On 2013 Nov 30, GianCarlo Panzica commented:

A previous study in the same rat model, demonstrated that also the nNOS system is altered in Tfm males, suggesting that also this system is depending by androgens for its full differentiation Martini M, 2008.

On 2014 Jan 02, Tom Kindlon commented:

Two letters were published in reply to this:

Two letters were published in reply to this piece. One is mentioned above, "What's the problem with sharing research committee's discussions?"

Then there is also my letter: BMJ. 2013 Sep 25;347:f5731. doi: 10.1136/bmj.f5731. "People want to learn as much as possible from the PACE trial for chronic fatigue syndrome" Kindlon T. Kindlon T, 2013

This second letter isn't free online. But it's just a slightly shortened version of an e-letter which can be read for free at: http://www.bmj.com/content/347/bmj.f5355/rr/659900 .

Following a response from the PACE Trial authors, I justified and expanded on my points in these two e-letters: (i) "Author's response: Criticisms of the PACE Trial were justified" http://www.bmj.com/content/347/bmj.f5963/rr/667107 (ii) "PACE trial: Simply giving a reason why an outcome measure was changed is not necessarily sufficient" http://www.bmj.com/content/347/bmj.f5963/rr/670755

On 2013 Oct 29, John Cannell commented:

Both isoforms of tryptophan hydroxylase are directly regulated by calcitriol and both isoforms have a vitamin D response element on their genes. Vitamin D down-regulates the peripheral hydroxylase and up-regulates the central tryptophan hydroxylase.

Wang, T. T. et al. Large-scale in silico and microarray-based identification of direct 1,25-dihydroxyvitamin D3 target genes. Mol Endocrinol 19, 2685-2695, doi:10.1210/me.2005-0106 (2005) Wang TT, 2005

Autistic children with vitamin D deficiency have high peripheral serotonin and low central serotonin and thus low central melatonin as they do not have the central serotonin necessary to make melatonin.

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

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take the American Pediatric Association's recommended vitamin D supplement of 400 IU/day.

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

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

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

However, these scientists appear to be in the minority. Until all autism researchers become cognizant of the wider body of autism research, we will continue to wonder how to prevent - and perhaps even treat - this modern day plague.

John J Cannell, MD Vitamin D Council http://www.vitamindcouncil.org

On 2014 Jan 08, Brett Snodgrass commented:

Dear Authors,

Thank you for the excellent article.

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

http://bit.ly/JTWearn

http://bit.ly/vasaThebesii

For additional commentary, please see

https://twitter.com/BrettSnodgrass1/status/417440058648428544

Comments and suggestions are welcome.

Thank you very much.

On 2013 Oct 31, John Cannell commented:

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

Prietl B, 2013

Kamen DL, 2010

Yang CY, 2013

Baeke F, 2010

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

John J Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org

On 2017 Oct 11, Bhaskar Chandra Mohan Ramisetty commented:

Does not seem like there is any useful information from this paper. The authors are apparently bold enough to correct their work!!! Good job. Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells. https://www.biorxiv.org/content/early/2017/10/09/200477.1

On 2016 Feb 29, Bhaskar Chandra Mohan Ramisetty commented:

http://biorxiv.org/content/early/2015/07/02/021162 http://journal.frontiersin.org/article/10.3389/fmicb.2016.01882/full

A biorxiv article with contradictory results. Regulation of yefM/yoeB TA system is independent of inorganic polyphosphate as well as ppGpp.

On 2014 Feb 19, james brophy commented:

Prompt revascularization of the culprit lesion with percutaneous coronary interventions (PCI) is a cornerstone in the treatment of acute myocardial infarction (STEMI). Numerous previous studies have suggested that simultaneous additional interventions of other non-culprit is at best unnecessary and at worst potentially dangerous. However this study that compared simultaneous ‘preventive angioplasty’ of non-infarct-related coronary arteries with ≥50% stenosis with primary PCI alone (with optimal medical treatment) found the composite endpoint of cardiac death, nonfatal myocardial infarction, or refractory angina was reduced by a staggering 65% (HR=0.35; 95% CI: 0.21-0.58, p<0.001). Is this result believable?

First, despite a very slow recruitment period of several years, the trial was prematurely stopped. Premature trial discontinuations for benefits are well known to overestimate treatment effects. This is especially problematic in this small unblinded study with only 16 excess 'hard' events and no formal statistical stopping rule described in their study protocol. The strongly positive results in prematurely stopped small trials are often not confirmed in bigger follow-up studies underlining the important role of chance that arises with repeated looks at the data. Moreover it has been shown that these small prematurely stopped trials have an increased likelihood of being published in high profile journals reinforcing this tendency to early stopping, as in the present case. Second, can medical treatment really be considered optimal in the control group when, despite STEMI and multi-vessel disease patients were discharged in less than 2 days without ischemic testing, the current standard of care (if additional angioplasty has not been performed during the original hospitalization). It seems only 1/3 of patients ever got any ischemic testing and this occurred only several weeks after the acute event, perhaps to late to influence potentially avoidable outcomes. Consequently was the “preventive” up front PCI group not being compared to an inferior "straw man" comparator? Third given the unblinded nature, could not the knowledge of untreated lesions have encouraged a detection bias in the search for clinical outcomes.

In an accompanying editorial, it was proposed that these additional interventions helped to pacify the inflamed coronary vasculature. However this argument seems specious as the coronary vasculature is diffusely and not locally inflamed. The biases discussed above seem a more likely explanation for this large and unexpected effect size.

On 2013 Sep 26, Carl Heneghan commented:

We wrote about all sorts of sports intervention in the BMJ last year and bare foot running was one of the interventions we looked. The evidence underpinning sports performance products: a systematic assessment.

Heneghan C, Howick J, O'Neill B, Gill PJ, Lasserson DS, Cohen D, Davis R, Ward A, Smith A, Jones G, Thompson M. BMJ Open. 2012 Jul 18;2(4). doi:pii: e001702. 10.1136/bmjopen-2012-001702. Print 2012. PMID: 22815461

Seems whilst there is lots of biomechanical evidence, as pointed out in the article, there is no actual clinical performance evidence that could aid the decision as to whether to use these shoes.

On 2017 Oct 18, Eric Lock commented:

None

On 2017 Oct 18, Eric Lock commented:

The software URL is yet again broken. Instead see

http://ericfrazerlock.com/Software.html , or https://github.com/lockEF/bayesCC

On 2015 Sep 03, Kenneth Daily commented:

Software URL broken - currently is:

http://www.tc.umn.edu/~elock/Software.html

On 2014 Jan 17, Amanda Capes-Davis commented:

A note regarding the tissue studied here: KB is not an epidermoid carcinoma cell line. The KB cell line is known to be cross-contaminated and is actually HeLa, a cervical adenocarcinoma cell line. For a database of cross-contaminated or otherwise misidentified cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2013 Dec 30, Ben A Inglis commented:

It seems to me that although the intent was to assess connectivity induced by reading a novel, in the absence of a control task there is no way to know whether the changes were due to the specific act of reading or due simply to the subjects' being engaged in a structured task over the study period. Surely, to be confident that the changes are due to reading, a second group of subjects should have been exposed to a control task that was as similar as possible to the novel reading. For example, control subjects could have been instructed to watch a dramatic TV mini-series, with each evening's exercise lasting approximately the same time as the reading. (Questioning of control subjects could have verified that the task was completed as instructed, in precisely the same manner as the test subjects had their reading task assessed.) An even better control would have been to use the same story but change the medium. For instance, the test subjects might have read the story while the control subjects listened to it on an audio book. Perhaps there is even need for a second control group; subjects are set a task to attend to each night, but there is no plot to follow. In sum, without assessing directly the effects of a structured attention task over the study period there is no way to be sure that reading per se is causing the connectivity changes.

On 2015 Jan 30, Peter Gøtzsche commented:

This meta-analysis was fatally flawed

Based on FDA trial data, Arif Khan et al. report that antipsychotic drugs lower total mortality in schizophrenia by more than 50% and that the drugs also lower suicides (1). These results agree very poorly with the fact that people with schizophrenia live about 20 years less than other people while almost all of them receive antipsychotics; that many experience excessive weight gains and diabetes because of the antipsychotics, which shorten their life substantially; and that a meta-analysis of old people found that double as many died when they got antipsychotics than when they got placebo (2).

It is difficult to understand how Khan, who has been principal investigator of more than 340 clinical trials sponsored by more than 65 pharmaceutical companies and 30 contract research organizations (1), can publish a meta-analysis that is so intensely misleading as this one (1). The fatal flaw in their analysis is that the authors used person-years instead of using persons. As pointed out in a letter to the editor, a person-year is not just a person-year (3). The average duration of placebo exposure was very short, only 33 days, as compared to 132 days on drug (1). Khan et al. seem to have included not only the double-blind phases of the trials but also safety extension studies (in which patients only receive active drug of course). Such analyses are notoriously unreliable, as those who continue on active drug are those who tolerate it. We need to look at deaths in relation to number of randomised patients, and then we can see that antipsychotics kill people, which we knew beforehand. The relative risk is 1.65, i.e. a 65% increase in total mortality on drug compared with placebo, and for suicides, the relative risk is 2.83.

Conflicts of interest: none.

1 Khan A, Faucett J, Morrison S, et al. Comparative mortality risk in adult patients with schizophrenia, depression, bipolar disorder, anxiety disorders, and attention-deficit/hyperactivity disorder participating in psychopharmacology clinical trials. JAMA Psychiatry 2013;70:1091-9.

2 Schneider LS, Dagerman KS, Insel P. Risk of death with atypical antipsychotic drug treatment for dementia: meta-analysis of randomized placebo-controlled trials. JAMA 2005;294:934–43.

3 Nordentoft M, Laursen TM. Was Risk of Suicide Underestimated? JAMA Psychiatry 2014;71:716.

On 2014 Oct 26, Nicholas Rosenlicht commented:

In evaluating the results of this trial it is important to note that the published results do not correspond to the primary outcomes specified in the trial’s original and updated registrations on ClinicalTrials.gov. The four primary outcome measures initially registered (10/7/2008) were: MADRS at 40 minutes, 120 minutes, 24 hours, and 7 days. These were expanded on 1/12/11 to include the MADRS at 240 minutes, 48 hours, 72 hours, biweekly for up to 4 weeks, and early termination. After publication (1/30/14) all Primary Outcomes except MADRS at 24 hours were removed from the ClincalTrials.gov registration. These changes can be tracked at: http://clinicaltrials.gov/archive/NCT00768430 It would be important to understand why the authors changed the outcome measures several times during the trial. These changes are not mentioned in the publication. The finding that ketamine, a dissociative anesthetic that is abused for its euphoric and other mind-altering properties, transiently suppresses MADRS scores is not surprising. It would be much more important clinically to demonstrate significant effects on the outcome measures at 2 to 4 weeks. These were not presented.

On 2013 Nov 01, Natalie Clairoux commented:

The submitted version of the manuscript is freely available here: https://papyrus.bib.umontreal.ca/xmlui/handle/1866/9023

On 2014 Apr 10, Alexander Klabnik commented:

I recomend as a collaborator

On 2014 Feb 04, Jean-Jacques Letesson commented:

In the bacteria and plasmid section of this paper, the readers should be aware that it is impossible to grow B. melitensis in the minimal medium stated "B. melitensis 16 M was routinely cultured in rich medium Tryptic Soy Broth (TSB) or in minimal medium GEM7.0 (MgSO4.7H2O 0.2 g/L, Citric acid•H2O 2.0 g/L, K2HPO4 10.0 g/L, NaNH4HPO4.4H2O 3.5 g/L, Glucose 20 g/L, pH 7.0)" All Brucella strictly require biotin, panthotenate, thiamine and nicotinamide as additional factors. In addition 20g/L of glucose is almost ten times as much as normaly needed.

On 2014 Mar 16, Jonathan Eisen commented:

Two of the authors of this paper have written a guest post on my "Tree of Life" blog discussing some of the "Story behind the paper". See Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

On 2013 Nov 08, Seth Bordenstei commented:

The Story Behind "Mom Knows Best: The Universality of Maternal Microbial Transmission"

What types of microbes do mothers transmit to their newborns and how universal is maternal microbial transmission throughout animals?

http://symbionticism.blogspot.com/2013/08/the-story-behind-mom-knows-best.html

On 2014 Oct 06, Anders von Heijne commented:

Yes, the abductive mode of thinking that Peirce described is really very crucial in all forms of diagnostics. Depending on the problem at hand we clearly use different logical strategies. This is a must read, together with Lawson AE1, Daniel ES. Inferences of clinical diagnostic reasoning and diagnostic error.J Biomed Inform. 2011 Jun;44(3):402-12. Sadly this sort of analysis seldom appears in clinical speciality journals. If you are lucky you can find articles on Dual System theory and Bayesian theory, but without abduction there is no place to start using these techniques. We all need a dose of metacognitive musings from time to time.

On 2015 Sep 25, Amanda Capes-Davis commented:

Great to see a paper looking at reproducibility of cell culture systems, in this case for replication of HuNoVs, important for the study of acute gastroenteritis. The authors note in their Materials and Methods that two cell lines are used for viral growth, INT-407 and Caco-2, and correctly state that INT-407 has been cross-contaminated with HeLa. So it makes sense that INT-407 is not a good model for culture of HuNoVs. INT-407 was found to be cross-contaminated with HeLa in the 1960s and there are no known authentic stocks remaining for the original intestinal culture; INT-407 has been completely replaced by HeLa cells. HeLa may form microvilli as shown here, but HuNoV replication is likely to require additional tissue-specific factors that HeLa cannot supply.

Failure of Caco-2 is more puzzling, considering that the authors used a well-known intestinal (colorectal adenocarcinoma) cell line that was successful for the previous study, and obtained their stock of Caco-2 from the same source. However, it is worth noting that viral replication can vary across different strains or subclones e.g. Carson & Pirruccello, PMID 23408555. Caco-2 is well documented as a cell line that can change phenotype with passaging e.g. Briske-Anderson et al, PMID 9083258.

For a list of known misidentified cell lines, please refer to http://iclac.org/databases/cross-contaminations/. It is also important to authenticate cell line stocks before use. Setting up in vitro culture systems takes a great deal of time - testing can save a great deal of heartache!

On 2015 Dec 02, David Keller commented:

Extended-release niacin reduced Lp(a) but not CV risk, when added to statin therapy

The AIM-HIGH trial yielded a 21% reduction in Lp(a) levels when high dose niacin was added to statin therapy, but without the expected additional reduction in cardiovascular (CV) events. This is puzzling because it is known that CV risk is correlated to Lp(a) level. Niacin is known to lower Lp(a) levels, which was again demonstrated in this study.

The Coronary Drug Project, conducted in the pre-statin era, demonstrated that monotherapy with high-dose niacin reduced recurrent nonfatal myocardial infarctions, cerebrovascular events, and overall mortality at 15 years compared with placebo [1]. However, more recent studies of patients taking appropriate baseline statin therapy did not demonstrate additional reduced CV risk due to the improvement in lipids caused by the addition of niacin.

All of the patients in this study were on appropriate statin therapy at baseline. Again, we see that adding niacin to baseline statin therapy somehow fails to yield the additional outcome benefits expected from niacin's improvements in cholesterol and Lp(a) levels.

Given the evidence of outcome benefits with niacin monotherapy, but not with niacin added to a statin, it may be that statins somehow negate niacin's outcome benefits, despite preserving its improvement of the lipid profile. If so, then statin-intolerant patients remain candidates for niacin therapy, unless and until future clinical trials fail to reproduce the outcome benefits niacin demonstrated in the Coronary Drug Project.

Reference

1: Canner PL, Berge KG, Wenger NK, Stamler J, Friedman L, Prineas RJ, Friedewald W. Fifteen year mortality in Coronary Drug Project patients: long-term benefit with niacin. J Am Coll Cardiol. 1986 Dec;8(6):1245-55. PubMed PMID: 3782631.

On 2013 Oct 23, Albert Erives commented:

The background motivation of this paper is well written and informative. The "fine structure" of transcriptional enhancers underlying animal development is worthy of study and it is refreshing to see affirmation that there may be a range of simple to structured regulatory DNAs. From this report on Svb target enhancers, it will be important to follow-up on whether there are functional consequences to the range of architectures.

Also of interest is the following. The authors note that: "[t]hese findings highlight a paradoxical discrepancy between the enrichment of putative BSs accumulated in Svb downstream genes and the limited number of those acting as cis-regulatory elements. Is there a role for this evolutionary accumulation of Svb-like motifs in Svb targets?" This is an important question that is related to the broader issues of homotypic site clustering and related phenomenon mentioned in this paper's background. Though my lab's work is nicely integrated into the introduction, there is one additional key study of ours that is most relevant to these issues: "Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers" (Crocker J, 2010). I suspect this one issue, and a difficulty in experimentally testing the function of every single sequence component of a homotypic site cluster, has facilitated the generally-assumed working model that each sequence component in a cluster or locus remains functional in the extant organisms from they have been isolated (I take issues with this model on several grounds). To some extent this is a question that preceded the more recent debate about "biochemical functionality" in the ENCODE data sets. This report is another step towards a more versatile, effective, and evolutionarily-grounded language of enhancer biology.

On 2014 Sep 15, Andrea Messori commented:

Bayesian models implemented under Winbugs: can they be considered the new standard for conducting a network meta-analysis?

When multiple agents are available to treat the same disease condition, network meta-analysis of randomized controlled trials (RCTs) has the purpose of synthesising the available evidence. In the application of this technique, both direct and indirect comparisons are made between individual treatments. Direct comparisons are those for which a “real” randomised study is available while indirect comparisons are those for which no real trial has been conducted.

Initial approaches for conducting network meta-analyses were designed to separately evaluate each indirect comparison; hence, there were as many separate analyses as the number of indirect comparisons [1,3]. More recently, the Bayesian approach for network meta-analysis has emerged as the new standard in this area [4-7]. This method relies on a sort of “all-in-one” modelling in which a single model incorporates the evidence available from all clinical trials and estimates, through a unified approach, all comparative results for both direct and indirect comparisons.

In network meta-analysis, the phases of literature search and data extraction do not differ from those commonly employed for standard meta-analysis [5,6]. As regards the type of end-points, network meta-analysis favours binary end-points [4] as opposed to continuous ones. Hence, irrespective of whether the analysis is aimed at evaluating effectiveness or safety, the starting material for conducting a network meta-analysis is given by the rates of end-point occurrence (i.e. numerator and denominator) for each arm of each RCT.

In present times, statistical modelling for network meta-analysis recognises its new standard in these Bayesian approaches based on an “all-in-one” model and implemented in the WINBUGS environment [4,7]. This approach has found a wide acceptance also because the methods and the software, developed by an authoritative institution (the NICE), are freely available [7]. The code for these estimations is available as fixed-effect model and random-effect model.

The Winbugs Bayesian model employs a random sequence of chains, called a Markov chain Monte Carlo simulation. Each chain must be run for a length of time sufficient to allow model convergence (burn-in) before estimating posterior probabilities. Typically, the random-effect logistic regression model is created according to the binary outcome of subjects reaching the end-point concerned. Randomization within each study is preserved by specifying each arm in each study separately, thus accounting for the effect of the comparator. Results are generally presented as odds ratio or log odds ratio. Heterogeneity among studies can be accounted by applying meta-regression techniques and by consequently generating an index of heterogeneity [4,7].

As regards the software, these analyses can be conducted by using the software package WinBUGS 1.4.3 (Cambridge, United Kingdom) in combination with the meta-analysis code developed by the National Institute for Health and Care Excellence[7]. Odds-ratio is the typical outcome measure of this software; however, odds-ratios can be converted into risk ratios or risk differences by application of standard equations [8,9]

Sobieraj and co-workers [10] have published an article that reviews all previously published studies that have adopted the Bayesian approach.

In conclusion, the present literature clearly indicates that Bayesian network meta-analysis can be considered the new standard in this field.

References

1. Lumley T. Network meta-analysis for indirect treatment comparisons. Stat Med 2002, 30; 21(16): 2313-24

2. Bucher HC, Guyatt GH, Griffith LE, Walter SD. The results of direct and indirect treatment comparisons in meta-analysis of randomized controlled trials. J Clin Epidemiol 1997;50(6):683–91

3. Wells GA, Sultan SA, Chen L, Khan M, Coyle D. Indirect treatment comparison [computer program]. Version 1.0. Ottawa: Canadian Agency for Drugs and Technologies in Health; 2009. Software available at:http://www.cadth.ca/preview/en/resources/itc-user-guide

4. Greco T, Landoni G, Biondi-Zoccai G, D'Ascenzo F, Zangrillo A. A Bayesian network meta-analysis for binary outcome: how to do it. Stat Methods Med Res. 2013 Oct 28.

5. Hoaglin DC, Hawkins N, Jansen JP,. et al. Conducting Indirect-Treatment-Comparison and Network-Meta-Analysis Studies: Report of the ISPOR Task Force on Indirect Treatment Comparisons Good Research Practices—Part 2. Value Health 2011;14:429-37.

6. Jansen JP, Fleurence R, Devine B, et al. Interpreting Indirect Treatment Comparisons and Network Meta-Analysis for Health-Care Decision Making: Report of the ISPOR Task Force on Indirect Treatment Comparisons Good Research Practices: Part 1. Value Health 2011;14:417-28.

7. NICE Clinical Guidelines, No. 92. National Clinical Guideline Centre – Acute and Chronic Conditions (UK). London: Royal College of Physicians (UK); 2010. Available at http://www.ncbi.nlm.nih.gov/books/NBK116530/ Accessed 14 August 2014

8. Zhang J, Yu KF. What's the relative risk? A method of correcting the odds ratio in cohort studies of common outcomes. JAMA. 1998 Nov 18;280(19):1690-1.

9. ClinCalc Website. Odds-ratio to risk ratio. http://clincalc.com/Stats/ConvertOR.aspx

10. Sobieraj DM, Cappelleri JC, Baker WL, Phung OJ, White CM, Coleman CI. Methods used to conduct and report Bayesian mixed treatment comparisons published in the medical literature: a systematic review. BMJ Open. 2013 Jul 21;3(7). pii:e003111. doi: 10.1136/bmjopen-2013-003111. Print 2013.

On 2014 Feb 23, Pei-Hui Wang commented:

PubM.Comm. is a funny tool!

On 2016 Dec 16, Alessandro Rasman commented:

CAREFUL APPLICATION OF THE RECOMMENDED PROTOCOLS IMPROVE REPRODUCIBILITY AND PERMIT COMPARISON AMONG CCSVI STUDIES. Posted by zambo on 15 Aug 2013 at 00:12 GMT http://journals.plos.org/plosone/article/comment?id=10.1371/annotation/a1ae22d2-49a5-4c0b-9b9d-dbb08773216b https://drive.google.com/file/d/0B_Ed_wxZvab3OWg4Y242NWFEQ3M/view?usp=sharing

On 2013 Oct 23, Stephen Shea commented:

What is the basis for the statement that CO2 is odorless? Because it is to humans? This paper that the authors cite (http://www.ncbi.nlm.nih.gov/pubmed/17702944) quite convincingly demonstrated low concentration responses to CO2 in the olfactory sensory neurons and main olfactory bulb?. What reason is there to conclude that these are trigeminal in origin? Aren't these neurons the most likely source of the responses you see in cortex? I don't see how you can make your central claim without inactivation of trigeminal and olfactory sensory neurons.

On 2014 May 22, Jacob Puliyel commented:

Post-marketing surveillance cannot properly estimate risks

The authors must be congratulated for conducting a study whose scope was so vast. However it must be recognized that RCTs are the best method to look for risks and benefits. Post-marketing surveillance is relied on to detect rare adverse events. It has severe limitations in quantifying the magnitude of risks. The present study highlights the problem well.

1 The authors estimate the risk of intussusceptions (IS) in two window periods after immunization. Previously surveillance had found that the incidence of IS was significantly increased in the first 3 weeks and more after the first dose than after the second dose. But that does not imply the risk of IS is limited to this window period alone. Only long term RCTs can really identify the full risk of IS after immunization and can categorically confirm that there is no risk in other periods.

2 For estimating reduction of diarrhea the authors use the hospital discharge diagnosis coded rota virus (A08.0) or acute gastroenteritis excluding rota virus (A01-A09, K32 excluding A08.0) multiplied by proportion of the cases estimated to be rota virus.

I am not sure how coding is done in the National Morbidity Database of the Australian Institute of Health and Welfare, but in many countries, diarrhea where rota virus is identified is coded as rota virus diarrhea, even where other pathogenic organisms are identified alongside and rota virus may not be the cause of the episode of diarrhea. The new rota virus vaccine strain from India, the monovalent human-bovine (116E) rotavirus, was cultured from an asymptomatic neonate in India. http://www.ncbi.nlm.nih.gov/pubmed/24629994. Some strains of rota virus could be a harmless commensals. The harmless rota virus may be protecting the individual imparting natural immunity without need for vaccines. Just because an organism is identified in a child with diarrhea, it does not necessarily imply that the organism is the cause of the diarrhea.

Furthermore, there are obvious problems in assuming that a fixed proportion of all diarrhea which are 'not coded as rota virus,' are due to rota virus.

Given these drawbacks, the estimate of 6500 rota virus hospitalizations avoided in Australia may not be accurate.

The judgment on acceptability of the risk-benefit equation pivots on the trade off between the putative 6500 rota virus admissions avoided on the one hand and the 14 cases of IS caused by the vaccine on the other, and these figures may not be reliable in the first place.

3 In their conclusions in the Abstract the authors say the "balance of risks and benefits at population level was highly favorable – a finding likely to extend to other settings despite varying incidence of IS and potentially higher morbidity and mortality from gastroenteritis and IS." This conclusion is clearly debatable.

The morbidity and mortality from gastroenteritis may be high in developing countries, but the morbidity and mortality for IS is disproportionately higher. Most developing countries can manage dehydration but facilities for surgical and radiological management of IS may not be available in large areas, making the risk unacceptable in accordance with the principle of primum non nocere.

4 Another factor the authors do not consider in their conclusion (that the findings are likely to extend to other countries,) is the varying vaccine efficacy seen in different countries. While the efficacy is nearly 90% in Western countries it is barely 50% in the tropics. Although the authors do not refer to the study by Madhi et al http://www.ncbi.nlm.nih.gov/pubmed/20107214 it is often quoted in this context. Severe rota virus gastroenteritis (SRVGE) was more common in Malawi than South Africa (13.1 vs. 5.4) and even though efficacy was lower in Malawi (49.4% vs. 76.9%) more cases of SRVGE were prevented by vaccination (6.7 vs. 4.2) in Malawi. This is often given as the justification for using the vaccine (with such low efficacy) in poor tropical countries.

This does not apply to all nations in the tropics. Although the incidence of gastroenteritis is high in India, the incidence of rota virus diarrhea was even less than South Africa. The incidence SRVGE in the unvaccinated in India was 3.4% compared to 13.1 in Malawi and 5.4 in South Africa. The absolute risk reduction (ARR) by vaccination was tiny in India (1.7). This is much lower than the benefit in Malawi (6.7) and even South Africa (4.2). It raises questions about the need for the vaccine in countries like India using the ‘disease burden’ argument. http://www.ncbi.nlm.nih.gov/pubmed/24629994#cm24629994_3808. Clearly each country needs to evaluate local risks and benefits and a blanket recommendation for all countries for the vaccine is perhaps not appropriate.

5 In conclusion: This study clearly shows the problems of relying on post marketing surveillance to evaluate harms. After unusual adverse events have been identified during post marketing surveillance, (if they are serious in nature) the vaccine must be withdrawn and reassessed in RCTs of sufficient size.

6 The data from the small 2-year follow-up RCT of the Indian vaccine 116E (4500 children received the new rota virus vaccine) will help understand if the '3 week window' is adequate to identify all adverse events. This follow-up paper is awaited. The preliminary report is available http://www.ncbi.nlm.nih.gov/pubmed/24629994#cm24629994. From the initial data it appears that the incidence of IS may be higher with this vaccine and so it may be a good vaccine to study the ‘window period’ of increased risk of IS.

On 2014 Nov 14, Curtis Corum commented:

Stephen,

Interesting comment...

I am not as familiar with standard imaging reporting for PC. For PC it is the various Gleeson scores that are of final interest, but structured imaging reporting is not necessarily as far along as in breast?

In Breast the BI-RADS reporting is standard, and now includes qualitative/semi-quatnitative DCE and morphological MRI. Efforts to process emerging modalities such as quantitative DCE and DWI/ADC are still research topics... for example http://www.ncbi.nlm.nih.gov/pubmed/23504036 as far as I can tell.

For treatment monitoring in breast (and many others icluding PC?) there are the various RECIST etc. http://www.ncbi.nlm.nih.gov/pubmed/18316345 that are continuously being updated as volumetric and other information becomes more readily available.

will review more...

On 2014 Aug 27, Stephen Strum commented:

My comment is limited by obviously not having read the full text of the article. What I have found in reviewing data on Multi-Parametric MRI (MPM) in PC (prostate cancer) is a lack of objective reporting, aka "structured" reporting. Therefore, I wonder if BC (breast cancer) reporting is similar.

What is needed is consensus on reporting the important objective data e.g., for DWI, indicating the Apparent Diffusion Coefficient (ADC) and b values; for DCE, reporting Ktrans (transfer constant min-1) or signal intensity-time curves (SITCs), and of course dimensional measurements for T2WI (T2 weighted images).

Such an attempt at a structured report would not only be of great value to clinicians for evaluating initial response to neoadjuvant therapy but also for ongoing responses to any form of treatment.

On 2014 Mar 14, Jonathan Eisen commented:

The last author of the paper, Amy Pruden, wrote a post for the "microbiology of the Built Environment network" (microBEnet) blog about this paper. See Probiotics for Plumbing?

On 2014 Feb 20, Markus Meissner commented:

Thank you very much for your feedback and the constructive criticism regarding our paper. We agree with some of the criticism regarding the nature of the localisation of TgStx6. Based on the co-localisation data with proM2AP, VP1 and GRASP we were initially convinced that Stx6 is localising to early endosomes, similar to the situation in ophistokonts. However, EM and IEM analysis did not result in the identification of EE but rather it appears that Stx6 is localising to the TGN as mentioned in the manuscript. However, we do not rule out that EEs exist and propose it as a hypothesis that apicomplexans have a more plant-like configuration.

With respect to other co-localisations with Rab5 or GalNac, we had some technical problems with these assays. As described in Kremer et al., 2013 overexpression of Rab5A (and Rab5C) leads to significant defects in the secretory system and therefore colocalisation analysis of parasites (over-) expressing both markers turned out to be not reliable. However, we agree that colocalisation with GalNac on transgenic parasites expressing endogenously tagged Stx6 would add additional information and should be performed in the future.

As you point out there is currently much confusion in the field if we can call something endosomal or endosomal-like. As one anonymous reviewer put it:” The authors are very generous in their use of the tern “endosome” in an organism where no form of endocytosis has even been seen. It might be better to define the process studied here as post-golgi membrane trafficking. “ We believe that unless one is very familiar with the terminology surrounding vesicular trafficking in Toxoplasma, the literature is very confusing. Therefore it might be the time where we have to agree on a common nomenclature based on the localisation of known markers, so that everyone has a clearer idea of the endomembrane system.

On 2014 Feb 19, Vernon B Carruthers, PhD commented:

Our group reviewed this paper for journal club recently. The group appreciated the novelty and importance of the study in defining new players in the elaborate vesicular transport system of the parasite. The main point raised was the unclear basis for stating that the study provided no "conclusive evidence for early endosomes in the parasite" and that the parasite likely harbors a fused TGN-EE similar to plants. The study did not attempt to look for early endosomes. It is widely acknowledged that there is limited published evidence that T. gondii can internalize exogenous material into its endocytic system. Nonetheless, Rab5, which is a classic marker for early endosomes has been used in several studies to define a mid-apical compartment that is associated with other markers of endosome-like compartments. Likewise, a previously characterized marker for the TGN, UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase or GalNac for short, was not tested. Comparing the localization of TgStx6 with these markers would help clarify the issue of a merged or separate TGN-EE in T. gondii.

On 2015 Sep 04, Casey M Bergman commented:

Orignally posted at PubPeer: https://pubpeer.com/publications/B37A9BD035CAEA3EEE79C48DDB0378

This paper provides a nice example of natural selection operating on a new gene duplicate at the Resistance to dieldrin (Rdl) locus in in D. melanogaster. Starting with an amino acid variant that is known to confer resistence to the insecticide dieldrin, the authors query whole genome sequences in the Drosophila Genetic Reference Panel (DGRP) [1] and find four strains that contain the resistance mutation. In three of the four strains, the resistance mutation is found unexpectedly in a heterozygous condition. The DGRP strains are highly inbred but are known to contain regions of residual heterozygosity scattered throughout the genome that could arise from incomplete inbreeding or segmental duplication.

By genotyping the offspring of "heterozygous" stocks, the authors find that 100% of progeny retain the heterozygous state, consistent with a segmental duplication. Analysis of the depth of sequence coverage in "heterozygous" strains confirms a 2-fold increase in the depth of coverage for a ~110 kb region containing Rdl and several other genes. The segmental duplication is flanked by two Roo transposable elements, suggesting it arose by ectopic recombination between repetitive sequences. The outcome of the duplication is that one duplicate contains the resitance allele and the other duplicate contains the susceptibility allele. Both copies are expressed. Transgenic analysis confirmed that the cause of the resistence allele is due to a single amino acid change in the Rdl gene only.

This paper shows how a newly arising allele with partial dominance can achieve a state of "permanant heterozygosis" by segmental duplication, conferring immediate adaptive advantage via the new allele while also retaining ancestral function via the old allele. This result nicely confirms a theoretical model developed by Spofford (1969) [2] (not cited in the current work) to explain selective forces that would govern the fixation of a new, polymorphic segmental gene duplicate. This work also shows that the "residual heterozygosity" in the DGRP lines may be more than just background noise from the vagaries of inbreeding, and may in fact point to many other functional segmental duplications in these lines.

[1] Mackay, Trudy FC, et al. "The Drosophila melanogaster genetic reference panel." Nature 482.7384 (2012): 173-178. http://www.nature.com/nature/journal/v482/n7384/full/nature10811.htm

[2] Spofford, Janice B. "Heterosis and the evolution of duplications." American Naturalist (1969): 407-432. http://www.jstor.org/stable/2458991

On 2013 Oct 31, John Cannell commented:

I congratulate the authors on a fine study. I wonder if they are aware that Mostafa et al found that an anti neural antibody found in autism had a -.86 correlation coefficient with 25(OH)D levels? If not it goes to show that scientists become experts in their own niche but apparently do not keep up with relevant science in other fields.

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

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

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take the American Pediatric Association's recommended vitamin D supplement of 400 IU/day. As milk consumption has fallen, so have toddler’s vitamin D levels.

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

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

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

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

John J Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org

On 2014 Sep 26, George Ntoumenopoulos commented:

The ability to determine the need for and deliver physiotherapy for patients managed on VV-ECMO is challenging, both from the acute respiratory and rehabilitative perspective. The cannulae type, location (e.g. femoral and/or jugular veins) and stability of delivery of VV-ECMO may impact on the clinicians opinions (physiotherapy and medical staff) about physiotherapy care. Deep sedation levels during ECMO may limit the ability the deliver physiotherapy and we need to explore this further. The use of ultra-low tidal volume delivery during mechanical ventilation for lung protective ventilation may also mask the detection of problems such as secretion retention, with standard methods such as"sawtooth" patterning on expiratory flow waveforms. We need to further investigate the role of physiotherapy (both acute respiratory and rehabilitative) in this complex patient group.

On 2014 Oct 15, Gerd Heusch commented:

The skepticism of Dr. Berthelsen is well taken. However, contrary to his expectation, the results of our study with its primary endpoint troponin release have already been replicated, see Candilio L, 2015.

On 2014 Oct 13, Preben Berthelsen commented:

This study was registered with ClinicalTrials (NCT01406678). According to the registration, the authors planned to include 500 patients in a randomised study of remote ischaemic preconditioning (RIP) in isoflurane anaesthetised patients. No interim statistical analyses were planned. The study was, however, stopped early after the inclusion of 162 patients in the RIP-group and 167 patients in the group where no RIP was used. (Only 121 and 137 patients could be included in a per protocol analysis).

It is an indispensable rule not to break the randomisation code before all patients have completed the investigation. The authors have not followed this imperative. They have kept running track of the results as can be seen from the admission on page 598 of this paper “After use in some patients, however, we became aware of apparent interference of propofol with remote ischaemic preconditioning and discontinued its use in the remainder of the study”. So at least theoretically, it has been possible for the authors to analyse the data continuously and therefore stop the investigation – when a statistical difference was demonstrated – and before the stipulated number of patients had been reached.

A re-calculation of the power of the study using the 17% difference in 72h-troponin AUCs and a SD of 200 (standardised difference 0.27) shows that there is less than a 50% chance that another study would replicate the authors’ findings. It is my opinion that the result of this investigation must be viewed with some scepticism. Preben G. Berthelsen MD. Charlottenlund, Denmark.

On 2014 May 21, Amanda Capes-Davis commented:

INT 407 is a widely used cell line. However, many scientists are unaware that it is NOT an intestinal cell line. INT 407 is cross-contaminated by HeLa, which comes from cervical carcinoma. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2013 Oct 26, Lorene M Nelson commented:

This article provides an excellent summary of the state of knowledge regarding the role of pesticides in the etiology of Parkinson’s disease, and nicely highlights the challenges faced by environmental epidemiologists in identifying specific pesticide chemicals that are associated with PD. I agree with Dr. Kamel that it has been difficult to make substantial progress in identifying specific pesticide chemicals that increase PD risk except in unique circumstances, such as the two recent high-quality cohort studies that she cites. Another notable example is the retrospective (case-control) study conducted in central California by Dr. Ritz (UCLA investigator) whose group has produced findings implicating workplace and ambient pesticide exposure in PD [Wang A, 2011; also cited by Dr. Kamel], well-water consumption Gatto NM, 2009, specific pesticide combinations Costello S, 2009, and gene-pesticide exposure interactions Manthripragada AD, 2010.

On 2014 Nov 17, Raphael Levy commented:

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

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

On 2014 Jun 30, Karel Koberna commented:

The method described in the article of Cappella et al. was patented by us in 2012 and at the end of the same year published in great detail in our article “Atomic Scissors: A New Method of Tracking the 5-Bromo-2′-Deoxyuridine-Labeled DNA In Situ” PLoS (7(12): e52584). This fact is not evident as the paper of Cappella et al. contains incorrect reference to our original paper. We asked editor of Cytometry A to correct this error so we believe that it will be corrected soon.

On 2013 Dec 02, Kenneth N Litwak commented:

This study, by Ruff et al, attempted to demonstrate negative effects of excess sugar consumption on mouse survival, competitive ability, and reproduction, as a means of demonstrating the utility of Organismal Performance Assays (OPAs) in quantifying toxicities. However, there are multiple methodological issues in the article affecting its value.<br> 1. In the discussion, the authors state that the diet was “analogous to human subjects consuming a healthy diet plus the equivalent of ~3 cans of soda per day”. This statement does not correctly reflect the study diet vs. control diet, as the two diets were isocaloric. Adding 3 cans of soda to the diet would add additional calories to a diet, not replace a source of carbohydrates.<br> 2. The authors correctly noted that this experiment would have ideally maintained the different groups on their original diets for duration of the study; however, all mice were given the F/G diet once they entered the OPA enclosures at 26 weeks of age and for the next 7 – 8 months. This change in diet is a major confounding point of the entire experiment. It might be reasonably assumed that initial outcomes in the OPA enclosures would be due to different diets, but the authors do not provide any data to support this premise, for initial or long-term outcomes.<br> 3. Mouse pups were only counted every six week to determine reproductive success (Methods). The long duration between counts would likely result in an under-count of reproductive success, as cannibalism and early pup death would be difficult to determine. Further, the duration between counts was sufficient to allow multiple litters to be born to founder mice and to F1 mice.<br> 4. The confounding effects of the OPA enclosures and their locations (Supplementary Figure S3) are potentially significant. Each enclosure was immediately adjacent to others. However, some enclosures were only bounded by two enclosures, while some were bounded on three sides by other enclosures. Stress associated with territorial boundaries has been repeatedly documented in mice. Due to the small size of this study, the potential space interaction could have had significant effects on the outcomes.

On 2017 Jul 08, David Keller commented:

Why Physicians Favored Lipitor Over Simvastatin

In their commentary on generic drug use, Alldredge and Kayser state the following:

"In 2011, fewer prescriptions for generic simvastatin were written than for Lipitor (atorvastatin calcium; Pfizer Inc) despite a significant cost differential and no apparent clinical differences in efficacy and safety." [1]

That statement is an unfair criticism of physicians and conflicts with the expressed views of the Food and Drug Administration (FDA). On June 8, 2011, the FDA issued a safety warning concerning simvastatin [2] in which physicians were advised to discontinue the use of simvastatin, 80 mg (except in patients who had already been taking it safely for over 1 year).

For patients taking amlodipine, the FDA warned against prescribing more than 20 mg of simvastatin, and for patients taking diltiazem or verapamil, the dose of simvastatin was limited to 10 mg. These safety warnings were based on reports of adverse events including serious myopathy caused by simvastatin, 80 mg, and by lower doses of simvastatin when combined with widely prescribed calcium channel blockers.

As a result, physicians were left with a maximum safe simvastatin dose of 40 mg, which lowers low-density lipoprotein cholesterol level by approximately 40%, whereas atorvastatin, 80 mg, lowers low-density lipoprotein cholesterol level by approximately 55%.[3] The FDA has not deemed it necessary to issue similar safety restrictions on the use of atorvastatin, which may explain why physicians favored Lipitor over generic simvastatin in 2011.

References

1: Alldredge BK, Kayser SR. Bending the curve toward increased use of generic drugs. JAMA Intern Med. 2013;173(3):233-234. PubMed Article

2: FDA Drug Safety Communication: new restrictions, contraindications, and dose limitations for Zocor (simvastatin) to reduce the risk of muscle injury. www.fda.gov/Drugs/DrugSafety/ucm256581.htm. Accessed February 21, 2013.

3: Law MR, Wald NJ, Rudnicka AR. Quantifying effect of statins on low density lipoprotein cholesterol, ischaemic heart disease, and stroke: systematic review and meta-analysis. BMJ. 2003;326(7404):1423. PubMed Article

Author's note: the format of the above letter is scrambled and difficult to read, as published online at the following URL:

https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/1726968

Due to the difficulty of getting the published version corrected, I have posted the corrected version above.

On 2014 Jan 15, Satoko Hattori commented:

"ImageLD" and "ImageEP", image analysis application softwares used in this article, are now freely available from http://www.mouse-phenotype.org/software.html.

On 2013 Nov 14, Gareth Highnam commented:

Awesome study, are cancerous areas changed to a uniform density across ethnicities? Or does density of cancerous areas also have an ethnic component? All factors for an optimized detection model, I suppose. [CoI - RH is my favourite published uncle :) ]

On 2013 Nov 20, Jamie Horder commented:

It would be wrong to say that reverse coded items are rarely not unconfusing!

On 2013 Nov 17, James C Coyne commented:

Formal Correction: This article has been formally corrected to address the following errors.

As a result of an error by PLOS ONE, an incorrect version of the article was typeset. Below is a link to a version of the article based on the correct manuscript.

http://www.plosone.org/annotation/listThread.action?root=71757

On 2013 Nov 05, Pedro Mendes commented:

This yeast metabolic reconstruction improves on the work described in Herrgård MJ, 2008, Dobson PD, 2010, and Heavner BD, 2012. The data set is available at http://yeast.sf.net/

On 2017 Jun 10, Casey Greene commented:

We used this method in our own preprint. Our preprint is available on bioRxiv: https://doi.org/10.1101/147645

For the convenience of the research community, we have made our implementation available as an open source python package. It is currently maintained on GitHub (https://github.com/kathyxchen/crosstalk-correction) and distributed via PyPI (pip install crosstalk-correction). We hope that others will also find this useful.

On 2014 Jul 12, Jorge H Ramírez commented:

The overall quality of this randomized clinical trial is poor:

• Limited time of follow-up (12 weeks) to determine the safety and effectiveness of an active pharmacological principle or a fixed-dose combination (i.e., solifenacin plus tamsulosin).

• The study evaluates surrogate instead of definitive outcomes.

• No description of allocation concealment mechanisms.

• No description of methods used to generate the random sequence used in the randomization of patients to each study arms

• The article does not describe methods for the implementation of the random sequence.

• No appropriate description of blindings in the study.

• No intention-to-treat analysis

• Cardiovascular adverse events were not appropriately described in this article.

• Haemodynamic variables were not included as primary or secondary outcomes in this study.

Tamsulosin is a nonuroselective alpha blocker associated with severe hypotension in men.(1,2) Moreover, over three quarters of the studies with tamsulosin in humans are unpublished.(3)

A recent publication entitled "Solifenacin/tamsulosin FDC squeezes out competitors."(4) supports that this combination is cost-effective only based in the pharmacoeconomic analysis of this study (Neptune trial. van Kerrebroeck and colleagues. Eur Urol 2013).

I have the following open-question for anyone reading this comment:

What would happen with pharmacoeconomic evaluations involving solifenacin/tamsulosin in the treatment of lower urinary tract symptoms after considering the risk of severe hypotension and the results of unpublished studies?

Finally, I personally think that the title "Solifenacin/tamsulosin FDC squeezes out competitors." resembles more a pharmaceutical marketing campaign (a misleading one) than a serious paper reporting the results of a pharmacoeconomic analysis.

References

1. Bird Steven T, Delaney Joseph A C, Brophy James M, Etminan Mahyar, Skeldon Sean C, Hartzema Abraham G et al. Tamsulosin treatment for benign prostatic hyperplasia and risk of severe hypotension in men aged 40-85 years in the United States: risk window analyses using between and within patient methodology BMJ 2013; 347:f6320 http://www.bmj.com/content/347/bmj.f6320

2. Ramirez Jorge. Severe hypotension associated with α blocker tamsulosin BMJ 2013; 347:f6492 http://www.bmj.com/content/347/bmj.f6492

3. Ramirez, Jorge H (2014): Expression of concern about tamsulosin: over three quarters of human studies are unpublished. figshare. http://dx.doi.org/10.6084/m9.figshare.1094338 URL:http://figshare.com/articles/Expression_of_concern_about_tamsulosin_over_three_quarters_of_human_studies_are_unpublished/1094338

4. Nazir, J. Solifenacin/tamsulosin FDC squeezes out competitors." PharmacoEconomics & Outcomes News 706 (2014): 10-5.

On 2013 Nov 01, Gerard Ridgway commented:

This is an updated version of Weiner MW, 2012, with additions highlighted in the PDF version. Somewhat confusingly, the abstract still refers to "results as of February 2011", but the masthead on the PDF clarifies that it was "Updated April, 18, 2013". To give a rough idea of the scale of the update, the number of cited references has increased from 225 to 349. Li Shen has been added as an author.

On 2013 Nov 19, Ilene Mizrachi commented:

The genome assembly is available in GenBank. The assembly was recently updated to version 2, APWK02000000 and is retrievable at http://www.ncbi.nlm.nih.gov/nuccore/APWK00000000

On 2013 Nov 19, Gustavo Costa commented:

The Genbank Acession APWK01000000 for the contigs, mentioned in the paper, is unavailable. Maybe the submitting authors should inform Genbank to release the sequences publicly.

On 2014 Dec 07, Harri Hemila commented:

Rerksuppaphol S, 2013 reports a highly significant baseline imbalance on age

Rerksuppaphol S, 2013 randomized 100 children to the zinc and placebo groups using blocks of two. According to their Table 1, average age was 10.0 yr (SD 0.5 yr) in the zinc group, but 11.4 yr (SD 0.8 yr) in the placebo group; the authors calculated P=0.0001 for the difference in baseline age. In their paper, Rerksuppaphol S, 2013 do not comment on their calculation of highly significant imbalance on age.

As the most interesting finding, Rerksuppaphol S, 2013 report that coughs and runny noses were shorter in the zinc group, with P=0.01. The median “duration for cough” was 1.0 days in the zinc group, and 6.0 days in the placebo group. The total duration of the trial was 3 months and it seems obvious that many participants had more than 1 cold episode per 3 months. However, the Methods and Results do not describe whether the “duration of cough” means duration per episode or duration per person. Thus the outcomes are not well described. Given the reported baseline imbalance and the lack of transparency in the outcomes, it is difficult to trust the reporting on coughs and runny noses.

Rerksuppaphol S, 2013 refer to the Cochrane review on zinc for the common cold by Marshall I, 2000 (ref. 19), which was withdrawn several years ago in Marshall I, 2007. Thereafter a new Cochrane review was written by Singh M, 2011 which is also cited (ref. 25), without any mention that the latter replaced the old withdrawn Cochrane review (2000), which was also cited (ie ref. 19). Such a presentation of previous literature on zinc and colds gives an impression of sloppiness.

Rerksuppaphol S, 2013 has been cited in JAMA by Das RR, 2014. Therefore the validity of this study is a relevant issue.

On 2017 Nov 29, Liz Dooley commented:

This Cochrane Review has been superseded. A new author team will publish a new protocol 'Vitamin C for pneumonia'. This information has been provided by the Cochrane Acute Respiratory Infections Group.

On 2014 May 14, Martine Crasnier-Mednansky commented:

The feedback strategy established by Doucette CD, 2011 relates to data obtained under conditions of 'extreme' catabolite repression elicited by nitrogen limitation. A direct inhibitory effect of α-ketoglutarate on Enzyme I inhibits phosphorylation of the components of the phosphotransferase system (PTS), including phosphorylation of EnzymeIIAGlc which activates adenylate cyclase. Therefore, cAMP-mediated catabolite repression occurs in these conditions. Another not-yet propounded effect of an increase in α-ketoglutarate is an enhanced inducer exclusion, which further hinders uptake of carbon sources other than PTS substrates. Under nitrogen-limited conditions, β-galactosidase synthesis in a wild-type strain growing on glucose is most likely affected by inducer exclusion. Thus, nitrogen-limited growth may not 'rely completely' on cAMP-mediated gene regulation as transcriptional regulation by cAMP and inducer exclusion both interfere with β-galactosidase synthesis Crasnier-Mednansky M, 2008. By not taking into account inducer exclusion the authors undermine the power of 'quantitative physiology'. Within the same frame of thought, using pts strains grown on lactose to measure β-galactosidase activity is physiologically irrelevant.

In sharp contrast with the present data, Daniel J, 1986 reported that α-ketoglutarate (or pyruvate indirectly by accumulation of α-ketoglutarate) caused repression of the lac operon - but not oxaloacetate. In addition repression did not occur in crr strains (lacking Enzyme IIAGlc) in support of Doucette CD, 2011.

On 2013 Oct 31, John Cannell commented:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take the Ameri

On 2014 May 07, Matthias Girndt commented:

The full title of this article in German is: "Paresthesia and muscle cramps after dialysis: can they be prevented?"

On 2016 Nov 20, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2013 Oct 31, John Cannell commented:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take the Ameri

On 2014 Jan 03, Ian Lyons commented:

In this paper, Park and Brannon showed that training adult subjects on an approximate, nonsymbolic arithmetic task (adding and subtracting estimates of the number of dots in various dot arrays) led to improvement on a symbolic arithmetic task (i.e., using Indo-Arabic numerals). The authors suggest this result points to a causal role for the ‘approximate number system’ (ANS) in more complex, symbolic math processing and may thus inform the development of interventions designed to improve mathematical competence in children and adults. We believe the authors’ work takes an important step forward in terms of understanding the building blocks of mathematical performance, and, using their work as a jumping board, we offer several points of reflection concerning (1) the nature of the ANS, and (2) what it means to train performance on a task versus the process it is meant to measure.

Park and Brannon’s crucial experimental condition trained participants using approximate, nonsymbolic addition. This differs from tasks used more commonly in the literature to measure individual differences in the ANS – adaptation and comparison – which involve simply distinguishing between two approximate quantities (e.g., in comparison tasks, one typically decides which of two arrays contains more dots). The difference in tasks is significant because previous attempts to train participants on just a nonsymbolic comparison task failed to show significant improvement in individuals’ symbolic math performance [Wilson et al., 2006 (http://www.ncbi.nlm.nih.gov/pubmed/16734906); DeWind & Brannon, 2012 (http://www.ncbi.nlm.nih.gov/pubmed/22529786)]. Why, then, does training on nonsymbolic arithmetic lead to improvement in symbolic arithmetic skills, but training on nonsymbolic comparison does not, even though both have been shown to correlate with symbolic arithmetic [e.g., Gilmore et al., 2010 (http://www.ncbi.nlm.nih.gov/pubmed/20347435); Halberda et al., 2012 (http://www.ncbi.nlm.nih.gov/pubmed/22733748)]? One possible conclusion is that it is not enough simply to tap the ANS; instead, accessing the ANS must be structured in a manner that more directly parallels the target skill – symbolic arithmetic. From a broader perspective, such a conclusion suggests that it is time to take a deeper look at what exactly we mean by an ‘approximate number system’, as Park and Brannon’s results may in fact point to an important division between approximate quantity representation and manipulation within the ANS. The view that the ANS is not a unitary construct is also leant support by the fact that performance on nonsymbolic quantity comparison and nonsymbolic arithmetic tasks are uncorrelated [Gilmore et al., 2011 (http://www.ncbi.nlm.nih.gov/pubmed/21846265)].

That nonsymbolic arithmetic (but not nonsymbolic comparison) training leads to improved symbolic arithmetic brings us to a second point: It is crucial to make a distinction between a task meant to measure or be an index of some underlying process, and the process itself. To cure a fever, one does not build a more precise thermometer; and by extension, if one demonstrated that using a more precise thermometer indeed failed to reduce one’s fever, it would be rather rash to conclude ambient bodily temperature is irrelevant to one’s health. A nonsymbolic number comparison task may act like a thermometer, where the underlying process it indexes is ANS acuity. Training on nonsymbolic comparison tasks does not improve math skills (Wilson et al., 2006; DeWind & Brannon, 2012), but this does not mean that the ANS is irrelevant for math. By training on nonsymbolic arithmetic instead of nonsymbolic comparison, Park and Brannon showed that one’s training regimen simply needs to tap the ANS in a way that better parallels the types of cognitive operations used in symbolic arithmetic.

One sees a similar distinction between tasks that index versus train an underlying process elsewhere in the numerical domain: when a person is asked to mark the location of a number on a number line, the linearity of their estimates predicts math achievement [Booth & Siegler, 2006 (http://www.ncbi.nlm.nih.gov/pubmed/16420128), 2008 (http://www.ncbi.nlm.nih.gov/pubmed/18717904)]; but rather than train on this task per se, researchers found success using a board game that trained children to linearize their visuo-spatial representations of symbolic numbers – i.e., the underlying process that was presumably being measured by the number line task. Training on the board game improved performance on both the numberline task as well as math achievement [Siegler & Ramani, 2009 (http://psycnet.apa.org/journals/edu/101/3/545/)].

Further, we believe that Park and Brannon’s own dataset provides yet another example illustrating the distinction between a task meant to measure or be an index of some underlying process, and the process itself. The authors show a correlation between numerical ordering ability and symbolic math ability, replicating our previous work [Lyons & Beilock, 2011 (http://www.ncbi.nlm.nih.gov/pubmed/21855058)]. Nevertheless, training on the ordering task did not lead to improvement in symbolic math beyond what was seen for vocabulary training. If one concludes from this result that understanding ordinality is irrelevant for developing math skills, one is in danger of mistaking a means of measurement for the thing being measured – much as one might have done with the dot comparison or number-line tasks discussed above.

In conclusion, Park and Brannon’s recent paper showing a causal relation between nonsymbolic and symbolic arithmetic, represents a step toward understanding the building blocks of complex arithmetic. Perhaps missed in the excitement, though, is that this work underscores the need for researchers – especially those interested in educational applications – to carefully consider what their tasks and paradigms truly mean with respect to the processes and representations they aim to investigate. Failing to do so risks conflating the means of measurement with what is being measured, and may in turn lead to recommendations for educators to train the wrong thing.

Signed, Ian Lyons and Sian Beilock

On 2017 Oct 10, L David Sibley commented:

We appreciate the posting of the comment by Dr. Meissner and also the primary data provided by the Kursula group (Kumpula et al., Kumpula EP, 2017). Although we agree that there are differences in the conclusions, we feel that these stem primarily from differences in methodology and biological substrates. As such, it would be premature from this new study to make sweeping statements about the polymerization behavior “apicomplexan” actins.

First, we note that our study used Toxoplasma gondii actin (TgACT1) Skillman KM, 2013, while Kursula group studied Plasmodium actin, PfACT1 more specifically. We agree that the two actins are somewhat similar, and so it would be surprising if they had an intrinsically different mechanism of polymerization. However, our previous studies have noted differences between these substrates and found that polymerization of PfACT1 is more efficient than that of TgACT1 as shown by light scattering and microscopy Skillman KM, 2011.

Second, Kumpula et al., suggest that sedimentation may not be a reliable method for monitoring polymerization kinetics of apicomplexan actins due to the formation of small oliogmeric species that do not fully sediment at 100,000g or even 450,000g. We are well aware of this limitation, and indeed it is also shown in our paper by several methods Gershon D, 1990. We considered the formation of heterogenous small oligomers in the experiments we performed, including in the simulations and determination of rate constants. Importantly all of our findings show that a simple isodesmic model can fit the data for assembly and turnover. These findings further predict that if there is a cooperative component, it is exceedingly small relative to conventional actins. Moreover, our conclusion that TgACT1 polymerizes by an isodesmic mechanism was not based solely on sedimentation but was supported by light scattering assays, which demonstrate a lack of a lag period associated with a normal critical concentration (Cc) Skillman KM, 2013.

Third, Kumpula et al., used a modified pyrene assay to monitor the “kinetics’ of filament formation. We agree that the pyrene assay is normally well suited for studying kinetics, but may not be ideal for monitoring thermodynamics associated with the intrinsic polymerization mechanism. Kumpula et al., report that at low concentrations of PfACT they detect evidence for a Cc, based on plotting the fluorescence signal vs. actin concentration. However, under these conditions where pyrene labeling was done at sub-stochiometric levels, the lack of a signal below a particular concentration may be due to lack of sensitivity, rather than an actual Cc. It would be important to determine whether such a Cc could also be detected by intrinsic tryptophan quenching, which may be more sensitive. We would also like to point out that unlike these two assays that attempt to monitor the Cc at very low concentration of protein, the estimate of Cc from sedimentation assays is based on behavior across a wide range of concentrations and thus it is more robust to small fluctuations, variability in protein levels, or assay differences.

Finally, we note than both our study and that of Kumpula used recombinant actin produced in insect cells. Hence, the previous suggestion that apicomplexan actins cannot be functionally expressed heterologously Olshina MA, 2016 is incorrect and not the reason for the differences described in polymerization behavior. Rather, it is clear that recombinant actins produced in an appropriate manner exhibit many interesting functional properties. Further studies may reveal to what extent these features are shared vs. unique among divergent actins.

On 2017 Sep 23, Markus Meissner commented:

A recent report from the Kursula group demonstrated that the sedimentation assays used in Skillmann et al., 2013 are unlikely to obtain reliable results for apicomplexan actins. In this study the Kursula group (see: https://www.nature.com/articles/s41598-017-11330-w) used a protocol based on pyrene labelling and demonstrated that polymerisation of apicomplexan (Plasmodium) actin is occurring in a cooperative manner, meaning it requires a critical concentration. Surprisingly, the Cc is very similar to canonical rabbit actin. Furthermore, it was shown that shorter filament lengths result from higher depolymerisation rate. In conclusion, it appears that -like all other known eukaryotic actins- apicomplexan actin polymerises in a cooperative manner, requiring a nucleation reaction (see Kumpula et al., 2017).

On 2016 Jul 06, David C. Norris commented:

In addition to the images above, an animation cited in the article may also be of interest: http://hemonc.org/docs/CMLhistory.avi

On 2013 Nov 18, vaigundaragavendran jegadeesan commented:

The review provides us with an in-depth overview of the multifarious mechanisms that underpin the pathophysiology of PCIBP. In particular, the pictorial representations are very informative and explain the critical steps more clearly. A nice read to concatenate PCIBP mechanisms to those underlying various other pain conditions to eventually form a string of plausible therapeutic approaches.

Highly recommended.

On 2013 Oct 28, John Cannell commented:

Didn't Finland start supplementing their children with vitamin D in 2003? I think increased vitamin D levels account for the reduction in type 1 diabetes in Finland.

On 2016 Apr 12, Oliver Kuss commented:

This is a clearly written paper on proportional hazards model for interval-censored data. I especially liked the authors sharing their SAS code for the piecewise constant model with which I was able to recalculate the results for the breast cancer data set as given by Lindsey/Ryan.

However, there are also two things that concern me a bit:

(1) The SAS code seems to be a only slightly shortened version of the %recurr macro of Lu/Liu (2008). It would have been fair by Gong/Fang to point to this source.

(2) The estimated hazard ratios for the breast cancer data set (table 6) do not coincide with the previous literature. For example, Lindsey/Ryan report 0.930 (0.287) as the hazard ratio from the piecewise constant model and I found the same results. However, the authors report 0.392 ...

Lindsey JC, Ryan LM. Tutorial in biostatistics methods for interval-censored data. Stat Med. 1998 Jan 30;17(2):219-38.

Lu L, Liu C. Analysis of Correlated Recurrent and Terminal Events Data in SAS®. www.lexjansen.com/nesug/nesug08/sa/sa16.pdf

On 2014 Nov 17, Raphael Levy commented:

I discuss the interpretation of the energy profiles shown in this paper (fig 4C) on my blog. I compare with two other articles addressing the same problem: Li Y, 2012 and Gkeka et al. One of the author of Gkeka et al, Lev Sarkisov (Edinburgh), left a detailed and helpful comment on the blog.

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

On 2013 Nov 16, M Mangan commented:

Oh, sure, now they changed the title so nobody will understand the issue. The original title was "Environmental stress and transposon transcription in the mammalian brian."

On 2013 Oct 31, M Mangan commented:

So does this affect only Brians? All Brians?

On 2013 Dec 09, John Cannell commented:

The authors report that immune system dysregulation is common in autism spectrum disorder (ASD). They discuss a number of nutritional relationships to the immune system. If it is dietary, the question is why does this immune dysregulation occur and what has caused such dysregulation to skyrocket in recent decades?

Vitamin D deficiency produces very similar immune dysregulation to what the authors reported.

Prietl B, 2013

Kamen DL, 2010

Yang CY, 2013

Baeke F, 2010

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

Gong ZL, 2014

Meguid NA, 2010

Mostafa GA, 2012

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

DeLuca GC, 2013

Eyles DW, 2013

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

Cannell JJ, 2010

Cannell JJ, 2008

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

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

Kočovská E, 2012

As the authors point out, immune dysregulation is common in ASD. The question is why now and what is causing it?

John J Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org

On 2013 Oct 29, John Cannell commented:

I congratulate the authors on an important work but it shows how little communication is occurring among autism scientists. Each scientist seems to be immersed in his or her own research interest but oblivious to the larger body of autism research.

The vitamin D theory of autism (vitamin D deficiency is the environmental risk factor for this highly heritable disorder) is entirely consistent with the authors work, as they briefly discuss in their paper. However, vitamin D's effect on the immune system is pervasive and robust and deserves much more attention as the factor implicated in both autism and immunity.

Schwalfenberg GK A review of the critical role of vitamin D in the functioning of the immune system and the clinical implications of vitamin D deficiency.Mol Nutr Food Res. 2011 Jan;55(1):96-108. doi: 10.1002/mnfr.201000174. Epub 2010 Sep 7. Review. Schwalfenberg GK, 2011

Three recent studies, using community controls, have found 25(OH)D levels are significantly lower in children with autism. Two of the studies below (Mostafa et al and Gong et al) also found autism severity, as rated on standard autism rating scales, is inversely correlated with 25(OH)D levels. Mostafa et al found an R value of -.86 for the association of serum 25(OH)D with autism severity.

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take the American Pediatric Association's recommended vitamin D supplement of 400 IU/day.

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

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

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

However, these scientists appear to be in the minority. Until all autism researchers become cognizant of the wider body of autism research, we will continue to wonder how to prevent - and perhaps even treat - this modern day plague.

John J Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org

On 2014 Jul 19, Chris Carter commented:

HSV-1/host interactome

On 2013 Nov 04, AARON HSUEH commented:

This paper neglected earlier work. For example: Extrapituitary action of gonadotropin-releasing hormone: direct inhibition ovarian steroidogenesis. Hsueh AJ, Erickson GF. Science. 1979 May 25;204(4395):854-5.

Gonadotropin-releasing hormone analogue binds to luteal cells and inhibits progesterone production. Clayton RN, Harwood JP, Catt KJ. Nature. 1979 Nov 1;282(5734):90-2.

Extrapituitary actions of gonadotropin-releasing hormone. Hsueh AJ, Jones PB. Endocr Rev. 1981 Fall;2(4):437-61. Review.

On 2014 Jan 07, Brett Snodgrass commented:

Dear Author,

Thank you for the excellent report. Please provide your kind attention to the difference between the vessels of Wearn and Thebesius. Approximately fifty percent of the medical literature applies the term "Thebesian veins" to the "vessels of Wearn."

Arteriosinusoidal vessels described by Wearn connect to myocardial sinusoids. The myocardial sinusoids are often pathologically altered and readily apparent on microscopy in pulmonary atresia with intact ventricular septum.

Dr. Wearn's work work detailing the difference between the Thebesian veins and the vessels of Wearn (which he referred to as arterioluminal vessels). http://bit.ly/JTWearn

The myocardial sinusoids are not phantom as they connect to the arteriosinusoidal vessels. The vessels of Wearn include the arteriosinusoidal and the arterioluminal vessels of the heart. Wearn's distinguished Harvey lecture of 1940 again reported the difference between the "Thebesian veins" and the "AL & AS" vessels (vessels of Wearn). However, this was soon obscured in the medical literature. My hypothesis is that with a lack of a pronoun such as the "vessels of Wearn," the vessels were described as Thebesian veins. Related references: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933738/ http://www.ncbi.nlm.nih.gov/pubmed/22704295 http://www.ncbi.nlm.nih.gov/pubmed/23332812 https://twitter.com/BrettSnodgrass1/status/419324443068874752

I appreciate comments, suggestions, and constructive criticism. Please feel free to E-mail me: brettsnodgrass@hotmail.com Alternatively, you may message me through Twitter https://twitter.com/BrettSnodgrass1

Thank you kindly.

On 2016 Aug 24, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT000004592. We believe the correct ID, which we have found by hand searching, is UMIN000004592.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2017 May 22, Christine Carson commented:

Full text of this Letter available in Swedish at: http://www.lakartidningen.se/07engine.php?articleId=18503

Full text of this Letter available in English from ResearchGate at: https://www.researchgate.net/profile/Christine_Carson/publication/236031981_Biverkningarnaar_overdrivna_Swedish_Tea_tree_oil_-_adverse_events_exaggerated/links/02e7e51cafbeed6002000000/Biverkningarnaaer-oeverdrivna-Swedish-Tea-tree-oil-adverse-events-exaggerated.pdf

On 2013 Oct 25, Gregory Francis commented:

I fear the science in this study does not back up the conclusions. An important part of the scientific process is to check whether the statistical data are consistent with the hypothesized theory. One way to do this is to compute the statistical power of the experiments. This analysis supposes that an experiment accurately measured the reported effect and then computes the probability that a randomly selected sample of data would satisfy the statistical criteria used to justify the scientific claims. For this study, these estimated probabilities are 0.56, 0.52, 0.48, and 0.57. That the values are close to one-half reflects the fact that the data were typically just to one side of the statistical criterion for finding an effect. Due to natural variation, data from some samples should fall on the other side of the criterion.

The power analysis suggests that, at best, the odds of showing the effect for each experiment is almost the equivalent of a coin flip. As such, the repeated success of the reported experiments is rather unbelievable (multiplying the power values gives 0.08). Scientists should doubt the veracity of the reported experiments; they are too good to be true.

A Excel file that computes the effect sizes used in the power analysis can be found at http://www1.psych.purdue.edu/~gfrancis/Publications/VohReddenRahinel2013.xls

On 2013 Nov 18, Gary Ward commented:

This paper describes a clever high-throughput assay to identify small molecules that disrupt the interaction of Plasmodium falciparum AMA1 and RON2, and can thereby block merozoite invasion of erythrocytes. The data provide promising proof-of-concept for the development of novel antimalarials that disrupt protein-protein interactions critical for invasion. This particular interaction is thought to happen extracellularly, within the blood, which could facilitate access of such drugs to their targets.

The three inhibitors described have IC50 values in the 20-30 uM range. The authors state that "small-molecule inhibitors will result in reduced or no emission signal depending on the strength of the inhibition". Our group was interested to know what the dynamic range of the AlphaScreen assay is and whether it can capture binding at both ends of the affinity spectrum (subnanomolar to millimolar).

A 1000-fold molar excess of inhibitor was required to disrupt RON2L-AMA1 interaction in the screen, perhaps because the compound is added after RON2L-AMA1 complex formation and must essentially displace the RON2L from AMA1. The assay may have been done this way purposely, to recapitulate what happens in the blood, i.e., secreted RON2 is probably not exposed on the surface of the red cell for long before it is bound by AMA1. It would nonetheless be interesting to know what happens to the IC50 if compound is added to AMA1 before the addition of RON2L.

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

On date unavailable, commented:

None

On 2014 Mar 22, Andrew R Kniss commented:

There are now two published criticisms of this work in New Phytologist, the journal that originally published the article.

• Letter from Gressel et al: http://onlinelibrary.wiley.com/enhanced/doi/10.1111/nph.12615/
• + author response to Gressel et al. http://onlinelibrary.wiley.com/enhanced/doi/10.1111/nph.12684/
• letter from Grunewald & Bury: http://onlinelibrary.wiley.com/enhanced/doi/10.1111/nph.12683/
• + author response to Grunewald & Bury: http://onlinelibrary.wiley.com/enhanced/doi/10.1111/nph.12748/

On 2013 Oct 23, Andrew R Kniss commented:

This is a very interesting paper, and it recieved wide media coverage after publication. There are some rather large oversights/deficiencies that should be noted. I have posted a rather long critique of this paper at my blog. There are several problems with the paper, all of which are described in detail at the link. In a nutshell:

• The breeding methods used did not ensure enough genetic uniformity between GE and non-GE hybrids to attribute differences to the transgene as they claim.
• The authors provided very little information about the the original transformation event, and how the transformed line differed from its parent line (even after presenting data suggesting the lines had different phenotypes).
• The authors do not adequately discuss other possibilities that may explain their results, particularly with respect to the promoter they used and the impact of closely linked genes.
• Closely related traits (tiller production, panicle production, seed production) are presented as independent evidence of an increase in fitness.
• None of the experiments presented in this study were repeated.

On 2013 Aug 10, Allison Stelling commented:

I find it a bit odd that the authors call for a national discussion on a very important topic in a journal that has put their words behind a paywall.

Biomedical science has a huge public impact, and the public needs to be aware how little we know about how to diagnose many diseases; let alone our lack of information on "cures". They are footing the majority of the bill and have a fundamental right to have the science explained to them. This is not a discussion that the researchers and "qualified experts" can keep within their own limited community; nor is it a one way lecture where interaction with the public is unidirectional. It's a conversation that needs to happen between medical doctors, the public taxpayers, and the scientific researchers.

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 body of the text of the article. The ID given is NCT0005937. We believe the correct ID, which we have found by hand searching, is NCT00059371.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 Sep 21, Annie De Groot MD commented:

I wonder if pathogens use this pathway to escape immune response? See our article at http://bit.ly/NTD_iVAX_2014

On 2014 Jan 31, Huiqi Qu commented:

This method is helpful to understand functional effects of some genetic variants.

On 2014 Apr 21, Morgan Price commented:

The annotation of DpigGOR10741-DpigGOR10744, which are important for hydrogen utilization and for growth in vivo by Desulfovibrio piger, as "hmc" is a bit misleading. This gene cluster is very similar to nhc (nine-heme cytochrome complex) of D. desulfuricans 27774 (Saraiva LM, 2001). While Hmc has subunits hmcABCDEF including a 16-heme periplasmic subunit (hmcA), nhc lacks the hmcE and hmcF genes, and the hmcA-like subunit is shorter and has nine hemes. Similarly, D. piger lacks hmcEF and has a shorter periplasmic subunit that is very similar to the nine-heme cytochrome (tree browser view).

On date unavailable, commented:

None

On 2017 Apr 23, Barbara L Fredrickson commented:

The following links provide the authors' responses:

• Cole SW, 2014
• Fredrickson BL, 2015
• Fredrickson BL, 2016

On 2017 Apr 11, Nicholas J L Brown commented:

The following articles comment directly on this article:

Brown et al., 2014: https://www.ncbi.nlm.nih.gov/pubmed/25157145 Walker, 2016: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068350/ Nickerson, 2017: http://www.collabra.org/article/10.1525/collabra.81/

On 2014 Dec 05, Gaetano Santulli commented:

Jiang and colleagues report that beta2-adrenergic receptor (B2AR) knockout (KO) mice exhibit a diabetic retinopathy phenotype. We recently demonstrated that B2AR KO mice display a progressive impairment in insulin release that leads to glucose intolerance (1). Our report, which seems to be mechanistically important in the pathophysiology of diabetic rethinopathy (if an animal is glucose intolerant a diabetic retinophaty phenotype appears to be more than obvious) is completely ignored by the Authors. A functional role for B2AR in the regulation of insulin secretion and thereby in the pathogenesis of diabetes had been suggested by the evidence of a decreased number of B2AR in type I diabetes patients (2, 3). Findings from other groups support such a mechanism (4-7). In addition, human polymorphisms in the B2AR gene have been associated with obesity and other metabolic disorders (8, 9). Moreover, the Authors state that B2AR KO mice exhibit attributes of retinal changes common in diabetes, despite normal glucose levels. However, they do not provide any experiment to show glucose (or insulin) levels, nor in basal conditions, nor after a challenge, nor during a clamp assay. Similarly, the Authors also state that in their previous studies they have shown that B1AR KO mice exhibit retinal changes similar to diabetic animals in spite of normal glucose levels, quoting a paper in which there is no experiment showing the claimed normal glucose levels, as well.

We believe that the Readers will appreciate a clarification on these studies by the Authors and the Editors.

Gaetano Santulli MD, PhD 1,2, and Guido Iaccarino MD, PhD 3,4

From the Departments of 1Translational Medical Sciences and 2Advanced Biomedical Sciences, Federico II University, Naples Italy; 3Department of Medicine and Surgery, University of Salerno, Salerno, Italy; 4Multimedica Research Hospital, Milan, Italy.

Essential References 1. Santulli G, Lombardi A, Sorriento D, Anastasio A, Del Giudice C, Formisano P, et al. Age-related impairment in insulin release: the essential role of beta(2)-adrenergic receptor. Diabetes. 2012;61(3):692-701. doi: 10.2337/db11-1027. PubMed PMID: 22315324; PubMed Central PMCID: PMC3282797; http://www.ncbi.nlm.nih.gov/pubmed/22315324

1. Schwab KO, Bartels H, Martin C, Leichtenschlag EM. Decreased beta 2-adrenoceptor density and decreased isoproterenol induced c-AMP increase in juvenile type I diabetes mellitus: an additional cause of severe hypoglycaemia in childhood diabetes? European journal of pediatrics. 1993;152(10):797-801. http://www.ncbi.nlm.nih.gov/pubmed/8223779. PubMed PMID: 8223779; http://www.ncbi.nlm.nih.gov/pubmed/8223779.
2. Noji T, Tashiro M, Yagi H, Nagashima K, Suzuki S, Kuroume T. Adaptive regulation of beta-adrenergic receptors in children with insulin dependent diabetes mellitus. Hormone and metabolic research. 1986;18(9):604-6. Epub 1986/09/01. doi: 10.1055/s-2007-1012385. PubMed PMID: 3023224; http://www.ncbi.nlm.nih.gov/pubmed/3023224.
3. Panagiotidis G, Stenstrom A, Lundquist I. Influence of beta 2-adrenoceptor stimulation and glucose on islet monoamine oxidase activity and insulin secretory response in the mouse. Pancreas. 1993;8(3):368-74. Epub 1993/05/01. http://www.ncbi.nlm.nih.gov/pubmed/8387193. PubMed PMID: 8387193; http://www.ncbi.nlm.nih.gov/pubmed/8387193.
4. Loubatieres A, Mariani MM, Sorel G, Savi L. The action of beta-adrenergic blocking and stimulating agents on insulin secretion. Characterization of the type of beta receptor. Diabetologia. 1971;7(3):127-32. http://www.ncbi.nlm.nih.gov/pubmed/4397807. PubMed PMID: 4397807; http://www.ncbi.nlm.nih.gov/pubmed/4397807.
5. Ahren B, Jarhult J, Lundquist I. Insulin secretion induced by glucose and by stimulation of beta 2 -adrenoceptors in the rat. Different sensitivity to somatostatin. Acta physiologica Scandinavica. 1981;112(4):421-6. http://www.ncbi.nlm.nih.gov/pubmed/6119001. PubMed PMID: 6119001; http://www.ncbi.nlm.nih.gov/pubmed/6119001.
6. Asensio C, Jimenez M, Kuhne F, Rohner-Jeanrenaud F, Muzzin P. The lack of beta-adrenoceptors results in enhanced insulin sensitivity in mice exhibiting increased adiposity and glucose intolerance. Diabetes. 2005;54(12):3490-5. Epub 2005/11/25. doi: 54/12/3490 [pii]. PubMed PMID: 16306366; http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16306366.
7. Large V, Hellstrom L, Reynisdottir S, Lonnqvist F, Eriksson P, Lannfelt L, et al. Human beta-2 adrenoceptor gene polymorphisms are highly frequent in obesity and associate with altered adipocyte beta-2 adrenoceptor function. The Journal of clinical investigation. 1997;100(12):3005-13. Epub 1998/01/31. doi: 10.1172/JCI119854. PubMed PMID: 9399946; PubMed Central PMCID: PMC508512; http://www.ncbi.nlm.nih.gov/pubmed/9399946.
8. Thomsen M, Dahl M, Tybjaerg-Hansen A, Nordestgaard BG. beta2-adrenergic receptor Thr164Ile polymorphism, obesity, and diabetes: comparison with FTO, MC4R, and TMEM18 polymorphisms in more than 64,000 individuals. The Journal of clinical endocrinology and metabolism. 2012;97(6):E1074-9. doi: 10.1210/jc.2011-3282. PubMed PMID: 22466342; http://www.ncbi.nlm.nih.gov/pubmed/22466342

On 2014 Sep 24, Michael Schroda commented:

Excellent study, a big step forward toward the understanding of Hsp70 function in chloroplasts.

On 2017 Oct 31, Morten Oksvold commented:

Please note that this article contains unreliable data, and should not be cited. The central ethical review board in Sweden found research misconduct in six articles by Macchiarini, including this one.

Please see the report from the Central ethical review board in Sweden: http://www.epn.se/media/2516/pressmeddelande-o-12-2016eng.pdf https://drive.google.com/file/d/0By2HqPi4t2RbYzZweVRieVVMajhJQUM0cmFMekwyRVJTUFVr/view

This information was provided by Leonid Schneider (forbetterscience.com).

On 2013 Oct 31, John Cannell commented:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

70% of American toddlers do not take

On 2014 Jan 29, Amanda Capes-Davis commented:

Please be aware that KB is NOT an oral epithelial cell line. The cell line is known to be cross-contaminated with HeLa and so comes from cervical carcinoma. For a list of known cross-contaminated or misidentified cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2016 Nov 15, Yuwei Fan commented:

Thermocycled for only 500 cycles seems to be insufficient to test aging effects.

On 2017 Jan 13, Yuwei Fan commented:

The description of CIELab a* and b* range in page 215 is incorrect. The range is ±100 or −128 to +127 (signed 8-bit integer). [https://en.wikipedia.org/wiki/Lab_color_space]. Delta-E equation in same page is wrong (or maybe a typo) apparently.

On 2017 Jan 11, Misha Koksharov commented:

It would be cool to also have data on evolution of decapod luciferases (Oplophorus, Systellaspis, etc). Unfortunately, only one is known so far. :( Although, there are plenty of them out there in the sea: http://dx.doi.org/10.1007/BF00347123 http://dx.doi.org/10.1016/j.ympev.2014.11.013

On 2013 Dec 16, Tarek Tawfik Amin commented:

This paper addresses a common problem in the developing countries, similar initiatives should be carried in other countries to make use of the available epidemiological data for the sake of comparison and trend exploration. i think the authors have used multiple data sources which strengthen their findings. best wishes and lots of respects.

On 2013 Dec 14, Mohsen Rostami commented:

I just read this paper and found it interesting! I think it will be highly cited by those who work in the related field! Reagrds

On 2013 Aug 08, Winston Timp commented:

Interesting paper highlighting a pathway which could grant predisposition to allergy. Perhaps more subtle effects on TGF-B signaling pathway (than mutation, e.g. epigenetic change) could lead to allergy in genotypically normal individuals.

On 2014 Mar 14, Jonathan Eisen commented:

The first author of this paper, Rachel Adams, wrote a post about the "story behind the paper" for the "microbiology of the Built Environment network" (microBEnet) blog. See How biomass can bias high-throughput surveys of microbial communities