On 2014 Feb 22, Christopher Southan commented:

The 46 PubChem structures refered to in this article can be retrieved via http://www.ncbi.nlm.nih.gov/sites/myncbi/collections/public/1zuPd27ihNyflkXH7XHUWAU5L/ The CIDs are specified in the text, with activity values aligned to the example numbers. Note SureChEMBL SIDs may connect to the patents where addtional SAR data can be found. An open version of the PMID:23506624 text can be found at http://figshare.com/articles/BACE2_as_a_new_diabetes_target_a_patent_review_2010_2012_/977844

On 2014 Nov 14, Christopher Southan commented:

While they followed Roche into BACE2-inhibition patents for diabetes, Novartis have since published a abstract contradicting the target status http://cdsouthan.blogspot.se/2014/12/bace2-as-diabetes-target-or-maybe-not.html

On 2016 Apr 03, Ariel Fernandez commented:

Protein folding in vitro is a spontaneous process [1]. This means it is irreversible in the thermodynamic sense [2]. The endpoints of the folding process, the native state and the denatured ensemble, may be recovered by restoring renaturing or denaturing conditions, respectively. Thus, at a variance with thermodynamics, this is what protein scientists usually mean when they claim that protein folding is reversible [1]. On the other hand, according to the tenets of thermodynamics, the folding and unfolding pathways themselves are untraceable and irreproducible [2]. In fact the very notion of “pathway” for a spontaneous process is thermodynamically meaningless or at least questionable. Dissipative forces intervene in the folding process producing a net increase in the entropy of the universe, and this is the hallmark of irreversibility. Therefore, the intermediate states associated with the folding process are irretrievable, as it would be the case for any spontaneous process in nature or in the lab.

Notwithstanding these thermodynamic considerations, a very active quest for folding intermediates continues to this day [3]. This search may be futile, probably meaningless from a thermodynamic perspective, unless some sort of paradox holds that, at the very least, needs to be properly dispelled. To the best of my knowledge this has not been done. Real folding intermediates are not only very difficult to trap: they do not exist per se, plain and simple. Any claim to the contrary inevitably violates the second law of thermodynamics.

Even more puzzling are the efforts to characterize folding intermediates by denaturing the native state (however carefully [4]). As the second law of thermodynamics tells us, the denaturation process is not the reverse of the folding process: only the endpoints are reversed. To discourage efforts in this direction, it would be more eloquent to resort to an analogy. Imagine you need to describe the way a standing house has been put together. No one in his/her right mind would address the problem by having the house demolished (however carefully), taking snapshots at different stages of demolition and then playing the movie backwards. Yet, intriguingly, a similar reasoning has been assumed to hold mutatis mutandis in the context of protein folding [5]. This accumulation of seeming contradictions may well lead to a paradox - and thermodynamics is full of those - and at the very least the paradox demands proper clarification in thermodynamic terms before the saga for the quest of folding intermediates continues. Ariel Fernandez

References

1. Anfinsen, C.B. Science 181, 223-230 (1973).

2. Planck, M. Treatise on Thermodynamics, 3rd edition, Dover, New York (2010).

3. Vendruscolo M. & Dobson, C.M. Nature Chem. Biol. 9, 216-217 (2013).

4. Jaremko, M., Jaremko, Ł., Kim, H.Y., Cho, M.K., Schwieters, C.D., Giller, K., Becker, S. & Zweckstetter, M. Nature Chem. Biol. 9, 264-270 (2013).

5. Fernandez, A. Biomolecular Interfaces (ISBN 978-3-319-16849-4), Springer, Berlin (2015).

On 2014 Mar 07, Arnaud Chiolero MD PhD commented:

A strong argumentation against the idea that having free access to all kind of (big-)data will lead eventually to better research

On 2016 Sep 27, Andrea Messori commented:

Comment deleted.... Please refer to: https://www.ncbi.nlm.nih.gov/pubmed/23534877#cm23534877_30166

On 2015 Jan 31, George McNamara commented:

I hope the US patent office rejects their patent application based on prior art - MVI has been selling DarkLite adapter since 2000 or earlier (possibly a decade earlier), see http://www.mvi-inc.com/products/microscopy-accessories/darklite-for-autoradiography/

On 2014 Dec 17, Sean Ekins commented:

some slides on this work http://www.slideshare.net/ekinssean/dual-event

On 2016 Sep 27, UFRJ Neurobiology and Reproducibility Journal Club commented:

We’d like to point out that in the legends of all figures in these article (except for Figure 7), the authors mention that data is presented as mean +- s.e.m.; nevertheless, in some of these figures (e.g. 2F, 3B, 3C and 3F), the error bars are clearly asymmetric. As standard errors of the mean are symmetric by definition, this seems to indicate that the data does not match the description in the legend. Therefore, the authors should clarify what the error bars presented stand for, as different kinds of error bars represent very different things and can lead to different inferences about the data (Cumming G, 2007; Krzywinski M, 2013).

On 2015 Mar 29, Harri Hemila commented:

Impure placebo as an unsound concept and other problems in the paper by Howick et al. (2013).

A number of problems in the Howick et al. paper are described at the PLoS ONE comment page and the comments are also available as a separate document with A4 layout.

The above mentioned criticism was formulated to a regular paper by Louhiala P, 2015.

On 2014 Jun 16, Allison Stelling commented:

I did a Spotlight Interview for this paper in Spectroscopy Online: Using Infrared Spectroscopy for Real-Time Diagnostics During Brain Surgery.

On 2014 Jan 31, Huiqi Qu commented:

Evolutionary selection evidence on synonymous codon usage was observed in this study. Email: huiqi.qu@gmail.com

On 2016 Jun 11, Daniel Schwartz commented:

The HOSPITAL score can be used online and in mobile apps here: http://qxmd.com/calculate/calculator_353/hospital-score

Conflict of interest: Medical Director, QxMD

On 2014 Jul 19, Torsten Seemann commented:

The URL in the abstract no longer exists, it has been moved to http://ccb.jhu.edu/software/EDGE-pro/

On 2013 Jun 14, Sebastian Schneeweiss commented:

Nice summary of assumptions and the issues arising when doing 1:1:1 matching with testing of several algorithms. If you plan PS matching of several treatment groups this is worth reading.

On 2014 Jul 20, Chris Carter commented:

The T.Gondii/host interactome Regularly updated

On 2016 Sep 27, Andrea Messori commented:

Modeling the economic consequences of inhibitor development in previously untreated patients with severe hemophilia A

By Andrea Messori, HTA Unit, Regional Health System, 50100 Firenze (Italy)

Background

If one performs a PubMed search using the keywords “Markov AND (haemophilia OR hemophilia) AND inhibitors”, only 4 articles are retrieved (published in 2013, 2003, 2003, and 2000). This demonstrates that, despite its potential advantages, the use of Markov models in haemophilia patients is still very limited. In the past 10 years, the study by Farrugia and co-workers (Haemophilia. 2013 Jul;19:e228-38.) is the only example of a Markov model designed to handle the data of patients with severe disease and inhibitors. Quite recently, we have developed a similar model that has not yet been formally published. Hence, this Comment has the purpose to describe the main characteristics of our model.

Model description

Our model is represented in Figure 1 (link to display this figure: http://www.osservatorioinnovazione.net/papers/markov-hemophilia-figure1.gif ). A commercial software (TreeagePro, Treeage Software Inc., 2011 version, Williamstown, MA, USA) has been employed for its development. Briefly, the core of the model is a decision node (not shown in Figure 1) from which two branches originate, the first describing the patients assigned to recombinant factor VIII (Panel A in Figure 1) and the second those assigned to plasma-derived factor VIII (Panel B in Figure 1). A total of 10 health states are included in the Markov model (see the Appendix reported below for further details). The purpose of the model is to carry out a budget impact analysis in which the replacement therapy and the treatment of inhibitors are the main cost items. The transition probabilities that manage how patients move across the health states are also presented in Figure 1 (Panels A and B). Probabilities with values of 0 or 1 are self-explanatory; accordin to the syntax of TreeagePro, the symbol “#” identifies a probability equal to the value needed to reach 100% after taking into account the other probability/probabilities directly expressed in numerical form and assigned to the other branch(es) of the same node. In each of the two main sections of the model (i.e. recombinant factor VIII [Panel A] and plasma-derived factor VIII [Panel B]), the Markov analysis incorporates the adjustment for annual discount rates and traces the number of cycles evaluated in the iterative process. According to the Markov approach, costs incurred in the model are iteratively summed upon each cycle. Three items participate in the cost analysis, namely the annual cost per patient treated with recombinant factor VIII (denoted as “annualcostric”), the annual cost per patient treated with plasma-derived factor VIII (denoted as “annualcostpd”), and the cost per patient of immunotolerance therapy (denoted as “costofIT”). As regards the syntax of the Treeage software, cost data are handled as “incremental rewards” (denoted as “Incr Rwd”). In other words, the variable “Rewards” was used to cumulate the various cost data at each cycle. The TreeagePro code needed for running the model is available from th author upon request.

Appendix. Detailed description of the 10 health states included in the Markov model

The main health states included in the recombinant branch of the model (ordered bottom-up according to Panel A of Figure 1) are the following: a) state denoted as “Without” in which patients assigned to heath-state ( c) are assumed not to develop high-titer inhibitors and then move to the health state “all-people-final-ric”; b) state denoted as “With” in which patients assigned to heath-state ( c) are assumed to develop high-titer inhibitors and then move to the health state “IT-ric”; c) state denoted as “all people ric” in which patients treated with recombinant factor VIII proceed in their Markov iterative process and are exposed to the risk of developing high-titer inhibitors; d) state denoted as “all-people-final-ric” in which patients treated with recombinant factor VIII (irrespective of whether they have developed or not high-titer inhibitors) proceed in their Markov iterative process until the end of the time horizon without being any longer exposed to the risk of developing high-titer inhibitors; e) state denoted as “IT-ric” in which patients treated with recombinant factor VIII who have developed high-titer inhibitors receive immune-tolerance therapy and move to the health state “post-IT-ric” and then to the health state “all-people-final-ric”. The main health states included in the plasma-derived branch of the model (ordered bottom-up according to Panel B of Figure 1) are the following: f) state denoted as “Without” in which patients assigned to heath-state (h) are assumed not to develop high-titer inhibitors and then move to the health state “all-people-final-pd”; g) state denoted as “With” in which patients assigned to heath-state (h) are assumed to develop high-titer inhibitors and then move to the health state “IT-pd”; h) state denoted as “all people ric” in which patients treated with recombinant factor VIII proceed in their Markov iterative process and are exposed to the risk of developing high-titer inhibitors; i) state denoted as “all-people-final-pd” in which patients treated with recombinant factor VIII (irrespective of whether they have developed or not high-titer inhibitors) proceed in their Markov iterative process until the end of the time horizon without being any longer exposed to the risk of developing high-titer inhibitors. j) state denoted as “IT-pd” in which patients treated with recombinant factor VIII who have developed high-titer inhibitors receive immune-tolerance therapy and move to the health state “post-IT-pd” and then to the health state “all-people-final-pd”. The model was designed to predict in these cohorts the expected expenditures, that were quantified on the basis of the (different) cumulative incidence of high-titer inhibitors and the (different) cost of the replacement products between the cohorts. It should be noted that some health states assigned, in Figure 1, to the first-level branches of both Panels A and B (governed by the Markov node) are not reachable at the first cycle of the Markov process (i.e. probability = 0 at this cycle), but are designed to be reached from the second-level branches, associated with the development or not of high-titer inhibitors. Finally, although the Treaage software allows to manage other variables participating in the calculation of rewards (namely: initial reward denoted as “Init Rwd”, which is summed upon entry in the health state; and: final reward denoted as “Fin Rwd”, which is summed upon exit from the health state), these were not necessary for the purposes of our model and were therefore kept at 0 (as illustrated in the two panels of Figure 1).

On 2014 Jun 20, Christos Chinopoulos commented:

Could it be that LPS-induced succinate over-production is due to itaconate formation? LPS induces Irg1, a gene

coding for cis-aconitate decarboxylase, specifically expressed in cells of macrophage lineage Proc Natl Acad Sci

U S A. 2013 May 7;110(19):7820-5. doi: 10.1073/pnas.1218599110, yielding itaconate. Itaconate is preferentially

used by succinyl CoA ligase forming itaconyl CoA, thus generating an accumulation of succinate when the ligase

operates towards succinyl CoA formation ADLER J, WANG SF, & Lardy HA (1957) The metabolism of itaconic acid by

liver mitochondria. J. Biol. Chem, 229, 865-879, and WANG SF, ADLER J, & Lardy HA (1961) The pathway of

itaconate metabolism by liver mitochondria. J. Biol. Chem, 236, 26-30.

On 2014 Jan 01, José Morales Roselló commented:

Like many other psicological disorders in the past, science goes behind reality. In this syndrome, children have an absolutely normal father (or mother) but have been programmed to hate him. The hate and the attitude of the children have no correlation with the father behaviour, and have more to do with a subtle denigration campaign with a mother (or father) origin. The original syndrome descriptions made by Gardner are easily found in most of the cases.

On 2013 Jul 17, James Troendle commented:

The section on the importance of interim monitoring leaves out one important drawback to sequential studies when the sequential design is motivated by reducing the sample size. Yes, sequential studies can on average reduce the sample size. However, they do that by delivering reduced precision of the effect estimate. This reduction in precision of the final estimate is often ignored when a decision is made about whether to adopt a sequential or fixed design.

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).

• No appropriate description of the interventions in each study arm

• The study evaluates surrogate instead of definitive outcomes.

• No description of allocation concealment mechanisms.

• No description of sample size calculation.

• The full text article does not specify dates for patient recruitment and follow-up

• 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)

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

On 2013 Jul 10, Julia Gilden commented:

This is a nice little paper that might explain the frustrations of researchers having trouble with consistent ectopic expression. The authors speculate in the discussion that reduced RNA Polymerase I transcription at high densities may reflect a developmental transition toward the short stumpy form of the parasite. It is not clear, however, what the authors think this reduced RNA Pol I activity might accomplish, particularly because (as they point out) procyclin transcription is RNA Pol I-dependent, and a switch to the procyclin coat must be induced upon uptake by the fly.

On 2013 Oct 24, Tom Kindlon commented:

Objective outcome data from the chronic fatigue syndrome specialist services would have been interesting

It is disappointing that Crawley et al.¹ presented no objective outcome data from the six chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) specialist services; an audit of Belgian CFS rehabilitation centres that used cognitive behavioural therapy (CBT) and graded exercise therapy (GET) found that, while improvements were reported with various subjective measures, no change was noted with exercise testing.^2-4 Moreover, there was actually a decrease in average hours in paid employment, from 18.3% of a 38 hour-working week to 14.9%.

Discrepancies between subjective and objective measures have also been found in trials of both CBT^5,6 and GET for CFS.⁷ Indeed, in the PACE Trial (which compared to the specialist services reported similar improvements on the Chalder Fatigue questionnaire (CFQ) but better SF-36 physical functioning (PF) scores), although moderate sized improvements were found with self-report instruments like the CFQ and SF-36 PF, differences with more objective measures were smaller, if they existed at all.^8,9 For example, there was no difference between the CBT and specialist medical care only (SMC) groups on the six minute walking test.⁸ And no difference between SMC and both CBT and GET in terms of employment losses, overall service costs, welfare benefits or other financial payments.⁹

Research on patient-reported outcome measures, and measures of improvement that CFS patients consider important, is underdeveloped.¹⁰ Given the known considerable impact of CFS/ME on productivity and employment in those attending such services, it is reasonable to speculate that many patients, and indeed other taxpayers, would find employment data of more interest.¹¹

References:

1 Crawley E, Collin SM, White PD, Rimes K, Sterne JAC, May MT, et al. Treatment outcome in adults with chronic fatigue syndrome: a prospective study in England based on the CFS/ME National Outcomes Database. QJM first published online March 28, 2013 doi:10.1093/qjmed/hct061

2 Rapport d’évaluation (2002-2004) portant sur l’exécution des conventions de rééducation entre le Comité de l’assurance soins de santé (INAMI) et les Centres de référence pour le Syndrome de fatigue chronique (SFC). 2006. http://www.inami.fgov.be/care/fr/revalidatie/general-information/studies/study-sfc-cvs/pdf/rapport.pdf. Accessed March 30, 2013 (French language edition)

3 Evaluatierapport (2002-2004) met betrekking tot de uitvoering van de revalidatieovereenkomsten tussen het Comité van de verzekering voor geneeskundige verzorging (ingesteld bij het Rijksinstituut voor Ziekte- en invaliditeitsverzekering) en de Referentiecentra voor het Chronisch vermoeidheidssyndroom (CVS). 2006. Available online: http://www.inami.fgov.be/care/nl/revalidatie/general-information/studies/study-sfc-cvs/pdf/rapport.pdf. Accessed March 30, 2013 (Dutch language version)

4 Stordeur S, Thiry N, Eyssen M. Chronisch Vermoeidheidssyndroom: diagnose, behandeling en zorgorganisatie. Health Services Research (HSR). Brussel: Federaal Kenniscentrum voor de Gezondheidszorg (KCE); 2008. KCE reports 88A (D/2008/10.273/58) https://kce.fgov.be/sites/default/files/page_documents/d20081027358.pdf Accessed March 30, 2013

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

6 Knoop H, Prins JB, Stulemeijer M, van der Meer JW, Bleijenberg G. The effect of cognitive behaviour therapy for chronic fatigue syndrome on self-reported cognitive impairments and neuropsychological test performance. Journal of Neurology, Neurosurgery & Psychiatry 2007; 78:434-446.

(references continue in next message)

On 2013 Oct 24, Tom Kindlon commented:

None

On 2013 Jun 29, Andries Zijlstra commented:

In addition to the specific experimental findings, this article demonstrates that: 1) Regulating a molecular mechanism of migration can be an independent predictor of patient survival. 2) For molecular mechanism that drive cancer, the protein availability and function and not gene-expression correlate to disease progression and patient outcome.

On 2014 Jan 28, Serge Ahmed commented:

This study is very interesting but it also has several potential problems that may limit its relevance to understand the neural basis of compulsive cocaine use. First, there is no solid evidence for compulsive cocaine use in this study. For instance, mice were clearly able to inhibit cocaine seeking at the onset of the signaled drug-off periods. What they seemed unable to do was to wait until the end of the drug-off periods before resuming responding. This behavior may merely reflect an anticipation of cocaine availability at the end of the drug-off periods and not a compulsion (see: http://www.ncbi.nlm.nih.gov/pubmed/22985696). In addition, PR responding for cocaine was very low in this study and, in fact, 10-30 times lower that PR responding for food (i.e., about 50 versus 1000 responses per PR sessions for cocaine and food, respectively). In other words, mice gave up quickly on cocaine, without spending much effort. Calling this behavior “compulsive” or even “compulsive-like” is excessive. Finally, the facilitatory effects of CNO-induced inhibition of D2-MSNs on PR responding for cocaine should be interpreted with caution. These effects were seen in a small group of mice (n = 6) that had an atypical low baseline (i.e., saline) level of PR responding compared to the other groups from this study (i.e., 18.7±6.1 versus 35±9.5, 41.5±18.2 or 59.2±24.1). In fact, PR responding following CNO-induced inhibition of D2-MSNs did not differ from baseline responding in these other groups.

On 2014 Jul 22, Veronica Alvarez commented:

Thanks for your interest in our study. These are interesting comments but based on incorrect assumptions. First, the behavioral score is a combination of breakpoint and responding during the time out period and thus it asses/compounds the individual variability in the incentive motivation for cocaine and the inability to restrain responding when the drug is not available (even when it is an anticipatory response and subjects “are unable to wait until the end of the drug period”). Second, the comparison of breakpoint for cocaine and food is an unfair comparison under these conditions. Mice responding for food were under caloric restriction and must work during the session to earn their remaining daily caloric requirement. This is a very different situation than for cocaine and the incentive motivation for food and cocaine are just incomparable. In addition, mice trained on FR1 for cocaine and FR10 for food which will influence the breakpoint values. The study was not designed to compare breakpoints for cocaine and food. Third, there is no effect of CNO per se. The effect seen corresponds to activation of Gi-coupled DREADDS in indirect-pathway D2-receptor expressing neurons in the NAc which is shown to inhibit the output (GABA transmission) of these neurons and increase the breakpoint for cocaine compared to days the same mice received saline (Fig. 4). The difference in responding between mice in Fig. 1-3 and mice in Fig. 4 and 5 is due to the fact that these are two different strains of genetically engineered mice. Experiments in Fig. 1-3 utilized Drd1a-GFP mice (Swiss Webster background) to identity direct- and indirect-pathway neurons while experiments in Fig. 4 and 5 used Adora2a-Cre-/+ mice (C57Bl6 background) to selectively manipulate the activity of indirect pathway neurons using DREADDs or ChR2. Contrary to the comment’s statement, responding was higher for mice of C57Bl6 background (35±9.5 mg/kg/day) than mice of SW background (18.7±6.1 mg/k/day) but the rate of responding might not be so different are the sessions were longer for C57Bl6 mice and there was no drug-off period.

On 2014 Jul 25, Serge Ahmed commented:

Thanks for your comments on my previous comments which, contrary to what you claim, were not based on “incorrect assumptions”. I leave the readers to judge for themselves. Here I just want to persist and sign for the sake of clarification. There is no solid evidence for compulsive cocaine use in your study. Mice gave up easily on cocaine and this apparently, I now learn from your comments, regardless of strain differences. I agree that your study was not designed to directly compare the motivation for food with that for cocaine. But still it shows that mice are able to produce hundreds of responses to obtain certain rewards of importance to them. The fact that mice are able to but do not expand a comparable level of effort to obtain cocaine shows that they are not that motivated for cocaine. More specifically, it shows that even after several weeks of cocaine intake, the motivation for cocaine fails to acquire a degree of intensity that approaches that for food in hungry mice. This is perhaps one of the reasons why mice were trained on a FR1 for cocaine in your study and not on a FR10 like for food. Finally, your operational measure of “perseverative responding” is difficult to interpret because the introduction of the drug-off periods also considerably influences cocaine self-administration during the drug-on periods. Judging from Figure 1, cocaine self-administration rapidly becomes very irregular, with short and long inter-injection intervals. As a result, some of the inter-injection intervals during the drug-on periods are much longer than the drug-off periods themselves, making behavior during the latter periods quite difficult to interpret!

On 2014 May 11, Chetan Mandelia commented:

Author Comment- This study was done back in 2009 when smart-phones and internet access through mobile phones were very limited, at least in India. Would be very interesting to see the prevalence of "Ringxiety" in present times.

On 2013 Nov 15, George McNamara commented:

Instead of citing this reference (IOS Press repackages many of its manuscripts to expand its bundles to make more money), please cite our original publication:

Spectral imaging in preclinical research and clinical pathology. Levenson R, Beechem J, McNamara G. Anal Cell Pathol (Amst). 2012;35(5-6):339-61. doi: 10.3233/ACP-2012-0062. Review. PMID: 22475632

On 2015 Oct 22, George McNamara commented:

This paper (ACP branded, the original publication) may now be open access at

http://downloads.hindawi.com/journals/acp/2012/904828.pdf

On 2014 Apr 05, Andrea Messori commented:

Incidence of new vertebral fractures in women treated with an antireabsorptive agent or placebo: re-analysis of 9 randomized trials

In the study of anti-reabsorptive agents for preventing vertebral fractures in women with post-menopausal osteoporosis, the systematic review published by Migliore et al[1] is the most recent contribution in this area and has also the merit that mixed treatment comparisons were carried out.

One limitation of the study by Migliore et al[1] is that, in studying the end-point of new vertebral fractures according to 9 randomized placebo-controlled trials [2-10], the crude event rates were not presented for individual trials. In fact, only the denominators of these rates were reported (see Table I of the publication by Migliore et al[1]). In addition, these denominators were affected by some typographical errors (eg. see the number of patients enrolled in the placebo arm of the trial by Lieberman et al. [3], N=42, which is erroneous and seems to be an inadvertent duplicate presentation of the age of the same patients).

We have previously stressed that the crude event rates extracted from individual trials should be reported in any meta-analysis study [11] because this presentation allows us to verify the quality of the extraction process and the reliability of the final results.

We have therefore re-extracted the event rates from the 9 trials [2-10] and we have reanalyzed these rates by redoing the same meta-analysis carried out by Migliore et al.[1] (see their Table II, first five comparisons vs placebo). Our analysis was based on the random-effect model as implemented in the OMA software [12]. We expressed our results as both odds-ratio and relative risk.

Figure 1 shows the results of this re-analysis. Our results are nearly identical to those published by Migliore et al. [1] and can therefore be seen as a useful confirmation of the findings of the referenced study.

Andrea Messori HTA Unit ESTAV Centro 50100 Firenze Italy

FIGURE 1 - Incidence of new vertebral fractures in women treated with an anti-reabsorptive agent or placebo.

The Forest plot shows the subgroup analysis for 5 treatments (alendronate, risedronate, zolendronate, ibandronate, and denosumab) compared with placebo. The original material was derived from 9 randomized trials [2-10]. The meta-analysis results are expressed as odds-ratio (Panel A) and relative risk (Panel B).<br> Abbreviations and symbols: horizontal black lines represent the 95CI% around the event rate (■); yellow diamonds represent the pooled (meta-analytical) rate with its 95%CI for the various subgroups, while the blue diamond represents the pooled overall rate across the two subgroups. The vertical dotted line (in red) represents the pooled rate from the overall series of 9 trials. I² is the index of heterogeneity and is accompanied by the p-value of its statistical significance. Abbreviations: RR, relative risk; Ev, number of events; Trt, number of patients in the treatment group; Ctrl, number of patient in the control group; ALE, alendronate; RIS, risedronate,; ZOL, zolendronate; IBA, ibandronate; DEN, denosumab.

This figure can be downloaded at the address: http://www.osservatorioinnovazione.net/papers/migliore2013fig1.jpg

References

1. Migliore A, Broccoli S, Massafra U, Cassol M, Frediani B. Ranking antireabsorptive agents to prevent vertebral fractures in postmenopausal osteoporosis by mixed treatment comparison meta-analysis. Eur Rev Med Pharmacol Sci. 2013 Mar;17(5):658-67.

2. Black DM, Cummings SR, Karpf DB, Cauley JA, Thompson DE, Nevitt MC, Bauer DC, Genant HK, Haskell WL, Marcus R, Ott SM, Torner JC, Quandt SA, Reiss TF, Ensrud KE. Randomised trial of effect of alendronate on risk of fracture in women with existing vertebral fractures. Fracture Intervention Trial Research Group. Lancet. 1996 Dec 7;348(9041):1535-41. PubMed PMID: 8950879.

3. Liberman UA, Weiss SR, Bröll J, Minne HW, Quan H, Bell NH, Rodriguez-Portales J, Downs RW Jr, Dequeker J, Favus M. Effect of oral alendronate on bone mineral density and the incidence of fractures in postmenopausal osteoporosis. The Alendronate Phase III Osteoporosis Treatment Study Group. N Engl J Med. 1995 Nov 30;333(22):1437-43. PubMed PMID: 7477143.

4. Cummings SR, Black DM, Thompson DE, Applegate WB, Barrett-Connor E, Musliner TA, Palermo L, Prineas R, Rubin SM, Scott JC, Vogt T, Wallace R, Yates AJ, LaCroix AZ. Effect of alendronate on risk of fracture in women with low bone density but without vertebral fractures: results from the Fracture Intervention Trial. JAMA. 1998 Dec 23-30;280(24):2077-82. PubMed PMID: 9875874.

5. Harris ST, Watts NB, Genant HK, McKeever CD, Hangartner T, Keller M, Chesnut CH 3rd, Brown J, Eriksen EF, Hoseyni MS, Axelrod DW, Miller PD. Effects of risedronate treatment on vertebral and nonvertebral fractures in women with postmenopausal osteoporosis: a randomized controlled trial. Vertebral Efficacy With Risedronate Therapy (VERT) Study Group. JAMA. 1999 Oct 13;282(14):1344-52. PubMed PMID: 10527181.

6. Reginster J, Minne HW, Sorensen OH, Hooper M, Roux C, Brandi ML, Lund B, Ethgen D, Pack S, Roumagnac I, Eastell R. Randomized trial of the effects of risedronate on vertebral fractures in women with established postmenopausal osteoporosis. Vertebral Efficacy with Risedronate Therapy (VERT) Study Group. Osteoporos Int. 2000;11(1):83-91. PubMed PMID: 10663363.

7. Black DM, Delmas PD, Eastell R, Reid IR, Boonen S, Cauley JA, Cosman F, Lakatos P, Leung PC, Man Z, Mautalen C, Mesenbrink P, Hu H, Caminis J, Tong K, Rosario-Jansen T, Krasnow J, Hue TF, Sellmeyer D, Eriksen EF, Cummings SR; HORIZON Pivotal Fracture Trial. Once-yearly zoledronic acid for treatment of postmenopausal osteoporosis. N Engl J Med. 2007 May 3;356(18):1809-22. PubMed PMID: 17476007.

8. Lyles KW, Colón-Emeric CS, Magaziner JS, Adachi JD, Pieper CF, Mautalen C, Hyldstrup L, Recknor C, Nordsletten L, Moore KA, Lavecchia C, Zhang J, Mesenbrink P, Hodgson PK, Abrams K, Orloff JJ, Horowitz Z, Eriksen EF, Boonen S; HORIZON Recurrent Fracture Trial. Zoledronic acid and clinical fractures and mortality after hip fracture. N Engl J Med. 2007 Nov 1;357(18):1799-809. Epub 2007 Sep 17. PubMed PMID: 17878149.

9. Chesnut III CH, Skag A, Christiansen C, Recker R, Stakkestad JA, Hoiseth A, Felsenberg D, Huss H, Gilbride J, Schimmer RC, Delmas PD; Oral Ibandronate Osteoporosis Vertebral Fracture Trial in North America and Europe (BONE). Effects of oral ibandronate administered daily or intermittently on fracture risk in postmenopausal osteoporosis. J Bone Miner Res. 2004 Aug;19(8):1241-9. Epub 2004 Mar 29. PubMed PMID: 15231010.

10. Cummings SR, San Martin J, McClung MR, Siris ES, Eastell R, Reid IR, Delmas P, Zoog HB, Austin M, Wang A, Kutilek S, Adami S, Zanchetta J, Libanati C, Siddhanti S, Christiansen C; FREEDOM Trial. Denosumab for prevention of fractures in postmenopausal women with osteoporosis. N Engl J Med. 2009 Aug 20;361(8):756-65. doi: 10.1056/NEJMoa0809493. Epub 2009 Aug 11. Erratum in: N Engl J Med. 2009 Nov 5;361(19):1914. PubMed PMID: 19671655.

11. Messori A, Fadda V, Maratea D, Trippoli S. The need to know crude event rates in meta-analysis. Am Heart J. 2013 Sep;166(3):e17. doi: 10.1016/j.ahj.2013.06.016. Epub 2013 Jul 25. PubMed PMID: 24016516.

12. OMA software (OMA, Open Meta-Analyst version 4.16.12, Tufts University, U.S., url http://tuftscaes.org/open_meta/)

On 2014 Mar 19, Arnaud Chiolero MD PhD commented:

A very good comment on a difficult topic

On 2013 Dec 20, Eric Johnson commented:

I get comments referring to this paper quite a bit, so I wanted to add a clarification that many casual readers seemed to have missed. The title uses "RADseq" generically, and then analyzes two different protocols: "RADseq" with the shearing step (Baird et al., 2008), and ddRAD which replaces the shearing step with a frequently-cutting enzyme (Peterson et al., 2012). The results are not the same for the two protocols. For example, Table 1 shows that "standard" RADseq deviates from the expected value of π by .995, while ddRAD deviates by .836.

All existing genotyping by sequencing methods that reduce the complexity of the genome will have biases and missing data when polymorphisms disrupt the sequence used to anchor the amplification and subsequent sequencing, and this paper shows how these biases can affect the calculation of population statistics. I just wanted to make clear the distinction between the two protocols, so when researchers use one or the other they can understand how to plan their projects and analyses accordingly.

[Conflict of interest note: I am an author on Baird et al.]

On 2017 Jul 23, David Keller commented:

Final Comments on "The Ethics of Commercial Testing"

Organizations such as the USPSTF issue guidelines which are based on the results of large clinical trials and therefore apply on average to entire populations, but may not apply to atypical individuals. We have all seen "outliers" who suffered a heart attack despite having few or no Framingham risk factors. Tests which are not justified on a population-wide basis can yield valuable information for atypical individuals. Since risk scores are not perfect at predicting who will have an adverse outcome, individuals should be allowed to decide for themselves how much risk they are willing to take, and how much of their own money they are willing to spend to assess their risk.

Consider the Affordable Care Act's mandate of free aneurysm screening for men aged 65 to 75 who have ever smoked: a man aged 65 who quit smoking 30 years ago gets a free ultrasound, but a 64 year old man who has been smoking 2 packs per day for the past 40 years does not. This makes no clinical sense, but is a perfect example of what Charles Dickens [1] meant when he said "the law is an ass [donkey]". Clinical decisions should be left to patients and their physicians, not written into law. Furthermore, these "free" ultrasounds will cost taxpayers a lot more if ordered by physicians and performed in hospital radiology departments than if patients can self-refer to commercial test companies which offer abdominal ultrasounds for $129, with carotid and peripheral artery screens included for no additional fee. The cost of hospital-based imaging is inflated in part due to excessive regulation. Commercial imaging companies can provide ultrasound at such a low cost partly because they are not yet burdened with providing mandatory counseling sessions which their customers may not even want.

Here is the crux of our disagreement. I believe that individuals in a free society should be allowed to purchase tests such as ultrasound and genetic testing, which pose no risk of direct harm. Stigmatizing commercial vendors of such tests as unethical for not providing counseling is the first step toward laws mandating counseling, which will increase the cost of the tests. To me, that outcome would be unethical.

The above comments were posted on an Annals of Internal Medicine website on March 26, 2013, and are being posted on PubMed Commons to complete the chain of comments for readers with no access to the Annals website.

[1] Mark Twain said it too, but was quoting Charles Dickens, through the character Mr. Bumble in the novel "Oliver Twist".

On 2013 Nov 07, Allison Stelling commented:

This paper found that an increase in volume in the brain's "irrigation system" (the ventricular area) could be observed in patients with age-related disorders like Alzheimer disease. This could suggest that imbalances in brain's delicate nutrient and chemical content may be one of the things that promotes the onset of these diseases.

On 2016 Mar 22, Joshua L Cherry commented:

This excellent study provides much useful information, but some important points are not apparent from the article. An important claim of the article is that the unmutated common ancestor (UCA) antibody binds the founder ENV protein with high affinity. However, several amino acids in the important CDR3 of the heavy chain “UCA” cannot have been encoded by germline sequences. These include most of the RGQLVN sequence that comprises six of the twelve paratope residues in the heavy chain. Either the nucleotide positions in question represent mutated germline residues, or they represent random additions by TdT. In the first case, the “UCA” that bound antigen with high affinity actually included mutations, presumably the product of affinity maturation. In the second case, we cannot know the identities of the original, unmutated nucleotides, and it is reasonable to suspect that the true UCA had a different sequence and a lower affinity for ENV. In any case, the fact that so many important residues are not encoded by the germline might mean that antibodies of this type are rare in the naive repertoire and therefore difficult to elicit.

The reconstructed UCA sequence contains 27 bases between the V and J regions. The longest perfect match to any germline D segment is just five bases. Five bases would be an unusually small size for a D region; less than 1% of the naive B cell repertoire contains a D region of five or fewer bases. Furthermore, a total of 22 N nucleotides, though not extraordinary, would be larger than typical. This suggests that some of the “UCA” bases in this region, including some of those encoding the critical RGQLVN sequence, are actually mutated D nucleotides, presumably selected for higher affinity to ENV.

Suppose, though, that the 22 bases that do not match the germline indeed represent N nucleotides, randomly added by TdT (with perhaps a small contribution from P nucleotides). In that case, we cannot know with any certainty what these bases were in the unmutated ancestor. If these bases changed early in the affinity maturation, perhaps greatly increasing the more modest affinity of the actual unmutated ancestor, there would be no way to know this.

The authors did construct three other candidate UCAs that differed at one or two amino acids. These, however, encompass only a small component of the uncertainty in the UCA sequence. Furthermore, results with these variants illustrate the concern raised here. Two of the variants bore an E at the third position of the critical hexapeptide, which is consistent with a longer D region. These more plausible UCA antibodies exhibited a 3.8- to 7-fold reduction in ENV affinity compared to the candidate containing RGQLVN.

If the UCA sequence is correct, the fact that several of the most important residues are encoded by randomly added nucleotides may have implications for the ease of eliciting similar antibodies through vaccination. Sequences encoded by commonly used germline segments will be present at reasonable frequencies in the naive B cell repertoire. Sequences encoded by N nucleotides will be rarer. If they must be associated with unusually short D regions, the combination will be rarer still. To the extent that a vaccination strategy is aimed at eliciting antibodies of this type, this may be a problem.

On 2014 Feb 12, David Keller commented:

The “Special Article” on Influenza Vaccines by Peter Doshi, PhD. (1) casts doubts on the benefits of influenza vaccination in a way which could dangerously mislead clinicians. He states that “influenza vaccines target a disease that is, for most people, self-limiting. While unpleasant, today, tragedies are rare”. This statement ignores the role the vaccine has played in preventing tragedies such as the 1918 flu pandemic, in which influenza was seen to be a highly contagious infection capable of quickly killing untold millions of humans, including the young and healthy. Doshi further states that between 33 and 100 adults would need to be vaccinated to prevent one case of influenza. This statistic is misleading because it pertains to the U.S. population, in which tens of millions get annual flu vaccinations, providing individuals with a broad-spectrum of antibodies to influenza, and partial herd immunity at a population level. The number needed to treat to prevent one case of influenza would undoubtedly be much lower if this huge segment of the population were not immunized. To achieve the full benefits of herd immunity, at least 80% of healthy Americans must be immunized (2), which is a worthy goal. Doshi cites retrospective cohort studies showing a 48% reduction in mortality among the elderly who are vaccinated, but decries the lack of evidence from placebo-controlled trials. However, given the evidence we do have, it would seem unethical to administer placebo instead of influenza vaccine to persons over age 75, for lack of equipoise (the same reason a randomized controlled trial of smoking has never been conducted). Doshi objects that the increase in influenza vaccination rates has not been accompanied by a decrease in total winter mortality. However, the relevant statistic to examine would be age-adjusted annual mortality. Everyone dies sooner or later, but I would rather die at age 85 than at age 75, regardless of the season, even if it means I have to get a flu shot annually. The problem among the elderly of inadequate antibody titer increase after influenza vaccine has been pointed out before, and is being addressed by such measures as increasing the dose of vaccine or changing the route of administration (3); it is not a reason to abandon the benefits of immunization in this population.

1) Doshi P. Influenza Vaccines: Time for a Rethink. JAMA Intern Med.2013;173(11):1014-1016. doi:10.1001/jamainternmed.2013.490.

2) Plans-Rubió P. The vaccination coverage required to establish herd immunity against influenza viruses. Prev Med. 2012 Jul;55(1):72-7. doi: 10.1016/j.ypmed.2012.02.015. Epub 2012 Mar 4.3.

3) DiazGranados CA, Dunning AJ, Jordanov E, Landolfi V, Denis M, Talbot HK. High-dose trivalent influenza vaccine compared to standard dose vaccine in elderly adults: safety, immunogenicity and relative efficacy during the 2009-2010 season. Vaccine. 2013 Jan 30;31(6):861-6. doi: 10.1016/j.vaccine.2012.12.013.

On 2013 Oct 28, Mick Watson commented:

We have now published the software behind many of the analyses in this paper:

Watson M, Schnettler E, Kohl A. (2013) viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. Bioinformatics. 29(15):1902-3

http://www.ncbi.nlm.nih.gov/pubmed/23709497

The website for the software is here: http://www.ark-genomics.org/bioinformatics/virome

On 2014 Dec 07, Eric Vallabh Minikel commented:

Please see our recent work in which we have provided evidence that the apparent anticipation in E200K families is driven by ascertainment bias: Minikel EV, 2014

On 2014 Dec 17, Sean Ekins commented:

Find out more about CDD here https://www.collaborativedrug.com/

On 2014 Dec 17, Sean Ekins commented:

slides using CDD for a collaboration http://www.slideshare.net/ekinssean/bio2014-ppt-sean-ekins-version-4

On 2014 Jun 02, Gerhard Nebe-von-Caron commented:

article is open access at http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22293/pdf

On 2013 Dec 15, Bonnie Barrilleaux commented:

The code used to generate Fig. S7 is available on Github.

On 2014 Nov 25, Harri Hemila commented:

Khan AA, 2013 reviewed potential interventions against neonatal tetanus. Vitamin C might also be included as a potential intervention worth further study.

According to WHO 2005, p. 27, Somalia has had particularly high rate of neonatal tetanus; 16.5 neonatal tetanus deaths per 1000 live births in 1999. The prevalence of vitamin C deficiency has also been particularly high in Somalia, WHO 1999, Table 2. The two conditions might have associations.

In dozens of animal studies, vitamin C increased resistance against diverse infections and purified bacterial toxins Hemilä, 2006. In particular, Dey PK, 1966 reported that five rats administered twice the minimal lethal dose of tetanus toxin all died, whereas 25 rats administered vitamin C either before or after the toxin all lived. CHAKRABARTI B, 1955 reported that tetanus patients had lower plasma vitamin C levels than healthy people, and tetanus patients who died had lower levels than those who survived. Furthermore, tetanus patients had elevated levels of dehydroascorbate, which is the oxidized form of vitamin C. Such changes in vitamin C metabolism suggest that it might be involved in the pathogenesis of tetanus.

One single controlled trial has examined the effect of vitamin C in the treatment of tetanus; the trial was undertaken in Bangladesh by Jahan K, 1984. Vitamin C at a dosage of 1 g/day was administered intravenously alongside conventional treatment. In tetanus patients aged 1 to 12 years, vitamin C treatment was associated with a 100% reduction in case fatality rate (95% CI from -100% to -94%): 74% (23/31) of the control children died but none in the vitamin C group (0/31). Although the Jahan trial has methodological shortcomings, the findings should not be ignored Hemilä H, 2013. Evidently the possible effects of vitamin C on neonatal tetanus patients should be studied.

On 2013 Oct 23, Stephen Turner commented:

This paper is a groundbreaking exploration of the use of metagenomics to investigate and determine the causal organism of an infectious disease outbreak. The authors retrospectively collected fecal samples from symptomatic patients from the 2011 Escherichia coli O104:H4 outbreak in Germany and performed high-throughput shotgun sequencing, followed by a sophisticated analysis to determine the outbreak's causal organism. The analysis included comparing genetic markers from many symptomatic patients' metagenomes with those of healthy controls, followed by de novo assembly of the outbreak strain from the shotgun metagenomic data. This illustrates both the power, but the real limitations, of using metagenomic approaches for clinical diagnostics. Also see David Relman's synopsis of the study in the same JAMA issue.

On 2014 Feb 20, Koji Ohira commented:

We made the electrophoresis chambers and performed the CLARITY according to the protocol. The chambers were made with the same materials/dimensions as the ones shown in the methods by a manufacturer. However, brains did not become transparent. I think that hydrogel tissue embedding is going well, but electrophoretic tissue clearing (ETC) is not. In our ECT, brain samples were applied with 30V at 37 °C for more than 10 days. Many air bubbles were generated around both electrodes during ETC and seemed to disturb the electricity. In fact, more than 50V cannot apply to the chamber in our system. I heard that some of our colleagues failed to make brain transparent with exactly same problems (i.e. a lot of air bubbles were generated). When you established the method, would you have a similar problem? Any tips? I wonder if I could get your comments and advice about that.

On 2014 Aug 29, Felicitas Merz commented:

!!Please note!! There was a mistake in the first version of the pdf. The formulation of the culture medium does NOT content N-hydroxysuccimide, but normal horse serum (25%). This will be corrected as soon as possible. For any further questions or comments, please contact us.

On 2013 Jun 16, Liam Paninski commented:

Seems very promising, along similar lines to recent work by Ahrens et al.

On 2014 Apr 08, David Reardon commented:

The authors of this study¹ concluded that smoking explains about one-third of the variation in preterm birth rates among low income and high income groups (SES) while reproductive history accounts for only one-fourth of preterm births.

Unfortunately this analysis and conclusion is marred by the incorrect assumption that smoking behavior is independent of prior reproductive history. It is not.

Smoking behavior is driven by many emotional factors, including loss and bereavement.² Women are especially more likely to explain a desire to smoke to cope with emotional upsets.³

Most importantly to the study at hand, research has consistently shown that women with a history of abortion smoke substantially more.^4,5 In addition, a dose effect has also been observed, with the number of abortions correlating with even higher rates of smoking.⁶

Research has also shown that women with a history of abortion are more likely to persist in or increase smoking (and alcohol or illegal drug use) during subsequent wanted pregnancies.^7,8 The most common explanation for this—provided by women themselves and by therapists experienced in treating post-abortion maladjustment⁹ is that subsequent wanted pregnancies may stir up unresolved feelings of loss, grief, or guilt relative to past abortions. From this perspective, smoking, drinking, and the use of other mood altering substances are just forms self-medication employed to assist in the repression of unresolved negative emotions.

A causal connection between abortion and smoking behavior is reported in a survey of 527 women interviewed one month after their abortions in which 23% reported using smoking specifically “to help deal with [their] abortion." Drinking and drug use were also reported as being used “to help deal with” their abortions by 18% and 9% respectively.10 Yet another follow up survey of women after their abortions found that higher post-abortion anxiety scores correlated to heavier smoking patterns.¹¹

It is also known that smoking rates increase with exposue to trauma and PTSD^12. This is important because studies of abortion patients, using multiple scales and assessments before and subsequent to abortion, show a significantly higher rates of PTSD following abortion.^13,14,15

In light of this evidence, it is clear that history of abortion should not be treated as simply an aspect of a woman’s physical history. It has psychological components more profound than, for example, a history of placenta previa. These psychological reactions can contribute to behaviors such as elevated smoking, drinking, and drug use which may not only persist through subsequent wanted pregnancies^16, but may even be accentuated by the emotions surrounding the pregnancy.⁹

In light of the above observations, I would encourage the authors to undertake additional analyses to tease out any possible distinctions between the direct biological effect associated with abortion and the possible indirect effects which may be associated with the psychological effects of abortion on behaviors like smoking.

Notably, the current study observe adjusted odds ratios for extremely preterm, very preterm, and moderately preterm for abortion (1.28, 1.16, 1.07, respectively) which were in a range similar to the adjusted odds ratios for smoking (1.21, 1.23, 1.15). Additional analyses could be performed to separate the potential effects of smoking and abortion.

In my proposed analysis, the first uninterrupted pregnancy outcomes (full term live singleton birth, stillbirth, moderate preterm, very preterm, extremely preterm, miscarriage, ectopic pregnancy) would be compared for three groups of women (no smoking, quit smoking during first trimester, smoked beyond first trimester) with results segregated for a prior exposure to induced abortion.

The proposed analysis would also allow us to determine if a history of abortion does reduce the likelihood that woman will stop smoking in the first trimester. In addition, comparing the two groups of women without any history of smoking would give us a clearer picture of the effects of abortion when smoking is not a confounding factor. This comparison would not eliminate other possible indirect, emotional factors (such as eating disorders, which can also be associated with abortion^9, might still play a role, but it would at least demonstrate whether smoking behavior in combination with abortion is confounding these currently published results.

References

1) Raisanen S, Gissler M, Saari J, Kramer M, Heinonen S (2013) Contribution of Risk Factors to Extremely, Very and Moderately Preterm Births – Register- Based Analysis of 1,390,742 Singleton Births. PLoS ONE 8(4): e60660.

2) Parkes CM, Brown RJ. Health after bereavement. A controlled study of young Boston widows and widowers. Psychosom Med. 1972 Sep-Oct;34(5):449-61.

3) United States Public Health Service, Adult Use of Tobacco. U.S. Dept of Health, Education and Welfare, CDC, Bureau of Health Education (1975)

4) Pedersen W. Childbirth, abortion and subsequent substance use in young women: a population-based longitudinal study. Addiction. 2007 Dec;102(12):1971-8.

5) Henriet L, Kaminski M. Impact of induced abortions on subsequent pregnancy outcome: the 1995 French national perinatal pregnancy survey, Br J Obstet Gynaecol 108:1036-1042, 2001.

6) Levin AA, Schoenbaum SC, Monson RR, Stubblefield PG, Ryan KJ. Association of induced abortion with subsequent pregnancy loss. JAMA. 1980 Jun 27;243(24):2495-9.

7) Coleman P, Reardon D, Rue V, Cougle J. A history of induced abortion in relation to substance use during subsequent pregnancies carried to term. Am J Obst Gynecol 2002; 187: 1673–8.

8) Coleman P, Reardon D, Cougle J. Substance use among pregnant women in the context of previous reproductive loss and desire for current pregnancy. Br J Health Psychol 2005; 10: 255–68.

9) Burke T, Reardon DC. Forbidden Grief: The Unspoken Pain of Abortion. Acorn Books. (2002) Springfield, IL.

10) Major B, Richards C, Cooper ML, Cozzarelli C, Zubek J. Personal resilience, cognitive appraisals, and coping: an integrative model of adjustment to abortion. J Pers Soc Psychol. 1998 Mar;74(3):735-52.

11) Henshaw R, et al, "Psychological responses following medical abortion (using mifepristone and gemepost) and surgical aspiration. Acta Obstet Gynecol Scand 73:812, 1994.

12) Feldner MT, Babson KA, Zvolensky MJ. Smoking, traumatic event exposure, and post-traumatic stress: a critical review of the empirical literature.. Clin Psychol Rev. 2007 Jan;27(1):14-45. Epub 2006 Oct 10.

13) Sharain Suliman et. al., Comparison of pain, cortisol levels, and psychological distress in women undergoing surgical termination of pregnancy under local anaesthesia versus intravenous sedation. BMC Psychiatry 2007, 7:24.

14) Rue VM, Coleman PK, Rue JJ, Reardon DC. Induced abortion and traumatic stress: A preliminary comparison of American and Russian women. Med Sci Monit, 2004 10(10): SR5-16.

15) Rousset, C. Brulfert, N. Séjourné, N. Goutaudier & H. Chabrol. Posttraumatic Stress Disorder and psychological distress following medical and surgical abortion. C. Journal of Reproductive and Infant Psychology, (2011) Volume 29(5), 506-517.

16) Coleman PK, Reardon DC, Cougle JR. Substance use among pregnant women in the context of previous reproductive loss and desire for current pregnancy.Br J Health Psychol. 2005 May;10(Pt 2):255-68.

On 2015 Nov 11, Nikolai Slavov commented:

This is a very insightful essay that presents the different sides in a balanced and reasonable framework. I agree that much of the controversy and tension arise from misrepresentation and not recognizing large-scale projects for what they really are. Such dissonance, I believe, is rooted in the politics of credit attribution and budget justification. The incentives for exaggeration are strong. Until these incentives are counterbalanced, we will continue to have problems with exaggeration, misrepresentation, and failure to recognize and credit large-scale projects for what they really are.

On 2014 Feb 27, James Carroll commented:

Kadhim-Saleh et al make significant errors and subsequently draw the wrong conclusion. A comprehensive rebuttal by Bjordal et al is published here Bjordal JM, 2014 but as as most readers are unlikely to pay $39.95 to read the letter I have listed some highlights here to help restore some balance.

The authors claim they used “A very strict study selection criterion” but they excluded Chow 2004 because it “most likely” included the same cohort as Chow 2006. It it is clearly stated in the Lancet review they cited Kimler WC IV, 1996 that one cohort was recruited in 1998 – 1999, and the other cohort recruited in 2002–2003.

Rather than contacting the trial authors to resolve uncertainty about the cohorts, which is normal practice for systematic reviewers Kadhim-Saleh et al. decided to base their decision on guess work, not stringent reviewing practice.

Kadhim-Saleh et al. had criticised the lancet review because “… investigators included trials that used different and more subjective tools for assessing the primary pain outcome measure”. Bjordal et al point out they only included studies that used well-recognized and validated scales for pain assessment including “weighted mean difference for continuous data from visual analogues scale (VAS) scores for pain intensity, relative risk for dichotomized data for global improvement, and standardized mean difference to combine different validated scales of disability including the Neck Disability Index, Neck Disability Scale and the Northwick Park Questionnaire”.

Bjordal et al said they enabled a comprehensive analysis of the available evidence and the finding was that the results were consistent across the different measurement tools actually strengthened the robustness of the Lancet conclusion. Kadhim-Saleh et al. only used a single outcome measure at a single time-point as their outcome measure of success.

Kadhim-Saleh et al. also added a study by Konstantinovic 2010 that they say “failed to detect a statistically significance difference between LLLT and placebo” based on only on VAS, but Konstantinovic had measured seven other outcomes and all were in favour of LLLT [but not reported by Kadhim-Saleh]. The study was on acute radiculopathy, which is a specific diagnosis for neck pain, and this would have increased heterogeneity not reduced it which which was their criticism of the Lancet review.

Kadhim-Saleh et al. criticized the Lancet review for having heterogeneity but Bjordal et al noted that Kadhim-Saleh et al was actually worse in their analysis (I2 = 94 % compared with the Lancet analysis I2 = 91 %). This revealed that the so called “stringent” criteria used by Kadhim-Saleh et al. had failed

Bjordal et al explained that in the Lancet they had included a 650-word paragraph that described a sensitivity analyses that found that most heterogeneity was attributed to interventions and that Kadhim-Saleh et al. gave no serious consideration to the appropriateness of LLLT technique including dosage, a priori in selection criteria or analysis protocol.

He pointed out that an example of how LLLT dose explains heterogeneity was provided by examining the two acute group trials included in the Lancet review. The negative trial using LLLT on acupuncture points by Aigner et al. was under-dosed (632 nm wavelength, 0.075 J) with an ineffective dose of only 0.02 % when compared with the positive trial by Soriano et al. (904 nm wavelength, 4 J). The additional acute radiculopathy trial by Konstantinovic et al. included in the review by Kadhim-Saleh et al. had similar doses and wavelength (904 nm wavelength, 2 J) to the positive trial by Soriano et al., and both were complying with the dosage recommendations from World Association for Laser Therapy (WALT). By conducting a meta-analysis that excludes the trial by Aigner et al. and substituting it with the new acute radiculopathy trial by Konstantinovic et al. Bjordal et al have found that heterogeneity disappears completely(from I2 =91% to I2 =0%). This results in a significant and clinically relevant RR for global improvement at 2.63 (95 % CI 1.73, 4.01).

Kadhim-Saleh et al also made an unsubstantiated claim about a re-analysis of the Lancet meta-analysis by Shiri and Viikari- Juntura 2010 “After applying a random-effects model Shiri and Viikari-Juntura found no significant difference between laser-treated and placebo-treated groups in pain reduction”. Bjordal et al emphatically state “This is simply untrue, as Shiri and Viika-Junturi 2010 confirmed that pain reduction on VAS with a weighted mean difference of 19.41 (95 % CI 9.67, 29.15) in a random-effects model. The inaccuracies in our original analysis brought to our attention by Shiri and Viikari-Juntura weakened slightly the size of effect on recalculation, yet the overall result remained that LLLT gave significant and clinically relevant relief for 6 out of 8 outcomes and lasting up to 22 weeks”.

Bjordal et al also criticised the Kadhim-Saleh paper because it “cited meta-analyses published over 20 years ago to demonstrate the consistency of their claim with previous reviews that found no effect from LLLT despite 80–90 % of RCTs on LLLT being published after these citations. The rate of publication of RCTs in recent years means that the survival period for systematic reviews is typically less than 5 years. In addition, they used literature published between 14 and 30 years ago to support descriptions of LLLT mechanisms. We stand by our original findings that LLLT gives clinically relevant neck pain relief and disability improvement after treatment and possibly follow-ups up to 5 months.”

DISCLOSURE

James Carroll

CEO

THOR Photomedicine Ltd

My publications

On 2017 Nov 27, Steven Watterson commented:

In our recent paper (https://www.ncbi.nlm.nih.gov/pubmed/28910500) we merge this pathway model with pharmacological data and explore how to create multi-drug therapies that optimally suppress cholesterol synthesis and eliminate off-target effects.

On 2017 Dec 14, Denise N Slenter commented:

The pathway model outlined in Figure 1 is available as free machine readable data in WP4190 in WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP4190

On 2014 Jun 20, Alexander (Lex) Nederbragt commented:

Together with three colleagues from my group, I was a reviewer of this paper. All review reports can be found on the journals website (including all versions of the manuscript) or on publons: https://publons.com/publon/4891/

On 2014 Mar 13, Jonathan Eisen commented:

Robert Lee Hotz wrote an article in the Wall Street Journal discussing (in part) this article. See Here's an Omical Tale: Scientists Discover Spreading Suffix

On 2014 Mar 13, Jonathan Eisen commented:

Richard Grant wrote an article for the Guardian discussing (in part) this article. See Say 'Ome': scientists get silly

On 2014 Apr 29, Amanda Capes-Davis commented:

Please be aware that HEp-2 is not a human laryngeal carcinoma cell line. It was shown to be cross-contaminated by Walter Nelson-Rees and is actually HeLa. For a list of known cross-contaminated or otherwise misidentified cell lines, see http://iclac.org/databases/cross-contaminations/.

On 2014 Feb 19, Valeria Fadda commented:

Co-authors of this Note: Roberta Gatto, Dario Maratea, Sabrina Trippoli, and Andrea Messori (all from the HTA Unit of Estav in Firenze, Italy).

The studies by Surder et al.[1] and by Traverse et al. [2] are a further improvement to the overall knowledge about the effectiveness of stem cell treatment in ischemic heart disease. Very few experiences are in fact available in the scientific literature about this relatively new therapeutic strategy. Since the systematic review of Clifford et al. [3] represents the most accurate previous attempt to shed light on this intervention for the acute treatment of myocardial infarction, adding the two trials (Surder et al.; Traverse et al.) to Clifford’s meta-analysis can be worthwhile. With reference to the end-point of left ventricular ejection fraction, we incorporated the results of the two trials (Surder et al.; Traverse et al.)into the meta-analysis of Clifford et al. The results of our analysis (Figure 1) show the superiority of treatment with intracoronary bone marrow-derived cells over placebo, thus confirming the results reported by Clifford et al. The main difference is that confidence intervals have become slightly wider after the addition of the two above mentioned trials.

References

1. Surder D, Manka R, Lo Cicero V et al. Intracoronary injection of bone marrow-derived mononuclear cells early or late after acute myocardial infarction: effects on global left ventricular function. Circulation. 2013 May 14;127(19):1968-79. doi: 10.1161/CIRCULATIONAHA.112.001035

2. Traverse JH, Henry TD, Pepine CJ et al. Cardiovascular Cell Therapy Research Network (CCTRN). Effect of the use and timing of bone marrow mononuclear cell delivery on left ventricular function after acute myocardial infarction: the TIME randomized trial. JAMA. 2012 Dec 12;308(22):2380-9. Erratum in: JAMA. 2013 Jan 23;309(4):343. PubMed PMID: 23129008; PubMed Central PMCID: PMC3652242.

3. Clifford DM, Fisher SA, Brunskill SJ et al. Stem cell treatment for acute myocardial infarction. Cochrane Database Syst Rev. 2012 Feb 15;2:CD006536. doi: 10.1002/14651858.CD006536.pub3

Figure 1. Comparison of intracoronary stem cell treatment with no stem cells in patients with acute myocardial infarction: pooled difference in mean change in LVEF from baseline to end of study. This figure is available at: http://www.osservatorioinnovazione.net/papers/Figure_1.jpg

Valeria Fadda HTA Unit Estav Regional Health System 50100 Firenze Italy

On 2017 Dec 18, Shaun Khoo commented:

Open Data: The underlying dataset for this paper is available on Figshare.

On 2015 Oct 08, thomas samaras commented:

There's a large body of research that indicates smaller humans live longer. Examples include studies of Okinawans, Spaniards,Sardinian,Japanese in Hawaii, US veterans, basketball players, Harvard male graduates, and US government reports on the age-adjusted mortality of five different ethnic groups.In addition, US males average 9% taller than females and have a 9% shorter life expectancy. Various areas of study supporting the thesis that smaller humans live longer is given in: Evidence from eight different types of studies showing that smaller body size is related to greater longevity: JSRR 2(16): 2150-2160, 2014; article no. JSRR.2014.16.003

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 2015 Jul 18, Jan Tunér commented:

A problem with most studies trying to treat tinnitus with laser light is the lack of proper diagnosis of the patients. Quite a few of these have a somatosensory background (the problem is basicly muscluar). Irradiation into the ear will then have no effect.

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

On 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 2015 Apr 25, Dorothy V M Bishop commented:

This is a pioneering study using a clever design with a unique dataset. I am grateful to the authors for making their raw data available. A colleague had suggested that I might be able to use the methods described in this paper with some of my own data, and it was good to have the opportunity to work through the analyses and gain more understanding of what was done.

Unfortunately, having done so, I became dubious as to whether the results show differentially methylated regions associated with ASD, as claimed. Over 23,000 sites were examined for methylation differences, and the numbers where discordant twins differed was not high. Most tellingly, when I used the authors' data to analyse concordant groups in similar fashion, the number of methylation differences was similar. This was true both for twins concordant for ASD (where there were 341 between-twin differences with p < .01, compared with 203 such differences in the discordant twins), and for twins who were concordant for low symptom scores on CAST (where there were 188 between-twin differences with p < .01 – here I selected the first 6 twins from this group to give an equivalent sample size to the discordant twins).

In addition, the findings of correlations between CAST scales and levels of methylation at given site is not impressive, given that the number of correlations computed was over 90,000 (4 per site), so some would be expected to achieve low p-values by chance.

I appreciate this is a new area, and exploratory work needs to be done, but given that the field of molecular genetics has learned the importance for controlling for chance findings when looking for associations with SNPs, I am wondering perhaps the same lesson will prove necessary when examining methylation data. With a twin data set such as this one, I would argue it is very useful to have concordant twins as a comparison group, as they can be used to give an indication of the amount of discordance between twins in methylation that is to be expected regardless of phenotype.

I have uploaded the analysis file I used to compare methylation patterns in different groups here: osf.io/z6w92 so that others can check my working.

On 2015 Apr 27, Chloe Wong commented:

Thank you for your interest and comments on our manuscript. As we hope is clear from the Discussion section of our paper, we are very conservative in our conclusions and are the first to recognize the many limitations of doing this type of work. Please also see our articles highlighting the many important issues to consider when undertaking and interpreting epigenetic epidemiological analyses (Mill & Heijmans, 2013; Heijmans & Mill, 2012).

There are many reasons why the standard research approaches developed for genetic epidemiology are not necessarily appropriate for epigenetic studies of common disease. To date, no real precedents have been set about the optimal sample-sizes needed to detect epigenetic changes associated with disease. The number of ASD-discordant twin-pairs available for this study was small - these are extremely rare samples, and we were only able to recruit and characterize six discordant monozygotic (MZ) pairs. Furthermore, it is recognized that standard multiple testing parameters (as used in GWAS analyses) are not necessarily appropriate for genome-wide DNA methylation data ­ first, most of the sites on the commonly-used Illumina EWAS array are actually non-variable, and second there is considerable non-independence between DNA methylation at proximal CpG sites. With the aim of identifying real, biologically relevant within-twin and between-group DNA methylation differences, we therefore decided to use an analytic approach that incorporated both the significance (that is, t-test statistic) and magnitude (that is, absolute DNA methylation difference) of any observed differences to produce a ranked list of DMRs. Of note, we confirmed the variation at selected loci using an independent technology (bisulfite-pyrosequencing) to rule out technical artifacts in the data.

Because individual studies such as this are, by necessity, small, it is absolutely clear that findings should be treated with caution until they are replicated and/or validated using complimentary approaches. In this regard, it is noteworthy that one of the top-ranked differentially methylated regions identified in our twin study ­ located in the vicinity of the OR2L13 gene - is also a top-ranked differentially methylated locus in a more recent epigenetic study of ASD by Berko and colleagues (2014). Furthermore, OR2L13 was found to be significantly differentially expressed in post-mortem brain tissue from ASD cases compared to unaffected controls in the most systematic transcriptomic analysis of autism brain yet undertaken (Voineagu et al, 2011). Finally, this gene has also been implicated in autism by genetic studies that have identified recurrent CNVs spanning the locus in cases.

The main concern raised by Professor Bishop is that methylomic differences are also identified within concordant affected and concordant unaffected twins. We would argue this is not necessarily surprising; given that it is not feasible to directly study brain tissue from our twins, and ASD is a subtle developmental brain problem, it's plausible (perhaps likely) that these individuals are discordant for other traits/exposures that are also associated with epigenetic variation detected in blood. That doesn¹t mean that differences specific to ASD discordant twin-pairs are not interesting. What is clear from our analyses is that i) the sites identified as differentially methylated in the six ASD-discordant twin-pairs are not differentially methylated in concordant-unaffected twin-pairs, and ii) the overall distribution of average within-pair DNA methylation differences is significantly skewed in ASD-discordant twins, with a higher number of CpG sites demonstrating a larger average difference in DNA methylation.

We acknowledge that our data represent only the first step in identifying molecular variation associated with autism. For example, we cannot begin to tackle issues regarding causality in this study, and it is possible (perhaps likely) that many of the changes we identified represent consequences of the disease. As discussed, we were also limited to using DNA derived from blood, and moving forward it will be important to understand the utility of peripheral tissues as a proxy for inaccessible organs such as the brain. We are currently undertaking more systematic analyses in larger samples of twins and post-mortem brain to address many of the limitations of this study.

Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, Greally JM. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet. 2014 May 29;10(5):e1004402.

Heijmans BT, Mill J. Commentary: The seven plagues of epigenetic epidemiology. Int J Epidemiol. 2012 Feb;41(1):74-8.

Mill J, Heijmans BT. From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet. 2013 Aug;14(8):585-94.

Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, et al. (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474: 380­384.

On 2016 Nov 01, Michael Axtell commented:

The URLs in this paper for software availability and data availability are out of date; here are the updated URLs:

The ShortStack program is now at github .. the latest release is at https://github.com/MikeAxtell/ShortStack/releases

The datasets used in this 2013 paper are now at https://psu.app.box.com/v/axtelldata in directory 'ShortStackPaperData'

A tutorial and test data for ShortStack are at https://psu.app.box.com/v/axtelldata in directory 'ShortStack_TestData'

Finally, I would like to point out that the current version of ShortStack is much enhanced relative to what was described in this 2013 paper. Many of the advancements are described by my group in Johnson et al. (2016) : https://www.ncbi.nlm.nih.gov/pubmed/27175019

Thanks, Mike Axtell

On 2016 Nov 01, Michael Axtell commented:

I should also add that the miscellaneous scripts mentioned in this 2013 paper have also been relocated, to https://psu.app.box.com/v/axtelldata in directory 'old_scripts'

On 2014 Feb 24, Olaf Hauk commented:

The Matlab tools used for the simulations in this paper are provided here: http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/DeFleCT_SpatialFiltering_Tools.

On 2013 Jun 29, Rahul Bakshi commented:

Fascinating. However, I am still puzzled by the emphatic use of the term 'artemisinin-resistant' to describe these parasites. The drug clearly still works. True resistance would have been reproduced using isolates and isolate-derived strains in vitro. More importantly,true resistance would lead to treatment failures all over the place. Is there a demonstrable increase in drug failure directly associated with these parasites?

On 2015 Oct 30, Christopher Southan commented:

The evolution of the beta secretase is described in http://www.ncbi.nlm.nih.gov/pubmed/24381583 which complements this useful analysis. Howerver, given the major differences in evolutionary trajectories co-evolution seems unlikely

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0071879. We believe the correct ID, which we have found by hand searching, is NCT00718796.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2016 Dec 02, Aurélie Névéol commented:

Follow-up work relying on the Scielo database led to the release of a large corpus of parallel scientific publications for biomedicine in three language pairs (EN/ES, EN/FR and EN/PT). The corpus is freely available and it was used in the 2016 conference on Machine Translation (WMT16).

On 2014 May 05, Neil Saunders commented:

Be aware that there is no available software implementation associated with this publication.

On 2013 Oct 29, Maurice Elphick commented:

This is a really important contribution to our understanding of the evolution of neuropeptide and peptide hormone signalling systems. By analysing genomic/transcriptomic sequence data throughout the animal kingdom, it provides new insights on the origins and evolution of peptide signalling systems. I strongly recommend it to anyone who has an interest in any aspect of neuropeptide/peptide hormone biology.

On 2014 Apr 10, Adam VanWert commented:

This article should be recognized as one of the best in its category. It is written very well with a very logical sequence. The information is presented in a highly understandable manner. Invaluable resource! I'm a pharmacology professor with GI pharmacotherapy/pharmacology as one of my course responsibilities. Thank you for this!

On 2016 May 31, Marc Robinson-Rechavi commented:

Link to extra supplementary data: Gene ages, processed expression data, etc http://bioinfo.unil.ch/supdata/Piasecka/datasets/

On 2013 Nov 13, Daniel Mietchen commented:

Fig. 3 and Animation S1 use materials from Google Earth, which are properly attributed but licensed under terms not compatible with the Creative Commons Attribution License that the entire article has been released under.

On 2013 Jun 30, Jonathan Eisen commented:

Data and higher resolution figures are available at Figshare at http://figshare.com/articles/Phylogeny_of_Bacterial_and_Archaeal_Genomes_Using_Conserved_Genes_Supertrees_and_Supermatrices/692979

On 2017 Apr 04, Atanas G. Atanasov commented:

Thanks a lot for this very interesting review, I have featured the manuscript at: http://healthandscienceportal.blogspot.com/2017/04/avocado-scientific-review-of-possible.html

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0029779. We believe the correct ID, which we have found by hand searching, is NCT00297791.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2015 Jul 12, Egon Willighagen commented:

The paper uses the CDK, which you can read about in these two papers:

Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E., Mar. 2003. The chemistry development kit (CDK):  an Open-Source java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43 (2), 493-500. URL http://dx.doi.org/10.1021/ci025584y

Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L., 2006. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Current pharmaceutical design 12 (17), 2111-2120. URL http://dx.doi.org/10.2174/138161206777585274

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 NCT017354435. We believe the correct ID, which we have found by hand searching, is NCT01735435.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2016 Sep 26, Lydia Maniatis commented:

Pelli and Bex (2013) make the following assertion:

"Neurally, Campbell and Robson (1968) revealed the presence of multiple channels in vision, each selective to a different band of spatial frequencies. This greatly increased interest in measuring the CSF. Today, the set of thresholds as a function of spatial frequency is usually fit with a contrast sensitivity function (Watson, 2000)."

The claim regarding Campbell and Robson (1968) is false.

It has been made previously by Pelli and coauthors, (and others), e.g. by Solomon and Pelli (1994). In a comment on that article (https://pubpeer.com/publications/6EA25EFC758D6B5C990CFDFD5899BD) I quote Robson and Campbell (1968), as follows:

"Thus, it seems that we cannot satisfactorily model the over-all visual system by a simple peak detector following a spatial filter...As a modification of this theory, we may assume...Thus, we may suppose that the visual system behaves not as a single detector mechanism preceded by a single broadband spatial filter but as a number of independent detector mechanisms each preceded by a relatively narrowband filter 'tuned' to a different frequency...Such a model could account for our findings...

In other words, Robson and Cambell's (1968) results did not bear out their original predictions, and they discuss purely speculative alternatives to account for their data. Between 1968 and 2013, no firmer references apparently became available.

Nevertheless, as is evident from the second part of Pelli and Bex (2013) statement, measurements based on Robson and Campbell's (1968) uncorroborated assumptions have become very popular. These measurements involve "fitting" a "constrast sensitivity function." As Pelli and Bex (2013) note, this fitting involves a minimum of four free parameters. What does this mean?

According to Wikipedia, a free parameter "is a variable in a mathematical model which cannot be predicted precisely or constrained by the model..." The mathematician and physicist Jon von Neumann is quoted as saying that "With four parameters I can fit an elephant, and with five I can make him wiggle his trunk." Investigators at the Max Planck institute have, in fact, fit an elephant with four free parameters (https://publications.mpi-cbg.de/Mayer_2010_4314.pdf).

What four free parameters means, in short, is that the model doesn't have to predict anything. The model assumptions (e.g., "the presence of multiple channels in vision, each selective to a different band of spatial frequencies") can be false, but still be fit to the (qualitatively generic) shape of the data.

The authors are advocating a method to be used to generate a certain score for individuals. But given the situation described above, we really can't say what that score means, in any theoretical sense.

On 2014 Jun 20, Alexander (Lex) Nederbragt commented:

I was a reviewer of this paper. My review reports can be found on publons: https://publons.com/review/3891/

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 2013 Oct 24, Tom Kindlon commented:

In 2011, I was accused by Professors Lloyd & van der Meer of an unscientific and personal attack in a published letter of mine.^1,2 The accusation was made without any explanation, and they never replied when I e-mailed them about this issue. I believe the accusation was clearly false on both counts. Now I find that Prof. Lloyd (while apologising to Stouten et al. for having wrongly claimed that their letter was an unscientific and personal attack, no less) has re-iterated the claim that this was an apt characterization for my letter, as well as letters written by others.³ I would like to take this opportunity to correct the record.

In the letter in question, I challenged the PACE Trial authors’ claims about the safety of cognitive behaviour therapy (CBT) and graded exercise therapy (GET) for chronic fatigue syndrome (CFS), distilling my points into 250 words, the maximum allowed by the journal.² At no point do I attack individuals. As is common in letters to the editor, I challenge points made in the original paper—it has been recognised that such correspondence can be an important part of the scientific process. I subsequently expanded on the points about that particular trial, and the reporting of harms for these interventions in general, in a peer-reviewed paper.⁴ I have had several letters published, before and since, on the subject of CBT and GET interventions in reply to different research groups in a variety of journals.⁵

Incidentally, I do not believe the description is suitable or appropriate for the other letters that the Lancet published either.

References:

1 van der Meer JW, Lloyd AR. A controversial consensus--comment on article by Broderick et al. J Intern Med. 2012;271:29-31. Epub 2011 Nov 11.

2 Kindlon T. The PACE trial in chronic fatigue syndrome. Lancet 2011;377:1833; author reply 4–5.

3 Lloyd AR. Apology. J Intern Med. 2013;273:628.

4 Kindlon T. Reporting of Harms Associated with Graded Exercise Therapy and Cognitive Behavioural Therapy in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Bulletin of the IACFS/ME. 2011;19:59-111.

5 https://www.researchgate.net/profile/Tom_Kindlon2/publications/

On 2017 Jan 24, Tom Weishaar commented:

This article was apparently published twice by mistake. For the non-retracted version, see https://www.ncbi.nlm.nih.gov/pubmed/23507683

On 2014 Feb 23, Vinay Gopalani commented:

@ conclusion: Human mesenchymal stem cells have a potential to adhere to plastic surface. I think its incorrectly mentioned as Human dermal fibroblasts.

On 2014 Apr 04, GREGORY CROWTHER commented:

I understand and agree with the central point of this article, i.e., that biology textbooks should emphasize scientific thinking and scientific investigation, but often don't. What is the solution to this problem? Duncan et al. imply that the textbook authors should simply prepare their books differently: "Textbook authors might better serve students by focusing more on how the information in their chapters was discovered, rather than devoting most illustrations to describing biology by representing what is known." This reasonable-sounding advice sidesteps the fact that authors do not have sole control of their books; the publishers exert much influence based on market considerations, and professional illustrators (who are actually responsible for preparing the figures) have input as well. Thus, making textbooks more research-based is not as simple as telling the textbook authors to "Make it so." An author of one of the texts reviewed by this article told me that he made his book "as data-intensive as reviewers would stand." In other words, he himself was not the bottleneck in getting more research data into the book. One hopes that publishers and editorial teams are now starting to expect more of a research flavor in their texts.

On 2013 Dec 06, John Cannell commented:

I congratulate the authors on their intresting paper. I found my self wondering however, how can they explain the dramatic increase in incidence in this centruy? Didn't Tylenol use remain fairly constant from the year 2000 to the present time?

The question is why do some children exposed to Tylenol may develop autism and some do not? The answer must lie in their immune system. Some mothers and fetuses have enough antioxidant reserve to protect themselves from the oxidative damage induced by paracetamol exposure and some do not.

Certainly, a controlling factor in such reserve is the amount of the key antioxidants superoxide dismutase and thioredoxin reductase expressed by the mother or fetus. It has been known for some time that both of these antioxidants have been shown to be upregulated rather dramatically by the neurosteroid calcitriol or activated vitamin D. Although it is not clear from the papers below, it is probable that a vitamin D response element is involved in directly or indirectly controlling the genetic expression of both antioxidants.

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.

Swami S, Raghavachari N, Muller UR, Bao YP, Feldman D. Vitamin D growth inhibition of breast cancer cells: gene expression patterns assessed by cDNA microarray. Breast Cancer Res Treat. 2003;80:49–62.

Palmer HG, Sanchez-Carbayo M, Ordonez-Moran P, Larriba MJ, Cordon-Cardo C, Munoz A. Genetic signatures of differentiation induced by 1α,25-dihydroxyvitamin D3 in human colon cancer cells. Cancer Res. 2003;63:7799–7806.

I propose that much of the autism epidemic is caused by the meeting of a dysfunctional antioxidant reserve with paracetamol. That is, gestational or early childhood vitamin D deficiency causes down-regulation of key antioxidants, which leave the fetus vulnerable to the oxidative damage induced by paracetamol. Thus a combination of vitamin D deficiency and paracetamol exposure is both a necessary and sufficient condition to trigger an unkown percentage of autism and explains the rapid rise in the prevalence of the disorder, at least in the 1980s and 90s.

As far as vitamin D deficiency is concerned, 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.

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.

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.

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

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.

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.

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

It is likely that much of the autism epidemic is caused by the perfect storm of paracetamol meeting a vitamin D deficient immune system.

John Cannell, MD

Vitamin D Council

http://www.vitamindcouncil.org/

On 2013 Oct 28, Egon Willighagen commented:

The data presented in this paper can be downloaded as CC-BY-SA from the Dutch Dataverse Network with this handle http://hdl.handle.net/10411/10279.

On 2014 Apr 18, Ivan Oransky commented:

This paper has been retracted: http://retractionwatch.com/2014/04/18/authors-retract-study-suggesting-magnesium-prevents-alzheimers-in-mice/

On 2014 Apr 20, Sergio Stagnaro commented:

None

On 2016 Nov 22, MICHAEL BALLARD commented:

This manuscript has been republished as Li, W., et al. (2014). “Elevation of brain magnesium prevents synaptic loss and reverses cognitive deficits in Alzheimer's disease mouse model.” Mol Brain 7(1): 65. See PubMed: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172865/ and journal site: https://molecularbrain.biomedcentral.com/articles/10.1186/s13041-014-0065-y

Figures 4 and 5D from the original article have been removed from the republished version.

According to the authors' retraction notice: “This article described the effects of elevating brain magnesium on preventing and reversing cognitive deficits in an Alzheimer's disease mouse model. During recent efforts to extend this work, we discovered errors in the quantification of the expression and/or phosphorylation of a subset of signaling pathways, particularly related to Figures 4 and 5D. Despite these errors, the major conclusions of the paper remain substantiated."

On 2014 Dec 17, Sean Ekins commented:

A post on what it took to get this paper published http://www.collabchem.com/2013/05/03/what-it-took-to-get-the-paper-out/

On 2014 Dec 17, Sean Ekins commented:

some slides on this work http://www.slideshare.net/ekinssean/acs-dispensing-processes-profoundly-impact-biological-assays-computational-and-statistical-analyses

On 2013 Jun 28, Julia Gilden commented:

Interesting paper. I would have enjoyed a greater focus on the functional differences between LPS-dependent and Leishmania-dependent exosomes. To me, the most interesting question is whether Leishmania might be have evolved a mechanism for highjacking exosomes for the delivery of GP63. I wish the authors had commented on the quantity of GP63 observed and whether it was enough to potentially effect neighboring cells. I'm also curious as to whether the LPS-dependent exosome preps contain any LPS, since if so, that might contribute to the strongly immunostimulatory effect of those exosomes compared to the other groups.

On 2015 Aug 23, David Keller commented:

Information theory contradicts Guideline Statement 4: more frequent PSA testing should benefit patients, not harm them

Information theory describes the reconstruction of continuous signals from discrete samples, and the extraction of signals from noise. Screening for prostate cancer involves scrutiny of a man's serial PSA measurements, with the goal of determining the likelihood that his prostate has developed a malignancy which could affect his longevity or quality of life (ie: his mortality or morbidity). Statement 4 from the 2013 Early Detection of Prostate Cancer: AUA Guideline [1] is as follows:

"Guideline Statement 4: To reduce the harms of screening, a routine screening interval of two years or more may be preferred over annual screening in those men who have participated in shared decision-making and decided on screening. As compared to annual screening, it is expected that screening intervals of two years preserve the majority of the benefits and reduce over diagnosis and false positives. (Option; Evidence Strength Grade C)"

Guideline Statement 4 can be proved false using the principles of information theory as follows. Individual PSA blood test results constitute discrete samples of the continuous signal which would result from continuous monitoring of the patient's PSA. The Nyquist-Shannon Sampling theorem states that the minimum sampling rate for perfect reconstruction of a signal is equal to twice the bandwidth of the signal [1]. Expressed another way, the maximum bandwidth of a signal to be perfectly reconstructed from samples taken at a sampling frequency f is f/2.

The crucial signal we wish to detect is a rising PSA consistent with a dangerous prostate cancer. Empirically, the faster a prostate cancer grows, the more rapid the rise in PSA and therefore the higher the bandwidth of the PSA signal. We would like to detect PSA signals which rise rapidly (have high bandwidth) in order to treat the patient while his cancer is confined to his prostate. The more frequently we sample the PSA, the higher the bandwidth of the PSA signal we can detect, meaning the more rapid rises in PSA will not escape detection. So, increasing the PSA sampling rate from once every 2 years to once every year can only improve the detection of the high-bandwidth signal caused by a rapidly growing prostate cancer. In fact, increasing the PSA sampling rate to twice per year, 4 times per year or even higher will only increase the maximum detectable bandwidth of the PSA signal.

Harms associated with PSA screening are generally associated with the prostate biopsy procedure and downstream diagnostic and therapeutic intervetions. The purpose of PSA sampling is to inform us when a prostate biopsy is likely to be more beneficial than harmful. The cumulative harm of multiple biopsies is proportional to the number of biopsies done, so we want to minimize the number of biopsies without missing a dangerous cancer. However, if the PSA signal includes useful information about the presence of cancer, the best way to reduce the number of biopsies is to improve the quality (bandwidth) of the detected PSA signal, which requires increasing the PSA sampling rate.

Reducing the PSA sampling rate in an attempt to reduce the harms caused by prostate biopsy is akin to hiding one's head in the sand. Continuous monitoring of the PSA signal would be ideal, but the maximum practical PSA sampling frequency should be employed to maximize the quality of the reconstructed PSA signal, and thereby increase the likelihood of detecting a fast-growing tumor while it is confined to the prostate. Application of a low-pass filter to the PSA signal should reduce the number of biopsies triggered by noise.

Lastly, the prostate biopsy rate need not be correlated with the PSA sampling rate, and indeed should be inversely correlated with it if the PSA signal has useful information about the presence of dangerous cancer in the prostate.

Reference

1: Shannon CE, Communication in the presence of noise, Proc. Institute of Radio Engineers, vol. 37, no. 1, pp. 10–21, Jan. 1949

On 2016 Aug 30, 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 NCT0053089. We believe the correct ID is NCT00530894.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 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

http://www.ncbi.nlm.nih.gov/pubmed/22704295

The vessels you describe are probably better described as vessels of Wearn as they are (1) not Thebesian veins*, (2) not studied by Thebesius, and (3) they were described by Wearn et al.

For additional commentary, please see the following link:

https://twitter.com/BrettSnodgrass1/status/417433946196942848

Comments and suggestions are welcome.

Thank you very much.

On 2014 Jan 31, George W Hinkal commented:

The National Cancer Institute has been investing in the development of an online webportal of curated cancer nanotechnology data called caNanoLab. The numerical data and additional nanomaterial characterizations related to this publication have been added to the database and can be found at:

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124992&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124993&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124994&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124995&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124996&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124997&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124998&page=0&tab=ALL

https://cananolab.nci.nih.gov/caNanoLab/characterization.do?dispatch=summaryView&sampleId=39124999&page=0&tab=ALL

The left navigation links on these pages provide information about each sample (under Navigation Tree).

For general information on how to use caNanoLab, please visit https://cananolab.nci.nih.gov/caNanoLab/home.jsp

On 2013 Dec 19, Raphael Stricker commented:

Our Letter to the Editor of Lancet Infectious Diseases (2014;14:12) expressed concern about the safety of the new Lyme OspA vaccine from Baxter Bioscience. This concern is based on safety issues related to the previous Lyme OspA vaccine, Lymerix®, which was taken off the market after these safety issues surfaced, as outlined in our letter.

In their response to our letter, the employees of Baxter Bioscience who studied the new vaccine made the following comment: “There are no data in Stricker and Johnson’s cited publications that support the statement that ‘joint-reactive and nerve-reactive antibodies’ are induced in human beings vaccinated with OspA antigen.” This comment is misleading because OspA vaccine-related antibodies against nerve and joint tissue have been detected in animals and humans described in the references below. Furthermore, the fact that antibodies with unknown reactivity were induced by Lymerix® vaccination presents an unresolved safety issue for the new OspA vaccine, and this issue was not addressed by the Baxter Bioscience employees who studied the vaccine.

Once again, the willingness of Baxter Bioscience to ignore legitimate safety concerns bodes ill for the new Lyme vaccine.

Raphael B. Stricker, MD, Lorraine Johnson, JD, MBA

References

1. Stricker RB. Lymerix® risks revisited. Microbe 2008;3:1-2.

2. Smith P, Gaito A, Marks DH. Transcript of FDA Lymerix Meeting, Bethesda, MD, January 22, 2002. Available at: http://www.lymediseaseassociation.org/index.php?option=com_content&view=article&id=532:lymerix-meeting&catid=129:hhsfood-a-drug-administration-fda&Itemid=531

3. Croke CL, Munson EL, Lovrich SD, et al. Occurrence of severe destructive Lyme arthritis in hamsters vaccinated with outer surface protein A and challenged with Borrelia burgdorferi. Infect Immun. 2000;68:658–63.

4. Rose CD, Fawcett PT, Gibney KM. Arthritis following recombinant outer surface protein A vaccination for Lyme disease. J Rheumatol. 2001;28:2555–7.

5. Latov N, Wu AT, Chin RL, Sander HW, Alaedini A, Brannagan TH. Neuropathy and cognitive impairment following vaccination with the OspA protein of Borrelia burgdorferi. Periph Nerv Syst. 2004;9:165–7.

6. Alaedini A, Latov N. Antibodies against OspA epitopes of Borrelia burgdorferi cross-react with neural tissue. J Neuroimmunol. 2005;159:192–5.

7. Souayah N, Ajroud-Driss S, Sander HW, Brannagan TH, Hays AP, Chin RL. Small fiber neuropathy following vaccination for rabies, varicella or Lyme disease. Vaccine 2009;27:7322-5.

8. Marks DH. Neurological complications of vaccination with outer surface protein A (OspA). Int J Risk Saf Med. 2011;23:89-96.

9. Molloy PJ, Berardi VP, Persing DH, Sigal LH. Detection of multiple reactive protein species by immunoblotting after recombinant outer surface protein A Lyme disease vaccination. Clin Infect Dis. 2000;31:42-7.

10. Fawcett PT, Rose CD, Budd SM, Gibney KM. Effect of immunization with recombinant OspA on serologic tests for Lyme borreliosis. Clin Diagn Lab Immunol. 2001;8:79-84.

11. Hanson MS, Edelman R. Progress and controversy surrounding vaccines against Lyme disease. Expert Rev Vaccines 2003;2:683–703.

12. Nigrovic LE, Thompson KM. The Lyme vaccine: a cautionary tale. Epidemiol Infect. 2007;135:1–8.

13. Nardelli DT, Munson EL, Callister SM, Schell RF. Human Lyme disease vaccines: past and future concerns. Future Microbiol. 2009;4:457-69.

14. Smith P. Remarks to Vaccines and Related Biological Products Advisory Committee, Bethesda, MD, January 31, 2001. Available at: http://www.lymediseaseassociation.org/index.php?option=com_content&view=article&id=262:vaccine-remarks&catid=80:controversy&Itemid=76

Disclosure: RBS and LJ are members of the International Lyme and Associated Diseases Society (ILADS) and directors of LymeDisease.org. They have no financial or other conflicts to declare.

On 2015 Jul 12, Egon Willighagen commented:

Dear authors, I just searched for your ontology on BioPortal (we do not seem to have a Chemistry equivalent), but could not find your ontology. Have you considered making it available via BioPortal?

On 2014 Feb 16, Lorene M Nelson commented:

This article provides a nice overview of the rationale for proposing a high-fat or ketogenic diet in ALS. A correction is needed, however, in one the authors' statements. ". . . a US case-control retrospective study reported a nonsignificant trend toward increased risk of amyotrophic lateral sclerosis in subjects who reported a diet high in fat calories, however this study was not adjusted for tobacco use [22]." As the author of that study, I would like to point out that the study results were adjusted for pack-years of smoking (see Methods section and Table 3 in Nelson LM, Matkin C, Longstreth WT Jr, McGuire V. Population-based case-control study of amyotrophic lateral sclerosis in western Washington State. II. Diet. Am J Epidemiol. 2000;151(2):164-173.)