On 2016 Jul 07, GianCarlo Panzica commented:

Further comments on this topic are on Bourguignon JP, 2016 and Kortenkamp A, 2016

On 2016 Aug 22, Anthony Jorm commented:

The Royal Australian and New Zealand College of Psychiatrists (RANZCP) has recently published clinical practice guidelines on schizophrenia Galletly C, 2016, eating disorders Hay P, 2014 and mood disorders Malhi GS, 2015. These guidelines contain a mixture of evidence-based recommendations where there were relevant intervention studies, and consensus-based recommendations where relevant studies did not exist. The consensus-based recommendations comprised a substantial proportion of the guidelines for mood disorders (59%) and schizophrenia (46%), but less so for eating disorders (10%), indicating that expert consensus is an important source of guidance on best practice in psychiatry.

Given the substantial contribution of expert consensus to these guidelines, it is important that the methods for establishing this consensus are adequate. The Australian National Health and Medical Research Council (NHMRC) has published requirements for development of clinical practice guidelines, but these do not give much guidance on how this should be done, simply mandating that “The method used to arrive at consensus-based recommendations or points (e.g. voting or formal methods, such as Delphi) is documented”. (National Health and Medical Research Council. Procedures and requirements for meeting the 2011 NHMRC standard for clinical practice guidelines. Melbourne: National Health and Medical Research Council; 2011.)

Another potential source of criteria for evaluating the quality of methods for developing consensus-based recommendations comes from research on ‘wisdom of crowds’ Lorenz J, 2011 Kattan MW, 2016 Baumeister RF, 2016. Based on such research, Surowiecki has proposed four conditions necessary for a group to make good decisions (Surowiecki J. The wisdom of crowds: why the many are smarter than the few. London: Abacus; 2004.): 1. Diversity of expertise. A heterogeneous group of experts will produce better quality decisions than a homogeneous one. For guidelines developers, this may mean that the experts should come from a range of relevant disciplines, including consumer experts where appropriate. 2. Independence. The experts must be able to make their decisions independently, so that they are not influenced by others. For guidelines developers, this means that voting on consensus-based recommendations is carried out privately so that strong individuals cannot dominate the group. 3. Decentralization. Expertise is held by autonomous individuals working in a decentralized way. For guidelines developers, it is important to specify what sources of information the experts had available to them. 4. Aggregation. There is a mechanism for coordinating and aggregating the group’s expertise. For guideline developers, this could involve an independent person who runs the voting and gives feedback to the group.

If we take these four conditions as appropriate for judging the quality of methods for developing consensus-based recommendations, how well do the RANZCP guidelines meet them?

An indication of diversity of expertise is the disciplinary composition of the guideline working groups. There was limited diversity for all working groups, with non-psychiatrists comprising 3 of the 8 members for eating disorders, 4 out of the 12 members for mood disorders and 2 out of the 10 members for schizophrenia working group. There were no consumer or carer members of any of the working groups. While the mood disorder and schizophrenia guidelines included consensus-based recommendations s for indigenous peoples, it is not stated whether any of the working groups included indigenous members.

The mood disorders and schizophrenia working groups did not appear to involve independent decision making. Both groups had discussions until consensus was reached. The eating disorders guidelines did not give relevant information about whether there was independence.

All three guidelines state that consensus-based recommendations were based on collective clinical and research knowledge and experience. The eating disorder guidelines additionally state that level IV articles were considered where higher-level evidence was lacking and this informed the consensus-based recommendations.

After drafting, all guidelines had input from a broader group of expert advisers with a wide diversity of expertise. However, it is not clear whether these advisers had the potential to persuade working group members to change consensus-based recommendations.

Where the guidelines included consensus-based recommendations relevant to indigenous peoples, it is not clear what sources of cultural expertise these were based on.

None of the guidelines state how judgements were aggregated to determine consensus. The mood disorders guidelines state that agreement on consensus-based recommendations was “in most cases unanimous but allowed one committee member to abstain”. The other guidelines did not define what constituted consensus.

In conclusion, there are major weaknesses in the procedures used to determine consensus-based recommendations for all three guidelines. These are lack of independence in decision making by experts, a lack of a formal mechanism for aggregating judgments, and a lack of diversity of expertise, particular in areas where consumers and carers could contribute and where cultural expertise is relevant.

While NHMRC gives quite detailed guidance on how to develop evidence-based recommendations, there is little guidance on best practice for developing consensus-based recommendations. While many of these weaknesses would be overcome by using formal consensus methods such as the Delphi process, there is a need for NHMRC and similar agencies to produce more rigorous quality standards for development of consensus-based recommendations.

On 2016 Sep 25, Lydia Maniatis commented:

I would respectfully ask the authors to justify their fundamental assumption, as this is straightforwardly asserted in their opening sentence:

“Visual sensitivity is limited by both the strength of the neural signals, and the noise in the visual nervous system1 (Levi DM, Klein SA, Chen I. 2005).”

I am interested in the reference to “the noise in the visual nervous system.” What is the basis of the claim that “noise in the visual nervous system" affects the percepts generated under the conditions of this study? What is the nature of this noise, where does it occur, and what is the evidence for it?

The single reference provided for the claim doesn’t provide answers as it, too, takes the it for granted. It does provide two other supporting references; but on inspection, these are equally inadequate.

According to Levi et al (2005) :

“It has been recognized for well over a century that visual perception is limited by both the strength of the neural signals, and by the noise in the visual nervous system…The notion that internal noise in the visual system acts like light, even in the absence of a stimulus, i.e., dark light, led Barlow (1957) to formulate a very influential model of visual detection which posits that visual sensitivity is limited “by the difficulty of distinguishing a weak signal from the background of spurious signals, or ‘noise’, which occurs without any light signal at all”. Barlow (1957) quantified the dark noise by determining the amount of actual light that produced the same amount of noise in the eye that is present in the dark, using the now widely used prescription for quantifying the noise, known as the equivalent input noise technique (Pelli, 1990).”

To clarify, Barlow (1957) is suggesting that there are “low levels of intrinsic retinal noise even in complete darkness.” He is interested in absolute thresholds. He states that his results “fit the theoretical predictions for the case of stimuli of short duration and small area (against a background of large area) for a range of background intensities up to about 10 scotopic trohinds [i.e. very, very low intensities].”

Levi, Klein and Chen (2005) however, are not referring to absolute thresholds or to retinal noise. They tell us that Pelli (1990); Pelli (1981) provided a new description of the equivalent input noise as a contrast function.

The theoretical rationale provided by Pelli (1990) is as follows:

Thus [in the case of electronic amplifiers] we can measure [“specify” would be more accurate] the intrinsic noise by finding an equivalent input noise. This is sometimes called 'referring the amplifier's noise to its input'. Essentially the same approach can be applied to vision. Indeed, this is analogous to Barlow's (1957) dark light measurements. By a similar analogy we can apply this idea to the contrast domain.”

More casual assumptions follow as Pelli (1990) elaborates the application of this analogy to the human visual system.

I submit that vague analogies should not be admitted the status of theoretical arguments.

It should be noted that Zomet et al (2016) in no way test the casually adopted and elaborated assumption that I am challenging. They simply interpret data as though it were true; their procedure can’t tell if it’s false. (The claim is, in fact, so vague that it’s not clear how one would go about testing it).

Postscript: The criteria for publication in Scientific Reports are that: "In this journal a paper is not assessed based on its perceived importance, significance or impact, but it is enough to be just scientifically valid." Testable hypotheses, and testing of assumptions prior to applying them as though they were true, is a fundamental criterion of scientific validity, which I believe is absent in the present case.

On 2016 Sep 08, Andrea Messori commented:

Active rheumatoid arthritis with inadequate response to methotrexate monotherapy: incremental benefit for infliximab plus methotrexate versus methotrexate alone

Andrea Messori, Sabrina Trippoli HTA Unit, ESTAR, Regional Health Service, Firenze, 50100 Italy

One strength of the meta-analysis by Hazlewood and co-workers [1] is that all pharmacological interventions aimed at rheumatoid arthritis have been evaluated in terms of efficacy. Since infliximab biosimilar has recently become available and its cost is lower than that of infliximab originator, evaluating the magnitude of the incremental benefit for infliximab plus methotrexate versus methotrexate alone is of interest.

In patients with active rheumatoid arthritis with inadequate response to methotrexate monotherapy, Hazlewood and co-workers [1] report a total of 5 randomised studies.

According to the end-point of ACR50 response at 30 weeks, the results found in these trials are shown in Table 1. The heterogeneity assessment (carried out according to Higgins and Thompson [2]) showed an I squared of 0% (with p=0.71).

If one analyses these data based on traditional pairwise meta-analysis (OMA software, Open Meta-Analyst, version 4.16.12, Tufts University, url http://tuftscaes.org/open_meta/), the pooled risk difference in favour of infliximab plus methotrexate vs methotrexate alone is +19.7% (95% confidence interval: +15.4% to +24.1%; fixed-effect model).

References

1. Hazlewood GS, Barnabe C, Tomlinson G, Marshall D, Devoe D, Bombardier C. Methotrexate monotherapy and methotrexate combination therapy with traditional and biologic disease modifying antirheumatic drugs for rheumatoid arthritis: abridged Cochrane systematic review and network meta-analysis. BMJ. 2016 Apr 21;353:i1777.

2. Higgins JP, Thompson SG. Quantifying heterogeneity in a meta-analysis. Stat Med. 2002 Jun 15;21(11):1539-58.

Table 1. Data of ACR50 response reported in 5 randomized trials: comparison between Remicade plus methotrexate (R+MTX) vs methotrexate alone (MTX). Detailed references for the 5 trials are given in the Appendix.

ACR50 response

Abe 2006: R+MTX=15/49 (30.6%) vs MTX=4/47 (8.5%)

Lipsky et al 2000 (ATTRACT): R+MTX=18/86 (20.9%) vs MTX=7/88 (8.0%)

Mac Isaac 2014: R+MTX=6/30 (20.0%) vs MTX=0/31 (0.0%)

Westovens et al 2006 (START): R+MTX=110/360(30.6%) vs MTX=33/361 (9.1%)

Zhang 2006: R+MTX=38/87 (43.7%) vs MTX=22/86 (25.6%)

Overall crude rate R+MTX=187/612 (30.5%) vs MTX=66/613 (10.8%)

Appendix

-Abe T, Takeuchi T, Miyasaka N, et al. A multicenter, double-blind, randomized, placebo controlled trial of infliximab combined with low dose methotrexate in Japanese patients with rheumatoid arthritis. J Rheumatol 2006;33:37-44

-Lipsky PE, Van Der Heijde DMFM, St. Clair EW, et al. Infliximab and methotrexate in the treatment of rheumatoid arthritis. New Engl J Med 2000;343:1594-602

-Mac Isaac KD, Baumgartner R, Kang J, et al. Pre-treatment whole blood gene expression is associated with 14-week response assessed by dynamic contrast enhanced magnetic resonance imaging in infliximab-treated rheumatoid arthritis patients. PLoS ONE 2014;9 (12) (no pagination)

-Westhovens R, Yocum D, Han J, et al. The safety of infliximab, combined with background treatments, among patients with rheumatoid arthritis and various comorbidities: a large, randomized, placebo-controlled trial.[Erratum appears in Arthritis Rheum. 2007 May;56(5):1675 Note: Dosage error in article text]. Arthritis Rheum 2006;54:1075-86

-Zhang FC, Hou Y, Huang F, et al. Infliximab versus placebo in rheumatoid arthritis patients receiving concomitant methotrexate: A preliminary study from China. APLAR Journal of Rheumatology 2006;9:127-30

On 2016 Apr 27, Ana Herrmann commented:

The authors state that 1) "animals were used for only one experiment and in a single behavioral test, to reduce interference from apparatus exposure", and later they state that 2) "Animals were allowed to freely explore the novel tank for 6 min, after which they were removed from it and exposed to the scototaxis tank". Which one was it?

On 2016 May 24, Stefan Hofmann commented:

See: http://www.ncbi.nlm.nih.gov/pubmed/27009055

On 2016 May 06, Margaret Sampson commented:

The initial posting for this article contained an error in the order of the authors, as did the article posted on the JCE website on 18 April 2016. The correct author order for "The Single-Case Reporting guideline In BEhavioural Interventions (SCRIBE) 2016 Statement" is as follows: Tate, Perdices, Rosenkoetter, Shadish, Vohra, Barlow, Horner, Kazdin, Kratochwill, McDonald, Sampson, Shamseer, Togher, Albin, Backman, Douglas, Evans, Gast, Manolov, Mitchell, Nickels, Nikles, Ownsworth, Rose, Schmid, and Wilson. As a check, please ensure that Vohra is the 5th author (Posted May 6, 2016, revised May 19, 2016)

On 2017 Mar 02, Melissa Rethlefsen commented:

I thank the authors for including the full version of their search strategies in the appendix. This is a valuable tool for readers to more comprehensively analyze the systematic review's methodology and outcomes.

In the appendix containing the full search strategies, the MEDLINE search and the Embase search appear identical. It is unclear if these databases were searched simultaneously using Ovid's multifile searching capability, or whether the search listed for MEDLINE is in fact not the search used for the MEDLINE search. It is of course also possible that the same search was used for each database, though searched individually.

The primary complication with the MEDLINE search as reported is that many of the search terms used are Embase-specific Emtree terms that are not searchable in MEDLINE. This includes: "crossover procedure"; "double blind procedure"; "single blind procedure"; "triple blind procedure"; "animal"; "nonhuman"; "human"; "human cell"; and "ulcerative colitis." Because these are not the correct MeSH terms for these concepts, searches for these terms as indicated would produce no results. This unfortunately impacts two major components of the search, from the recommended Cochrane Embase sensitive search for randomized control trials (lines 1-18) and the disease state section (lines 21-24). Multifile Ovid searching does try to map thesaurus terms to corresponding thesaurus terms across databases, which may resolve some of these issues. However, a best practice would be to include both Emtree and MeSH terms in a search instead of relying on multifile term mapping. If the authors did rely on multifile searching, it would be appropriate to note this in the methods section to alert readers.

In addition, lines 26 and 27 both search for the MeSH heading "Mesalamine," and lines 28 and 29 both search for the MeSH heading "Sulfasalazine." This was perhaps adapted from the previous version of this review (Feagan BG, 2012), which also utilizes this duplication. It is not clear why these terms were duplicated in either case, though this version of the review did update the rest of the search strategy to be more comprehensive and also more specific.

On 2016 Aug 18, Andrew Kewley commented:

Expression of concern over un-interpretable statistics of multiple candidate gene association studies.

The lack of replication of candidate gene association studies has led to much discussion and debate. It is generally considered that each candidate cannot be considered to be an independent hypothesis, hence the alpha level needs to be corrected for multiple comparisons. There is no discussion of this in the paper.

This research group have published multiple candidate gene manuscripts in addition to this study [1,2,3,4] (Most of which are not listed on pub-med), and may have other unpublished data. Hence it is difficult to know what alpha should be used for significance, after correcting for multiple comparisons. If correcting for 678 comparisons, then none of the results reach significance and the overall conclusion should be quite different.

In general, future genetic studies should utilise genome-wide association methodology to avoid such biases.

[1] Examination of Single Nucleotide Polymorphisms (SNPs) in Transient Receptor Potential (TRP) Ion Channels in Chronic Fatigue Syndrome Patients. Sonya M. Marshall-Gradisnik, Peter Smith, Ekua W. Brenu, Bernd Nilius, Sandra B. Ramos and Donald R. Staines Immunology and Immunogenetics Insights 2015:7 1-6

[2] Genotype Frequencies of Transient Receptor Potential Melastatin M3 Ion Channels and Acetylcholine Muscarinic M3 Receptor Gene Polymorphisms in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis Patients. Marshall-Gradisnik, SM; Chacko, A; Johnston, S; Smith, P; Nilius, B; et al. Immunology and Immunogenetics Insights 8 (2016): 1-2.

[3] Examination of Single Nucleotide Polymorphisms in Acetylcholine Receptors in Chronic Fatigue Syndrome Patients. Marshall-Gradisnik, Sonya; Smith, Peter; Nilius, Bernd; Staines, Donald R. Immunology and Immunogenetics Insights 7 (2015): 7-20.

[4] Killer Cell Immunoglobulin-like Receptor Genotype and Haplotype Investigation of Natural Killer Cells from an Australian Population of Chronic Fatigue Syndrome/Myalgic Encephalomyelitis Patients. T. K. Huth, E. W. Brenu, D. R. Staines, and S. M. Marshall-Gradisnik. Gene Regulation and Systems Biology 2016:10 43-49

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 NCT0255810. We believe the correct ID, which we have found by hand searching, is NCT02558101.

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 2017 Mar 29, Zvi Herzig commented:

Despite the fact that this study relates to e-cigarette (EC) vapor dissolved in a liquid medium, the authors surprisingly attribute outcomes to fine particulate matter:

… our findings suggest it is not nicotine or toxic combustion product that activates the hemostatic system, but instead the hemostatic system is most responsive to fine particulate matter

This conclusion is puzzling because particulate matter of EC aerosol are in fact liquid droplets. When these are merged with the liquid medium, their former particle sizes become irrelevant. (Solid particles emitted from EC hardware are at quantities below safety limits Farsalinos KE, 2015 and thus unlikely to be of significance).

It is also unclear what the causes or the relevance of these in vitro platelet effects are. For example, propylene glycol and glycerol are not rapidly metabolized here as they are in vivo. Indeed, Hom et al write:

There are some important limitations to the work presented here, including the use of an ex vivo static system, without negative hemostatic regulators (such as endothelial cells), to evaluate the effects of e-vapor on platelet functions.

In contrast, a recent clinical study of smokers switching to Tobacco Heating System 2.2 (whose emissions also include the limited cigarette smoke toxicants present in EC vapor Schaller JP, 2016) shows a level of reduction in platelet activation among switchers approaching those of quitters Lüdicke F, 2018:

Reductions in 8-epi-prostaglandin F2α (biomarker of oxidative stress), 11-dehydro-thromboxane B2 (biomarker of platelet activation)… occurred in the menthol tobacco heating (mTHS) system group compared with the menthol conventional cigarette group. The changes in the mTHS group approached those in the smoking abstinence group.

This would indicate that the outcomes of Hom et al are not manifested in real use. While it can be countered that perhaps EC flavorants not emitted by heated tobacco have induced the platelet effects, this is unlikely considering that outcomes were similar for two disparate EC products tested.

It would also be interesting to consider the effects of air bubbles present from bubbling the aerosol through the extraction buffer. It's well-known that air bubbles induce platelet activation Sandgren P, 2011 and this might help explain the strange outcome.

On 2016 May 23, Jonathan Heald commented:

Posted on behalf of the American Academy of Sleep Medicine:

These recommendations for the use of adaptive servo-ventilation for the treatment of congestive heart failure related central sleep apnea are updates to the 2012 recommendations found in the guideline "The treatment of central sleep apnea syndromes in adults: practice parameters with an evidence-based literature review and meta-analyses." These recommendations serve as an essential supplement to the 2012 practice parameter document:

Aurora RN, 2012

On 2016 Jun 06, Christopher Southan commented:

Since the molecular structure of HM71224 is not disclosed the journal has allowed the publication of work that cannot be reproduced. This consequently obfuscates the clinical trial entry from Eli Lilly

https://clinicaltrials.gov/ct2/show/NCT02628028

On 2017 Sep 13, Seán Turner commented:

According to the CCM catalog of strains, the type of Paenibacillus cucumis Kampfer et al. 2016 is CCM 8655, not CCM 8653. The authors have later assigned CCM 8653 as the type of Isoptericola cucumis Kampfer et al. 2016 (PMID 27045419) which is consistent with the assignment in the CCM catalog of strains.

On 2017 Sep 13, Seán Turner commented:

None

On 2016 Jul 14, Marcus Munafò commented:

This study provides deeper theoretical insights than might be imagined from a cursory reading. Evolutionary life history theory addresses how organisms, including humans, vary in the allocation of resources to growth, survival and reproduction across the life course. Life history strategies are defined by key decisions that trade off finite resources against competing demands to achieve reproductive goals [1, 2]. Both across and within species, the trade-off between the allocation of resources to growth and to reproductive efforts results in organisms employing varying strategies that can be characterised, loosely, as ‘slow’ or ‘fast’. A ‘slow’ life history strategy is characterized by later maturity and proportionally greater investment of resources in a smaller number of offspring, while a ‘fast’ life history strategy involves more effort directed towards reproduction, such as earlier puberty and sexual activity [2, 3]. Typically, animals pursue a fast life history strategy (‘live fast, die young’) under adverse environmental conditions of high extrinsic mortality. In such conditions, as Day and colleagues suggest, earlier sexual maturation may increase reproductive fitness. However, Day and colleagues also suggest that associations between earlier puberty and a greater propensity for risk-taking behaviours, lower educational attainment, and adverse health outcomes, contradicts this evolutionary perspective. On the contrary, directing effort into risky and aggressive behaviour is best considered as an important part of a fast life history strategy, in which competition for mates is crucial [1]. Viewed in this light, adolescent behaviours of unprotected sex and earlier pregnancy, as well as violence, law breaking, and substance abuse, can be seen as central components or consequences of a fast strategy in which the future is discounted relative to the present [1, 4]. Variation in these physiological and behavioural traits in response to changing environments may reflect a suite of adaptations – psychological and somatic – that increase fitness on average despite poor social and health consequences [5], as resources are diverted from longevity towards short-term reproductive goals under conditions of adversity.

The human life history literature suggests strategies are contingent on variation in the environment rather than variations in genotype. Day and colleagues illustrate the central role genetics can play in testing key hypotheses arising out of life history theory, where reliance on observational data has previously limited causal inference. The key point is that variants identified in GWAS studies may reflect environmental (and hence modifiable) risk factors, as well as direct genetic effects [6]. An ever-increasing range of social and psychological traits relevant to life history theory are proving tractable to GWAS, including, for example, social deprivation [7] and endocrine biomarkers including cortisol [8] and sex steroids [9]. Genetic instruments associated with social outcomes could be used as a proxy for environmental harshness, while instruments for endocrine status may provide causal evidence for status seeking and reproductive behaviours known to occur in other species, but that are not amenable to experimental analysis in humans. The results of emerging GWAS therefore provide us with unprecedented opportunities for testing the predictions of life history theory, with implications for our understanding of the determinants of health and social behaviour. The elegant demonstration by Day and colleagues of causal links between earlier puberty and both key reproductive traits and adverse outcomes provides compelling evidence that evolutionary life history theory can shed light on human reproductive behaviour, health and disease, even in a modern Western environment. Combining causal analysis from genetic epidemiology and theoretical insights from evolutionary models may help to launch a science of evolutionary social epidemiology, combining knowledge of ‘how’ exposures lead to certain outcomes with an understanding of ‘why’ these relationships may exist. Reframing our understanding of the development of significant social and health outcomes in this way may lead to novel insights to inform future interventions.

Rebecca Lawn, Abigail Fraser, Marcus Munafò and Ian Penton-Voak

1. Ellis, B.J. and Bjorklund, D.F. Beyond mental health: an evolutionary analysis of development under risky and supportive environmental conditions: an introduction to the special section. Developmental Psychology, 2012. 48(3): p. 591.
2. Chisholm, J.S., Death, hope and sex: Steps to an evolutionary ecology of mind and morality. 1999, Cambridge: University of Cambridge Press.
3. Ellis, B.J., et al., Fundamental dimensions of environmental risk. Human Nature, 2009. 20: p. 204-268.
4. Simpson, J.A., et al., Evolution, stress, and sensitive periods: the influence of unpredictability in early versus late childhood on sex and risky behavior. Developmental psychology, 2012. 48: p. 674-686.
5. Gluckman, P.D. and Beedle, A.S. Match fitness: development, evolution, and behavior: comment on Frankenhuis and Del Giudice (2012). Developmental Psychology, 2012. 48: p. 643– 646.
6. Gage, S.H., et al., G= E: What GWAS can tell us about the environment. PLoS Genet, 2016. 12: e1005765.
7. Hill, W.D., et al., Molecular genetic contributions to social deprivation and household income in UK Biobank (n= 112,151). bioRxiv, 2016.
8. Bolton, J.L., et al., Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin. PLoS Genet, 2014. 10: e1004474
9. Vandenput, L. and C. Ohlsson, Genome-wide association studies on serum sex steroid levels. Molecular and cellular endocrinology, 2014. 382: p. 758-766.

On 2016 May 15, Arnaud Chiolero MD PhD commented:

In a life course epidemiology perspective, this is a great review to understand strengths and limitations of intergenerational approach of prevention of obesity and related conditions. In this domain, the words are elegant and the concepts are appealing; the evidence is however weak, letting us short of knowing how to act. We need trials to go further.

On 2017 Mar 02, Simina Boca commented:

Code for analyzing the processed data available at https://github.com/SiminaB/DMD-metabolomics

On 2016 Jul 26, Fernando Castro-Chavez commented:

Dear Reader, This is my most recent article and in it I present the match between the Vigesimal Numerical System of the Maya Culture from the Yucatan Peninsula, in Mexico, and the twenty amino acids with suggested systems of anatomical mnemonics in the Education of Molecular Biology, i.e., using the twenty appendages of our extremities (fingers and toes), and another to remember the purines and pyrimidines with hands and feet. Furthermore, by the suggestion of my chemistry tutoring student Ana Baleva, I have also explored the Icosahedron as an alternate way to represent the twenty amino acids for the Graphics Design in Bioinformatics, containing in one of its triangular cells, an on/off switch. To see the rest of a suggested set of correspondences, please go to my Facebook page and (if you wish) befriend me: https://www.facebook.com/fernando.castrochavez.90. I deeply appreciate feedback, and/or constructive comments, for this and for The Rest of my: Publications in PubMed, by Fernando Castro-Chavez:. And my LinkedIn: https://www.linkedin.com/in/fernando-castro-chavez-6744a322. Sincerely, Fernando Castro-Chavez. P.D. An updated image inspired by this research:

The First Ten plus Zero Numerals of the Vigesimal Mayan System

On 2016 Jun 29, Fernando Castro-Chavez commented:

None

On 2017 Nov 30, Joe G. Gitchell commented:

Readers may find the follow-up letter to this article (http://ajph.aphapublications.org/doi/full/10.2105/AJPH.2016.303456) and the authors' reply to the letter (http://ajph.aphapublications.org/doi/full/10.2105/AJPH.2016.303476) of interest.

On 2016 Apr 25, Dita Gratzinger commented:

Dr. Itkin and colleagues provide a tour de force overview of hematopoeitic stem and progenitor cell maintenance and trafficking within the context of distinctive capillary/arteriolar and sinusoidal vascular beds in the mouse. In parallel to their findings in mouse, we have previously described the analogous vascular beds in intact human marrow, particularly the nestin+ capillary/arteriolar bed, which is tightly wrapped in SMA/CD146+ pericytes/vascular smooth muscle which in turn is wrapped in CD271+ mesenchymal stromal cells (MSCs), as distinct from the nestin-negative sinusoidal endothelium in direct contact with MSCs; the MSCs are then in direct contact with CD34+ hematopoietic progenitor or stem cells Flores-Figueroa E, 2012. CD105 is a specific sinusoidal vascular marker and nestin as a specific capillary/arteriolar marker in intact human bone marrow, allowing for quantification of the distinct vascular beds in the setting of myelodysplastic syndromes Ewalt MD, 2016.

On 2016 Apr 14, Fernando Suarez-Obando commented:

Great paper

On 2016 Dec 15, Victoria MacBean commented:

Plain English Summary:

Parasternal intercostal electromyography (EMGpara) is a new way to measure breathing difficulty. Research needs to be carried out because body parts used in breathing, like the lungs, need to be properly checked over for breathing problems to be managed, but the testing methods aren’t always suitable for children who are very young or ill. The parasternal intercostal muscles are muscles that move at the same time as the diaphragm (a thin sheet of muscle under the lungs) when you breathe in and out. EMGpara measures signals from the brain which are sent to these muscles without putting any instruments into the body, so it is ideal for children. EMGpara was measured using stickers on the front of the chest while the participants (92 healthy, 20 wheezy and 25 with a machine (ventilator) to help them breathe) were breathing in and out in a resting state. For the wheezy children, measurements were taken before and after a substance to widen air passages (reliever inhaler, or bronchodilator) was used; for the critically ill children, these were taken during ventilator-assisted breathing, then with just mild air pressure to keep the airways open (continuous positive airways pressure). It was found that as age, weight and height increased, EMGpara decreased. This is because when children are growing up, big changes take place in the respiratory system, decreasing the effort needed for breathing. EMGpara in the healthy children was the lowest; in the wheezy children it was higher before the bronchodilator was used, dropping to similar levels to the healthy children afterwards. In the critically ill children, EMGpara was higher than in the wheezy children when the ventilator was used, and even higher with continuous positive airways pressure when they were having to breathe without support. This study has shown that measuring EMGpara is possible in children of a range of ages and levels of health. The results from the healthy children have shown important age-related changes in EMGpara, and those from the wheezy and critically ill children have shown that EMGpara is affected by changes in how hard the breathing muscles have to work because of different diseases and treatments. EMGpara could be a really helpful method in testing the breathing ability of patients who are usually difficult to assess.

This summary was produced by Lottricia Millett, Year 12 student from Burntwood School, London, as part of the investigators' educational outreach programme.

On 2016 Aug 31, Joanna Hudson commented:

We thank Ben Goldacre and the opentrials.net project for bringing this to our attention. We have informed the journal of this anomaly and will ensure all future publications are cited with the correct trial registry ID.

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 NCT023528702. We believe the correct ID, which we have found by hand searching, is NCT02352870.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2016 May 12, Heidi Schulz commented:

Note that according to HGVS guidelines, the novel variant described as c.717delG in the paper should be referred to as c.718del p.Val240*.

On 2016 Apr 20, Anderson Santos commented:

Dear users of the MED pipeline, The MED web server address has been migrated to this new one: http://med.compbio.sdu.dk/ in the Denmark. The MED web server administrator is negotiating a web address forward but no responses from Saarland till now. An important clue about MED: keep the proteins names small and simple, avoid punctuation characters or your processing can fail. I hope to correct such weakness in a further version. Best regards, Anderson Santos - Author

On 2016 Apr 30, Clive Bates commented:

Missing the Point

The priorities elaborated in Matthew Myers' editorial are misplaced will have only trivial impact on the cigarette market. I have proposed five more fundamental tobacco-related regulatory issues for FDA or Congress to address. Please see this e-letter response to the journal Tobacco Control: e-letter Missing the point

An expanded version of this is available with links in this posting The tobacco control high command has lost its way - what we learn from its views on FDA priorities

On 2016 May 27, Carmine Pariante commented:

We are grateful to Dr. Carroll for his comment, which has allowed us to clarify this point. Dr. Carroll is right that we use 'specific' as indicating the outcome of statistical analyses. However, we refer to pathways and genes 'specifically' regulated in depressed patients (or, indeed, in the group that does not develop depression) because these genes/pathways are only regulated in the depressed (or in the non-depressed) group. In this sense, we are using 'specific' to differentiate these genes/pathways from the many genes/pathways that are regulated equally in both groups. We also agree that there are limitations in using IFN-alpha as a model of ordinary major depressive disorder, although we are confident that our findings are relevant to at least the subgroup of depressed patients with high levels of peripheral inflammation. We hope that this reply is helpful.

On 2016 May 08, Bernard Carroll commented:

Several issues arise with this report. 1. Authors claimed that "specific signatures" of gene expression changes distinguished depressed versus non-depressed patients. After reading the full paper plus the Supplemental material it is clear that specificity was not established. No data were presented on conditional probabilities or on diagnostic confidence or prognostic confidence. 2. Multiple, misleading, references to specificity in the article actually just denote statistically significant differences in gene expression between the 2 groups of patients. 3.No group-wise differences in cytokine concentrations were found. 4. Validity of IFN-alpha induced depression as a model of ordinary major depressive disorder has not been established.

On 2016 Jul 20, Rohan Maddamsetti commented:

While gene flow is certainly important in the evolution of gut microbiota, given current evidence I do not believe that gene flow is a good explanation for synonymous variation in E. coli. I've written a short post on my blog explaining my thinking: http://rohanmaddamsetti.weebly.com/blog/a-retraction-of-sorts

On 2017 Apr 27, Randi Pechacek commented:

Katherine Dahlhausen wrote an engaging blog post on microBEnet about this review. She explains how this review emphasizes our "knowledge gaps in the understanding of the fate of antibiotics in our environments."

On 2016 Apr 13, Anders von Heijne commented:

Recommended reading - Note the important aspect of including the scale/lexicon as a footnote in all radiology reports!!

On 2016 Apr 16, Aiguo Ren commented:

The lowest and highest point estimates of NTD prevalence were obtained from two studies in China. However, these two studies are not comparable in terms of geographical area, time period, and, most importantly, method of calculation. The estimate from Beijing was obtained from a maternity hospital and the numerator was the number of NTD cases in pregnancies of 28 weeks of gestation or greater. In Beijing, every pregnant woman receives ultrasound scanning for fetal structural defects around 20 weeks of gestation, and virtually all fetuses with NTDs will be detected by 28 gestational weeks, and terminated based on informed choice of the mother. This explains, in a larger part, the low NTD prevalence in Beijing. Other national or hospital-bases data from China suffer from the same problem. Please see our most recent report PMID: 26879384.

On 2016 Jun 22, Vatsalya Vatsalya commented:

Research highlight at NIAAA June 2016 Council Meeting: http://www.niaaa.nih.gov/about-niaaa/our-work/advisory-council/directors-reports-council/niaaa-directors-report-institute-12

On 2016 Aug 01, Joaquim Radua commented:

Re: the previous comment, I think there may be some unfortunate confusion. Raw p-values of current voxelwise meta-analyses have not the same meaning as usual p-values because they are not derived from the usual null hypothesis (“there are no differences between groups”), but from another null hypothesis (“all voxels show the same difference between groups”). Thus, up to the moment one of the only ways to "approximately" know if the results of a voxelwise meta-analysis are neither too liberal nor too conservative is to compare them with the results of a mega-analysis of the same data, and that's what it was done.

On 2016 Jul 22, Christopher Tench commented:

Control in statistics is not achieved by fixed p-value threshold when there are many tests. There are very fundamental reasons for using FWE and FDR, and as a minimum these must be estimated to quantify the risk of false positives. Applying a fixed p-value and fixed cluster extent is a bit like having a fixed steering wheel in a car: it will work really well when the road is straight, but fail terribly when there is a bend! Controlled methods necessarily adapt themselves to the data. Without them, there is no quantifiable evidence that an effect is truly critical of the null.

I appreciate the validation study. Unfortunately it only tested known positive data. In statistics this cant be considered validation as it promotes confirmation bias. I am aware of the claim that the threshold is equivalent to corrected 0.05, but unfortunately this is not correct. Correction implies adaptation to the data and its null, but fixed thresholds are not able to do this.

On 2016 Jun 21, Fabio Richlan commented:

1) Whether or not a study can be considered a meta-analysis does not depend on the use of a correction for multiple comparisons. 2) As usual for coordinate-based meta-analyses, statistical significance was assessed by a permutation test (thresholded at a voxel-level (height) of p < 0.005 and a cluster-level (extent) of 10 voxels). Note that the use of a cluster extent threshold is a way of controlling false positives. In addition, only voxels with z > 1.0 were considered statistically significant. Based on an empirical validation, it was shown that, at least for seed-based d Mapping (SDM), this combination of voxel-level and cluster-level thresholds optimally balances sensitivity and specificity and corresponds to a corrected p-value of 0.05 (http://www.ncbi.nlm.nih.gov/pubmed/21658917). More details on the SDM method can be found at http://www.sdmproject.com/

On 2016 Jun 15, Christopher Tench commented:

The method employed in this study offers no control over the 10⁵ statistical tests performed. The results are can not be considered statistically significant or a meta-analysis.

On 2017 Apr 09, Harri Hemila commented:

A manuscript version is available at HDL.

On 2016 Apr 30, Morten Oksvold commented:

Please note that this publication is actually a retraction of the Leukemia article. There is no indication in this PubMed notice that this is a retraction.

I will strongly suggest that all retractions in the future are written clearly in the beginning of the article title.

On 2017 Jul 24, Joseph J Drabick commented:

Thank you for the comment for our article. We will clarify the literature searching strategy we used in the meta-analysis here. We used Pubmed, Cochrane Library, Ovid Medline and Ovid Healthstar databases, which are accessible from our medical center library. Other details for the search strategy, such as keywords, inclusion and exclusion criteria, are shown in our manuscript.

On 2017 Jul 20, Irma Klerings commented:

Remarks concerning the literature search

The authors state that they conducted the review in accordance with Cochrane guidance, which is commendable. However, both the Cochrane Handbook for Systematic Reviews of Interventions and the Methodological Expectations of Cochrane Intervention Reviews state that the full search strategies for each database need to be included in an appendix of the review.

Unfortunately, this is not the case here. As far as I can see, this article does not include a replicable search strategy in the text or in an appendix.

The description of the databases used is also puzzling: “PubMed database, Cochrane database, and Ovid database”

Ovid is not a database, but a platform that hosts many different databases. Which one(s) were used is not discernible. Similarly, it is not quite clear what is meant by “Cochrane database”. This might refer to the Cochrane Library which contains a number of databases or it might refer to only one of the databases produced by Cochrane (CDSR, CENTRAL).

In short, the authors may have adhered to Cochrane guidance when they conducted this review. But when it comes to the literature searches there is no way to tell because the reporting is insufficient. This means the reader has no way of judging the comprehensiveness and the quality of the literature search process.

On 2016 May 08, Amitav Banerjee commented:

The study by Deshmukh et al,[1] entitled, “Taken to Health Care Provider or Not, Under-Five Children Die of Preventable Causes: Findings from Cross-Sectional Survey and Social Autopsy in Rural India,” published in the current issue of Indian Journal of Community Medicine, raises some serious debatable issues which need to be revisited.

1. On the whole this cross sectional study, covering rural areas from 16 districts in 8 states of India to identify the causes of death among under-five children and health seeking behavior of caregivers by verbal autopsy, does not yield any novel information. No one with a basic understanding of public health in India would find surprising that mortality was mostly due to neonatal etiologies and preventable causes such as acute respiratory infections, diarrhea, and so on. The fact that most caregivers preferred private health care facilities over government health centers is also to be expected given the poor quality and availability of public health facilities in rural areas. Many studies have brought out these factors ad-nauseam.

2. This study would have passed as a benign redundant study but for the fact that it has raised a serious debatable issue by some very casual inferences which can misguide the reader, the policy makers and the lay public.

3. The issue concerns the authors’ claim that this study is the first study on Sudden Unexplained Deaths (SUDS). They found 1.4% (21 out of 1488) of deaths among under-five children otherwise healthy before death which they labeled as SUDS. Well, so far, so good. However, while discussing the implications of this finding vis-à-vis Adverse Effects Following Immunization (AEFI), one wonders why they drag in AEFI in their discussion since it was not one of the study objectives. Further, they also claim, naively, that no vaccination histories were available for these cases. So one would like to know by what stretch of imagination one can conclude, in either direction, the relationship between immunization and these cases of SUDS from the data they provide. Authors have resorted to speculation in absence of scientific reasoning.

4. They claim that the findings regarding SUDS in their study could serve as a baseline for future assessment of SUDS in Indian children and could be used for analysis and in contextualizing SUDS and AEFI deaths in India. Well, again, so far, so good. Now follows the gaffe.

5. The authors have made the following statement, “…SUDS and AEFI deaths in India …have been wrongly attributed to new vaccine in the lay press (here they have cited two references, 25 and 26).” This statement and the references labeled as “lay press” are very misleading. Reference number 25 (cited as “lay press”) is a very balanced editorial, published in the Indian Journal of Medical Ethics, a reputed journal indexed in PubMed and Scopus among others. Reference number 26 is “Weekly Epidemiological Record from WHO Geneva!!” One wonders whether the authors have read these references before citing them, otherwise they would not have made this blunder of labeling them as “lay press.”

6. One would strongly recommend all readers who read Deshmukh et al’s paper[1] to also read these references cited as “lay press” by the authors. Puliyel in his editorial in the Indian Journal of Medical Ethics,[2] has very elegantly with simple calculation (he resorted to all causes mortality since SUDS specific mortality was not available) demonstrated that unexplained deaths after introduction of pentavalent vaccine increased much beyond the base rate for all causes infant mortality rate in Kerala. If Deshmukh et al[1] suggest that data from their present study regarding SUDS be used to contextualize AEFI and SUDS then Puliyel’s caution about adverse effect of pentavalent vaccine becomes stronger as only 2.3% of all cause infant mortality would be expected as SUDS (and co-incidental to administration of pentavalent vaccine). While their data on SUDS supports Puliyel’s concerns about AEFI deaths after pentavalent vaccine (in fact more than Puliyel’s own editorial, since based on this data SUDS would be only a fraction of all causes infant mortality), they casually dismiss his editorial as “lay press.”

7. Similarly the other reference cited by the authors as “lay press”, i.e. The Weekly Epidemiological Record from WHO[3] cautions that in the context of evaluating a safety signal, it is important that countries understand their own infant mortality rates and underlying causes. If a particular serious AEFI is identified as a concern, additional epidemiological studies should be conducted to ascertain factors that can be used to evaluate the evidence for risk hypothesis. SUDS, among other causes of infant mortality, would benefit from detailed epidemiological studies. The report by WHO in this issue of the WER, concedes that there have been deaths following pentavalent vaccine in Sri Lanka, Bhutan, India and Vietnam leading to temporary suspension of vaccination in some countries. Albeit in the end the report concludes that pentavalent vaccine is to be considered safe. This perhaps may be due to lack of proper baseline data on SUDS and inadequate epidemiological investigations of AEFI.

8. Based on Deshmukh et al[1] findings on SUDS, the WHO may be persuaded to reconsider its position on safety of pentavalent vaccine. Lastly, we hope Deshmukh et al appreciate their contribution to understanding AEFI – they have raised the bar of vaccine safety – not realizing they have done so!!

References

1. Deshmukh V, Lahariya C, Krishnamurthy S, Das MK, Pandey RM, Arora NK. Taken to health care provider or not, under-five children die of preventable causes: Findings from cross-sectional survey and social autopsy in Rural India. Indian J Community Med 2016;41:108-19

2. Puliyel J. AEFI and the pentavalent vaccine: Looking for a composite picture. Indian J Med Ethics 2013;10:142-6.

3. Weekly epidemiological record. Geneva: World Health Organization 2013; 88: 301 – 12. .

Dr Amitav Banerjee, Professor Community Medicine, Dr DY Patil Medical College, Hospital and Research Centre, Pune, India

On 2016 Apr 08, Dr. Kam Cheong Wong commented:

Dear readers,

The full article can be freely accessed via the following open access link: http://jmedicalcasereports.biomedcentral.com/articles/10.1186/s13256-016-0850-6

In a spirit of continual improvement, I have updated Figure 3 in this article. The haematological and endocrinological causes of pain in the right upper quadrant of the abdomen have been grouped in “other systems” in the Figure 3, which can be freely downloaded via the following link:

https://www.researchgate.net/publication/299760713_How_to_apply_clinical_cases_and_medical_literature_in_the_framework_of_a_modified_failure_mode_and_effects_analysis_as_a_clinical_reasoning_tool_-_an_illustration_using_the_human_biliary_system/figures

This article has referred to the use of Ishikawa diagram. Readers who would like to revisit “how to apply Ishikawa diagram in a clinical setting” can freely access the article via the following link:

http://jmedicalcasereports.biomedcentral.com/articles/10.1186/1752-1947-5-120

I look forward to receiving your feedback.

Thank you.

Yours sincerely, Dr. Kam Cheong WONG; MBBS(UQ),MSc(NUS),BE(NUS),FRACGP.

On 2017 Apr 21, Randi Pechacek commented:

Katherine Dahlhausen, or as I know her, Katie, is the first author on this paper. She wrote an entertaining and honest post on microBEnet about the whole process of using crowdfunding for research. As someone who personally works on her "Koala Project," I highly recommend reading her blog post here.

On 2016 Dec 18, Laura Williams commented:

Our online journal club discussed this paper on April 25, 2016. https://www.youtube.com/watch?v=aj8mqOw83Bo

On 2016 Aug 24, Jim Woodgett commented:

A relatively minor point, but the inhibitors used here, lithium and SB216763 (and also BIO, which is mentioned in the Discussion) are not selective for GSK-3beta as they are equipotent towards the GSK-3alpha isoform. This could be simply remedied by deleting the "beta" from each mention of GSK-3beta. Of note, there are currently no isoform-selective small molecule antagonists of GSK-3. Both isoforms are largely redundant (though there are some differences), similarly regulated and widely expressed.

On 2016 Apr 06, Donald Forsdyke commented:

PROTEIN SIZE AND CONCENTRATION DETERMINE DOSAGE-SENSITIVITY?

With the goal of understanding “the evolution of incomplete sex chromosome dosage compensation mechanisms in general,” the authors confirm that, among dosage-sensitive genes, those whose products specifically engage in stoichiometric complexes with other gene products, have a high degree of dosage-compensation. However, most genes are not dosage-limited by stoichiometry and “perplexing questions” remain. It is suggested that “certain loci … simply lack dosage effects” (my italics). In other words, certain loci “simply” contribute more to dosage effects than others.

While far from simple, this proposal is consistent with dosage compensation being more concerned with collective protein functions than with the specific functions of individual proteins (1). In the crowded cytosol the protein collective should exert an entropy-driven aggregation pressure on individual proteins, as part of a process of intracellular self/not-self discrimination (2). It is predicted that small, low concentration, proteins, will hardly influence aggregation pressure, so here there is no necessity for dosage compensation between the sexes. However, large, high concentration, proteins will greatly influence aggregation pressure, so here regulation of dose, on a gene-by-gene basis or otherwise, should be critical. Failure to regulate such dosage in human females would explain their susceptibility to autoimmune diseases (3-5).

1.Forsdyke DR (1994) Relationship of X chromosome dosage compensation to intracellular self/not-self discrimination: a resolution of Muller's paradox? J Theor Biol 167:7-12. Forsdyke DR, 1994

2.Forsdyke DR (2009) X chromosome reactivation perturbs intracellular self/not-self discrimination. Imm Cell Biol (2009) 87:525-528.Forsdyke DR, 2009

3.Dillon SP et al. (2012) Sex chromosome aneuploidies among men with systemic lupus erythematosus. J Autoimmun 38:J129-J134. Dillon SP, 2012

4.Forsdyke DR (2012) Ohno's hypothesis and Muller's paradox: sex chromosome dosage compensation may serve collective gene functions. BioEssays 34:930-933. Forsdyke DR, 2012

5.Wang J et al. (2016) Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Proc Natl Acad Sci USA doi/10.1073/pnas.1520113113 Wang J, 2016

On 2016 Sep 30, Jackie Marchington commented:

The Global Alliance of Publication Professionals (GAPP) submitted a timely response to this article to BMC Medical Ethics in May 2016. In September 2016 we received the author’s response to our correspondence. In the light of current (as of September 2016) correspondence on a subsequent, similar article by the same author in the British Medical Journal (http://www.bmj.com/content/354/bmj.i4578/rapid-responses), we consider our original response to this article to be redundant, but would encourage readers to visit the BMJ correspondence.

Disclosure: All members of GAPP declare that we have provided or do provide ethical medical writing services to academic, biotechnology, or pharmaceutical clients, and are active in national and international not-for-profit associations that encourage ethical medical writing practices. Details of GAPP members can be found at http://gappteam.org

On 2016 Apr 05, Christophe Dessimoz commented:

The paper is published as open access and thus freely available from the publisher: http://dx.doi.org/10.1038/nmeth.3830

Furthermore we wrote a blog post with the story behind this paper: http://lab.dessimoz.org/blog/2016/04/05/ortholog-benchmark-service

On 2016 May 02, Ricky Turgeon commented:

This review required withdrawal for additional important reasons to the outdated search described by the editors, including inappropriate study inclusion, factually incorrect statements and conclusions not supported by the included evidence. As these reasons were not described in the reasons for withdrawal, we share a letter sent to the Cochrane Heart Group on March 30, prior to withdrawal, highlighting these issues:

"Dear Cochrane Heart Group,

In performing our own review and synthesis of the evidence for impact of diuretics on mortality and hospitalization in patients with heart failure, we identified critical issues in Cochrane review CD003838 that warrant immediate withdrawal of the review for revision.1 For the purposes of this letter, we focus on the analyses of ‘mortality’ and ‘heart failure worsening’ and 3 of the 4 randomized controlled trials (RCTs) that provided data for at least one of these analyses.2-4

First, the reviewers defined eligible participants as “adult participants with chronic heart failure, […] a clinical syndrome characterised by breathlessness and fatigue that is caused by an inability of the heart to support an adequate circulation, that may limit exercise tolerance and may lead to pulmonary congestion and peripheral oedema”. Based on these criteria, reviewers should have excluded the trials by Burr, de Jonge, and Myers from this Cochrane review as none or few patients in these trials met this disease definition.1-3

In the trial by Burr et al,2 investigators excluded patients if “they had had congestive cardiac failure during the previous three months” or “they had ever had left ventricular failure”. The published report further notes that “an attempt was made to discover the original reason for which each patient had been given a diuretic” and that “in most cases, however, this information was not in the hospital notes”. They furthermore note that “ankle oedema was often mentioned in the notes, but in the majority there was no reference to cardiac failure”.

The trial by de Jonge et al specifically excluded patients with heart failure.3 First, the authors describe their objective as “to determine the effect of withdrawing diuretic drugs on oedema in patients prescribed them for only ankle oedema, excluding patients with cardiac […] failure”. In their methods, the authors describe their approach to excluding patients with a clear diagnosis of heart failure, such as those “[having] congestive heart failure or increased risk of developing it after stopping diuretic drugs,” or “heart failure previously established by a cardiologist, history of severe dyspnoea treated by the general practitioner as cardiac failure, atrial fibrillation, symptoms of right sided heart failure, palpable right ventricular pulsations, or hepatomegaly”. Therefore, de Jonge et al appeared to include only patients in whom heart failure was unlikely or ruled-out as the cause of ankle edema. Additionally, the Cochrane authors describe this trial as only including “participants with decreased ejection fraction (EF) measured by echocardiography”, but this is not described in the published report of the de Jonge trial.1,3

Similarly, the eligibility criteria in the trial by Myers et al excluded patients with definite or probable heart failure.4 In this trial, “concurrent digoxin therapy” was the most common reason for exclusion, with additional relevant reasons for exclusion being “active heart failure […] (clinical or radiological evidence of heart failure)” or hypertension. Corroborating this is the fact that only 9 out of 77 included patients were noted to have had “previous CHF” according to the study report’s patient characteristics table.

Based on the above published trial details, it is clear that 3 of the 4 studies contributing data to the Cochrane review’s ‘mortality’ and ‘worsening heart failure’ outcome analyses should be excluded according to the reviewers’ predefined review eligibility criteria.1-4 Exclusion of the Burr and Myers trials leaves only the Sherman trial for the ‘mortality’ analysis, demonstrating no statistically significant difference between diuretics and control (0 versus 2 deaths).1 Additionally, no trials remain for analysis for the ‘heart failure worsening’ outcome with exclusion of the Burr and de Jonge trials. As a result, exclusion of trials not meeting this Cochrane review’s predefined eligibility criteria substantially changes the review’s conclusions.

Second, further issues arise from attributing a causal role of diuretics in the reported reduction in mortality. In the trial by Burr et al, none of the 3 deaths in the control group were attributable to heart failure.2 Similarly, only 1 of the 8 deaths reported in the control group of the trial by Myers et al was attributable to heart failure, with the others attributed to cancer (3), respiratory disease (2), stroke (1) or gastrointestinal bleed (1).4 Such inconsistencies between all-cause mortality and heart failure-related mortality would deserve, at minimum, description by the reviewers in their Discussion section. Ideally, the impact of inconsistency between outcomes should be considered in the determination of quality of the body of evidence, such as by using the framework provided by the GRADE approach as described in the Cochrane Handbook.5

Third, the reviewers inappropriately exclude the results of the Myers trial from their analysis of ‘worsening of heart failure’.1 According to the authors, they excluded Myers from this analysis “because of heterogeneity for heart failure worsening in the diuretic group versus placebo (chi-square, 16.03; P = 0.001)”. The heterogeneity noted resulted from the increase in “withdrawal due to heart failure” in the diuretic group compared to the placebo group in this trial (6/29 versus 2/29). Such arbitrary exclusion from analysis constitutes selective outcome reporting bias. Rather than excluding the trial by Myers et al, which contributed greater statistical weight (38.9%) than either trials by Burr or de Jonge, the appropriate course of action according to the Cochrane Handbook would have been to evaluate methodological and clinical sources of heterogeneity, and to abstain from performing a meta-analysis of this outcome.5

Based on the above appraisal of critical issues present in Cochrane review CD003838, we urge editors of the Cochrane Heart Group to withdraw the aforementioned review from the Cochrane Library and issue a report on the Cochrane Heart Group website describing reasons for withdrawal. Authors of the review should then be provided with the opportunity to revise the review to meet the standards set by their protocol.

Thank you for your consideration,

Ricky Turgeon BScPharm, ACPR, PharmD Michael Kolber BSc, MD, CCFP, MSc

References 1. Faris RF, Flather M, Purcell H, Poole-Wilson PA, Coats AJS. Diuretics for heart failure. Cochrane Database Syst Rev 2012;2:CD003838. 2. Burr ML, King S, Davies HE, Pathy MS. The effects of discontinuing long-term diuretic therapy in the elderly. Age Ageing 1977;6:38-45. 3. de Jonge JW, Knottnerus JA, van Zutphen WM, de Bruijne GA, Struijker Boudier HA. Short term effect of withdrawal of diuretic drugs prescribed for ankle oedema. BMJ 1994;308:511-3. 4. Myers MG, Weingert ME, Fisher RH, Gryfe CI, Shulman HS. Unnecessary diuretic therapy in the elderly. Age Ageing 1982;11:213-21. 5. Higgins JPT, Green S (editors). Cochrane Handbook for Systematic Reviews of Interventions Version 5.1.0 [updated March 2011]. The Cochrane Collaboration, 2011. Available from www.cochrane-handbook.org."

On 2016 Aug 29, CREBP Journal Club commented:

The three comparisons included in the Hope-3 trial show the effect of a) blood pressure lowering medication b) lipid lowering medication and c) the combination in patients who would traditionally be considered low risk (a risk over 5.6 years of approximately 5% or about 1% pa). The results are broadly consistent with previous trials of blood pressure and lipid lowering therapy, showing similar reduction in risk of cardiovascular events as a proportion of baseline risk. The non-significant results of the blood pressure lowering trial might be explained by either the hypothesis put forward by the study authors (greater effect in patients with higher baseline blood pressure) but could also be explained by the high proportion of patients using non-trial blood pressure lowering drugs at baseline and the difference in the number of patients using non-trial drugs between the active and the placebo arms of the trial. From the results of the lipid lowering arm of the trial, 1000 people would need to take the drug for 5.6 years to prevent 11 events. Whether this is worthwhile needs consideration at both a public and individual patient level.

On 2016 Aug 29, Jenny Doust commented:

None

On 2016 Jun 11, Madhavi Bhargava commented:

MDR-TB household contacts in 2016

Madhavi Bhargava, Dept of Community Medicine, Yenepoya Medical College, Yenepoya University, Mangaluru-575018, Karnataka, India

The opinion piece by David Moore (Moore DA, 2016) regarding multidrug resistant tuberculosis (MDR-TB) is a very important document for caregivers and policy makers alike. One cannot agree more with the author that pending the results of three drug trials until 2020 the alternative to preventive therapy is not to do nothing at all. There is indisputable scientific merit in registering MDR-TB contacts, screening them for active disease, drug-susceptibility testing in co-incident cases and follow-up of remaining MDR-exposed household contacts. The subsequent dilemma of deciding what, if more can be offered to the remaining MDR-exposed household contacts is what is discussed in this comment.

• Learning from the experiences in treating drug-sensitive tuberculosis (DS-TB) is last but not the least of the seven guiding principles of the policy brief of November 2015 (http://sentinel-project.org/wp-content/uploads/2015/11/Harvard-Policy-Brief_revised-10Nov2015.pdf). Contacts of MDR-TB cases are no different from contacts of DS-TB cases of pre-chemotherapy era. Which means that addressing the social determinants such as reduced stress, reduced intensity of TB exposure, proper housing and adequate food supply cannot be ignored (Bhargava A, 2012).

Moreover, the guidance on prevention of MDR-TB from World Health Organization (“(1) Early detection and high quality treatment of drug susceptible TB, (2) early detection and high quality treatment if drug resistant TB, (3) effective implementation of infection control measures, (4) strengthening and regulation of health systems. (5) Addressing underlying risk factors and social determinants)” needs careful consideration.

• Regarding effective implementation of infection control, one of the most cost-effective measures is airborne infection control (AIC) and cough-hygiene. In countries like India, AIC systems are found to be poorly developed and implemented (Parmar MM, 2015). Provision for safe sputum disposal and adequate patient education for the same at individual and family level, often gets neglected in chemotherapy centered approach in high-burden developing countries.This has obvious implications on the burden of MDR-TB in a country.

• Lastly, undernutrition which is often considered a social determinant, should be considered a biological risk factor of tuberculosis (resistant or sensitive) since it has definite influence on immune mechanism of an individual (Schaible UE, 2007). Nutritional support at family level can be added in the battery of interventions for household contacts of MDR-TB patients pending much desired definitive chemotherapeutic agents.

Conflict of interest: Author declares no conflict of interest

On 2016 Apr 04, Sujai Kumar commented:

Disclaimer: I am one of the authors of this paper.

This is the peer-reviewed version of the bioRxiv preprint that systematically refutes each of the 8 lines of evidence provided by Boothby et al for extensive HGT.

We hope this paper will correct the scientific record. A blog post describing the behind-the-scenes aspects of this paper is available at Eight things I learnt from #tardigate

On 2016 Apr 11, Hilda Bastian commented:

The strongly declarative title of this paper makes a claim that is not supported by its contents.

The authors argue that only one study (Galesic M, 2009) has reported "a substantial benefit" of natural frequencies. That claim is not based on an up-to-date systematic review of the studies on this question. A systematic review is needed, because there are multiple studies now with varying methods, in various populations, and in relevant contexts, that need to be considered in detail.

These authors cite some studies that support their position (all in the context of treatment decisions). However, this is only a part of the relevant evidence. Among the studies not cited in this paper, there is at least one looking at medical tests (Garcia-Retamero R, 2013), others at treatments (e.g. Cuite CL, 2008, Carling CL, 2009, Knapp P, 2009 and Sinayev A, 2015), and at least one in a different field (Hoffrage U, 2015). Some find in favor of natural frequencies, others for percentages, and others find no difference. I don't think it's possible to predict what a thorough systematic review would conclude on this question.

This study by Pighin and colleagues is done among US residents recruited via Mechanical Turk, and includes some replication of Galesic M, 2009 (a study done in Germany). The authors conclude that Galesic and colleagues' conclusion is attributable to the outcome measure they used (the "scoring artifact" referred to in the abstract here). However, their study comes to the same conclusion - better understanding with natural frequencies - when using the same outcome measure. They then applied more stringent outcome measures for "correct" answers, but the number of people scoring correct were too small to allow for any meaningful conclusion. For their two studies, as well as for Galesic M, 2009, both methodological detail and data are thin. Neither the original study nor this replication and expansion, provide "the answer" to the questions they address.

On 2016 Sep 11, Seth Bordenstei commented:

The authors write that the hologenome concept is strictly based on a premise that the holobiont evolves as a "single cooperative unit". This central argument is unfortunately not accurate and misrepresents the framework. Holobionts and hologenomes are structural entities subject to ecological and evolutionary forces at varying levels. A clarification and review of the literature can be found here:

http://msystems.asm.org/content/1/2/e00028-16

Abstract: Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

On 2016 Apr 02, Harald HHW Schmidt commented:

This paper relies on two anti-NOX4 antibodies for which no validation is presented. One alternative interpretation of the finding that two antibodies give different localisations would be that at least one of them has specificity issues. I have yet to see a commercial NOX4 antibody that is specific. The paper also discusses splice variants without showing any data on them.

On 2016 Dec 20, Pertti Hakkinen commented:

Readers of this BraCVAM-focused publication might be interested in a 2016 "International Harmonization and Cooperation in the Validation of Alternative Methods" publication ( https://www.ncbi.nlm.nih.gov/pubmed/27671730 ) that notes "the International Cooperation on Alternative Test Methods (ICATM) was established in 2009 by validation centres from Europe, USA, Canada and Japan. ICATM was later joined by Korea in 2011 and currently also counts with Brazil and China as observers."

On 2016 Oct 05, Cicely Saunders Institute Journal Club commented:

The Cicely Saunders Institute journal club discussed this paper on 5th October 2016.

We thought that this review addressed an important question in relation to the pharmacological management of breathlessness at the end of life, and agreed that an update to the previous Cochrane review in this area was warranted.

We were interested in the selection of papers and the fact that some of the studies in the original Jennings et al review were deemed of insufficient quality to include in the update. We also wondered if more information could have been included about the authors’ definition of “advanced progressive illness”.

There was a lively discussion about the heterogeneity of included studies, which was attributed to variations in individual study design, and in the drug, dose and route used for the intervention. Some argued that focusing solely on studies evaluating morphine sulphate, which has high affinity for the µ opioid receptor (the subtype present in the lung) and also appeared to have the most promising results in sub-group analysis, might have provided a clearer picture of the benefit of opioids. Others pointed out that pooling studies for meta-analysis provides a larger sample, and that focusing on morphine alone would exclude patients with renal impairment.

We noted that when reporting the breathlessness outcomes, it would have been useful to define a minimal clinically important difference in breathlessness as well as an effect size, since it is difficult to tell if the standardised mean differences from the meta-analysis would be clinically relevant. In addition lack of standardisation of outcome measurements limited the potential meta-analysis.

We considered that as presented in this paper, the evidence on opioids in breathlessness is insufficient to guide practice. We agreed with the authors that larger, fully powered studies with adequate wash out periods and standardised dosing schedules are the starting point to improve the evidence base. We thought that focusing future studies on a single opioid (morphine sulphate seems the most promising candidate) might reduce heterogeneity and allow clearer measurement of any benefit.

Comment written by Dr Simon Etkind and Dr Sabrina Bajwah

On 2016 May 03, Marcus Munafò commented:

Joshi and colleagues report that genetic variants in the CHRNA5-A3-B4 gene cluster and the APOE gene are associated with lifespan. This is not surprising – the former influences smoking behaviour, which in turn leads to a number of adverse health outcomes, while the latter influence Alzheimer disease risk. The critical insight here is that genetic studies can provide information about the role of modifiable, behavioural determinants of health and disease, such as smoking [1]. In many cases, this will be the most parsimonious explanation. For example, while we agree with Joshi and colleagues that the effects of CHRNA5-A3-B4 on lung cancer remain after adjustment for self-reported smoking intensity, this is most likely because self-report measures poorly capture actual tobacco exposure, given inter-individual differences in smoking topography (e.g., number of puffs taken per cigarette, depth of inhalation, etc.) [2]. When the association between and CHRNA5-A3-B4 smoking intensity is estimated using cotinine, a precise biomarker of exposure, this is sufficient to fully account for the observed association between CHRNA5-A3-B4 and lung cancer [3]. Joshi and colleagues describe the genes they identify as associated with lifespan as “very pleiotropic”, but the distinction between biological (or horizontal) and mediated (or vertical) pleiotropy is important here (4). The former refers to a genetic variant influencing multiple separate biological pathways, while the latter refers to the effects of a genetic variant on multiple outcomes via a single biological pathway. In our opinion, many effects of CHRNA5-A3-B4 on health outcomes are likely to be the result of mediated pleiotropy. In other words, smoking kills.

Marcus Munafò and George Davey Smith

1. Gage, S.H., et al. G = E: What GWAS Can Tell Us about the Environment. PLoS Genetics, 2016. 12(2): e1005765.

2. McNeill, A. and Munafò, M.R. Reducing harm from tobacco use. Journal of Psychopharmacology, 2013. 27(1): p. 13-8.

3. Munafò, M.R., et al. Association between genetic variants on chromosome 15q25 locus and objective measures of tobacco exposure. Journal of the National Cancer Institute, 2012. 104(10): p. 740-8.

4. Davey Smith, G. and Hemani G. Mendelian randomization: genetic anchors for causal inference in epidemiological studies. Human Molecular Genetics, 2014. 23(R1): p. R89-98.

On 2016 Sep 04, Raphael Stricker commented:

Study Conclusion is Incorrect This study did not have a true control group because all chronic Lyme disease patients received an additional two weeks of intravenous ceftriaxone therapy. The study clearly shows that this additional antibiotic treatment was associated with significant improvement in the SF-36 quality of life scale in all patient groups (see Figure 2). Thus the conclusion that additional antibiotic therapy was ineffective for chronic Lyme disease is incorrect.

Disclosure: RBS is a member of the International Lyme and Associated Diseases Society (ILADS) and a director of LymeDisease.org. He has no financial or other conflicts to declare.

On 2017 Mar 15, Michelle Fiander commented:

My comment on this paper pertains to the authors' methodology and rationale for it. This paper is not a systematic review and it does not claim to be, but it describes its literature search as systematic, refers to duplicate screening, and includes a study flowchart--each of which are part of systematic review methodology.

Despite describing its lit search as 'systematic,' there is insufficient detail to reproduce the strategies or to confirm the number of results identified and screened for the review. Table 1 which is not a flowchart but is labeled "Flowchart of all clinical studies included for the final analysis" implies that terms i-v, and "secondary" terms were combined using Boolean OR to create two sets of concepts which were then combined using Boolean AND. If this is the case, the search finds about 100 in Pubmed; 87 in Embase, 7 in Cochrane, 1690 in Google Scholar, 32,200 in Science Direct (sciencedirect.com), and 8 articles and 9 book chapters in Springer Link (springerlink.com). These numbers do not correspond with the number of citations retrieved per Table 1.

In terms of how references were screened and studies selected for inclusion, the authors describe the process as follows: "Study eligibility was assessed independently by two observers and all assessments were then crosschecked." What is absent here are the stages at which duplicate screening occured, e.g. title/abstract? full-text? both? Further, with dual screening there are typically conflicts, but we are not told how they are resolved.

Systematic reviews are popular; some might say they are "flavor of the ....decade." Perhaps it is this popularity that has led to a glut of poor quality systematic reviews in the literature. Whatever the reason, using the adjective 'systematic' to describe one or two aspects of a review in the absence of a full and complete systematic approach does, I suspect, contribute to misunderstandings of the purpose, process and value of true systematic reviewing and evidence synthesis.

On 2016 Dec 31, David Keller commented:

If placebo works as well as acupuncture, reduce healthcare costs with placebo acupuncture

The disadvantages of sending patients to a licensed acupuncturist for treatment include the high cost of acupuncture, which must be administered by a licensed acupuncturist, exposure of the patient to the influence of the acupuncturist, who may prescribe other unapproved treatments, such as untested herbal medicines, and the small but finite possibility of injury or infection from the needles. The sham acupuncture procedure in this study employed sharp toothpicks, tapped and twisted on the patient's skin without piercing it, which nevertheless yielded good patient blinding (by standard assessment).

The investigators chose not to include an observation-only arm in this study, to avoid introducing negative expectation effects and other complications. However, they cite the typically long-lasting duration of the fatigue encountered with Parkinson's disease [PD], and its treatment-refractory nature, thus making a strong argument in favor of treatment of PD-associated fatigue with acupuncture to achieve the substantial placebo benefit seen in both the acupuncture and control groups of this study.

The fact that acupuncture provides the same benefit as placebo sham acupuncture suggests that the observed benefits can be achieved at a lower cost by having physicians administer sham acupuncture as an office procedure. Sham acupuncture should be easy to learn and administer because it does not require the practitioner to study the concepts of Qi ("chee", life energy), meridians, nor any of the other complex conjectures at the basis of traditional Chinese folk medicine, nor to obtain a special license.

The question of whether it is ethical for a physician to perform and bill for a sham placebo procedure begs a similar question regarding the ethics of referral to an acupuncturist for treatments which do not differ, in effect, from placebo.

On 2016 Mar 31, Mojtaba Heydari commented:

Iranian herbal distillates, as harmful as eating an apple!

In this paper, Shirani et al, have measured methanol content of 84 samples of herbal distillates from Iran market. The results showed the methanol concentration ranging from 43 to 277 mg/L, more than half of samples (45/84) containing methanol levels beyond the standard limits according to the Iranian standard (100mg/L). The authors concluded necessity for" warning to watch out for the latent risk problem of methanol uptake".

However the hazard mentioned in conclusion seems to be so exaggerating. Comparing to a potential exposure of 1,000 mg of methanol per day from fruits and vegetables (1), it seems that 277 mg/L (as the maximum amount of methanol in samples of the present study) can not be that hazardous. To become more understandable, each glass (200 cc) from the distillates with the highest amount of methanol, contains just about 50% of methanol in one medium size apple (200 gram, contains about 100 mg of methanol). (1)

In fact, the problem is the mentioned maximum standard level (100mg/L) for methanol (which is presented without any reference). As author has mentioned the American standard limit for methanol in juices is 460 mg/L, which is far more than highest Iranian distillate sample. According to Australian Register of Therapeutic Goods for complementary medicines, Health Canada for natural products, and European Medicines Agency for Herbal medicinal products, 3000 ppm is mentioned as limit for methanol intake . (2)

So it can be concluded that, despite the importance of monitoring the methanol content of herbal distillates, current samples shows far less amount of methanol than the upper limits of worldwide standards. If the national scale standard recommends the upper limit of 100 mg methanol, it should be revised to allow eating more than one apple a day!

References: 1. Food Standards Agency, Committee on Toxicity of Chemicals in Food, Consumer Products and the Environment. COT statement on the effects of chronic dietary exposure to methanol. Available here 2. Mundkinajeddu D, Agarwal A. Residual Methanol in Botanical Dietary Ingredients - Perspectives of a Manufacturer. HerbalEGram 2014, 11(8). Available here

On 2016 Nov 23, Ricky Turgeon commented:

Critical appraisal of this study is available at http://nerdcat.org/studysummaries/dapt-score

On 2016 May 22, Daniel Schwartz commented:

The DAPT Score can be used online or via a mobile app http://qxmd.com/calculate/calculator_373/dapt-score

Conflict of interest: Medical Director, QxMD

On 2016 Mar 31, Christophe Dessimoz commented:

The article is published as open access and is thus freely available from the publisher here: http://dx.doi.org/10.1016/j.tplants.2016.02.005

Furthermore, the "story behind the paper" is available in this blog post: http://lab.dessimoz.org/blog/2016/03/24/what-are-homoeologs

On 2016 May 04, Richard Unwin commented:

Hmmm,

Care should be taken with the interpretation of results in this study. The age matching between the case (HD) and control groups is not great.

Cases have a mean +/- s.d. age at death of 57+/-12.3, while the controls are 79 +/- 13.45. A Welch’s T-test comparing these data gives p=0.00011. The observations made in this study could therefore simply be normal changes in the ageing brain, rather than as a result of HD?

On 2016 Apr 09, Lydia Maniatis commented:

Turning a blind eye to the well-established role of stimulus structure in all aspects (including thresholds, salience, etc) of perception is a good method for proliferating either reliably falsifiable generalisations or generalisations that can't be challenged because they're so vague.

In other words a. results are contingent on the stimulus and a different stimulus could well lead to different results, and b. words like "weak target" "highly visible stimuli" describe the percept not the stimulus, and so avoid specifying conditions in physical terms.

Anyway, what is interesting about "perisaccadic compression"?

On 2016 Dec 18, Laura Williams commented:

Our online journal club discussed this paper on May 18, 2016. https://www.youtube.com/watch?v=N5x4t0eRts8

On 2016 Aug 18, Peter Hajek commented:

Cigarette smoke killed the cells within 24 hours, e-cig vapour damaged them after extended exposure over up to 8 weeks. The abstract ignores this. The authors of this study are Yu et al., the authors listed above are not responsible for this paper, they in fact published a critique explaining the problems in it and in the accompanying media release - see below.

On 2016 May 19, Clive Bates commented:

For clarity, it is important to point out that the abstract above is drawn from a different paper Yu V, 2016. It is not the abstract for this PubMed entry.

This PubMed entry actually refers to a highly critical commentary on the Yu V, 2016 paper and the abstract shown above. Please use the full-text link at the top right of this page or access the commentary here:

Holliday R, Kist R, Bauld L. Commentary on Yu et al, Evidence-Based Dentistry (2016) 17, 2–3. doi:10.1038/sj.ebd.6401143

On 2017 Sep 23, Karim Abbas commented:

I see the data in Figure 3 confusing and might involve a bias. Figure 1 clearly depicts a stable PS-LTP recorded for 15 minutes every day for successive 14 days. However, in Figure 3b the magnitude of PS-LTP with anisomycin (but without "reactivation" (Sic1)) looks decreasing from the values between 0-3 days, albeit non significantly (I guess the lack of significant differences was due to high SD; the values of SD were not reported in the article but can be seen in the figures). There is no explanation though for that tendency of decreasing PS magnitude compared to stable values depicted in Figure 2. More intriguing is why the recording interval following "reactivation" was restricted to 2 days (total 5 days), which is much shorter than the one depicted in Figure 1 (14 days)?

On 2016 Sep 19, Saurabh Gupta commented:

This article discusses which of the vascular channels may represent fifth arch artery based on current knowledge of embryogenesis.

On 2016 Sep 19, Saurabh Gupta commented:

Fifth arch artery, one of the most controversial topics in the embryology of cardiovascular system.

On 2016 May 09, M Mangan commented:

An interesting discussion of this study can be found here: http://www.marklynas.org/2016/04/deformed-gmo-franken-butterflies-not-fast/

Edit to add: a response from the Rothamsted researchers can be found here as well: <http://rothamsted.ac.uk/sites/default/files/Comment on Hixson et al. 2016_Deformed butterfly wings when feeding on artificial diets containing EPA and DHA.pdf>

On 2016 Apr 19, S. Hong Lee commented:

Many thanks for your comments. The two models (response variables) do not simply represent association between genome-wide markers, previously associated with schizophrenia, and woman’s age at first birth. The two models (response variables) are the functions derived from the relationship between the schizophrenia risk in children and their mother’s age, studied in a large national-wide study (please see reference #11 in the paper). So what we tested was that the relationship between the schizophrenia risk in children and their mother’s age found from the previous (totally independent) study was associated with the relationship between schizophrenia risk profile score (inferred from SNP effects estimated in another independent SCZ GWAS data set) and age at first birth. Although we used SNP effects to infer risk profile score, we did not think the test should be corrected for the number of SNPs. We used a response variable and one set of risk profile score (N x 1) in a single test (not multiple sets of risk profile score).

In addition, I would like to explain a bit more about the variance explained by the predictor in the target data set (R2 in Table 2). The variance explained by the predictor in the target data set is not the actual variance of the underlying effects. It means it can increase more when there is less sampling error (i.e. with a larger samples size). For example, if you estimate SNP effects in a discovery (or training) data set, and the estimated SNP effects are projected into an independent target data set, the R2 explained by the predictor (from the estimated SNPs effects) depends on the estimation error of the SNP effects. So, if the sample size in the discovery data set (SCZ GWAS in our case) is increased, the R2 can be increased (hence lower p value).

On 2016 Mar 31, Anastasia Levchenko commented:

Reading the paper, I did not see a clear mention that the calculated p-values (Table 2) were corrected for multiple testing (and if they were, it is not clear which statistical method was used). For instance, “statistically significant” association between a genome-wide marker and a phenotype is represented by a p-value ≤ 5E-08, if the Bonferroni correction is used. Don’t the two models (response variables), used in the present study, represent association between genome-wide markers, previously associated with schizophrenia, and woman’s age at first birth? If they do, then it is not clear based on what grounds the authors claim that the p-value = 4.1E-04 is “statistically significant” in the present study setting. Near the end of Discussion the authors state that “A caveat of our findings is that the genetic association between risk of SCZ and delayed AFB was only marginally significant given the number of analyses performed, perhaps reflecting smaller sample size and correspondingly larger standard errors for women with delayed AFB, and so require replication in a larger sample”, probably referring to the p-value = 1.4E-02. Again, the reader sees no support for the statement that p = 1.4E-02 is “significant”, although “marginally”.

On 2016 Mar 29, Ludovic Barault commented:

Hi, People who are interesting in this research area should also read some of the recent studies (from our lab and others) currently unreferenced in the above manuscript:

• Tumor MGMT promoter hypermethylation changes over time limit temozolomide efficacy in a phase II trial for metastatic colorectal cancer. PMID: 26916096

• Dose-Dense Temozolomide in Patients with MGMT-Silenced Chemorefractory Colorectal Cancer. PMID: 26538496

• Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer. PMID: 26113646

• Activity of temozolomide in patients with advanced chemorefractory colorectal cancer and MGMT promoter methylation. PMID: 24379162

• A phase II study of temozolomide in patients with advanced aerodigestive tract and colorectal cancers and methylation of the O6-methylguanine-DNA methyltransferase promoter. PMID: 23443801

• Promoter CpG island hypermethylation of the DNA repair enzyme MGMT predicts clinical response to dacarbazine in a phase II study for metastatic colorectal cancer. PMID: 23422094

• Works from B. Kaina's lab

Sincerely,

On 2016 Apr 04, Donald Forsdyke commented:

COLLECTIVE GENE FUNCTIONS SHOULD BE TAKEN INTO ACCOUNT

Gene products have both individual and collective functions (e.g. the Donnan equilibrium; 1). Wang et al. suggest that female susceptibility to autoimmune diseases may reflect incomplete dosage-compensation, which results in overexpression of certain X chromosome-located, immunity-related, genes (2). However, they refer to studies by Scofield and colleagues [ref. 11] on diseases with changes in numbers of entire X chromosomes (e.g. XXY), indicating biallelic expression of many genes. Scofield has noted that collective, as well as specific, gene functions must be considered (3). This is in keeping the hypothesis that the cytosolic aggregation pressure exerted by the protein collective is immunologically important (4, 5). <br>

1.Loeb J (1921) Donnan equilibrium and the physical properties of proteins. 1. Membrane potentials. J Gen Physiol. 3:667-90. Loeb J, 1921<br>

2.Wang J et al. (2016) Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Proc Natl Acad Sci USA doi/10.1073/pnas.1520113113 Wang J, 2016<br>

3.Dillon SP et al. (2012) Sex chromosome aneuploidies among men with systemic lupus erythematosus. J Autoimmun 38:J129-J134.Dillon SP, 2012<br>

4.Forsdyke DR (2009) X chromosome reactivation perturbs intracellular self/not-self discrimination. Imm Cell Biol (2009) 87:525-528. Forsdyke DR, 2009<br>

5.Forsdyke DR (2012) Ohno's hypothesis and Muller's paradox: sex chromosome dosage compensation may serve collective gene functions. BioEssays 34:930-933. Forsdyke DR, 2012

On 2017 Feb 17, Arturo Martí-Carvajal commented:

Trial authors did not report randomization process. Randomization is oly mentioned into abstract. Where are inclusion and exclusion criteria? This "RCT" is not clear.

On 2016 May 23, Maurizio Battino commented:

The post released by AG Atanasov, revealed the wide interest that CoQ has arisen in health debates. He explained, in a a few words and for a public which is not professionally involved in health care, where, how and why CoQ has a critical/strategic role in our physiology and well-being. When I began to investigate CoQ antioxidant properties in health and disease in addition to the well-known role in the mitochondrial respiratory chain of this molecule, about 25 years ago, I was considered one of the pioneer in the field and several criticisms arose from reviewers (e.g., it took more than 2 years to publish DOI: 10.1016/0003-2670(91)80070-A and DOI: 10.1016/0098-2997(94)90016-7 and also DOI: 10.1024/0300-9831.69.4.243 suffered important delays). 25 years later, CoQ is widely recognized as an active compound with important features which go beyond its primitive redox role and also those antioxidant properties my group proposed at the beginning. Nowadays, we have clear proofs of its involvement in several pathologies and we directly found evidences it has, among others, key roles in aging (doi: 10.1093/gerona/glv063, doi: 10.1016/j.freeradbiomed.2011.02.004, doi: 10.1016/j.mad.2009.11.004, DOI: 10.1023/A:1023754305218), in periodontal diseases (doi: 10.1016/j.phrs.2014.10.007, doi: 10.1016/j.fct.2009.06.026, doi: 10.1016/j.numecd.2009.03.003), in fibromialgia (doi: 10.1089/ars.2013.5198, doi: 10.1089/ars.2013.5260), in Papillon-Lefevre Syndrome (DOI:10.1080/1071576031000083116) and in modulating the effects of nutrients as outlined by this very last review (doi: 10.3390/molecules21030373).

On 2016 May 12, Atanas G. Atanasov commented:

Consumer Health Digest Scientific Abstract of this article is available at: https://www.consumerhealthdigest.com/anti-aging/coenzyme-q-role-in-dietary-therapy-against-aging.html

On 2016 Apr 22, Toby Gibson commented:

Dr. Gack, Thank you for taking the time to comment. One interesting way in which NS3 could potentially regulate 14-3-3 epsilon would be to bind across the top of the groove. Such a binding mode could act as a gatekeeper for phosphopeptide entry/exit into the deep binding pocket. This presupposes that the interaction is direct and strong enough and for this, bacterially expressed proteins need to be assessed in vitro for their dissociation constant.

Incidentally, regarding the work that you are building upon (Liu et al., 2012, PMID:22607805), there was no attempt to identify a candidate motif. But again, RIG-I is also unlikely to have a 14-3-3 phosphopeptide binding mode. RIG-I is almost entirely structured with a few short interdomain linkers. I don’t see good candidates for canonical 14-3-3 binding motifs in RIG-I. So, in this whole system, in my opinion there are no strong clues toward elucidating the molecular details of how 14-3-3 epsilon might be interacting. Assuming that this interaction also validates in vitro, there is some useful structural biology to be done.

On 2016 Apr 19, Michaela Gack commented:

Dr. Gibson’s comment about our manuscript solely stated that the viral RxEP motif identified in the Dengue NS3 protein does not fulfill all of the criteria of conventional 14-3-3-binding motifs found in cellular 14-3-3-interacting proteins. The main conclusions of our study, that the NS3 protein of Dengue virus binds to 14-3-3epsilon and thereby antagonizes RIG-I translocation to mitochondria and type I interferon induction, were never questioned by Dr. Gibson.

Using mapping experiments and site-directed mutagenesis, we identified that the 64-RxEP-67 motif in the Dengue NS3 protein is essential for 14-3-3epsilon binding. Mutation of the central Glu66 (E66) residue to positively-charged Lys66 (K66) markedly reduced the binding of NS3 to 14-3-3epsilon. Additional mutation of Arg64 to Lys64 (termed ‘NS3(KIKP)’ mutant) led to a nearly complete loss of binding to 14-3-3epsilon. These data together with the similarity of the viral RxEP motif with the cellular 14-3-3-binding motif Rxx(pS/pT)xP, where pS/pT indicates a phosphorylated Ser/Thr residue, suggested that the negatively charged E66 serves as a phosphomimetic residue. Although our study indicated that the RxEP motif is required for 14-3-3epsilon binding, our data also suggested that additional as-yet-unidentified residues in the Dengue NS3 protein are important for 14-3-3epsilon interaction, as introduction of the RxEP motif into the NS3 protein of Yellow Fever virus, which is unable to bind 14-3-3epsilon, did not result in gain of 14-3-3epsilon binding. Thus, the full characteristics of the binding mode of Dengue NS3 and 14-3-3epsilon and their binding affinity remain to be determined in future studies, as well as additional residues in NS3 and 14-3-3epsilon that are engaged in the interaction.

On 2016 Apr 08, Toby Gibson commented:

Is there an RxEP motif in Dengue NS3 protein?

This comment addresses the plausibility that the reported RxEP motif in Dengue NS3 is a genuine 14-3-3 binding motif and as such a target for rational design of therapeutics. It does not address other aspects of this published work, in particular that the NS3 protease plays a role in antagonising the cellular relocation and antiviral activity of RIG-I.

Viral mimicry of cellular protein motifs is very common and frequently provides a useful insight into the cellular mechanisms that are being disrupted (Davey et al., 2011). Given our interest in these interactions, I was keen to read this new viral motif paper. Given the current importance of flaviviral infections in human health, it then seemed desirable to post here the explanation as to why RxEP cannot be a phosphomimetic for 14-3-3 proteins. It is my hope that this comment will be of value to the Dengue research field e.g. in how follow up experiments might be planned.

There are several molecular structural issues relevant to 14-3-3 / phosphopeptide interactions:

Proline is disallowed at the +1 position. There is no ambiguity about this. Phosphopeptide arrays probed by (yeast) 14-3-3 clearly show that Pro is disallowed at +1 (Panni et al., 2011). The structural explanation is that there is no physical space for proline because the backbone peptide bond NH group hydrogen bonds to the 14-3-3 protein (residue Asn176 in the epsilon isoform) as part of local geometry that orients the adjacent phosphorylated side chain (See e.g. Fig. 1D, Molzan et al., 2012). Biologically, rejection of proline at +1 is crucial for separate readout of sites phosphorylated by basophilic kinases (PKA, CAMK etc.) vis-a-vis proline-directed kinases (MAPKs, CDKs etc.) as discussed by Panni et al. (2011).

Arginine is typically present at either positions -3 or -4 in many well-studied phosphopeptides binding to 14-3-3 proteins. Presence of Arginine at position -2 is also sometimes observed and structures show that the residue orients to H-bond with the phosphate group. Therefore Arg at the -2 position is not an issue in the present context.

14-3-3 phosphomimetics. We already know that aspartic acid cannot function as a mimetic (de Chiara et al., 2009). This means that the proposed RLDP motif in WNV NS3 can’t work. I am unaware whether a glutamic acid mimetic has previously been evaluated in vitro for its binding affinity. The reason why it may not be possible for any 14-3-3 phosphomimetic is that the PO3- group is complemented by three H-bond donor ligands: in epsilon they are Arg57, Arg130, Tyr131 (Fig. 1D, Molzan et al., 2012). The single negative charge and planar geometry of the carboxyl group rule out an equivalent interaction for glutamate.

The well-studied 14-3-3-binding phosphomotifs are overwhelmingly, perhaps exclusively, found in regions of intrinsically disordered protein (IDP). As the authors note, the motif postulated in NS3 is on the protein surface but is very well folded. Structurally-embedded motif candidates require a high standard of proof. It is essential that the affinity of the interaction between purified NS3 and 14-3-3 be measured in vitro. In our recent motif discovery guidelines paper, we have explained why a short linear motif is never reliably assigned unless in vitro binding assays using purified components have been undertaken in addition to the in-cell experiments (Gibson et al., 2015).

In my view the experiments reported here also do not rule out indirect interaction modes. The most direct experiment, in Fig. 1G, used HEK293T cell extracts for the GST-NS3 bead attachment and this might allow bridging proteins to be complexed with NS3 that can secondarily bind the added 14-3-3.

To recap, the data presented in the paper here indicate that NS3 and 14-3-3 epsilon associate within the same macromolecular complex. In my view, whether the interaction may be direct or indirect has not been unambiguously determined.

I wish to conclude with two straightforwardly testable predictions:

1. A synthetic peptide encompassing the viral RxEP sequence will bind 14-3-3 epsilon with an affinity that is millimolar or weaker when measured by ITC or an equivalent solution-based assay.

2. If NS3 directly and convincingly binds 14-3-3 epsilon at micromolar or nanomolar affinity, when measured by ITC or equivalent, it will do so by an interface that does not involve phosphomimicry.

References

Davey NE, Travé G, Gibson TJ. How viruses hijack cell regulation. Trends Biochem Sci. 2011 Mar;36(3):159-69.

de Chiara C, Menon RP, Strom M, Gibson TJ, Pastore A. Phosphorylation of S776 and 14-3-3 binding modulate ataxin-1 interaction with splicing factors. PLoS One. 2009 Dec 23;4(12):e8372.

Gibson TJ, Dinkel H, Van Roey K, Diella F. Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal. 2015 Nov 18;13:42

Molzan M, Weyand M, Rose R, Ottmann C. Structural insights of the MLF1/14-3-3 interaction. FEBS J. 2012 Feb;279(4):563-71.

Panni S, Montecchi-Palazzi L, Kiemer L, Cabibbo A, Paoluzi S, Santonico E, Landgraf C, Volkmer-Engert R, Bachi A, Castagnoli L, Cesareni G. Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens. Proteomics. 2011 Jan;11(1):128-43.

On 2016 Mar 24, Jeromy Anglim commented:

Thanks for posting a comment. I just wanted to add a few thoughts on your points.

Relationship between type D and outcomes were not moderated by illness group. For us, this was the important conclusion that we want researchers to think about. There is a lot of research done examining Type D in specific illness groups. To some extent implicit in such research is the idea that the effect of Type D might vary based on illness type. While this may be true, this study presents some evidence that at least for the illness groups and variables studied, this is not the case.

The effect of negative affect on social support and the effect of social inhibition on health behaviours failed to reach statistical significance. I would not say that it failed. This is actually an important finding that supports the idea that the subscales of Type D provide different correlates (i.e., negative affectivity is related more to affective processes, and social inhibition is related more to social processes). Presumably, this is as we would expect. Although if you wanted to be critical, there is the idea that NA is merely neuroticism, and SI is a mix of neuroticism and introversion (see Horwood, Anglim, Tooley, 2015). Whether that is a problem probably depends on how primary you view Big 5 personality.

Limitations: I think we note the limitations you mention in the limitations section. That said, those limitations only relate to certain points of the paper. For me personally, I think that the paper has two fairly important implications for researchers working with Type D personality. The first relates to the general lack of variation in effects by group as discussed above. Second, we did a comparative regression analysis comparing a range of different scoring systems for Type D personality. The results suggested that binary Type D is a poor predictor, and there was limited evidence for NA by SI interactions effects. Rather entering NA and SI as two separate predictors generally resulted in the best prediction of outcomes. This goes agains the implicit claims of Type D that there is an interactive effect and that cut-offs are appropriate for Type D. Importantly, all these analyses also speak to the novelty of the Type D construct and the rationale for choosing the two particular subscales for inclusion.

Thus, for me, the paper provides a nuanced and critical assessment of the predictive validity of Type D personality. In particular, I'd encourage other researchers working with Type D personality (and some are doing this already) to run the comparative regression analyses in their samples.

On 2016 Mar 23, Andrew Kewley commented:

Given that the main hypothesis was unsupported by the evidence, it seems strange that there is no mention of this in the abstract.

The hypothesis was stated: "that functional somatic syndromes, conditions that are characterized primarily by general somatic complaints of unclear etiology, such as chronic fatigue syndrome or fibromyalgia, may be more susceptible to the effects of Type D personality than illnesses of known etiology such as type 2 diabetes or arthritis."

The authors did not find a difference in the prevalence of "Type D personality" between the two chronic illness groups. Likewise, the effect of negative affect on social support and the effect of social inhibition on health behaviours failed to reach statistical significance between the two chronic illness groups after correcting for multiple comparisons.

The study had key limitations, in particular it was based on a convenience sample and self-report questionnaires rather than objective measures of symptom impact and social support. The sample size was adequate.

While there was much speculation in the discussion, the most likely directional association between the questionnaire results and illness is simply that chronic illness contributes to affective suffering.

On 2016 Apr 29, Geriatric Medicine Journal Club commented:

This article was critically appraised at the April 2016 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). While there were concerns about the level of commercial influence in the included studies, the overall young age of the patients, the lack of inclusion of other treatment modalities (exercise, narcotics), and the absence of analysis of harm; this paper brought forth important doubts about effectiveness of acetaminophen. How to reconcile the known harms of NSAIDs and the clinical effectiveness on pain and function is the essence of ongoing discussion.

Did you miss the #GeriMedJC tweetchat? Check out the transcript in our Archives section: http://gerimedjc.utorontoeit.com/index.php/2015/12/01/missed-gerimedjc-all-archived-here/

On 2016 Jun 21, Evelina Tutucci commented:

We have also recently discussed Nelles et al. Nelles DA, 2016. Since we are interested in developing new techniques for studying gene expression and mRNA localization at the single molecule level, a potential tag-less system to detect mRNAs in fixed and live cells would be a further advance. As pointed out by the Duke RNA Biology journal club we think that Nelles et al. represents an attempt to apply the Cas9 System to detect endogenous mRNA molecules. Unfortunately, no evidence is presented to demonstrate that this system is ready to be used to study gene expression at the single molecule level, as the MS2-MCP system allows. The RNA letter by Garcia and Parker Garcia JF, 2015 showed that in S. cerevisiae the binding of the MS2 coat protein to the MS2-loops diminished tagged mRNA degradation by the cytoplasmic exonuclease Xrn1. However, these observations were not extended to higher eukaryotes. Previous work from our lab described the generation of the beta-actin-MS2 mouse, whereby all the endogenous beta-actin mRNAs were tagged with 24 MS2 loops in the 3’UTR (Lionnet T, 2011, Park HY, 2014). This mouse is viable and no phenotypic defects are observed. In addition, control experiments were performed to show that the co-expression of the MS2 coat protein in the beta-actin-MS2 mouse allowed correct mRNA degradation and expression (Supplementary figure 1b, Lionnet T. et al 2011). Furthermore, multi-color FISH (Supplementary figure 6, Lionnet T. et al 2011) showed substantial co-localization between the ORF FISH probes and MS2 FISH probes, demonstrating the validity of this model. We think that the observations by Garcia and Parker are restricted to yeast because of the short half-life of their mRNAs, wherein the degradation of the MS2 becomes rate-limiting. Based on our extensive use of the MS2-MCP system, we think that higher eukaryotes may have more time to degrade the high affinity complexes formed between MS2-MCP, providing validation for this system to study multiple aspects of gene expression. In conclusion, we think that the MS2-MCP system remains to date the best method to follow mRNAs at the single molecule level in living cells. For the use of the MS2-MCP system in S. cerevisiae we have taken the necessary steps to improve it for the study of rapidly degrading mRNAs and are preparing this work for publication.<br> Evelina Tutucci and Maria Vera, Singerlab

On 2016 May 17, Duke RNA Biology Journal Club commented:

These comments were generated from a journal club discussion:

We were excited to read and discuss this paper as many of us have questions pertaining to mRNA localization. This technique theoretically allows for imaging of mRNAs without genetic manipulation meaning mRNAs at native expression levels can be tracked in live cells. However, as with many cutting-edge papers, more work is needed before this will become commonplace in the lab.

Most current methods to track mRNAs in live cells involve aptamer based methods which require genetic manipulation of mRNA PMCID: PMC2902723. Additionally, the most commonly used aptamer system, the MS2-MCP system, has become controversial in light of recent findings that the MS2 coat protein stabilizes the aptamer bearing constructs Garcia JF, 2015. In this paper, Fig 1F and 1G replicated these findings and also reassured us that the RCas9 technique would not have the same downfall. While this is certainly a good thing, we were unconvinced this technique was better than FISH (Fig 2), other than having the potential for live cell imaging.

Unfortunately, we found the live cell imaging, which was limited to Fig 3B, to be disappointing. First, we observed that unless an mRNA is strictly localized, as in stress granules, live imaging shows a diffuse mass within the cytosol. Second, imaging was performed with ACTB mRNA which is highly abundant. We don’t think live cell imaging would work as well for low abundance mRNAs due to high background signal. Finally, while specialized imaging software can detect the pile-ups of mRNA in localized foci, we are concerned that tracking individual mRNA may prove a hurdle. Cell models for mRNA localization are large cells such as fibroblasts and neurons, we would be interested to see the ability of this system within these cell types.

One major flaw with this system is the lack of ability to monitor nuclear localized RNA such as lncRNA or splicing machinery. Since since the RCas9 and sgRNA have to first be produced in the nucleus, the majority of the signal in all the figures came from the nucleus. There is a split-GFP-PUM-HD system that has been used to successfully track mRNA in mitochondria Ozawa T, 2007. Perhaps a similar concept could be used with the Cas9 system. This would prove an advantage to the Pumilio system since only the sgRNA needs to be modified instead of the entire protein.

Overall, this is a great start towards a new, tagless, method of mRNA tracking. We look forward to future developments and improvements of this exciting technique.

On 2017 Jul 01, David Keller commented:

A randomized, controlled trial of ethanol for reduction of cardiovascular mortality is needed

The reduction of overall mortality observed with moderate regular ethanol ingestion is driven by the much larger and more significant reduction in cardiovascular mortality which is observed [1]. The beneficial effects of moderate ethanol consumption on the lipid profile are significant, along with hypothetical benefits from antithrombotic and relaxation-inducing effects of ethanol. Many cardiologists have lamented the lack of quality data that would allow them to prescribe moderate alcohol intake to patients with elevated cardiovascular risk, and no elevated risk of addictive or hepatic adverse effects of alcohol. In addition, it is clear that the topical carcinogenic effects of ethanol on the gastrointestinal epithelium vary directly with the cytotoxic effects caused by ethanol concentration, with the greatest risk of esophageal cancers seen with high-proof beverages such as straight whiskey, and no significant elevation of risk due to comparatively dilute beer, with its 5% ethanol concentration causing little if any topical cytotoxicity.

I am calling for a randomized, placebo-controlled interventional trial of ethanol, taken at bedtime to reduce automobile accidents as a source of traumatic mortality, in persons at elevated risk of cardiovascular mortality. Expectation effects could be minimized by administration of the ethanol in capsules, several of which might be required. Oil of peppermint could be included in both the ethanol capsules and in the placebo, for further masking when belching or reflux occur. We have been speculating and correcting observational data for long enough. If a randomized, controlled, interventional trial of ethanol proves to have powerful benefits in persons at high risk of cardiovascular mortality, then populations with average cardiovascular risk can be tested next. Such clinical trials are long overdue. The potential benefits of ethanol are substantial, if properly ascertained.

Reference

1: Vogel RA. Alcohol, heart disease, and mortality: a review. Rev Cardiovasc Med. 2002 Winter;3(1):7-13. Review. PubMed PMID: 12439349.

On 2017 Jul 01, David Keller commented:

A randomized, controlled trial of ethanol capsules for reduction of cardiovascular mortality is called for

The reduction of overall mortality observed with moderate regular ethanol ingestion is driven by the much larger and more significant reduction in cardiovascular mortality which is observed. The beneficial effects of moderate ethanol consumption on the lipid profile are significant, along with hypothetical benefits from antithrombotic and relaxation-inducing effects of ethanol. Many cardiologists have lamented the lack of quality data that would allow them to prescribe moderate alcohol intake to patients with elevated cardiovascular risk, and no elevated risk of addictive or hepatic adverse effects of alcohol. In addition, it is clear that the topical carcinogenic effects of ethanol on the gastrointestinal epithelium vary directly with the cytotoxic effects caused by ethanol concentration, with the greatest risk of esophageal cancers seen with high-proof beverages such as straight whiskey, and no significant elevation of risk due to comparatively dilute beer, with its 5% ethanol concentration causing little if any topical cytotoxicity.

I am calling for a randomized, placebo-controlled interventional trial of ethanol, taken at bedtime to reduce automobile accidents as a source of traumatic mortality, in persons at elevated risk of cardiovascular mortality. Expectation effects could be minimized by administration of the ethanol in capsules, several of which might be required. Oil of peppermint could be included in both the ethanol capsules and in the placebo, for further masking when belching or reflux occur.

We have been speculating and correcting observational data for long enough. If a randomized, controlled, interventional trial of ethanol proves to have powerful benefits in persons at high risk of cardiovascular mortality, then populations with average cardiovascular risk can be tested next. Such clinical trials are long overdue. The potential benefits of ethanol are substantial, if properly ascertained.

Reference

1: Vogel RA. Alcohol, heart disease, and mortality: a review. Rev Cardiovasc Med. 2002 Winter;3(1):7-13. Review. PubMed PMID: 12439349.

On 2016 Apr 12, Martin Hofmeister commented:

Do not forget published reviews

I thank Dr Mat Eil Ismail et al, for their interesting article "Preoperative physiotherapy and short-term functional outcomes of primary total knee arthroplasty", published in the March 2016 issue of the Singapore Medical Journal (SMJ). There is one aspect worth mentioning. In my opinion, systematic reviews of the past five years should be included in an original article consistent with good scientific practice. The reviews of Kwok et al, Jordan et al, Simmons et al and the Australian Agency for Clinical Innovation about the evidence of preoperative physiotherapy on outcomes following total knee arthroplasty are not mentioned in the discussion (1-4). The results of the SMJ study reconfirm the above-mentioned reviews: No statistically significant effect in patient key outcomes (1-4). I refer readers to the latest meta-analysis "Does preoperative rehabilitation for patients planning to undergo joint replacement surgery improve outcomes?" that can be found in the February 2016 issue of the BMJ Open (5).

REFERENCES

1) Kwok IH, Paton B, Haddad FS. Does Pre-Operative Physiotherapy Improve Outcomes in Primary Total Knee Arthroplasty? - A Systematic Review. J Arthroplasty. 2015;30:1657-63. Kwok IH, 2015

2) Jordan RW, Smith NA, Chahal GS, Casson C, Reed MR, Sprowson AP. Enhanced education and physiotherapy before knee replacement; is it worth it? A systematic review. Physiotherapy. 2014;100:305-12. Jordan RW, 2014

3) Simmons L, Smith T. Effectiveness of pre-operative physiotherapy-based programmes on outcomes following total knee arthroplasty: a systematic review and meta-analysis. Phys Ther Rev. 2013;18:1-10. http://www.tandfonline.com/doi/abs/10.1179/1743288X12Y.0000000035?journalCode=yptr20

4) NSW Agency for Clinical Innovation (NSW ACI). Musculoskeletal Network: NSW Evidence Review: preoperative, perioperative and postoperative care of elective primary total hip and knee replacement. Chatswood, Australia: Agency for Clinical Innovation, 2012. Available at: http://www.aci.health.nsw.gov.au/__data/assets/pdf_file/0020/172091/EJR-Evidence-Review.PDF. Accessed 22 March 2016.

5) Wang L, Lee M, Zhang Z, Moodie J, Cheng D, Martin J. Does preoperative rehabilitation for patients planning to undergo joint replacement surgery improve outcomes? A systematic review and meta-analysis of randomised controlled trials. BMJ Open 2016;6:e009857. Wang L, 2016

On 2016 Apr 30, Ivan Oransky commented:

Ben Ashby, who reviewed a later paper by Hanna Kokko, one of the authors, in which she corrected an error in this paper, says it should not have been retracted: http://retractionwatch.com/2016/04/29/why-that-evolution-paper-should-never-have-been-retracted-a-reviewer-speaks-out/

On 2016 Mar 29, Wan map Ni commented:

It sounds effective. But in fact the gates could be more effective. Furthermore, it is not suitable for many patients with hematological malignancy , especially MDS.

On 2016 Jul 10, Jihoon Yoon commented:

I found that the author cited my case report in this article. (Citation No. 121.) However, the citation is inappropriate. The patient in our case represented duplication in 14q11.2 to 14q21.1 region, but the genes mentioned in this article, AMN and HSP90AA1, are located on 14q32 which does not duplicated in our case. There is no overlapping area with the genes and the duplicated region in our case. Therefore, the author should revise the citation or the content. (Contacted with the author.)

On 2016 May 04, Simon Young commented:

This review raises a number of issues related to the content and interpretation of articles that are cited.

1. Paragraph 6 on page 347, about side effects of TRP, cites two placebo controlled trials of TRP (Thomson et al and Steinberg et al) and mentions side effects of TRP. However, the article fails to mention that the study by Thomson et al reported no significant differences in side effects between TRP and placebo, and that in the study of Steinberg et al only 1 of 20 side effects measured (dizziness) was significantly greater after TRP group than after placebo. The same paragraph also contains the sentence “In a study in which 3 g TRP daily was administered to participants for 12 weeks, one patient reported diarrhea as a side-effect of TRP intake (Van Praag et al., 1972)”. However, the van Praag article states “The precursor we used was not tryptophan but dl-5-HTP”. 5-Hydroxytryptohan has a different side effect profile from that of TRP.

2. Paragraph 6 on page 347 mentions that the dose of TRP in the study of Steinberg et al was 6g daily for 3 months and suggests that “Such high doses might not be recommendable not only because of such side-effects, but also because the TPH enzyme is likely to already be saturated by a dose of TRP up to 3g”. While it is true that the daily dose was 6g it was given in three doses of 2g each (after breakfast, after lunch, and before bed), which would not be likely to saturate TRP hydroxylase, and explains why only 1 of 20 side effects measured was significantly greater in the TRP group than in the placebo group. Also, the article did not mention that TRP altered social behavior, specifically a decrease in irritability, in the study of Steinberg et al.

3. The article lists the dose of TRP in the study of Volvaka et al as “6g for 3 weeks”. It fails to mention that the daily dose of 6g was given in divided doses, either 3 or 4 times per day. The article lists the dose of TRP in the study of Nemzer et al as 100mg/kg daily for 1 week. TRP was given in divided doses in the morning and afternoon. The article gives the dose of TRP in the study of Cerit et al as “2.8g per day for 6 days”. The TRP was given in 3 doses per day, 0.8g in the morning and afternoon and 1.2g in the evening. These differences are important as a divided dose is likely to increase serotonin synthesis for longer during each day than the same amount given as a single dose, as well as possibly reducing side effects.

4. Five of the articles listed in Table 1 and discussed in the text involve a technique called acute TRP depletion (ATD). The discussion of all these articles lacks important information. In ATD participants are given a mixture of amino acids that is devoid of TRP (T-), or the same amount of amino acids plus the appropriate amount of TRP as in a balanced protein (B mixture), which for the studies described is 2.3g Young SN, 2013. When the T- mixture is given the amino acid mixture induces protein synthesis and TRP in the blood and tissues is incorporated into protein. Over 5 hours TRP levels fall dramatically and the rate of serotonin synthesis in human brain can decline by more than 90% Nishizawa S, 1997. The B mixture, which contains TRP, will not increase brain TRP or serotonin synthesis, for reasons explained in the paragraph 2 of section 1.1 of the article. Sometimes in ATD studies an additional 8g of TRP is added to the B mixture to raise brain TRP (T+). The problems in the discussion of these articles are: (i) The study of Marsh et al compared the T- mixture, the B mixture, and fasting participants. None of these treatments would increase brain TRP so this was an ATD study, not a TRP supplementation study. The study demonstrated that ATD increases aggressive responding relative to the B mixture. This does not necessarily mean that TRP supplementation would have decreased aggression relative to the B mixture. The fact that the B mixture decreased aggressive responding relative to the fasting condition is irrelevant as the B treatment does not increase brain TRP. While the B and T- mixtures were given under blind conditions, the fasting day occurred after both days in which amino acid mixtures were given, and the participant knew they were not receiving an amino acid mixture. Any effect could have been due to lack of blinding or an order effect, issues not mentioned in the article. Also (a minor point) the article mentions “a control condition (i.e. a low monoamine diet)”. The participants were on a low monoamine diet throughout the study, and the control condition was fasting. (ii) The study of Bjork et al (2000) compared ATD treatment with a T+ treatment containing 10.3g TRP, and a fasting condition. The conclusion given in Fig. 1 of the article by Steenbergen et is that TRP supplementation “Decreased aggressive responding”. However, the article by Bjork et al (2000) states that “TRP depletion increased aggression relative to TRP loading in aggressive men”. Any difference could have been due to increased aggression after ATD, or decreased aggression after TRP loading, or both, so this study did not demonstrate an effect of TRP loading. (iii) The study of Cleare and Bond looked at the effect of ATD and a T+ mixture containing 10.3g TRP. As reported by Steenbergen et al TRP supplementation “was found to reduce self-report ratings of angriness, quarrelsomeness, hostility, and annoyance, but only for males with high trait levels of aggression”. These were changes over time after administration of the amino acids and were relatively small (at most 20%). Given the absence of any control group with unaltered TRP levels these changes cannot necessarily be attributed to the effect of TRP supplementation. (iv) The study of Finn et al compared the effect of a B mixture and a T- mixture. As there was no treatment that increased brain TRP this paper should not have been included in the article.

5. Section 3 of the article includes the statement “if the TPH1 enzyme in the gut is very active, more TRP is converted there and less will be available to pass through the BBB and be converted into 5-HT in the brain. Thus TRP might have less impact on social behavior in individuals with highly active TPH1 enzyme.” Under normal circumstances only about 1% of ingested TRP is converted into serotonin by TPH (see section 4, paragraph 5 of the article and SJOERDSMA A, 1956). Only in a rare condition, the carcinoid syndrome, which is due to neuroendocrine tumors metastasizing in the liver and producing large amounts of serotonin Molina-Cerrillo J, 2016, is metabolism via TPH quantitatively significant, with up to 60% of TRP converted to serotonin SJOERDSMA A, 1956. The main catabolic route of TRP is along the kynurenine pathway, and flux along this pathway is increased in patients with major depressive disorder Teraishi T, 2015. However, TRP is an effective antidepressant according to a Cochrane review Shaw K, 2002. Therefore, it is unlikely that increased peripheral catabolism of TRP will mitigate the effect of TRP on social behavior to any great extent.

6. Section 4 of the article states “some of the effects of TRP administration on social behavior might in fact be a result of enhanced sleep and mood”. An effect on sleep cannot apply to the majority of the studies discussed, which were carried out during a single day. When TRP was given for many days TRP was usually given in a divided dose with only a small dose (usually around 1g) given in the evening, sometimes with dinner. When TRP is given as a hypnotic it is usually given shortly before bedtime, as plasma TRP rises quickly after ingestion. Whether the low doses of TRP given in the evening in the studies lasting longer than a day would have had an effect on sleep is not clear. In relation to improved mood as a mediator of more positive social behavior, the study of Moskovitz et al (2001) demonstrated that TRP resulted in more positive social behavior without any change in mood.

On 2016 Jun 28, Lydia Maniatis commented:

No real objection to this study, which is refreshingly sensible. I want to note, though, that the term "geometric figure-ground cues" is no more specific than the term "good shape cues," both of which are essentially place-holders for further specification (e.g. convex shape). I want to note this because "good shape" is a Gestalt concept which was trivialised and dismissed, but which evidently is necessary. It's not reducible to points, orientations, angles, "features," "signals," or probabilities. (The probability of a particular seen shape can be, essentially, zero.)

On 2016 May 11, Wan map Ni commented:

When will flow cytometry immunophenotyping be included in the classification?

On 2017 Dec 07, M Mangan commented:

There was a major correction to this paper, but it's not linked from this page. Their concentrations were 1000x off. de Aguiar LM, 2017 94-101].")

On 2016 Dec 06, Atanas G. Atanasov commented:

Excellent, thanks a lot for sharing your experience, I have enjoyed a lot reading :-)

On 2017 Oct 29, David Keller commented:

Pharmacists should be enlisted to help physicians monitor PDMP data

Recommendation #9 is: "Clinicians should review the patient’s history of controlled substance prescriptions using state prescription drug monitoring program (PDMP) data to determine whether the patient is receiving opioid dosages or dangerous combinations that put him or her at high risk for overdose. Clinicians should review PDMP data when starting opioid therapy for chronic pain and periodically during opioid therapy for chronic pain, ranging from every prescription to every 3 months."

Prescribing physicians should obtain and review the patient's PDMP data, if possible, prior to initiating any opioid prescription. In addition, pharmacists must be enlisted to check the PDMP databases whenever they fill a prescription for a Schedule 2, 3 or 4 medication. If the pharmacist discovers evidence of concurrent opioid prescriptions or other red flags, they should inform the prescriber and the patient.

The 2016 CDC Guideline for Prescribing Opioids for Chronic Pain establishes a de facto standard of care for prescribing opioids, which will enhance patient safety, and thereby increase access to opioids for patients who really need them. Prescribers will gain a degree of protection from lawsuits for adverse outcomes related to opioid therapy by documenting careful adherence to the 12 recommendations in the CDC Guidelines. This adherence (and documentation) will increase the cost of caring for pain patients, as measured in physician time and effort.

Pharmacists should be required to cross-check the PDMP databases with every opioid fill and refill, and transmit their findings to the prescribing physician, especially red-flag findings. This will be an easy task for pharmacists, and will free up physician time to perform the extensive discussions and documentation required by these Guidelines.

On 2016 Sep 19, Preben Berthelsen commented:

The consequence of the statistical problems in this study must be considered before accepting the authors’ contention that dexmedetomidine is better than saline in ICU patients with agitated delirium.

In the power/sample size calculation and the pre-trial ClinicalTrials registration, a difference of at least 20 hours in ventilator-free time was defined as the minimum difference of clinical interest. The authors found difference of only 17 hours. This finding was statistically significant but not clinically important as the authors - a priori - had defined the 20 hour difference as the minimum difference of interest.

The trial was stopped early when the sponsor – the manufacturer of dexmedetomidine – lost patience due to slow recruitment of patients. As a consequence, only 71 of the 96 stipulated patients could be included in the final statistical analysis – severely limiting the power of the trial. The authors state in the paper that “no data analysis by the study investigators had occurred prior to this decision.” The decision alluded to is the decision taken by the pharmaceutical company sponsoring the trial. But the essential point is when or why the investigators decided not to finish the trial according to the original plan. Was the decision taken before or after the finding of a statistically significant result? The answer cannot be found in the paper.

Additionally, analyses of the “hard” secondary end points (length of ICU stay, hospital stay or mortality) do not support the authors’ view that dexmedetomidine is superior to saline in ICU patients with agitated delirium.

In conclusion, I find that the authors’ hypothesis that dexmedetomidine is effective in ICU patients with agitated delirium not proven. Moreover, I suspect that the chance of reproducing the positive result of this trial to be no better than fifty-fifty.

P.G.Berthelsen. MD, MIA, DCHA. Charlottenlund, Denmark

On 2017 Jun 26, David Marks commented:

This trial was neither randomised, nor controlled, and needs to be retracted. The trial did not compare an abrupt method to a gradual method, as stated, it compared an abrupt method with a mixed bag of complicated gradual methods about which it is impossible to draw solid conclusions. The lead authors have either declared significant conflicts of interest in products used in the research (Aveyard and West) or the ICMJE Form for Disclosure of Potential Conflicts of Interest is incorrect, being the form for the wrong study(Michie). The conclusion that abrupt cessation produces superior cessation rates to gradual cessation cannot be maintained on the basis of this flawed trial for the reasons given below. 1) The gradual-cessation group received short-acting nicotine replacement therapy (NRT) and nicotine patches before the quit day. The abrupt-cessation group received only nicotine patches before the quit day. The treatments are therefore confounded with different pre-exposure levels of NRT. 2) Eligible smokers were booked for an appointment with a research nurse during which the study was explained, eligibility was confirmed, and written informed consent was obtained. What research training did the so-called 'research nurses' receive or were the key study personnel basic grade practice nurses given the task of running the trial? 3) The gradual-cessation group were were supposed to reduce smoking to half of the baseline amount by the end of the first week (known as visit −1) and to a quarter of the baseline amount at the end of the second week (visit 0) in daily increments using a complex variety of procedures that were likely to have been confusing and difficult to follow. 4) The nurses provided the gradual-cessation group with nicotine patches, 21 mg/d, and a choice of short-acting NRT products (gum, lozenges, nasal spray, sublingual tablets, inhalator, or mouth spray) during the reduction period. For such products as gum and lozenges, the instruction was to use 1 dose per cigarette missed. Again, apart from the confounding, and different pre-exposure for the gradual-reduction group, the procedure is unnecessarily complex. 5) Before quitting, participants in the abrupt-cessation group were asked to use nicotine patches, 21 mg/d, but no short-acting NRT. Nicotine patches were used in this group before the quit day, a protocol that aimed to balance the effect between groups. Instead of aiming to balance the effect between groups, there should have been precise balancing, otherwise the trial cannot be described as 'controlled'. 6) Allocation of participants was the responsibility of the so-called 'research nurse' who put patients into blocks of 2, 4, and 6. This allocation was manifestly non-random: “After the participant granted consent, the research nurse opened sealed, numbered envelopes in turn. However, for pairs (for example, husband and wife), one person was allocated randomly and the other was allocated to the same group”. This was a clustered method of allocation, not randomisation. 7) The loss of 300 potential participants also raises questions about how the remaining 697 differed from the original applicants. 8) Unsurprisingly, given their complicated and non-matched treatment, significantly fewer participants in the gradual-cessation group attended visit 0, (67.0% [229 of 342] vs. 83.4% [296 of 355] in the abrupt-cessation group; P < 0.001). Fewer participants in the gradual-cessation group (61.4% [210 of 342]) than the abrupt-cessation group (71% [252 of 355]) (P = 0.007) made a quit attempt. In sum, the trial was a mish-mash of umatched 'treatments', one of which was actually three different treatments counted as one, both confounded by differing pre-cessation exposure to a variety of NRT products chosen by the participants themselves. The trial was carried by 'research nurses' working in GP practices using a batch method for allocating participants. A deliberately uncontrolled, improperly randomised trial, confounded by different NRT products between groups.