On 2015 Feb 25, Oliver Gillie commented:

There is a serious flaw in the scientific reasoning of Autier et al 1,2. A negative result in a clinical trial of a vitamin in adult disease does not prove that the vitamin cannot have caused the disease. A vitamin deficiency may have occurred earlier in life causing irreversible metabolic damage.

Title: Clinical trials, causation and type 2 error. By Oliver Gillie PhD Health Research Forum, 68 Whitehall Park, London N19 3TN Tel: ++44 20 7561 9677

I have pointed out Autier’s mistake which may be classified as a “type 2 statistical error” 2. Regrettably The Lancet (diabetes and endocrinology) has refused to publish a correction even though the error may be seen as one of editing as much as of original research.

Autier et al point out that raising the blood level of 25(OH)D (the standard reference measure of vitamin D) with a vitamin D supplement in clinical trials has not generally been found to modify the occurrence or clinical course of diseases associated with low D in observational studies. And they conclude: “Hence, associations between 25(OH)D and health disorders reported by investigators of observational studies are not causal.” 1

Autier is even more forthright in a Lancet press release where he is quoted as saying: "If the health benefits of high vitamin D concentrations shown by data from observational studies are not reproduced in randomised trials (the gold standard method for assessing a causal relation between an exposure and an outcome) then the relation between vitamin D status and disorders are probably the result of confounding or physiological events involved in these disorders… What this discrepancy suggests is that decreases in vitamin D levels are a marker of deteriorating health." 3

However, Autier et al have misunderstood the literature on trials and causation. They reference Byar et al.4 as referring to RCTs as a “gold standard” in establishing causation. However Byar et al. do not use the term “gold standard” and only consider causation very briefly. Causation may be proved in a clinical trial when supplementation succeeds in correcting a defect, but not when it fails to do so. A null result may be obtained simply because the trial took place too long after an irreversible insult occurring at a much earlier time.

A “type 2 error” mistakenly accepts the null hypothesis, when an alternative hypothesis is or could be the true state of nature. That is: Autier et al find no significant difference between treated and untreated subjects in adult trials of vitamin D supplements and use this finding to support a null hypothesis. In doing so they wrongly rule out an alternative hypothesis that treatment at an earlier stage, e.g. during growth and development, might be effective. Much more extensive trials in all age groups and in pregnancy are required before a null conclusion could be safely reached.

Rickets is the classical example of a disease which may be cured in early life but not in adulthood.5 It causes alteration of normal bone formation and deformation of limbs which may be corrected in childhood by supplementation with vitamin D. If however the deformations, whether gross or minor, are not corrected by vitamin D while the bones are growing, the bones become set in a pathological form that cannot be corrected by later supplementation.

Cardiac structure and some cardiac diseases such as hypertension may be associated causally with low 25(OH)D levels. The Baltimore Longitudinal Study of Aging has found that 25(OH)D levels are positively correlated with left ventricle wall thickness and there is a relationship between 25(OH)D and left-ventricle concentric remodelling.6 Hypertension in this study was also linked to left ventricle hypertrophy and low 25(OH)D. Experiments with young rats show that deprivation of vitamin D causes specific cardiac abnormalities similar to those found in the Baltimore study: cardiac hypertrophy, left-chamber alterations and systolic dysfunction, which follow on from cardiac inflammation, fibrosis and apoptosis.6 This strongly suggests that the association of low 25(OH)D with cardiac pathology is the result of lifelong low vitamin D levels which caused heart abnormalities during early growth. These observations can reasonably be regarded as proof that heart anatomy, and diseases arising from pathological changes in heart anatomy, can be caused by early vitamin D deficiency.

However, if we follow the reasoning of Autier et al. failure of vitamin D to induce beneficial heart remodeling in adults with abnormal heart anatomy would lead us to misleading conclusions i.e. that low vitamin D associated with abnormal heart anatomy in the Baltimore study is the result of reverse causation.

Autoimmune and other diseases are associated in significantly elevated rates with hospital admission for vitamin D deficiency, osteomalacia and rickets.8 Failure in determination of the immune system early in life by escape of T cells from thymic deletion could explain this common association of low vitamin D with autoimmune disease. Vitamin D is well known to be involved in immune processes.9

Many of the molecular mechanisms involving vitamin D are well known and provide a substantial basis for further exploration with clinical trials.9 However clinical trials of vitamin D must be conducted bearing in mind the additional difficulties presented when testing a nutrient rather than a drug.10 It is very difficult and enormously expensive to undertake clinical trials which continue for 20 or 30 years. Indeed it may not be possible. Other approaches are therefore required such as the animal experiments which complement the Baltimore study.

Further examples showing how vitamin D deficiency may cause disease at various stages of life are given in an article2 by the author together with examples of the serious harms which may ensue from literal or dogmatic adherence to policy advice provided by Autier and colleagues. Conflicts of interest: I have no conflicts of interest.

References 1. Autier PBM, Boniol M, Pizot C & Mullie P (2013) Vitamin D status and ill health: a systematic review. Lancet Diabetes Endocrinol 2, 76–89. 2. Gillie O. Controlled trials of vitamin D, causality and type 2 statistical error. Public Health Nutrition 2014. 3. Anon. (2013) Further doubt cast on benefit of vitamin D supplementation for disease prevention. Press release promoting Autier et al. (2013); available at : http://www.eurekalert.org/pub_releases/2013-12/l-fdc120313.php 4. Byar DP, Simon RM, Friedewald WT et al. (1976) Randomized clinical trials. Perspectives on some recent ideas. N Engl J Med 95, 74–80. 5. Holick MF (2006) Resurrection of vitamin D deficiency and rickets. J Clin Invest 116, 2062–2072. 6. Ameri P, Canepa M, Milaneschi Y et al. (2013) Relationship between vitamin D status and left ventricular geometry in a healthy population: results from the Baltimore Longitudinal Study of Aging. J Intern Med 273, 253–262. 7. Assalin HB, Rafacho BP, dos Santos PP et al. (2013) Impact of the length of vitamin D deficiency on cardiac remodeling. Circ Heart Fail 6, 809–816. 8. Ramagopalan SV, Maugeri NJ, Handunnetthi L et al. (2013) Hospital admissions for vitamin D related conditions and subsequent immune-mediated disease: record-linkage studies. BMC Med 11, 171. 9. Pludowski P, Holick MF, Pilz S et al. Vitamin D effects on mitochondrial health, immunity, autoimmunity, cardiovascular disease, cancer, fertility, pregnancy, dementia and mortality – a review of recent evidence. Autoimmune Rev 2013; 12: 976-89 10. Grant WB. Using findings from observational studies to guide vitamin D randomized controlled trials. J Int Med. Published online: 5 May 2014 DOI: 10.1111/joim.12260

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Jun 18, Ryan Radecki commented:

Post-publication commentary:

"Abscess Management in the Era of MRSA"

Every so often, it’s good to circle back from the esoteric to the basics, and remind ourselves how to provide the best, evidence-based treatment for some of the most common diseases – in this case, abscesses....

http://www.emlitofnote.com/2014/06/abscess-management-in-era-of-mrsa_16.html

On 2015 Jun 02, thomas samaras commented:

Additional research on height, body size and longevity is available from the following publications.

Samaras TT. Evidence from eight different types of studies showing that smaller body size is related to greater longevity. Journal of Scientific Research & Reports. 2014: 3 (16): 2150-2160, 2014; article no. JSRR.2014.16.003.

Samaras TT. Human Scaling and Body Mass Index. In: Samaras TT (ed): Human Body Size and the Laws of Scaling: Physiological Performance, Growth, Longevity and Ecological Ramifications. New York: Nova Science Pub; 2007: pp 17-32.

He Q, Morris BJ, Grove JS, Petrovitch H, Ross W, Masaki KH, et al. Shorter men live longer: Association of height with longevity and FOXO3 genotype in American men of Japanese ancestry. Plos ONE 9(5): e94385. doi:10.1371/journal.pone.0094385.

Salaris L, Poulain M, Samaras TT. Height and survival at older ages among men born in an inland village in Sardinia (Italy), 1866-2006. Biodemography and Social Biology, 58:1, 1-13.

Bartke A. Healthy Aging: Is Smaller better? A mini-review. Gerontology 2012; 58:337-43.

On 2016 Mar 27, Gustav van Niekerk commented:

So called ‘sickens associated anorexia’ (SAA) is one of the major manifestations of an infection. I am very curious regarding the extent to which this response is evolutionary conserved: I have come across articles on describing a SAA in vertebrate [1-4] and invertebrates [5-8] (sorry, not using the NCBI PMID codes as I am cut-and pasting from a draft) such as Drosophila and African army worm but not primitive animals such as corals and sea anemone. In your manuscript, you make reference that “no feeding occurred after the infection” as well as the “retraction of tentacles”. Is this because you stopped feeding, or because the animal stopped feeding? More explicitly, would you consider the sea anemone enacting a form of SAA? Also, is there any similar study describing a decrees in feeding when infected by other primitive animals such as see sponges?

References 1. Crespi EJ, Denver RJ: Roles of stress hormones in food intake regulation in anuran amphibians throughout the life cycle. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 2005, 141(4):381-390. 2. De Voe RS: Nutritional support of reptile patients. Vet Clin North Am Exot Anim Pract 2014, 17(2):249-261. 3. Islam AN, Woo PT: Anorexia in goldfish Carassius auratus infected with Trypanosoma danilewskyi. Dis Aquat Org 1991, 11(1):45-48. 4. Johnson R, Curtis S, Dantzer R, Bahr J, Kelley K: Sickness behavior in birds caused by peripheral or central injection of endotoxin. Physiol Behav 1993, 53(2):343-348. 5. Povey S, Cotter SC, Simpson SJ, Lee KP, Wilson K: Can the protein costs of bacterial resistance be offset by altered feeding behaviour? J Anim Ecol 2009, 78(2):437-446. 6. Povey S, Cotter SC, Simpson SJ, Wilson K: Dynamics of macronutrient self‐medication and illness‐induced anorexia in virally infected insects. J Anim Ecol 2014, 83(1):245-255. 7. Adamo SA, Fidler TL, Forestell CA: Illness-induced anorexia and its possible function in the caterpillar, Manduca sexta. Brain Behav Immun 2007, 21(3):292-300. 8. Ayres JS, Schneider DS: The role of anorexia in resistance and tolerance to infections in Drosophila. PLoS Biol 2009, 7(7):e1000150.

On 2014 Mar 21, Kostas Lasithiotakis commented:

Very nice illustrations!

On 2014 Aug 26, Anders von Heijne commented:

PML in the posterior fossa remain a clinical and radiological challenge. It is important to keep in mind that JCV infections come in different forms. There are some mutations of JCV that seem to target the cerebellar granule cells specifically, causing granular cell neuronopathy, that at least in early stages only show rapid cerebellar atrophy but with obvious cerebellar symtoms. See for example a recent report on JCV GCN in natalizumab treated MS: Agnihotri et al Neurology. 2014 Aug 19;83(8):727-32

On 2014 Aug 12, Miguel Lopez-Lazaro commented:

Most of the patients with advanced cancers die because the drugs used in their treatment have a low ability to kill their cancer cells at concentrations that do not significantly affect their normal cells. Although these patients need drugs that kill their cancer cells selectively, we typically look for drugs that kill cancer cells at low concentrations or that have specific mechanisms of action. These strategies do not reliably predict the ability of a drug to kill cancer cells selectively and many times result in the selection of compounds with low therapeutic potential and in the failure to detect compounds with therapeutic potential.

In vitro therapeutic potential can be easily and efficiently assessed answering the following question:

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

In this article, the authors demonstrate that organoiridium complexes improve the ability of platinum complexes to kill cancer cells at low concentrations. They also show that their cytotoxic activity is mediated by a pro-oxidant mechanism of action. One of their complexes could also match the selectivity of cisplatin when tested in ovarian cancer cells versus lung nonmalignant cells.

In my opinion, additional nonmalignant cell lines (or primary cells) from appropriate tissues should be used to assess the therapeutic potential of these compounds further. If one only uses one cancer cell line and one non-malignant cell line originated from different tissues, the observed selective anticancer effect could be caused by tissue differences in sensitivity. In addition, cells from other tissues commonly affected by chemotherapy could be highly sensitive to the cytotoxic activity of organoiridium complexes. In view of the possible relevance of the results presented by the authors, I think that these additional experiments are worth considering.

Dr. Lopez-Lazaro

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

On 2015 Apr 24, BSH Cancer Screening, Help-Seeking and Prevention Journal Club commented:

The HBRC journal club read Scherer et al’s paper with interest. While flu vaccination is not the focus of our work, using metaphors as a manipulation to increase the likelihood of a behaviour and the methods used to test the efficacy of doing so, resonated with our research team. Most of the group were unfamiliar with the metaphor literature and found the introduction to provide a useful summary of the field. The authors present a discussion of the role of risk perceptions and affect, but a more detailed discussion of how the two interact and their complexities might have provided a truer representation of the field.

The group liked that the authors attempt to measure whether participants were likely to move beyond intention (measuring participants’ desire to receive a reminder email to get a flu vaccination), without having to measure behaviour (which is difficult to do objectively). However, contrary to the authors, the finding that individuals who occasionally get a flu vaccine were more likely to request an email reminder was unsurprising to us because individuals who always get a flu vaccination seemingly do not need reminding. A further strength of the paper is that non-emotive metaphors were considered (the flu as a weed), as this helped dispel the suggestion that the effect was due to vividity or violence (as might be the case with metaphors such as ‘beast’ and ‘riot’). The group wondered if a virus could also be considered to be a metaphor, given its use in computing. Additionally, it may have been of interest if the vaccination itself was also part of the metaphor, for example the flu virus being described as a ‘weed’ and the flu vaccine as ‘weed killer’. In Hauser DJ, 2015 using congruent metaphors to describe an illness and the measure to prevent the illness increased behavioural intentions compared to just using a metaphor to describe the illness.

While metaphors may increase the vividness of the flu and encourage individuals to engage, the group were concerned about how use of metaphors to manipulate behaviour may not be congruent with informed decision making, instead being considered coercive. We disagreed with the authors suggestion that metaphors might have a use in decision aids, which we believe have a role in helping individuals make informed decisions and not swaying their opinion. We suggested that metaphors might be useful when the aim is to increase individuals’ understanding, rather than increasing intentions to engage in a behaviour. It may also be important to consider the unintended consequences of using metaphors, for example in the cancer field (the focus of our work), describing cancer as a battle may lead to suggestions that people who do not survive the disease did not fight hard enough. However, we acknowledge that metaphors are used ubiquitously in the media, which is difficult to control.

The group felt that flu vaccination was a complex example to choose to conduct these studies. Flu is a fairly common illness, which might result in participants having an accurate estimate of their risk of contracting the illness or how serious it is. This might explain why the manipulation did not affect the mediators in the main analysis. Individuals are likely to have existing beliefs about vaccination (for example, beliefs about side effects, effectiveness) and the benefits of vaccination might not always be obvious (the individual does not contract the flu - a non event and herd immunity benefiting the population). It would have been helpful to have been informed about the flu vaccination recommendations in the USA where the study was conducted. Cultural differences in how the flu is appraised, treated and prevented between countries might alter the effect of metaphors. For example, in the group’s opinion, the metaphor ‘beast’ was an exaggerated conceptualisation of the flu and felt removed from the actual consequences of the virus.

Study 3 was perceived by the group to be the most useful study of the paper as it used a validated measure of affect and a larger sample than Study 1. The ecological validity of studies 2 and 3 could have been increased if Study 1 had been a ‘think aloud’ study, whereby the authors could have gained a justification for the mediators of flu vaccination that were tested. The group thought that a strength of the studies is that the authors did consider the possible mediators of any effect of the metaphor. Other mediators that could have been considered include attitudes and a measurement of arousal (engagement). A ‘think aloud’ study might also help to ensure that metaphors are used appropriately, for example in Hauser DJ, 2015, use of an enemy metaphor reduced intentions for self-limiting cancer prevention behaviours (such as stopping smoking or limiting alcohol intake). The group also wondered how novel the ‘novel’ metaphors used in the studies actually were, something that pilot work could have investigated.

The group thought it was interesting that the findings were not wholly consistent across the studies reported and considered that this could have been a product of differences in the sample. The authors do not describe whether participants were randomised to each condition, and no baseline measurements were reported, both of these factors leave readers unclear about whether the sample was similar across each of the studies. It would also have been helpful to have a justification for the sample size chosen for each of the studies.

Scherer et al. present a novel paper, which has provided readers with examples of how to measure the impact of using metaphors to increase intentions to receive a flu vaccination. Future work in this field should consider conducting pilot work to ensure the topic, manipulation and measures used are relevant to the population of interest. We caution readers to consider the unintended consequences of using metaphors to manipulate behaviour, including concern about the ethical implications this might have.

Conflicts of interest We report no conflict of interests and note that the comments produced by the group are collective and not the opinion of any one individual.

On 2017 Sep 26, Eric Vallabh Minikel commented:

A full text pre-print is available via Zenodo.

On 2015 May 17, Maya Guglin commented:

It is true that patients with advanced HF typically have low blood pressure. That is why almost none of them are tolerating thiazide diuretics. In fact, not a single patient from our cohort was on thiazides, so their contribution to the reported effect of LVADs can be completely excluded. Admittedly, we did not record the doses of ACE inhibitors before and after LVADs, although cardiologists are known for neglecting uptitration of HF meds after LVAD implant.

However, other publications on the same topic can shed some light on ACE doses, because I am sure some authors did record them. We summarized their findings in our recent paper "What did we learn about VADs in 2014?" published in our newborn "The VAD Journal". The text below is the excerpt from this paper.

Several reports, including ours, unanimously confirmed the discovery made by Uriel et al.in 2011: diabetes improves after LVAD. Choudhary et al. also found that fasting blood glucose improved from 136 +/- 35 to 108 +/- 29 mg/dl post-LVAD (p < 0.001), and daily insulin dose decreased from 43 +/- 37 to 29 +/- 24 units (p = 0.02). Mohamedali et al. presented similar findings and added that some patients were able to completely discontinue oral hypoglycemics. Other groups published similar findings. The nature of this phenomenon is unclear; however, Koerner et al. measured cortisol and plasma catecholamine levels and found that both decreased after the LVAD implant. (6). This may mean that reduction of the systemic inflammatory and stress response may play a role. Otherwise, improved hemodynamics in either pancreas or peripheral tissues or both may be the cause of improvement of glucose metabolism. In any case, diabetes should not be considered a contraindication to LVAD.

Uriel N, Naka Y, Colombo PC et al. Improved diabetic control in advanced heart failure patients treated with left ventricular assist devices. European journal of heart failure 2011;13:195-9.

Choudhary N, Chen L, Kotyra L, Wittlin SD, Alexis JD. Improvement in glycemic control after left ventricular assist device implantation in advanced heart failure patients with diabetes mellitus. ASAIO journal (American Society for Artificial Internal Organs : 1992) 2014;60:675-80.

Mohamedali B, Yost G, Bhat G. Mechanical circulatory support improves diabetic control in patients with advanced heart failure. European journal of heart failure 2014;16:1120-4.

Subauste AR, Esfandiari NH, Qu Y et al. Impact of left ventricular assist device on diabetes management: an evaluation through case analysis and clinical impact. Hospital practice (1995) 2014;42:116-22.

Koerner MM, El-Banayosy A, Eleuteri K et al. Neurohormonal regulation and improvement in blood glucose control: reduction of insulin requirement in patients with a nonpulsatile ventricular assist device. The heart surgery forum 2014;17:E98-102.

On 2015 May 17, David Keller commented:

Reduced diuretic doses & increased ACE-inhibitor doses account for some of the improvement in blood sugars after LVAD

Implanting a left ventricular assist device (LVAD) should reduce the doses of diuretics required to treat congestive heart failure (CHF). Thiazide diuretics are well-known to promote insulin resistance, and are often used with loop diuretics to treat CHF. Therefore, the reduced need for diuretics after LVAD implantation could account for some or all of the observed decrease in blood sugars.

Also, CHF patients often do not tolerate maximal doses of ACE-inhibitors, due to hypotension. After LVAD implantation, these patients should be able to tolerate a higher dose of ACE inhibitor, which would also have the side effect of improving insulin sensitivity.

How much of the benefit in blood sugar control in diabetic CHF patients who received LVAD implantation was due to their decreased need for diuretics (especially thiazides) and increased tolerance of ACE-inhibitors? The results of this study should be corrected for these well-known medication side-effects. Only the residual improvements in blood sugar control which are not explained by these medication effects should be attributed to improvement in the CHF itself.

On 2015 Sep 29, Jan Egger commented:

Videos demonstrating the interactive real-time segmentation can be found under the following YouTube channel: https://www.youtube.com/c/JanEgger/videos

Best wishes, Jan

http://www.janegger.de/

On 2014 Mar 19, Salvatore Chirumbolo commented:

This interesting paper refers to previous mouse models of anxiety and developed a molecular investigation on human neuroblastoma cell line SH-SY5Y to explain mouse behaviour. Why do not use a mouse neuroblastoma model? The authors refer to a paper by Li et al (2009) which is in Chinese and does not deal with the related issue mentioned within the manuscript. probably, the correct ref should be a paper by Li et al on Neuropsychopharmacology 2009. Authors should consider an ERRATUM for their paper, to make it more readable.

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Nov 26, Guillaume Filion commented:

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

On 2015 Feb 27, Geriatric Medicine Journal Club commented:

This pharmaceutical company sponsored trial of Mirabegron for treatment of overactive bladder symptoms in older people was discussed at the September 2014 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full transcript of the conversation can be found here: http://gerimedjc.blogspot.com/2014/09/to-two-articles-critically-appraised.html?spref=tw Highlights include concern for lack of reporting on cognitive outcomes.

On 2014 Apr 10, Patrick Hiepe commented:

nicely presented data, congratulations !

On 2014 Apr 10, Patrick Hiepe commented:

Congratulations, really nice paper! RPBM-offered information are quite impressive!

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Mar 18, Paul Glasziou commented:

A 5 minute video abstract is also available at: https://www.youtube.com/watch?v=ZmX5MPopeDw

A Word template is available as appendix 3 here: http://www.bmj.com/content/suppl/2014/03/07/bmj.g1687.DC4

On 2014 Jul 11, Mirko Spiroski commented:

Retraction

The article published by Ilankovic et al., 2013 [1] has been retracted by Editor-in-Chief because corresponding author published the similar paper in Psychiatria Danubina in 2014 [2]. An internal investigation has raised sufficient evidence of the originality in the first paper [1] and self plagiarism in the second paper [2]; as such, we retract this article from the literature on request by corresponding author and in accordance with guidelines and best editorial practices from the Committee on Publication Ethics. We apologize to our audience about this unfortunate situation.

References

[1] Ilankovic A, Damjanovic A, Ilankovic V, Milovanovic S, Petrovic D, Ilankovic N. Sleep Organisation in Depression and Schizophrenia: Index of Endogenous Periodicity of Sleep as a State Marker. Maced J Med Sci. 2013 Dec 15; 6(4):408-413.

[2] Ilanković A, Damjanović A, Ilanković V, Filipović B, Janković S, Ilanković N. Polysomnographic sleep patterns in depressive, schizophrenic and healthy subjects. Psychiatr Danub. 2014;26(1):20-6.

The retraction is located here: http://www.mjms.mk/Online/MJMS_2014_7_2/MJMS.1857-5773.2014-0380.pdf and here: http://www.degruyter.com/view/j/mjms.2014.7.issue-2/mjms.1857-5773.2014.0380/mjms.1857-5773.2014.0380.xml?format=INT

The retracted paper is located here: http://www.mjms.mk/Online/MJMS_2013_6_4/MJMS.1857-5773.2013-0335.pdf

On 2014 Jul 03, Jeffrey Beall commented:

The text in this article very closely matches the text in an article published in Volume 6, Issue 4 (Dec 2013) of the Macedonian Journal of Medical Sciences. That article is entitled "Sleep Organisation in Depression and Schizophrenia: Index of Endogenous Periodicity of Sleep as a State Marker."

The other article is located here: http://www.degruyter.com/view/j/mjms.2013.6.issue-4/mjms.1857-5773.2013.0335/mjms.1857-5773.2013.0335.xml?format=INT

Both articles have six authors. There are four authors common to both papers. Each article also has two authors that are not listed as an author on the counterpart paper.

I cannot tell which was published first; they both came out at about the same time. I request that both journals investigate this possible case of duplicate publication / plagiarism.

On 2014 Mar 31, Sergio Stagnaro commented:

None

On 2014 Mar 30, Allison Stelling commented:

The accuracy isn't totally surprising, mass spec would be quite sensitive to pathogenic phenotype markers like those phosopholipids. These smaller biological molecules- lipids, sugars, etc- are linked to the mechanisms of pathogenesis. As biomarkers go, they're pretty solid.

What I worry about is that the algorithm they use to sort the data may have a contaminated "healthy vs normal" training set. I see this in a lot of the spectral diagnostic literature. It is making the assumption that the "gold standard" test for the disease is in fact accurate and reliable itself.

I also see a lot of use of non-open source software in the field. This may hinder our efforts to establish ourselves in the medical realms. We must make these analyses reproducible and reliable across many, many sites for medical work; and that means having many eyes on the code.

On 2014 Mar 27, Robert Tibshirani commented:

This paper shows some impressive results, predicting phenoconversion to either amnestic mild cognitive impairment or Alzheimer's disease, from ten lipids in peripheral blood, with 90-95% accuracy over a 2-3 time frame. The research appears to be well done, but as is often the case, it is impossible to judge the strength of the results without digging into the details. The statistical analysis has multiple steps and is quite complicated. The raw data needs to be made available, and ideally, an R script that carries out the calculations in full.

On 2015 May 22, University of Kansas School of Nursing Journal Club commented:

Team 9: Sage Peterson, Jessica Joslin, Dahnika Sachs, Melissa Ryan, Erin Ekholm, Brittney DuBois, Halie McCombs (Class of 2015)

Background Introduction

This article focuses on the transnational migration of nurses worldwide and the uneven distribution of nurse labor in a current nursing shortage (Prescott, 2014). This plays in directly with our class discussion on global nurse migration. Our team chose this article because it ties in the reasoning for migration of nurses to the US from other countries with our class discussion of integrating these nurses into our American healthcare system.

The article brings up the issue of our current nursing shortage and how it is not evenly distributed. There is more demand for nurses in less developed countries because the desire to work there is not as high as in the more developed countries such as the US or UK (Prescott, 2014). In class, we discussed the role of migrating nurses in our own culture and health care system and how important it is to be culturally open and competent. We are seeing a lot of internationally educated nurses migrating to the US to work because we do have a shortage and we are a more desirable place to work than other less wealthy countries. A lot of the nurses that we see migrating into America are from the Philippines and India. These foreign educated nurses help cut down on the nursing shortage here, but they could be potentially causing shortages in the home countries. The article also discusses this and other political “push and pull” that leads to nurse migration.

Methods

We were able to find this article by searching “global nursing” in PubMed. The article reviews the literature on nurse migration and its current and future impact on healthcare systems worldwide. There is a focus on the “push/pull” of economic logic and the cause and effect of nurse migration (Prescott, 2014). The concepts of political-economic, historical, and cultural factors are all covered in the article and their impact on nurse migration. The data was collected from reviews of nursing literature in order to analyze and provide directions for future anthropologic studies. The target population that this issue of nursing shortage and migration has the greatest impact on is the global healthcare systems.

Findings

What was mainly discussed and found in the article is that we have a big problem with an uneven distribution of nurses globally. This is causing inadequate migration to some countries and an abundance of migration to others. An example of this would be the migration of Philippine educated nurses to the US. Because of this, we are seeing the need to integrate them properly to our healthcare system in order for them to be successful. What also needs to be considered is the impact this has on the sending countries (like the Philippines) that are seeing more and more nurses leaving to work in more developed countries with better jobs and pay (Prescott, 2014). This unbalanced labor is creating problems globally and this study brings up these issues in order to bring attention to the matter for future studies.

Implications

The article is relevant to our nursing practice in many ways. It gives us an understanding and reasoning behind nurse migration around the world and gets us thinking about what we can do to solve this issue. Also, since there is so much transnational migration of nurses, it is important for us to be culturally competent and open about providing other culturally different nurses the opportunity to assimilate to our healthcare system. By better understanding the reasoning and method that many foreign nurses have for migrating out of their home countries to others, we are able to assimilate them to the local health care system better.

References Prescott, M., & Nichter, M. (2014). Transnational nurse migration: Future directions for medical anthropological research. Social Science & Medicine, 107113-123. doi:10.1016/j.socscimed.2014.02.026

On 2015 Mar 06, Andrew Brown commented:

See Erratum at: http://www.ijbnpa.org/content/11/1/33/comments

On 2014 Aug 13, Jim Woodgett commented:

This is an open access article (just click on the full text link). I don't know why this isn't indicated by PubMed.

On 2014 Mar 13, Jonathan Eisen commented:

The first author of the paper, Rachel Adams, has a post on the "microbiology of the Built Environment network" blog discussing some background to this study. See Bacteria in a university housing complex

On 2014 Mar 26, Dan Laks commented:

This study ignores the dramatic rise in blood inorganic mercury over that same time period. Why? Inorganic mercury may be a better bioindicator of chronic mercury exposure than organic mercury which is really a bioindicator of recent exposure. Please see this article for a full description of a more accurate assessment of chronic mercury exposure:

http://www.ncbi.nlm.nih.gov/pubmed/24368746

On 2014 Mar 13, Jonathan Eisen commented:

There have been a variety of blog posts and news stories about this work. I am compiling a list of links here: Links about new work from BioBE center’s on “microbiology of the built environment”

On 2014 Jul 03, Torsten Seemann commented:

The source code for the MGA project can be found at https://github.com/crukci-bioinformatics/MGA

On 2014 Mar 23, Adrian Heilbut commented:

A supplementary website for easily searching and browsing the data presented in this paper is accessible at http://pd.sciencespace.org

Source code for statistical analyses and plots is available at https://github.com/aheilbut/pdmouse/

On 2016 Sep 06, Hilda Bastian commented:

The authors of this paper state: “Our own findings as well as research by others show that the effect of children on women’s academic careers is so remarkable that it eclipses other factors in contributing to women’s underrepresentation in academic science”.

This paper fails to support this contention in 5 ways:

1. Addressing only a subset of the range of factors that potentially contribute to women’s underrepresentation.

2. Relying on a selected set of literature that fails to discount alternative explanations, in particular that there is no one single factor that accounts for the phenomenon of women’s underrepresentation in science. Multiple contributing factors, even small ones, can contribute to cumulative advantage for men in science (National Academy of Sciences (US), National Academy of Engineering (US), and Institute of Medicine (US) Committee on Maximizing the Potential of Women in Academic Science and Engineering, 2007).

3. No method to quantify and comparatively weigh contributing factors that could underpin the single remarkable factor hypothesis.

4. Not satisfactorily demonstrating that motherhood consistently results in high levels of underrepresentation across disciplines of academic science, and not in all other academic careers.

5. It generalizes to all of academic science, based exclusively on American data of family responsibilities and science careers.

The authors rely heavily on their previous work: Ceci SJ, 2011. I have addressed that in a PubMed Commons comment (link to comment). That paper also does not contain adequate evidence to sustain the contention of the claim about the motherhood hypothesis presented here.

The only data sets presented in support of this hypothesis are (in order of appearance):

• A study including 586 graduate students in 1992 in the US, surveyed again in 2003 and 2004 (Lubinski D, 2006).

• A figure of the number of ovarian follicles women have by age from birth to 51, overlaid with key scientists’ career stages.

• A national faculty survey on career and family in 1998 (with over 10,116 respondents across scientific and non-scientific disciplines) (Jacobs, 2004).

• 2 selected examples of studies from their previous review chosen to illustrate their argument that there is a level playing field for women in the science workforce, along with a blanket claim that I do not believe the evidence in their review supports (Ceci SJ, 2011).

• A study that included 2 major components (Goulden, 2009):

  (a) Modeling of data from the Survey of Doctorate Recipients (SDR), which had limited data on potential contributing factors to women’s careers (see for example (Bentley 2004). Women with young children had a 4-13% lower odds of achieving tenure than women without, which is not a considerably higher contribution to gender differences than has been in other studies. (Note that age of children is one of the areas with relatively high missing data in the SDR (Hoffer 2002.)

  (b) A survey of 45 female doctoral and postdoctoral at the University of California, including 16 “new mothers”.

• A survey with 2,503 respondents from 2008/2009 which found that women were more likely than men to wish they had more children (Ecklund EH, 2011) (although it is not included in the article’s list of references, the study was readily identifiable). Williams and Ceci report “Often this regret is associated with leaving the academy”. However, Ecklund and Lincoln report that there was no gender difference in the desire to leave academic science among these respondents. Further, they conclude, “the effect on life satisfaction of having fewer children than desired is more pronounced for male than female faculty, with life satisfaction strongly related to career satisfaction”.

• A study of people early in their careers, graduating with MBAs from a single US business school between 1990 and 2006. It had a low response rate (31%) and including 629 women (Bertrand, 2010).

This data basis is inadequate to support the paper’s conclusions and presents highly selected data. The article included a separate extended bibliography, but the basis for the identification and selection of the studies in the bibliography and in the article is not given. In relation to the major review on which they rely (Ceci SJ, 2011), an unsystematic approach and lack of methods to minimize bias has resulted in a very misleading sample of data, and biased reporting and interpretation of that data (see my comment in PubMed Commons).

Finally, central to the argument presented here is the hypothesis that as societal and policy changes have reduced the impact of blatant and conscious discrimination, the salience of motherhood as a relative barrier to the progression of women’s scientific careers has assumed greater significance.

However, those same societal changes have also been affecting how people manage and accommodate family responsibilities and careers. For example, later childbirth and fewer children is an ongoing trend in the US (Matthews TJ, 2009, Matthews TJ, 2014), which partially results from, and contributes to, changing attitudes to motherhood and parenting over time. Similarly, increasing workforce participation by women has been changing, and continues to rapidly change, men’s roles in parenting Cabrera NJ, 2000. The authors acknowledge that there has been some accommodation by academic institutions, but their analysis remains largely one-sided.

For example, this statement is made with neither current nor longitudinal data cited in support: “Men more often have stay-at-home spouses or spouses in flexible careers who bear and raise children while the men are free to focus on academic work”. Indeed, a study they cite in another context found that both men and women scientists with children worked fewer hours than those without children, but similar hours to each other (Ecklund EH, 2011).

I agree with the authors that much remains to be done to accommodate family responsibilities of all types, not just motherhood. But that will not be a single magic bullet that counteracts the cumulative impact of biases and barriers affecting women related to gender, race, and more as well as family responsibilities. These authors have not made their case for the claim that, “It is when academic scientists choose to be mothers that their real problems start”.

In addition to comments here on PubMed Commons on the previous review by these authors that supports this paper, I have discussed it on my blog

Disclosures: I work at the National Institutes of Health (NIH), but not in the granting or women in science policy spheres. The views I express are personal, and do not necessarily reflect those of the NIH. I am an academic editor at PLOS Medicine and on the human ethics advisory group for PLOS One. I am undertaking research in various aspects of publication ethics.

On 2016 Apr 08, Lydia Maniatis commented:

This article is a follow-up to Gheiratmand, Meese & Mullen (2013) and is vulnerable to the same criticisms, which can be found here: https://pubpeer.com/publications/23283693

Other comments: In the first sentence of the article the authors state that: "The processing shape and form begins with the encoding of local orientation information in the visual scene by arrays of neural mechanisms selective for different orientations."

What is the basis for this statement? The local orientation of what? Of points? Of horizontal rows of points, vertical rows of points, diagonal rows of points, points having identical luminance, points varying in their luminance? How many points per locally oriented item? On what principle are the points linked into rows, so that they can be "detected"? How about subjective contours, or curves? How about orientations in 3D? How about amodal contours?

Given the well-established fact that non-local, high level principles mediate the percept, the notion that the percept can reveal "low-level" detector mechanisms and their "tuning" lacks, as Teller (1984) would put it, face validity. Even threshold effects have been clearly shown to be stimulus-dependent, i.e. the results of "tried and true" Gabor patches don't generalise.

In other words, the authors foundational claim is as obsolete and invalid as it could possibly be. But they assert it, and proceed accordingly.

The absence of a defensible rationale is (as is typical in this category of studies) complemented by a casual approach to assumptions in general (caps mine). Thus, "a von Mises function is used in part because "it IS THOUGHT TO BE the best function to fit to neurophysiological orientation tuning data. (Swindale, 1998)." So basically, Swindale thought this 1998, and Gheiratmand and Mullen apparently think it because Swindale thought it. Nuff said. Similarly: "m is fixed at 4, which has been CONSISTENTLY USED in the literature for approximation of the probability summation rule." I'm sure those other people had a good reason to use it. And: "we use a model involving arrays of orientation and spatial frequency tuned filters whose outputs are combined across the visual extent of the stimulus using a Minkowski summation rule. This method HAS BEEN USED previously to determine orientation and spatial frequency tuning for achromatic stimuli."Well, as long as its been used before. Some people must have thought it was good enough. Summing up: "We have used the classical psychophysical method of subthreshold summation to measure orientation tuning of the visual detectors underlying human colour vision at different spatial frequencies." Because old (classic) is best, e.g. some people think classical music is better than modern, or that old Coke tastes better than new. And if our: "visual detectors at different spatial frequencies" assumption is invalid (which it certainly is), our experiments will never reveal it, thanks to our other insulating, arbitrary (though confirmed by popularity) assumptions and restricted choice of stimulus features, that allow us to interpret our results in terms of those features (whether they are, in fact, relevant or not).

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Apr 16, Claudiu Bandea commented:

What if we have totally missed the true nature of viruses? (Part II)

(Due to size limitations, this comment was entered as two parts)

Another way to react to the critical question raised by Wolkowicz and Schaechter (24) is to invoke the notion that viruses are not even living entities, and come up with “Ten reasons to exclude viruses from the tree of life” (26). As discussed in more detail elsewhere (8), many of the reasons presented by David Moreira and Purificación López-García (26) were rationalized within the framework of the misleading conventional paradigms about their nature and evolution, so their scientific validity is compromised. Interestingly, Moreira and López-García were well aware of the problems with the dogma of viruses as virus particles, as they wrote: “Claverie recently proposed a provocative redefinition of the viral identity wherein the true nature of a virus is not the virion (the infective viral particle)” (26). However, they dismissed the entire issue by justifiably arguing that the solution to the problems associated with the dogma of viruses as virus particles as proposed by Claverie, “The virus factory should be considered the actual virus organism when referring to a virus” (4), is nonsensical, as the identity of an organism should rely solely on its components and properties, not those of its environment (i.e. the host cell; for more discussion on this issue see Ref. 9); incidentally, this rationale also questions the ‘virocell concept,’ which was developed by Patrick Forterre as a novel solution to the misleading dogma of viruses as virus particles (11, 27). Moreover, in their response to a flurry of comments prompted by their article (see the published correspondence associated with Ref. 26 in the journal Nature Rev. Microbiol.), Moreira and López-García explained the reasons for much of the scientific confusion afflicting the current paradigms on the evolution of viruses: “We realize that much of this confusion comes from the fact that many virologists and other biologists are not familiar with the theory and practice of molecular phylogeny.” That might be true. However, generating correct data and observations is only half of the scientific process, the other half is their interpretation; and, as previously discussed (9), the interpretation of their own (presumably valid) molecular phylogeny data by Moreira and López-García was compromised by the current misleading paradigms on their nature and evolutionary origin.

The allegations outlined here against the conventional paradigms on the nature and evolution of viruses are strong and implicating, climaxing with the assertion that the life and welfare of tens of millions of people suffering from neurodegenerative diseases might have been affected by the constrains imposed by the dogma of viruses as virus particles on understanding the true etiology of these devastating diseases and on the development of preventive and treatment approaches (14-16). It should be expected, therefore, that scientists working in these basic and applied biomedical fields would timely and openly refute or embrace these allegations. That might not happen, though, as it is well recognized by the historians and philosophers of science (28, 29) that the scientific theories, paradigms and dogmas, even if blatantly wrong, have a life of their own, which doesn’t necessarily follow Peter Medawar’s sensible recipe for conducting science: “The scientific method is a potentiation of common sense, exercised with a specially firm determination not to persist in error” (30). However, in this particular case, there is hope that some of the millions of patients affected by neurodegenerative diseases, as well as their family members and friends, might put some pressure on the scientists working these fields to either dismiss or to embrace these allegations.

References:

(1) Edwards, RA, Rohwer F. Viral metagenomics. 2005. Nat. Rev. Microbiol. 3:504-510. Edwards RA, 2005

(2) Suttle C.A. 2007. Marine viruses--major players in the global ecosystem. Nat Rev Microbiol. 5:801-12. Suttle CA, 2007

(3) Forterre P. 2006. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res. 117:5-16. Forterre P, 2006

(4) Claverie JM. 2006. Viruses take center stage in cellular evolution. Genome Biol. 7, 110. Claverie JM, 2006

(5) Koonin EV, Senkevich TG, Dolja VV. 2006. The ancient Virus World and evolution of cells. Biol Direct. 1-27. Koonin EV, 2006

(6) Bandea CI. 2009. A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains. Nature Precedings; http://precedings.nature.com/documents/3888/version/1

(7) Rohwer F, Barott K. 2013. Viral information. Biol Philos. 28:283-297. Rohwer F, 2013

(8) Bandea CI. 1983. A new theory on the origin and the nature of viruses. Journal of Theoretical Biology 105:591-602. Bândea CI, 1983

(9) Bandea CI. 2009. The origin and evolution of viruses as molecular organisms. Nature Precedings; http://precedings.nature.com/documents/3886/version/1

(10) Watson, JD. 1976. Molecular Biology of the Gene. Benjamin-Cummings, Menlo Park.

(11) Forterre P. 2010. Giant viruses: conflicts in revisiting the virus concept. Intervirology. 53:362-78. Forterre P, 2010

(12) Legendre M et al. 2014. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A. 111:4274-9. Legendre M, 2014

(13) Zimmer C. 2011. A Planet of Viruses. University of Chicago Press, Chicago.

(14) Bandea CI. 1986. From prions to prionic viruses. Med Hypotheses. 20:139-142.Bândea CI, 1986

(15) Bandea CI. 2009 Endogenous viral etiology of prion diseases. Nature Precedings; http://precedings.nature.com/documents/3887/version/1

(16) Bandea CI. 2013. Aβ, tau, α-synuclein, huntingtin, TDP-43, PrP and AA are members of the innate immune system: a unifying hypothesis on the etiology of AD, PD, HD, ALS, CJD and RSA as innate immunity disorders. bioRxiv; http://biorxiv.org/content/early/2013/11/18/000604

(17) Prusiner, SB. 1998. Prions. Proc. Natl. Acad. Sci. U. S. A. 95:13363-13383. Prusiner SB, 1998

(18) Raoult D et al. 2004. The 1.2-megabase genome sequence of Mimivirus. Science. 306:1344-50. Raoult D, 2004

(19) Philippe N et al. 2013. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341:281-6. Philippe N, 2013

(20) Hoffmann R et al. 1998. Archaea-like endocytobiotic organisms isolated from Acanthamoeba sp. (Gr II). Endocytobiosis & Cell Res.12, 185.

(21) Michel R et al. 2003. Endocytobiont KC5/2 induces transformation into sol-like cytoplasm of its host Acanthamoeba sp. as substrate for its own development. Parasitol Res. 90:52-6. Michel R, 2003

(22) Scheid P et al. 2008. An extraordinary endocytobiont in Acanthamoeba sp. isolated from a patient with keratitis. Parasitol. Res.102, 945, (2008). Scheid P, 2008

(23) Scheid P, Hauröder B, Michel R. 2010. Investigations of an extraordinary endocytobiont in Acanthamoeba sp.: development and replication. Parasitol Res.106:1371-7. Scheid P, 2010

(24) Wolkowicz R, Schaechter M. 2008.What makes a virus a virus? Nat Rev Microbiol. 6:643. Wolkowicz R, 2008

(25) Raoult D, Forterre P. 2008. Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol. 6:315-9. Raoult D, 2008

(26) Moreira D. & López-García P. 2009.Ten reasons to exclude viruses from the tree of life. Nature Rev. Microbiol. 7:306–311. Moreira D, 2009

(27) Forterre P. 2013. The virocell concept and environmental microbiology.ISME J. 7:233-6. Forterre P, 2013

(28) Kuhn TS. 1962. The Structure of Scientific Revolutions. University of Chicago Press, Chicago.

(29) Popper K. 1963. Conjectures and Refutations: The Growth of Scientific Knowledge. Routledge, London

(30) Medawar PB. 1969. Induction and Intuition in Scientific Thought. Methuen, London.

On 2014 Apr 16, Claudiu Bandea commented:

What if we have totally missed the true nature of viruses? (Part I)

(Due to size limitations, this comment was entered as two parts)

Viruses are the most abundant life forms on Earth and the repertoire of their genes is greater than that of cellular organisms (reviewed in 1, 2). Considering also their extraordinary medical and ecological significance as well as their critical role in shaping the evolution of cellular species and their genome (3-7), it would be expected that the paradigms about the nature and evolution of viruses were on solid scientific grounds.

However, in what might be the most enduring misconception in biology, ever since they were discovered more than a century ago, viruses have been conceptually misidentified with the virus particles and defined based on the physical, biochemical, and biological properties of these particles (8, 9). Because of the dogma of viruses as virus particles, thousands of scientific articles and books about viruses contain errors that border the pseudo-science realm. Take, for example, the following quote, which is representative of the scientific description of viruses: “all viruses differ fundamentally from cells, which have both DNA and RNA, in that viruses contain only one type of nucleic acid, which may be either DNA or RNA” (italics added to all quotes; 10). Despite common knowledge that during their life cycle many viruses have both nucleic acids, even James Watson, the eminent scientist, who arguably knows nucleic acids better than anyone, has fallen victim to the dogma of viruses as virus particles (for additional examples and quotes outlining this dogma see Ref. 9).

Although the scientific flaws associated with the dogma of viruses as virus particles were outlined more than three decades ago (8), along with a new hypothesis on their nature and evolutionary origin, these flaws have only become acute after the discovery of giant viruses (reviewed in Ref. 11). Perhaps no one has questioned the dogma of viruses as virus particles more explicitly, and in stronger terms, than Jean-Michel Claverie, the senior author of the article by Legendre et al. (12) and one of the leading researchers in the field of giant viruses, who asked: “what if we have totally missed the true nature of (at least some) viruses?” (4). Claverie answered this intriguing question in a rather revealing way: identifying viruses with the virus particles, he wrote, might “be a case of ‘when the finger points to the stars, the fool looks at the finger.”

As previously emphasized, however, questioning the dogma of viruses as virus particles is challenging (9). After all, it can be argued that, even if scientifically flawed, the dogma has ‘guided’ several generations of scientists to extraordinary discoveries in virology and in related biomedical fields. By analogy, it is also true that many scientific studies about our planet, which is increasingly thought of as “A Planet of Viruses” (13; see also Ref. 7), can be successfully performed in context of the theory that Earth is flat. So, why question the dogma of viruses as virus particles? First, this dogma is scientifically flawed and, therefore, academically unacceptable. More importantly, though, it has constrained progress not only in basic research, such as that on the origin and evolution of viruses and cells, but also in some applied biomedical fields, in which the life and welfare of many people is at stake.

For example, in the field of neurodegenerative diseases, which affect tens of millions of people and have a negative economic impact that dwarfs the entire global investment in biomedical research, the misleading dogma of viruses as virus particles led to the formulation of the prion hypothesis, which has apparently misdirected much of the thinking and research for decades (14-16). Briefly, in the context of dogma of viruses as virus particles, in order to prove or disprove the viral etiology of Transmissible Spongiform Encephalopathies (TSEs), the scientists searched for viruses (i.e. virus particles containing the viral genome) in the material used for the transmission of the disease. Hundreds of studies using this experimental approach were performed, but no TSE virus was found, which led to the triumph of the prion hypothesis and the dismissal of the virus hypothesis: “the 50-year quest for a virus has failed because it does not exist!” it was exclaimed (17). However, a decade earlier, it was proposed that the scientific rationale and the experimental approach that were used to investigate the etiology of TSEs were misleading; specifically, it was proposed that the so called ‘prion protein’ was encoded by an endogenous virus, and that this virus could not be identified by the experimental approaches that were employed or in the context of the scientific rationale imposed by the dogma of viruses as virus particles; indeed, none of the thousands of endogenous viruses can be identified using these scientifically flawed approaches. Nevertheless, the pseudoscientific aberration imposed by conventional view about the nature and identity of viruses did not stay in the way of making the prion hypothesis one of the top novelties in modern biology and promoted and rewarded accordingly (17).

Regarding P. sibericum and other giant viruses, the current dogma about the nature and evolution of viruses has delayed their identification for many years, if not decades, and have confused the interpretation of the experimental data and observations in the field. For example, the original mimivirus isolate was classified as a small Gram-positive bacterium for a decade before realized that it was a virus (18). Since then, several viruses with large genomes size have been identified, culminating with the remarkable reports on the discovery of pandoraviruses (19) and P. sibericum (12) by Claverie and his colleagues. Interestingly, it appears that some of these ‘novel’ giant viruses have also been isolated and characterized many years ago, but classified as cellular organisms. Indeed, two free-living amoeba intracellular parasites, labeled KC5/2 and KLaHel, which were discovered by a German research group in samples collected form a water-treatment-plant sample (20, 21) and the inflamed eye of a patient with keratitis (22, 23), respectively, are highly similar P. sibericum and pandoraviruses.

So, “What makes a virus a virus?” (24). Incited by a new proposal by Didier Raoult and Patrick Forterre for defining the nature of viruses (25), Roland Wolkowicz and Moselio Schaechter (24) have come to realize that the identity of viruses, as traditionally defined (i.e. virus particles), or as proposed by Raoult and Forterre (i.e. capsid-, or virus particle-encoding organisms), is missing the “the most fundamental aspect of what makes a virus a virus: it breaks up and loses its bodily integrity, with its progeny becoming reconstituted after replication from newly synthesized parts.” And, reflecting more broadly on the nature of viruses and on the field of virology, Wolkowicz and Schaechter wrote: “We are surprised from our own experience that the world of virology has not fully embraced this outlook” (24). However, this outlook, along with a comprehensive theory on their evolutionary origin, nature, and identity, has been presented more than three decade ago (8, 9), but until recently (see, for example, Ref. 11) it has received little attention.

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Apr 15, Ronald Perez commented:

Good review on checkpoint inhibitor immuno-oncology, however, I was hoping the authors had mentioned cancer vaccines. I believe cancer vaccines (i.e. T-VEC and MAGE-A3) are also included in the realm of immuno-oncology and deserved to be mentioned in a future review.

On 2016 Jul 21, Judy Slome Cohain commented:

The term, avulsion means ‘forcibly detached from its normal point of insertion by either trauma or surgery’. It is unusual nowadays to have a medical term that by definition blames the practitioner for the problem. Probably this term is going to be replaced with cord snapping asap. But whatever the terminology, Yes, cord snapping or avulsion is caused by force. The cord only snaps if you pull too hard on it. If the cord is only 10 -14 cm, it is hard not to pull on it, so even if you dont intend to pull hard, if the cord is very short, you will have a cord snap if you do enough births. If you pay attention and have your clamp readily accessible (which is what you are being paid for) you clamp it right away and lose very little blood. To be perfectly clear, cord snapping after the baby is born is never a problem except when the practitioner is not acting expediently as they should be or if there is no birth attendant present or if the water is so murky that one cannot see what is going on or if the woman is in the middle of a large pool and inaccessible.

It was not pointed out that after coming out of the uterus, cords keep pulsing nicely in hot water. This is a great advantage when delivering breech babies because the cord keeps pulsing, even after half the baby is out, if it is under hot water, the fetus continues to be well supplied with oxygen. However, since hot water causes cords to keep pulsing, even the ones that snapped, perhaps that is why there are more cases described of babies who delivered into water, who had a snapped cord, who also lost significant amount of blood. But maybe it is not waterbirth, but pool birth. In most pool births, the midwife is not in the pool with the woman, so would not be able to expediently clamp the cord if it snaps. This is not true for bathtub births. This is another reason to recommend bathtub over pools. In a bathtub waterbirth, if the cord snaps, the midwife can easily clamp it. The other advantages of bathtubs over pools are: it is possible to get rid of the feces by draining the bathtub, it is much easier to keep hot, it is easier to get the woman out in the event of shoulder dystocia, and it enables the husband more time to bond with the baby instead of having to empty the pool.

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Mar 05, Dale D O Martin commented:

The authors state that the protein has multiple predicted N-myristoylation sites that probably plays a role in telomere maintenance. However, myristoylation can only occur on N-terminal Glycines, hence the name N-myristoylation. I've commented on this on two other papers by these authors (here http://www.ncbi.nlm.nih.gov/pubmed/18071584 & here http://www.ncbi.nlm.nih.gov/pubmed/23007995 and the same comment I made is pasted below). I have also contacted the senior author and the editor of the journal regarding the second paper (http://www.ncbi.nlm.nih.gov/pubmed/23007995), but they have not changed it despite agreeing with me that it was incorrect. So, I am highlighting it here once again.

Previous comment: It should be noted that N-myristoylation can only occur on N-terminal Glycines, hence the name N-myristoylation. This occurs either co-translationally on the nascent polypeptide following the removal of the initiator Met or it can occur posttranslationally following proteolysis, which exposes a new N-terminal Gly. The latter has only been shown to occur in caspase-cleaved proteins. In this case, the Gly follows an Asp residue where caspase will cleave. The authors here predict internal myristoylation at very unlikely positions. Furthermore, the general consensus sequence for myristoylation is GXXXS/C/T where X is any amino acid, except for large bulky residues, and S/C/T are preferred in position 5 (counting from Gly). The first site they predict is GAAPP and is very unlikely to be myristoylated. Caution should be taken when predicting internal myristoylation sites. Unless it is predicted to be cleaved to expose an N-terminal Gly.

On 2014 Mar 11, Daniel Kripke commented:

These wonderful data add important additions to our understanding of long and short sleep. There are some additional issues to which the data might contribute.

1) It appears that like the Cancer Prevention Studies and many others, this study suggests that the longest survival was associated with sleep durations slightly below the mean. According to Table 5, among females, the risk was consistently just a bit less with -1 hour adjusted sleep than with mean sleep. (Incidentally, perhaps the squared age-adjusted sleep regressions for females would be significant if centered at the minimum risk.) Among males, Table 5 indicated that death risk rose much more rapidly above the mean age-adjusted sleep duration than below it. Long sleep was associated with more risk than short sleep. Would the lowest risk for males be associated with sleep durations about 30 min. below the mean, as was the case in the adult data?

2) Increased mortality risk has been found associated with delayed sleep phase disorder, that is, with late bedtimes. Is a late bedtime a mortality risk factor in data from these children?

3) Several studies of risk factors among adults have indicated that use of hypnotic drugs (sleeping pills) is an independent risk factor for increased mortality, though sometimes confounded with short sleep or insomnia. Does this remarkable data set offer any information about mortality risks associated with hypnotics?

On 2014 Mar 10, LEE ELLIS commented:

can the authors or editors please provide an explanation for the retraction. I cannot see the link to any article describing the reasons for the retraction.

On 2014 Jun 19, Sacchetti Maria Luisa commented:

This study demonstrate a high prevalence of the nerve dysfunction and a significant correlation with the severity of SDB, in acute stroke patients. Due to the recording technique limitations, the Authors do not classify patients' SDB as central or obstructive. As cases affected by previous peripheral neuropathy or previous OSA were excluded, what might have caused the deficit? Hypoglossal nerve function - and more in general upper airways patency- is regulated by serotonin (5HT). Several studies have demonstrated that altered central networks, particularly serotoninergic, can contribute to OSA Brown RE, 2012 as well as to central sleep apnea Buchanan GF, 2010. Moreover, Sunderram et al.Sunderram J, 2000 observed that a selective serotonin reuptake inhibitor (SSRI), paroxetine hydrochloride,may activate motor neurons in the hypoglossal nucleus and increase genioglossal electromyographic (EMG) activity. Therefore we can hypothesize that the hypoglossal nerve dysfunction observed in the study is -at least in part- the direct consequence of stroke on the serotoninergic network. The incidence of depression after stroke<PMID: 18728805 >, together with effectiveness of its treatment independently to the clinical relevance depressive symptoms Mead GE, 2012, partially support this hypothesis.

On 2014 Oct 01, Anthony Tweedale commented:

PubMed soon should be adding the published Erratum to this Letter to the Editor (responding to academics' research important to risk assessment (Krauth D, 2013), but as I prompted the Erratum, I wish to add that it, concerning the declared interests (DoI) of two of these industry and industry-affiliated authors (Pr.'s Leist & Boobis), even now fails to say 'industry' or a synonym; whereas my investigations revealed that these two also work regularly for industries.

On 2016 Apr 05, Marko Premzl commented:

The third party data gene data set of eutherian Mas-related G protein-coupled receptor genes HG426065-HG426183 was deposited in European Nucleotide Archive under research project "Comparative genomic analysis of eutherian genes" (https://www.ebi.ac.uk/ena/data/view/HG426065-HG426183). The 119 complete coding sequences were curated using tests of reliability of eutherian public genomic sequences included in eutherian comparative genomic analysis protocol including gene annotations, phylogenetic analysis and protein molecular evolution analysis (RRID:SCR_014401).

Project leader: Marko Premzl PhD, ANU Alumni, 4 Kninski trg Sq., Zagreb, Croatia

E-mail address: Marko.Premzl@alumni.anu.edu.au

Internet: https://www.ncbi.nlm.nih.gov/myncbi/mpremzl/cv/130205/

On 2014 Jun 16, S Sundar commented:

Medical paternalism in prostate radiotherapy.

Authors: Dr S.Sundar & colleagues (E.F, G.W, R.T)

The MRC RT01 randomised trial has shown no overall survival benefit for escalated doses of radiation in prostate cancer( 1). This complete lack of overall survival benefit for higher doses of radiation is a consistent finding across many well designed randomised trials (2). It is a fundamental radiobiological fact that radiation toxicity is directly proportional to total dose of radiation administered. So, not surprisingly, escalated doses of radiation has been associated with higher toxicity across the randomised trials (2).

In spite of the lack of overall survival benefit coupled with higher radiation toxicity, escalated doses of radiation have inexplicably become the international standard of care. Various guidelines including National Institute for Health and Care Excellence (NICE) guideline (CG 175) recommend escalated doses of radiation with the NICE guideline making a specific recommendation of at least 74 Grays of radiation.

If escalated radiation dose is treated in the same way as a pharmacological drug, it certainly would not have been accepted as a universal standard of care due to higher toxicity and lack of overall survival benefit. Medical paternalism seems rife in prostate radiotherapy. A patient preference study from Netherlands has demonstrated that prostate patients prefer lower toxicity and are happy to trade off efficacy for better quality of life. However,more importantly, physicians were poor in predicting this patient preference(3)(4).

Radiation oncologists need to shed medical paternalism and engage patients. They should explain the pros and cons of escalated doses of radiation, may be with the us of decision aids, and help patients make an informed choice. Radiation oncologists need to demonstrate evidence based medicine particularly when there is an ongoing debate about appropriate use of prostate radiotherapy in urologist owned radiation facilities (5).

References: 1 Dearnaley DP, Jovic G, Syndikus I, et al. Escalated-dose versus control-dose conformal radiotherapy for prostate cancer: long-term results from the MRC RT01 randomised controlled trial. Lancet Oncol 2014. doi:10.1016/S1470-2045(14)70040-3.

2 Viani GA, Stefano EJ, Afonso SL. Higher-than-conventional radiation doses in localized prostate cancer treatment: a meta-analysis of randomized, controlled trials. Int J Radiat Oncol Biol Phys 2009; 74: 1405–18.

3 Van Tol-Geerdink JJ, Stalmeier PFM, van Lin ENJT, et al. Do patients with localized prostate cancer treatment really want more aggressive treatment? J Clin Oncol Off J Am Soc Clin Oncol 2006; 24: 4581–6.

4 Stalmeier PFM, van Tol-Geerdink JJ, van Lin ENJT, et al. Doctors’ and patients’ preferences for participation and treatment in curative prostate cancer radiotherapy. J Clin Oncol Off J Am Soc Clin Oncol 2007; 25: 3096–100.

5 Mitchell JM. Urologists’ use of intensity-modulated radiation therapy for prostate cancer. N Engl J Med 2013; 369: 1629–37.

On 2014 Mar 19, Alexander Lerchl commented:

The symbol "*" in Fig. 1 is misplaced. According to the text, the "Total time carrying phone/week (hrs)" was not significantly different.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0104446. We believe the correct ID, which we have found by hand searching, is NCT01044446.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 Sep 01, Francois Cachat commented:

In this study, the authors demonstrated that the outcome of children with a single kidney is not as good as it was thought previously. As they pointed out rightfully, poor outcome (proteinuria, hypertension, chronic kidney disease (CKD)) is (mostly) related to the addition of other injury to the single kidney such as (recurrent) pyelonephritis or obstruction. That was the case in 4 of 5 patients they described with CKD. Genetics might play a role as well (as with their 5th patient with hypodysplasia). Other studies also reported chemotherapy after Wilms tumor and nephrectomy as a risk factor for poor outcome. In addition to CKD, it would be interesting to know if hypertension (3 patients) and proteinuria (2 patients) was found only in the "high risk" group of patients with a single kidney. It is my understanding that a child with a congenital single kidney, with no other anomalies, with renal length above 95th percentile, and no other aggression such as hypertension or diabetes, is probably not at higher risk than the general population of developping renal disease (but that remains to be demonstrated in long-term follow up cohort studies)(hyperfiltration might be deleterious as well on a long-term basis). Thank you and congratulation to the authors for their work.

On 2014 Apr 08, Steve Herman commented:

This abstract, and the authors' press releases, fail to adequately clarify the fact that the hazard ratios shown in the abstract are "adjusted", and do not represent the real risks to real offspring in the population. Some of the "adjustments" are staggering. For example, the actual population risks that were found in this study can be correctly summarized as follows:

Compared with offspring born to fathers 20 to 24 years old, offspring of fathers 45 years and older were 1.5 times more likely to have autism, .7 times less likely to have ADHD, 1.3 times more likely to have a psychotic disorder, 1.5 times more likely to have bipolar disorder, .9 times less likely to have suicidal behavior, .8 times less likely to have a substance abuse problem, .7 times less likely to have failing grades in school, .9 times less likely to have low educational attainment, .8 times less likely to have a low IQ; and 1.5 times more likely to have some higher education.

Please see http://ow.ly/v6ehS for more information.

On 2014 Sep 21, Bernard Baars commented:

Dear Leonard, --- I admire your range of interesting papers on fundamental questions.

In regard to esthetic pleasure and behavior, I would call your attention to a sizable evolutionary anthropology literature on the cost of social display of primary and secondary sexual signals --- the classical case being the male peacock.

Dan Zahavi called this the Handicap Principle in 1975, and the idea is essentially that sexual selection for mating with the fittest available other-gender mates is so important as an evolutionary driver (only comparable to individual survival itself) that hominins like us, and all of our ancestors among primates, mammals and vertebrates, dedicated a great percentage of biological resources to it. The male peacock posing for sexual selection (by the well-camouflaged females) is endangering his life by attracting predators (by blatant visual, auditory, and presumably olfactory signaling.) The female peahen takes no such chances. Thus the male handicaps himself to look beautiful, and interestingly, humans have used peacock feathers historically to decorate themselves as well.

It is precisely the apparently inutility of esthetic enjoyment that is evolutionarily important, along the lines of Thorstein Veblen's "conspicuous consumption." Biologically, the male peacock is signaling "looking how strong and fertile I am!!!" I can even afford to waste immense personal risk of predation, great metabolic energy, attacks from competing males in heat, the strength to shiver my tail feathers and preen for hours, simply to attract the best female! What healthy offspring we shall have! The easy analogy would be to men who buy muscle cars or Cadillacs when they could drive a mini-car instead. Among recent entertainment stars, Kim Kardashian and her many imitators among women spending hugely on breast and buttocks enlargements imitates varieties of H sapiens sapiens morphology among peoples who evolved large breasts, steatopigous buttocks, and large stomachs in evolutionarily recent times. Fat storage is a great advantage in certain climates (Siberian-descended Inuits and Amerindians are a good example), but encounter handicaps to survival in the face of massive droughts and famine conditions. Since human ancestors are known to have encountered massive drought conditions in the desertification of the Sahara in the millennia prior to the "African Exodus," when the Hss population is thought to have collapsed to 5,000 individuals in North East Africa, famine-adaptibility is plausibly a major Darwinian constraint on human survival.

(Note that the term "African Exodus" does not apply to African humans who escaped the desertification of the Sahara by migrating southwards, and who never left Africa. Nor does it apply to the peoples who remained sub-Saharan, such as plausibly the Khoi San of the Kalahari Desert. Khoi San body morphology is gracile rather than robust, as befits a desert-dwelling people, and their cultural and personal knowledge of semi-arid survival tactics is vast.)

Nicholas Wade has also pointed out the fact that tribal peoples very often perform frequent, vigorous and long-lasting community dancing, and universally harbor other-worldly religious beliefs, which are thought to enhance group harmony and therefore survival. (Mating in tribal peoples tends to obey strict kinship rules, either within the birth group, or between allied groups). The very wide distribution of these human cultural habits has been very well studied since the publication of Stephen Brown's Human Universals (1992) (also called Cultural Universals today).

In human evolution the earliest evidence for artificial body decoration comes from human-related diggings in South Africa of ancient colored clay deposits, thought to have been used for spectacular body decoration by men and women, especially during and after puberty. (At least 200KYA) Personal jewelry involving trading over sizable distances, such as seashells found far from their origins in North Africa, are also ancient. In more recent years mating-related body decoration, hair styles, special clothing, vigorous dancing, music-making, singing and use of instruments (!), seductive movements and gestures, open competition within genders, verbal facility, display of cooking and hunting skills, and an essentially unlimited number of novel attention-catching behaviors can be related to sexual display. Among the American Sioux the male warriors showed their physical size (often 6' or taller), and created new clothing fashions each year (while the women took a more modest role). "Counting coup" --- rushing into an enemy village, physically touching a fierce enemy warrior, and rushing out again to safety was a quantitative measure of masculine heroics. Precisely analogous behavior can be seen today in ever-changing female fashions, in male body building, and in military uniforms for men, including medals and honor ribbons displayed on the left chest, reflecting both combat experience, military skills, and rank in the male hierarchy. The bodily posture of "pride" is also on display (see palace guards throughout Europe, including the Kremlin in Russia). Mammalian positions of pride are anti-gravity postures (head back, body erect, goose-stepping high) which require great physical training, and which oppose the body posures of social defeat, depression and surrender (head down, bowing low, slow non-threatening approach to the victors, etc.) Notice that we instantly recognize those body postures in lions, horses, and humans --- the standard Napoleonic pride statue in European capitals is a proud-looking man on a horse, bearing a sword. The upward direction of the sword, spear or rifle in heroic sculptures may hark back in evolution to the upward-pointing position of the penis during courtship display in our primate relatives. In classical art this is highly visible in 19th century paintings of Napoleon on a white horse, surrounded by battle. The link between male heroics, female fashions, secondary and primary sexual signals, music and the arts is unavoidable in the art of the Romantic period in Europe.

Notice that this bio-anthropological hypothesis accounts for a number of features of esthetics you have raised in your interesting article.

On 2014 Aug 30, Jorge H Ramírez commented:

Ramirez, Jorge H (2014). A story about oxygen nanobubbles (RNS60). figshare. http://dx.doi.org/10.6084/m9.figshare.1135796

No further comments.

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Jun 19, Swapnil Hiremath commented:

This guideline was discussed on June 10th 2014 on the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available on PBFluids and at the NephJC website. It was quite a spirited discussion, with participation from nephrologists, clinical pharmacologists, internists, and more. A transcript and three different curated (i.e. Storified) versions of the tweetchat are available at the same NephJC link.

On June17th 2014, we conducted a video chat via Google Hangout, among the NephJC editors, Dr Richard Sterns and Dr Hatim Hassan, an archived version of which can be viewed on Youtube.

The highlights of the tweetchat and the hangout were: 1. These guidelines are extensive and exhaustive and will serve as an extremely useful resource for students, residents and practicing physicians. 2. There was widespread agreement that 'asymptomatic' hyponatremia is rarely asymptomatic, and doing away with that qualifier is a good move. 3. The recommendation against use of vasopressin antagonists in chronic hyponatremia is appropriate given lack of superiority in comparison against standard treatment, and possibility of neurological sequelae from rapid correction (and the high cost of these agents remains a concern). 4. The empiric treatment with hypertonic saline in hyponatremic patients with moderate to severe symptoms will be quite handy, particularly since the intricate calculations otherwise needed are often found to be daunting. 5. The lack of strong evidence (made especially apparent by the use of the GRADE methodology) is disappointing, especially given how common hyponatremia is, and highlights a need for future research.

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

This comment is cross-posted at the other two versions of the guidelines also.

On 2014 Jun 19, Swapnil Hiremath commented:

This guideline was discussed on June 10th 2014 on the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available on PBFluids and at the NephJC website. It was quite a spirited discussion, with participation from nephrologists, clinical pharmacologists, internists, and more. A transcript and three different curated (i.e. Storified) versions of the tweetchat are available at the same NephJC link.

On June17th 2014, we conducted a video chat via Google Hangout, among the NephJC editors, Dr Richard Sterns and Dr Hatim Hassan, an archived version of which can be viewed on Youtube.

The highlights of the tweetchat and the hangout were: 1. These guidelines are extensive and exhaustive and will serve as an extremely useful resource for students, residents and practicing physicians. 2. There was widespread agreement that 'asymptomatic' hyponatremia is rarely asymptomatic, and doing away with that qualifier is a good move. 3. The recommendation against use of vasopressin antagonists in chronic hyponatremia is appropriate given lack of superiority in comparison against standard treatment, and possibility of neurological sequelae from rapid correction (and the high cost of these agents remains a concern). 4. The empiric treatment with hypertonic saline in hyponatremic patients with moderate to severe symptoms will be quite handy, particularly since the intricate calculations otherwise needed are often found to be daunting. 5. The lack of strong evidence (made especially apparent by the use of the GRADE methodology) is disappointing, especially given how common hyponatremia is, and highlights a need for future research.

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

This comment is cross-posted at the other two versions of the guidelines also.

On 2014 Mar 03, mohamed salah abbassi commented:

iT IS VERY INTERESTING ARTICLE

On 2014 May 14, David Keller commented:

Still waiting for anyone to answer my criticisms of this USPSTF report

When I first read the 2014 USPSTF update on vitamins for disease prevention, I expected, based on the headlines, to find evidence that there is no reason to take a multivitamin. Instead, I became convinced by the data presented by the USPSTF that the evidence of benefits versus harms favors men over 50 taking a multivitamin to prevent cancer and possibly reduce overall mortality. At the very least, the USPSTF would be fully justified in recommending that men over 50 who do not consume a diet rich in vegetables and fruits should consider adding a multivitamin. For some reason, most editorials and comments have completely ignored the significant reductions in cancer for men randomized to multivitamins in the 2 studies cited by USPSTF, and the significant reduction in overall mortality for men randomized to the high dose multivitamin tested in the French study. Instead, we saw headlines and editorials stating or implying that we now have proof that multivitamins are useless. I request that an expert in this area reply to my comments, giving good reasons why you are not convinced by the data we have, and what it would take to convince you. If you are knowledgeable in this area, and especially if you are a member of the USPSTF, I would greatly appreciate your pointing out where my thinking on this issue is wrong or even debatable. For details, data and references, please see my Open Letter to the USPSTF on the following PubMed Commons web page:

http://www.ncbi.nlm.nih.gov/pubmed/24566474#cm24566474_4093

Lastly, it is not helpful to tag a comment as "not helpful" without specifying why. PubMed Commons should foster meaningful debate, not merely anonymous unexplained contradiction of each other.

On 2014 Apr 23, David Keller commented:

Open letter to the USPSTF: the evidence shows multivitamins reduce cancers in men

The United States Preventative Services Task Force (USPSTF) recently updated their report on multivitamin supplements, and again found "insufficient evidence" to recommend their general use. The USPSTF report dismissed the significant reduction in cancers seen in men in both the SU.VI.MAX and Physicians' Health Study (PHS II), stating: "The lack of effect in women and the use of different supplement formulations in the 2 trials make extrapolating these findings to the general population difficult."(1) However, since men constitute approximately half of the general population, there is no need to extrapolate any benefit which men obtain from supplements to women. A benefit proven to accrue to men would justify a recommendation that men should take supplements, and the USPSTF could state that the issue was still unresolved for women. After all, the USPSTF makes other sex-specific recommendations, such as aortic ultrasound screening for male smokers but not females. Alternatively, the USPSTF may have doubted the biological plausibility of supplements preventing cancers in men but not in women. The SU.VI.MAX authors explained that difference by pointing out that women have a higher baseline nutritional status than men (2), and thus have less to gain by adding a multivitamin supplement. The USPSTF failed to mention or rebut that seemingly reasonable explanation.

The second reason USPSTF gave for not being able to interpret the results of the PHS II and SU.VI.MAX studies was that these two clinical trials tested 2 different multivitamin supplement formulations. However, the 5 antioxidants used in the SU.VI.MAX supplement are a subset of the micronutrients in the Centrum Silver administered in PHS II. I have pointed out in PubMed Commons (3) that there is evidence of a dose-response effect when one compares the effects of the Centrum Silver supplement versus the higher-dose SU.VI.MAX supplement, with regard to the significant reduction in cancer seen in men in both studies. Each of the 5 ingredients of the SU.VI.MAX supplement (vitamin C, vitamin E, beta carotene, selenium and zinc) is present in a higher dose than in Centrum Silver, yielding a correspondingly higher reduction in the risk of cancer in men (see Table 1). A dose-response effect tends to corroborate the findings of the individual studies, and it also suggests the need for a dose-ranging study of the SU.VI.MAX supplement. Would increasing the doses of these 5 antioxidant nutrients reduce cancer rates and mortality even further in men? Would a significant effect in women become evident?

Lastly, the updated USPSTF report completely omitted any mention of the significant reduction in all-cause mortality which benefitted the men taking the SU.VI.MAX supplement (2).

At this time, there is consistent evidence from 2 large, prospective, randomized, placebo-controlled trials that the low-dose multivitamin supplement used in PHS II significantly reduces the incidence of cancer in men, and that the higher-dose SU.VI.MAX supplement (consisting of 5 antioxidant nutrients in higher doses than in Centrum Silver) reduces cancer rates even more in men, and adds a significant reduction in all-cause mortality. The USPSTF report did not indicate how many more studies must replicate these results before they find the data persuasive. Until such trials are completed, the evidence we have indicates that men will continue to suffer cancers and deaths which are preventable by taking a multivitamin. If future studies fail to replicate these results (perhaps as a result of improved nutritional status among men) then the only known harm or cost would be the 6 cents per pill retail price of the Centrum multivitamin used in PHS II, or the inexpensive combination of supplements which duplicates the SU.VI.MAX formula.

The USPSTF should modify their assessment of multivitamin supplements to reflect the significant dose-related benefits multivitamins have demonstrated for men over the age of 50, who can benefit from reduced cancer rates and overall mortality, according to the best evidence we have. The USPSTF should call for dose-ranging studies to determine whether the benefits of the five antioxidants administered in SU.VI.MAX can be increased by increasing their doses. If the USPSTF has evidence or reasons other than those I have refuted above for not recommending multivitamins for men over age 50, they should make them public.

At the very least, the USPSTF report should be amended to include the fact that overall mortality was significantly decreased in men taking the SU.VI.MAX supplement. The absence of that data from their report was a disservice to men who are deciding whether or not to take a supplement.

Table 1: Dose-Response Effect? Vitamin doses versus relative risk of cancer:

Centrum Silver 50+............SU.VI.MAX multivitamin....................................................

Beta-Carotene 1000 IU.......Beta-Carotene 6mg = 9960 IU...............................................

Vitamin C 60 mg.................Vitamin C 120 mg..........................................................

Vitamin E 50 IU...................Vitamin E 30 mg = 67 IU ..................................................

Zinc 11 mg..........................Zinc 20 mg................................................................

Selenium 55 mcg..................Selenium 100 mcg..........................................................

RR of cancer = 0.93............RR of cancer = 0.69.......................................................

References

1: Moyer VA. Vitamin, Mineral, and Multivitamin Supplements for the Primary Prevention of Cardiovascular Disease and Cancer: U.S. Preventive Services Task Force Recommendation Statement. Ann Intern Med. 2014 Feb 25. doi: 10.7326/M14-0198. [Epub ahead of print] PubMed PMID: 24566474.

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

3: Keller DL. Multivitamins: "Expensive Urine" or inexpensive cancer prevention? Comment posted on PubMed Commons, last edit dated 3/29/2014. http://www.ncbi.nlm.nih.gov/pubmed/24566474#cm24566474_3700

On 2014 Apr 19, David Keller commented:

Men taking multivitamins had significantly lower overall mortality and lower cancer risk

The USPSTF report did not disclose that men randomized to antioxidant supplements in the large prospective SU.VI.MAX trial had significantly lower risk of death, in addition to significantly fewer overall cancers than men assigned to placebo (1). This important information should be considered by any man over age 50 who is deciding whether or not to take multivitamins. In addition, please see my accompanying comments regarding the apparent dose-response effect of the SU.VI.MAX supplement with regard to cancer prevention in men.

(1) Hercberg S, Kesse-Guyot E, Druesne-Pecollo N, Touvier M, Favier A, Latino-Martel P, Briançon S, Galan P. Incidence of cancers, ischemic cardiovascular diseases and mortality during 5-year follow-up after stopping antioxidant vitamins and minerals supplements: a postintervention follow-up in the SU.VI.MAX Study. Int J Cancer. 2010 Oct 15;127(8):1875-81. doi: 10.1002/ijc.25201. PubMed PMID: 20104528.

On 2014 Mar 29, David Keller commented:

Multivitamins: "Expensive Urine" or inexpensive cancer prevention?

The USPSTF guideline statement on multivitamins and cancer risk (1) includes the following statements:

Statement 1: “Two large trials, the Physicians' Health Study II (PHS II) and the SU.VI.MAX (Supplementation in Vitamins and Mineral Antioxidants) study, showed a decrease in overall cancer incidence in men (pooled unadjusted relative risk, 0.93 [95% CI, 0.87 to 0.99])“

Statement 2: “Use of dietary supplements is common in the U.S. adult population. Forty-nine percent of adults used at least 1 dietary supplement between 2007 and 2010, and 32% reported using a multivitamin–multimineral supplement. Supplement use is more common among women and older adults than men and younger adults.”

Statement 3: “The lack of effect in women and the use of different supplement formulations in the 2 trials make extrapolating these findings to the general population difficult.”

The lack of benefit of multivitamins and mineral supplements (MVMS) in women might have been due to the higher background use of MVMS by women (Statement 2). Intention-to-treat analysis would count women in control groups who took MVMS in violation of experimental protocol as if they were not taking MVMS; this would tend to reduce the apparent benefit of MVMS in women, perhaps explaining Statement 3. A hypothesis-generating per-protocol analysis of these trials is warranted; if an anti-cancer effect of MVMS is thereby discerned in women, a more rigorous follow-up study would be justified.

As a male physician, I will continue to take a MVMS, based on Statement 1, unless evidence emerges which disproves the results of these 2 large trials. While awaiting further information, and considering the minimal potential harms and cost of multivitamins, and the possible benefits, I see no reason to dissuade women from taking a MVMS.

The USPSTF report also states that "the use of different supplement formulations in the 2 trials makes extrapolating these findings to the general population difficult", which refers to the fact that the Physician's Health Study tested "a commercially available multivitamin that contained 30 ingredients" (which was Centrum Silver), while the SU.VI.MAX Study (2) tested a supplement which "included nutritional doses of vitamins C and E plus β-carotene, selenium, and zinc".

In fact, the 5 nutrients included in the SU.VI.MAX supplement are a subset of the 30 nutrients included in Centrum Silver, and each of these 5 nutrients is present at a substantially higher dose in the SU.VI.MAX supplement than in Centrum Silver (3). Furthermore, use of the SU.VI.MAX supplement led to a larger reduction in the average relative risk of cancer than did the use of Centrum Silver, suggesting a possible dose-response effect for the ingredients of the SU.VI.MAX supplement with regard to lowering the relative risk of cancer. See Table 1:

Table 1: Dose-Response Effect? Vitamin doses versus relative risk of cancer:

Centrum Silver 50+............SU.VI.MAX multivitamin....................................................

Beta-Carotene 1000 IU.......Beta-Carotene 6mg = 9960 IU...............................................

Vitamin C 60 mg.................Vitamin C 120 mg..........................................................

Vitamin E 50 IU...................Vitamin E 30 mg = 67 IU ..................................................

Zinc 11 mg..........................Zinc 20 mg................................................................

Selenium 55 mcg..................Selenium 100 mcg..........................................................

RR of cancer = 0.93............RR of cancer = 0.69.......................................................

A dose-response effect, if present, would tend to support the hypothesis that the decrease in cancers observed in these 2 studies was real and not due to the play of chance. Proving a dose-response effect requires more than just two data points taken from 2 different studies on 2 different populations. However, this observed trend suggests the need for a follow-up study to determine whether further increases in the doses of the ingredients of the SU.VI.MAX supplement will lead to further declines in the average relative risk of cancer. Of course, all relevant cautions must be taken, such as not administering beta-carotene to persons with a smoking history.

References

1: Moyer VA. Vitamin, Mineral, and Multivitamin Supplements for the Primary Prevention of Cardiovascular Disease and Cancer: U.S. Preventive Services Task Force Recommendation Statement. Ann Intern Med. 2014 Feb 25. doi: 10.7326/M14-0198. [Epub ahead of print] PubMed PMID: 24566474.

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

3: Centrum Silver 50+ website, accessed on 3/24/2014:<br> http://www.centrum.com/centrum-silver-adults-50-plus#tablets

4: The following websites were referenced for converting vitamin doses from mg to IU, accessed on 3/24/2014: http://ods.od.nih.gov/factsheets/VitaminE-HealthProfessional/

http://ods.od.nih.gov/factsheets/VitaminA-HealthProfessional/

http://dietarysupplementdatabase.usda.nih.gov/ingredient_calculator/help.php

On 2017 Jul 23, Randi Pechacek commented:

Embriette Hyde made a blog post about this paper on microBEnet as part of a larger discussion on the microbiome of the built environment of our cars.

On 2014 Jun 19, Swapnil Hiremath commented:

This guideline was discussed on June 10th 2014 on the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available on PBFluids and at the NephJC website. It was quite a spirited discussion, with participation from nephrologists, clinical pharmacologists, internists, and more. A transcript and three different curated (i.e. Storified) versions of the tweetchat are available at the same NephJC link.

On June17th 2014, we conducted a video chat via Google Hangout, among the NephJC editors, Dr Richard Sterns and Dr Hatim Hassan, an archived version of which can be viewed on Youtube.

The highlights of the tweetchat and the hangout were: 1. These guidelines are extensive and exhaustive and will serve as an extremely useful resource for students, residents and practicing physicians. 2. There was widespread agreement that 'asymptomatic' hyponatremia is rarely asymptomatic, and doing away with that qualifier is a good move. 3. The recommendation against use of vasopressin antagonists in chronic hyponatremia is appropriate given lack of superiority in comparison against standard treatment, and possibility of neurological sequelae from rapid correction (and the high cost of these agents remains a concern). 4. The empiric treatment with hypertonic saline in hyponatremic patients with moderate to severe symptoms will be quite handy, particularly since the intricate calculations otherwise needed are often found to be daunting. 5. The lack of strong evidence (made especially apparent by the use of the GRADE methodology) is disappointing, especially given how common hyponatremia is, and highlights a need for future research.

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

This comment is cross-posted at the other two versions of the guidelines also.

On 2014 Feb 25, Patrick Morcillo commented:

Let me add a few points to clarify and avoid misunderstandings, mostly for the lay public: 1) There is no "placebo effect" in mice, and therefore, the results are real 2) When no voltage (or current) is applied, there is no effect 3) When the current is applied in a non-acupoint, there is no effect 4) Please be aware that many promising results in mice do not work with humans

Disclaimer: I am acknowledged in the article

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0024451. We believe the correct ID, which we have found by hand searching, is NCT00244517.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 Jun 25, Ryan Radecki commented:

Post-publication commentary:

"Should Paramedics Intubate Out-of-Hospital Cardiac Arrest?"

Airway management of out-of-hospital cardiac arrest is a controversial topic. Most patients transported for OHCA have receive prehospital airway management. However, attempts at establishing an airway can interrupt compressions, over-ventilation can decrease cerebral perfusion, and delays in airway acquisition impact transport to definitive care....

http://www.emlitofnote.com/2014/06/should-paramedics-intubate-out-of.html

On 2014 Feb 25, Maciej Wójcik commented:

very nice work

On 2014 Feb 23, Hilda Bastian commented:

This paper tackles an important issue. We definitely need better ways to keep up with the evidence - and the rate of growth of that evidence makes it both more difficult and more urgent (Bastian H, 2010). It's particularly helpful that the paper addresses the risks of multiple testing in continuous updating models.

In calling for "a shift to continuous work process," though, it's important to remember that this shift has long occurred for many organizations and groups. A 2010 survey of agencies that sponsor and conduct systematic reviews (sometimes with clinical practice guidelines as well), found 66 that were already doing this to some extent at least (Garritty C, 2010).

In this latest proposal for living systematic reviews, several issues reach Table 1 as key challenges, that are unquestionably important. But "validation and acceptance by the academic community" and "ensuring conventional academic incentives are maintained" did not prevent the development of continuous updating models.

The restriction of access to key databases does contribute to keeping many groups trapped in duplicative updating hamster wheels, though. Poor access leads to critical research waste (Glasziou P, 2014). Making the preservation of conventional academic incentives foundational in Table 1, rather than, say, opening databases, runs the risk of focusing us on technical issues within restricted models, slowing down and limiting both innovation and the entry of new players.

On 2015 Dec 11, Mark Johnston commented:

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

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT011583309. We believe the correct ID, which we have found by hand searching, is NCT01583309.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 Mar 24, Karen Woolley commented:

FINALLY...more attention is being paid to PRACTICAL issues about data sharing!

Well done to Wilhelm, Oster, and Shoulson for reminding us that it takes resources (financial and nonfinancial) to share data. We should also remember that it takes resources (financial and nonfinancial) to publish data. This issue seems to have been lost in the hand-wringing taking place over low and slow publication rates.

A robust systematic review, presented at the 2013 Peer Review Congress (organised by JAMA and the BMJ) identified “lack of time” as the main reason why researchers don’t write up manuscripts.¹ Clearly, many researchers need writing support (ie, from legitimate, ethical, highly trained and qualified professional medical writers; NOT ghostwriters). Similar to Wilhelm et al., we outlined the need to consider the cost issue if we want to enhance publication speed and quality.² We think our paper struck a chord - it was among the top 5 most downloaded papers from Current Medical Research & Opinion that year.

Professional medical writers are trained to help make complex data understandable to different target audiences (eg, researchers, regulators, patients) and could, therefore, help address another critical point made by Wilhelm et al., “Standardization costs for data-sharing models include the additional effort required to share, beyond what is required of any high-quality clinical research, because it takes considerably more effort to organize and make data understandable to others.”

Wilhelm et al. conclude that “Understanding and planning for the costs [for data sharing] at the outset of research can help realize the full potential of data sharing.” The same sentence could apply to publications ie, understanding and planning for the costs of manuscript writing at the outset of research can help realise the full potential of peer-reviewed publications.

Authors and affiliations Karen L. Woolley PhD CMPP,a Art Gertel MS,b Cindy Hamilton PharmD,c Adam Jacobs PhD,d Jackie Marchington PhD CMPPe (Global Alliance of Publication Professionals; www.gappteam.org) a. Division Lead. ProScribe – Envision Pharma Group; Adjunct Professor, University of the Sunshine Coast, Australia. b. VP, Regulatory and Medical Affairs, TFS, Inc.. USA; Senior Research Fellow, CIRS. c. Assistant Clinical Professor, Virginia Commonwealth University School of Pharmacy; Principal, Hamilton House, USA. d. Director, Dianthus Medical Limited, UK. e. Director of Scientific Operations, Caudex Medical, UK.

Disclosures All authors declare that: (1) all authors have or do provide ethical medical writing services to academic, biotechnology, or pharmaceutical clients; (2) KW’s husband is also an employee of ProScribe – Envision Pharma Group; all other authors’ spouses, partners, or children have no financial relationships that may be relevant to the submitted work; and (3) all authors are active in national and international not-for-profit associations that encourage ethical medical writing practices. No external sponsors were involved in this study and no external funding was used.

References 1. Scherer RW, Ugarte-Gil C. Authors’ reasons for unpublished research presented at biomedical conferences: A systematic review. http://www.peerreviewcongress.org/abstracts_2013.html#1 Accessed 27 February 2014. 2. Woolley KL, Gertel A, Hamilton C, Jacobs A, Snyder G (GAPP). Poor compliance with reporting research results – we know it’s a problem…how do we fix it? Curr Med Res Opin 2012;28:1857-1860.

On 2014 Feb 21, Rafael Najmanovich commented:

For a in depth look at the method and its validation, take a look at Najmanovich R, 2008.

On 2014 Feb 27, guoan zhang commented:

axl and Tyro3 and Mer are important regulator of natural killer cell maturationCaraux A, 2006, and now those receptors are revealed to be players in the regulation of NK cells function in tumor immunology.it seems tumor ,through gas6 which could be secreted by tumor cells or stromal cells , suppressed the function of NK cells.and cbl-b takes a important role in gas6/TAM-mediated NK cells malfunction. and more important, the authors found a TAM kinase inhibitor and warfarin exerts anti-metastatic activity in mice via Cbl-b/TAM receptors in NK cells, suggesting possible clinical use.

On 2014 Feb 26, M S Muthu commented:

Another scientific vision from Prof Feng. Great....

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 May 23, Germana Bancone commented:

The authors state that the patient had a low G6PD enzymatic activity "The spectrophotometric assay showed a mildly reduced level of the enzyme: 7.2% (normal range: 8-18%)." Does 7.2% refer to the activity compared to a normal control? Could the authors specify the value expressed in international units per grams of hemoglobin (IU/gHb)? Could the authors explain this line "Though this X-linked disease is known to affect males exclusively, Errico et al., [2] have described it in females as well.", are they referring to G6PD deficiency or to hemolysis caused by ketoacidosis with G6PD deficient subjects?

On 2014 Nov 16, Ivan Oransky commented:

A medical resident explains how this paper came to be retracted: http://retractionwatch.com/2014/11/12/know-how-to-recognize-pseudoscience-whistleblower-fills-in-the-blanks-on-fish-oil-retraction/

On 2014 Apr 27, Jeff Kiefer commented:

The author seems to have mistakenly interpreted ref 80 Fantin VR, 2006. In the author's article he says, "Rats were fed fish oil or beef tallow." I could not find a mention of the diets that the animals used by Fantin et al were fed. In addition, the animals used in the Fantin VR, 2006 were not rats, they were FVB female mice. Lastly, in the authors discussion on Fantin VR, 2006, he states that mitochondrial enzyme activity was measured in kidney cells, which is wrong also. The mitochondrial experiments were performed on breast cancer cell lines. I doubt the veracity of the authors conclusions, as they relate to fish oil damaging mitochondria, do to the gross misrepresentation of Fantin VR, 2006 to support that particular hypothesis.

On 2016 Feb 18, Kristina Hanspers commented:

The pathway in figure 2 is available in the "Open Access Publication" collection at WikiPathways: http://www.wikipathways.org/index.php/Pathway:WP2637. This pathway can be downloaded for use in network analysis tools such as Cytoscape and PathVisio.

On 2014 Mar 01, L David Sibley commented:

It is interesting to see that most of the comments are about why we choose to study AMA1 and whether or not AMA1 is essential. We feel that there may be some misunderstanding about the rationale for our study, so hopefully the following points will help to clarify a few things.

The first misunderstanding deals with the findings of our previous work on ALD mutants and binding to the MIC tail (Starnes et al 2009). When we in a previous comment that these studies “were not able to definitively separate the functions of energy metabolism from motility vs. invasion”, we meant that while the studies did identify a mutant (TgALD K41E-R42G) that separates the functions of energy production from invasion, they did not fully explain why such mutants had no effect on gliding. One plausible explanation was provided in that paper: decreased occupancy of ALD-MIC2 in the cell (a product of altered affinity and protein concentrations) might differentially affect gliding vs. invasion. However, an alternative explanation is that ALD might also bind to another adhesin that is important in invasion but not gliding. When it became apparent that mutants in the AMA1 tails (AMA1t) also affect ALD binding in vitro (i.e. FW/AA) (Sheiner and Soldati et al, 2010), this provided a logical candidate, since AMA1 was known to be involved in host cell invasion but not motility (Mital et al., 2005).

Perhaps a second point of confusion is that our study did not try to address the essentiality of AMA1, something that has been studied by others, who ascribe various roles to the protein including attachment, MJ formation, and cell penetration. We were not aware at the outset of our study of the data contained in Bargieri et al. 2013, as the paper was published online while our work was under review. However, this likely would not have changed our approach as were not concerned with whether AMA1 is essential, or what factors might compensate for its loss, but rather with how it functions when it is expressed. Because the FW/AA mutations are located in the tail of the protein, we reasoned they were more likely to be involved in functions in the cytosol, rather than influencing the roles of the extracellular domains. Hence, this mutant provided an excellent candidate to test whether decreased cell invasion was due to alteration in ALD binding. As it turned out, study of additional mutants did not provide support for this model. Moreover, by re-examining the role of ALD in energy production, our study newly revealed that the previously ascribed role in adhesin binding does not play an essential role in vivo. We believe this is the only aspect of the apicomplexan invasion model that is directly addressed by our studies. We also hope that our work will inspire further studies to figure out the real function of AMA1t, which in turn will help us to understand the invasion process better.

Bang Shen, David Sibley

On 2014 Feb 27, Robert Menard commented:

The goal of the paper was to see whether aldolase plays a mechanical role during motility and/or internalization, the motor-dependent processes of the zoite. AMA1, using AMA1 KOs, was shown by the Bargieri paper (not cited in the current paper) to have NO detectable role in these processes, which would imply that the putative aldolase-AMA1 interaction does not either. The sound rationale appears to be that of the Starnes paper, which asked the question using the MIC2-aldolase interaction, since MIC2 is a bona fide motor-binding protein and is clearly important for motile processes. The data of the Starnes paper clearly indicate that aldolase has no mechanical role. For example, mutants K41A and K41E:R42G bind to MIC2t with 18% and 5% efficiency, respectively, and to actin with 13% and 9% efficiency, respectively. Fig 5C shows that these mutants have no detectable defect in motility. It is surprising to see that the author now says the Starnes data ‘was not able to definitely separate the functions’. This is clearly contrary to the straightforward title and abstract, which reads: “we generated a series of mutations in Toxoplasma gondii aldolase (TgALD1) that delineated MIC2 tail domain (MIC2t) binding function from its enzyme activity”.

Regarding the role of AMA1 in the TJ, the redundancy theory by AMA paralogs is presented incompletely. The author omits the crucial point that while AMA1 was not found to have any role in internalization at the TJ, it has an important role in adhesion to the host cell. AMA1 paralogs are expected to have a similar function, in promoting proper adhesion. Examination of Fig 1 shows overexpression of AMA1 paralogs in the AMA1 KO, but complete citation of the paper should also state increased paralog expression decreases the adhesion defect. In other words, AMA1 paralogs appear to be adhesins like AMA1, and are not expected to do at the TJ what AMA1 does not do itself. Lastly, we again point out that it is incorrect to state that inhibition experiments showed that the AMA1-RON interaction is important for TJ formation; they only indicate that its inhibition blocks invasion. This might occur by other scenarios than the interaction being the TJ, as further discussed in the Bargieri paper.

While we agree that it might be premature to draw a model of the TJ, it is equally dangerous to discard data that do not fit with the original model.

On 2014 Feb 26, L David Sibley commented:

As was discussed in our paper, and the previous Starnes paper, prior mutants of aldolase or MIC2t were not able to definitively separate the functions of energy metabolism from motility vs. invasion. Indeed, several mutants made in other systems have shown these later two functions can be independently controlled. Hence showing that one behavior is affected while the other one is not, cannot be used to argue that the process is not essential at some point. Combined with the hypothesis that AMAt binding to aldolase might be important for invasion (while playing no role in motility), this dichotomy provided more than adequate rationale for our present study. We also do not agree that prior work on AMA1 rules out a role in invasion, it merely shows that individual genes may be dispensable under some circumstances. Examination of Figure 1D in Bargierri et al., reveals evidence for 15-fold upregulation of a paralog of AMA1 (incorrectly called a homologue) in the TgAMA1 KO, suggesting that this gene may mask the phenotype by compensating for AMA1. Whether Plasmodium has recognizable paralogs of AMA1, or uses another adapter, one could still argue that the mechanism is conserved since the MJ is preserved. Independent of these genetic studies, there is a strong body of work that AMA1 is critical to the MJ formation. At this point it is premature to discard the existing model based on an incomplete assessment of potential compensatory mechanisms for loss of individual genes.

On 2014 Feb 25, Robert Menard commented:

The demonstration that aldolase plays no bridging role between actin and the MIC2/TRAP tails during zoite motility was provided by Starnes et al, who introduced mutations in aldolase that specifically abolished its capacity to bind MIC2 but not its energy producing capacity; these mutations had no effect on tachyzoite motility, which demonstrated the point. Regarding AMA1, previous work in Toxoplasma and Plasmodium has conclusively demonstrated not just that AMA1 is not essential for internalization, but that it has no detectable role in the process: AMA1 KO tachyzoites form a normal TJ and enter cells at a normal speed. The argument of redundancy by AMA1 paralogs has no basis, since (i) we showed that AMA1 - and paralogs - play a role in adhesion to the host cell, not directly in invasion at the TJ, and (ii) Plasmodium expresses no AMA1 paralog. These genetic data (Giovannini et al, CHM, 2011; Bargieri et al, Nat Comm, 2013) strongly argue against any motor-dependent function of AMA1 in any zoite and thus question the rationale of the present study. R. Menard, M. Meissner and D. Bargieri

On 2014 Feb 22, L David Sibley commented:

We welcome the opportunity to clarify the reasoning behind our study. We chose the AMA1-aldolase interaction to study because it demonstrates the requirement of two residues in the tail (FW) of AMA1 for cell invasion in a conditional knockdown, as reported previously (Sheiner et al., 2010 (PMID:2054586)). This AMA1t mutant also fails to bind aldolase in vitro, leading to the testable hypothesis that these two phenotypes are linked. We chose AMA1 not to address whether it is essential or not (indeed the jury is still out on this important question), but rather to test the model that binding of adhesin tails to aldolase is critical for linking the motor complex (as suggested previously by Jewett et al., 2003 (PMID12718875), and Starnes et al., 2009 (PMID19380114)). We are aware that others have questioned the requirement for AMA1 during invasion, but these studies also failed to account for possible redundant roles of paralogs, for which there is clear evidence of up-regulation in at least the one study that looked (Bargieri et al., Nature Comm 2013 (PMID24108241)). The use of knockout strains also runs the risk that suppressor mutations may have arisen in the background, given the length of time required to obtain such knockouts, at least by conventional means. In contrast, the conditional system we employed is less prone to such issues of compensation.

By studying a broader collection of AMAt mutants than previously, we show that there is no correlation between AMA1t-aldolase binding in vitro and invasion. This led us to further investigate the role of aldolase using more efficient techniques for gene disruption (Andenmatten et al., Nat Meth 2013 (PMID23263690)). The results show conclusively that aldolase is required for energy metabolism, but not binding to adhesin tails during invasion. This insight could not have been provided by any of the previous studies, as outlined in the discussion to our paper. Although we have not tested MIC2t, or other adhesins shown to bind aldolase, this no longer seems worthwhile given the clear lack of a phenotype for aldolase negative cells when grown in the absence of glucose. As we further point out in the discussion, there are clearly important roles for conserved residues in the tails of adhesins and the search is on for what those functions might be.

In terms of the model for invasion, our studies indicate that some other protein(s) must be responsible for linking the adhesin tails to the motor complex, and that if aldolase participates, it is redundant. This finding is consistent with the view that redundancy in biology is likely the norm for essential pathways. The work by Andenmatten et al., Nat Meth 2013 (PMID23263690) offers an exciting new tool to explore such redundancy with greater precision than previously possible, and indeed this was the basis for the final test in our study. Andenmatten et al., show that under conditions where genes can be rapidly excised by inducible Cre, it is possible to delete some of the core components of the glideosome. However, this is not without consequence as such mutants are severely impaired in gliding and invasion. Hence, we would interpret the available data as providing strong support for the current glideosome model for motility and invasion, rather than cause to abandon it. What remains unanswered by current studies is what is the backup or alternative mechanism(s), by which such deletion parasites still invade? There are a number of possibilities including: 1) residual levels of proteins remaining in knockout cells; 2) redundancy (i.e. paralogs that are upregulated), as are clearly evident in the genome, or 3) alternative mechanisms that serve as backup, albeit clearly less efficient. The remaining challenge for the field is to fill in these details, at which point it may be possible to provide a revised model for gliding and invasion by apicomplexans.

On 2014 Feb 20, Markus Meissner commented:

This nice study re-adresses the role of the glycolytic enzyme aldolase as a critical component of the gliding and invasion machinery of apicomplexan parasites as suggested previously by the same group. Aldolase has been described as a critical linker molecule between the tail domain of microcemal transmembrane proteins, such as AMA1 or MIC2 and the actin-myosin motor, thereby playing a crucial role for force transmission during motility and invasion. Here the authors tested if the interaction between AMA1 and ALD is important for host cell invasion. However, previous analysis of AMA1 knockdown (the same mutant as used in this study) and knockout mutants ruled out an important role of AMA1 as force transmitter during gliding motility (Mital et al., 2005) and host cell invasion (Giovannini et al., CHM 2011; Bargieri et al., Nature Comm 2013). Why did the authors expect a critical role of aldolase binding to AMA1, when AMA1 itself is not required for force transmission? Did the authors also investigate the role of MIC2 in binding to aldolase?

The authors continued to analyse the phenotype of an ALD knockout and demonstrate that these parasites can invade the host cell normally, ruling out an important function of aldolase during this process.

It would have been very informative for the reader if the authors would have discussed their finding in a more holistic view that also incorporates recent findings on the gliding and invasion machinery. The authors mention that the current model needs to be revised, which is certainly true, since several of the core components for invasion appear to be not essential for invasion, including actin itself (Andenmatten et al., Nat Meth 2013). It would have been very interesting to hear the opinion of the senior author how he currently perceives the molecular mechanisms involved in gliding and invasion. As it stands now it seems that we do not have a model that is sufficiently backed up by experimental data.

On 2014 Nov 05, Gary Ward commented:

This is a beautiful and clear demonstration of how Toxoplasma gondii can serve as both a useful model organism for the study of other apicomplexan parasites, and powerful surrogate system for small molecule screening. By complementing TgCDPK3 with Plasmodium falciparum CDPK1 (PfCDPK1), the group was able to confirm the functional localization dependence of PfCDPK1 and identify compounds that inhibit both PfCDPK1 and TgCDPK3, as well as those that inhibit PfCDPK1 alone. This work and the work of Sharling et al. PLOS Negl Trop Dis [2010] 4: e794 and others provide good examples of how studying T. gondii may be useful to understanding other apicomplexan parasites from a drug development standpoint.

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

On 2014 Feb 26, David Keller commented:

Why is citalopram still being used instead of safer escitalopram?

In the CitAD trial, the use of citalopram predictably led to its known adverse side-effect of QT-interval prolongation, which is a dose-dependent risk factor for toursades de pointes, an often-fatal cardiac arrhythmia. The QT-interval is prolonged further by interactions with numerous common medications, including over-the-counter omeprazole, which the patient may take or be prescribed inadvertently (1). As I have pointed out before (2), (3), the use of escitalopram instead of citalopram reduces the amount of QT-interval prolongation for any given degree of intended therapeutic antidepressant or antianxiety effect. The reason is that the therapeutic benefits of racemic citalopram are caused only by the levorotatory optical isomer (S-citalopram or escitalopram). The dextrorotatory molecule (R-citalopram) causes a roughly equivalent degree of QT-interval prolongation as escitalopram without contributing any known therapeutic effects. The last remaining reason to prescribe citalopram vanished when escitalopram went generic.

Are the cognitive adverse effects of citalopram caused roughly equally by both optical isomers, similar to the cardiac risks? If so, then the significant benefits of citalopram on agitation in Alzheimer's disease could have been achieved with roughly half the degree of cognitive impairment by substituting escitalopram at half the milligram dose instead of citalopram.

(1) Yee Guan Yap, A John Camm. Drug induced QT prolongation and torsades de pointes. Heart. 2003 November; 89(11): 1363–1372.PMCID: PMC1767957

(2) Keller DL. Prescribe escitalopram instead of citalopram. Am J Med. 2013 Jun;126(6):e21. doi: 10.1016/j.amjmed.2012.10.024. No abstract available. PMID: 23684405 [PubMed - indexed for MEDLINE]

(3) Keller DL. Comments and questions regarding the safety of citalopram. Mayo Clin Proc. 2013 Apr;88(4):420. doi: 10.1016/j.mayocp.2013.01.023. No abstract available. PMID: 23541017 [PubMed - indexed for MEDLINE]

On 2014 Nov 11, Eva Kottenberg commented:

Contrary to his statement, we have not been contacted by Dr. Berthelsen from Denmark. Also, contrary to his statement, ethics approval was explicitly mentioned in our paper (page 454 line 52). We had also clearly and explicitly reported in our paper, that our study is a retrospective analysis of a subgroup in an ongoing trial. Finally, we had specifically reported in which respect the patient selection of the current analysis differed from that of our prior Lancet paper. Dr. Berthelsen could have avoided his mathematical speculations simply by reading our paper much more carefully, so as to avoid obvious false statements which question the integrity and honesty of our scientific work. PD Dr. med. E. Kottenberg, Prof. Dr. med. J. Peters

On 2014 Oct 29, Eva Kottenberg commented:

None

On 2014 Oct 22, Preben Berthelsen commented:

Before accepting the authors’ results it must be realized that the conclusions are based on a non-randomized, unplanned, post hoc subgroup analysis of a larger study on remote ischaemic preconditioning in CABG surgery (ClinicalTrials NCT01406678). The results of the primary study were published in The Lancet (August 17, 2013). There are severe methodological problems with The Lancet paper as can be seen in the PubMed Commons comment to the paper (PMID:23953384).

In the present paper, the authors have selected, as a control group, 130 patients of the 167 controls included in the original Lancet paper. The patients were anaesthetized with isoflurane and no remote ischaemic preconditioning was used. The results are peculiar. The average 72h troponin release AUC in the original 167 patients was 321 (SD 213) and in the present subgroup of 130 patients 514 (SD 600). It is a mathematical impossibility that that so large a difference - in both mean and SD values - can be correct when 78% of the patients/results are shared. Furthermore, in the present study 14 of 130 (11%) are reported to be ACE/ARB treated while 75 of 167 (45%) in The Lancet paper are so treated. Again, it is not mathematically possible that the reported numbers are correct. I have tried to contact the corresponding author twice to determine if these discrepancies are printing errors. I have not received a response.

The authors have not statistically compared the difference in troponin release between sulphonylurea-treated diabetics and patients without diabetes. Their conclusions are instead solely based on within-group statistical analyses. And as Bland & Altman lucidly put it “this approach is biased and invalid, producing conclusions which are potentially highly misleading” (Trials 2011,12:264).

The investigation has no approval from an ethics committee. Taken in all, I feel it justified to view the results of this paper with scepticism. P.G.Berthelsen, Charlottenlund, Denmark.

On 2014 Jul 29, Jesper M Kivelä commented:

1) Under the Author information and after Children's Hospital there should be Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland.

2) My academic degree, in addition to MD, is not PhD as indicated in Wiley Online Library under Author Information. I'm a PhD student at the moment.

On 2016 Jan 09, Chao Liu commented:

Findings from our studies are consistent with the authors’ point. We found that glucocorticoids could promote renal water and sodium excretion in heart failure.

1. Liu C, Chen Y, Kang Y, Ni Z, Xiu H, Guan J, et al. (2011). Glucocorticoids Improve Renal Responsiveness to Atrial Natriuretic Peptide by Up-Regulating Natriuretic Peptide Receptor-A Expression in the Renal Inner Medullary Collecting Duct in Decompensated Heart Failure. J Pharmacol Exp Ther 339(1): 203-209.

2. Liu C, Liu G, Zhou C, Ji Z, Zhen Y, Liu K (2007). Potent diuretic effects of prednisone in heart failure patients with refractory diuretic resistance. Can J Cardiol 23(11): 865-868.

3. Liu C, Liu K (2014a). Effects of glucocorticoids in potentiating diuresis in heart failure patients with diuretic resistance. Journal of cardiac failure 20(9): 625-629.

4. Liu C, Liu K (2014b). Reply to Day et al.--hypouricemic effect of prednisone in heart failure: possible mechanisms. Can J Cardiol 30(3): 376 e373.

5. Liu C, Zhao Q, Zhen Y, Gao Y, Tian L, Wang L, et al. (2013). Prednisone in Uric Acid lowering in Symptomatic Heart Failure Patients With Hyperuricemia (PUSH-PATH) study. Can J Cardiol 29(9): 1048-1054.

6. Liu C, Zhao Q, Zhen Y, Zhai J, Liu G, Zheng M, et al. (2015). Effect of Corticosteroid on Renal Water and Sodium Excretion in Symptomatic Heart Failure: Prednisone for Renal Function Improvement Evaluation Study. J Cardiovasc Pharmacol 66(3): 316-322.

7. Meng H, Liu G, Zhai J, Zhen Y, Zhao Q, Zheng M, et al. (2015). Prednisone in Uric Acid Lowering in Symptomatic Heart Failure Patients with Hyperuricemia - The PUSH-PATH3 Study. The Journal of rheumatology 42(5): 866-869.

On 2014 Nov 26, Guillaume Filion commented:

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

On 2014 Mar 01, Christopher Southan commented:

Source updates related to this paper and the availabilty of UniProt cross-references as PMC outlinks or suplementary data are detailed at http://cdsouthan.blogspot.se/2014/02/getting-to-know-databases-by-comparing.html. Our earlier paper mentioned in the abstract above, is http://www.ncbi.nlm.nih.gov/pubmed/22821596

Nov 2015 contextual comments added to Kudos http://goo.gl/OlK8xM

On 2015 Jan 24, Madhusudana Girija Sanal commented:

How cancer stem cells may originate-the three hit hypothesis-the importance of epigenetic hit!

There are thousands (if not millions) of dangerous cancer associated mutations in every "healthy" human being. However, only a few get cancer. First of all one mutation may not lead to cancer, but two or more hits (the classic two hit hypothesis) might. What happens is: (A) a genetic mutation (usually associated with proliferation) (B) another genetic mutation (associated with proliferation, cell attachment, a protein regulating the epigenetic status etc.) (C) Epigenetic instability or change (induced by another mutation or by the environment-mechanical, transcription factor induced or cytokine/growth factor induced). However, some mutations are very strongly proliferative/oncogenic that an epigenetic change is seldom required during the cancer initiation.

The events can be in any direction- ABC, CBA, CAB. Each of these has clinical examples, although there could be significant overlap. Esophagial cancer (some forms) is an example of CAB. Persistent acid reflux from the stomach (GERD) will induce the esophagial epithelium to undergo metaplasia. A transdifferentiation to columnar cells. May be columnar cells are more resistant to acid reflux or it is a futile attempt of our body to resist acidity. However, the transdifferentiation requires an epigenetic change from the stratified squamous epithelium epigenome to columnar cell epigenome which involves activation or repression of several transcription factors. This weakens the stability of epigenomic landscape (which is unique to each cell type). At this point, if an oncogenic mutation occurs, in any of these dysplastic cells it may lead to cancer. But it is possible that an oncogenic mutation pre-exists in these cells and the "loose" epigenetic atmosphere now helped the oncogene to express taking over the normal cell cycle which is followed by another mutation which helped the cells to invade (ACB). Now at this point which cell one would call a cancer stem cell? Probably, it is possible that the very cell which initiated the cancer may not express even a single cancer stem cell marker! These stem cell markers may come and go at a later stage and they are dictated by the tumor environment. In short, cancer stem cell markers are the need of the time because, at some point of cancer evolution they help cancer cells to adapt and survive. In short cancer cells, which are not cancer stem cells can give rise to a cancer stem cells and cancer stem cells can give rise to cancer cells which are not qualified to be called cancer stem cells. Therefore, to conclude, cells which have a "loose" epigenetic status (on a background of one or more 'oncogene' mutations) are the ideal candidates for cancer "stem" cells. It is an epigenetically dynamic state. It is epigenetic 'anarchy' and 'promiscuity' for survival as a cancer cell.

On 2015 Nov 25, Thomas Cleveland commented:

Very nice work, and the associated software they developed, "WillItFit," has well-organized code that is relatively easy for an outsider to understand and modify. This is the best work I've seen so far, in terms of analyzing nanodiscs by small-angle scattering (not to disparage others---there is a large literature and I've only recently started exploring it).

On 2014 Oct 18, Pavel Baranov commented:

What is the difference between Open Reading Frame (ORF) and Coding Sequence (CDS)?

Thank you for the reply. I think the disagreement lies in our understanding of what Open Reading Frame is.

A simple and effective definition of ORF is a sequence of codons not interrupted with stop codons: nucleotide sequence is open for reading in one of the three (for RNA) or six (dsRNA) frames. ORF is an abstract notion, it can be found in any sequence. Both protein-codng and non-coding sequences have ORFs.

Coding Sequence (CDS) is the part of RNA that encodes protein. CDS often, but not always (exceptions are ribosomal frameshifting, stop codon readthrough, etc.), is located within a single ORF. A single ORF may contain more than one Coding Region if, for example, translation begins at different start codons within the same ORF.

From your reply I presume that you suggest to define ORF as a sequence of codons from start to stop (like CDS). But the problem with this detention is that it is unclear what should we consider as a start of ORF. AUG? But not all AUGs are starts and not all starts are AUGs. Also there are no starts in non-coding RNAs, but there are ORFs in non-coding sequences.

Besides if we use this definition, all eukaryotic mRNAs coding for multiple protein isoforms would need to be described as bi- or even polycistronic.

I hope that this discussion brings some clarity to the terminology used or at least it draws attention to a potential confusion when terms such as ORF, CDS and cistron are not explicitly defined.

On 2014 Oct 03, Jonathan C Kagan commented:

In response to the comment by Baranov, we would first like to thank you for your interest in our work. We agree that alternatively translated eukaryotic proteins most commonly share a reading frame, as our study mentioned. In fact, we discuss this point in the analysis of our ribosomal profiling data. For instance, we observed that truncations are more common than internal out-of-frame translation products. Regardless of whether the products share a reading frame, however, a point of interest is the regulation allowing ribosomes to initiate translation at more than one location on a transcript. We chose to use the terms polycistronic and bicistronic for two reasons. First, bicistronic mRNAs are operationally defined as transcripts that produce two stable proteins of distinct functions, regardless of whether the two proteins share sequence similarity. Our study clearly demonstrated that this is the case with the MAVS transcript. Whether these functionally distinct proteins share coding sequence with each other is functionally irrelevant. Second, a transcript producing a truncated protein (such as MAVS) conforms to generally accepted definitions of a polycistronic transcript, such as you provided: “…protein products of distinct coding ORFs are translated from the same transcript.” While the two MAVS proteins are encoded in the same reading frame, their production is initiated at unique start sites; thus, they have distinct coding sequences. In short, we consider them to be distinct ORFs that share a reading frame and therefore produce two proteins from a bicistronic mRNA.

On 2014 Aug 06, Pavel Baranov commented:

What is a polycistronic mRNA?

This is an interesting research article that provides insights into distinct functions of two proteoforms that differ at their N-termini due to the use of alternative translation initiation starts. Terming the corresponding mRNA bicistronic is, however, somewhat misleading. When we refer to a bacterial mRNA as polycistronic we imply that protein products of distinct coding ORFs are translated from the same transcript. Here the ORF is the same, but the translation initiates at different codons of that ORF. There are several examples of human proteins with truncated or extended N-termini produced from alternative translation initiation starts, see a recently discovered extension of PTEN for a startling example, see Hopkins BD, 2013. True bicistronic mRNAs are rare. Molybdopterin subunits MOCS2A and MOCS2B were reported to be produced from two different but overlapping ORFs at the same mRNA, see Stallmeyer B, 1999. If this were true the corresponding mRNA could be classified as bicistronic, however, further evidence suggested that these proteins are produced from alternatively spliced transcript variants, see Hahnewald R, 2006. A good example of an eukaryotic polycistronic mRNA could be found in Drosophilla tal (aka pri) mRNA that codes for four peptides produced from four distinct ORFs, see Kondo T, 2010. Perhaps, human mRNAs with uORFs encoding functional proteins should also be classified as polycistronic, but not mRNAs that encode multiple protein isoforms translated from the same ORF.

On 2014 Feb 20, Anne Marie Cunningham commented:

Pre-publication version of this commentary can be found here