On 2015 Sep 14, Tom Kindlon commented:

Comment 2 of 2 formally submitted on September 9, 2015 using instructions here: http://www.cochranelibrary.com/help/submitting-comments-on-cochrane-reviews.html

(This is available in one piece at: http://forums.phoenixrising.me/index.php?threads/my-two-detailed-comments-on-the-cochrane-exercise-therapy-for-cfs-review-2015.39801/ )

Second comment:

I have decided to split my comment into two as it was getting very long. This is part two.

Variation in interventions

It would have been useful to have some more information on the “exercise with pacing” intervention tested in the Wallman et al. (2004) trial and how it was distinct from some other exercise interventions tested. The authors say (1): “On days when symptoms are worse, patients should either shorten the session to a time they consider manageable or, if feeling particularly unwell, abandon the session altogether” (p. 143). I don't believe the description given in the review conveys this. In the review, this approach is described as "Exercise with pacing: exercise in which the incremental increase in exercise was personally set." But Wallman et al.’s approach allows patients to decrease as well as increase how much exercise they do on the day. This approach also contrasts with how White (an investigator in two of the trials) has described graded exercise therapy: "if [after increasing the intensity or duration of exercise] there has been an increase in symptoms, or any other adverse effects, they should stay at their current level of exercise for a further week or two, until the symptoms are back to their previous levels" (2). In the PACE Trial manual White co-wrote (3), the GET intervention was guided by the principle that “planned physical activity and not symptoms are used to determine what the participant does” (p. 21); similarly, “it is their planned physical activity, and not their symptoms, that determine what they are asked to do” (p. 20). Compliance data would help us examine which approach patients are actually using: I suspect many patients are in fact doing exercise with pacing even in trials such as the PACE Trial (i.e. when they have increased symptoms, often reducing levels of exercise and sometimes doing no exercise activities at all on that day).

Bimodal versus Likert scoring in Wearden et al. (2010)

I find it odd that the fatigue scores for the Wearden et al. (2010) trial (4) are given in the 0-33 format rather than the 0-11 scoring method. The 0-11 scoring system is what is mentioned as a primary outcome measure in the protocol and is what is reported in the main paper reporting the results (4, 5). It is even what your own report says on p. 44 is the scoring method (“Fatigue Scale, FS; 11 items; each item was scored dichotomously on a 4-point scale [0, 0, 1 or 1]”). This is important because using the scoring method for which you don't report data (0-11), there is no statistically significant difference at the primary outcome point of 70 weeks (5).

Diagnostic criteria

One problem with using these trials as an evidence base, which I don't believe was mentioned, is that all the trials used the Oxford and Fukuda diagnostic criteria (6, 7). Neither of these criteria require patients to have post-exertional malaise (or something similar). Many consider this to be a core symptom of ME/CFS and it is mandatory in most of the other major criteria (8-11). [Aside: The London criteria were assessed in the PACE Trial (12) but they seem to have been operationalised in an unusual way. Ninety seven per cent of the participants who satisfied the (broad) Oxford criteria who didn't have a psychiatric disorder satisfied the definition of M.E. used (13). Ellen Goudsmit, one of the authors of the London criteria, has rejected the way they were used in the PACE Trial (14)]. So this lack of requirement for patients to have post-exertional malaise (or a similar description) means we cannot be sure that the evidence can be generalised to such patients. An independent National Institutes of Health committee this year concluded "continuing to use the Oxford definition may impair progress and cause harm. Therefore, for progress to occur, we recommend that this definition be retired" (15). An Agency for Healthcare Research and Quality review of diagnostic methods this year reached a similar conclusion: "Consensus groups and researchers should consider retiring the Oxford case definition because it differs from the other case definitions and is the least restrictive, probably including individuals with other overlapping conditions” (16). An Agency for Healthcare Research and Quality review of ME/CFS treatments said: "The Oxford CFS case definition is the least restrictive, and its use as entry criteria could have resulted in selection of participants with other fatiguing illnesses or illnesses that resolve spontaneously with time" (17).

Exclusion of some data from analyses due to baseline differences

It seems unfortunate that some data cannot be used due to baseline differences e.g. "Four trials (669 participants) contributed data for evaluation of physical functioning at follow-up (Jason 2007; Powell 2001; Wearden 2010; White 2011). Jason 2007 observed better results among participants in the relaxation group (MD 21.48, 95% CI 5.81 to 37.15). However, results were distorted by large baseline differences in physical functioning between the exercise and relaxation groups (39/100 vs 54/100); therefore we decided not to include these results in the meta-analysis". It would be good if other methods could be investigated (e.g. using baseline levels as covariates) to analyse such data.

Thank you for taking the time to read my comments.

Tom Kindlon

Conflict of Interest statement:

I am a committee member of the Irish ME/CFS Association and do a variety of unpaid work for the Association.

References

1 Wallman KE, Morton AR, Goodman C, Grove R. Exercise prescription for individuals with chronic fatigue syndrome. Med J Aust. 2005;183:142-3.

2 White P. How exercise can help chronic fatigue syndrome. Pulse: 1998. June 20:86-87.

3 Bavinton J, Darbishire L, White PD -on behalf of the PACE trial management group. Graded Exercise Therapy for CFS/ME (Therapist Manual) http://www.pacetrial.org/docs/get-therapist-manual.pdf

4 Wearden AJ, Riste L, Dowrick C, Chew-Graham C, Bentall RP, Morriss RK, Peters S, Dunn G, Richardson G, Lovell K, Powell P. Fatigue Intervention by Nurses Evaluation--the FINE Trial. A randomised controlled trial of nurse led self-help treatment for patients in primary care with chronic fatigue syndrome: study protocol. [ISRCTN74156610]. BMC Med. 2006 Apr 7;4:9.

5 Wearden AJ, Dowrick C, Chew-Graham C, Bentall RP, Morriss RK, Peters S, Riste L, Richardson G, Lovell K, Dunn G; Fatigue Intervention by Nurses Evaluation (FINE) trial writing group and the FINE trial group. Nurse led, home based self help treatment for patients in primary care with chronic fatigue syndrome: randomised controlled trial. BMJ. 2010 Apr 23;340:c1777. doi: 10.1136/bmj.c1777.

6 Sharpe M, Archard L, Banatvala J, Borysiewicz LK, Clare AW, David A, et al. Chronic fatigue syndrome: guidelines for research. Journal of the Royal Society of Medicine 1991;84 (2):118–21.

7 Fukuda K, Straus SE, Hickie I, et al. The chronic fatigue syndrome: A comprehensive approach to its definition and study. Ann Intern Med. 1994; 121: 953‑959.

8 Carruthers BM, Jain AK, De Meirleir KL, et al. Myalgic Encephalomyelitis/chronic fatigue syndrome: Clinical working case definition, diagnostic and treatments protocols. Journal of Chronic Fatigue Syndrome. 2003; 11: 7-115.

9 Carruthers BM, van de Sande MI, De Meirleir KL, et al. Myalgic encephalomyelitis: International Consensus Criteria. J Intern Med. 2011; 270: 327-338.

10 IOM (Institute of Medicine). Beyond myalgic encephalomyelitis/chronic fatigue syndrome: Redefining an illness. Washington, DC: The National Academies; 2015.

(continues)

On 2015 Sep 14, Tom Kindlon commented:

(continues)

References:

1 Turner L, Boutron I, Hróbjartsson A, Altman DG, Moher D: The evolution of assessing bias in Cochrane systematic reviews of interventions: celebrating methodological contributions of the Cochrane Collaboration. Syst Rev 2013, 2:79.

2 Chalder T, Goldsmith KA, White PD, Sharpe M, Pickles AR. Rehabilitative therapies for chronic fatigue syndrome: a secondary mediation analysis of the PACE trial. Lancet Psychiatry. 2015;2:141-152.

3 White PD, Goldsmith KA, Johnson AL, Potts L, Walwyn R, DeCesare JC, et al. Comparison of adaptive pacing therapy, cognitive behaviour therapy, graded exercise therapy, and specialist medical care for chronic fatigue syndrome (PACE): a randomised trial. The Lancet 2011;377:823-36.

4 Kindlon T. Reporting of Harms Associated with Graded Exercise Therapy and Cognitive Behavioural Therapy in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Bull IACFS ME. 2011;19:59-111. http://iacfsme.org/ME-CFS-Primer-Education/Bulletins/BulletinRelatedPages5/Reporting-of-Harms-Associated-with-Graded-Exercise.aspx

5 Lipkin DP, Scriven AJ, Crake T, Poole-Wilson PA (1986). Six minute walking test for assessing exercise capacity in chronic heart failure. British Medical Journal 292, 653-5.

6 Kadikar A, Maurer J, Kesten S. The six-minute walk test: a guide to assessment for lung transplantation. J Heart Lung Transplant. 1997 Mar;16(3):313-9.

7 Friedberg F, Sohl S. Cognitive-behavior therapy in chronic fatigue syndrome: is improvement related to increased physical activity? J Clin Psychol. 2009 Feb 11.

8 Friedberg F. Does graded activity increase activity? A case study of chronic fatigue syndrome. Journal of Behavior Therapy and Experimental Psychiatry, 2002, 33, 3-4, 203-215

9 Results and In-depth Analysis of the 2012 ME Association Patient Survey Examining the Acceptability, Efficacy and Safety of Cognitive Behavioural Therapy, Graded Exercise Therapy and Pacing, as Interventions used as Management Strategies for ME/CFS. Gawcott, England. http://www.meassociation.org.uk/2015/05/23959/ Accessed: September 3, 2015

10 Critical Illness - A Dreadful Experience with Scottish Provident. http://forums.moneysavingexpert.com/showthread.php?t=2356683 Accessed: September 4, 2015

11 McCrone P, Sharpe M, Chalder T, Knapp M, Johnson AL, Goldsmith KA, White PD. Adaptive pacing, cognitive behaviour therapy, graded exercise, and specialist medical care for chronic fatigue syndrome: a cost-effectiveness analysis. PLoS One. 2012;7(8):e40808.

12 Rapport d’évaluation (2002-2004) portant sur l’exécution des conventions de rééducation entre le Comité de l’assurance soins de santé (INAMI) et les Centres de référence pour le Syndrome de fatigue chronique (SFC). 2006. http://health.belgium.be/internet2Prd/groups/public/@public/@shc/documents/ie2divers/14926531_fr.pdf (Starts on page 223.) Accessed September 4, 2015 (French language edition)

13 Evaluatierapport (2002-2004) met betrekking tot de uitvoering van de revalidatieovereenkomsten tussen het Comité van de verzekering voor geneeskundige verzorging (ingesteld bij het Rijksinstituut voor Ziekte- en invaliditeitsverzekering) en de Referentiecentra voor het Chronisch vermoeidheidssyndroom (CVS). 2006. http://health.belgium.be/internet2Prd/groups/public/@public/@shc/documents/ie2divers/14926531.pdf (Starts on page 227.) Accessed September 4, 2015 (Dutch language version)

14 Stordeur S, Thiry N, Eyssen M. Chronisch Vermoeidheidssyndroom: diagnose, behandeling en zorgorganisatie. Health Services Research (HSR). Brussel: Federaal Kenniscentrum voor de Gezondheidszorg (KCE); 2008. KCE reports 88A (D/2008/10.273/58) https://kce.fgov.be/sites/default/files/page_documents/d20081027358.pdf Accessed September 4, 2015

15 Wiborg JF, Knoop H, Stulemeijer M, Prins JB, Bleijenberg G. How does cognitive behaviour therapy reduce fatigue in patients with chronic fatigue syndrome? The role of physical activity. Psychol Med. 2010; 40:1281-1287.

16 Van Kessel K, Moss-Morris R, Willoughby, Chalder T, Johnson MH, Robinson E, A randomized controlled trial of cognitive behavior therapy for multiple sclerosis fatigue, Psychosom. Med. 2008; 70:205–213.

17 Powell P. FINE Trial Patient Booklet http://www.fine-trial.net/downloads/Patient PR Manual ver9 Apr05.pdf Accessed September 7, 2015

18 Twisk FNM, Maes M. A review on Cognitive Behavorial Therapy (CBT) and Graded Exercise Therapy (GET) in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS): CBT/GET is not only ineffective and not evidence-based, but also potentially harmful for many patients with ME/CFS. Neuro Endocrinol Lett. 2009;30:284-299.

19 Carruthers BM et al. Myalgic Encephalomyelitis – Adult & Paediatric: International Consensus Primer for Medical Practitioners. ISBN 978-0-9739335-3-6 http://www.investinme.org/Documents/Guidelines/Myalgic Encephalomyelitis International Consensus Primer -2012-11-26.pdf Accessed September 5, 2015

20 Twisk FN. Objective Evidence of Post-exertional “Malaise” in Myalgic Encephalomyelitis and Chronic Fatigue Syndrome. J Sports Med Doping Stud 2015. 5:159. doi: 10.4172/2161-0673.1000159

21 Higgins JPT, Green S: Cochrane Handbook for Systematic Reviews of Interventions Version 5.1.0 [updated March 2011]. Table 8.5.d. The Cochrane Collaboration; 2011. http://handbook.cochrane.org/chapter_8/table_8_5_d_criteria_for_judging_risk_of_bias_in_the_risk_of.htm Accessed: September 5, 2015

22 White PD, Sharpe MC, Chalder T, DeCesare JC, Walwyn R; on behalf of the PACE trial group. Protocol for the PACE trial: A randomised controlled trial of adaptive pacing, cognitive behaviour therapy, and graded exercise as supplements to standardised specialist medical care versus standardised specialist medical care alone for patients with the chronic fatigue syndrome/myalgic encephalomyelitis or encephalopathy. BMC Neurology 2007, 7:6 http://www.biomedcentral.com/1471-2377/7/6 Accessed: September 5, 2015

On 2015 Sep 14, Tom Kindlon commented:

(contd.)

Compliance

The review doesn't include any information on compliance. I'm not sure that there is much published information on this but I know there was a measure based on attendance at therapy sessions (which could be conducted over the phone) given for the PACE Trial (3). Ideally, it would be interesting if you could obtain some unpublished data from activity logs, records from heart-rate monitors, and other records to help build up a picture of what exercise was actually performed and the level of compliance. Information on adherence and what exercise was actually done is important in terms of helping clinicians, and indeed patients, to interpret and use the data. I mention patients because patients' own decisions about their behaviour is likely to be affected by the medical information available to them, both within and outside of a supervised programme of graded exercise; unlike with an intervention like a drug, patients can undertake exercise without professional supervision.

"Selective reporting (outcome bias)" and White et al. (2011)

I don't believe that White et al. (2011) (the PACE Trial) (3) should be classed as having a low risk of bias under "Selective reporting (outcome bias)" (Figure 2, page 15). According to the Cochrane Collaboration's tool for assessing risk of bias (21), the category of low risk of bias is for: "The study protocol is available and all of the study’s pre-specified (primary and secondary) outcomes that are of interest in the review have been reported in the pre-specified way". This is not the case in the PACE Trial. The three primary efficacy outcomes can be seen in the published protocol (22). None have been reported in the pre-specified way. The Cochrane Collaboration's tool for assessing risk of bias states that a “high risk” of bias applies if any one of several criteria are met, including that “not all of the study’s pre-specified primary outcomes have been reported” or “one or more primary outcomes is reported using measurements, analysis methods or subsets of the data (e.g. subscales) that were not pre-specified”. In the PACE Trial, the third primary outcome measure (the number of "overall improvers") was never published. Also, the other two primary outcome measures were reported using analysis methods that were not pre-specified (including switching from the bimodal to the Likert scoring method for The Chalder Fatigue Scale, one of the primary outcomes in your review). These facts mean that the “high risk of bias” category should apply.

Thank you for taking the time to read my comments.

Tom Kindlon

Conflict of Interest statement:

I am a committee member of the Irish ME/CFS Association and do a variety of unpaid work for the Association.

(continues)

On 2015 Sep 14, Tom Kindlon commented:

Comment 1 of 2 formally submitted on September 9, 2015 using instructions here: http://www.cochranelibrary.com/help/submitting-comments-on-cochrane-reviews.html

(This is available in one piece at: http://forums.phoenixrising.me/index.php?threads/my-two-detailed-comments-on-the-cochrane-exercise-therapy-for-cfs-review-2015.39801/ )

I would first like to thank those involved for their work in preparing this document. Even for those of us who have read the individual Chronic Fatigue Syndrome (CFS) papers it is useful to have the results collated, as well as details regarding the interventions. Also it is interesting to see the results of sensitivity analyses, subgroup analyses, standardised mean differences, etc.

I would like to make a few comments. I’m splitting them into two submissions as the piece had become very long. I’ve added some loose headings to hopefully make it more readable.

Objective measures

The review assessed the studies as having a high risk of bias regarding blinding, since neither participants nor assessors were blinded. Evidence suggests that subjective outcomes are more prone to bias than objective outcomes when there is no blinding (1). It is thus unfortunate that the review concentrated almost exclusively on subjective measures, failing to include results from nearly all the objective outcome measures that have been published with trials. (The exception was health resource use for which you presented follow-up data from one trial).

I hope objective outcome data can be included in a future revision or edition of this review.

Examples of objective outcomes include: exercise testing (work capacity by oxygen consumption); fitness test/step test; the six minute walking test; employment status; and disability payments.

Adding in these results would allow a more rigorous assessment of the effectiveness and relevance of the therapies, their causal mechanisms, therapeutic compliance, and safety.

On exercise testing, for example, in the PACE Trial (the largest trial in the review) there was no improvement in fitness levels as measured by a step test (2). The fitness data contrasts sharply with the many positive results from subjective self-report measures in the trial, so one is left wondering how much the subjective measures reflect reality.

On another exercise test used in the PACE Trial, the 6 minute walk test, there was a small (mean) increase from 312 metres at baseline to 379 metres at 12 months: this was 35.3 metres more than the "passive" control group when adjustments were made. However, the final result of 379 metres remains very poor compared to the more than 600 metres one would expect from healthy people of a similar age and gender make-up (3,4). By comparison, a group with Class III heart failure walked an average of 402 metres (5). A score of less than 400 metres has been suggested as the level at which somebody should be put on a lung transplant list (6). Such information from objective measures helps to add important context to the subjective measures and restraint to the conclusions that can be drawn from them.

Objective data is also needed to check compliance with a therapy. If patients diligently exercised for 12 months one would expect much better results on fitness and exercise testing than the aforementioned results in the PACE Trial. This is important when considering adverse events and safety: such trials may not give us good information on the safety of complying with such interventions if patients haven't actually complied.

Employment and receipt of disability payments are practical objective measures of general functional capacity so data on them would help establish whether patients can actually do more overall or whether they may just be doing, for example, a little more exercise but have substituted that for doing less in other areas (7,8). Also, CFS patients are sometimes pressured by insurance companies into doing graded exercise therapy (GET) programs so it would be useful to have data collated on employment outcomes to see whether pressure can in any way be justified (9,10). In the PACE Trial, there was no significant improvement in employment measures and receipt of disability payments in the GET group (11). Outside the realm of clinical trials, the quantitative and qualitative data in a major (UK) ME Association survey also found that GET didn't lead to higher levels of employment and lower levels of receipt of disability payments on average (9). Also, extensive external audits were performed of Belgian CFS rehabilitation clinics that treated using cognitive behavioural therapy (CBT) and GET. The main reports are in French and Dutch (12,13), with an English summary available (14) that says, "Employment status decreased at the end of the therapy, from an average of 18.3% of a 38h working week, to 14.9% [...] The percentage of patients living from a sickness allowance increased slightly from 54 to 57%." This contrasts with the average improvements reported in the audit for some symptoms like fatigue.

While data on (self-reported) symptoms like fatigue (one of your two primary outcomes) is interesting, arguably more important to patients is improving their overall level of functioning (and again, objective measures are needed here). Being able to work, for example, despite experiencing a certain level of fatigue would likely be more important for many than being unable to work but having slightly lower levels of fatigue.

An example of how reductions in the reported levels of fatigue may not lead to improvements in functioning can be seen in an analysis of three graded activity-oriented CBT therapy interventions for CFS (15). The analysis showed, compared to controls, there were no improvements in overall activity levels as measured by actometers despite improvements in self-reported fatigue (15). Activity in these trials was assessed using actometers. Another study that exemplifies the problem of focusing too much on fatigue scores after behavioural interventions is a study of CBT in multiple sclerosis (MS) patients with “MS fatigue”(16). The study found that following the intervention, patients with MS reported significantly lower (i.e. better) scores on the Chalder Fatigue Scale (0-33 scoring) than those in a healthy, nonfatigued comparison group! This significant difference was maintained at 3 and 6 months’ follow-up. It is difficult to believe that patients with MS fatigue (at baseline) truly subsequently had less fatigue than healthy nonfatigued controls: a much more likely scenario is that undertaking the intervention had led to response biases.

You mention that "many patient charities are opposed to exercise therapy for chronic fatigue syndrome (CFS)". One reason for concern about the way in which exercise programmes are promoted to patients is that they are often based upon models which assume that there is no abnormal physiological response to exercise in the condition, and make unsupported claims to patients. For example, in the FINE trial (Wearden et al., 2010) patient booklet (17), it is boldly asserted that: "Activity or exercise cannot harm you" (p. 49). However, a large number of studies have found abnormal responses to exercise, and the possibility of harm being done simply cannot be excluded on the basis of current evidence (discussed in 4, 18-20)."

(continues)

On 2015 Feb 24, Laurie Thomas commented:

Clinical studies of chronic fatigue syndrome are plagued by serious problems in the inclusion/exclusion criteria. These problems stem from the fact that the syndrome consists of nonspecific symptoms that are "medically unexplained." However, there is a major difference between medically unexplained and medically inexplicable. The symptoms of chronic fatigue syndrome can result from a serious circulatory problem that is easily overlooked. In 2003, Peckerman and coworkers showed that low cardiac output, as measured by impedance cardiography, predicts the severity of symptoms in CFS patients.[1] Miwa and Fujita found a small left ventricular size leading to low cardiac output in CFS patients with orthostatic intolerance.[2] Porter and coworkers reported that a case of femoral arteriovenous fistula causing high-output cardiac failure was originally misdiagnosed as chronic fatigue syndrome.[3]

The studies of graded exercise for management of CFS are based on the presumption that CFS is the result of laziness and deconditioning and that the solution to the problem is to persuade the patient to exercise. Yet in many reported cases, the real problem was unrecognized cardiac decompensation. This state of cardiac decompensation could account for the push-crash phenomenon (serious, prolonged adverse events from overexertion) among people with CFS. Thus, a graded exercise program that might be beneficial for the large number of people who are tired and achy because of major depressive disorder could be catastrophic for the relatively small number of people whose problem is due to cardiac decompensation. Unfortunately, the existing studies of exercise for management of CFS do not shed light on this problem. The patients whose exercise intolerance is too severe to allow them to participate in the exercise program might refuse to enroll or might be dismissed as noncompliant if they try but fail to exercise. Yet as a result of the positive results of graded exercise for subjects whose real problem is major depressive disorder, patients with unrecognized cardiac decompensation are being scolded for failing to exercise.

For ethical and scientific reasons, the protocol for a clinical study of subjects with CFS should be based on the best possible model for clinical management of CFS patients. It would begin with a careful assessment of the subject's circulatory status. This assessment should include a tilt-table test, or at least a measurement of supine, sitting, and standing pulse and blood pressure. Any circulatory problem should be addressed appropriately. (Note that once the patient's condition is found to be due to a circulatory problem, the patient no longer fits the inclusion criteria of "medically unexplained" symptoms.)

As improper diet is the most prevalent cause of chronic ill-health, the cardiology assessment should be followed by a run-in period of at least a week of optimal dietary management. Subjects should be fed a low-fat (<10% of calories), purely plant-based diet that excludes the most common causes of food allergies or intolerance syndromes (i.e., wheat, rye, barley, corn, soy, strawberries, and citrus fruits). To ensure adherence, the diet should be administered in a residential setting. This kind of low-fat, plant-based diet can bring about a significant drop in blood pressure in hypertensive patients within 7 days, even if the patients stop taking blood pressure medication at baseline.[4] This correction of hypertension results from the decrease in systemic resistance. Thus, this diet could lead to a significant improvement in circulation, which would be beneficial to patients whose symptoms are due to poor circulation, even if they are not hypertensive. Note also that the elimination of poorly tolerated foods is the only reliable way to establish that the patient's problem is due to a food intolerance. Of course, once the subject's problem has been shown to be dietary in origin, the subject no longer has "medically unexplained" symptoms and thus no longer fits the inclusion criteria for a study of CFS.

Many patients with a diagnosis of CFS are inactive, but they may be inactive because they are sick, rather than being sick because they are inactive. Thus, any study of exercise and CFS should be structured to establish the direction of causality. If a study of subjects with a diagnosis of CFS involves exercise, the outcome variables must involve some measurement of the subjects' overall activity levels, not just to assess compliance with the exercise program but to assess whether the subjects are merely wasting their energy on the exercises and thus become less able to perform activities of daily living. In that situation, the exercise program could actually decrease the subject's quality of life.

[1] Peckerman A, LaManca JJ, Dahl KA, Chemitiganti R, Qureishi B, Natelson BH. Abnormal impedance cardiography predicts symptom severity in chronic fatigue syndrome. Am J Med Sci. 2003 Aug;326(2):55-60.

[2] Miwa K1, Fujita M. Small heart with low cardiac output for orthostatic intolerance in patients with chronic fatigue syndrome.Clin Cardiol. 2011 Dec;34(12):782-6. doi: 10.1002/clc.20962. Epub 2011 Nov 28.

[3] Porter J1, Al-Jarrah Q1, Richardson S. A case of femoral arteriovenous fistula causing high-output cardiac failure, originally misdiagnosed as chronic fatigue syndrome. Case Rep Vasc Med. 2014;2014:510429. doi: 10.1155/2014/510429. Epub 2014 May 20.

[4] McDougall J1, Thomas LE, McDougall C, Moloney G, Saul B, Finnell JS, Richardson K, Petersen KM.Effects of 7 days on an ad libitum low-fat vegan diet: the McDougall Program cohort. Nutr J. 2014 Oct 14;13:99. doi: 10.1186/1475-2891-13-99.

On 2015 Feb 19, Joan Crawford commented:

This review states: “Chronic fatigue syndrome (CFS) is characterised by persistent, medically unexplained fatigue, as well as symptoms such as musculoskeletal pain, sleep disturbance, headaches and impaired concentration and short-term memory.”

This is important because the above description of CFS and the addition of trials in the review only requiring chronic fatigue as an inclusionary requirement (Sharpe et al, 1991) makes generalisation of the findings problematic as many patients with major depressive disorder (MDD) would also meet the above description of CFS and Sharpe et al.'s (1991) criteria if their condition was fatiguing – a common feature - along with muscular aches and pains, sleep disturbance, cognitive difficulties and so on. The high percentage of patients included in these trials suffering from depression (Table 1. Study demographics) indicates this may be their primary condition – confounding the results. Exercise, through behavioural activation programs, has a moderately positive impact on patients with depression (Cooney et al., 2013). It is unclear whether the modest improvement seen in some of these trials can be accounted for by an improvement in low mood caused by depression. Moreover, where there is data there is a high usage of antidepressants in patients included in the reviewed trials (Table 1. Study demographics).

Of the eight exercise trials included in this review, five used broad inclusion criteria (Sharpe et al, 1991) (N=1287) – 85% of all participants. Two of these studies also used a version of the London criteria, which did not exclude patients with depression and other psychiatric conditions as originally specified by the authors making it hard to assess how these criteria were operationalised. Three further trials used the CDC Fukuda (1994) CFS criteria (N=231). While these purport to be more selective, they do not necessary include patients whose primary difficulties include post exertional weakness and debility and flu-like symptoms and so on beyond broadly defined fatigue and other general symptoms which could be attributed to CFS or MDD.

There is also an issue with lack of evidence of patients’ fidelity to exercise programs using objective measures. We do not know if patients increased their activity as suggested to them by their clinicians. Without using devises such as actimeters or pedometers to track daily activity levels we have no accurate way of assessing whether an increase in activity occurred and whether this helps. Black & McCully’s (2005) study demonstrates objectively the difficulties patients face when trying to increase activity and concluded that they were exercise intolerant, unable to sustain activity targets.

The report is bold in stating “no evidence suggests that exercise therapy may worsen outcomes“. Many patient surveys from across the world report numerous instances of harm and worsening of symptoms from taking part in exercise programs. For a summary of the difficulties and limitations of the reporting of harms, in and outside of clinical trials, and why these might be underestimated please see Kindlon (2011).

References

Cooney GM, Dwan K, Greig CA, Lawlor DA, Rimer J, Waugh FR, McMurdo M, Mead GE (2013). Exercise for depression. The Cochrane Library. http://onlinelibrary.wiley.com/doi/10.1002/14651858.CD004366.pub6/abstract

Fukuda, K., Straus, S.E., Hickie, I., Sharpe, M.C., Dobbins, J.G., & Komaroff, A. (1994). The chronic fatigue syndrome: A comprehensive approach to its definition and study. International chronic fatigue syndrome study group. Annals of Internal Medicine, 121(12), 953-959.

Kindlon T. (2011). Reporting of harms associated with graded exercise therapy and cognitive behavioural therapy in Myalgic Encephalomyelitis/chronic fatigue syndrome. Bulletin of the IACFS/ME. 19(2): 59-111.

M, Archard L, Banatvala J, Borysiewicz LK, Clare AW, David A, et al. (1991). Chronic fatigue syndrome: guidelines for research. Journal of the Royal Society of Medicine, 84(2):118–21.

On 2015 Feb 14, Ellen M Goudsmit commented:

I had contact with the main author to alert her to certain misconceptions published earlier. Sadly, I found I had wasted my time.

For example, we can not tell how many, if any, patients in the PACE trial met the London criteria. Having read that the researchers planned to select individuals with ME and had listed the criteria in the protocol, I checked that Prof. White would use the original version which had not been published. I had been the Chair of the Research Working Group at AFME when they were being tested and still had a copy. They came with a questionnaire as well as a physician to establish their reliability. Prof. White was unwilling to confirm that he would use the original so in light of the uncertainty, I requested that he did not cite me as a co-author. I did not work on the lay version published in the Westcare report which I felt was deeply flawed. I was right to be cautious. The trial manual indicates that the researchers adapted the lay version and I could tell from the results that the London criteria were not used as they exclude individuals with psychological disorders so the percentage for that variable should have been nil. It wasn’t.

A second point. The review does not pay the required attention to the lack of actigraphy, an objective measure to confirm fidelity to the protocol. This has been included in most studies conducted in the USA and the Netherlands. The results from actigraphy indicate that, except for 7 individuals, there were no significant increases in activity after GET and similar therapies. According to Friedberg who assessed the phenomenon, patients on exercise trials tend to reprioritise their activities, choosing those that result in less stress etc. In short, they learn to pace themselves (Goudsmit et al 2012). That is why they feel better and less fatigued, but it's not possible to attribute improvement to an increase in activity (or fitness).

Pacing was not defined and adaptive pacing therapy (APT) refers to a programme consisting of several components including stress management, advice on sleeping etc. There are no data for pacing alone in the PACE trial, so to conclude that GET is superior to pacing therapies is premature. There is only one pacing therapy. Pacing is not a therapy. It's a simple strategy. Research by Jason suggests that people who pace themselves feel better, irrespective of the protocol they are on.

Finally, we know that many patients have adverse reactions to activity. It's a criterion for diagnosis. To dismiss them ("no evidence that exercise therapy worsens outcomes") is hard to comprehend. Every survey in every country to date has revealed that GET does have marked adverse reactions and can result in relapse. See also Sisto et al and Black and McCully, cited in Goudsmit et al 2012.

To summarise: lack of a definition of pacing resulting in confusion, repetition of incorrect information, failure to consider the findings from objective measures suggesting patients did not adhere to the protocol and ignoring consistent reports from surveys that undermine one's conclusions. I expect more objectivity and attention to detail from the Cochrane Library.

Goudsmit, EM., Jason, LA, Nijs, J and Wallman, KE. Pacing as a strategy to improve energy management in myalgic encephalomyelitis/chronic fatigue syndrome: A consensus document. Disability and Rehabilitation, 2012, 34, 13, 1140-1147. Online 19th December. doi: 10.3109/09638288.2011.635746.

On 2015 Mar 12, Donald Forsdyke commented:

ADAPTATION DECOUPLED FROM SPECIATION. The authors begin by noting that gene flow among populations, rather than assisting speciation, has a “greater impact” when acting “as a homogenizing force, reuniting populations that might otherwise have had separate evolutionary trajectories.” This blending effect, which thwarts speciation, is prevented by some form of reproductive isolation dependent upon an internal or external barrier. The nature of the barrier varies with time. The present work reflects on the order in which barriers arise, an early barrier being superceded by a later.

The two fern types, having diverged 60 million years ago, can still transfer gametes abiotically (so there are no genic incompatibilities conferring prezygotic isolation), and the resulting zygotes can still develop (so there are no genic incompatibilities conferring hybrid inviability). Thus, they are reproductively isolated to a degree sufficient to prevent blending, solely by virtue of hybrid sterility.

Following a line of reasoning that dates back to Romanes (1886), a failure of meiotic pairing, due to the accumulation of base differences in parental DNA sequences (that would not necessarily affect genes), results in sterile hybrids. The line cannot advance, so that in evolutionary terms the parents are reproductively isolated from each other. Over 60 million years, this chromosome pairing barrier would have been elevated by addition of macroscopically observable deletions, duplications or inversions. Accompanying genic changes would have affected phenotypic functions other than those affecting fertilization and development. Thus secondary adaptations would be decoupled from the primary speciation event. This is in keeping with the recent conclusion of Hedges et al. (2015) that “if adaptation is largely decoupled from speciation, we should not expect it to be a driver of speciation” (see: http://1.usa.gov/1ESNM0W where further references may be found).

On 2015 Jun 10, Paul Golding commented:

Baggott and Tamura imply that my experiment was flawed because: “The study design by Golding (2014) should have included a balanced supplementation of micronutrients at the level of generally recommended dietary intakes.” and advise that “Therefore, the data presented by Golding (2014) must be cautiously interpreted”.

My full response is available here.

Was the 500 mg/day vitamin C supplement excessive, and could it have abnormally extended the time taken to deplete the liver folate store?

Baggott and Tamura claim that my 500 mg/day vitamin C supplement was excessive, and that my saturated vitamin C status was abnormal. They propose that by abnormally protecting the reduced (unstable) form of folate from oxidation, which they claim would not have been preserved by recommended vitamin C intakes, the “excessive” vitamin C preserved the liver folate store. I strongly disagree with these assertions.

Carr et al (2012), Levine et al. (1996) and Lykkesfeldt and Poulsen (2010) recommend that vitamin C intake should be sufficient to ensure plasma saturation. If the plasma vitamin C concentration is insufficient to prevent oxidation of fully reduced folate, although sufficient to prevent scurvy, there would be sub-optimal vitamin C status.

There is no evidence that, once there is sufficient vitamin C present to ensure plasma saturation, and thereby protect the fully reduced folates, additional amounts will affect the time taken to develop folate deficiency.

Levine et al. (1996) recommend 200 mg vitamin C daily, very significantly higher than the 70 mg taken by Herbert (Herbert 1962), and a level that ensures plasma saturation. They plotted plasma vitamin C concentration against the daily vitamin C dose (Levine et al. 1996 Figure 1C); this produced a sigmoid curve with 200 mg the lowest dose to reach a plateau.

I used data from Levine et al. (1996 Table 1) to produce a chart to illustrate the relationship between vitamin C dose and the plasma concentration, at relevant levels. At Herbert’s dose of 70 mg/day, plasma concentration is 32 µmol/L; at 200 mg/day recommended by Levine et al. (1996), plasma concentration is 66 µmol/L; at my dose of 500 mg/day, plasma concentration is 71 µmol/L. A 500 mg dose of vitamin C will not produce a significantly higher plasma concentration than the 200 mg dose recommended by Levine et al. (1996), but a 70 mg dose will produce a very significantly lower plasma concentration. The Excel file, high-resolution PDF and Microsoft PowerPoint slide for my chart are available at the link above.

The predicted plasma vitamin C concentration of 71 µmol/L, produced by my intake of 500 mg/day, is very close to the value considered by Carr et al. (2012) to be necessary for good health.

The vitamin C supplement used by me was integrated with the iron tablets taken to prevent the iron deficiency reported by Herbert. As stated in Golding (2014), the iron tablets (Abbott Australia Ferro-Grad C) comprised 325 mg ferrous sulphate (equivalent to 105 mg elemental iron), with 562 mg sodium ascorbate (equivalent to 500 mg vitamin C). Sodium ascorbate is necessary to ensure adequate absorption of the iron (Hurrell 2002, McCurdy 1968).

Was the 1000 µg/day vitamin B12 supplement excessive, and could it have abnormally extended the time taken for me to deplete my liver folate store?

Although Baggott and Tamura raise the possibility of such a confounding effect, they have not suggested any mechanism for it, or cited any published reports of such findings.

I found no published reports of vitamin B12 used to overcome a dietary folate deficiency, or any findings of interference by vitamin B12 supplements with folate metabolism where there was no initial vitamin B12 deficiency. An initially untreated vitamin B12 deficiency can cause a secondary functional folate deficiency; the “methylfolate trap” (Tisman and Herbert 1973). Such a secondary folate deficiency might be corrected by vitamin B12 supplements, depending on the cause of the vitamin B12 deficiency, but there is no published evidence that increasing the vitamin B12 intake beyond that will have any effect on folate metabolism.

As explained in Golding (2014), the 1000 µg/day vitamin B12 supplement was necessary to prevent vitamin B12 deficiency. Extensive testing during my previous vitamin B12 investigation showed that my vitamin B12 is absorbed and transported to cells normally but is not utilised adequately within the cells, presumably because of a deficiency of one of the B12 cofactors. At least 250 µg was needed to avoid deficiency but 1000 µg is the most readily available, allows a reasonable margin for error, and is within the recommended range for the oral vitamin B12 dose (Kuzminski et al. 1998).

Did the experiment include appropriate supplementation of micronutrients and was the title adequate?

Baggott and Tamura have not provided any evidence that taking either of these supplements could have interfered with the development of folate deficiency in my experiment, and have not offered any plausible mechanism for such confounding effects. In addition, my supplementation with vitamin C and vitamin B12 was reasonable, in the doses used, to prevent deficiencies.

I therefore disagree with their advice that “Therefore, the data presented by Golding (2014) must be cautiously interpreted”, and with what they imply in their conclusion; that my experiment was flawed because the study design failed to include “a balanced supplementation of micronutrients at the level of generally recommended dietary intakes.”

I also disagree with their assertion that “The title … should have contained words clearly indicating that the subject had a high initial folate status and was saturated with ascorbate.” My replete folate status was clearly stated in Objective, Experiment Design and The Subject. According to Levine et al. (1996), Carr et al. (2012) and Lykkesfeldt and Poulsen (2010), plasma saturation is the normal optimal vitamin C status.

References

Baggott JE, Tamura T (2014) The second study of experimental human folate deficiency. SpringerPlus 3:719

Carr AC, Pullar JM, Moran S, Vissers MC (2012) Bioavailability of vitamin C from kiwifruit in non-smoking males: determination of 'healthy' and 'optimal' intakes. J Nutr Sci 1:e14

Golding PH (2014) Severe experimental folate deficiency in a human subject – a longitudinal study of biochemical and haematological responses as megaloblastic anaemia develops. SpringerPlus 3:442

Herbert V (1962) Experimental nutritional folate deficiency in man. Trans Assoc Am Physicians 75:307–320

Herbert V (1987) Recommended dietary intakes (RDI) of folate in humans. Am J Clin Nutr 45(4):661–670

Hurrell RF (2002) Fortification: overcoming technical and practical barriers. J Nutr 132(4 Suppl):806S–812S

Kuzminski AM, Del Giacco EJ, Allen RH, Stabler SP, Lindenbaum J (1998) Effective treatment of cobalamin deficiency with oral cobalamin. Blood 92(4):1191-1198

Levine M, Conry-Cantilena C, Wang Y, Welch RW, Washko PW, Dhariwal KR, Park JB, Lazarev A, Graumlich JF, King J, Cantilena LR (1996) Vitamin C pharmacokinetics in healthy volunteers: evidence for a recommended dietary allowance. Proc Natl Acad Sci 93(8):3704–3709

Lykkesfeldt J, Poulsen HE (2010) Is vitamin C supplementation beneficial? Lessons learned from randomised controlled trials. Br J Nutr 103(9):1251-1259

McCurdy PR, Dern RJ (1968) Some therapeutic implications of ferrous sulfate-ascorbic acid mixtures. Am J Clin Nutr 21(4):284–288

Tisman G, Herbert V (1973) B12 dependence of cell uptake of serum folate: an explanation for high serum folate and cell folate depletion in B 12 deficiency. Blood 41(3):465–469

On 2015 Mar 10, Ben A Inglis commented:

The parameters for the magnetization preparation (MP) RF pulse are not given in the paper, the supplemental material nor in the authors' previous work (Franklin et al 2013, Franklin et al 2014) on blood flow effects in gray matter measured with MP-RAGE. Was a non-selective or slab-selective inversion pulse used? The latter is expected to have more flow weighting than the former. Also, what was the inversion time (TI)? The value of TI will also influence flow weighting. In this report as well as the two prior reports, the TR quoted is considerably shorter than the TR typically employed when using a TI of 700-900 ms at 3 T. Was the magnetization preparation actually enabled? Finally, given that the paper contends there is an effect of blood flow in assessing gray matter with MP-RAGE, discussion of the effects of the MP scheme on flow weighting is essential. As given the paper fails to explain the mechanism of the blood flow weighting and whether there might be ways to minimize effects, e.g. by using a non-selective inversion and particular inversion times.

On 2016 Jan 12, Tamás Ferenci commented:

I have replied to this paper criticizing certain aspects of it (Ferenci T, 2017), available for download here, to which the original authors also responded (Diamond DM, 2017), available for download here.

On 2015 Nov 01, John Tucker commented:

The authors correctly point out that the use of relative risk information in isolation can be misleading, but this is true of their preferred measure of absolute risk reduction as well. The examples chosen by the authors to illustrate their point are 2 to 5 year trials of drugs that are taken prophylactically for much longer periods. Further, two were stopped early for ethical reasons after crossing the threshold for showing clear clinical benefit, which placed an upper limit on the level of benefit that could be demonstrated. The survival curves from longer term trials such as 4S and WOSCOPS show a progressively larger absolute benefit with longer duration of treatment.

Presented in isolation, both relative and absolute risk reduction can be misleading.

On 2015 Feb 17, Ryan Radecki commented:

Post-publication commentary: "Inappropriately Promoted tPA "Drip and Ship" Safety"

“More community hospitals are giving a powerful clot-busting medication to stroke victims, improving their chances of survival and recovery, new research shows.”

This statement comes from coverage of the American Heart Association release regarding this synopsis of the Get-With-the-Guideline Registry. Part of this statement is true – more community hospitals are using tPA for acute ischemic stroke. In this review of 44,667 patients treated with tPA over the past decade, 23.5% received tPA outside of a specialized stroke or academic center.

The second half of this press statement is false.

Patients treated by the “drip and ship” method, as community administration of tPA is described, did not have an improved chance of survival. Patients treated at community hospitals were younger, had less-severe strokes, and had fewer prior strokes – yet their in-hospital mortality was 10.9%, compared with 9.7%....

http://www.emlitofnote.com/2015/02/inappropriately-promoted-tpa-drip-and.html

On 2015 Feb 17, Ryan Radecki commented:

Post-publication commentary: "Christmas Comes Early for Endovascular Therapy in Stroke"

Quite literally, in fact, considering the timing of the publication of MR-CLEAN – and, now, the triple fall-out from those results.

Due to the positive findings presented by the MR-CLEAN investigators in December 2014, three other ongoing major endovascular trials used this opportunity to check their results early. ESCAPE, EXTEND-IA, and SWIFT-PRIME – all products of the Covidien Solitaire FR clinical trial machine – ceased recruitment and looked to see if they’d met statistical measures of efficacy. Obviously, if you’re reading about all three of these trials here today – presented at the International Stroke Conference yesterday – they all found the results they hoped. ESCAPE and EXTEND-IA were published simultaneously in the NEJM, while SWIFT-PRIME is still in the manuscript drafting stages.

The more robust of the two trials is ESCAPE, whose original target enrollment was 500 patients based on a primary outcome of “ordinal shift analysis” on the modified Rankin scale.....

http://www.emlitofnote.com/2015/02/christmas-comes-early-for-endovascular.html

On 2015 Feb 17, Ryan Radecki commented:

Post-publication commentary: "Christmas Comes Early for Endovascular Therapy in Stroke"

Quite literally, in fact, considering the timing of the publication of MR-CLEAN – and, now, the triple fall-out from those results.

Due to the positive findings presented by the MR-CLEAN investigators in December 2014, three other ongoing major endovascular trials used this opportunity to check their results early. ESCAPE, EXTEND-IA, and SWIFT-PRIME – all products of the Covidien Solitaire FR clinical trial machine – ceased recruitment and looked to see if they’d met statistical measures of efficacy. Obviously, if you’re reading about all three of these trials here today – presented at the International Stroke Conference yesterday – they all found the results they hoped. ESCAPE and EXTEND-IA were published simultaneously in the NEJM, while SWIFT-PRIME is still in the manuscript drafting stages.

EXTEND-IA was a much smaller trial, targeting only 100 patients, with coprimary outcomes of reperfusion and NIHSS improvement at 24 hours....

http://www.emlitofnote.com/2015/02/christmas-comes-early-for-endovascular.html

On 2015 Apr 22, Melissa Raven commented:

Inappropriate analysis of mortality in mental disorders

There are serious problems with this analysis of mortality in mental disorders. Walker et al. have very inappropriately generalized mortality estimates derived from their analysis of clinical samples (primarily tertiary treatment samples), which include high proportions of patients (often inpatients) with psychotic disorders, to cases of common mental disorders (primarily anxiety disorders and mood disorders) identified in population surveys (World Mental Health (WMH) surveys). The authors have thereby grossly exaggerated the population-level mortality due to mental disorders. Unfortunately this has been accepted uncritically by the reviewers, the editors, and many readers.

I have posted a more detailed comment on JAMA Psychiatry http://archpsyc.jamanetwork.com/article.aspx?articleid=2110027

On 2015 Mar 10, Harri Hemila commented:

Vitamin C may help against exercise-induced bronchoconstriction

Boulet LP, 2015 reviewed the treatment options for exercise-induced bronchoconstriction (EIB) and stated that there is insufficient data to recommend vitamins or antioxidants as treatment. This statement is misleading.

Three randomized trials examined the effect of vitamin C on exercise-induced FEV1 decline in asthmatics, see Schachter EN, 1982, Cohen HA, 1997, and Tecklenburg SL, 2007. Each trial found that vitamin C halved the FEV1 decline, with the pooled estimate indicating a reduction of postexercise FEV1 decline by 48% (95%CI: 33% to 64%), see Hemilä H, 2013 and Hemila H, 2014. The studies were carried out in three different decades and on two different continents, and the mean ages of the participants were 14 yr in Cohen HA, 1997 and 25-26 yr in Schachter EN, 1982 and Tecklenburg SL, 2007. It is not evident how far the estimate of effect can be generalized, but similar findings from such dissimilar studies indicate that vitamin C may be effective for a wider population who suffer from EIB.

Boulet LP, 2015 refers to the Cochrane review by Wilkinson M, 2014 as a justification for the statement that there are insufficient data on vitamins or antioxidants as treatment of EIB. However, Wilkinson M, 2014 does not include any of the above mentioned three RCTs in their analyses, since their analysis is restricted to studies that used both vitamin C and vitamin E together. Those studies are not relevant to the question whether vitamin C alone has effects on EIB.

Given the safety and low cost of vitamin C and the consistency in the findings of the three RCTs on vitamin C and EIB, it would seem reasonable to encourage physically active people to test whether vitamin C is beneficial on an individual basis, if they suffer from EIB.

On 2015 Apr 02, Marcus Munafò commented:

Carter and colleagues [1] report that 17% of the excess mortality among smokers is due to causes to yet established. This is an important insight – we know that smoking kills, but do not fully understand how. Nevertheless, there are reasons for being cautious about ascribing a direct causal role to smoking for some of the outcomes reported. The supplementary appendix indicates substantial excess mortality among smokers for “all other mental diseases”, including suicide. However, homicide is related to smoking in a similar way to suicide [2], which casts doubt on the possibility that smoking may be acting via a biological pathway. Mendelian randomization [3] offers a possible solution, protecting against confounding and reverse causality and enabling stronger causal inference. Since we do not yet fully understand why smoking kills, we have established the Causal Analyses for Research on Tobacco and Alcohol (CARTA) consortium to use Mendelian randomization to elucidate the causal role of smoking on a range of health outcomes and intermediate markers (http://www.bris.ac.uk/expsych/research/brain/targ/research/collaborations/carta/), which has failed to provide evidence that smoking causes depression [4].

Marcus Munafò, Amy Taylor and George Davey Smith

1. Carter, B.D., et al., Smoking and mortality--beyond established causes. N Engl J Med, 2015. 372(7): p. 631-40.
2. Davey Smith, G., A.N. Phillips, and J.D. Neaton, Smoking as "independent" risk factor for suicide: illustration of an artifact from observational epidemiology? Lancet, 1992. 340(8821): p. 709-12.
3. Davey Smith, G. and S. Ebrahim, 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease? Int J Epidemiol, 2003. 32(1): p. 1-22.
4. Taylor, A.E., et al., Investigating the possible causal association of smoking with depression and anxiety using Mendelian randomisation meta-analysis: the CARTA consortium. BMJ Open, 2014. 4(10): p. e006141.

On 2015 May 05, Arthur Yin Fan commented:

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

On 2015 Feb 11, Robert Eibl commented:

Better understanding of the immune system appears to be the key element for cancer cure, but not all cancer research agencies share this priority.

On 2015 Oct 24, Geriatric Medicine Journal Club commented:

There is already strong evidence for comprehensive geriatric assessment in the inpatient setting. This orthogeriatrics trial also incorporates a cost-effectiveness evaluation. This article was critically appraised at the October 2015 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full discussion can be found at: http://gerimedjc.blogspot.com/2015/10/october-2015-gerimedjc.html?spref=tw Despite more resourcing, when patients are cared for on a comprehensive geriatric care ward, outcomes of mobility of function are better. An important point raised during the journal club discussion is that by creating specialized wards, we may be distracting from a larger effort to make an entire hospital senior-friendly.

On 2015 Jul 13, Graham Coop commented:

After our paper appeared we were made aware of a great potential example of paternal control of female meiotic transmission (Herrera et al. 1996). In many species dispensable supernumerary B-chromosomes are preferentially transmitted to offspring, with this preferential segregation (drive) often occurring through female meiosis (Jones 1991, Burt and Trivers 2006). Herrera et al. studied a widespread B chromosome polymorphism in the grasshopper, Eyprepocnemis plorans. In crosses between 1B females and males from the same focal population in which B-chromosomes were present, B-chromosomes were transmitted following Mendelian ratios. However, when the same females were crossed to males from a population where the B chromosome was not present, they transmitted their B-chromosome to much more than half of their progeny. There was no obvious reduction in fertility, suggesting that this was not due to lethality and potentially due to meiotic drive. Herrera et al suggested that the male control of female meiosis is exerted during the first meiotic division, perhaps due to an effect of substances in the male ejaculate. These results are consistent with our hypothesis that sperm-based suppressors of drive may arise and spread in response to the spread of female meiotic drive elements (such as B-chromosomes), such that female meiotic drive can re-emerge when eggs are exposed to specific sperm from a population where drive suppression had not evolved. We thank Juan Pedro M. Camacho (Universidad de Granada) for kindly bringing this example to our attention and for feedback on this note.

Yaniv Brandvain and Graham Coop

Cited References:

Jones, R.N. 1991. B-Chromosome Drive. American Naturalist 137: 430-442.

Burt, A. and R. Trivers, 2006. Genes in conflict. Belknap Press, Cambridge.

Herrera, J. A., M. D. López-León, J. Cabrero, M. W. Shaw and J. P. M. Camacho. 1996. Evidence for B chromosome drive suppression in the grasshopper Eyprepocnemis plorans. Heredity 76: 633–639.

On 2015 Jun 16, Andrew Brown commented:

Read the commentary by Nwudu VC, 2015 for important considerations regarding the quality and completeness of this systematic review.

On 2015 Feb 13, Heping Zhang commented:

Thanks for your comments. Our work regarding the comparative genomic analysis of genus Bifidobacterium began in 2013, which was finished in early 2014. As we found, the manuscript from your side had not been published elsewhere when we were submitting the manuscript or revising the manuscript according to the reviewers’ suggestions from PLOS ONE. Anyway, it’s very glad that consistent conclusions were reached by two teams independently, which proved the reliability of both researches. In future, Bifidobacterium genomics is likely to be one of our interests. We sincerely wish to cooperate with the team of Prof. Ventura, and all of the colleagues worldwide with enthusiasm on promoting advancement of this certain area.

On 2016 May 10, Morten Oksvold commented:

Please pay attention to the following report by ORI (Office of Research Integrity) before reading this article:

https://ori.hhs.gov/content/case-summary-walker-kenneth

On 2016 Dec 17, John Tucker commented:

The problem with the conclusions of this article, is of course, that the most impassioned arguments made from first principles and in vitro results carry little weight when used to argue against the results of multiple phase 3 trials involving tens of thousands of patients.

Statins reduce MI and cardiovascular death. The data is clear.

On 2015 Aug 17, Guangchuang Yu commented:

the original idea of using bubble chart to compare annotations was published in OMCIS, 2012, http://www.ncbi.nlm.nih.gov/pubmed/22455463 by clusterProfiler package.

On 2016 May 31, Marcelo G Bonini commented:

Thank you Rick!

On 2016 May 26, FREDERICK DOMANN commented:

References for the MnSOD over-expressing MCF-7 cells used in this study can be found here:

1. http://www.ncbi.nlm.nih.gov/pubmed/11929863
2. http://www.ncbi.nlm.nih.gov/pubmed/16170370

On 2016 May 31, David C. Norris commented:

Following Hardin's model¹ , Roman² advances an argument characteristic of that "intolerance of reason" which stands "not often on the side of liberty"³ : A crisis looms, having no technical solution; my analysis of human nature proves coercion indispensable.

Hardin's crisis was the 1960s' looming Malthusian apocalypse. "The necessity of abandoning the commons in breeding" demanded "mutual coercion, mutually agreed upon"¹ -- words that could hardly sound more chilling except against the background of Hardin's eerie silence on all details of said "coercion". Roman for his part volunteers specifics, but only to conflate as "coercion" such divergent measures as cost-sharing (a decidedly non-coercive remedy for the moral hazard which Roman misreads as a 'tragedy of the commons') and outright healthcare rationing: "giv[ing] local communities responsibility for governance of common-pool resources."²

Ironically, Hardin's crisis now yields to technical innovation⁴ plus the spread of liberal values and liberty itself.⁵ Can these same forces not solve also an artificial crisis in which -- unlike Nature's common-pool oceans and atmosphere -- our Treasury has become a healthcare commons purely by an accident of our politics?

[1] Hardin G, 1968 Full text

[2] Roman BR, 2015

[3] Hayek, F. A. The Road to Serfdom: Text and Documents--The Definitive Edition. Edited by Bruce Caldwell. 1 edition. Chicago: University Of Chicago Press, 2007. See p. 200 in Ch. 13, titled 'The Totalitarians in Our Midst'. The fuller quotation is as follows:

The influence of these scientist-politicians was of late years not often on the side of liberty: the "intolerance of reason" so frequently conspicuous in the scientific specialist, the impatience with the ways of the ordinary man so characteristic of the expert, and the contempt for anything which was not consciously organized by superior minds according to a scientific blueprint were phenomena familiar in German public life for generations before they became of significance in England.

[4] Whitty CJ, 2013

[5] Bongaarts J, 2011

On 2017 Jan 11, Thomas E Sussan commented:

Extrapolation of the levels of exposure in this model to those of human users is difficult due to a number of factors, including differences in respiratory mechanics, altered metabolic rates of nicotine and other constituents, and the fact that mice are passively breathing rather than actively puffing. Development of an appropriate animal model that is both representative of a human condition and also amenable to investigation can be challenging. As a result, animal models often push the limits of a typical human exposure in order to obviate the need for a protracted disease course. Additionally, due to interspecies differences, toxicity studies generally employ a 10-fold uncertainty factor when extrapolating from laboratory animals to humans, and further uncertainty factors are also typically used to account for vulnerable/susceptible populations. Findings in animal toxicity studies are generally applicable to humans, and animal studies have been used for decades to provide the basis for human studies.

Mice are frequently more resistant than humans to toxicant exposures, as is the case for cigarette smoke. The most widely accepted mouse model of cigarette smoke-induced lung disease utilizes daily exposure to high levels of cigarette smoke for 4-7 hours per day for 6 mo, resulting in a phenotype that is morphologically similar to that of a chronic smoker with mild COPD. Additionally, unlike humans, mice rarely progress beyond mild stages of disease. Due to the relative short history of e-cigarettes, we don’t have the ability to compare the pulmonary responses in mice to those of chronic e-cig users. Thus, while animal models have been indispensible for providing the basis of human studies, they all have limitations, and our model is no different. Based on duration of exposure, we believe that our published model is reasonable, although we do not dispute that the level of exposure is elevated compared to that of a typical e-cig user.

In our exposure model, mice breathed freely in a chamber containing a constant mix of 20% e-cig vapor/80% air for 1.5h twice per day. In 3 hours, a human would take approximately 2160-3600 breaths (12-20 breaths/minute), and thus a 20% e-cig vapor would be equivalent to 432-720 breaths. However, it is notable that a typical human breath is substantially larger than a typical e-cig puff. Thus, breaths and puffs are not equivalent, and our exposure is higher than that of a typical human e-cig user.

Drs. Mukhin and Rose used a different approach to estimate exposure in our model based on our measured cotinine levels and previously published values of metabolic rates for nicotine and cotinine in mice and humans, a published equation to calculate steady state cotinine, published steady state cotinine levels in mice after nicotine infusion, and a published volume of e-cig liquid consumption per puff. Based on these values, they determined that our model was equivalent to 3600-4600 puffs by a human user (although our e-cigs contained 1.8% nicotine, not 1.6%, which reduces these estimates slightly to 3333-4111). This puff estimate is approximately 10x higher than the average number of daily puffs taken by a typical e-cig user. These published estimates for nicotine and cotinine metabolism can vary considerably due to genetic variation within and between species, age, sex, diet, etc, making it difficult to accurately compare exposures based on nicotine. Regardless, I am not disputing the validity of their estimate nor questioning their intentions. In fact, our exposure estimate (based on number of breaths) is consistent with their estimate (based on nicotine metabolism). The reported serum cotinine concentrations demonstrated that these levels were consistent with those of human e-cig users, but it is correct that this is actually indicative of an elevated exposure due to differences in nicotine metabolism between mice and humans.

Drs. Mukhin and Rose also stated that due to lack of clarity in the methods, it is possible that the puff estimate could be as high as 13000 puffs per day. To clarify this area of confusion that was not clear in our methods, blood was collected from 5-10 mice almost immediately after conclusion of exposure, but the process of collecting blood from each mouse required a certain amount of time. Thus, we wrote in the methods that blood collection was made within 60 min of exposure, but we strived to collect it as soon as possible.

Regarding the claim by PHE that we simply made the mice sick and thus reduced their recovery, the mice displayed no overt signs of sickness (ie vomiting, diarrhea, dizziness, lethargy, etc). They exhibited only mild effects in the absence of infection. However, in response to infection they demonstrated immunosuppression, which was evident even when the airway macrophages were infected ex vivo. This demonstrates a clear impairment at the cellular level.

The relevance of this study’s findings is unclear. The phenotypes demonstrated in this model certainly warrant further exploration of potential immunosuppressive effects in human e-cig users, especially considering the well-published impaired immune responses observed in both humans and mice exposed to cigarette smoke, which are similar to the findings in the current study. Our current study should not serve as the definitive body evidence, but should instead guide future studies. There is some more recent evidence to suggest that human e-cig users exhibit gene expression signatures indicative of immunosuppression (PMID: 27288488), although it’s noteworthy that this commenter has also criticized this human study and several other e-cig studies. Another group has shown in a retrospective study that switching from cigarettes to e-cigs may reduce the number of COPD exacerbations (PMID: 27986085), suggesting that the immune response is improved as a result of switching. Additional studies are still greatly needed to determine the relevance of our current animal study to e-cig users.

The point by Pruen is interesting. We previously did some preliminary testing to compare the disposable NJOY e-cigs versus the rechargeable NJOY e-cigs, and we noted considerable differences between the two with respect to the average life of a cartridge. We expected them to be similar, but were surprised to see that the rechargeable e-cigs lasted much longer than the disposables. Our animal exposure used the rechargeable e-cigs. Our exposure included a real-time light scattering monitor connected to the inlet of the exposure chamber to determine when the output of each e-cig began to wane. E-cig cartridges were replaced whenever the monitor detected a drop in vapor density. No one was puffing the e-cigs to ensure that the vapor remained pleasant to the taste, but we can definitively state that there was no dry puffing and thus overheating. We also puffed each e-cig for 2 seconds, once per minute to further prevent overheating of the coil and dry wicking.

Our study compared e-cig exposure to room air, but did not directly compare e-cig vapor to cigarette smoke. The questions of whether e-cigs are safe and whether they are safer than cigarettes are both valid questions, but our current study only addressed the first question. While our study demonstrated an effect on the immune response that was similar in nature to that previously seen with cigarette smoke, we did not directly compare the relative effects between cigarettes and e-cigs. No individual study can address all questions, and as stated above, further studies are needed to determine the effect of e-cigs on never-smokers, former-smokers, and dual users.

Dr Farsalino’s comment is simply a restatement of a paragraph in the Discussion of our publication, which stated the following: “Cigarette smoke contains 1014 free radicals per puff…We determined that E-cig vapor contains 7x1011 free radicals per puff…this concentration is several orders of magnitude lower than in cigarette smoke.”

On 2016 Dec 20, Zvi Herzig commented:

Important methodological issues have been raised in response to this study.

• Mukhin and Rose calculate, based on cotinine levels, that aerosol exposure levels in this study are the mouse equivalent of 11,000-13,000 puffs per day! link
• Public Health England's 2015 report on e-cigarettes notes that suddenly exposing nicotine-naive subjects to quantities of nicotine tolerated only by heavy smokers would be expected to result in stress, sickness and vomiting, which explains the reduced recovery from infection in exposed mice. link
• Mayer notes that it has been known for decades that nicotine has anti-inflammatory effects associated with immune suppression in mice and rats, but this is apparently not reflected in humans. Thus, this study's findings of reduced recovery after infection are not surprising, but lack relevance. link
• Pruen explains that this study's design protected poorly from inadvertent overheating, likely resulting in unrealistic toxicant exposures from pyrolysis. link
• Without cigarette smoke exposed controls it's quite difficult to estimate magnitude of effect in relation to real-world human consumption.

Additionally, Farsalinos notes:

"Concerning free radicals, the authors found 7x1011 spins/puff compared to 1014 spins/puff for smoking (other reports have measured up to 1017 spins/puff for smoking). That is about 150 times lower compared to tobacco cigarettes." link

On 2015 Feb 05, William Grant commented:

Increasing vitamin D levels can reduce unplanned hospital readmissions

The paper by Merkow and colleagues points out that readmissions after surgery are largely due to new postdischarge complications related to the procedure [1]. The information about the characteristics of the patients and the factors associated with unplanned readmission provide important clues as to the causes of the readmissions. This comment examines the possible role of low 25-hydroxyvitamin D [25(OH)D] concentration as an important underlying cause of readmission.

One aspect is that blacks have higher unplanned readmissions than whites (Table 4). Blacks have much lower mean 25(OH)D concentrations than whites [2] due to the facts that most vitamin D is made from solar UVB exposure and blacks have darker skin.

The next clue is the types of disease with significantly higher unplanned readmission rates (Table 4). Risk of congestive heart failure death is significantly inversely correlated with 25(OH) concentrations [3]. Treating those with heart failure increases heart function [4]. Prevalence of chronic pulmonary obstructive disease is inversely correlated with 25(OH)D concentration [5]. Those with COPD and severe vitamin D deficiency are more likely to be hospitalized [6].

Incidence of diabetes is inversely correlated with 25(OH)D concentration [7]. Incidence and mortality rates for many types of cancer are inversely correlated with solar UVB doses and 25(OH)D concentrations [8]. Would infection: an observational study in Massachusetts found that surgical site infections for those undergoing Roux-en-Y gastric bypass surgery were linearly inversely correlated with 25(OH)D concentrations below about 30 ng/mL (75 nmol/L) [9]. Vitamin D has a number of antimicrobial actions such as inducing production of cathelicidin and defensins [10]. It has been proposed that increasing 25(OH)D concentrations would reduce the risk of hospital acquired infections [11]. Renal failure: A study in Boston found that preadmission 25(OH)D concentrations below 20 ng/mL is predictive of acute kidney injury [12]. Peripheral vascular disease: 25(OH)D concentrations are significantly inversely correlated with peripheral vascular disease [3]. Sepsis: 25(OH)D concentrations are significantly inversely correlated with risk of sepsis [13, 14].

The general finding in many observational studies is that 25(OH)D concentrations below 30 ng/mL have increased risk of many chronic and infectious diseases [15, 16].

Looking at Table 2, the two most frequent reasons for unplanned readmissions directly related to 25(OH)D concentrations are surgical site infection and sepsis. Together they account for about 22% of readmissions. This portion of the readmissions can be reduced significantly if those undergoing surgery in hospitals have higher 25(OH)D concentrations.

To reduce this portion of readmissions, it would be worthwhile to measure 25(OH)D concentrations of those planning surgery or admitted to the hospital. Giving loading doses of vitamin D3 should increase 25(OH)D concentrations rapidly. A loading dose of 250,000 IU vitamin D3 increased 25(OH)D concentrations by 58 nmol/L (23 ng/mL) after 5 days in a study with healthy adults in one study [17]. A study in Austria found that giving 550,000 IU of vitamin D3 shortly after admission to the intensive care unit followed by 90,000 IU/mo thereafter found a significant reduction in mortality rates between 28 days and 6 months after admission for those with 25(OH)D concentrations below 12 ng/mL [18]. There were no significant adverse effects associated with this dose of vitamin D in this patient population although some of the patients had elevated serum calcium levels. 550,000 IU is higher than would typically be given to raise 25(OH)D concentrations rapidly. Prescription grade 50,000 IU capsules of vitamin D3 are now available.

References 1. Merkow RP, Ju MH, Chung JW, et al. Underlying Reasons Associated With Hospital Readmission Following Surgery in the United States. JAMA. 2015;313(5):483-495 2. Ginde AA, Liu MC, Camargo CA Jr. Demographic differences and trends of vitamin D insufficiency in the US population, 1988-2004. Arch Intern Med. 2009;169(6):626-32. 3. Anderson JL, May HT, Horne BD, et al. Relation of vitamin D deficiency to cardiovascular risk factors, disease status, and incident events in a general healthcare population. Am J Cardiol. 2010;106(7):963-8. 4. Dalbeni A, Scaturro G, Degan M, et al. Effects of six months of vitamin D supplementation in patients with heart failure: a randomized double-blind controlled trial. Nutr Metab Cardiovasc Dis. 2014;24(8):861-8. 5. Skaaby T, Husemoen LL, Thuesen BH, et al. Vitamin D status and chronic obstructive pulmonary disease: a prospective general population study. PLoS One. 2014;9(3):e90654. 6. Malinovschi A, Masoero M, Bellocchia M, et al. Severe vitamin D deficiency is associated with frequent exacerbations and hospitalization in COPD patients. Respir Res. 2014;15(1):131. 7. Song Y, Wang L, Pittas AG, et al. Blood 25-hydroxy vitamin D levels and incident type 2 diabetes: a meta-analysis of prospective studies. Diabetes Care. 2013;36(5):1422-8. 8. Moukayed M, Grant WB. Molecular link between vitamin D and cancer prevention. Nutrients. 2013;5(10):3993-4023. 9. Quraishi SA, Bittner EA, Blum L, et al. Association between preoperative 25-hydroxyvitamin D level and hospital-acquired infections following Roux-en-Y gastric bypass surgery. JAMA Surg. 2014;149(2):112-8. 10. Youssef DA, Miller CWT, El-Abbassi AD, et al. Antimicrobial implications of vitamin D. Dermatoendocrinol, 2011;3(4):220 – 9. 11. Youssef DA, Ranasinghe T, Grant WB, Peiris AN. The potential of vitamin D to reduce the risk of hospital-acquired infections, Dermatoendocrinol. 2012;4(2):167-75. 12. Braun AB, Litonjua AA, Moromizato T, et al. Association of low serum 25-hydroxyvitamin D levels and acute kidney injury in the critically ill. Crit Care Med. 2012;40(12):3170-9. 13. Moromizato T, Litonjua AA, Braun AB, et al. Association of low serum 25-hydroxyvitamin D levels and sepsis in the critically ill. Crit Care Med. 2014;42(1):97-107. 14. Rech MA, Hunsaker T, Rodriguez J. Deficiency in 25-hydroxyvitamin D and 30-day mortality in patients with severe sepsis and septic shock. Am J Crit Care. 2014;23(5):e72-9. 15. Hossein-Nezhad A, Holick MF. Vitamin D for health: A global perspective. Mayo Clin Proc. 2013;88(7):720-55. 16. Pludowski P, Holick MF, Pilz S, et al. Vitamin D effects on musculoskeletal health, immunity, autoimmunity, cardiovascular disease, cancer, fertility, pregnancy, dementia and mortality- a review of recent evidence. Autoimmun Rev. 2013;12(10):976-89. 17. Kearns MD, Binongo JN, Watson D, et al. The effect of a single, large bolus of vitamin D in healthy adults over the winter and following year: a randomized, double-blind, placebo-controlled trial. Eur J Clin Nutr. 2015;69(2):193-7.<br> 18. Amrein K, Schnedl C, Holl A, et al. Effect of high-dose vitamin D3 on hospital length of stay in critically ill patients with vitamin D deficiency: The VITdAL-ICU Randomized Clinical Trial. JAMA. 2014;312(15):1520-30.

Disclosure I receive funding from Bio-Tech Pharmacal, Inc. (Fayetteville, AR), MediSun Technology (Highland Park, IL), and the Vitamin D Council (San Luis Obispo, CA).

On 2015 May 12, University of Lausanne Genomics, Ecology and Evolution Journal Club commented:

The article nicely highlights the need for a reference genome panel consisting of African variants and understanding African population history. This is a summary of the discussion at our journal club. By sequencing a large number of single sperm DNA molecules, the authors showed that meiosis is an important source not only of genetic diversity of gametes with different alleles combinations as products of chromosomal crossovers (COs), but it is also the source of sequence variation, knowing that recombination may cause local mutagenic effect at crossover sites with recurrent double strand breaks (DSBs). This study contributes to the understanding of the sequence evolution at recombination hotspots. Observed de novo mutations changed strong (S) CG into weak (W) TA base pairs and they all occurred mainly at CpG sites. As it is shown that GC base pairs are preferentially transferred during crossover, the authors suggested that GC-biased gene conversion (gBGC) is the dominant force shaping the nucleotide composition at hotspots and potentially in other recombination products, which might explain the high GC content associated with recombination. It is possible that gBGC is an adaptation to reduce the opposing mutational load of recombination, knowing that mutation favors weak over strong nucleotides. Still, small sample size gives little power for detecting potential differences between COs and NCOs.

On 2015 Feb 04, Robert Eibl commented:

fascinating!

On 2015 May 20, NephJC - Nephrology Journal Club commented:

This study was discussed on May 12th and 13th in the open online nephrology journal club, #NephJC, on twitter.

Introductory comments are available at the NephJC website. The discussion was quite detailed, with more than 65 participants, including nephrologists, gastroenterologists and also input from the senior author, Professor Paulo Angeli.

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

The highlights of the tweetchat were:

• The authors, with research funding from the University of Padova, should be commended for conducting this elegant and well-thought out trial, which was stopped early after the interim analysis reported a superiority of the intervention (terlipressin) compared to the standard therapy (midodrine+ octreotide).

• There was some discussion around a few factors/issues: the fact that acute kidney injury in hepatorenal syndrome is a heterogenous entity and whether using biomarkers in conjunction to guide patient selection would have been helpful; concern about the early stopping and whether power/sample size should have taken interim analysis into account; the possibility that the continuous terlipressin infusion, used in this study, perhaps is more effective than bolus dosing used previously (and which will be tested in an ongoing trial by the same group of authors).

• There was a transatlantic divide in the approach to such patients. Terlipressin is not available in North America, and the evidence from this trial did not convince most participants in the American chat; on the other hand, terlipressin is available in most of Europe and UK, and the participants in that chat felt this data supported their standard of care.

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

On 2015 Mar 22, Gholson J Lyon commented:

In regards to TAF1 reported in this paper, we also published a finding involving TAF1 in this paper:

http://www.ncbi.nlm.nih.gov/pubmed/?term=seqhbase

And we also posted the TAF1 discovery on BioRxiv: http://biorxiv.org/content/early/2015/01/21/014050

We are looking for other families with TAF1 mutations and any phenotypes overlapping with our family, so please contact me if you find any. My contact info can be found on my website: http://lyonlab.labsites.cshl.edu/

On 2015 Feb 03, David Mage commented:

From the perspective of a chemical engineer, a most critical parameter for calculating the extent of rebreathing of exhalations with high CO2 and low O2 from the presence of a facial obstruction is the exact millimeters of clearance, if any, between the infant's nostrils and the obstruction. Because the usual natural practice of the shocked discoverer of an apparently moribund infant is to immediately pick the infant up to revive it, that critical measurement is lost forever.

On 2016 Feb 27, Jomar Rabajante commented:

Corrigendum: The authors regret the following minor errors

In Fig.5a, the caption should state n=5 instead of n>=5. This is correct in the accepted manuscript but was changed in the published manuscript. We were not able to correct this in the galley proof. Moreover, in the captions for Fig. 5a and Fig 5b, X5 should be X{i not equal to 5} and X4 should be X{i not equal to 4}, respectively. The readers could immediately correct these errors by looking at Fig. 5a and 5b. We also rearranged the first sentences in Fig. 5 for clarity. In summary, the caption for Fig. 5 should be read

“Fig. 5. Examples of oscillating pathways. See Supplementary Figs. 13-15 and 17 for the stochastic simulations and for the parameter values used. (a-b) There are no deep valleys only continuous zigzag canals. (a) n=5; X{i not equal to 5} are initially silenced. (b) n=4; X{i not equal to 4} are initially silenced. (c) Damped oscillations towards multipotency or pluripotency. The rates of decline of the timescale factors are all equal to 0.001. (d) Damped oscillations resulting in partial differentiation and reversal of dominant GRF. The rates of decline of the timescale factors are not all equal. The initial dominant regulatory factor is GRF 5 but eventually becomes inferior as oscillations dampen.”

In Supplementary Figure 20, we were not able to change the legend in the graph when we were rearranging the figures. The legend should state that the red broken line pertains to the entropy corresponding to Fig. 5c (instead of 3d), and the blue broken line pertains to the entropy corresponding to Fig. 5d (instead of 3e). The caption for Supplementary Figure 20 is correct.

These two errors do not affect or change the information in the figures, the results and the discussion in the manuscript.

On 2015 Feb 06, Ryan Radecki commented:

Post-publication commentary: "Which Review of Tamiflu Data Do You Believe?"

Ever since its introduction, there have been skeptics regarding the utility of oseltamivir and other neuraminidase inhibitors for the treatment of influenza. Roche has profited tremendously off strategic stockpiling by many governments as a response to pandemic influenza – yet, nearly all the data comes from Roche-conducted trials, and the data has been persistently cloaked from independent review. This past year, after much strife and public shaming, the Cochrane Collaboration received some access to clinical trial reports to conduct an independent review. This review found, on average, adults receiving early treatment with oseltamivir benefited by reduction in symptom duration from 7 days to 6.3 days. No benefit was found for reduction in respiratory infectious complications or hospitalization, the truly critical need during influenza outbreaks.

However, a second group also conducted an independent review – the “Multiparty Group for Advice on Science”. Their results, based on an individual-patient meta-analysis, are published in the Lancet and offer similar – yet wildly different – conclusions....

http://www.emlitofnote.com/2015/02/which-review-of-tamiflu-data-do-you.html

On 2015 Apr 16, Paul Brookes commented:

Figure 5 of this paper contains images that appear more similar to each other than one would expect by coincidence.

http://imgur.com/tXdWQwE

A corresponding post. has been made at PubPeer... https://pubpeer.com/publications/BBC278257761C0C12E5D38844873DF

The journal has been notified.

On 2015 Feb 18, David Keller commented:

Should Parkinson patients with low LDL cholesterol increase dietary cholesterol intake?

Patients with Parkinson Disease (PD) tend to have lower LDL and total cholesterol levels than matched subjects without PD (and concomitantly lower rates of cardiovascular atherosclerotic diseases). The association of elevated cholesterol levels with reduced risk for PD incidence suggests that PD patients with abnormally low LDL and total cholesterol levels may benefit by elevating these lipid levels into the normal range, perhaps by consuming more dietary saturated fat or cholesterol itself. Of course, increasing LDL levels would also tend to increase cardiovascular risk; if increasing LDL by diet is found to slow down PD progression, then each PD patient will have to decide how much cardiovascular risk increase they are willing to accept in exchange for the concomitant neurological benefits. A randomized trial of atherogenic diet in PD patients would require careful attention to fully-informed consent, and should not raise the cardiovascular risk profile of any subject higher than the age-adjusted lower limit of normal for that patient.

On 2015 Feb 18, David Keller commented:

Evidence that high cholesterol, not statin use, is protective against Parkinson disease.

Prior studies have demonstrated decreased incidence of Parkinson disease (PD) with statin use, and with elevated LDL and total cholesterol. Subjects who are taking a statin are generally doing so because of a history of elevated LDL cholesterol. The reduced incidence of PD in these patients is difficult to interpret; is it due to their use of statins, or to their history of underlying elevated cholesterol levels? This uncertainty is due to "indication bias", so named because one factor of interest (elevated cholesterol) is an indication for the other factor of interest (a statin drug) to be prescribed. Prior studies which attributed a decreased risk for PD to statin use instead of the underlying elevated cholesterol may have suffered from indication bias.

Huang and colleagues addressed this problem by adjusting statin use for prior cholesterol levels, and adjusting cholesterol levels for current statin use. They found that high LDL and total cholesterol are associated with lower risk of incident Parkinson Disease (PD), and that statin use is actually a risk factor for PD. These findings imply that prior studies which reported a lower risk of PD with statin use may have suffered from indication bias, due to higher statin use among subjects with a past history of high cholesterol, and to lower current cholesterol levels among patients currently taking a statin. Huang's findings suggest that statin drugs are not candidates to slow or stop the progression of PD, based on the 56 PD cases analyzed.

Would it be possible to apply the statistical adjustments employed in this study to re-analyze the data used in prior studies, to reduce the effects of indication bias and determine whether prior reports of a protective effect of statin use were actually measuring the effects of the history of high cholesterol in these subjects?

On 2015 Feb 23, William Grant commented:

Vitamin D disparities may explain some of the findings regarding risk of primary cesarean delivery

The paper by Min and colleagues found many interesting results regarding correlations with primary cesarean delivery [1]. However, one additional important factor was overlooked: 25-hydroxyvitamin D [25(OH)D] concentration. This comment briefly summarizes how 25(OH)D concentrations are related to the findings of Ref. 1.

First, 25(OH)D concentrations have been found inversely correlated with primary cesarean delivery [2]. Second, black Americans have much lower 25(OH)D concentrations than white Americans due to dark skin pigmentation and the fact that most vitamin D comes from solar UVB exposure. In the period 2001-4, 25(OH)D concentrations for women aged 20-39 years were 14 ng/mL for blacks and 28 ng/mL for whites [3]. Vitamin D disparities has been proposed to explain black-white disparities in adverse birth outcomes [4]. Low 25(OH)D concentrations are also associated with adverse pregnancy outcomes such as preterm birth [5,6], and obesity [7]. Parathyroid hormone concentration has been found directly correlated with gestational diabetes [8], but parathyroid hormone concentrations are inversely correlated with 25(OH)D concentrations although also modified by age [9].

A vitamin D randomized controlled trial conducted with black, Hispanic, and white pregnant women in South Carolina found that it took 4000 IU/d vitamin D3 to raise 25(OH)D concentrations to above 40 ng/mL and normalize 1,25-dihydroxyvitamin D concentrations [10]. 1,25-dihydroxyvitamin D controls expression of many genes, so this function is very important during fetal development. No adverse effects were reported such as hypercalcemia.

References 1. Min CJ, Ehrenthal DB, Strobino DM. Investigating racial differences in risk factors for primary cesarean delivery. Am J Obstet Gynecol. 2015 Jan 28. pii: S0002-9378(15)00085-X. 2. Merewood A, Mehta SD, Chen TC, Bauchner H, Holick MF. Association between vitamin D deficiency and primary cesarean section. J Clin Endocrinol Metab. 2009;94(3):940-5. 3. Ginde AA, Liu MC, Camargo CA Jr. Demographic differences and trends of vitamin D insufficiency in the US population, 1988-2004. Arch Intern Med. 2009;169(6):626-32. 4. Bodnar LM. Simhan HN. Vitamin D may be a link to black-white disparities in adverse birth outcomes. Obstet Gynecol Surv. 2010; 65(4): 273–284. 5. Bodnar LM, Klebanoff MA, Gernand AD, et al. Maternal vitamin D status and spontaneous preterm birth by placental histology in the US Collaborative Perinatal Project. Am J Epidemiol. 2014;179(2):168-76. 6. Wagner CL, Baggerly C, McDonnell SL, et al. Post-hoc comparison of vitamin D status at three timepoints during pregnancy demonstrates lower risk of preterm birth with higher vitamin D closer to delivery. J Steroid Biochem Mol Biol. 2014 Nov 13. pii: S0960-0760(14)00268-4. doi: 10.1016/j.jsbmb.2014.11.013. [Epub ahead of print] 7. Drincic AT, Armas LA, Van Diest EE, Heaney RP. Volumetric dilution, rather than sequestration best explains the low vitamin D status of obesity. Obesity (Silver Spring). 2012;20(7):1444-8. 8. Kramer CK, Swaminathan B, Hanley AJ, et al. Vitamin D and parathyroid hormone status in pregnancy: effect on insulin sensitivity, β-cell function, and gestational diabetes mellitus. J Clin Endocrinol Metab. 2014;99(12):4506-13. 9. Valcour A, Blocki F, Hawkins DM, Rao SD. Effects of age and serum 25-OH-vitamin D on serum parathyroid hormone levels. J Clin Endocrinol Metab. 2012;97(11):3989-95. 10. Hollis BW, Johnson D, Hulsey TC, et al. Vitamin D supplementation during pregnancy: double-blind, randomized clinical trial of safety and effectiveness. J Bone Miner Res. 2011;26(10):2341-57.

Disclosure I receive funding from Bio-Tech Pharmacal, Inc. (Fayetteville, AR), MediSun Technology (Highland Park, IL), and the Vitamin D Council (San Luis Obispo, CA).

On 2015 Feb 12, Brian Clark commented:

We (Brian C. Clark and Jack Blazyk) published an opinion article in the “In My View” section of the August 2014 issue of The Journal of The American Osteopathic Association (JAOA) titled “Research in the Osteopathic Medical Profession: Roadmap to Recovery.” Four of our clinical colleagues in the Department of Osteopathic Manipulative Medicine (OMM) at our home institution, the Ohio University Heritage College of Osteopathic Medicine, responded to our article with the letter-to-the-editor indexed above. As stated in the “Editor’s Note” at the end of their letter-to-the-editor, "The JAOA declined to publish the response submitted by Drs. Clark and Blazyk.”

Since the JAOA denied us the opportunity to reply to the letter in print, we are posting our response here on PubMed Commons (see follow-up post below). When the journal editors attempted to alter our reply, we stated that "we are not willing to make any further changes to our response. Since our article was clearly defined as an opinion piece, we feel that we are entitled to state our opinion, particularly with regard to our response to Walkowski et al.'s letter-to-the-editor. Is it the JAOA's intent to edit or censor their letter? If not, we believe that we should be afforded the opportunity to reply according to our beliefs and principles. If the decision is not to publish our response, we request a brief statement that the authors and the journal were unable to agree on an acceptable response.”

On 2015 Feb 12, Brian Clark commented:

We welcome the correspondence from Walkowski and colleagues submitted in response to our article titled “Research in the Osteopathic Medical Profession: Roadmap to Recovery.” We address their questions and criticisms as follows:

Use of NIH Funding Data to Compare Research by Institutional Type

While it might be useful to compare different disciplines according to the number of institutional research FTE, these data are not easily obtainable nor publicly available. It seems highly unlikely, though, that any normalization procedure would reveal serious research strength within osteopathic medical schools in this regard, as our NIH funding levels are negligible. Is not this criticism by the correspondents an admission of the unfortunate reality that our osteopathic medical schools lack sufficient numbers of faculty trained in and committed to research?

We recognize that there are many impactful research findings arising from non-NIH funded studies and did not mean to imply, that for research to be valued, it must be funded by NIH. We simply chose this metric because the NIH peer-review process is rigorous and respected, and NIH funding is the typical standard by which medical schools as well as other health professional schools are compared for stature in research and scholarly activity.

OMM & EBM

Due to word limitations we were unable to provide more examples of unsubstantiated applications of osteopathic manipulation. We agree that there is clearly growing evidence for the efficacy of OMM to treat certain conditions, particularly low back pain, and that more work needs to be done. An example of the tension between reliance on historical tradition vs. evidence-based practice, however, is the intense training that many osteopathic medical schools offer in the use of diagnostic palpatory tests. For more than three decades, scientists and clinicians have investigated the reliability of many diagnostic tests, with systematic reviews of the literature finding that motion and landmark location diagnostic tests have poor inter-rater reliability [1-3]. Even the most rigorous reliability studies fail to demonstrate acceptable reliability rates for most diagnostic palpatory tests [4]. In light of the poor inter-rater reliability of palpatory diagnosis, validity cannot possibly be addressed. This raises the question of why so much time and effort is invested in palpatory diagnosis training and in promoting its value in osteopathic clinical decision-making. We simply provide this as one example to support our argument.

Why hold OMM to a different standard than other fields of medicine?

We did not intend to single out OMM as the only area that lacks a sufficient evidence base to warrant acceptance as a medical standard of care. The following example was included in our original manuscript, but was excised by the JAOA editors. The AOA recognizes a specialty college in ‘Prolotherapy Regenerative Medicine’ despite the lack of evidence of its efficacy for the treatment of musculoskeletal pain (e.g., to our knowledge, all MedLine-indexed systematic reviews or meta-analysis reports suggest that prolotherapy is either ineffective or inconclusive, at best) [5-13]. Since the osteopathic profession is ideally positioned and has an inherent responsibility to take the lead in musculoskeletal research, examining the utility of interventions such as prolotherapy by an objective, systematic approach is certainly reasonable. Whether or not physicians should be using prolotherapy to treat their patients may be debatable, but is it appropriate for the AOA itself to recognize Prolotherapy Regenerative Medicine as a specialty college? We strongly encourage the AOA, as well as osteopathic medical schools, to examine the balance between creating a unique identity versus the importance of accepting and assimilating scientific and clinical evidence that must ultimately determine best treatments and advances in healthcare.

Should OPP (osteopathic principles and practices) research be encouraged and supported?

While we concur that OPP research should be encouraged and supported, we questioned whether the AOA Council on Research should focus all of its attention and resources on OPP-related research at the expense all other areas of research critical to advancing human health, particularly related to the delivery of primary care.

Other thoughts:

• We did not intend for this article to be perceived as divisive or territorial (as stated by Walkowski and colleagues). In fact, one of our peer reviewers in the JAOA review process noted that “…every critical statement is substantiated with data and cannot possibly be taken as mean-spirited or as an attack on the profession. On the contrary, the tone of this paper is one of genuine concern for the DO profession, attempting to help in a positive way to shape the future research agenda.” To be explicitly clear, our goal in publishing this paper was not only to point out the relative lack of scholarly activity and research focus in osteopathic medical schools, but to offer specific steps to improve this situation.

• The AOA Commission on Osteopathic College Accreditation (COCA) must begin to enforce its research accreditation standards. Many of the existing osteopathic medical schools have little or no infrastructure to support research. Moreover, there are an additional 13 proposed osteopathic medical schools on the drawing board (as of 17-June-2014, 13 entities that have requested ‘Applicant status’, which is the first step in seeking accreditation). Will COCA continue to approve new schools, as well as renew accreditation to existing schools, that do not significantly contribute to developing new knowledge and improving healthcare through scientific inquiry, as mandated by COCA Standard Seven? The time is long overdue for the leadership of the osteopathic profession to act by putting teeth into its accreditation standards.

• Lastly, we agree wholeheartedly with Walkowski and colleagues that a team-based approach that synthesizes the respective expertise of clinicians and scientists is critical to impactful health-related research; however, we strongly disagree with their suggestion that: “We are first osteopathic, and it is that quality that serves to primarily employ and support our basic science faculty. To that end, it is the job of each researcher in our colleges to support the philosophy and practice of osteopathic medicine by actively designing and engaging in studies that support or refute the current science around that practice.” The notion that non-physician researchers at osteopathic institutions should confine their research to the philosophy and practice of osteopathic medicine is antithetical to free and unfettered scientific inquiry and discovery. As we stated in our article, “this approach marginalizes our profession by ceding new developments in the vast panoply of modern health care not only to MDs but also to all other research-driven health care professionals.” We argue that the job of folks like us (i.e., PhD researchers) is not to support any particular philosophy, but rather to constructively criticize and question the rational basis underlying any area of medical practice that might advance medical care. This is what medically-oriented PhD scientists, like ourselves, are trained to do.

Are osteopathic medical schools, the AOA, and COCA ready and willing to take the first steps toward improving our stature in research and scholarly activity in order to elevate our standing among our healthcare colleagues and the general public? Now is the time for action.

Brian C. Clark, PhD and Jack Blazyk, PhD Ohio University

On 2015 Feb 12, Brian Clark commented:

REFERENCES

1.Seffinger et al. Spine, 2004. 29(19): p. E413-25.

2.Stochkendahl et al. J Manip Physiol Thera, 2006. 29(6): p. 475-85, 485 e1-10.

3.van der Wurff et al. Manual Therapy, 2000. 5(1): p. 30-6.

4.Degenhardt et al. J Am Osteo Assoc, 2010. 110(10): p. 579-86.

5.Chou et al. Spine, 2009. 34(10): p. 1078-93.

6.Dagenais et al. Spine J, 2005. 5(3): p. 310-28.

7.Dagenais et al. Spine J, 2008. 8(1): p. 203-12.

8.Krogh et al. Am J Sports Med, 2012.

9.Rabago et al. Clin J Sport Med, 2005. 15(5): p. 376-80.

10.Rabago et al. Br J Sports Med, 2009. 43(7): p. 471-81.

11.Staal et al. Cochrane Rev, 2008(3): p. CD001824.

12.Staal et al. Spine, 2009. 34(1): p. 49-59.

13.Yelland et al. Spine, 2004. 29(19): p. 2126-33.

On 2015 Feb 12, Brian Clark commented:

None

On 2015 Feb 12, Brian Clark commented:

None

On 2013 Jun 13, Karl Broman commented:

A hugely influential paper, worth spending the time to work out the unmentioned details. It covers basically everything except the permutation test (see Churchill GA, 1994)

On 2015 Apr 27, David Keller commented:

How much conflict of interest is acceptable for an author arguing for a controversial treatment?

The authors of the review paper “Testosterone and Cardiovascular Risk” [1] argue for the safety and therapeutic benefits of treating aging men with supplemental testosterone (which they call "T"), claiming health-enhancement beyond the simple correction of any T deficiency which may be present. Unfortunately, there is a lack of data from randomized, controlled trials to prove the safety or efficacy of widespread T supplementation for aging men. The authors use the existing observational data to argue that the benefits of routine testosterone treatments will far outweigh the faint signals of cardiovascular harm which have been detected. Their implied message is that aging men should not be denied the benefits of testosterone supplementation while we await the definitive large, randomized study confirming the observed associations of “T” with positive health outcomes.

Their arguments are reminiscent of those favoring routine post-menopausal estrogen replacement, prior to the Women's Health Initiative's disappointing results. Is it possible that the decline of sex hormone levels with age in both men and women is a natural process that should not be tampered with? Apparently not, according to the many pharmaceutical companies which market testosterone products, listed in the “Competing Interests” section of this paper.

For example, Auxilium, a pharmaceutical company specializing in trans-dermal testosterone products, paid doctors over $1.5 million last year [3]. The fifth-listed author of this paper received $82,445.33 in speaker’s fees, mostly for the Auxilium testosterone product Testim [4], at times giving talks at the rate of almost one per week. It is hard to imagine that any physician could remain unbiased by such payments. If he were to express doubts about the level of evidence supporting the safety or efficacy of administering testosterone for general health enhancement, he would risk losing risk a substantial chunk of income. Other authors of this paper accepted similar payments, including the lead author [2].

The degree of financial conflict of these authors causes me to question the pro-testosterone message of this paper. The pharmaceutical manufacturers could have funded a definitive randomized, controlled trial of testosterone with the money they have paid in speaker’s fees for “T” proponents to rehash observational data. Epidemiologists caution us that observational data may be used to generate hypotheses, but not to prove them; such data cannot establish the safety or efficacy of any intervention.

That is why reasonably cautious physicians should not prescribe testosterone to aging men for general health enhancement until a randomized, controlled trial proves the safety and benefits of doing so.

References

1: Morgentaler A, Miner MM, Caliber M, Guay AT, Khera M, Traish AM. Testosterone Therapy and Cardiovascular Risk: Advances and Controversies. Mayo Clin Proc. 2014 Nov 1. Review. PubMed PMID: 25636998.

2: Open Payments CMS Website, searched for “Morgantaler” on 3/1/2015 https://openpaymentsdata.cms.gov/

3: Open Payments CMS Website, searched for “Auxilium” on 3/1/2015 https://openpaymentsdata.cms.gov/

4: Open Payments CMS Website, searched for “Mohit Khera” on 3/1/2015 https://openpaymentsdata.cms.gov/

On 2015 Feb 01, William Grant commented:

The paper by Jorde and Grimes outlines the case for conducting more vitamin D randomized controlled trials (RCTs) [1]. They also point out that RCTs conducted on those with low baseline 25-hydroxyvitamin D [25(OH)D] concentration are more likely to find beneficial effects of vitamin D supplementation than those with higher baselines. In agreement with this point, we just published a review of vitamin D RCTs and biomarkers of inflammation. Among the 22 trials with baseline 25(OH)D concentration below 47 nmol/L, 49% found reduced biomarkers of inflammation while for the 12 trials with baseline 25(OH)D concentration above 48 nmol/L, only 27% did [2]. In addition, achieved 25(OH)D concentration was relatively unimportant.

Robert Heaney recently presented guidelines for designing nutrient RCTs. The key steps for vitamin D RCTs include starting with an understanding of the 25(OH)D concentration-health outcome relation, generally from observational studies, measure 25(OH)D concentrations of prospective participants, include only those with 25(OH)D concentrations near the low end of the relation, supplement with enough vitamin D3 to raise 25(OH)D concentrations to near the upper end of the relation, remeasure 25(OH)D concentrations, and optimize conutrient status [3]. Few vitamin D RCTs have been designed in accordance with these guidelines, including the major ones currently underway.

As to the concern about J- an U-shaped 25(OH)D concentration-health outcome relations, one of the reasons for such findings appears to be that those with the highest 25(OH)D concentrations started taking vitamin D supplements late in life, possibly after developing some vitamin D deficiency conditions such as osteoporosis. In support of this hypothesis, two similar observational studies of 25(OH)D concentration and frailty conducted in the United States found different results: for men, there was a nearly linear inverse relation between 25(OH)D and frailty [4] while for women, there was a U-shaped relation [5]. In the United States, postmenopausal women are often advised to take vitamin D but older men are not.

One of the emerging topics of research is whether the observational studies finding inverse correlations between health outcomes and 25(OH)D concentrations might be due to non-vitamin D effects of solar UV exposure. There is mounting evidence that this may be the case for at least three types of health outcomes.

For many types of cancer, geographical ecological studies find inverse correlations between solar UVB doses and cancer incidence and/or mortality rates [6]. A mouse model study recently found that UVB exposure was more effective in slowing the progression of intestinal tumors than was oral vitamin D intake when both raised 25(OH)D concentrations by similar amounts [7].

Several recent studies have found that there are non-vitamin D effects associated with solar UVB exposure for multiple sclerosis [8-11].

Long wave UV (UVA) has been found to lower blood pressure [12], a risk factor for cardiovascular disease.

The mechanisms whereby UVB reduces the risk of disease independent of vitamin D are not well known and determining what they are remains an active field of research.

Based on the knowledge to date, what seems to be a prudent policy is spending time in the sun daily when it is possible to make vitamin D, generally when the solar elevation angle is greater than 45 deg. [13] and taking vitamin D supplements when not.

References 1. Jorde R, Grimnes G. Vitamin D and health: The need for more randomized controlled trials. J Steroid Biochem Mol Biol. 2015 Jan 27. pii: S0960-0760(15)00033-3. doi: 10.1016/j.jsbmb.2015.01.021. [Epub ahead of print] Review. 2. Cannell JJ, Grant WB, Holick MF. Vitamin D and inflammation. Dermato-Endocrinology. 2015;6(1): e983401-1-10. DOI:10.4161/19381980.2014.983401 3. Heaney RP. Guidelines for optimizing design and analysis of clinical studies of nutrient effects. Nutr Rev. 2014;72(1):48-54. 4. Ensrud KE, Blackwell TL, Cauley JA, Cummings SR, Barrett-Connor E, Dam TT, Hoffman AR, Shikany JM, Lane NE, Stefanick ML, Orwoll ES, Cawthon PM; Osteoporotic Fractures in Men Study Group. Circulating 25-hydroxyvitamin D levels and frailty in older men: the osteoporotic fractures in men study. J Am Geriatr Soc. 2011;59(1):101-6. 5. Ensrud KE, Ewing SK, Fredman L, Hochberg MC, Cauley JA, Hillier TA, Cummings SR, Yaffe K, Cawthon PM; Study of Osteoporotic Fractures Research Group. Circulating 25-hydroxyvitamin D levels and frailty status in older women. J Clin Endocrinol Metab. 2010;95(12):5266-73. 6. Moukayed M, Grant WB. Molecular link between vitamin D and cancer prevention. Nutrients. 2013;5(10):3993-4023. 7. Rebel H, der Spek CD, Salvatori D, van Leeuwen JP, Robanus-Maandag EC, de Gruijl FR.UV exposure inhibits intestinal tumour growth and progression to malignancy in intestine-specific Apc mutant mice kept on low vitamin D diet. Int J Cancer. 2015;136(2):271-7. 8. Lucas RM, Ponsonby AL, Dear K, Valery PC, Pender MP, Taylor BV, Kilpatrick TJ, Dwyer T, Coulthard A, Chapman C, van der Mei I, Williams D, McMichael AJ. Sun exposure and vitamin D are independent risk factors for CNS demyelination. Neurology. 2011;76(6):540-8. 9. Zivadinov R, Treu CN, Weinstock-Guttman B, Turner C, Bergsland N, O'Connor K, Dwyer MG, Carl E, Ramasamy DP, Qu J, Ramanathan M. Interdependence and contributions of sun exposure and vitamin D to MRI measures in multiple sclerosis. J Neurol Neurosurg Psychiatry. 2013;84(10):1075-81. 10. Bjørnevik K, Riise T, Casetta I, Drulovic J, Granieri E, Holmøy T, Kampman MT, Landtblom AM, Lauer K, Lossius A, Magalhaes S, Myhr KM, Pekmezovic T, Wesnes K, Wolfson C, Pugliatti M. Sun exposure and multiple sclerosis risk in Norway and Italy: The EnvIMS study. Mult Scler. 2014;20(8):1042-1049. 11. Knippenberg S, Damoiseaux J, Bol Y, Hupperts R, Taylor BV, Ponsonby AL, Dwyer T, Simpson S, van der Mei IA. Higher levels of reported sun exposure, and not vitamin D status, are associated with less depressive symptoms and fatigue in multiple sclerosis. Acta Neurol Scand. 2014;129(2):123-31. 12. Liu D, Fernandez BO, Hamilton A, Lang NN, Gallagher JM, Newby DE, Feelisch M, Weller RB. UVA irradiation of human skin vasodilates arterial vasculature and lowers blood pressure independently of nitric oxide synthase. J Invest Dermatol. 2014;134(7):1839-46. 13. Engelsen O. The relationship between ultraviolet radiation exposure and vitamin D status. Nutrients. 2010;2(5):482-95.

On 2017 Dec 16, Y Uncu commented:

We would like to state that this comment might be misleading for the readers, since the issues mentioned in the comment has been previously brought into question and extensively evaluated. It was concluded that there is no scientific flaw accordingly. We would be glad to provide further information should the readers require. (yuncu@uludag.edu.tr)

On 2017 Dec 08, Nazan Bilgel commented:

How you've done a controlled randomized clinical trial by using a drug (misoprostol) that has been banned in Turkey since August 2012? When was this research done? I assume that you have done before 2012. Does this research have ethics committee approval? In the text you gave the dose of misoprostol 400 mg and on tables 400 microg, which is correct? Are vaginal and rectal forms of misoprostol in Turkey available? According to my knowledge misoprostol in Turkey is available only in oral form. How did you use a drug that is only available in oral form for vaginal and rectal usage? You should have to explain this in your text. Why did you use SPSS Version 10.0? This is a very old version of SPSS. Today version 23.0 is available. Could this study be a translation of the study which was presented at the 7th Uludag Gynecology and Obstetric Winter Congress in 2005 (7. Uludag Jinekoloji ve Obstetrik Kıs Kongresi, 2005) under the Turkish title “Postpartum Kanamanın Önlenmesinde Profilaktik Misoprostol Kullanımı Randomize Klinik Çalışma: Uncu G, Omak M, Karahasan M, Yılmaz A.” However the names of some authors are different in this Turkish study but the translation of the title from Turkish into English is same as your study: Prophylactic misoprostol for the prevention of postpartum hemorrhage: a randomized controlled trial

On 2015 Feb 08, Francis Collins commented:

I completely agree with Greg -- and access to data by participants is the explicit intention of the initiative. More details will be forthcoming in the next few months.

On 2015 Feb 05, Greg Lennon commented:

This initiative has great potential and deserves support, assuming participants are given direct access to the data collected about them.

On 2015 Feb 16, John Friesen commented:

The authors report that an atropine dose of 0.5 mg was dangerously low in this morbidly obese patient. They present evidence to support scaling the dose according to lean body weight. However, lean body weight cannot be used directly as a weight scalar: it must be increased(1) such that it is normalized to ideal body weight(2). In this way, safe adjustments can be made for drugs whose dosages scale with lean body weight.

1 Bouillon T, Shafer SL. Does size matter? Anesthesiology. 1998 Sep;89(3):557-60. Bouillon T, 1998

2 Friesen JH. Lean-scaled weight: a proposed weight scalar to calculate drug doses for obese patients. Can J Anesth. 2013 Feb;60(2):214-5. Friesen JH, 2013

On 2016 Nov 02, Zvi Herzig commented:

Thank you. Indeed, a mean daily caffeine intake for coffee drinkers of 374.7 mg/day is below EFSA's level for concern, but still rises to "high risk" using the approach of this study.

On 2016 Nov 02, Dirk Lachenmeier commented:

Thank you for providing the data about caffeine. While coffee was outside of our scope of addictions included in this research project, we actually published a previous paper Lachenmeier DW, 2012, which included a BMD for caffeine of 63 mg/day (human data for systolic pressure increase). While caffeine may not be associated with mortality, there is a range of reported adverse effects (see review in EFSA (2015) cited below). For this reason, the EFSA suggests that single doses of caffeine of more than 200 mg (about 3 mg/kg bw for a 70-kg adult) and habitual caffeine consumption of more than 400 mg per day may give rise to safety concerns (DOI: 10.2903/j.efsa.2015.4102).

On 2016 Nov 01, Zvi Herzig commented:

Had coffee been included it would be assigned a "high risk" MOE of ~4 for personal exposure, between cigarettes and cocaine.

This is based on the average animal oral LD50 for caffeine of 190.5 mg/kg (BMDL10 = 18.7) (link) and daily caffeine intake for coffee drinking of 374.7 mg (5.1 mg/kg) (link).

However, drinking coffee is not positively associated with mortality Crippa A, 2014, highlighting the limitations noted by the authors.

On 2015 Jan 31, Christopher Southan commented:

This atricle is complemented by resolution of the molecular structures in PubChem http://cdsouthan.blogspot.se/2015/01/the-drugs-of-2014-in-pubchem.html

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 NCT0158718. We believe the correct ID, which we have found by hand searching, is NCT01587183.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2016 Aug 27, Santosh Kondekar commented:

Its nice to note that medical fraternity globally is getting aware that childhood asthma is getting over diagnosed. By all means, it says that Asthma should not the diagnosis that is made empirically but should always be a diagnosis by exclusion. It may not sound easy but an attempt has been made to separate OTA[other than asthma] . So if we could exclude OTA, what remains is most likely asthma. Thus giving a refined knowledge/criteria to help in diagnosis of childhood asthma.Weinberger M et al had published such cases as pseudo asthma. I have enumerated criteria for OTA diagnosis at following link. http://childasthma.weebly.com/ota-other-than-asthma-or-asthma-like-illnesses.html

On 2016 Mar 15, Kathryn Kaiser commented:

A letter to the editor regarding errors observed in this article may be found at this link:

http://www.wjgnet.com/1007-9327/full/v22/i9/2867.htm

Re: Errors in Zhao et al (2015), Impact of enteral nutrition on energy metabolism in patients with Crohn's disease

World J Gastroenterol. Mar 7, 2016; 22(9): 2867-2868 Published online Mar 7, 2016. doi: 10.3748/wjg.v22.i9.2867

Kathryn A Kaiser, Brandon J George, David B Allison

On 2016 Apr 12, Bernard Baars commented:

This possibility is almost always dismissed or ignored in the general media. See a recent story in the Guardian, which is uniformly positive about LSD, based on a single brain imaging study. Like THC, which has long been associated with risk of psychotic episodes in vulnerable teenagers, basic cautionary messages do not seem to reach the public.

On 2015 Feb 25, Vincent DiGiacomo commented:

Note that support for the ability of RPSA to homo- and heterodimerize within cells was recently generated using bimolecular fluorescence complementation (BiFC) by Alqahtani F, 2014. It is unclear whether these dimers represent the protein forms referred to as "higher molecular weight (HMW) species" in this review.

For those wishing to examine this evidence, note that HMW RPSA/LAMR species (i.e. 67LR, 67-kDa LAMR, etc.) are generally accepted to be stable under the denaturing and reducing conditions of SDS-PAGE – as noted in the review. Alqahtani F, 2014 helpfully provides an immunoblot detecting the tagged-RPSA constructs within the cells used for the BiFC (supplemental information).

Each individual can evaluate the strength of the new evidence to determine whether it constitutes evidence that the identity of HMW species has been resolved. In my opinion, definitive identification remains unclear.

On 2015 Jan 30, John Denning commented:

So would this provide evidence to the VA administration that lower paid masters-level providers can be hired instead of Psychologists? Similar outcomes...so go with a lower-cost provider. I have not read the article, but this is an interesting point to consider.

On 2015 Jun 30, Jung Weon Lee commented:

Indeed, Na J, Ryu J, Kim HJ, and Nam SH should be recognized as the co-second authors.

2015.06.30 Jung Weon Lee

On 2015 Feb 18, Airton Stein commented:

This is quite an interesting article and reaching a conclusion in which it is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality.

On 2015 Jan 28, William Grant commented:

Vitamin D does reduce risk of upper respiratory infections!

The paper by Yawn and colleagues reported that the evidence for vitamin D for the treatment of respiratory diseases was weak since random controlled trials (RCTs) have not supported the observational studies finding inverse correlations between 25-hydroxyvitamin D [25(OH)D] concentrations and incidence of respiratory diseases [1]. However, the analysis of the RCTs and the literature search were not conducted well.

There have been two vitamin D RCTs that demonstrated a beneficial effect in reducing risk of influenza. The first was conducted on black post-menopausal women living on Long Island. Those taking 800 or 2000 IU/d vitamin D3 had significantly lower incidence of colds and influenza than those taking the placebo [2]. However, the same research group conducted a second vitamin D RCT on a similar group without finding a beneficial effect as noted in Ref. 1 [3]. The primary difference between the two trials was the baseline 25(OH)D concentration. As reported in Ref. 3, in the first one, it was 46.9±20.6 nmol/l (95% CI 43.9–50.39) while in the second one it was 64.3±25.4 nmol/L. The second was a vitamin D RCT conducted on school children in Japan. For those not taking vitamin D prior to entering the trial, there was a 64% reduction in incidence of type A influenza for those taking 1200 IU/d vitamin D3 compared to the placebo [4].

Another vitamin D RCT overlooked was conducted in Mongolia. In this study, school children with mean baseline 25(OH)D concentration of 7.0 (5.0–9.9) ng/mL (to convert ng/mL to nmol/L, divide by 2.5). were given 300 IU/d vitamin D3 which raised 25(OH)D concentration to 18.9 (15.5–22.9) ng/mL [5]. A significant reduction in acute respiratory infections was found.

Two negative studies were reviewed in Ref. 1. A study from New Zealand started with a baseline 25(OH)D concentration of 29 (SD, 9) ng/mL, achieved a 25(OH)D concentration of 48 ng/mL, and found no beneficial effect [6]. Another vitamin D RCT followed two groups, each with mean baseline 25(OH)D concentration near 25 ng/mL and achieved 25(OH)D concentration near 32 ng/mL [7]. Again, no significant effect of vitamin D supplementation was found.

Summarizing the findings from vitamin D trials, those trials that had baseline 25(OH)D concentrations below 50 nmol/L (20 ng/mL) found reduced risk of respiratory tract infections from taking vitamin D3 while those with higher baseline concentrations did not.

Robert Heaney recently outlined guidelines for optimizing designs of nutrients such as vitamin D [8]. The important points for vitamin D are to start with an understanding of the 25(OH)D concentration-health outcome relation, measure 25(OH)D concentrations, enroll only those with low 25(OH)D concentrations, supplement with enough vitamin D3 to raise concentrations high enough to see an effect, and remeasure 25(OH)D concentrations. Very few vitamin D trials satisfied these steps. Many 25(OH)D concentration-health outcome relations show rapid changes below 15 ng/mL with very little change after 30 ng/mL [9, 10]. Thus, vitamin D RCTs should seek to enroll people with baseline 25(OH)D concentrations below 20 ng/mL.

Additional evidence that vitamin D reduces risk of respiratory tract infections comes from an ecological study of influenza case-fatality rates in 12 communities in the United States from the 1918–1919 influenza pandemic. Case fatalities were generally due to pneumonia and occurred about 10 days after the influenza infection. In a comparison with solar UVB doses for summer or winter, rates were significantly lower in communities with higher solar UVB doses [11]. The mechanisms proposed were that vitamin D induces cathelicidin, which can kill bacteria, and reduction in the cytokine storm that often accompanies influenza. The cytokine storm can damage the lining of the lungs, thereby permitting the ever present bacteria to give rise to pneumonia. The influenza in that pandemic was type A H1N1.

Thus, there is plenty of evidence that vitamin D can prevent and treat upper respiratory tract infections.

References 1. Yawn J, Lawrence LA, Carroll WW, Mulligan JK. Vitamin D for the treatment of respiratory diseases: Is it the end or just the beginning? J Steroid Biochem Mol Biol. 2015 Jan 24. pii: S0960-0760(15)00029-1. doi: 10.1016/j.jsbmb.2015.01.017. [Epub ahead of print] 2. Aloia JF, Li-Ng M. Re: epidemic influenza and vitamin D. Epidemiol Infect. 2007;135(7):1095-6; author reply 1097-8. 3. Li-Ng M, Aloia JF, Pollack S, et al. A randomized controlled trial of vitamin D3 supplementation for the prevention of symptomatic upper respiratory tract infections. Epidemiol Infect. 2009;137(10):1396-404. 4. Urashima M, Segawa T, Okazaki M, Kurihara M, Wada Y, Ida H. Randomized trial of vitamin D supplementation to prevent seasonal influenza A in schoolchildren. Am J Clin Nutr. 2010;91(5):1255-60. 5. Camargo CA Jr, Ganmaa D, Frazier AL, et al. Randomized trial of vitamin D supplementation and risk of acute respiratory infection in Mongolia. Pediatrics. 2012;130(3):e561-7. 6. Murdoch DR, Slow S, Chambers ST, et al. Effect of vitamin D3 supplementation on upper respiratory tract infections in healthy adults: the VIDARIS randomized controlled trial. JAMA. 2012;308(13):1333-9. 7. Rees JR, Hendricks K, Barry EL, et al. Vitamin d3 supplementation and upper respiratory tract infections in a randomized, controlled trial. Clin Infect Dis. 2013;57(10):1384-92. 8. Heaney RP. Guidelines for optimizing design and analysis of clinical studies of nutrient effects. Nutr Rev. 2014;72(1):48-54. 9. Grant WB. Relation between prediagnostic serum 25-hydroxyvitamin D level and incidence of breast, colorectal, and other cancers. J Photochem Photobiol B, 2010;101(2):130–6. 10. Garland CF, Kim JJ, Mohr SB, et al. Meta-analysis of all-cause mortality according to serum 25-hydroxyvitamin D. Am J Pub Health. 2014;104(8):e43-50. 11. Grant WB, Giovannucci E. The possible roles of solar ultraviolet-B radiation and vitamin D in reducing case-fatality rates from the 1918–1919 influenza pandemic in the United States. Dermatoendocrinol. 2009;1(4): 215-9.

Disclosure I receive funding from Bio Tech Pharmacal (Fayetteville, AR), MediSun Technology (Highland Park, IL), and the Vitamin D Council (San Luis Obispo, CA).

On 2015 May 20, Bill Cayley commented:

This is a useful study, but it would have been helpful to know whether or not the non-everted wound closure was QUICKER.

On 2015 Feb 27, T Eugene Day commented:

This is an excellent use of simulation to tease out how complex factors influence ED crowding. In the real world, the (as the authors put it) "chaotic" nature of the ED can make identifying factors associated with crowding extremely difficult to understand. However, simulation allows us to make controlled experiments which reveal insight into system dynamics. This is an interesting and thoughtful approach to a difficult problem.

On 2016 Jan 03, Sargis Dallakyan commented:

Visit http://pyrx.sourceforge.net to learn about the new features in the latest PyRx releases.

On 2015 Feb 26, Anders von Heijne commented:

It would be of great interest if the thalamic volumes in this study were to be correlated with a simple linear measurement, such as Third Ventricular Witdh. If changes in TVW can be shown to correlate with cognitive impairment in multiple cohorts it would be much easier to implement in clinical practice than volumetric measures.

On 2015 May 25, Tove Alm commented:

Response to letter by Islam

Shahidul Islam refers to our research article in Science “Tissue-based map of the human proteome” (M. Uhlén et al 23 January, 2015, p. 394) and claims that “they have skipped the control experiments because that would slow down the productivity”. This is of course not true; a large portion of the resources for the project are invested in validation of the antibodies.

A considerable amount of the resources in the program have been used to perform control experiments for the antibodies displayed in the portal and a lot of effort has been put into the visualization of the primary data to allow the scientific community to explore the data behind the control experiments. At present, more than 60,000 antibodies have been validated using Western blots and high-density micro arrays and these efforts have been published in hundreds of articles from our group (www.proteinatlas.org/about/publications). The result in each application is also compared to RNA expression levels and what is known in literature. In addition, to further examine the antibodies, a pipeline for validation of antibody specificity using gene silencing has been established. The results are currently available for a subset of the antibodies in the Protein Atlas.

The open-source policy applied to all antibodies published on the Atlas allows transparency and users may themselves review the experiments supporting the specificity of a particular antibody through the “Antibody/antigen” page (see example: www.proteinatlas.org/ENSG00000141510-TP53/antibody).

The statement by Islam that the antibodies are available through Atlas Antibodies and therefore “reduces the reliability of the immunohistochemistry images” is also difficult to understand. The Human Protein Atlas includes antibodies from more than 40 commercial providers and all primary data supporting the respective antibody is shown as an open resource on the antibody/antigen page for each antibody (see example link above). In the Human Protein Atlas program, a requirement for including an antibody has from the start been that the corresponding antibody must be available to the scientific community through a commercial provider. This is important, since it allows for the use of the same antibody by all researchers interested in human biology and medicine.

As far as we know, there are no past or current efforts with a more comprehensive pipe-line of systematic antibody validations.

On 2015 Apr 19, Md. Shahidul Islam commented:

Immunohistochemistry images published in the “Human Protein Atlas” are not reliable

IN THE ARTICLE “Tissue-based map of the human proteome” (M. Uhlén et al 23 January, 2015, p. 394), the authors point out that they have produced more than 13 million tissue-based immunohistochemistry images by using 24,028 antibodies. These images are freely available from the “Human Protein Atlas” portal. However, when it comes to the interpretation of the images, the key issue is whether the antibodies detect only the proteins that they are intended to do, under the conditions of the immunohistochemistry experiments. What is not widely known is that the scientists behind the “Human Protein Atlas” publish the immunohistochemistry images without performing the proper control experiments. For interpreting immunohistochemistry images, it is essential to perform the appropriate control experiments (1, 2). They have skipped the control experiments because that would slow down the productivity. They have tested the specificity of the antibodies mainly in the protein microarray experiments, and assumed that the antibodies that turn out to be specific in the protein micro array experiments will be specific also in the immunohistochemistry experiments. This assumption is not correct. Only about 45% of these antibodies detect the intended protein in the Western Blot. Scientists cannot publish immunohistochemistry images in peer-reviewed journals, without appropriate control experiments (1, 2). “Human Protein Atlas” is an exception. Here, millions of immunohistochemistry images have been published without requiring any independent peer-review process. The antibodies used for generating the images are being sold by the “Atlas Antibodies”, founded by the researchers from the “Human Protein Atlas” project. This conflict of interest further reduces the reliability of the immunohistochemistry images.

Md. Shahidul Islam Department of Clinical Sciences, and Education, Södersjukhuset, Karolinska Institutet, SE-118 83, Stockholm, Sweden and Department of Internal Medicine, Uppsala University, Uppsala, Sweden. E-mail: shahidul.islam@ki.se

Reference List

1.  R. W. Burry, J. Histochem. Cytochem. 59, 6 (2011).
2.  A. Lorincz, Z. Nusser, J. Neurosci. 28, 9083 (2008).

On 2015 Apr 24, Björn Hallström commented:

We agree that it is not immediately obvious what the colors in Fig 1F refer to, and that this could have been better explained in the figure legend. However, the yellow bands refer to genes that have RNA evidence either from this study or from Uniprot. Since the categories ("Not detected" etc) are determined solely from our RNA data it is possible that Uniprot has RNA evidence for a gene that we could not detect. This is what the yellow band above "Not detected" in Fig 1F refers to. These are generally genes that are expressed in more specialized tissues that were not part of our panel of 32 tissues, such as retina, olfactory bulb and related to hair growth.

On 2015 Mar 05, University of Kentucky Systems Biology and Omics Integration Journal Club commented:

Figure 1F appears to have a significant discrepancy. The definition for the "Not Detected" category in the first column section of Figure 1F is defined as "FPKM < 1 for all tissues" in Table 1. The definition would indicate that there is no RNA evidence for putative protein coding genes in this category; however, there is a yellow band indicating significant number of these genes have RNA evidence.

On 2015 Jul 12, Guo-Liang Jiang commented:

Proposed revision of CT-based cervical and thoracic lymph node levels for esophageal cancer in UICC 7th version.Radiother Oncol. 2014 Nov;113(2):175-81. We correct the first author Liu M's affiliation as the following: 1. Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; 2.Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; 3.Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China

On 2016 Jun 03, Ewen Gallagher commented:

A detailed review on MEKK1 (encoded by Map3k1) and MAPK signaling, and looking at the roles of Map3k1 in cell death, survival and differentiation. Recent research relating to the genetic analysis of the MEKK1 PHD motif is included in the review (1).

Related work.(1) Charlaftis N, Suddason T, Wu X, Anwar S, Karin M, Gallagher E. The MEKK1 PHD ubiquitinates TAB1 to activate MAPKs in response to cytokines. The EMBO journal 2014; 33:2581-96.

On 2017 Jul 13, Randi Pechacek commented:

Katherine Dahlhausen described this paper after traveling to South America. She wrote of its important findings on microBEnet.

On 2017 May 04, Jeremy Horst commented:

Can the actual results of this study be extended to infer a role of human genes in the disease? The influence of sex on the relationship to and influence of the environment is known to be strong for this disease. No assessment of any genotype besides assumed XX vs XY was performed.

Also, a role for horizontal transmission of dental plaque bacteria from parents to children has been established. This obfuscates simple heritability estimates.

Are there any loci that have shown an association with disease or disease severity in different studies? Perhaps lactoferrin. Clearly there is a role when tooth-development genes are mutated, but these are rare and do not extend to the general population.

The conclusions here go to far in purporting genes as the cause of the difference in disease outcomes by sex.

On 2015 Feb 13, Amanda Capes-Davis commented:

The two cell lines used here are both HeLa. KB is not an oral cancer cell line. It was cross-contaminated by HeLa - most likely during establishment of the cell line in 1955 - and no authentic stocks are known.

A number of studies have used KB for testing of therapeutic activity and concluded that an effect will be relevant for oral cancer. Unfortunately that is not the case.

Cell lines can be easily tested for cross-contamination and an increasing number of journals require authentication testing before publication. In my view, authentication testing would address the widespread use of KB as a model for oral cancer.

Short tandem repeat (STR) profiling is the current consensus for authentication testing. Online databases can be used to compare a laboratory's result to HeLa and other commonly occurring contaminants.

For more information on STR profiling see: http://iclac.org/resources/human-cell-line-authentication/.

For a list of known cross-contaminated cell lines see: http://iclac.org/databases/cross-contaminations/.

On 2015 Nov 12, RUBEN ABAGYAN commented:

Additional disclosure. One of the authors, R.A., has an equity interest in Molsoft, LLC. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.

On 2015 Sep 20, Ralph Brinks commented:

Most guidelines in health economic modeling stress the importance of the quality of the input data for the results of an economic model [1]. The input data of the transition probabilities between the BMI groups in the model of this work is based on empirical data from Germany and a method, which is stated to be described in [3]. Essentially, the transition probabilities are estimated from age-specific prevalence data, which is a well-known problem in epidemiology [4]. The method used in [2], however, is inappropriate, which I will demonstrate by showing the magnitude of the error. Terminology here is similar to [2], the BMI groups are numbered: normal (1), overweight (2), obese (3). The transition probability from state x to state y is denoted by tpxy

Given the data of 53 year old males tp12 = 0.02159, tp23 = 0.01035, [2], and assumed that the probability of dying is 0.006 for all BMI groups [5], then at age 53 the prevalences in the respective BMI groups are about P(53) = (0.45, 0.3, 0.25), see Figure 2 of [2]. After simulating one cycle of the Markov model, we obtain the prevalence at age 54 as P(54) = (0.4402, 0.3067, 0.2531). If we now use Equation (1) in [2] to estimate tp12, we obtain (0.3067-0.3)/0.45 = 0.01489. Compared to tp12 = 0.02159, this is an relative error of -31%, a magnitude which exceeds the relative errors in the sensitivity analysis (+/-20%) by far. This is not acceptable.

Thus, I query whether the results of [2] are valid. Instead of using the inappropriate Equations (1) and (2) in [2] I suggest to use studies surveying the transition probabilities between BMI groups directly.

[1] Penaloza Ramos MC, Barton P, Jowett S, Sutton AJ. A systematic review of research guidelines in decision-analytic modeling. Value Health 2015; 18: 512-29.

[2] Sonntag D, Ali S, Lehnert T, Konnopka A, Riedel-Heller S, König HH. Estimating the lifetime cost of childhood obesity in Germany: Results of a Markov Model. Pediatr Obes 2015 [Epub ahead of print]

[3] Miller DK, Homan SM. Determining transition probabilities: confusions and suggestions. Med Dec Making 1994; 14: 52-58.

[4] Keiding N. Age-specific incidence and prevalence: a statistical perspective. J R Statist Soc A 1991; 154: 371-412

[5] Statistisches Bundesamt. Generationensterbetafeln Deutschland: Wiesbaden 2011.

On 2015 Nov 11, Luis Quadros commented:

It's impressive to reach such a conclusion with only 36 patients.

On 2016 Oct 13, Lydia Maniatis commented:

In addition to the circularity of the noise revelation, the claim in the abstract regarding "spatial pooling" is also misleading:

" Our results suggest that chickens use spatial pooling of cone outputs to mitigate photon-shot noise."

The results show nothing of the sort, since "spatial pooling" was introduced as a free parameter to aid in data-fitting. If we were to label this parameter "the tooth fairy" then the data would "suggest" that the tooth fairy mediates color discrimination.

Again, we are talking about cosmetic applications of concepts to data-fitting techniques and arguments consisting of multiple casual assumptions that license no such interpretation.

On 2016 Oct 05, Lydia Maniatis commented:

Thanks for your reply, Peter. I've copied it below and respond to the various points in the order they came up.

You: There are measurements of noise in the visual system of animals which we have cited in the paper, so I can not agree with you that there is no evidence for noise in the visual systems of animals.

Me: I think that all of the cited papers assume they are measuring "noise", without actually testing that assumption.

You: In this paper we are describing the smallest colour difference that chickens were able to discriminate to figure out the equivalent Weber fraction which describe these limits. Whether that is actually caused by noise or not we can not say from our experiment, but it is adressed in some of the cited literature.

Me: The title of your paper says "behavioural thresholds reveal receptor noise" and the abstract states that your "experiments allowed us to compare behavioural results wtih model expectations and determine how different noise types limit colour discrimination." So it sounds like a claim that your experiments did, in fact, corroborate the "noise" assumptions. In fact, the noise argument was never in any danger of falsification, because it was not tested, only assumed to be indirectly measurable. The confusion about this issue has seeped into other publications; the reason I was looking at yours was that Scholtyssek, Osorio and Baddeley (2016) claim that your paper "validated experimentally" the "receptor-noise limited model of Vorobyev and Osorio (1998)." This didn't seem likely, so I wanted to check.

You: We find, similar to other experiments, that there this Weber fraction is the same in relatively brighter light (thresholds are very similar) but that the Weber fraction we need to assume to describe the thresholds needs to be higher in dim light, consistent with addition of photon-shot noise.

Me: "consistent with" doesn't mean causally connected to. If the claim is about causality, this needs to be tested, not assumed. The adjustments and assumptions in general seem ad hoc.

You: Which has been shown to limit visual sensitivity in many experiments.

I think this applies in very, very low light conditions. But your experiment does not constitute a test that this is relevant to your results. Again, it is simply assumed, even though the idea that raw responses of neurons early in the hierarchy are transmitted directly to visual experience is not credible.

You: We are using the Receptor Noise Limited model to describe the data, it is a tool that can be used to make predictions in other scenarios as well.

Me: Why do you consider it a useful tool? Have its "noise" related assumptions ever been tested and corroborated? How? When Vorobyev and Osorio (1998) say that the model "predicted" some psychophysical data, they just mean that they were able to find some datasets that fit more or less, and some that didn't, not that they predicted beforehand which datasets would match. And again, general consistency alone does not justify uncritical acceptance of whatever qualitative assumptions are tacked onto the math.

You: Regarding Percepts: We are not talking about how the animals perceive the colours, but rather how they are able to discriminate them. Absolutely, there is much more in the visual system going on that we yet do not understand. But the photoreceptor cells are the input of the system and the limits of the photoreceptors are going to be important.

Me: First, discrimination implies perception, at least to the extent that two surfaces are perceived as same or different. Second, the limits of photoreceptors are not discernible in ordinary percepts. Correct me if I'm wrong, but you don't even seem to be acknowledging the complexity of the neural code for color, which involves combining cone activity to produce color experiences that can't be qualitatively analyzed on the basis of the individual cone activity, for example the fact that "red" plus "green" plus "blue" cone activity (or, e.g. "red plus green") produces the experience of grey or white. With four cones, the code will be even more complicated.

On 2016 Oct 05, Peter Olsson commented:

Dear Lydia Thank you for your interest and comments.

There are measurements of noise in the visual system of animals which we have cited in the paper, so I can not agree with you that there is no evidence for noise in the visual systems of animals.

In this paper we are describing the smallest colour difference that chickens were able to discriminate to figure out the equivalent Weber fraction which describe these limits. Whether that is actually caused by noise or not we can not say from our experiment, but it is adressed in some of the cited literature.

We find, similar to other experiments, that there this Weber fraction is the same in relatively brighter light (thresholds are very similar) but that the Weber fraction we need to assume to describe the thresholds needs to be higher in dim light, consistent with addition of photon-shot noise. Which has been shown to limit visual sensitivity in many experiments. We are using the Receptor Noise Limited model to describe the data, it is a tool that can be used to make predictions in other scenarios as well.

Regarding Percepts: We are not talking about how the animals perceive the colours, but rather how they are able to discriminate them. Absolutely, there is much more in the visual system going on that we yet do not understand. But the photoreceptor cells are the input of the system and the limits of the photoreceptors are going to be important.

On 2016 Oct 01, Lydia Maniatis commented:

From the article (I've broken up a single continuous paragraph for clarity (caps mine):

"We ASSUME that discrimination thresholds of visual systems are set by noise (Vorobyev and Osorio, 1998; Lind and Kelber, 2009b) and that noise can arise from different sources in different light conditions. Over a wide range of relatively high light intensities...

...we EXPECT that Weber's law holds, so that sensitivity changes proportionally to light intensity and a constant Weber fraction (थscribes the signal-to-noise ratio that sets discrimination thresholds (Donner et al., 1990; Osorio et al, 2004; Lind et al., 2014). Under these conditions...

...the main source of noise is PROBABLY transducer noise (Lillywhite and Laughlin, 1979; Howard and Snyder, 1983) originating at the later stages of signal transduction in the photoreceptors, possibly by fluctuations in cGMP levels (Angueyra and Rieke, 2013).

There are no electrophysiological measurements of noise in bird photoreceptors, but rough estimates of noise have been deduced from the results of behavioural experiments on spectral sensitivity (Maier, 1992; Vorobyev et al., 1998; Lind et al., 2014)."

There is no empirical evidence that there is "noise" in the visual system and that this noise affects perception. The assumption is, furthermore, so vague that it could not be tested; and in our experience as observers, percepts certainly aren't "noisy." The reference to deduction of "rough estimates of noise" is contingent on this same untested, untestable, and empirically implausible assumption.

In addition, the idea that the formed, conscious percept, the product of complex processing with outcomes that resemble inferential logic, (such as, for example, lightness constancy (which has been shown even in chicks)) can be used to detect the neural properties of particular sets of neurons (here photoreceptors) is untenable.

Explicitly, the authors assume that "the discrimination thresholds are set by photoreceptor noise, which is propagated into higher order processing." This is a huge assumption, given what is known about the very different receptive field properties of neurons as we go up the hierarchy, and in view of the fact that these higher levels affect the activity of lower levels via feedback. It implies, in effect, that we can ignore, suppress or control for the participation of all other neural populations and interactions in this system. It is a claim that clearly requires a bit more effort at argument, rather than the casual assumptions, expectations, references to "established" or "standard" methods, etc. being offered here.

I see the bun, the catsup, the mustard and the onion rings...but where's the beef?

Another fascinating though not original aspect of this article is that it assumes that if we fit two arbitrary "models" to a dataset, and one of them fits this dataset better than the other, then the former is "more probable" than the other. This is the "Bayesian" way (though I don't think Bayes himself would agree). The fact that both models are too vague even to test doesn't interfere with these probabilities, which are in any case "subjective" and thus reflect the authors' (and the reviewers and editor's, I guess) personal beliefs.

On 2015 Jan 25, David Mage commented:

We (Mage and Donner) agree 100% with the authors' conclusion that there could be a commonality of the terminal mechanisms of SIDS and SUDEP. Our research on SIDS, based upon the universal 50% SIDS male excess for equal numbers of males and females at risk, predicts that the SIDS causation is X-linked resulting in acute anoxic encephalopathy (See our abstracts 9076695, 15384886 and 24164639). We suggested that a presently unknown gene locus on the X with a protective dominant allele with frequency p = 1/3 is involved. It would code for a protein enzyme that would allow the respiratory control neurons in the brainstem to shift from aerobic oxidation to anaerobic oxidation during a transient episode of acute cerebral anoxia. The XY male would be at risk of not having this dominant ability with frequency q = 2/3 and the XX female would be at identical risk with frequency q x q = 4/9. For equal numbers of male and female infants at risk the ratio 2/3 to 4/9 = 1.5, giving the expectation of 3 males dying of SIDS for every 2 females dying of SIDS. The authors report that for their cited 85 cases of prone SUDEP that there were 51 male and 34 female patients which is exactly in the ratio of 3 male to 2 female as we predicted. They propose that the main mechanism of SUDEP in their study is the peripheral hypoventilation and suffocation secondary to complete or partial airway obstruction which could lead to potentially terminal acute cerebral anoxia. We suggest that this may be a fertile field for further investigation because, to our knowledge, there is no other hypothesis in the medical literature that can predict that both SIDS and SUDEP would have the same 50% male excess.

On 2015 Feb 06, Ryan Radecki commented:

Post-publication commentary: "Prednisone … for Pneumonia?"

The utility of antibiotics for eradication of bacterial pathogens from the lower respiratory tract is a given. Use of steroids – also known for their immunosuppressive properties – not so much.

But, one can imagine clinical utility for steroids in acute infection. Not every function of the immune system results in desirable patient-oriented effects. Immunologic host responses include release of many inflammatory cytokines responsible for organ dysfunction, and steroids are already part of accepted therapy for several specific manifestations of pneumonia. Based on prior results in smaller trials, these authors suspected use of steroids might be of benefit – both in mortality and in time to symptom resolution.

http://www.emlitofnote.com/2015/01/prednisone-for-pneumonia.html

On 2017 Sep 18, Konstantinos Farsalinos commented:

Although Jensen et al. mentioned in the 2015 NEJM research letter that the health risks of formaldehyde hemiacetal inhalation are unknown ("How formaldehyde-releasing agents behave in the respiratory tract is unknown..."), they made a calculation that the formaldehyde-attributable cancer risk from e-cigarette use is 5 to 15 times higher than from long-term smoking. These two statements are clearly contradictory, and the calculation of any cancer risk from formaldehyde hemiacetal emissions is invalid since no such risk has been established for these compounds. It is simply based on an unsubstantiated assumption that "inhaling formaldehyde-releasing agents carries the same risk per unit of formaldehyde as the risk associated with inhaling gaseous formaldehyde...". Additionally, the latter statement was further misinterpreted by the media that reported the cancer risk of e-cigarettes (total risk, not formaldehyde-attributable risk) being 5 to 15 times higher than smoking. This is extremely important because, according to Fowles and Dybing (http://tobaccocontrol.bmj.com/content/12/4/424.long), the formaldehyde-attributable cancer risk is less than 1% of the total cancer risk of smoking. Prof Peyton, one of the authors of the NEJM research letter, now claims that formaldehyde hemiacetals are different from gaseous formaldehyde. But then, why did he and his co-authors use the hemiacetal measurements to present the cancer risk of e-cigarettes relative to tobacco cigarettes, considering that literature data for gaseous formaldehyde emissions from tobacco cigarettes were used in the comparison?

In the recently published paper (https://www.nature.com/articles/s41598-017-11499-0), Salamanca et al. are comparing the results of an experimental method (NMR) with the results of an established and validated analytical method used to identify and measure aldehyde emissions. In our study, using a validated and widely accepted method, we found 89% higher levels of formaldehyde at 5 V than the level of formaldehyde hemiacetal reported by Jensen et al. in the NEJM research letter. Therefore, we did not underestimate formaldehyde levels. We did not reject the findings by Jensen et al. that, high formaldehyde levels can be produced when blindly testing e-cigarettes at inappropriately high power settings relevant to the atomizer used (in fact we found more, but in general our findings support their observations). However, this cannot be used as an indication that e-cigarette users are exposed to such extreme formaldehyde levels in their daily routine.

I would also like to remind that we used a product which is outdated and inefficiently designed, a design that has been abandoned since 2012. These products are not even available in the market in the European Union anymore. Recent atomizers release formaldehyde at levels orders of magnitude lower than the one we tested. Even if we assume, despite the lack of evidence, that formaldehyde hemiacetals carry the same health risk as formaldehyde and that DNP derivatization underestimates the total formaldehyde exposure, still e-cigarettes developed over that last 3 years (at least) emit by far lower formaldehyde than tobacco cigarettes. Finally, the comparison between tobacco and electronic cigarettes in formaldehyde emissions is based on measurements performed using the same analytical method (DNPH derivatization) for both products. The assumption about underestimation of formaldehyde by DNPH derivatization applies equally to tobacco cigarettes and electronic cigarettes (tobacco cigarettes contain a lot of PG and VG); thus the relative difference remains the same.

Recent studies have found that e-cigarettes release formaldehyde at levels corresponding to > 1900 cigarettes consumed per day (e.g. https://www.ncbi.nlm.nih.gov/pubmed/27461870). All these studies, which have been accompanied by press statements and wide media coverage, need to be replicated under verified realistic conditions. Science is defined by replication, and we hope that journal editors will accept the challenge of publishing studies that reject findings previously reported in the same journal. In any case, all our replication studies will be published in peer-reviewed journals.

In conclusion, our purpose was to replicate an experiment using a specific e-cigarette device, atomizer and liquid under verified realistic conditions in order to verify or reject the conclusion that e-cigarettes carry 5 to 15 times the cancer risk of tobacco cigarettes. Our study clearly identified that this statement is false, and this was evident even when we used a very outdated and inefficient e-cigarette product. Therefore, our study was a valid replication experiment that presented the clinical relevance of previous findings.

On 2017 Sep 14, David H Peyton commented:

We appreciate the feedback on our manuscript, and respect the concerns of the posters here as well as those of the authors of the 2017 Food Chem Toxicol. paper by Farsalinos et al., cited by Clive Bates below. We share in the common goal of maximizing harm reduction. However, the claim that the aforementioned manuscript embodies a “replication” of our study in NEJM is false and misleading. Unfortunately, this misunderstanding continues to propagate prior misinformation disseminated about our work published in the 2015 NEJM paper. As clearly stated in our 2015 manuscript, we discovered and measured the levels of formaldehyde hemiacetals, not gaseous carbonyl formaldehyde. The 2017 study by Farsalinos et al. only measured levels of carbonyl formaldehyde. The ongoing omission of this critical detail, as reflected in the posts below as well as in the recent claimed “replication” of our work, has led the authors (yet again) to the conclusion that high levels of formaldehyde are detectable by e-cigarette users only under “dry puff” conditions. As we have described in a very recent manuscript (https://www.nature.com/articles/s41598-017-11499-0), 35-45 % of the formaldehyde hemiacetals are not converted to the detectable form of formaldehyde using DNPH impinger or related sorbent tube methods. Accounting for an approximately 40% loss of detectable formaldehyde at a power level of 4V, which the authors described as “realistic use conditions,” affords levels of > ca. 1400 ug of formaldehyde consumed. This is essentially the same level of formaldehyde from smoking combustible cigarettes, again according to data in the manuscript by Farsalinos and co-workers. This means that the cancer risk from formaldehyde in the e-cigarette that was investigated in the so-called replication study, even at this modest power level, is the same as that for combustible cigarettes. In other words, e-cigarettes do not emit very high formaldehyde levels only in conditions that are averse to users. In addition, discussing ‘dry puffs’ with the study subjects and increasing the power levels in a non-random way do not seem best practice for generating unbiased human subject study results. Our further studies of the chemistry and health effects of e-cigarettes are ongoing, and will be reported in due course, in peer-reviewed journals.

On 2017 Sep 02, Clive Bates commented:

This study has now been replicated and its obvious flaws confirmed.

Farsalinos KE, Voudris V, Spyrou A, Poulas K. E-cigarettes emit very high formaldehyde levels only in conditions that are aversive to users: A replication study under verified realistic use conditions. Food Chem Toxicol. 2017; . [link]

Conclusion

The high levels of formaldehyde emissions that were reported in a previous study were caused by unrealistic use conditions that create the unpleasant taste of dry puffs to e-cigarette users and are thus avoided.

The high levels of formaldehyde reported by the authors occur only in "dry puff" conditions that would be too acrid and aversive for human users to withstand. The authors completely missed this human control mechanism yet went on to calculate cancer risks based on conditions that humans would never experience. The resulting media storm was deeply misleading and the result of the authors inappropriate reporting of cancer risks based on unrealistic exposures.

This research letter should have been withdrawn or corrected by the NEJM once the flaws were pointed out. Given the controversy and impact on public health arising from people being given misleading information about health risks, the journal should have proactively commissioned a replication study or at least published this one.

A correction by the authors could at least admit that cancer is a human condition and that the cancer risk calculations have no validity given that humans are not exposed toxins generated under dry puff conditions.

At the time of writing the paper has 138 academic citations and 386 media articles. How many people will have been misled into making decisions harmful to their health by this paper?

On 2016 Apr 20, Clive Bates commented:

The fundamental weakness in this study is a failure to control the vapourising temperature to the levels experienced by real human subjects, rather operating temperatures that create a sensory experience that can only be tolerated by laboratory machines. The artifically high operating temperatures account for the high levels of formaldehyde and similar detected in the study.

At high temperatures, e-cigarette vapour undergoes thermal decomposition and aldehydes, such as formaldehyde, will form. For human subjects, there is a control feedback that avoids this exposure - namely that the aerosol takes on a horrible harsh taste and the e-cigarette user stops vaping. This phenomenon is widely understood among users and is known as 'dry puff' or 'dry hit' and it is always avoided. No such control feedback exists for laboratory machines.

This is one of several studies that ignores this important effect - something that could have been easily remedied by involving human users to verify the puffing protocol and device configuration and voltage settings create a realistic human vaping experience.

While it is not incorrect, merely pointless, to measure and report the decomposition of vapour in these unrealistic conditions, it is not legitimate to go on to make and publicise calculations of cancer risk, which can only arise from human exposures.

A critique of this short but damaging paper was published in the journal Addiction with an exchange of letters (Disclosure - I am a co-author): Bates CD, Farsalinos KE. Research letter on e-cigarette cancer risk was so misleading it should be retracted. Addiction 2015;110:1686–7. doi:10.1111/add.13018 Link to critique in Addiction

A detailed critique and case for retraction under the COPE guidelines was provided and published as supplementary material in Addiction. Link to Complaint under the Code of Conduct of the Committee on Publication Ethics

Forty experts wrote to the New England Journal of Medicine to express concern about the paper. Their letter was also published as supplementary material in Addiction. Link to letter

The New England Journal of Medicine has not provided a substantive response to this complaint or offered a route for escalation at the journal, as it should do under COPE. The full engagement with NEJM is described here with a annotated document file here - Google Doc

On 2015 Sep 14, Ivan Oransky commented:

Critics have called for this paper to be retracted, and there has been extensive correspondence about it in Addiction: http://retractionwatch.com/2015/09/11/researchers-call-for-retraction-of-nejm-paper-showing-dangers-of-e-cigarettes/

On 2015 Mar 15, IGSJC - The International General Surgery Journal Club commented:

Author Tom Varghese (@TomVargheseJr) joined IGSJC and moderator Amalia Cochran (@AmaliaCochranMD) to discuss "Nonsteroidal Anti-inflammatory Drugs and the Risk for Anastomotic Failure" on Twitter March 10-11, 2015, from 5-9pm PDT. For the remainder of the month of March, JAMA Surgery has opened access to the article (available at http://j.mp/IGSJC-201503), and all are still welcome to contribute to the discussion on Twitter using the #IGSJC hashtag.

A transcript of the journal club chat is available at: https://storify.com/AmaliaCochranMD/march-2015-igsjc

On 2015 Mar 09, IGSJC - The International General Surgery Journal Club commented:

Author Tom Varghese (@TomVargheseJr) will be joining IGSJC and moderator Amalia Cochran (@AmaliaCochranMD) to discuss "Nonsteroidal Anti-inflammatory Drugs and the Risk for Anastomotic Failure" on Twitter March 10-11, 2015, from 5-9pm PDT. For the month of March, JAMA Surgery has opened access to the article (available at http://j.mp/IGSJC-201503), and all are welcome to contribute to the discussion.

For tips on getting started, read http://igsjc.wordpress.com/guide-for-new-twitter-users/. Then, read the article, and return to Twitter on March 10 to take part!

Search on Twitter for #IGSJC (https://twitter.com/hashtag/igsjc) for the latest info and to join the chat.

On 2015 Jul 18, Jan Tunér commented:

Not arguing against the results of this paper, but a problem with most studies trying to treat tinnitus with laser light is the lack of proper diagnosis of the patients. Quite a few of these have a somatosensory background (the problem is basicly muscluar). Irradiation into the ear will then have no effect.

References: Bjorne A, Agerberg G. Reduction in sick leave and costs to society of patients with Ménière´s disease after treatment of temporomandibular and cervical spine disorders: A controlled 6-year cost-benefit study. Cranio. 2003; 21 (2): 136-143. Bernhardt O, Gesch D, Schwahn C, Bitter K et al. Signs of temporomandibular disorders in tinnitus patients and in a population-based group of volunteers: results of the Study of Health in Pomerania. J Oral Rehabil. 2004; 31 (4): 311-319. Levine RA, Abel M, Cheng H. CNS somatosensory-auditory interactions elicit or modulate tinnitus. Exp Brain Res. 2003; 153 (4): 643-648. Tullberg M, Ernberg M. Long-term effect on tinnitus by treatment of temporomandibular disorders: a two-year follow-up by questionnaire. Acta Odontol Scand. 2006; 64 (2): 89- 96.

On 2015 Jan 22, Larry Parnell commented:

This paper was my selection for Paper of the Week for 19-23 Jan 2015.

On 2015 Feb 18, Arnaud Chiolero MD PhD commented:

Primordial prevention is a key strategy for initiating prevention of cardiovascular diseases early in life. This commentary gives an elegant point of view on some experimental evidence on childhood intervention to improve cardiometabolic health.

On 2016 Mar 28, Mones Abu-Asab commented:

The positive aspect of this review is that it highlights phylogenetics as “likely to have an important impact on patient care.” However, this is a rambling review on metastasis without a critical evaluation of the literature on the topic or good conclusions on how phylogenetics would make a difference in studying metastasis. It doesn’t discuss some experimental work on metastasis (e.g., PMID: 18755941), or analytical phylogenetic approaches that discuss metastasis or the conceptual framework of cancer progression (e.g., PMID: 21319991, 23548567).

On 2015 Feb 08, Arnaud Chiolero MD PhD commented:

Contrary to statements of several experts, this study suggests that cardiovascular health of children may not have worsened despite the increase in obesity.

On 2015 Jan 30, Alvaro Alonso commented:

It is well-known that food-frequency questionnaires (FFQ) are suboptimal tools to assess dietary sodium intake. Thus, not finding an association between FFQ-assessed sodium and the study endpoints is expected, but does not provide any useful information about the health effects of sodium intake.

On 2015 Feb 08, KEVIN BLACK commented:

This is a fascinating clinical problem. The following quote may be of interest:

"[T]hree of 20 patients with both TS and OCD met criteria for bipolar disorder [53]. Given a population prevalence for bipolar disorder of <1%, the 15% prevalence here is remarkable. However, a study from Spain found that 12% of 90 consecutively examined patients with TS had either bipolar disorder or schizoaffective disorder, and an additional 21% had bipolar II disorder or cyclothymia [54]. The majority of these patients (80%) also had OCD, and many of them reported fewer tics during depressive episodes and more with manic episodes [54]. This surprising prevalence of manic illness in TS+OCD patients is probably not due to excessive symptom reporting in general, as this group reported less panic disorder or agoraphobia than the other groups [53]. Further studies of this difficult to treat subgroup are warranted. ...

"53.    Coffey BJ, Miguel EC, Biederman J, Baer L, Rauch SL, O'Sullivan RL, et al. Tourette's disorder with and without obsessive-compulsive disorder in adults: are they different? J Nerv Ment Dis 1998; 186:201-206. ...

"54.    Berthier ML, Kulisevsky J, Campos VM. Bipolar disorder in adult patients with Tourette's syndrome: a clinical study. Biol Psychiatry 1998; 43:364-370."

-- from Black KJ, Mink JW: Neuropsychiatry of movement disorders. Curr Opin Psychiatry 1999; 12(3):313-319.

On 2015 Feb 25, Gerard Ridgway commented:

In relation to the failure "to replicate all the group differences in GMV reported in previous studies", it would be very helpful to extract GMV for the previously reported coordinates (or clusters) and to report the magnitudes of the group differences on the new data, for example like the plot in Figure 2 does for the significant cluster here. It would be more compelling to support an assertion of an absent effect on such an extracted summary by demonstrating that the confidence interval is reasonably narrow (i.e. confined to trivially small group differences) rather than just that the region is not significant (in this case, after correction for multiple comparisons).

It is also not made clear whether the methods closely match the unreplicated studies. For example, the smoothing of 4mm here seems very low for a VBM study (particularly one using cluster-extent inference), and it would be interesting to know whether previous studies have used similarly low smoothing, or more typical values such as 8mm. As another example, did all previous studies adjust for total intracranial volume? In cases like this, where there is a significant group difference in TIV, I think both the adjusted and unadjusted analyses can be of interest.

On 2015 Jan 26, David D Leedahl commented:

We appreciate this comment. The patient had an extensive list of allergies to antimicrobials, which included multiple beta lactams (penicillin, ertapenem, aztreonam) in addition to several additional antibiotics from other classes. The decision to initiate a desensitization protocol to ceftaroline on the general medical floor outweighed the risk of potentially inducing an allergic reaction. Whether or not the patient would have experienced an allergic reaction to ceftaroline without completing a desensitization protocol, we agree, is uncertain.

On 2015 Jan 20, Eric Macy commented:

An IgE-mediated allergy to ceftaroline was not confirmed in this patient by either skin testing or challenge. Only a very small minority of even clinically significant penicillin allergy confirmed individuals will have IgE-mediated reactions to any specific cephalosporin. Only a small minority of individuals with multiple drug intolerance syndrome have any underlying IgE-mediated allergy to any of the medications they have noted reactions associated with.

On 2016 Jan 20, Stephen Royle commented:

The analysis of cell migration presented in this paper was done using an early version of software which is now maintained at http://github.com/quantixed/CellMigration

On 2015 Mar 13, Albert Erives commented:

Animal genomes do not encode the eukaryotic ClpB chaperones, Hsp104 and Hsp78 (See: Metabolic and chaperone gene loss marks the origin of animals: evidence for hsp104 and hsp78 sharing mitochondrial enzymes as clients, PMID: 25710177). The so-called CLPB gene annotated in the human genome is a partial bacterial clp family sequence fused to an ankyrin-repeat containing domain. Phylogenetic analysis of this gene from humans and other animals puts it outside of the clpB/HSP104/HSP78 family (see Fig. S2 in the above reference).

On 2015 May 29, Hongjian He commented:

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

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

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

On 2015 Jan 27, William Grant commented:

The paper on hypovitaminosis D by Daniel Podd [1] is useful in drawing attention to the problem but has a number of factual errors. This comment suggests a number of corrections.

Ref. 1 states that vitamins D2 and D3 have equivalent biological activity. Vitamin D researchers disagree on this point [2]. A recent meta-analysis of vitamin D trials found that supplementation with vitamin D3 lowered mortality rate significantly by 10% while supplementation with vitamin D2 increased mortality rate by a non-significant 3 to 15% [3].

Regarding lower vitamin D levels for those who are obese, another suggestion is that volumetric dilution rather than fat sequestration that explains the findings [4]. However, both may be important.

Regarding cancer, the findings for vitamin D levels and breast cancer are very similar to those for colorectal cancer [5]. The problem in determining this has been that prospective observational studies with longer than three-years follow up have not found a significant inverse correlation between vitamin D levels and breast cancer incidence rates [6]. The reason is that breast cancer develops very rapidly, which is why mammography is recommended annually. Case-control studies consistently find strong inverse correlations between vitamin D levels and breast cancer incidence rates [6]. The evidence that solar UVB and vitamin D reduce the risk of cancer incidence and mortality rates for many types of cancer is strong based on geographical ecological studies and laboratory investigations of the mechanisms [7]. Vitamin D plus calcium supplementation has also been found to reduce risk of breast cancer [8].

Regarding vitamin D production from solar UVB: it is very difficult to impossible to make vitamin D in winter for about six months in locations pole ward of about 40 degrees [9]. When the solar elevation angle is below 45 degrees, it is difficult to make vitamin D since most of the UVB is scattered out [9]. Thus, time of day and season are very important considerations regarding vitamin D production. Also important is skin pigmentation. Black Americans have vitamin D levels about 40% lower than white Americans [10].

Regarding calcium supplementation, 1.5 to 2.0 g/d is too high. There is increased risk of cardiovascular disease with higher calcium intake [11]. A recent meta-analysis found that dietary calcium intake of 800 to 1000 mg/d was associated with the lowest risk of cardiovascular disease, with intakes above 1200 mg/d associated with significantly increased risk [12].

Regarding the best time to take vitamin D, it is with the largest meal of the day [13]. That way vitamin D stays in the intestines longer.

Regarding frequency of dosing, daily may be optimal. A meta-analysis found "Supplementation of intermittent, high dose vitamin D may not be effective in preventing overall mortality, fractures, or falls among older adults." [14]. By intermittent, they meant once or once a month. Others have shown good results for weekly dosing. Daily dosing is similar to being in the sun daily, which is the physiological way to produce vitamin D.

While there is mounting evidence that vitamin D has important health benefits [15], there is also mounting evidence that some of the benefits attributed to vitamin D may, in fact, be due to other effects of solar UVB exposure. Non-vitamin D effects of UV exposure have been found for multiple sclerosis [16, 17], hypertension/cardiovascular disease [18] and intestinal cancer [19]. Thus, midday sun exposure may be a better option for increasing vitamin D levels when possible.

An additional critique of Ref. 1 can be found at http://vitamindwiki.com/tiki-index.php?page_id=6196

References 1. Podd D. Hypovitaminosis D: A common deficiency with pervasive consequences. JAAPA. 2015;28(2):20-26. 2. Heaney RP, Recker RR, Grote J, et al. Vitamin D3 is more potent than vitamin D2 in humans. J Clin Endocrinol Metab. 2011;96(3):E447-52. 3. Chowdhury R, Kunutsor S, Vitezova A, et al. Vitamin D and risk of cause specific death: systematic review and meta-analysis of observational cohort and randomised intervention studies. BMJ. 2014;348:g1903. 4. Drincic AT, Armas LA, Van Diest EE, Heaney RP. Volumetric dilution, rather than sequestration best explains the low vitamin D status of obesity. Obesity (Silver Spring). 2012;20(7):1444-8. 5. Grant WB. Relation between prediagnostic serum 25-hydroxyvitamin D level and incidence of breast, colorectal, and other cancers. J Photochem Photobiol B, 2010;101(2):130–6. 6. Grant WB. Effect of interval between serum draw and follow-up period on relative risk of cancer incidence with respect to 25-hydroxyvitamin D level; implications for meta-analyses and setting vitamin D guidelines. Dermatoendocrinol. 2011;3(3):199-204. 7. Moukayed M, Grant WB. Molecular link between vitamin D and cancer prevention. Nutrients. 2013;5(10):3993-4023. 8. Bolland MJ, Grey A, Gamble GD, Reid IR. Calcium and vitamin D supplements and health outcomes: a reanalysis of the Women's Health Initiative (WHI) limited-access data set. Am J Clin Nutr. 2011;94(4):1144-9. 9. Engelsen O. The relationship between ultraviolet radiation exposure and vitamin D status. Nutrients. 2010;2(5):482-95. 10. Ginde AA, Liu MC, Camargo CA Jr. Demographic differences and trends of vitamin D insufficiency in the US population, 1988-2004. Arch Intern Med. 2009;169(6):626-32. 11. Bolland MJ, Grey A, Reid IR. Calcium supplements and cardiovascular risk: 5 years on. Ther Adv Drug Saf. 2013;4(5):199-210. 12. Wang X, Chen H, Ouyang Y, et al. Dietary calcium intake and mortality risk from cardiovascular disease and all causes: a meta-analysis of prospective cohort studies. BMC Med. 2014;12:158 13. Mulligan GB, Licata A. Taking vitamin D with the largest meal improves absorption and results in higher serum levels of 25-hydroxyvitamin D. J Bone Miner Res. 2010;25(4):928-30. 14. Zheng YT, Cui QQ, Hong YM, Yao WG. A meta-analysis of high dose, intermittent vitamin D supplementation among older adults. PLoS One. 2015;10(1):e0115850. 15. Pludowski P, Holick MF, Pilz S, et al. Vitamin D effects on musculoskeletal health, immunity, autoimmunity, cardiovascular disease, cancer, fertility, pregnancy, dementia and mortality- a review of recent evidence. Autoimmun Rev. 2013;12(10):976-89. 16. Knippenberg S, Damoiseaux J, Bol Y, et al. Higher levels of reported sun exposure, and not vitamin D status, are associated with less depressive symptoms and fatigue in multiple sclerosis. Acta Neurol Scand. 2014;129(2):123-31. 17. Wang Y, Marling SJ, Beaver EF, et al UV light selectively inhibits spinal cord inflammation and demyelination in experimental autoimmune encephalomyelitis. Arch Biochem Biophys. 2014;567C:75-82. 18. Liu D, Fernandez BO, Hamilton A, Lang NN, et al. UVA irradiation of human skin vasodilates arterial vasculature and lowers blood pressure independently of nitric oxide synthase. J Invest Dermatol. 2014;134(7):1839-46. 19. Rebel H, der Spek CD, Salvatori D, et al. UV exposure inhibits intestinal tumour growth and progression to malignancy in intestine-specific Apc mutant mice kept on low vitamin D diet. Int J Cancer. 2015;136(2):271-7.

Disclosure I receive funding from Bio Tech Pharmacal (Fayetteville, AR), MediSun Technology (Highland Park, IL), and the Vitamin D Council (San Luis Obispo, CA).