardiac ''enhancer'' therapies. What we can say is it appears that the majority of enhancer templated lncRNAs, at least their -cis activity is dependant on the nascent endogenously produced transcript recruiting and activating in a ''proximity-transfer'' manner chromatin remodelling complexes. This tends to mean that exogenous over-expression is not sufficient. However examples exist of exogenous over-expression impacting upon endogenous -cis loci. A recent study specifically addressed this issue and provides an excellent experimental framework for how such experiments to test these ideas should be conducted. This group mechanistically characterised an enhancer associated lncRNA named CCAT1-L.

1: Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z, Zhang S, Wang HB, Ge J, Lu X, Yang L, Chen LL. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 2014 Sep;24(9):1150. doi: 10.1038/cr.2014.117. PubMed PMID: 25174407; PubMed Central PMCID: PMC4152739.

Finally Hofmann and Boon ask whether ''enhancer RNAs functionally affects the response to cardiac stress in a disease model like acute myocardial infarction''. This is a major questions ourselves and others in the community are trying to address using various strategies. We do suspect that considering the unique context and tissue specific expression profiles of enhancer associated lncRNAs, they would represent ideal specific therapeutic targets for ''enhancer-therapy'' type approaches post acute cardiac stress. We look forward to see how these concepts will emerge and evolve in the coming years.

Finally it is worth noting that many adult heart specific lncRNAs are also associated with adult heart specific active enhancer sequences. Furthermore, heart specific lncRNAs associated with such enhancers are preferentially modulated post myocardial infarction in the mouse, implicating them in the global enhancer reprogramming that underpins maladaptive cardiac remodelling. More on this can be found ...

Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa S, Nemir M, Sarre A, Johnson R, Dauvillier J, Burdet F, Ibberson M, Guigó R, Xenarios I, Heymans S, Pedrazzini T. Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J. 2014 Apr 30. [Epub ahead of print] PubMed PMID: 24786300.

On 2016 Apr 30, Morten Oksvold commented:

Please be aware that this article represents one of eleven publications which were found to contain false data, after an investigation led by ORI in 2015:

https://ori.hhs.gov/content/case-summary-dasmahapatra-girija

On 2015 Apr 22, Clyde Francks commented:

Study authors Tulio Guadalupe and Clyde Francks reply to comment by Dorothy Bishop:

We thank Dorothy Bishop for insightful comments. We considered the HO measurement of PT grey matter volume as a region-of-interest index 'within and around the human planum temporale', rather than a direct measurement of its neuroanatomical definition. The HO measurement was weighted on the voxels that most probably belonged to the PT, based on 37 brains used in constructing the atlas. The HO definition of PT is lateralized to the left and the measurement of PT regional asymmetry in our datasets reflected this. We agree that this spatial restriction probably contributed to the lower inter-subject variability measured with the HO approach compared to FreeSurfer's parcellations. However, because of the large variability in landmarks in the superior temporal lobe, these regions are among the least reliable in Freesurfer parcellations, and also the Freesurfer-Destrieux definition of the planum temporale includes the planum parietale which is not usually recognized as part of its extent. Reassuringly, we found PT regional lateralization to be sexually dimorphic with both approaches (PT region was the most sexually dimorphic of all 44 regions using the HO atlas and the third most dimorphic of 74 regions using the FreeSurfer-Destrieux atlas). We agree that the measurement issues do not obviously explain the sex effect.

Because of the normalization pre-processing of the GM maps to the MNI template, subjects with departures from average PT lateralization are already somewhat 'pre-fitted' for the HO probabilistic atlas before it is applied (and we saw no major departures based on the random thirty normalized subjects we visually inspected, which would have been expected to contain three or four subjects with rightward PT lateralization). If normalization was perfect, someone with a larger-than-average right PT in relation to that hemisphere would have their right PT morphed into an equivalent normalized space as someone with a smaller than average right PT, prior to atlas application.

Our additional requirement with our HO PT lateralization index was to support genome-wide association meta-analysis across multiple datasets, for which a single and comparable index was required across datasets, after which individual genetic associations would be further interrogated in a voxel-based-morphometry context without use of the HO atlas. We argued that, for measuring group and individual differences, regional identification was likely to be more accurate with an asymmetrical atlas than with a left-right symmetrized atlas, for structures that were asymmetrical both in the atlas and, on average, in our datasets. Using a symmetrized atlas would affect the mean and range of lateralization in the dataset, and probably allow some individuals to be measured with rightward lateralization, but then the fit would be worse for people with leftward lateralization (the majority) than for the un-symmetrized HO atlas.

Genomewide association analysis requires thousands of participants to achieve sufficient statistical power to detect the effects of individual polymorphisms that are individually expected to account for a fraction of 1% of trait variation. Even the sex difference that we found only explained 1.2-1.6% of trait variance. The use of large and multiple datasets was required within a single collaborative study, and the creation of dataset-specific atlases, based on large numbers of participants, by each of the contributing teams matched to their particular scanning setup and population demographic, was not practical. We agree that there is an urgent need for manually created brain atlases based on larger numbers of participants, together with improved methods of automated application that are robust to dataset heterogeneities and flexible for the full range of individual differences.

On 2015 Apr 18, Dorothy V M Bishop commented:

The literature on sex differences in cerebral asymmetry does appear to be very confusing, and this paper does a thorough job in attempting to address the inconsistencies. I'm not sure it completely resolves the issue, but it sets a high methodological standard by using much larger sample sizes than previous studies and including two replication samples. It also includes a genetic analysis, which I won't discuss here.

Structural asymmetry of the planum temporale, with larger PT on the left, was described 47 years ago by Geschwind and Levitsky. Since that time it has become clear that the proportion of the population showing asymmetry varies substantially according to how it is measured. There have been claims of sex differences in PT asymmetry, but, as noted by Guadalupe et al, there have also been counterclaims, and a recent meta-analysis concluded that there is no sex difference, and the impression of one arose because of publication bias.

Guadalupe et al, however, found a reliable sex difference in PT asymmetry that replicates across three samples. However, their method of measurement does have one characteristic that I found puzzling: in a sample of 2337 adults they found nobody with reversed asymmetry (i.e., R>L planum). This contrasts with the original sample of Geschwind and Levitsky, where 11% had reversed asymmetry, and 24% had equal size PT on left and right. G&L's study was based on examination of post mortem specimens, but Watkins et al (2001) found similar proportions in a voxel-based analysis of grey matter from 142 MRI scans.

I assume the finding of universal left-biased PT in the current study had to do with the method by which this was defined: this was different from the method used by Watkins et al.

In the current study, grey matter was quantified in cortical regions based on a template taken from a average brain, then weighting each voxel by the probability that it belonged to that specific cortical region. The authors note that there are regional asymmetries in the atlas they used that will necessarily influence the mean – presumably, the left planum map is bigger than the right planum map, and so there are more voxels to count on the left. The authors argue that we already know that the left and right perisylvian regions differ systematically in their anatomy on average, and the interest here is in individual differences. They argued therefore that an averaged left-right template would not capture the systematic differences between the two sides.

I have trouble understanding how the template they used could adequately capture cases where someone had a larger than average PT. If the template represents the PT from an average brain, there will be variation around that average, with some people have larger and others having smaller PTs. If voxels were counted if they were within the template and not otherwise, anyone who had a PT that actually extended beyond the template would not have all their voxels counted. I appreciate that in practice, a more sophisticated probabilistic approach was used, but I'm not sure this would solve the problem. The template is based on 37 brains; we know that around 11% of people have R>L planum temporale, so around 3-4 contributors to the template would have that pattern. So, if I understand it correctly, voxels in the outskirts of a core region would have a low weighting, because in only a small proportion of the template subjects would this region be included in PT. But this means that for a new subject who genuinely had PT in that region, the amuont of grey matter in PT would be underestimated, because the weighting would be low. And there may be some people with rare PT configurations who may have parts of their PT not represented at all in the template. In this regard, given the known individual variation in PT, 37 people seems rather small a number on which to base probabilistic weightings.

I wondered whether this aspects of methodology explained why the volume measures for the Freesurfer analysis had standard deviations that were about 1.7 times as large as the standard deviations for the HO atlas analysis – is the HO atlas analysis in effect minimising or excluding values for those whose PTs are more extensive than the average?

I can't see an obvious reason why this should generate spurious sex differences, but I wondered if it could explain the absence of cases of reversed asymmetry in this sample.

Overall, I thank the authors for providing such comprehensive data on this vexed topic; it is remarkable how the measurement of asymmetry, which looks on the surface like such a simple issue, is exceedingly complex, with specific analytic choices leading to different patterns of findings. It is good to see examples like this where alternative approaches are used to give one the opportunity to observe their effects.

Geschwind, N., & Levitsky, W. (1968). Human brain: left-right asymmetries in temporal speech region. Science, 161, 186-187. Watkins, K. E., Paus, T., Lerch, J. P., Zijdenbos, A., Collins, D. L., Neelin, P., . . . Evans, A. C. (2001). Structural asymmetries in the human brain: a voxel-based statistical analysis of 142 MRI scans. Cerebral Cortex, 11, 868-877.

On 2014 Sep 23, Vojtech Huser commented:

This is interesting study. The trial http://clinicaltrials.gov/show/results/NCT01658254 deposited no results itself to the registry.

On 2015 Mar 08, David Keller commented:

Arguments against the use of cannabidiol or other cannabis derivatives to treat Parkinson's disease

Arguments against the use of cannabidiol to treat Parkinson's disease patients:

1) Persistent cannabis users show neuropsychological decline from childhood to midlife [1], which is abnormal and worrisome.

2) Cannabidiol (CBD) is a "major constituent of cannabis" [2]

3) We do not know which one, or which combination of cannabis constituents, contributes to the neuropsychological decline observed in persistent users. The possible culprits include CBD, THC, and other compounds present in cannabis.

4) The study by Chagas and colleagues [3] did not prove that long-term chronic CBD use does not contribute to neuropsychological decline.

5) The alleged benefit demonstrated by CBD was a minor improvement in PDQ-39 score of borderline statistical significance. CBD use did not affect the 3 other reported outcomes significantly.

6) The borderline improvement in PDQ-39 score observed with CBD use [3] does not justify the risk of neuropsychological decline which CBD, as a major constituent of cannabis, may cause [1].

7) Researchers who work with cannabis, CBD, THC or any combination of cannabis derivatives, should declare whether they currently use any such substances, as should those who comment, review or editorialize about these substances, because such use constitutes a source of potential bias, which I shall designate as "Cannabis Derivatives User Bias".

8) I do not use cannabis or any of its derivatives. I request that Dr. Kevin McKernan and all other commenters make similar disclosures.

References

1: Meier MH, et al. Persistent cannabis users show neuropsychological decline from childhood to midlife. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):E2657-64. PubMed PMID: 22927402

2: Gallily R, Yekhtin Z, Hanuš LO. Overcoming the Bell-Shaped Dose-Response of Cannabidiol by Using Cannabis Extract Enriched in Cannabidiol. Pharmacology & Pharmacy,2015,6,75-85

3: Chagas MH, Zuardi AW, Tumas V, Pena-Pereira MA, Sobreira ET, Bergamaschi MM, dos Santos AC, Teixeira AL, Hallak JE, Crippa JA. Effects of cannabidiol in the treatment of patients with Parkinson's disease: an exploratory double-blind trial. J Psychopharmacol. 2014 Nov;28(11):1088-98. doi: 10.1177/0269881114550355. Epub 2014 Sep 18. PubMed PMID: 25237116.

On 2015 Mar 05, David Keller commented:

The first reference given by Kevin McKernan contradicts him, and also contradicts itself

The first sentence of Dr. McKernan's first reference is: "Cannabidiol (CBD), a major constituent of Cannabis, has been shown to be a powerful anti-inflammatory and anti-anxiety drug, without exerting a psychotropic effect."[1] This sentence starts out by contradicting McKernan's assertion that "marijuana and Cannabidiol (CBD) are very rarely related", given that cannabis and marijuana are synonymous, and CBD is "a major constituent of Cannabis". Moreover, this sentence goes on to contradict itself by stating that CBD has been shown to be an "anti-anxiety drug" but "without exerting a psychotropic effect". It is clearly contradictory to state that an anti-anxiety drug has no psychotropic effect.

My main point is that it is perfectly acceptable for a basic scientist, like Dr. McKernan, to explore the properties of "cocktails of cannabinoids" in his laboratory. However, before exposing human subjects suffering from Parkinson's disease to cannabidiol, or any other "major constituent of cannabis", the neurological safety of these cannabinoids must be established. I see nothing "controversial" about the study conducted by Meier and colleagues (2); rather, it confirms the widely-held perception that chronic users of cannibis (marijuana) suffer neuropsychological degeneration. Until this worrisome safety signal is addressed, I do not consider it ethical to test CBD, THC or any other major constituent of cannabis on patients with Parkinson's disease, Alzheimer's disease, or any other neurodegenerative condition. The borderline-insignificant gain in the PDQ-39 score observed in this study is simply not worth the risk, even if the benefit had been statistically significant.

The amount of research into the beneficial effects of cannabidiol and other chemicals found in marijuana seems excessive, given the scant benefits demonstrated in this study, and others like it. How much of this zeal to promote the benefits of marijuana-derived compounds is driven by the wish for full legalization of this drug? I propose the following experiment: legalize marijuana in all 50 states and also by the Federal government. Once its advocates are free to grow, smoke, and consume this plant in any form or fashion without restrictions of any kind, I predict that the amount of research into the benefits of marijuana-derived chemicals will drop significantly.

Lastly, it is reasonable to expect that a regular user of cannabis or any of its derivatives might exhibit bias when reporting results of a trial, or when commenting on them ("user bias"). For this reason, use of cannabis or any of its derivatives should be disclosed in the same fashion as a financial bias. Full disclosure: I do not use any of these substances, and I call on Dr. McKernan to make a similar disclosure.

References

1: Gallily R, Yekhtin Z, Hanuš LO. Overcoming the Bell-Shaped Dose-Response of Cannabidiol by Using Cannabis Extract Enriched in Cannabidiol. Pharmacology & Pharmacy,2015,6,75-85

2: Meier MH, et al. Persistent cannabis users show neuropsychological decline from childhood to midlife. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):E2657-64. PubMed PMID: 22927402

On 2015 Feb 26, Kevin McKernan commented:

Marijuana must not be conflated with Cannabidiol

David Keller highlights a few controversial studies pointing out the adverse effects of "marijuana". This is known as a straw man argument as marijuana and Cannabidiol (CBD) are very rarely related. Most Marijuana is THC enriched and lacking CBD as a direct result. Pathways in the plant that synthesize THCA are in competition for GPP required to make CBDA (CBD's carboxylated precursor). Most "Marijuana" is devoid of CBD as a result. Likewise, most recreational "Marijuana" is consumed with a route of administration via smoking and cannot deliver 300mg/day via the hepatic portal system which is known to metabolize many cannabinoids into other active molecules not experienced with smoking "marijuana". Likewise, THC is pharmaceutically very different than CBD such that any reference to studies investigating the non descriptive 'Marijuana' are obsolete and irrelevant. The investigator bias on display here is clearly in the camp of Dr. Keller not understanding some of the basics of Cannabidiol research. For reference I would point to the following references highlighting the very distinct nature of CBD compared to THC. Any attempt to conflate these two molecules has already been thoroughly established as foolhardy in the endocannabinoid sciences. For instance, CBD does not get patients 'stoned' and its mechanism of action is not related to the CB1 receptor. Some of the most exciting work in this field is exploring cocktails of cannabinoids found in more raw forms of the plant as these cocktails appear to widen the dose response curve. The above studies p-value will likely improve utilizing the methods recently published by Gallily et al.

In summary, the Parkinsons genetic pathways continue to highlight the relevance of Parkin, LRRK2 and mitochondrial dysfunction. These genes are involved in the ROS pathway and lipid soluble antioxidants with very tolerant therapeutic indexes are a perfectly rational approach for Parkinsons disease. Future studies stratifying the genetics of the disease and widening the dose response curve with work like Gallily et al are likely to be very productive for the field.

References

Gallily- http://www.scirp.org/journal/PaperDownload.aspx?paperID=53912 http://www.sciencedirect.com/science/article/pii/S0006899306034718 https://www.google.com/patents/US6630507 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942876/ http://onlinelibrary.wiley.com/doi/10.1002/jat.2828/abstract;jsessionid=33248CFFF91EA20AE26A6C2EFE120DEE.f04t03?deniedAccessCustomisedMessage=&userIsAuthenticated=false http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797438/ http://www.pnas.org/content/95/14/8268.short http://jop.sagepub.com/content/early/2008/11/21/0269881108096519.short

On 2014 Sep 26, David Keller commented:

The cognitive adverse effects of cannabidiol must be discussed

Chronic cannabis use causes irreversible cognitive impairment, and is considered neurotoxic for that reason (1). Many marijuana addicts cite acute cognitive dysfunction as their intended goal; in street terms, this is known as being "stoned". Any proposal to treat Parkinson disease with cannabidiol, cannabis or marijuana itself which fails to assess and report cognitive impairment raises the question of investigator bias.

Lastly, the results of a clinical trial are commonly deemed statistically significant when the probability that the findings are the result of chance is less than 5% (2). A p-value equal to 0.05 is usually described as being of borderline or marginal statistical significance.

References

1: Meier MH, et al. Persistent cannabis users show neuropsychological decline from childhood to midlife. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):E2657-64. PubMed PMID: 22927402;

2: Higgins JPT and Green S. Cochrane Handbook for Systematic Reviews of Interventions, Version 5.1.0, revised March, 2011

On 2015 Apr 22, Fillip Port commented:

I would like to add that inadvertent integration of a bi-cistronic plasmid, such as the one reported here, into the gRNA target site would create an autonomous gene drive. Genomic integration in the absence of homology arms is expected to be a rare event, but has been reported before. I would therefore suggest to take such a possibility into account. Further reading: PMID:25035423; http://biorxiv.org/content/early/2015/04/01/017384; http://www.sciencemag.org/content/early/2015/03/18/science.aaa5945.abstract.

On 2014 Oct 29, Fillip Port commented:

The following comment was initially posted on the technology blog igtrcn.org

As is the case for many other organisms, CRISPR has rapidly become the method of choice for targeted genome modification in insects. Much of the method development has been taking place in the model organism Drosophila melanogaster, where, in little over a year, 17 publications have demonstrated various ways to harness the CRISPR system for fly genome editing.

However, this flurry of papers has not resulted in a consensus about which protocol is best suited to modify the fly genome, not least because each method comes with certain strengths and weaknesses. CRISPR components – i.e. the Cas9 endonuclease and short gRNAs - can be delivered into fly embryos by microinjection of either plasmid DNA, in-vitro transcribed RNA or purified protein. Microinjection is the most rapid way to introduce CRISPR components into flies and is independent of genetic background, but often suffers from a high degree of variability that leads to overall reduced efficiency. In contrast, transgenic CRISPR in which both Cas9 and gRNAs are expressed from previously integrated transgenes results in reproducible gene targeting at very high rates, but generating the transgenes in the first place is a time consuming process that makes this approach rather slow. Since all gene targeting experiments require Cas9, a popular compromise is to inject gRNA into cas9 expressing transgenic embryos. This approach benefits from good success rates due to the reliable source of Cas9, and is as rapid as microinjection of both components once a lab has acquired one of the publically available cas9 lines.

Now Peter Duchek and colleagues (Gokcezade et al. 2014) present a new protocol for microinjection-based CRISPR in Drosophila melanogaster. The method uses microinjection of DNA plasmids, but rather than injecting a mix of two plasmids encoding Cas9 and gRNA as was done previously, they combine both components on a single plasmid. This small change proves an effective one. In their paper Gokcezade et al. present data from targeting five genes and achieve efficiencies of around 10% mutant offspring when monitoring random InDel mutations and around 5% for precise genome modifications by homology directed repair.

Efficiencies of that range start to make it practical to screen for mutations by PCR based assays, a requirement for scarless genome engineering without the use of visible markers. If such high efficiencies can be routinely achieved on more target genes and in different laboratories then the method presented by Duchek and colleagues will present an attractive alternative to gRNA injections into transgenic cas9 embryos. This is particularly good news for researchers working on insects where transgenic cas9 strains are not available or for those who want to modify a specific genetic background of D. melanogaster. However, in another recent paper Frank Schnorrer and colleagues use the bi-cistronic plasmid presented in Gokcezade et al. to knock-in a RFP selection cassette into the Drosophila genome and achieve efficiencies that are substantially lower than the ones reported in Gokcezade et al. (Zhang et al., 2014, G3, PMID:25324299). This might be because of the larger size of the integration cassette, different target genes and gRNAs or differences in the microinjection procedure.

Like with all other CRISPR protocols proposed today, it will be interesting to see how the bi-cistronic cas9/gRNA plasmid fares in the hands of other insect genome engineers. To aid this Gokcezade et al. have made their plasmids available from the non-profit repository Addgene (Plasmid number 59984 and 59985).

On 2015 Dec 27, Gwinyai Masukume commented:

In the Introduction it is written, "Currently, health expenditure accounts for 4.6% of the Gross Domestic Product."

South Africa spent between 8.5 - 9% of Gross Domestic Product on health expenditure, 2001 - 2015. THE WORLD BANK - Health expenditure, total (% of GDP)

On 2014 Sep 24, Jim Woodgett commented:

Interesting study and raises a number of questions. I wonder if MVB sequestration is a rescue/escape mechanism in cells to deal with constant signalling (since the initial studies used a constitutively active LRP6 variant)? I always wondered why so much (80+%) GSK-3 was reported to be sequestered when we could only ever find 5% of the entire cellular content of this kinase associated with Axin.

P.S. GSK-3alpha plays an equal role in Wnt signalling in mammals, although there is no equivalent in Drosophila. No small molecule inhibitor is able to discriminate between the GSK-3 isoforms (despite extensive literature).

On 2016 Sep 14, Kevin Hall commented:

An Erratum for this article was published 10 AUG 2016 DOI: 10.1002/oby.21634.

We recently identified an error in the measured resting metabolic rate (RMR) data in participants of “The Biggest Loser” competition (BLC) at 7 months. In Table 1, the corrected RMR at 7 months in BLC is (mean ± SD) 1967 ± 331 kcal/d such that there was a significant metabolic adaptation of −308 ± 165 kcal/d (P<0.0001) that was not significantly different from metabolic adaptation in Roux-en-Y gastric bypass surgery (RYBG) patients at 6 months (P=0.118). The corrected RMR at 7 months in BLC was significantly different from measured RMR in RYGB at 6 months (P<0.05). Figure 2 was corrected in the published Erratum.

Metabolic adaptation was significantly correlated with energy imbalance (r=0.72, P<0.0001), rate of weight loss (r=0.67, P=0.0002), and percent change in leptin (r=0.52, P=0.006) in combined BLC at 7 months and RYGB at 1 year. Similarly, when including RYGB data at 6 months, metabolic adaptation was significantly correlated with energy imbalance (r=0.62, P=0.0001), rate of weight loss (r=0.61, P=0.0001), and percent change in leptin (r=0.38, P=0.02). Figure 3 was corrected in the published Erratum. Finally, the authors previously reported a non-significant association between metabolic adaptation and changes in T3; however, the corrected data demonstrate a trend for a positive association between metabolic adaptation and changes in T3 (r=0.48, P=0.06). The authors regret this error.

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13776?shared_access_token=fMVtUmzLTKsGdrY8ug0-MdRgN0jAjWel9jnR3ZoTv0MkNtytsQI8CrxALVSINUBXvrtPrDww46idbEIbq9tEM9pcRtzbcW-BZUxCCN1TU-l6YirUq5Z3zzofA_hjpoe1_RNiEbzs48Gyn0fpn0qckc5ViYvsDvFyfbUI01fos2iX76CCaivFA0CDEk0X8N4mEEsKamvynFg0TIWzPmClU0N59nciGTVGbckfrGWiekQ=

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13775?shared_access_token=XkFK-FGuyU9OCZD5dwA6JtRgN0jAjWel9jnR3ZoTv0Of-Ay0arX2-wZ07ZoCpD0eycCn7er0iLlXFSSijJFd-1l-LXcuvFEwenumzV16fwW2TwHrpJ8GocXfmbXiq2ny8bisr28X4o_YPXEKvnROC2LRUjaqBME14AvHcYcZH3f9djLHkKhioJeDl15WD27MAUloTQiQ3WRMlcPC_TbF5R-UMXzJA7yUKPj9Xz0nXrA=

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 NCT0192052. We believe the correct ID, which we have found by hand searching, is NCT01920529.

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 Mar 24, Michelle Lin commented:

Video interview with first author, Dr. Rebecca Smith-Bindman (UCSF Department of Radiology), and co-author Dr. Ralph Wang (UCSF Department of Emergency Medicine) hosted at the Academic Life in Emergency Medicine website. In this video, questions and nuances in this landmark paper were addressed.

http://www.aliem.com/author-insight-ultrasonography-versus-ct-for-suspected-nephrolithiasis-nejm/

Four questions were posed:

• Q1: About 1/3 of patients in the ultrasound study arms eventually went on to get CT’s in the same ED stay. What would you recommend to clinicians about when that should be?

• Q2: Can you address generalizability issues in this 15-center study whereby the cohort has 40% with a history of previous kidney stones and only 60% demonstrating microscopic hematuria. Also what are your recommendations for obese patients (men >280 lb, women >250 lb) who were excluded from your study? CT them all?

• Q3: What has been the feedback from urologists since the paper was published? What are the drivers of CT ordering?

• Q4: What’s next? What’s NOT in your paper?

Ultimately, this paper advocates for bedside ultrasonography over CT as the first-line diagnostic modality for patients with suspected kidney stones. In this 15-center study, the ~1800 ultrasounded patients had good primary and secondary outcomes despite the fact that 2/3 did NOT undergo a CT in the first ED visit.

On 2014 Nov 02, Swapnil Hiremath commented:

This study was discussed on Oct 7th 2014 in the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available at the NephJC website and cross-posted at the eAJKD blog. It was a great discussion, with more than 20 participants, including nephrologists, urologists and emergency medicine physicians. A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website. A summary is also posted on the eAJKD blog. The highlights of the tweetchat were:

• The investigators and the funding agency (AHRQ) should be commended for designing and funding this pragmatic trial to answer a key diagnostic question

• There was broad agreement about the validity of the results, suggesting that an ultrasound should be performed first in case of suspected kidney stones; however, many participants look forward to more data being published, on patient characteristics that predicted subsequent CT scan use and details of the economic analysis

• A concern was raised about the availability of point-of-care ultrasound in emergency departments, and the expertise and/or experience necessary to do these. It was recognized that this expertise is indeed rapidly becoming the standard for emergency room physicians

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

On 2014 Sep 30, Ryan Radecki commented:

Post-publication commentary:

"Farewell, CT Stone Protocol"

Ureterolthiasis has become a poster child for over-utilization of advanced imaging. Despite the relative level of distress kidney stones cause our patients, the use of computed tomography has never been associated with improved outcomes – yet, CT is widespread for its diagnostic utility, contributing substantially to $2 billion in annual healthcare expenditures for this condition in the U.S. alone.

This, however, is a comparative effectiveness evaluation promoting ultrasound for the diagnosis of ureterolithiasis in the Emergency Department, a three-pronged evaluation comparing CT, formal ultrasonography by radiology technicians, and bedside Emergency Department ultrasonography. Essentially, the objective of this study was to compare safety – regarding, in a sense, whether the additional information supplied by CT was valuable for the detection of life-threatening alternative diagnoses. And, with respect to this outcome all strategies had, essentially, the same number of “misses” during the follow-up period – mostly acute cholecystitis, one case of appendicitis, and a smattering of other thoracoabdominal diagnoses. And so – ultrasonography, even our amateur sort in the ED, is "just as good"....

http://www.emlitofnote.com/2014/09/farewell-ct-stone-protocol.html

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 NCT10528605. We believe the correct ID, which we have found by hand searching, is NCT01528605.

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 2014 Sep 21, David Keller commented:

Was the ulcerative colitis patient status post colectomy, or taking corticosteroids during treatment with ipilimumab?

In the case of the ulcerative colitis patient who tolerated ipilimumab and achieved partial remission of metastatic melanoma, this abstract does not indicate whether this patient was status post colectomy, or taking corticosteroids while being treated with ipilimumab. Ipilimumab treatment is associated with a high risk of autoimmune enterocolitis. This is important information for other patients with autoimmune diseases contemplating treatment with ipilimumab for metastatic melanoma.

On 2014 Oct 09, Arturo Casadevall commented:

We thank Joshua L. Cherry for the additional comments. We also feel that our original response applies to much of the new comments but will try again to clarify our answers. As we have done previously, we copy Joshua L. Cherry’s comments and respond below.

Joshua L. Cherry states “We have all encountered writing that refers to science or its subfields and uses scientific language but lacks scientific content. The editorial does something similar with respect to philosophy. It defines epistemology and makes use of its vocabulary, but the arguments that it makes are not epistemological. The only general principle about knowledge that it invokes is the Faberite notion that knowledge is good. This is not an epistemological proposition or a philosophical insight, nor a revelation to scientists”.

We feel that Joshua L. Cherry misses the point in continuing to argue that our essay is not about philosophy and its branch epistemology. GOF experiments are the gold standard for acquiring certain times of information including the capacity of a virus to become mammalian transmissible. GOF experiments are accepted methodology in the field and commenting on their power and their standing within the normative standards of the field of molecular microbiology clearly constitutes epistemological content for scientific methodology is part of the epistemology of science. These experiments provide information with the highest standard of rigor that is unobtainable in any other way.

Joshua L. Cherry states that “The benefits of GOF experiments commonly discussed are indeed benefits of the resulting knowledge. (What else would they be? The economic benefits of creating employment for laboratory personnel?) These have mostly been supposed direct practical applications of this knowledge for preventing human H5N1 infections. The response above suggests that the authors intended to emphasize “the many other possible future uses of that knowledge, some of them practical, but some of them purely theoretical”. As I stated, most or all scientific knowledge has many possible future uses, and it is common knowledge, not a philosophical insight, that science works this way.”

We have no disagreement with this paragraph although we note that if this is indeed ‘common knowledge’ then we have trouble understanding why it is necessary for us to point this out in the context of weighing the epistemic value of GOF experiments.

Joshua L. Cherry states that “Exceptional risks demand exceptional benefits. Satisfaction of normative standards does not imply exceptional benefits. The authors indeed make a logical leap in concluding that GOF experiments must be powerful because they share certain formal properties with experiments that proved to be powerful. The literature is filled with results of experiments that meet these normative standards, with importance ranging from great to nearly nil. Thus, we must consider the value of these particular experiments, using scientific reasoning and judgment. That is exactly what most of the debate has been concerned with.”

We see several problems with this paragraph. First, there is no evidence that the experiments done carry ‘exceptional risks’. These have been done in laboratories with rigorous biosafety protocols and high level bio-containment capabilities. Furthermore, we do not know whether transmissibility in Ferrets confers transmissibility in humans. Second, we never argued that GOF experiments yielded "exceptional benefits," alone capable of balancing exceptional risks. Instead, we merely argued that the epistemological value of GOF experiments must be part of the bookkeeping, and we questioned the objectivity of the claimed exception character of the risk. These experiments have already provided important information regarding the biological potential of highly pathogenic avian influenza virus to acquire the capacity for mammalian transmissibility. We did not assign a specific value to this epistemic gain: we simply argued that it needed to be part of the risk-benefit analysis. We have no problem with the comment that “we must consider the value of these particular experiments, using scientific reasoning and judgment” and if Joshua L. Cherry feels that this “is exactly what most of the debate has been concerned with” then we are mostly on the same page.

On 2014 Oct 02, Joshua L Cherry commented:

I thank the author(s) for responding. My original comment applies to much of the response, but a few points should be clarified.

We have all encountered writing that refers to science or its subfields and uses scientific language but lacks scientific content. The editorial does something similar with respect to philosophy. It defines epistemology and makes use of its vocabulary, but the arguments that it makes are not epistemological. The only general principle about knowledge that it invokes is the Faberite notion that knowledge is good. This is not an epistemological proposition or a philosophical insight, nor a revelation to scientists.

The benefits of GOF experiments commonly discussed are indeed benefits of the resulting knowledge. (What else would they be? The economic benefits of creating employment for laboratory personnel?) These have mostly been supposed direct practical applications of this knowledge for preventing human H5N1 infections. The response above suggests that the authors intended to emphasize “the many other possible future uses of that knowledge, some of them practical, but some of them purely theoretical”. As I stated, most or all scientific knowledge has many possible future uses, and it is common knowledge, not a philosophical insight, that science works this way.

Exceptional risks demand exceptional benefits. Satisfaction of normative standards does not imply exceptional benefits. The authors indeed make a logical leap in concluding that GOF experiments must be powerful because they share certain formal properties with experiments that proved to be powerful. The literature is filled with results of experiments that meet these normative standards, with importance ranging from great to nearly nil. Thus, we must consider the value of these particular experiments, using scientific reasoning and judgment. That is exactly what most of the debate has been concerned with.

On 2014 Oct 01, Arturo Casadevall commented:

We thank the writer for his comments. The writer is critical of several of the statements in our editorial. We respond to each individually:

Joshua L Cherry states that: ‘The arguments are framed in philosophical terms, but there is no philosophical content, and the underlying question is one of scientific judgment.’

We found this comment puzzling. Our paper includes discussion on two of the branches of philosophy: epistemology and ethics (by the writer’s own admission). Framing the GOF experiments within the normative standards of the field microbiology explores how we seek knowledge in the area. This together with discussion of ethical issues constitutes philosophical content.

Joshua L Cherry states that: “[W]hen one does a risk-benefit analysis of this issue, the epistemic gain from GOF experiments should be included in the bookkeeping: if one does that, the benefits of GOF experiments are potentially so great as to warrant our risking more than we otherwise might.” This is a puzzling assertion. All of the benefits that have been considered are benefits of the resulting knowledge (“epistemic gain”). Perhaps the authors mean to refer to an intrinsic good of having knowledge, independent of any practical applications. If so, it is possible, and helpful, to state this more plainly, as I have just done. If there is a philosophical issue here, it is one of ethics, not epistemology. Perhaps the authors are referring to the practical value of the knowledge beyond its direct applicability to the case at hand. In either case the argument is weak. These are common properties of experiments, not special properties of potentially dangerous GOF experiments. The resources used for such experiments could be reallocated to other experiments that lack the serious safety concerns yet also have epistemic value (on any meaning), and quite possibly more of it.’

The writer states that ‘all the benefits that have been considered are benefits of the resulting knowledge’. This is not the case. A reading of our paragraph describing the knowledge gained from GOF experiments considers the information that highly pathogenic avian influenza viruses can become mammalian transmissible useful because it provides a warning that these viruses have the biological potential to acquire this property. Prior to these experiments there was debate as to whether these viruses could become transmissible. Now we know that they can and that is a clear epistemic gain. But that epistemic gain goes beyond the utilitarian gain from any immediate application of this new knowledge, in part because of the many other possible future uses of that knowledge, some of them practical, but some of them purely theoretical. We have no disagreement with the notion that the subject of ethics is interwoven into considerations for GOF experiments. However, the idea that we should reallocate resources away from this type of work would accomplish nothing in helping us prepare against an influenza pandemic. As the currently developing Ebola epidemic in West Africa shows us we must continue research into highly dangerous pathogens for it is knowledge in medicine and science that provide the defenses against new threats from nature.

Joshua L. Cherry states that: ‘The authors make much of the claim that the GOF experiments meet the “normative standards of the fields of microbiology and infectious diseases”. This is faint praise for experiments that, many fear, might cause pandemics. We might question the merits of these standards, despite their being normative, and might ask whether they are sufficient conditions for value, or merely necessary. Even putting those questions aside, at best this point establishes that the experiments have nonzero value, not that they are exceptionally powerful, as must be the case to justify exceptional danger. Again, there are plenty of other experiments that also satisfy these standards without posing the same threat.’

Meeting the normative standards of the fields of infectious diseases and microbiology is high praise for GOF experiments for these fields have delivered some of the greatest successes in medicine. The writer appears to be mixing two issues that are very different: the fear and the power of GOF experiments. Fear can be minimized with strict laboratory safeguards that greatly reduce the likelihood of accidents. With regards to the power of GOF experiments, these have already taught us that highly pathogenic avian influenza virus has the capacity for mammalian transmission, as noted above. Since mammalian transmission is necessary for a pandemic this information is incredibly important. Humanity now stands warned that with a few sequence changes H5N1 influenza virus can acquire the property of mammalian transmissibility. The writer states that ‘there are plenty of other experiments that also satisfy these demands without posing the same threat’ but provides no examples. In fact, we counter that there is no other technology or mechanism short of waiting for epidemic to occur that could have provided this information. If there were, it is likely that a scientist would have pursued it by now. Hence, we stand by the words that these experiments are exceptionally powerful and that we lack alternatives if we are to seek certain types of knowledge.

Joshua L. Cherry states that: The editorial seems to suggest such fallacious reasoning as this: The discovery that HIV causes AIDS established a cause-and-effect relationship about a pathogen and was very powerful; GOF experiments have established cause-and-effect relationships concerning pathogens; therefore, GOF experiments are very powerful.

The key word here is “seems”: it is unclear how the writer infers this from what we wrote. GOF experiments trace their ancestry to the powerful scientific techniques that that have been responsible for some of the greatest successes in medicine including establishing disease causation and intervening against such diseases with vaccines and drugs. GOF experiments are fully within the normative standards of microbiology and molecular biology and as such they are incredibly powerful investigative tools that humanity can use to learn about microbial threats. As noted above GOF experiments have already produced highly valuable information that is not available from any other source.

On 2014 Sep 23, Joshua L Cherry commented:

This editorial purports to offer new considerations that favor the continuation of potentially dangerous “gain of function” (GOF) experiments with pathogens with pandemic potential. The arguments are framed in philosophical terms, but there is no philosophical content, and the underlying question is one of scientific judgment. The philosophical language serves only to obscure and to create the illusion that a new consideration is being introduced.

The authors state that

“[W]hen one does a risk-benefit analysis of this issue, the epistemic gain from GOF experiments should be included in the bookkeeping: if one does that, the benefits of GOF experiments are potentially so great as to warrant our risking more than we otherwise might.”

This is a puzzling assertion. All of the benefits that have been considered are benefits of the resulting knowledge (“epistemic gain”). Perhaps the authors mean to refer to an intrinsic good of having knowledge, independent of any practical applications. If so, it is possible, and helpful, to state this more plainly, as I have just done. If there is a philosophical issue here, it is one of ethics, not epistemology. Perhaps the authors are referring to the practical value of the knowledge beyond its direct applicability to the case at hand. In either case the argument is weak. These are common properties of experiments, not special properties of potentially dangerous GOF experiments. The resources used for such experiments could be reallocated to other experiments that lack the serious safety concerns yet also have epistemic value (on any meaning), and quite possibly more of it.

The authors make much of the claim that the GOF experiments meet the “normative standards of the fields of microbiology and infectious diseases”. This is faint praise for experiments that, many fear, might cause pandemics. We might question the merits of these standards, despite their being normative, and might ask whether they are sufficient conditions for value, or merely necessary. Even putting those question aside, at best this point establishes that the experiments have nonzero value, not that they are exceptionally powerful, as must be the case to justify exceptional danger. Again, there are plenty of other experiments that also satisfy these standards without posing the same threat.

Through reference to “normative standards”, the authors make an unjustified connection between GOF experiments and such important findings as the discovery that HIV causes AIDS. They tell us that “GOF experiments are very powerful because such experiments can give direct information on cause-and-effect relationships” about infectious agents. In reality, not all experiments that provide such information are “very powerful”. The editorial seems to suggest such fallacious reasoning as this: The discovery that HIV causes AIDS established a cause-and-effect relationship about a pathogen and was very powerful; GOF experiments have established cause-and-effect relationships concerning pathogens; therefore, GOF experiments are very powerful.

Debate about GOF experiments has always been about whether the value of the knowledge they might yield is sufficient to justify their risks. Many claims for particular benefits have been abandoned, and some have been undermined by arguments put forth to downplay safety concerns. Referring to knowledge as “epistemic gain” adds nothing to the debate.

On 2014 Sep 17, Attila Csordas commented:

associated dataset available via PRIDE/ProteomeXchange: http://www.ebi.ac.uk/pride/archive/projects/PXD000661

On 2016 Aug 17, Mohammed AlJasser commented:

I have noticed that the language in which this article was written was labelled as Hebrew. However, the text is written in Arabic.

Thank you.

On 2017 Jan 11, Vinay Pasupuleti commented:

The abstract was erroneously deleted by journal editors and was published as an erratum at a later date. The full text clearly mentions that 6 articles were included (one article had results from a retrospective cohort study as well as a prospective cohort study)....therefore, a total of 7 observational studies. Total N in Table 1 is 102,767 as mentioned in the abstract (351+58+625+27+1848+246+170+160+96806+322+1077+1077 = 102,767).

On 2016 Jul 04, Swapnil Hiremath commented:

Looks like the abstract was erroneously deleted, see the erratum.

On the other hand, the point about number of studies is valid (6 in full text, 7 in abstract) - also the total N in full text (from table 1) adds up to > 200,000, compared to 102, 767 above in abstract. Does need to be clarified and addressed by the authors, in my opinion.

On 2016 Jun 30, Gabriel Rada commented:

This abstract contains several mistakes, most of them minor formatting issues. However, it states there are 7 included studies, when the actual number reported in the full text is 6. On the other hand, there is no abstract in the journal website, so it seems it was created for indexing purposes. I don't see any indication of this abstract being 'in process' in Pubmed/MEDLINE. My main issue is who is responsible of the information displayed here? The publisher or Pubmed?

On 2014 Sep 19, Ian Dworkin commented:

In addition to all of the data and scripts for analysis being available at Dryad, we have also made it available on github as a repository. https://github.com/DworkinLab/PitchersJEB2014_cricket_wings

On 2014 Sep 16, Mohamed Soliman commented:

I think this can be a subject of a prospective study to clarify this issue.

On 2014 Dec 17, Sean Ekins commented:

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

On 2014 Dec 02, Ross Mounce commented:

If you're not blind or visually-impaired you can read the full-text of this article here: http://www.readcube.com/articles/10.1038/nature13704?shared_access_token=yHbnKF1lQFfG6Yqg_0gr2tRgN0jAjWel9jnR3ZoTv0Npz8zRHm1DgGX6oHtfBFPcgnPUjlPawFWnxeOTbLrOjGH7l3QlaEbnesc2IXtHTVeOuMZDQmqTT1RwKvWt4cAzxfDdjGfUP69A9Nf_tsDhVyBIs8FPRuBKNpKDNqaeyuJ5LXzTuwk2lutlAMO8YfELzhepvyjx-hWRLbdqmtGvS4XaEtKELfoAAphhAFk0RmY=

On 2014 Oct 11, Igor Zwir commented:

Pre-selected SNPs The list of 2,891 pre-selected SNPs from the MGS study (1) utilized in (2) (see supplemental material) is available at http://m4m.ugr.es/resources/2891-SNP-PreSelection.txt. This list contains 99% of the SNPs reported in the supplemental material of (1).

(1) Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R, Gejman PV. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 2009;460I:753-7.

(2) Arnedo J, Svrakic DM, del Val C, Romero‑Zaliz R, Hernández-Cuervo H, Molecular Genetics of Schizophrenia Consortium, et al. Uncovering the Hidden Risk Architecture of the Schizophrenias: Confirmation in Three Independent Genome-Wide Association Studies. American J of Psychiatry 2014 (in press);172:1–15. Epub 9/15/2014.

On 2014 Oct 07, Igor Zwir commented:

Interdisciplinary work not so fast … Geneticist with a statistic background vs. engineers/computer scientists with a genetic background

Unfortunately, interdisciplinary works have been concurrently stimulated and frozen at the same time. Much of this contradiction is due to the lack of universal reviewers that know about everything. Science is specialized, in terms of education and consequently in terms of results. For example, most studies of complex disorders usually focus on single sources of data (genetics, neuroimages), eliminating the possibility of having complementary perspectives of the patients. In addition, there is a sort of disrupted communication between the biomedical researchers and math or computer science investigators. Biologist and physicians use to search for articles in pubmed (http://www.ncbi.nlm.nih.gov/pubmed), however, most of the engineers look for the Institute of Electrical and Electronics Engineers (IEEE) communications (https://www.ieee.org) and many of them ignore Pubmed. In contrast, many molecular biologists ignore what IEEE exists and what it represents. There are few IEEE publications that are available in pubmed and most of them are old. However, many of those that are not in Pubmed are much more rigorous than any method proposed in the best biomedical journals. This comment encourages both Pubmed and IEEE sites to solve their differences, which in turn, will help to have more and more informed reviewers for novel techniques in the post genomic era.

On 2014 Oct 07, Igor Zwir commented:

Rationale of the method applied in Arnedo et. al.

Clustering methods have been applied for long time in pattern recognition problems and in a variety of fields and actually are embedded in most of our devices, from a simple refrigerator to a Boing engine. In biomedical sciences there is a trend of considering that few classes of clustering exist (e.g., hierarchical cluster of K-Means). However, datamining, knowledge discovering, and machine leaning are fields of computer sciences with very rich and different either theoretical or empirical methods. Much of the power of these methods is based on the fusion of them, taking advantages of each one.

The methodology and framework proposed in this Arnedo et. al encodes a generalized factorization method (GFM) that was designed to identify structural patterns or clusters (substructures) that characterize complex objects (1-8) embedded in databases (6, 7, 9, 10). Unfortunately, solving these kinds of complex problems cannot be performed by a single clustering method but utilizing and combining the advantages of many of them, as were implemented in the GFM and summarized below.

First, we utilized the notion of Model-based clusters (5, 11, 12), where the centroid/prototype of a cluster is not a point but a model (e.g., line segment, ellipsoids, (5, 13, 14) or see C-varieties algorithm (12)) -or a family of models (8) - defined as a relation between cohesive subset of points that meet certain constraints (e.g., Relational clustering (12), undirected graph (12)). When the subjacent equations of the models are unknown, they can be estimated from the data by identifying relations between subsets of observations that show similar patterns under a specific subset of relevant descriptive features (attributes) (4, 5, 15). Here we proposed that in a pure data driven analysis these unknown models (grey boxes) can be learned as local relationships between subsets of features and observations, which are termed biclusters. The biclusters are often represented as sub-matrices (4, 5, 15). Other models proposed in this work (black boxes) consist of those that are encoded by a particular method devoted to recognize certain classes of patterns.

Second, to identify a family of models (8) or biclusters we planned the use of the NMF (16) factorization algorithms (tensor analysis), which can uncover cohesive data represented as sub-matrices (factors). When sorted and thresholded, each sub-matrix represents a bicluster. Notably, biclustering produces several local models of the data (17), each one capturing intrinsic relationships between subsets of observations sharing subsets –instead of all- features. Diverse biclusters –instead of uniform data explanations- provide a better understanding of the described object that is diluted when together, all features are used in a single global model of data typically performed by clustering methods (17).

Third, we proposed in this work that biclusters can be fuzzy (overlapping, see Fuzzy clustering (18)), where voxels and/or subjects can belong to more than one bicluster), as well as possibilistic (non-exhaustive partitions, see Possibilistic clustering (12)), where certain voxels and/or subjects may not be assigned to any bicluster, and thus, outliers can be detected.

Fourth, we demonstrated that biclusters could be identified without choosing a priori a particular number of clusters (11, 13, 14, 19). Setting this parameter as a small number may eventually generate few but large data partitions here defined as general biclusters that may underfit the data. In contrast, using a big number of clusters will generate many clusters with partitions of small size (i.e., more granular partitions) here defined as specific biclusters that may overfit the data (1, 5, 11, 13, 14, 19-21). Although there are many different validity indices (12, 18) that suggest the best number of clusters for a given dataset, they often produce contradictory results (11, 13, 14, 19). This problem is exacerbated when Centroid-based (e.g., k-means, NMF) or Distribution-based clustering (e.g., EM) is utilized because two successive numbers of clusters may generate completely different cluster arrangements (see (12, 18) for a review). Instead of fighting over the lost battle of uncovering a single optimal number of clusters, biclusters were calculated from partitions generated by all number of clusters between 2 and √n (12), where n is the number of observations (subjects). We postponed the selection of the best clusters until all partitions were examined to select a set of clusters that together provide an optimal description of the sample. These clusters could be chosen from different partitions that were generated by different number of clusters (see Consensus clustering (1, 5, 11, 13, 14, 19-21)).

Fifth, formulation of the bicluster identification problem from different partitions may produce redundant, excessively specific and/or excessively general biclusters (4, 5, 15, 22, 23). To select optimal biclusters, we proposed a GFM that performs the following Consensus clustering strategy: (i) eliminates all redundant biclusters by comparing the similarity between their subjacent sub-matrices using Hypergeometric statistics (see Methods and Material in Supplement 1), and selecting only one representative bicluster from each set of equivalent sub-matrices. Biclusters harboring <10% of the total number of subjects were not considered to avoid a trend to obtain singleton biclusters. (ii) From the non-redundant biclusters, GMF selects all biclusters that are optimal in terms of specificity, generality and diversity. To do so, it selects all non-dominated biclusters where one bicluster is not worse (i.e. dominated) than another in both objectives: specificity and generality (4, 5, 15, 22, 23). Moreover, to ensure diversity, GMF applies the non-dominance metric only among biclusters within a neighborhood (22, 23) (i.e., biclusters with a relatively high overlapping of subjects and voxels with). This Multiobjective and Multimodal optimization process is analogous to Minimum Description-Length methods (24) and was carried out as described in (1-8). (iii) The remaining optimal biclusters are hierarchically organized by inclusion of their subjects into connected or disjoint hierarchies (i.e., subgraphs or subnetworks).

Sixth, and after the first step of identifying interesting patterns describing objects embedded in the data, we went one step further by also finding characteristic descriptions for each group, where each group represents a concept or class using Conceptual clustering. In this work we incorporated factors such as the generality and simplicity of the derived bicluster descriptions by (1) relational clustering validation against data driven independent descriptions obtained in other domains of knowledge, and (2), incorporate the previous structured knowledge into predictive multiclassifiers mixing machine learning and multiobjetive optimization techniques.

On 2014 Oct 07, Igor Zwir commented:

References

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16. Pascual-Montano A, Carazo JM, Kochi K, Lehmann D, Pascual-Marqui RD (2006): Nonsmooth nonnegative matrix factorization (nsNMF). IEEE transactions on pattern analysis and machine intelligence. 28:403-415.
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On 2014 Oct 07, Igor Zwir commented:

None

On 2014 Oct 07, Igor Zwir commented:

None

On 2014 Oct 07, Igor Zwir commented:

None

On date unavailable, commented:

None

On 2014 Oct 06, C. Robert Cloninger commented:

References

1. Arnedo J, Svrakic DM, Del Val C, Romero-Zaliz R, Hernandez-Cuervo H, Fanous AH, et al. Uncovering the Hidden Risk Architecture of the Schizophrenias: Confirmation in Three Independent Genome-Wide Association Studies. The American journal of psychiatry. 2014.
2. Arnedo J, del Val C, de Erausquin GA, Romero-Zaliz R, Svrakic D, Cloninger CR, et al. PGMRA: A web server for (Phenotype X Genotype) many-to-many relation analysis in GWAS. Nucleic Acids Res. 2013(Web Server issue). PMCID: 2447763.
3. Risch N. Linkage strategies for genetically complex traits. I. Multilocus models. American journal of human genetics. 1990;46(2):222-8. PMCID: 1684987.
4. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014;511(7510):421-7. PMCID: 4112379.
5. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. American journal of human genetics. 2007;81(3):559-75. PMCID: 1950838.
6. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, et al. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 2009;460(7256):753-7. PMCID: 2775422.
7. Graves JA. Review: Sex chromosome evolution and the expression of sex-specific genes in the placenta. Placenta. 2010;31 Suppl:S27-32.
8. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, et al. Linkage disequilibrium in the human genome. Nature. 2001;411(6834):199-204.
9. Slatkin M. Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. Nat Rev Genet. 2008;9(6):477-85.
10. Wiehe T, Slatkin M. Epistatic selection in a multi-locus Levene model and implications for linkage disequilibrium. Theor Popul Biol. 1998;53(1):75-84.
11. Pritchard JK, Donnelly P. Case-control studies of association in structured or admixed populations. Theor Popul Biol. 2001;60(3):227-37.
12. Koch E, Ristroph M, Kirkpatrick M. Long range linkage disequilibrium across the human genome. PLoS One. 2013;8(12):e80754. PMCID: 3861250.
13. Wright S. The shifting balance theory and macroevolution. Annual review of genetics. 1982;16:1-19.
14. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, et al. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet.86(6):929-42. PMCID: 3032061.
15. Zwir I, Shin D, Kato A, Nishino K, Latifi T, Solomon F, et al. Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. Proc Natl Acad Sci U S A. 2005;102(8):2862-7.
16. Zwir I, Huang H, Groisman EA. Analysis of Differentially-Regulated Genes within a Regulatory Network by GPS Genome Navigation. Bioinformatics. 2005;21(22):4073-83.
17. Romero-Zaliz R, Del Val C, Cobb JP, Zwir I. Onto-CC: a web server for identifying Gene Ontology conceptual clusters. Nucleic Acids Res. 2008;36(Web Server issue):W352-7.
18. Romero-Zaliz R, C. Rubio R, Cordón O, Cobb P, Herrera F, Zwir I. A multi-objective evolutionary conceptual clustering methodology for gene annotation within structural databases: a case of study on the gene ontology database. IEEE Transactions on Evolutionary Computation . 2008;12:6:679-701.
19. Harari O, Park SY, Huang H, Groisman EA, Zwir I. Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria. PLoS Comput Biol. 2010;6(7):e1000862. PMCID: 2908699.
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On 2014 Oct 06, C. Robert Cloninger commented:

Conclusion

We appreciate the opportunity to clarify the fundamental differences between the assumptions and goals of traditional GWAS and our novel approach that addresses the complexity of common disorders with sophisticated and well-validated machine-learning and data-mining methods. We hope that the profound differences in the approaches with which Breen and colleagues are familiar and those developed by us should stimulate greater understanding of the challenges faced by the fields of psychiatric and medical genetics. We recognize that this new approach will cause a period of reexamination of standard methodology in this field, but every major advance in genetics, and in all of science for that matter, has always required flexibility and creative thinking. There are always things that we can improve upon in any method, and we recognize that many incremental improvements are essential for the advance of science.

We have put forth a new data-driven method that allows the uncovering of complex genotypic-phenotypic relations when they are present without imposing this as an a priori assumption. We uncovered relationships are in fact highly complex, which allowed us to identify individuals at high risk and to associate specific SNP clusters with specific clinical syndromes despite the presence of extensive pleiotropy and heterogeneity. This approach, like all those that have preceded it, is undoubtedly imperfect and will also require refinement and may ultimately give way to yet another approach that will explain more. Such methodological evolution is nothing more than the typical course of advancement in science. We hope that these exciting developments will lead to new ways to push the boundaries of accepted science, and help us to question a priori assumptions that restrict our understanding of all the information embedded in data.

If this discussion has shown us nothing else, it is that this process of questioning and reflection has already begun. Ultimately, beyond all of the technical issues, our main goal is to help those in need. With schizophrenia, we know the need is great from the tremendous outpouring of requests for guidance and help that we have received, and we know that there are many people with other diseases who may benefit from our new approach. We can all be comforted knowing that our debate can bring us closer to doing what we are really here to do – that is, helping those suffering from debilitating diseases and finding ways to promote their health and well-being. Whatever path leads us there is worth considering. So let us not permit our philosophical or scientific differences to prevent us from allowing for a sufficient diversity in our tactics, because we never know what path will lead us towards our common goals of improving health and reducing the burden of disease.

On 2014 Oct 06, C. Robert Cloninger commented:

The Facts about Replication and Significance Testing of SNP Selection

B-S expressed concern about our replication process. Of course in traditional GWAS, replication has always been a serious problem, which is the basis for the rationale of PGC to carry out meta-analysis of large collections of samples despite their heterogeneity and limited phenotypic description. It was most challenging for us to identify samples with adequate clinical description to apply our novel approach, but the reward was in identifying strong effects that replicated consistently across three samples, including the Portuguese Islands study that used the same diagnostic instrument in a specific ethnic sample. The samples were independently recruited and independently analyzed, as we stated clearly in the published report. SNP sets, phenotypic sets and associations were separately calculated for the three samples to avoid weighted or biased aggregations. Then, we used a well-known co-clustering test based on the hypergeometric distribution to establish the replicability of results from one sample in the other. This test has been used widely in molecular biology (15, 16, 25), and as a general strategy for validating clusters. For example, it has also been implemented into software packages such as TIBCO/Spotfire. The concerns expressed by B-S about replication have no reasonable justification. Thus we feel that the concerns expressed by B-S about replication are overstated and empirically unfounded. Again, the strength of this new approach is it allows us to avoid some of the major problems that plague traditional GWAS approaches.

B-S also expressed their concern about the use of a permutation test, claiming that "because SNP sets differ in allele frequency between cases and controls, this procedure does not generate a valid null distribution". The permutation test was used not to establish the significance of the SNP sets, which was evaluated by the SKAT method (14), but rather to test the validity (and approximate probability) of the association between SNP sets and symptom sets. Controls were not used in this test at all, as they have no symptoms of psychosis. Moreover, these symptoms were not even evaluated in the reported inventories. The misunderstanding of B-S is probably due to a lack of familiarity with this new statistical procedure, which highlights the previously discussed difficulties people have when first trying to understand a novel approach.