On 2017 Sep 12, Daniele Marinazzo commented:

Dear authors

thanks a lot for this paper, that has collected quite some attention.

I agree that interpretation issues of Granger Causality in Neuroscience exist (partially due to the historical unfortunate use of the name “causality”, as nicely described in previous literature).

On the other hand I think that the paper uses a formulation of Granger causality which is outdated (albeit still used), and in doing so it dismisses the measure based on a suboptimal use of it.

In order to provide a more balanced view, we replicated their simulations used the updated State Space implementation, proposed already some years ago, in which the pitfalls are mitigated or directly solved.

You can find the report here https://arxiv.org/abs/1708.06990

Another reply has been also posted, addressing more fundamental issues https://arxiv.org/abs/1708.08001

Best regards

On 2017 Nov 24, James Friel commented:

This research demonstrates that infants suffering from gastrointestinal distress when fed bovine fortifier benefit from human milk based fortifier. Our research found in similar infants that systemic oxidative stress increased with increasing amounts of bovine fortifier. (Friel JK, Diehl-Jones B, Cockell KA, Chiu A, Rabanni R, Davies SS, Roberts LJ2nd. Evidence of oxidative stress in relation to feeding type during early life in premature infants. Pediatr Res. 2011 Feb;69(2):160-4).Using more subtle indicators than feeding intolerance supports the current findings. It may be that most premature infants would benefit from the human milk based fortifiers. Hopefully as their use increases they will become more affordable and thus more available.

On 2017 Aug 26, Christopher Southan commented:

The chemical structures and protein targets for this exellent review have been resolved in this blog post https://cdsouthan.blogspot.se/2017/08/name-to-struc-resolution-for-yet.html

On 2017 Sep 02, Randi Pechacek commented:

Marcus Leung, first author of this article, wrote a blog post on microBEnet. It discusses his personal thoughts on the air microbiome of zero carbon buildings.

On 2017 Aug 09, Jacob H. Hanna commented:

This is the third paper from Smith group describing deriving human transgene free naïve "pluripotent" reset cells. However, in all three papers, the authors have failed to describe whether they are able to generate teratomas from any of the described cell lines. It should be noted that mouse naive pluripotent cells have the intrinsic "self organizing capacity" to enter a formative/primed state after in vivo sub-cutaneous injection into immunodeficient mice and robustly make teratomas within 4-8 weeks. In our opinion, without evidence for teratoma formation competence of such transgene free naive cells they do not qualify to be annotated as pluripotent cells at all (neither naive nor primed). We raise the possibility that the cells being propagated in this study may be more akin to a non-pluripotent pre-iPSC/pre-ESC state. I hope the authors can clearly point out and directly address this critical caveat in their future publications.

On 2017 Sep 11, NephJC - Nephrology Journal Club commented:

This randomised controlled trial of oral methylprednisolone on clinical outcomes in patients With IgA nephropathy was discussed on August 29th and September 6th 2017 on #NephJC, the open online nephrology journal club. Introductory comments written by Amit Langote are available at the NephJC website here.

As one of the commoner conditions we Nephrologists face, there was lots of interest in the controversial results of this trial.

The highlights of the tweetchat were:

• There remains some uncertainty regarding the pathogenesis of IgA Nephropathy and the disease may actually comprise a spectrum of conditions. As such treatment should likely be stratified and this limits our ability to interpret RCTs of all-comers.

• It would have been useful to see renal biopsy findings determine or influence randomization procedures.

• The fact that the population were mostly Chinese may limit the generalizability of the results to western populations.

• The GFR decline was much faster than expected or previously reported but this can be the case with certain Asian populations.

• There is a general reluctance to use steroids in the absence of crescents or rapid GFR decline among Nephrologists currently and this trial further re-enforces this sentiment. We keenly await the results from the low-TESTING trial.

Transcripts of the tweetchats, and curated versions as storify will be shortly available from the NephJC website.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC on twitter, liking @NephJC on facebook, signing up for the mailing list, or just visit the webpage at NephJC.com.

On 2017 Sep 15, Robin Kok commented:

Regarding bias, this 'review' is an exercise in confirmation bias.

The rationale and execution of this systematic review are confusing at best, and misleading at worst. The authors invoke some metric of 'strength of evidence', which consists of tallying up positive conclusions from meta-analyses. For example, they conclude: "Protocols improve anxiety in adults: 8/9 meta-analyses", which we are to believe is strong evidence for cognitive bias modification (CBM).

However:

a) many of these meta-analyses draw from the same pool of primary studies, resulting in a great deal of overlap. Yet the authors treat these as if they are independent data points - demonstrably, they are not. If one would perform 10 meta-analyses on 40 studies, then it should come as no surprise that these meta-analyses report comparable outcomes. This greatly exaggerates positive effects by counting single studies multiple times. It is disconcerting that the peer reviewers did not spot this serious and elementary flaw. Then again, given that the entire process of submission, reviews and editorial acceptance took just over a month, reviewers and/or editor(s) must have been particularly pleased with this manuscript to favour it with an expedient review process.

b) many of these meta-analyses - and the primary outcomes from which they draw data - fail even the most basic quality criteria for rigorously conducted meta-analyses and randomised controlled trials.

c) many of these meta-analyses and primary studies reported therein were conducted by investigators with an investigator allegiance or other conflicts of interest. Studies performed by independent researchers often fail to find effects.

d) there is evidence for extreme publication bias in the field of CBM, as apparent by both statistical indicators (which the authors mostly ignore), as well as by the great number of trials in official trial registries which are still awaiting publication - some for almost 10 years. The reader can easily find an abundance of file-drawered CBM studies in the WHO, ISRCTN, ANZCTR, and Clinicaltrials.gov trial registries.

In short, this review is strongly biased in favour of cognitive bias modification and serves only to promote CBM as a 'promising therapy'. It adds to an already overwhelming number of positively biased reviews and analyses which essentially draw from the same pool of biased literature, strengthening the echo-chamber effect that seriously diminishes the scientific credibility of the CBM field. Reviews such as these are no more than opinion/promotion pieces in disguise, and should be interpreted with extreme caution as a reader unwary of these issues might easily conclude that there is overwhelming evidence for the efficacy of CBM - which there is not.

If there is any value in CBM, it deserves fair testing - which means pre-registered, transparent replication efforts by disinterested, independent researchers. The disturbing phenomenon where biased CBM trials are recycled in reviews and meta-analyses in quick succession by biased investigators is the academic equivalent of an echo-chamber. And if CBM is to be seen as a serious alternative to psychotherapy, it is to be held to the same standards of methodology and transparency and step away from the cargo cult science we have seen so far.

DECLARATION OF INTEREST: I have co-authored two (mostly critical) meta-analyses included in this review.

On 2017 Aug 07, DAVID ALLISON commented:

A letter to the editor (and response) have been published indicating erroneous statistical inferences in the article such that the conclusions regarding differential effectiveness by pubertal status are unsubstantiated.

See: http://pediatrics.aappublications.org/content/early/2017/06/08/peds.2016-4285.comments

On 2017 Oct 10, Shaun Khoo commented:

Green Open Access: The accepted manuscript is available from the UNSW Institutional Repository.

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

On 2017 Oct 13, Martine Crasnier-Mednansky commented:

The authors really should not write in legend of figure 7, "Our results indicate that for robust growth on chitin, the transporters responsible for uptake of [ABC-transported] chitobiose and [PTS-transported] GlcNAc play the largest role". In fact, data in figure 6A indicate lack of either one of these two transporters does not impair growth on chitin at all. Also, the 'chitosan' PTS (PTS^Chs, VC1282 in the figure), cannot possibly be a major player considering there is little glucosamine in chitin. Moreover, PTS^Chs transport is most likely inhibited by Enzyme IIA^Glc-dependent PTS transports (including PTS^Nag), as it was reported chs expression is positively regulated by cAMP (Berg T, 2007).

A proper question is whether or not the two transporters can be used simultaneously, as depicted in figure 7. Upon in vitro characterization of the periplasmic chitodextrinase activity (VCA0700 in Vibrio cholerae), Keyhani NO, 1996 proposed the ABC transport at first predominates up to a threshold concentration of (GlcNAc)n, n≥3, above which the PTS transport predominates. The two transport systems are not physiologically redundant.

On 2017 Aug 14, David Mage commented:

Hauck et al., prepared an interesting report on Sudden Unexpected Infant Death (SUID) and priorities for research to explain it. They state in the very first sentences of their introduction that 25 years ago, research into SIDS led to a ‘breakthrough’ which identified that “infants who slept on their stomachs were significantly more likely to die of SIDS than infants who slept on their backs [1].” Breakthrough? Schmakethrough!

Almost 75 years ago, Harald Abramson [2] published a proscription against the daytime practice of placing the infant in the prone position for sleep – unless constantly guarded. “The practice should, furthermore, be entirely done away with at night.” Fortunately, my thesis professor taught me the importance of reading the references of references to prevent such oversights when a blind eye is turned to the past literature. Reference 20 [Gilbert et al.] of their first reference [1] [Horne et al.] cites the Abramson 1944 paper.

1. Horne RSC, Hauck FR, Moon RY. Sudden infant death syndrome and advice for safe sleeping. BMJ 2015;350:h1989 doi: 10.1136/bmj.h1989

2. Abramson H. Accidental mechanical suffocation in infants. The Journal of Pediatrics 1944;25:404-413.

On 2017 Oct 19, Polina Vishnyakova commented:

Dear colleagues, in order to maintain a healthy scientific debate we need to clarify the statement, which you provided in Discussion of this paper. You wrote: «These findings are inconsistent with the findings of Vishnyakova et al. who reported that OPA1 was upregulated in PE placentas. […] The findings of Vishnyakova et al. were mainly based on gene expression. Levels of DNA or RNA may be unable to predict protein levels accurately, as they do not account for post-transcriptional/translational modifications». It is important to note than in our work we observed changes both on mRNA and protein content level of OPA1 and these findings surely disagree with your data. But we think that this could be explained by the difference in patients characteristic: we divided patients with preeclampsia basing on gestational age while you included women only with severe preeclampsia. Plus in current paper you analyzed only OPA1-L form, but not both forms (full OPA1-L and cleaved OPA1-S). So obtained difference in our findings could be explained with these points. Best regards.

On 2018 Jan 01, DAVID ALLISON commented:

A letter to the editor has been published indicating unsubstantiated conclusions in this article due to the use of difference in nominal significance (DINS) analyses.

See: http://onlinelibrary.wiley.com/doi/10.1111/1753-6405.12755/full

A response from the authors has also been published: http://onlinelibrary.wiley.com/doi/10.1111/1753-6405.12767/abstract

On 2017 Aug 05, Pedro Moreno commented:

Regarding the authors: No (A Moreno P). It is Moreno PA. Please correct this.

On 2018 Jan 27, Viktor Müller commented:

While it is true that there is considerable overlap in the recognition of self and (possibly pathogenic) non-self epitopes (Calis et al [1] estimated an overlap of around one third for HLA class I alleles), this is likely to make the job of the immune system harder, rather than easier. The overlapping peptides tend to be non-immunogenic, indicating tolerance, and the immune system needs to be able to target epitopes that are distinguishable from self peptides even with the degenerate recognition of T cell receptors [1]. Furthermore, even if the recognition task was indeed reduced to self and similar peptides, this would still vastly exceed the capacity of a fixed germline-encoded receptor repertoire. The number of distinct potential epitopes (for HLA class I) is of the order of magnitude 10⁷ in humans [2] and in mice [3]; this exceeds the maximum number of germline immune receptors found in any species by several orders of magnitude.

We still maintain that "Distinguishing tumours from normal self is likely to be the most challenging task for Darwinian immunity that could only be added at advanced stages of its evolution" [4], but have never claimed the same for positive selection. Amphioxus has proto-MHC, and positive selection might indeed be an ancient characteristic of (vertebrate) Darwinian immunity. It will be instructive to elucidate whether and how the divergent adaptive system of jawless fish handles positive selection, or anything analogous to MHC restriction in general.

Finally, we note that the origin of vertebrate adaptive immunity is a notoriously difficult problem. We certainly do not know the whole truth about the complex events that took place more than half a billion years ago -- but we hope that, by surveying the most recent evidence, we have taken a small step in the right direction.

[1] Calis JJA, de Boer RJ, Keşmir C (2012) Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire. PLoS Comput Biol 8(3): e1002412. https://doi.org/10.1371/journal.pcbi.1002412

[2] Burroughs, N.J., de Boer, R.J. & Keşmir, C. Immunogenetics (2004) 56: 311. https://doi.org/10.1007/s00251-004-0691-0

[3] Müller, V. & Bonhoeffer, S. (2003). Quantitative constraints on the scope of negative selection. Trends Immunol 24, 132-5. https://doi.org/10.1016/S1471-4906(03)00028-0

[4] Müller V, Boer RJ de, Bonhoeffer S, Szathmáry E (2018) Biol Rev 93:505-528. https://doi.org/10.1111/brv.12355

On 2018 Jan 20, Donald Forsdyke commented:

PATHOGEN COEVOLUTION AND THE ANTIGENIC UNIVERSE

The distinction between selective and instructive (Lamarckian) systems of immunity (1) – originating with Paul Ehrlich – was clearly set out in 1957 by Talmage (2) who, with Burnet, can be considered a "father of clonal selection theory" (3, 4). Its historical omissions aside, this bold attempt to place the evolution of immune systems in a broad context raises other concerns.

Although mentioning "the complex adaptation of the immune repertoire to the antigenic environment," and the need "continuously to acquire and store open-ended information about the antigenic environment," the coevolution of that antigenic environment (e.g. the coevolution of pathogens) does not seem to have been considered.

While the authors agree with Burnet that "distinguishing tumours from normal self is likely to be the most challenging task for Darwinian immunity," it is not recognized that the most successful pathogens are those that, through mutation, can come close to self. Whereas tumours represent mutations away from self, successful pathogens represent mutations towards self (by means of which they seek to exploit 'holes' in immune repertoires; 5). In both circumstances, this greatly simplifies the evolutionary task of a host. It does not have to depend on "the open-ended nature of the receptor repertoire." It does not have to "constitute a system of 'unlimited heredity' within the immune system." It does not have to "be broad enough to recognize the 'potential universe of antigens'." The scope of its task is greatly reduced.

As long ago proposed (6), and increasingly recognized (7, 8), it would be evolutionarily advantageous for organisms to focus their immune cell receptors on 'near self' antigenic specificities, rather than to attempt to anticipate the entire universe of antigens. Organisms achieve this, not through negative, but through positive selection of their immune repertoires. From the outset, organisms and their pathogens have coevolved and it would seem incorrect to suppose for the immune system that positive selection "could only be added at advanced stages of its evolution" (9). It is fundamental to immune system evolution.

1.Muller V, Boer RJ de, Bonhoeffer S, Szathmary E (2018) Biol Rev 93:505-528. Müller V, 2018

2.Talmage DW (1957) Allergy and immunology. Ann Rev Med 8:239-256 TALMAGE DW, 1957

3.Forsdyke DR (1996) The origins of the clonal selection theory of immunity. FASEB J 9:164-166.Forsdyke DR, 1995

4.Lederberg J (2002) Instructive selection and immunological theory. Immunol Rev 185:50-53.Lederberg J, 2002

5.Calis JJA, de Boer RJ, Kesmir C (2012) Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol 8:e1002412.Calis JJ, 2012

6.Forsdyke DR (1975) Further implications of a theory of immunity. J Theoret Biol 52:l87-l98.Forsdyke DR, 1975

7.Vrisekoop N, Monteiro JP, Mandl JN, Germain RN (2014) Revisiting thymic positive selection and the mature T cell repertoire for antigen. Immunity 41:181-190.Vrisekoop N, 2014

8.Marrack P. et al. (2017) The somatically generated portion of T cell receptor CDR3alpha contributes to the MHC allele specificity of the T cell receptor. eLife 6:e30918.Marrack P, 2017

9.Forsdyke DR (2016) Evolutionary Bioinformatics. 3rd Edition. Springer, New York.

On 2017 Aug 25, Jason R Richardson commented:

Drs. Blakely and Melikian, thank you both for your insightful comments. In working with these cells over a number of years, we have found that while the cell line expresses all of the necessary components to be identified as dopaminergic, it neither synthesizes a significant amount of dopamine nor has functional dopamine uptake. This is likely because of the diffuse nature of the protein expression identified by Dr. Melikian, which may be because it was generated by immortalizing cells from embryonic day 12 rat. I believe when I was a postdoc, I did some co-labeling and observed that the DAT was primarily present in the ER and golgi in these cells, suggesting that the intracellular machinery may not be mature enough to fully generate a functional and fully glycosylated DAT. I should note that the original group that made the N27 line recently re-cloned it and purified cells from this new clone had higher expression levels of both TH and DAT (Gao et al., 2016). Although, there were no functional studies for DAT-mediated uptake with the re-cloned line, they did show a modest increase in susceptibility to 6-OHDA and MPP+. Our primary goal for this paper was to better characterize the role of histone acetylation and transcription factor binding in the epigenetic regulation of DAT expression based on our previous studies in SK-N-AS cells (Green et al., 2015) in a rat cell line that we could then translate to in vivo studies. I certainly agree that additional studies in cells that display a more mature phenotype that allow for determination of function are warranted. I think both comments bring out a very important point regarding the study of transporter regulation. That is, cell context and system are critical to the interpretation and translation of mechanisms regulating the DAT to in vivo systems.

On 2017 Aug 19, Randy Blakely commented:

Thanks Haley for your note. The field studying dopamine transporter regulation would greatly benefit from a a cell line expressing endogenous transporter protein, validated through RNA, western blotting and critically transport activity measurements demonstrating pharmacological sensitivities appropriate to brain DAT. Some cell lines are said to be "dopaminergic", e.g. SH-SY5Y, but these express NET activity not DAT activity, like PC-12 cells.

On 2017 Aug 19, Haley Melikian commented:

We have also used the cell line in this study (N27), but have neither detected DAT protein by immunoblot, nor measured specific DA uptake using a standard radiotracer flux assay. While low DAT mRNA levels may be expressed, the evidence presented does not strongly support endogenous DAT protein expression. The immunofluorescence signal shown appears primarily diffuse and intercellular, and not in agreement with the typical plasma membrane DAT localization. Indeed, these cells have been used by transporter biologists, but only in the context of heterologous DAT expression. I would be curious to know whether the authors have measured specific DA uptake in these cells.

On 2017 Dec 05, Karen Woolley commented:

Congratulations to Dr Pushparajah on this editorial and congratulations again to her and her colleagues at UCB for generating evidence on the value of making the results of clinical research more accessible to the public via plain-language summaries. http://journals.sagepub.com/doi/abs/10.1177/2168479017738723. Ironically, when clinical research results go public (eg, through a peer-reviewed PUBLIC-ation), the public is rarely involved. This needs to change. Publications should be "of the people, BY the people, FOR the people". We need patients to be engaged - ethically and meaningfully - in the publication ecosystem. We know patients are diverse, but some patients are accessing the peer-reviewed literature for information. We need to work with patients, journal editors, sponsors, and publication professionals to help make the "patient-to-peer-reviewed publication" journey better, easier, and more reliable than their journey to Dr Google.Disclosures: Financial: I am a paid employee of Envision Pharma Group, which provides medical communication services and technology solutions. I have shares in Johnson & Johnson and have been a government-appointed director on the board of 5 hospitals. Nonfinancial: I am an active member and past director of associations that advocate for ethical publication practices. I am a research partner with international patient leaders and advocacy organisations

On 2017 Oct 11, Harri Hemila commented:

Zinc lozenges and vitamin C are promising approaches for the common cold

Papadopoulos NG, 2017 reviewed promising approaches for the treatment and prevention of viral respiratory tract infections, but did not include any meta-analyses or trial reports on zinc lozenges and vitamin C.

Three randomized trials using zinc acetate lozenges found that common cold duration was shortened by 2.7 days (95% CI: 1.8-3.3 days), Hemilä H, 2016, and that the rate of recovery from colds was increased 3.1-fold (2.1-4.7), Hemilä H, 2017. Although zinc lozenges are dissolved in the oro-pharyngeal region, they also shortened the duration of symptoms in the nasal region: nasal discharge by 34% (17-51%) and nasal congestion by 37% (15-58%), Hemilä H, 2015.

The binding of zinc to acetate is weaker than to gluconate and there have been suggestions that zinc acetate might therefore be a better salt for lozenges. Nevertheless, it is not evident that differences at the chemical level between these salts are translated into substantial differences at the clinical level. A meta-analysis found no evidence that lozenges formulated from either of these 2 salts differed in their effects on common cold duration, Hemilä H, 2017. In addition, 2 zinc gluconate trials found that the rate of recovery from colds was influenced to a similar extent as that for the 3 zinc acetate trials, Hemilä H, 2017.

In the trials that reported benefits of zinc lozenges, the total daily dose of elemental zinc was over 75 mg/day. This dose is higher than the recommended intake of 11 mg/day for men and 8 mg/day for women in the USA. However, 100-150 mg/day of zinc has been administered to certain patient groups for months with few adverse effects, and 150 mg/day of zinc is currently one standard treatment for Wilson’s disease, Hemilä H, 2017. Thus, it seems unlikely that 80-100 mg/day of zinc for about a week for treating a cold might lead to long-term adverse effects. There are therefore good reasons for classifying zinc lozenges as a promising approach to treat colds.

A Cochrane review showed with a narrow confidence interval that vitamin C does not prevent colds in the general community, Hemilä H, 2013. However, a meta-analysis of 5 randomized trials with participants under heavy short-term physical stress showed that vitamin C decreased the incidence of colds by 52% (36-65%). Thus, vitamin C seems to have prophylactic effects albeit only in special conditions.

A meta-analysis of more than 2 dozen placebo-controlled trials calculated that ≥1 g/day of vitamin C shortens the duration of colds in children by 18% (9-27%) and in adults by 8% (4-12%), Hemilä H, 2013. Furthermore, 2 trials found a linear dose-response association in the effects on common cold duration by up to 6- and 8-g/day of vitamin C, with colds being shortened by about 20% with the higher dose, Hemilä H, 2017. Still higher therapeutic dosages might lead to greater benefits but such dosages have not been investigated yet. More research also on vitamin C is evidently warranted.

On 2017 Oct 11, Clive Bates commented:

The most misleading thing about this paper is not merely the paper itself, but the way authors chose to present the findings to the media. As so often happens in academic work in this field, association became causation, uncertainty became confidence and very weak methods became the foundations of an assertive press release.

The press notice headline is:

Vaping doubles risk of smoking cigarettes for teens.

Of course, that is a made-for-media headline but deeply misleading about causation and grossly over-confident, given the study's limitations.

Much more likely is that the characteristics (personality, social and family context) that cause people to smoke also cause them to vape and the effects measured are the result of uncorrected confounding or reverse causation. It is quite possible that vaping acts to prevent smoking in people who would otherwise be susceptible to taking up smoking - an obvious possibility given the decline in teenage smoking in the US that coincided with the rise of vaping (albeit mostly experimentation and mostly without nicotine) - trends charts here.

My more detailed review of this study is here: Review of controversial Canadian ‘gateway effect’ study

On 2017 Sep 18, Neil McKeganey commented:

This paper will be interpreted by some as proof that using e-cigarettes acts as a gateway to smoking. That misleading impression is actually encouraged by one of the lead authors of the paper who in an interview for the Business New under the headline "E-cigarettes may double risk of tobacco smoking in teenagers" comments that the study provides a "yes" answer to the question of whether vaping lead to smoking. That statement is however in direct conflict with the stated limitations included within the published paper to the effect that "..the current study makes no claim of cause and effect". In fact this study is not even about the relationship between e-cig use and actual smoking but about e-cig use and a constructed variable for individual's susceptibility to smoke with the latter defined in terms of adolescents indication that they had not taken a firm decision not to smoke. So not having decided not to smoke is interpreted here as an indication that the individual is susceptible to future smoking. The authors rightly acknowledge that not all of those who are judged to be susceptible to smoking will actually go on to smoke in the future. Clearly that definition is problematic since it may well have been that many of the younger pupils had not found themselves in a situation where they felt they felt compelled to establish a clear view for themselves on the possibility of their future smoking. What the researchers have found here is that those pupils who in their definition were susceptible to smoking were more likely to have used e-cigarettes. As with other similar studies there is an entirely different possible explanation for that finding which has to do with the possibility that those pupils who reported past e-cig use were indeed more likely to smoke in the future because of the influence of a different variable e.g. willingness to experiment with different substances with that variable influencing both the likelihood of smoking and the likelihood of e-cig use rather than the latter influencing the former. As the authors acknowledge they have no measure here of intensity of e-cig use; rather they used a measure of any past use (of whatever actual frequency) and any use over the last 30 days (again of whatever actual frequency). As a result the e-cig using group could contain individuals who had used e-cigs on a single occasion in the past or a single occasion in the last 30 days. The only real conclusion which the authors can draw from this study is as they say that "use of e cigarettes among never smokers may increase the risk of future cigarette use.." It could equally be pointed out, though the authors choose not to say this, that "e-cigarette use amongst non-smokers may not increase future cigarette use."

On 2017 Aug 16, Deepa Bhartiya commented:

Authors report primitive, rare Oct-4 positive neural stem cells (pNSCs) in adult mouse brain that form spheres in vitro and also participate in endogenous regeneration. The pNSCs are activated in response to a stress produced by treatment with an antimitotic agent. Authors claim credit for pNSC to be the only adult stem cell to express OCT-4. But this is not true.

We have similarly reported that rare, small sized, pluripotent OCT-4 positive stem cells exist in adult testis, survive chemotherapy (https://www.ncbi.nlm.nih.gov/pubmed/27663915) and rather get activated in response to stress produced by busulphan treatment. Similarly OCT-4 expressing stem cells in adult bone marrow survive and are activated after radiotherapy (https://www.ncbi.nlm.nih.gov/pubmed/21034791) and chemotherapy (https://www.ncbi.nlm.nih.gov/pubmed/27095238). OCT-4 positive stem cells exist in all adult organs and are not limited to only the adult brain as claimed by the authors of this study. This needs to be corrected and a bigger picture of existence of pluripotent OCT-4 positive stem cells in various adult tissues needs to emerge.

On 2017 Oct 31, ANTHONY BAUGHN commented:

My coauthors and I stand firmly behind the design of our study, methods for data collection, presentation and interpretation, and the major conclusions that were drawn in our manuscript. We look forward to continued dialogue and the objective responses of others in the tuberculosis and antimicrobial drug communities regarding this matter.

On 2017 Oct 19, Wanliang Shi commented:

Please see the response: https://www.nature.com/articles/s41598-017-06415-5

On 2017 Dec 05, Joseph M Barnby commented:

This letter to the editor was originally submitted to JMIR uHealth and mHealth. The letter was later withdrawn as we became aware it was eligible to have an APC applied to it; in spite of what we understood the JMIR APC policy to be regarding letters to the editor. Neither of our institutions at the time of publication were able to cover the relevant fees. We have posted our reviewed letter here and invited Clare Killikelly to post her submitted response.

Authors:

Mr J M Barnby - Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 8AF. (Corresponding Author; joe.barnby@kcl.ac.uk)

Dr S A J Fonseca - Division of Psychiatry, University College London, WC1E 6BT.

The Editor JMIR mHealth and uHealth

On 20th July 2017, your journal published a useful and wide-ranging systematic review of mobile and web-based technologies for people with psychosis [1] – a field of mental health which has huge potential to shape the way service users are able to take control of their treatment. Authors found service user aid in design, length of intervention, and social support were all important factors in whether a participant would stop using a digital intervention.

Part of the authors’ summary was that, a) symptom severity may not have a significant effect on drop-out, and b) continuing to develop these interventions alongside users is vital. However, we believe that point a) is not clearly supported by the evidence presented in the article, and point b) misses out (or doesn’t plainly state) a crucial aspect of the technology.

We believe concluding that symptom severity doesn’t have a significant effect on drop-out is premature. The authors reviewed 20 studies that used web-based or mobile technologies and found 6 that measured the impact of symptom severity, chronicity, and duration on drop-out [2, 3, 4, 5, 6, 7]. However, the review only presents the results of those who stayed in the trials, and we believe it’s safe to assume that participants did not drop out randomly. As there were several individuals who declined to take part or dropped out of the study, and since we have no data for this group, we cannot assume that symptom severity does not affect drop-out. In fact, we would argue that it is likely this group were more symptomatic than those who took part. We believe the authors should have stated this more clearly and commented on it in their conclusions about drop-out, including suggesting ways to test this.

The authors only mention that intensity, frequency, and duration of interventions are all vital to adherence, but don’t specifically discuss the role of User Experience/User Interface (UXUI) – a role in software design which tries to make interaction with content as smooth and intuitive as possible. This is a separate but related concept to ‘co-production’ – the involvement of service users in intervention design. Commercial mobile-phone and web-based software is continuously developing more sophisticated and visually pleasing versions. It’s reasonable to hypothesise that better UXUI may result in less drop-out of interventions. Testing this hypothesis may give insight into how a more pleasing user experience may affect drop-out, and how extra investment into UXUI with user input may improve symptom control through better engagement. Indeed, research has suggested this approach might be useful in other areas of healthcare [9] and proposed it might be an important aspect to health intervention design [10]. UXUI focus is increasingly more relevant as mainstream software designers find more ways to keep users engaged, and we believe this highlights that digital interventions may have to compete for attention to meet the expectations of the users they wish to benefit.

In future research aimed at improving user adherence we suggest testing, a) whether simple, text-based designs are as effective as visually pleasing well-designed interfaces when the content is constant (for example, computerised cognitive behavioural therapy), and b) if gamification of therapeutic content improves engagement.

We would like to thank the authors for their current review in this important and emerging area of mental health research, and hope that these comments serve to constructively build upon the discussion.

Yours sincerely, Joseph M Barnby & Dr J Andres S Fonseca

References:

[1] Killikelly C, He Z, Reeder C, Wykes T. Improving Adherence to Web-Based and Mobile Technologies for People With Psychosis: Systematic Review of New Potential Predictors of Adherence. JMIR Mhealth Uhealth 2017; 5(7):e94

[2] van der Krieke L, Emerencia A, Boonstra N, Wunderink L, de JP, Sytema S. A web-based tool to support shared decision making for people with a psychotic disorder: randomized controlled trial and process evaluation. J Med Internet Res 2013 Oct 07;15(10):e216

[3] Ben-Zeev D, Brenner C, Begale M, Duffecy J, Mohr D, Mueser K. Feasibility, acceptability, and preliminary efficacy of a smartphone intervention for schizophrenia. Schizophr Bull 2014 Nov;40(6):1244-1253

[4] Palmier-Claus J, Ainsworth J, Machin M, Dunn G, Barkus E, Barrowclough C, et al. Affective instability prior to and after thoughts about self-injury in individuals with and at-risk of psychosis: a mobile phone based study. Arch Suicide Res 2013;17(3):275-287.

[5] Schlosser D, Campellone T, Kim D, Truong B, Vergani S, Ward C, et al. Feasibility of PRIME: a cognitive neuroscience-informed mobile app intervention to enhance motivated behavior and improve quality of life in recent onset schizophrenia. JMIR Res Protoc 2016 Apr 28;5(2):e77

[6] Kimhy D, Vakhrusheva J, Khan S, Chang RW, Hansen MC, Ballon JS, et al. Emotional granularity and social functioning in individuals with schizophrenia: an experience sampling study. J Psychiatr Res 2014 Jun; 53: 141-148

[7] Hartley S, Haddock G, Vasconcelos ES, Emsley R, Barrowclough C. An experience sampling study of worry and rumination in psychosis. Psychol Med 2014 Jun;44(8):1605-1614.

[8] Gleeson J, Lederman R, Wadley G, Bendall S, McGorry P, Alvarez-Jimenez M. Safety and privacy outcomes from a moderated online social therapy for young people with first-episode psychosis. Psychiatr Serv 2014 Apr 01;65(4):546-550

[9] Boulos MN, Gammon S, Dixon MC, MacRury SM, Fergusson MJ, Rodrigues FM, Baptista TM, Yang SP. Digital games for type 1 and type 2 diabetes: underpinning theory with three illustrative examples. JMIR Serious Games. 2015 Jan;3(1).

[10] Wilhide III CC, Peeples MM, Kouyaté RC. Evidence-based mHealth chronic disease mobile app intervention design: development of a framework. JMIR research protocols. 2016 Jan;5(1).

On 2017 Aug 28, Daniel Corcos commented:

Haymart et al. recommend active surveillance by mammography for ductal carcinoma in situ (DCIS) of the breast, on the basis that it is a low-risk cancer. Actually, DCIS is at low-risk because it is removed soon after diagnosis, so there is no direct evidence for an intrinsic low malignant potential of this form of early breast cancer. The idea that breast cancer is overdiagnosed rests on the observation of an excess of breast cancers concomitant to mammography screening implementation, which is persistent over years. However, mammography-induced cancers better explain this excess, as they occur with a delay and in older women, like the excess cancers that are observed. Delayed surgery has a dramatic effect on breast cancer survival (1). Active surveillance of DCIS would worsen the prognosis of this otherwise low-risk cancer.

1) Bleicher RJ, Ruth K, Sigurdson ER, et al. Time to Surgery and Breast Cancer Survival in the United States. JAMA Oncol 2016;2:330-9.

On 2017 Oct 04, Gurpreet K. Rana commented:

The MEDLINE search strategies are available upon request from the authors as they were not included in article as intended. - G.K. Rana

On 2017 Jul 30, Zvi Herzig commented:

The RCTs instructing controls to avoid artificial sweeteners (Peters et al and Blackburn et al) show significantly reduced BMI in the treatment group. It shouldn't be surprising that the other trials, merely assigning controls to water or placebo, fail to show reduced BMI in the treatment group. Artificial sweeteners can only reduce BMI if they're positioned to displace sugar intake. This isn't the case where the controls are given water or placebo instead of the artificial sweetener.

On 2017 Sep 05, William Davies commented:

CCN3 has recently been associated with vulnerability to Obstructive Sleep Apnea (Weingarten JA, Bellner L, Peterson SJ, Zaw M, Chadha P, Singh SP, Abraham NG. The association of NOV/CCN3 with obstructive sleep apnea (OSA): preliminary evidence of a novel biomarker in OSA. Horm Mol Biol Clin Investig. 2017 doi:10.1515/hmbci-2017-0029); this is interesting in light of the fact that sleep disruption may precipitate postpartum psychosis (Lewis KJ, Foster RG, Jones IR. Is sleep disruption a trigger for postpartum psychosis? Br J Psychiatry. 2016 May;208(5):409-11)

On 2017 Jul 31, Tom Kindlon commented:

Overall averages for Table 2, "Mean change (95% CI) in patient-reported measures between assessment and 1-year follow-up across CFS/ME specialist services":

Frustratingly, the overall weighted averages for the measures included in Table 2 were not included in the paper.

Two people have independently calculated them. Here they are: n = 432

Chalder Fatigue Scale (range 0–33) -6.05

SF36 Physical Function Subscale (range 0–100) 4.19

Work & Social Adjustment Scale (range 0–40) -3.40

Visual analogue pain rating scale (range 0–100) -4.42

HADS Anxiety Score (range 0–21) -0.56

HADS Depression Score (range 0–21) -1.35

Epworth Sleepiness Scale (range 0–24) -1.07

Jenkins Sleep Jenkins (range 0–20) -1.37

CIS20R Fatigue Subscale (range 8–56) -4.73

CIS20R Concentration Subscale (range 5–35) -2.67

CIS20R Motivation Subscale (range 4–28) -2.42

CIS20R Activity Subscale (range 3–21) -1.95

On 2017 Sep 07, Pranay Jindal commented:

Thank you for your comments and feedback.

The purpose of the article was to critically analyze the Flesch Reading Ease (FRE) and Flesch-Kincaid Reading Grade Level (FKRGL) and their use in assessing the reading level/perceived difficulty of a written text. We agree with you that grade level as assessed by readability formulas do not equate with readers understanding. In the article, we mention “in their assessments, FRE and FKRGL do not take into account (1) document factors (layout, pictures and charts, color, font, spacing, legibility, and grammar), (2) person factors (education level, comprehension, health literacy, motivation, prior knowledge, information needs, anxiety levels), and (3) style of writing (cultural sensitivity, comprehensiveness, and appropriateness), and thus, inadequately assess reading level”.

We do not explicitly support the use of readability formulas to assess the reading level/perceived difficulty of a written text, and in our article recommended that “future research needs to develop generic and disease-specific readability measures to evaluate comprehension of a written document based on individuals' literacy levels, cultural background, and knowledge of disease”. We encourage researchers and clinicians to move towards assessment of comprehension of written documents. However, in the absence of a reliable and valid measure to measure comprehension and the ease of using Flesch Reading Ease (FRE) and Flesch-Kincaid Reading Grade Level (FKRGL) via Microsoft office makes them a popular and easy choice.

On 2017 Jul 24, Donna Berryman commented:

While the authors do a pretty good job of pulling together the basic information about some popular readability formulas, they tend to support the idea that these formulas are somehow worthwhile. It is time to focus on the idea that grade level or readability formula results do not equate to reader understanding. As Leroy, Kauchak and Hogue (2016) write: "The lack of strong evidence for increased comprehension after using readability formulas may indicate that it is perceived difficulty that is being manipulated: The text looks easier but may not necessarily be easier to understand." (PMID 27043754) Wan et al (2013) do a good job of showing how different readability formulas vary in their calculations (see PMID 22835706). They conclude that "the SMOG formula appears to be more ideally suited for use in a health care context, as it has been validated against 100% comprehension..." But, beyond that, I would heartily encourage that we start thinking beyond written materials. I'd recommend the work of Donald L. Rubin on listenability (see PMID 23030569 for one example). Most health information is dispensed orally.

On 2017 Sep 01, Seán Turner commented:

Alou et al. (2016) [PMID 27330818] write that strain Marseille-P2366 (= CSUR P2366 = DSM 102091) is the type strain of Bacillus mediterraneensis. Contradictorily, Cadoret et al. (2017) [PMID 28706723] write that the type strain of Bacillus mediterraneensis is Marseille-P2384 (= CSUR P2384 = DSM 102091), and that strain Marseille-P2366 (= CSUR P2366 = DSM 102112) is the type strain of Bacillus massilinigeriensis.

On 2017 Oct 02, Serge Ahmed commented:

This article reports an interesting set of experiments showing that ravens repeatedly choose among a set of different objects, an object that will prove several minutes or hours later to be useful to obtain food. The authors interpret this preference as evidence that ravens would be able to plan for the future. However, since the preferred object was repeatedly and selectively paired with food reward during initial training, one cannot definitively rule out the involvement of non-planning processes. For instance, ravens could prefer the would-be useful object, not because they anticipate its future utility, as hypothesized by the authors, but merely because they attach more affective and/or motivational value to the object due to its past selective association with food reward. To rule out this associative mechanism, it is important to add a control condition where, all else being equal, choice of the previously food-paired object is not followed by an opportunity to use it to obtain food (for a similar criticism and a specific example of a control condition, see: Redshaw et al. https://www.ncbi.nlm.nih.gov/pubmed/28927634).

On 2017 Sep 05, MARK VRABEL commented:

Good to see the "Librarian AS" author has been corrected.

On 2017 Aug 16, MARK VRABEL commented:

Thanks for commenting after seeing my MEDLIB-L post and #medlibs tweet about this "Librarian AS" error.

On 2017 Aug 14, Melissa Rethlefsen commented:

Sam Johnson is the Academic Support Librarian, and he is named as an author. Let's hope this gets updated, though!

On 2017 Aug 14, Donna Berryman commented:

It's quite jarring to see that "Academic Support Librarian" - a position, not a person - is listed as an author on this paper. Assuming that an academic support librarian actually did participate, then the person (not the position) should be named. I'm hoping this will be corrected by the time the article is in print (rather than the epub ahead of print status).

On 2017 Jul 31, George McNamara commented:

Please note that supporting materials.zip (Word document inside) is available online at http://onlinelibrary.wiley.com/doi/10.1002/cphg.42/full#hg0404-sec-0023

On 2017 Jul 28, Morten Oksvold commented:

“Dunoyer has been a long-time colleague and collaborator of Olivier Voinnert, and recently a number of their studies, three with Dunoyer as first author, have been retracted while a number more have had formal corrections published to address problems with presented data."

Please note that Olivier VOINNET is his correct name and Dunoyer's master has so far eight retractions and twenty corrections(only 12 of them are directly searchable in PubMed):

https://www.ncbi.nlm.nih.gov/pubmed?term=(voinnet o[Author]) AND "retracted publication"[Publication Type]

https://www.ncbi.nlm.nih.gov/pubmed?term=(Voinnet o[Author]) AND "published erratum"[Publication Type]

(Link to full report here: https://www.ethz.ch/content/dam/ethz/news/medienmitteilungen/2015/PDF/untersuchungsbericht/Report_of_ETH_Commission_Voinnet.pdf )

Please also note that in reference 7 in the mentioned article (Incarbone, M et al., Nature Plants, June 2017) they cite Deleris A et al., Science 2006, which represents one of the articles that supposed to be retracted (see quote from the report below).

From the investigation report: "Although it is obviously the journal's prerogative, the former (category 2) papers, particularly those containing well documented intentional manipulations (PLoS Pathogens 2013 9:e1003435; Plant Cell 2004 16: 1235; Science 2006 313: 68; PNAS 2006 103: 19593 and EMBO J 2010 29: 1699), should be retracted through OV's requests as being non-factual, irrespectively of whether the reported observations have been reproduced by others."

I find it problematic that Nature Plants accept this kind of practice, by apparently legitimating well documented intentional manipulations as facts.

On 2017 Aug 20, Daniel Weiss commented:

This review of Tickborne diseases other than Lyme by Drs. Eickhoff and Blaylock paints a frightening picture of diverse illnesses increasing in prevalence in the United States.

A recent survey found over 20% of U.S residents reporting a tick attached to themselves or a family member within the previous year(1). Yet, as Eickhoff and Blaylock point out, the absence of a known tick bite “never precludes the diagnosis of a tick-borne infection” and “co-infections with multiple pathogens may occur”. Throughout their review, the authors emphasize that insensitive laboratory testing methods increase the complexity of diagnosis, and result in an unknown risk to the blood supply. All health care practitioners require a high index of suspicion and sound clinical judgment to identify individual tick-borne infections. Simultaneous co-infections increase the diagnostic and therapeutic challenge.

As examples of the challenges faced, Borrelia miyamoti infection may not demonstrate the erythema migrans rash occurring with B. burgdorferi—the agent of Lyme disease. But up to 70% of patients with Lyme disease have no history of this rash(2). Similarly, there is no proven clinical difference between the rash seen with B. lonestari and B. burgdorferi. Lonestar ticks can transmit both spirochetes(3).

Because no gold standard exists to prove the absence of any of these infections, practitioners must avoid declaring with certitude that no infection is present—especially if an acute infection has gone untreated or undertreated. In his accompanying editorial, Dr. Mandell reiterated the difficulty of identifying acute tick-borne infection. Therefore, we were confused by his concluding paragraph. Given the diagnostic uncertainties, one must not dismiss dogmatically the possibility of an infection, either acute or chronic. A call for improved diagnostics and more effective therapeutics is the more logical response to the issues raised by this important review.

1. Hook SA, Nelson CA, Mead PS. U.S. public's experience with ticks and tick-borne diseases: Results from national HealthStyles surveys. Ticks Tick Borne Dis. 2015;6(4):483-8. doi: 10.1016/j.ttbdis.2015.03.017. PubMed PMID: 25887156.
2. Aucott JN, Seifter A, Rebman AW. Probable late lyme disease: a variant manifestation of untreated Borrelia burgdorferi infection. BMC Infect Dis. 2012;12:173. Epub 2012/08/03. doi: 10.1186/1471-2334-12-173. PubMed PMID: 22853630; PMCID: PMC3449205.
3. Clark KL, Leydet B, Hartman S. Lyme borreliosis in human patients in Florida and Georgia, USA. Int J Med Sci. 2013;10(7):915-31. doi: 10.7150/ijms.6273. PubMed PMID: 23781138; PMCID: PMC3675506.

On 2017 Aug 09, David Keller commented:

Two Large Epidemiological Studies Reach Opposite Conclusions Regarding Dementia Risk From PPI Use

A recent German study [1] found a significant 44% increased incidence of dementia with regular proton-pump inhibitor (PPI) antacid use, in a cohort of 73,679 baseline non-demented persons over age 75, of whom 29,510 developed dementia over 8 years, and 2950 were regular PPI users. The authors of that study boldly concluded that "avoidance of PPI medication may prevent the development of dementia" and called for a randomized controlled trial of PPIs to better assess this risk.

The current study [2] looked at the 70,718 cases of Alzheimer disease (AD) diagnosed in Finland over a 7-year period and found no difference in risk based on regular PPI use, and a confirmatory lack of association of risk with dose of PPI, or duration of PPI use.

Which of these two large, painstaking studies in similar populations is correct? PPI use either does or does not increase the risk of dementia, and it is crucial to know which is true. Millions take PPI medication daily to control acid reflux, but would be better off taking less effective or tolerable treatments if PPIs increase the risk of dementia.

Taipale and colleagues identified PPI users from medication-purchase data, whereas Gomm and colleagues identified PPI users from prescription data, which did not indicate whether the prescriptions were actually filled. Obviously, persons who purchase a medication are more likely to be taking it than persons who are merely prescribed it. However, the effect of non-compliance with prescribed PPI therapy in the Gomm study is to actually increase the risk of dementia caused by taking PPI medication. The more non-compliance among patients in Gomm's PPI group, the greater the dementia-increasing effect PPIs must have had on compliant patients to explain the observed overall increased dementia in the PPI group. So, the difference in how PPI-takers were identified cannot account for the discrepant results of these studies.

How much credence can we place in epidemiological results if two large studies can report polar opposite conclusions with such apparent certainty? Is it ethical, or even possible, to randomize patients to less-effective medications than PPIs in a controlled trial, to definitively determine whether PPIs truly increase the risk of dementia?

References

1: Gomm W, von Holt K, Thomé F, Broich K, Maier W, Fink A, Doblhammer G, Haenisch B. Association of Proton Pump Inhibitors With Risk of Dementia: A Pharmacoepidemiological Claims Data Analysis. JAMA Neurol. 2016 Apr;73(4):410-6. doi: 10.1001/jamaneurol.2015.4791. PubMed PMID: 26882076.

2: Taipale H, Tolppanen AM, Tiihonen M, Tanskanen A, Tiihonen J, Hartikainen S. No Association Between Proton Pump Inhibitor Use and Risk of Alzheimer's Disease. Am J Gastroenterol. 2017 Jul 11. doi: 10.1038/ajg.2017.196. [Epub ahead of print] PubMed PMID: 28695906.

On 2017 Jul 14, Seán Turner commented:

The authors cite strain CECT 9186 as type, but this is also cited as the type strain of Blastomonas quesadae (PMID 28631592) and is listed as such in the CECT online catalog.

On 2017 Jul 17, Donald Forsdyke commented:

IF G-QUADRUPLEXES, WHY SO MANY ADENINES?

It is good to see the problem of EBV immune evasion focused, not on the translation product of EBNA1 mRNA (1), but on the mRNA itself (2). However, it is puzzling that the sequence encoding the glycine-alanine repeats is enriched not only in guanines (Gs), but also in adenines (As). In such a GC-rich genome (60% GC), there is a scarcity of As, yet they are concentrated in the glycine-alanine repeat-encoding region. In other words, codons have been selected for their general purine-richness, not just for their G-richness (3). While it is conceivable that the As somehow assist consecutive Gs to form G-quadruplexes, consideration might have been given to the hypothesis that the G-quadruplexes may merely be helpful by-products of the fundamental need to purine-load the mRNA.

EBV is not alone in this respect. EBV and HTLV-1 share common characters. Both are deeply latent, GC-rich viruses. They persist in their human hosts for long periods often with no obvious detrimental effects. Most of their proteins are encoded by pyrimidine-rich mRNAs. The HTLV-1 provirus encodes its pyrimidine-rich mRNAs in its "top" sense strand. But there is a "bottom" strand transcript. This is heavily R-loaded and is translated into a basic zipper protein (HBZ) which is poorly immunogenic and is increasingly seen, like EBNA-1, as playing a major role in immune evasion (4-6).

1. 1.Levitskaya, J. et al. (1995) Inhibition of antigen processing by the internal repeat region of the Epstein-Barr virus nuclear antigen-1. Nature 375:685–688. Levitskaya J, 1995
2. 2.Lista MJ et al. (2017) Nucleolin directly mediates Epstein-Barr virus immune evasion through binding to G-quadruplexes of EBNA-1 mRNA. Nature Commun 8:16043. Lista MJ, 2017
3. 3.Cristillo AD et al. (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load. J Theor Biol 208:475–491.Cristillo AD, 2001
4. 4.Cook LB et al. (2013) HTLV-1: Persistence and pathogenesis. Virology 435:131–140. Cook LB, 2013
5. 5.Shiohama et al. (2016) Absolute quantification of HTLV-1 basic leucine zipper factor (HBZ) protein and its plasma antibody in HTLV-1 infected individuals with different clinical status. Retrovirology 13:29 Shiohama Y, 2016
6. 6.Forsdyke DR EBV Webpage

On 2017 Sep 08, Falk Leichsenring commented:

Toward a more Balanced Perspective on Anxiety Treatment

Falk Leichsenring 1, Allan Abbass 2, Patrick Luyten13

1 Department of Psychosomatics and Psychotherapy, Justus-Liebig-University Giessen, Ludwigstr. 76, D-35392 Giessen, Germany 2 Department of Psychiatry, Dalhousie University; Centre for Emotions and Health, Halifax, 8203 5909 Veterans Memorial Lane, Halifax, NS, Canada, B3H 2E2 3 Faculty of Psychology and Educational Sciences, University of Leuven, Klinische Psychologie (OE), Tiensestraat 102 - bus 3722, 3000 Leuven, Belgium, and Research Department of Clinical, Educational and Health Psychology, University College London, Gower Street, London WC1E 6BT, UK

Stein and Craske recently published a viewpoint article entitled "Treating Anxiety in 2017".1 Yet, the treatment section excludes other evidence-based, widely-used non-medical treatment options while exclusively recommending pharmacotherapy and Cognitive Behavioral Therapy (CBT).

The authors state that most empirical support exists for CBT. However, a recent meta-analysis showed that only one sixth of studies are of high quality.2 In more than 80% of the studies CBT was compared to a waiting list, that is to a relatively weak comparator that may even represent a nocebo condition.2 In panic disorder, CBT was not superior to treatment-as-usual, only to waiting list.2 There was also significant evidence of publication bias.2 Based on these and other findings, this meta-analysis concluded that CBT was “at best probably effective” in anxiety disorders, which markedly contrasts with the overly optimistic depiction of the effects of CBT by Stein and Craske.

In exclusively recommending CBT, Craske and Stein completely bypass other forms of psychotherapy such as interpersonal therapy or psychodynamic therapy, even though both are efficacious in anxiety disorders. 3,4 Moreover, comorbidity is the norm in anxiety disorders but there is lack of evidence to support CBT in complex or comorbid anxiety populations, whereas brief psychodynamic therapy has been found to be more effective than other treatments in reducing anxiety in patients with depression. 5 The evidence for the proposed working mechanisms in anxiety disorders is also far less clear than Craske and Stein suggest, and their assertion that working mechanisms of CBT are different from other types of psychotherapy is similarly largely unsupported.

It is also quite perplexing that the authors recommend benzodiazepines for patients for whom SSRIs or CBT failed without consideration of the above mentioned other commonly used, non-medical treatments. Given evidence that long-term effects of pharmacotherapy in anxiety disorders are unknown due to the lack of follow-up studies6, such a suggestion biases patient care in favour of often endless medication treatments.

This unbalanced discussion of treatments for anxiety disorders is the more perplexing since the authors' attention was recently called to the fact that other types of psychotherapy have been found to be equally effective in anxiety disorders7, based on studies of good quality .4

Biased clinical guidance such as the one by Stein and Craske is highly undesirable from a scientific and clinical perspective, and can be easily avoided by including proponents of rival approaches (adversarial collaboration).

References

1. Stein MB, Craske MG. Treating Anxiety in 2017: Optimizing Care to Improve Outcomes. JAMA. Jul 18 2017;318:235-236.
2. Cuijpers P, Cristea IA, Karyotak E, Reijnders M, Huibers MHJ. How effective are cognitive behavior therapies for major depression and anxiety disorders? A meta-analytic update of the evidence World Psychiatry. 2016;15:245-258.
3. Markowitz JC, Petkova E, Neria Y, Van Meter PE, Zhao Y, Hembree E, Lovell K, Biyanova T, Marshall RD. Is Exposure Necessary? A Randomized Clinical Trial of Interpersonal Psychotherapy for PTSD. Am J Psychiatry. May 2015;172:430-440.
4. Keefe JR, McCarthy KS, Dinger U, Zilcha-Mano S, Barber JP. A meta-analytic review of psychodynamic therapies for anxiety disorders. Clin Psychol Rev. Jun 2014;34:309-323.
5. Driessen E, Hegelmaier LM, Abbass AA, Barber JP, Dekker JJ, Van HL, Jansma EP, Cuijpers P. The efficacy of short-term psychodynamic psychotherapy for depression: A meta-analysis update. Clin Psychol Rev. Aug 1 2015;42:1-15.
6. Leichsenring F, Leweke F. Social Anxiety Disorder. N Engl J Med. Jun 08 2017;376:2255-2264.
7. Steinert C, Leichsenring F. No psychotherapy monoculture for anxiety disorders. Lancet. May 13 2017;389:1882-1883.

On 2017 Sep 02, Randi Pechacek commented:

Aaron J. Prussin II, second author of this article, and Amy J. Pruden wrote a blog post on microBEnet. The blog post explores the topic of the exposome of the built environment.

On 2017 Aug 18, NephJC - Nephrology Journal Club commented:

The position paper for the ISPD on the length of time on peritoneal dialysis (PD) and encapsulating peritoneal sclerosis (EPS) was discussed on July 11th and 12th 2017 on #NephJC, the open online nephrology journal club. Introductory comments written by Nikhil Shah are available at the NephJC website here

There was a lot of interest in this updated position paper, with 98 participants in the discussion and nearly 700 tweets. Of note, the PDI editor and the UK authors also joined in to provide further background and context to this paper.

The highlights of the tweetchat were:

• There participants agree with the epidemiological challenges as outlined by the authors – difficulty defining EPS, lack of interventions, conflicting data on effect of time on PD, difficulty applying available evidence into individual risk assessment. As such, they recognise that this is only a position statement as opposed to a set of guidelines.

• Ascertainment bias may affect reported incidence rates. Clearer diagnostic criteria may encourage earlier diagnosis and intervention.

• Applying empiric time-limitations to PD is probably not the solution.

• Aggressive nutrition, switching dialysis modality and referral to a specialist surgical centre were the preferred management strategies of this group. Some advocate tamoxifen or steroids in addition.

Transcripts of the tweetchats, and curated versions as storify are available from the NephJC website.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC on twitter, liking @NephJC on facebook, signing up for the mailing list, or just visit the webpage at NephJC.com.

On 2017 Aug 04, Luis Mauricio T. R. Lima commented:

This is an interesting article showing the pramlintide and zinc interaction, and the role of His18 in zinc interaction such as previously reported for human amylin. https://www.ncbi.nlm.nih.gov/pubmed/20536124 https://doi.org/10.1021/ja1007867

We have also recently reported (2016) the amyloid aggregation of pramlintide, spontaneously and without zinc. https://www.ncbi.nlm.nih.gov/pubmed/27665170 https://doi.org/10.1016/j.bpc.2016.09.007

Murine amylin, another "stable" (compared to human) amylin analogue, also behaves as amyloid in solution. https://www.ncbi.nlm.nih.gov/pubmed/23974296 https://doi.org/10.1016/j.bpc.2013.07.013

Murine amylin can also interact with zinc, and this peptide has no His18, and interaction is mediated by several other contacts, and can result in modulation of the amyloid aggregation process. https://www.ncbi.nlm.nih.gov/pubmed/27693831 http://dx.doi.org/10.1016/j.bpc.2016.09.008

Collectively, these data suggest an universal amyloid behavior of amylin analogues and interaction with zinc, regardless of the presence of proline or His18.

On 2017 Jul 05, Jim Woodgett commented:

Kudos for a super study (and bonus for getting the GSK3 isoforms right).

On 2017 Jul 15, James Tsung commented:

Video of vaginal foreign body on transabdominal ultrasound: https://youtu.be/B22Ae0z7i64

On 2017 Jul 04, Parmit Singh commented:

Very interesting finding that sad-7 is showing localization in cytoplasm, peripheral and in nuclear regions. Understanding the correlation of localization with its function in meiotic silencing might be interesting. Interestingly, its expression is similar to sad-4. Also like sad-4, it produces 50% round spores in a heterozygous cross. Homozygous cross is barren in case of sad-7 whereas it is very less productive in case of sad-4. In case of sad-5 and sad-6 (both sad-5 and sad-6 are nucleus localized suppressors, homozygous crosses are fertile. This suggests that the meiotic function of sad-7 might be related to its perinuclear localization or peripheral part of meiotic silencing similar to sad-4. This is further supported by the fact that recently identified two other suppressors cbp20 and cbp80 (cap - binding proteins) produce 80% round spores (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386863/pdf/1149.pdf). Proteins of both genes cbp20 and cbp80 are localized in nucleus and homozygous crosses are fertile like sad-4.

On 2017 Oct 22, George Kunos commented:

We read with interest the above article (Varga B, 2017), comparing the pharmacological properties of a series of cannabinoid receptor 1 (CB1R) blockers, including first generation brain-penetrant compounds and more recently introduced peripherally restricted compounds in various tests, including their anti-obesity effects in a mouse diet-induced obesity (DIO) model. The complete lack of effect of the peripheral CB1R inverse agonist JD-5037 in the DIO mouse model was of particular interest to us, as we have earlier documented its high anti-obesity efficacy in DIO mice (Tam J, 2012, Cinar R, 2014) and in a mouse model of Prader-Willi syndrome (Knani I, 2016), as well as its anti-diabetic efficacy in a rat model of type 2 diabetes (Jourdan T, 2013, Jourdan T, 2014). In these as well as in more recent studies (Tam J, 2017, Hinden L, 2018, Udi S, 2017), JD-5037 was dissolved in 4% DMSO/1% Tween-80 in PBS (vehicle #1) for administration by oral gavage (see Jourdan T, 2013), whereas Varga et al. used a 5% Tween-80 solution (vehicle #2). Because in our hands the inclusion of DMSO was critical for keeping this highly lipophilic compound in solution, we compared the oral bioavailability and peripheral target engagement of JD-5037 dissolved in these 2 vehicles. Using vehicle #1, the peak plasma concentration of JD-5037 measured by LC-MS/MS 1 h after oral administration to lean, male C57Bl6/J mice was 1076 ± 208 ng/mL (1840 nM), similar to values we published earlier (Tam J, 2012). In contrast, using vehicle #2, the plasma level of JD-5037 was 0.38 ± 0.02 ng/mL (0.67 nM), more than 1,000-fold lower and barely detectable. JD-5037 is 99.6% protein-bound in plasma (Tam J, 2012), so its calculated free concentration was 7.4 nM using vehicle #1 versus 2.7 pM using vehicle #2, the latter value being 2 orders of magnitude below the binding Kd of JD-5037 for CB1R (0.4 nM), which predicts no significant CB1R occupancy. We further verified this by using the upper GI motility test as a measure of peripheral CB1R occupancy (Tam J, 2012). In vehicle-treated mice, an oral charcoal bolus traveled 54 ± 3% of the length of the small intestine in 30 minutes, whereas In mice treated with a maximally effective dose of the CB1R agonist ACEA, the charcoal bolus traveled only 25 ± 3%, indicating a 54% inhibition. The inhibitory effect of ACEA was completely blocked by pretreatment with a single dose of 3 mg/kg JD-5037 in vehicle #1 (53 ± 3%), in agreement with our published data (Tam J, 2012). In contrast, the same dose of JD-5037 administered in vehicle #2 was completely without effect, the distance traveled by the charcoal bolus (29 ± 2%) being the same as with ACEA alone. Thus, the negative findings of Varga et al. can be attributed to lack of absorption and a consequent lack of peripheral CB1R occupancy by JD-5037, due to the use of an inappropriate vehicle. Such pitfalls are avoidable by verifying bioavailability and target engagement, which is a basic requirement when testing the in vivo efficacy of novel compounds.

George Kunos, Joseph Tam^1, Resat Cinar, Tony Jourdan; National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA

¹ Current address: School of Pharmacy, The Hebrew University, Jerusalem, Israel

On 2017 Sep 15, Cicely Saunders Institute Journal Club commented:

We chose this paper for our monthly Journal Club on 6th September 2017 and some comments from our discussion are below.

This is a useful paper to explore the experiences of clinicians and relatives to determine why hospital deaths predominate in haematological cancers. This paper focused on an important and under-researched topic. We felt that this paper would be improved if the authors could

1) Use Consolidated criteria for reporting qualitative studies (COREQ): 32-item checklist.

2) State what methodological orientation underpinned the study? E.g. grounded theory, ethnography, phenomenology.

3) Explain the reasons for the imbalance of sample (45 clinicians vs. 10 relatives) and why patients’ perspectives were not included.

4) Elaborate the views of ‘co-dependency’ in more detail.

5) Provide more in-depth cross-comparison of perspectives between different groups of participants (healthcare practitioners across different settings and relatives of deceased patients)

The paper generated a lively discussion among clinicians, researchers and academics, and we thank the authors for drawing attention to this important area.

On 2017 Sep 08, Ping Guo commented:

None

On 2017 Jul 12, Felipe Santiago commented:

I don't disagree with their main message, but I think is not addressing the problem at all. I do believe the current environment makes the job look "unattainable" but still is very "desirable". Less than 10% of all the postdocs in my current research-intensive institution actually successfully complete an academic job search, but almost all still try! Most go elsewhere after trying at least 2 cycles. So I disagree with the statement that PIs are discouraging grad students and postdocs to follow this path, they are just been good, realistic mentors, that know the many problems postdocs can face in today's hypercompetitive academic job search.

On 2017 Oct 10, Shaun Khoo commented:

Green Open Access: The accepted manuscript is available from the UNSW Institutional Repository (subject to a 12 month publisher embargo).

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

On 2017 Jul 26, Mohammed AlJasser commented:

I cannot access this article although it is labelled as "Free full text".

On 2017 Sep 12, John Roger Andersen commented:

Read publishers pdf version in ReaderCube for free: click here.

On 2017 Aug 09, Thomas Jeanne commented:

The statement "...with infectious Zika able to be cultured from semen up to 80 days after the onset of symptoms" cites reference 55 (Matheron S, 2016), which does not support it. Matheron et al. found Zika virus RNA in semen at 80 days, but "infectious virus was not cultured." It appears that the longest reported period between symptom onset and detection of infectious Zika virus in semen is 69 days, in a vasectomied patient (Arsuaga M, 2016).

On 2017 Jul 11, Martine Crasnier-Mednansky commented:

The cya crp* mutant strain CA-8404 isolated by L. Soll (Sabourin D, 1975), which has been widely used for transduction of its crp* gene (also used in the present work), was finally characterized by Karimova G, 2004 as containing three mutations in the crp gene. Karimova G, 2004 further reported this CRP* was indeed capable of responding to cAMP and therefore was still sensitive to Carbon Catabolite Repression (CCR). Of interest to the present study, and any other studies aimed at releasing CCR in Escherichia coli, Karimova G, 2004 also characterized a novel CRP* with two mutations which totally relieved CCR as compared to the three-mutation CRP*.

Here cAMP-dependent CCR may not be the main culprit for preventing xylose utilization by the Escherichia coli wild type W strain (the Waksman’s strain). Generally, an increase in cAMP upon glucose depletion allows utilization of less-preferred sugar like xylose. Figure S7-A indicates that upon glucose exhaustion, E. coli W was still unable to use xylose after 96 hours, even though it could use xylose quite efficiently in the absence of glucose (Figure 2-D). In addition, the CRP* isolated by the authors (G141D) for specifically increasing xylose catabolism (Figure 1), and which doubled xylose utilization in the parent strain XW043, did not improve E. coli W xylose consumption at all in the presence of glucose (Figure 4-A). Thus, based on current knowledge, the inability of the Waksman’s strain to use xylose in the presence of a large excess glucose does not appear to relate to cAMP-dependent CCR. Interestingly, E. coli B, unlike W, is unable to use glucose fully when grown in excess glucose, and the typical increase in cAMP does not occur after cessation of growth (figure 2 in Peterkofsky A, 1971). Thus, if some glucose remains unused in the medium, cells may fail to use xylose.

On 2017 Jul 26, Sally Satel commented:

Dartmouth demographer Samir Soneji and his co-authors find that the probability of cigarette smoking at follow-up is significantly higher among all e-cigarette users than among individuals who never used a nicotine product. Based on this finding, they conclude that “strong e-cigarette regulation” by the federal, state, and local governments are needed to minimize the potential “future population-level burden of tobacco.” This conclusion is unwarranted based on the nature of their results.

The article compares the probability of smoking in the post-period conditional on e-cigarette use without smoking to the probability of smoking in the post-period conditional on neither e-cigarette use nor smoking. This is not the relevant comparison for the purpose of assessing public-health risk. The relevant comparison is between smoking behavior conditional on access to e-cigarettes and smoking behavior conditional on no access to e-cigarettes, as such a comparison incorporates both the potential gateway and deterrent/diversion effects of e-cigarette use.

Such a comparison would take into account any beneficial effects of e-cigarettes on potential smokers who choose to reduce their cigarette smoking or to limit themselves to e-cigarette use altogether, as well as on smokers in the pre-period who switch to e-cigarettes partially or fully, or successfully use e-cigarettes as a cessation aid. It is on this comparison that regulatory choices should be based.

The nascent market for e-cigarettes in the United States can make robust empirical research on the consequences of these products on tobacco use challenging. The importance of a proper analytical framework is illustrated in a recent National Bureau of Economic Research working paper by economists Mike Pesko of Weill Cornell Medical College and Janet Currie of Princeton. The economists identify an important unintended consequence of minimum legal sale age laws restricting access to e-cigarettes: smoking among underage pregnant teenagers increased by more than 2 percentage points.

With teen smoking at a new low, policymakers should be celebrating a public health success instead of seeking a new regulatory expansion. Empirically, it is certainly not clear that more vaping has any causal effect on smoking among youth, as Soneji and his co-authors imply but do not demonstrate. Moreover, the type of analyses reported in JAMA Pediatrics fails to offer a reliable basis for developing an optimal regulatory framework for e-cigarettes and other modified risk tobacco products.

-Alex Brill, Sally Satel, Stan Veuger

NBER paper: http://www.nber.org/papers/w22792

On 2017 Jul 21, Samir Soneji commented:

We thank Joel Nitzkin for his interest in our article, which systematically reviewed 9 US-based longitudinal studies that assessed e-cigarette use and cigarette smoking among >17,000 adolescents and young adults. Our research concluded that e-cigarette use among adolescents who had never tried a cigarette was associated with subsequent cigarette smoking initiation and past 30-day cigarette smoking, with similar effect size across studies of adolescents and young adults. All of the studies used multivariable analysis to adjust for other factors that might make adolescent e-cigarette users at higher risk for use of multiple substances—risk factors such as friends who smoke, sensation seeking tendencies, and use of other substances like alcohol.

Nitzkin asserted three claims about the research. First, Nitzkin claimed that the studies provided no evidence that e-cigarette use is related to consistent daily cigarette smoking. Second, he claimed that e-cigarette use was simply a marker for high-risk youth who were more likely to smoke anyway. Third, he claimed that the decline in youth cigarette smoking over time at the population level proves e-cigarette use does not increase the probability of cigarette smoking at the individual level. Empirical evidence contradicts these claims, as we describe below.

Regarding Nitkin’s first claim that e-cigarette use is not related to consistent daily cigarette smoking, few adolescents smoke on a daily basis, which makes assessment of daily smoking impractical for most longitudinal studies that have a 1-2 year timeframe. Logically, smoking initiation is a necessary requisite to daily smoking. Moreover, recent longitudinal research found that smoking initiation identifies about two-thirds of adolescents who will be daily smokers two years later, with a false positive rate of 8 percent.1 In other words, smoking initiation is about as good at predicting eventual daily smoking as screening mammography is at predicting breast cancer.² Although not perfect, smoking initiation presents a public health concern especially given the growing body of evidence that e-cigarettes are used by some youth unlikely to have ever smoked cigarettes.^1,3,4 Furthermore, a recent longitudinal study by Leventhal et al. (2016) found that more frequent e-cigarette use at baseline was associated with more frequent and heavier patterns of cigarette smoking at follow-up using data from >3000 adolescents.⁵ Thus, smoking initiation, which the studies examined, is a sensible predictor of future daily smoking, and the pattern of e-cigarette use seems to predict the pattern of eventual cigarette smoking.

Regarding Nitzkin’s second claim that e-cigarette users are just high-risk youth, the combined risk estimate represents a risk that adjusts for many risk factors, as we mentioned above, that would cause some adolescents to be at risk for using multiple substances. The fact that the adjusted estimate is very strong (odds ratio of almost 4) suggests to us that it is unlikely that one or more added covariables would completely confound the e-cigarette effect. Moreover, several studies concluded that adolescents who use e-cigarettes are medium-risk youth, not those who are necessarily destined to begin cigarette smoking anyway.^6–10 Furthermore, several longitudinal studies have reported that the association between e-cigarette use and smoking initiation was strongest among the lowest risk youth (i.e., youth who stated that they were unlikely to try smoking in the future).^9,11,12

Regarding Nitzkin’s third claim that the recent decline in youth cigarette smoking proves e-cigarette use does not lead to cigarette use, youth cigarette smoking has been declining steadily in the US for the past 20 years and predates e-cigarettes.^13,14 In other words, this steady decline in youth cigarette smoking began long before the introduction of e-cigarettes into the US in 2007 and before e-cigarette use became prevalent in youth around 2011. So the decline in youth cigarette smoking cannot be attributed to the advent of the e-cigarette.

We believe our research underlines that the potential risks of e-cigarette use are significant and should not be discounted. Tobacco control efforts, including taxation, youth smoking prevention programs, and restrictions on tobacco advertising reduce youth smoking. The nearly twenty-year decline in youth smoking demonstrates the success of these tobacco control efforts despite youth e-cigarette use. We must acknowledge and address the public health harm posed by youth e-cigarette use to prevent a new generation of nicotine-addicted adult tobacco users.

References

¹ Sargent JD, Gabrielli J, Budney A, Soneji S, Wills TA. Adolescent smoking experimentation as a predictor of daily cigarette smoking. Drug Alcohol Depend. 2017;175:55-59. doi:10.1016/j.drugalcdep.2017.01.038.

² Ferrini R, Mannino E, Ramsdell E, Hill L. Screening mammography for breast cancer: American College of Preventive Medicine practice policy statement. Am J Prev Med. 1996;12(5):340-341.

³ Barrington-Trimis JL, Urman R, Leventhal AM, et al. E-cigarettes, Cigarettes, and the Prevalence of Adolescent Tobacco Use. Pediatrics. July 2016:e20153983. doi:10.1542/peds.2015-3983.

⁴ Dutra LM, Glantz SA. E-cigarettes and National Adolescent Cigarette Use: 2004–2014. Pediatrics. January 2017:e20162450. doi:10.1542/peds.2016-2450.

⁵ Leventhal AM, Stone MD, Andrabi N, et al. Association of e-Cigarette Vaping and Progression to Heavier Patterns of Cigarette Smoking. JAMA. 2016;316(18):1918-1920. doi:10.1001/jama.2016.14649.

⁶ Wills TA, Knight R, Williams RJ, Pagano I, Sargent JD. Risk Factors for Exclusive E-Cigarette Use and Dual E-Cigarette Use and Tobacco Use in Adolescents. Pediatrics. 2015;135(1):e43-e51. doi:10.1542/peds.2014-0760.

⁷ Kristjansson AL, Mann MJ, Sigfusdottir ID. Licit and Illicit Substance Use by Adolescent E-Cigarette Users Compared with Conventional Cigarette Smokers, Dual Users, and Nonusers. J Adolesc Health Off Publ Soc Adolesc Med. 2015;57(5):562-564. doi:10.1016/j.jadohealth.2015.07.014.

⁸ Thrasher JF, Abad-Vivero EN, Barrientos-Gutíerrez I, et al. Prevalence and Correlates of E-Cigarette Perceptions and Trial Among Early Adolescents in Mexico. J Adolesc Health Off Publ Soc Adolesc Med. 2016;58(3):358-365. doi:10.1016/j.jadohealth.2015.11.008.

⁹ Barrington-Trimis JL, Urman R, Berhane K, et al. E-Cigarettes and Future Cigarette Use. Pediatrics. June 2016:e20160379. doi:10.1542/peds.2016-0379.

¹⁰ Leventhal AM, Strong DR, Sussman S, et al. Psychiatric comorbidity in adolescent electronic and conventional cigarette use. J Psychiatr Res. 2016;73:71-78. doi:10.1016/j.jpsychires.2015.11.008.

¹¹ Primack BA, Soneji S, Stoolmiller M, Fine MJ, Sargent JD. Progression to traditional cigarette smoking after electronic cigarette use among US adolescents and young adults. JAMA Pediatr. September 2015:1-7. doi:10.1001/jamapediatrics.2015.1742.

¹² Wills TA, Knight R, Sargent JD, Gibbons FX, Pagano I, Williams RJ. Longitudinal study of e-cigarette use and onset of cigarette smoking among high school students in Hawaii. Tob Control. January 2016:1-6. doi:10.1136/tobaccocontrol-2015-052705.

¹³ Johnston L, O’Malley PM, Miech R, Emerson P, Bachman J, Schulenberg J. Monitoring the Future National Survey Results on Drug Use, 1975-2015: Overview, Key Findings on Adolescent Drug Use. Ann Arbor: Institute for Social Research, The University of Michigan; 2016.

¹⁴ Office on Smoking and Health. Trends in Current Cigarette Smoking. Centers for Disease Control and Prevention http://www.cdc.gov/tobacco/data_statistics/tables/trends/cig_smoking/. Accessed July 13, 2017.

On 2017 Jul 07, Joel Nitzkin commented:

This Soneji meta-analysis dealing with e-cigarettes and subsequent teen smoking,1 summarized data from nine studies, all of which share the same flaws, leading to an incorrect conclusion. These studies did not differentiate one-time or occasional use from consistent daily use. None compared smoking at follow-up in e-cigarette experimenters with kids who had experimented with or otherwise used cigarettes at baseline. Such a comparison would have reflected rates of smoking at follow-up in these same populations, had e-cigarettes not been available. Given these flaws, the only conclusion that can reasonably be drawn from the individual studies or this meta-analysis is that teens who are inclined to experiment with products disapproved by adult leadership are more likely to use both e-cigarettes and cigarettes than kids not prone to such experimentation. Neither the individual studies nor this meta-analysis give us reason to expect that reducing access to e-cigarettes or making them unattractive to potential users would reduce the numbers of teens recruited to nicotine addiction. The question as to whether e-cigarettes recruit American teens to nicotine addiction has already been answered. In June 2017, the Centers for Disease Control (CDC) published its 6th annual report showing use of tobacco-related products by high school students, by type or product, including e-cigarettes.2 During this period, e-cigarette use has gone from 1.5% of high school students in 2011 to 16.0% in 2015 and 11.3% in 2016, with significant reductions in cigarette use almost every year and no significant change in the percentage of high school students using any tobacco-related product. The data on middle school students reflects the same pattern, with much smaller numbers. If, as alleged by Soneji et al, e-cigarettes were attracting significant numbers of teens who otherwise would not have used tobacco products, there would have been significant year to year increases in the percent of teens using tobacco-related products. This did not occur. The fact that this has occurred year after year validates the impression that the teens attracted to e-cigarettes are those who would have used cigarettes, had e-cigarettes not been available. The time has come for public health authorities to consider the possibility that e-cigarettes, while not risk free, could be promoted for prevention of smoking and smoking cessation among teens inclined to smoke, without attracting yet more teens to nicotine experimentation. Joel L. Nitzkin, MD, MPH, DPA References 1. Soneji S, Barrington-Trimis JL, Wills TA et al. Association Between Initial Use of e-Cigarettes and Subsequent Cigarette Smoking Among Adolescents and Young Adults. JAMA Pediatrics. 2017 June 26:E1-E10. doi:10.1001/jamapediatrics.2017.1488 2. Jamal A, Getrzke A, Hu SS et al. Tobacco Use Among Middle and High School Students --- United States, 2011-2016. Morbidity and Mortality Weekly Report. 2017;66(23) (June 16):597-603. https://www.cdc.gov/mmwr/volumes/66/wr/pdfs/mm6623a1.pdf

On 2017 Sep 12, Ryan Jajosky commented:

For trainees, knowing that Bernard-Soulier syndrome protects against TTP can help you remember the pathogenesis of these conditions.

Ultra-large vWF multimers bind to GP Ib-IX-V on platelets and cause TTP, but patients with Bernard-Soulier syndrome have deficient / defective GP Ib-IX-V, so the disease process is blocked.

On 2017 Jun 29, Edward Morrow commented:

The authors state "Hyslop et al. (2016) demonstrated that global gene expression in early PNT blastocysts did not differ from unmanipulated controls".

Morrow & Ingleby (2017) demonstrate why the size and experimental design of Hyslop et al (2016) cannot provide conclusive evidence that expression profiles of manipulated or control samples are indistinguishable from one another, due to low power.

References

Hyslop et al. (2016) Towards clinical application of pronuclear transfer to prevent mitochondrial DNA disease. Nature 534:383–386. doi:10.1038/nature18303 Hyslop LA, 2016

Morrow EH and Ingleby FC (2017) Detecting differential gene expression in blastocysts following pronuclear transfer. BMC Res Notes. 2017 Feb 15;10(1):97 Morrow EH, 2017 DOI: 10.1186/s13104-017-2421-3

On 2018 Jan 09, Tom Kindlon commented:

I submitted it to the journal but it was not accepted: "Thank you for submitting your Letter to The Lancet. Having discussed your Letter with the Editor, and weighing it up against other submissions we have under consideration, I am sorry to say that we are unable to accept it for publication. Please be assured that your Letter has been carefully read and discussed by the Editors."

I will await to see whether any other letters cover the same or similar points.

There's a reasonable possibility those in the group with an initial score of 45+ on the SF-36 physical functioning subscale actually decreased on average. Unfortunately as this letter wasn't published (unless they publish another letter making the same point or Lucy White, Peter White and the GETSET investigators reply here), I doubt anyone outside the GETSET team will ever know.

On 2018 Jan 09, Tom Kindlon commented:

Response to: Guided graded exercise self-help plus specialist medical care versus specialist medical care alone for chronic fatigue syndrome (GETSET): a pragmatic randomised controlled trial

The SF-36 physical functioning (PF) outcomes for those in the guided graded exercise selfhelp (GES) group who had a baseline SF-36 PF score ≥45 (call them group B) must have been particularly poor in the GETSET trial.1 We are told that those with a baseline score ≤40 (group A) made up approximately 40% of the sample and ended with average score of 56.9. This means the average outcome for group B, the higher functioning group at baseline, was actually lower, at around 54.9. Also, by definition, group A increased by an average of at least 16.9 (56.9-40). However the whole sample only increased by an average of 8.4. This means that an upper bound on the average increase for group B would be only approximately 2.7, in comparison to the increase of 16.9 for group A. This is an extreme scenario and the difference in improvements was most likely higher than 14.2. It would be interesting if Clark and colleagues could give the exact figure so everyone would be aware of the magnitude of the difference in the response.

Clark and colleagues say the poor results may be due to a ceiling effect. More than 90% of healthy working-age people score 90 or more.2 Therefore, the mean score of 54.9 for group B and 55.7 overall suggests that if there is a ceiling in the effectiveness of GES, it is a long way below normal functioning. I do not believe this was made clear to readers.

Tom Kindlon

Competing interests: I work in a voluntary capacity for the Irish ME/CFS Association.

References:

1 Clark LV, Pesola F, Thomas J, Vergara-Williamson M; Beynon M, White PD. Guided graded exercise self-help plus specialist medical care versus specialist medical care alone for chronic fatigue syndrome (GETSET): a pragmatic randomised controlled trial. The Lancet. June 22, 2017 doi:10.1016/S0140-6736(16)32589-2

2 Wilshire CE, Kindlon T, Matthees A, McGrath S. Can patients with chronic fatigue syndrome really recover after graded exercise or cognitive behavioural therapy? A critical commentary and preliminary re-analysis of the PACE trial. Fatigue. 2017;5:1–4.

On 2017 Jul 18, Mohamed Rady commented:

Kitzinger et al argued in favor of applying “the ‘holistic’ approach outlined in the Briggs judgment” to ascertain, in Court and ‘on the floor’, what in accordance with the Mental Capacity Act 2005 (MCA) ought to be considered a patient’s best-interest assessment.[1] They highlighted the significance of the Briggs judgment because of “the great weight Charles J gave the person’s own views, even when set against ‘sanctity of life’.” There are theoretical and practical problems with Kitzinger et al’s position.

First, it is incorrect to describe the Briggs case as the clash of ‘sanctity of life’ and ‘self-determination’. There was no self-determination because there was no advance directive that clearly expressed the preference that, if affected by a disorder of consciousness, assisted nutrition and hydration (ANH) is to be discontinued. It was a third-party determination of the acceptability of Paul Briggs’ future quality of life and judgment of what was to be in his best interests. Therefore, the Briggs case is the clash of ‘sanctity of life’ and ‘third-party determination’ of best interests of a disabled person. Kitzinger et al incorrectly labeled the holistic approach to the best interest standard as an extension of self-determination. [1] They validated their claim of superiority of this approach to a best-interest assessment over ‘sanctity of life’ by quoting an article from 1973 calling the concept of ‘sanctity of life’ “impossibly vague and misleading’.” [3] However, the concept of ‘best interests’ is no less vague than the concept of ‘sanctity of life’ in justifying treatment withdrawal. A best-interest assessment of the acceptability of future quality of life on behalf of a disabled person is subjective. Even with today’s dominance of principlism in ethics, none of the four principles (autonomy, beneficence, non-maleficence, and justice) are clear, unambiguous, and uncontested. For instance, the notion of autonomy, which constitutes the foundation underlying the moral and legal notion of the best-interest standard, has evolved over time and continues to do so with significant moral, legal, and social implications.[4] The question is not if treatment can be withdrawn but under which circumstances it is justified. In first-person decision-making, individuals have the right to refuse treatment either through in-person communication or, if unable to express their opinion, through clear expression of preferences of that particular treatment in advance directives. Considering the weight of such decision in life-sustaining treatment, it appears that the judgment in W v M & Ors (2011) requiring clear and convincing evidence that the person had specifically directed not to have ANH administered in case of the presence of a disorder of consciousness is indeed more consistent with the medical principle of first do-no-harm. In absence of an unambiguous, substantive conception of what constitutes ‘the best-interest’ of human beings, mandating clear and convincing evidence of a person’s wishes in matters of life and death reflects without a doubt commitment to both the principle of sanctity of life and that of respect for persons. As it stands, adherence to the ‘sanctity of life’ standard and practicing medicine in accordance with the Hippocratic Oath both uphold the moral obligation of practitioners to avoid inflicting harm on patients.

Second, as the concept of ‘best interests’ in MCA is grounded in a third-party rather a first-person real time determination of acceptability of future quality of life, its interpretation legitimizes also nonconsensual treatment withdrawal in persons with severe disabilities. Many survivors of serious illnesses adapt to their new reality, cope with severe disabilities, and are satisfied with their quality of life even if greatly diminished from the past. [5-8] Therefore, the reliance on previously held opinions can misrepresent real-time or future preferences of individuals with serious disabilities. As has been argued elsewhere, treatment withdrawal decisions based on third-party determination of best interests can result in fatal errors.[9] Although Kitzinger et al endorsed the introduction of a holistic approach to the third-party determination of best interests, they failed to provide a convincing rationale that it (1) provides a more reliable (and therefore a superior) instrument for making substitute end-of-life decisions, and (2) results in decisions that are more closely aligned with respect for autonomy. The basic tenet of “do-no-harm” in medicine appears to provide more practical guidance towards decision-making under these conditions.

Third, other commentators have asserted that the ‘sanctity of life’ value in medicine, commonly associated with commitment to religious values, should not be allowed to stonewall secular determination of best interests.[10] It is clear to many that withdrawing of ANH is the proximate cause of a pre-planned death and, thus, a form of physician-assisted death. In other cases, where a patient is dependent on both mechanical ventilation and ANH (e.g., The Supreme Court in the matter of Charlie Gard [2017] EWHC 972 (Fam); https://www.supremecourt.uk/news/latest-judgment-in-the-matter-of-charlie-gard.html), withdrawing these life-sustaining interventions will lead, for the same reasons, to an act of physician-assisted death. In reality, the observed clash is the consequence of secular intolerance and exclusion of equally respected religious values in a pluralistic society.

From a practical perspective, without additional legislative revisions in the MCA to protect religious values, the best-interest standard and a holistic approach to assessing these interests has now been transformed into a widening of a backdoor approach to justifying nonconsensual euthanasia of vulnerable individuals. The best-interests standard with an expanded domain of potential surrogate decision makers increases the potential for legitimizing a “kill switch” in the MCA. Finally, patients’ religious beliefs and values should be taken into account to ensure that surrogate decisions made reflect commitment to the respect for autonomy.

Mohamed Y. Rady, Joseph L. Verheijde,

REFERENCES [1] Kitzinger J, Kitzinger C, Cowley J. When ‘Sanctity of Life’ and ‘Self-Determination’ clash: Briggs versus Briggs [2016] EWCOP 53 – implications for policy and practice. J Med Ethics.2017; 43(7):446-449.

[2]Briggs v The Walton Centre NHS Trust & Another: [2017] WLR(D) 25, [2016] EWCOP 53 http://www.bailii.org/ew/cases/EWCOP/2016/53.html.

[3]Clouser K. "the sanctity of life": An analysis of a concept. Ann Intern Med.1973; 78(1):119-125.

[4]Saad TC. The history of autonomy in medicine from antiquity to principlism. Med Health Care Philos.2017; First Online:10 June 2017. DOI: 10.1007/s11019-017-9781-2.

[5]Antonak RF, Livneh H. Psychosocial adaptation to disability and its investigation among persons with multiple sclerosis. Soc. Sci. Med.1995; 40(8):1099-1108.

[6]Lulé D, Zickler C, Häcker S, Bruno MA, Demertzi A, Pellas F, et al. Life can be worth living in locked-in syndrome. Prog. Brain Res.2009; 177:339-351.

[7]Demertzi A, Jox RJ, Racine E, Laureys S. A European survey on attitudes towards pain and end-of-life issues in locked-in syndrome. Brain Inj.2014; 28(9):1209-1215.

[8]Buono VL, Corallo F, Bramanti P, Marino S. Coping strategies and health-related quality of life after stroke. Journal of Health Psychology.2017; 22(1):16-28.

[9]Napier S. Perception of Value and the Minimally Conscious State. HEC Forum.2015; 27(3):265-286.

[10]Brierley J, Linthicum J, Petros A. Should religious beliefs be allowed to stonewall a secular approach to withdrawing and withholding treatment in children? J Med Ethics.2013; 39(9):573-577. Disclosure: This comment is an edited version of the original Rapid Response published online in JME on 4 July 2017 [http://jme.bmj.com/content/43/7/446.responses]

On 2017 Jul 13, Thomas Littlejohns commented:

Thank you for your comment as well as the link to your informative article on selection and collider bias.

The overall aim of the current paper was to investigate the representativeness of UK Biobank participants on a number of characteristics and health outcomes. The cohort has been described as healthier than the general population (due to the low response rate and voluntary recruitment process), however this is the first time the evidence has been provided to confirm this. Whilst UK Biobank was not set up to be representative, providing the empirical evidence for this, as opposed to informing the research community anecdotally, will hopefully help clarify what questions the resource is well-designed to address. Primarily, exposure-outcome associations and not deriving prevalence and incidence rates that apply to the general population.

However, we are in complete agreement with Marcus Munafo and colleagues that researchers also need to be aware of the potential for biases to be introduced due to the ‘healthy volunteer’ nature of the cohort and included the following on pg.10 – “As with all observational studies, it is incumbent on researchers to acknowledge potential sources of bias on a case-by-case basis that might affect the generalisability of exposure-disease associations, such as residual confounding, reverse causation and self-selection bias”.

Essentially, the take home message is that UK Biobank is well designed for providing generalisable associations between exposures and outcomes. But as with all observational studies, researchers should take care when interpreting their findings and acknowledge the range of biases that could drive any associations, including selection bias if applicable.

On 2017 Jul 05, Marcus Munafò commented:

This is an important study which makes explicit the very low response rate within UK Biobank (~5%) and presents some of the factors associated with participation, then discusses their potential impact. However, in our opinion the view that this will make little or no difference to association analyses is overly optimistic. We have recently examined the potential impact of selection bias on results obtained from studies with low response rates [1]. We argue that, because selection can induce collider bias (which occurs when two variables independently influence a third variable, and that variable is conditioned upon), selection can lead to biased estimates of associations in some circumstances. The extent to which this will occur will depend on the particular association being explored, and the selection mechanisms operating. We suggest that researchers consider the potential for selection bias affecting their analyses, and carry out sensitivity analyses to assess robustness of their conclusions to selection bias.

Marcus R Munafò, Deborah A Lawlor, Kate Tilling

1. Munafò MR, Tilling K, Taylor AE, Evans DM, Davey Smith G. Collider Scope: How selection bias can induce spurious associations. bioRxiv, doi: https://doi.org/10.1101/079707

On 2017 Jul 02, Louise B Andrew MD JD commented:

A prior study by this author among others explaining how these ADA impermissible questions that discriminate against those with mental health issues by not differentiating between illness and impairment discourage mental healthcare seeking by physicians (and therefore could contribute to physician suicide) can be found at https://www.ncbi.nlm.nih.gov/pubmed/27796258 and at www.physiciansuicide.com

On 2017 Aug 21, Luiza Rodrigues commented:

Hi. Why is the Supplement 2 not available? I would like to see the eFigures 3, 4 and 5. Couldn't find them in the link. Thanks Dr Luíza

On 2017 Oct 18, Nicoletta Villa commented:

1. The first question is: how to define this chromosome? It had a complete X banding exactly symmetrical above and below the primary constriction and presented an active centromere in an anomalous position definable as neocentromere, though canonical (repositioning).
2. According to the International System for Human Cytogenetic Nomenclature (ISCN) 2016, the definition of centric fission is: “break in the centromere resulting in two derivative chromosomes composed of the short and long arms, respectively”. This does not happen in the chromosome X here described since the whole chromosome (old centromere included) constitutes the isochromosome. This was also confirmed by the paracentric inversion that offers us a complicated but responsive mechanism for the isochromosome formation. Regarding the cited review (Lin and Yan, Mutat Res 2008; 658:95), we mentioned it in the introduction and discussion sections. In both cases, we reported general aspects of telomeric-like sequences. We speculated that the paracentric inversion of the entire Xp arm could be a result of a non-allelic homologous recombination mediated by inverted repeats, as reported by Warburton and Dittwald (see article for details). FISH data with pan-telomeric probes revealed the anomalous presence of TTAGGG repeats near the inactive centromeres in a highly symmetrical manner, absent in the Xp terminations. Therefore, we used BAC probes and identified the paracentric inversion of the entire short arm that made the telomere common sequences completely interstitial. Silahtaroglu et al (J Med Genet 1998; 35:682) reported a paracentric inversion that did not involve telomeric region in a XXY male (“Simultaneous hybridisation with biotin labelled "All Centromere" and digoxigenin labelled "All Telomere" probes showed that the telomeric sequences were not inverted). This is not our case.
3. Rivera et al. (Clin Genet 1999, 55:122) reported a case showing a rearrangement due to a centric fission of chromosome 12 and a translocation on chromosome 8p. This last rearrangement resulted in a fusion between 8ptel and 12cen mediated by interstitial telomeric sequences, as well written in the abstract. In our case there was not a fusion between two different chromosomes, but an isochromosome, confirmed by banding, FISH and by means of microsatellite segregation study. Moreover, we demonstrated the presence of telomeric sequences near to the old centromeres.
4. We did not perform the androgen receptor inactivation test because the itrc(X) was always inactivated in reverse banding (RBA) as it is possible to see in figure 1B and also the microsatellite polymorphisms never showed a third allele. Moreover, the mosaic situation made a quantitative analysis very difficult or even impossible due to the loss of Xq.
5. The frequency of chromosomal abnormalities in couples subjected to medically assisted procreation appears to be increased (literature data), but we couldn’t correlate the chromosomal rearrangement here described with PMA. We don’t know parental origin of the rearrangement and parents refused further analyses.

On 2017 Jul 19, Horacio Rivera commented:

Centromere repositioning or neocentromere in a tricentric X chromosome? As for the unique tricentric X-cromosome described by Villa et al. (2017), I do the following remarks: 1. The apparent discrepancy between title and content regarding the paper’s key concept illustrates how difficult is to classify the single functional centromere of the rearranged X: did it result from centromere repositioning and is a class III neocentromere as stated in the title or is it a novel kind of neocentromere? Since the former mechanism implies the emergence of a new non-alphoid centromere in otherwise intact chromosomes (Marshall et al. Am J Hum Genet 2008, 82: 261; Liehr et al. Cytogenet Genome Res 2010,128:189), it seems better to opt for the more general term neocentromere despite it being composed of alphoid sequences. 2. Since the authors plausibly ascribe the emergence of the functional centromere at an unexpected place to an initial paracentric inversion of the entire Xp arm “shifting a part of the centromere at the p end”, then they may have designated such centromeric breakage with the specific term centric fission. It is significant that the hypothetical telomere-like sequences mapping at Xp11.21 or 22 and thought by the authors to be involved in the rearrangement, are simply not referred to in the cited review (Lin and Yan, Mutat Res 2008; 658: 95); moreover, the authors appear to contradict themselves when they conclude that “the first event could be a result of a non-allelic homologous recombination mediated by inverted low-copy repeats”. Regardless of the concerned sequences, the exact breakpoint should be revised to Xp10 and the Xp rearrangement designated as a centric inversion after Silahtaroglu et al. (J Med Genet 1998, 35: 682) who described an inverted 12p resulting from a centric fission coupled with a subtelomeric breakpoint. 3. According to the underlying mechanism advanced by the authors, two true centromere-telomere fusions (Rivera et al. Clin Genet 1999, 55: 122) occurred in the rearranged chromosome. Yet, the authors also fail to recognize this phenomenon. 4. Despite the analysis of microsatellite polymorphisms, the parental derivation of the tricentric X chromosome was not determined. Likely, the HUMAR assay could have resolved this point. 5. The fact that the patient was conceived after intracytoplasmic sperm injection recalls other chromosome rearrangements and gonosomal aneuploidies found in children conceived by means of such a technique (Venkataraman and Craft, Hum Reprod 2002, 17: 2560; Alfonsi et al. Cytogenet Genome Res 2012, 36: 1; Rivera and Domínguez, Clinics 2012, 67: 669).

On 2017 Oct 26, Duke RNA Biology Journal Club commented:

This paper was chosen based on the well written abstract. The observation in the title appeared interesting and novel with implications for a role of miRNA in epigenetics with response to environmental conditions. However, upon further reading and analysis of the paper, we expect more work will be done to solidify these initial conclusions. We agree that miRNAs are divergent when flies are grown at different temperatures, additionally, piRNAs do seem to be expressed more at lower temperatures. That this holds true when flies are subsequently switched to different temperatures was also fascinating. However, this paper remained mostly observational. We expected, from general patterns observed in narratives of other papers, that the authors would attempt looking at the protein expression of machinery associated with each process, miRNA and piRNA processing, at each temperature to help elucidate a mechanism for these observations. However, what followed was a speculative section on these observations based on RNA-expression, which does not always correlate with protein expression. Overall, we think this article provides a great starting point for future work involving the functional impact that these molecular changes to environmental stimulus can have on an organism.

On 2017 Jul 28, Morten Oksvold commented:

In this article the authors cite Deleris, A. et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313, 68–71 (2006) (reference number 7).

This article represents one of the articles that supposed to be retracted (see quote from the report below):

From the investigation report: "Although it is obviously the journal's prerogative, the former (category 2) papers, particularly those containing well documented intentional manipulations (PLoS Pathogens 2013 9:e1003435; Plant Cell 2004 16: 1235; Science 2006 313: 68; PNAS 2006 103: 19593 and EMBO J 2010 29: 1699), should be retracted through OV's requests as being non-factual, irrespectively of whether the reported observations have been reproduced by others."

Link to full report here: https://www.ethz.ch/content/dam/ethz/news/medienmitteilungen/2015/PDF/untersuchungsbericht/Report_of_ETH_Commission_Voinnet.pdf

I find it problematic that Nature Plants accepts this kind of practice, by apparently legitimating well documented intentional manipulations as facts.

On 2018 Jan 21, Atanas G. Atanasov commented:

Thank you so much for the excellent joint work dear Colleagues! I have featured our manuscript on the INPST website: https://sites.google.com/view/inpst/1-xanthohumol

On 2018 Feb 04, Sin Hang Lee commented:

The medical profession, including medical schools and hospitals, is now a part of the health care industry, and implementation of editorial policies of medical journals is commonly biased in favor of business interests. PubMed Commons has offered the only, albeit constrained, open forum to air dissenting research and opinions in science-based language. Discontinuation of PubMed Commons will silence any questioning of the industry-sponsored promotional publications indexed in PubMed.

On 2017 Jun 24, Sin Hang Lee commented:

Jorge Cervantes proposed a new theory to argue against the existence of chronic Lyme disease with persistent infection [1]. According to this theory, “after antibiotic eradication of Bb, its DNA is able to persist in anatomical locations that coincide with sites of inflammation.” He assumed that the free, naked and water-soluble DNA molecules released from the dying Borrelia burgdorferi spirochetes remain in the extracellular matrix of the patient’s tissues. However, under section “3. Borrelia DNA persistence” of his article, the references cited did not test for free borrelial DNA at all, and therefore do not back up his theory. For examples, in the reference by Li et al. [2], the authors concluded that the DNA detected was in moribund or dead B burgdorferi cells, not in free form. In the reference by Schmidt et al. [3] and the reference by Aberer et al. [4], borrelial DNA was detected in the pellet of patients’ urine samples after centrifugation at 14,000 x g and 36,000 × g, respectively. Since soluble free DNA molecules cannot be pelleted by such a low centrifugal force, the borrelial DNA detected by these authors must be still bound to bacterial cells or cell fragments in the urine. In the reference by Kubanek et al. [5], the authors actually showed by electron microscopy that the tissues tested positive for borrelial DNA clearly contained borrelial bacteria, not free DNA.

Free, extracellular, naked bacterial DNA is very prone to decay. Foreign DNA experimentally introduced into a mammal is degraded and eliminated from the host’s blood within 48 hours [6]. But the stability of extracellular DNA still depends on its form or even on the sequence of its nucleotide bases. Circular plasmid DNA is more stable in vitro than a segment of linear chromosomal DNA after release from the bacterial cell. Even DNase I does not cleave DNA randomly although not base nor sequence specific. Extracellular bacterial 16S rDNA is known to be degraded much more rapidly in the environment than those bound to cell fragments [7]. Borrelial 16S rDNA extracted by ammonium hydroxide stored in TE buffer is stable, but is degraded rapidly in human serum at room temperature (unpublished personal observation). DNA sequencing-confirmed detection of borrelial 16S rDNA in the pellet of serum or plasma samples derived from patients’ venous blood constitutes solid molecular evidence of spirochetemia in Lyme borreliosis [8, 9]. Whether spirochetemia in chronic Lyme disease needs to be treated with prolonged antibiotics is an important heath care issue which should be further discussed. To push an elusive DNA-binding AMP treatment of chronic Lyme disease can only direct the attention away from the real issue of how to define Lyme disease, acute or chronic, as an emerging infectious disease, like Ebola and Zika, for proper patient management. There is no evidence that free naked borrelial DNA has been demonstrated in any patient samples.

The author should also cite a reference to back up his claim that human macrophages can remove extracellular Bb DNA. The reference by Brencicova and Diebold [10], cited by the author, clearly stated “Endosomal TLR are situated in the membrane of the endolysosomal compartment of APC and sample the content of these compartments for the presence of nucleic acid agonists. Pathogens or dead cells gain access to the compartment by endocytosis. Alternatively, infection-induced autophagy can shuttle viral nucleic acids and antigens into the endolysosomal compartment and allow for recognition of replicating virus within infected cells by endosomal TLR.” Free DNA was not mentioned.

References [1] Cervantes J. Doctor says you are cured, but you still feel the pain. Borrelia DNA persistence in Lyme disease. Microbes Infect 2017 Jun 15. pii: S1286-4579(17)30090-4. doi: 10.1016/j.micinf.2017.06.002. [Epub ahead of print] Review. [2] Li X, McHugh GA, Damle N, Sikand VK, Glickstein L, Steere AC. Burden and viability of Borrelia burgdorferi in skin and joints of patients with erythema migrans or lyme arthritis. Arthritis Rheum 2011;63: 2238-47. [3] Schmidt B, Muellegger RR, Stockenhuber C, Soyer HP, Hoedl S, Luger A, et al. Detection of Borrelia burgdorferi-specific DNA in urine specimens from patients with erythema migrans before and after antibiotic therapy. J Clin Microbiol 1996;34:1359-63. [4] Aberer E, Bergmann AR, Derler AM, Schmidt B. Course of Borrelia burgdorferi DNA shedding in urine after treatment. Acta Derm Venereol 2007;87(1):39-42. [5] Kubanek M, Sramko M, Berenova D, Hulinska D, Hrbackova H, Maluskova J, et al. Detection of Borrelia burgdorferi sensu lato in endomyocardial biopsy specimens in individuals with recent-onset dilated cardiomyopathy. Eur J Heart Fail 2012;14:588-96. [6] Schubbert R, Renz D, Schmitz B, Doerfler W. Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA. Proc Natl Acad Sci U S A. 1997;94:961-6. [7] Corinaldesi C, Danovaro R, Dell'Anno A. Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl Environ Microbiol 2005;71:46-50. [8] Lee SH, Vigliotti JS, Vigliotti VS, Jones W, Shearer DM. Detection of borreliae in archived sera from patients with clinically suspect Lyme disease. Int J Mol Sci. 2014;15:4284-98. [9] Lee SH. Lyme disease caused by Borrelia burgdorferi with two homeologous 16S rRNA genes: a case report. Int Med Case Rep J. 2016;9:101-6. [10] Brencicova E, Diebold SS. Nucleic acids and endosomal pattern recognition: how to tell friend from foe? Front Cell Infect Microbiol 2013;3:37.

On 2017 Oct 26, Duke RNA Biology Journal Club commented:

We were excited to see another paper on ribosome heterogeneity from Maria Barna’s lab since their 2011 paper linking loss of a ribosomal protein (RP) with developmental phenotypes in mice PMCID: PMC4445650. In comparison, we found this paper less of a complete story but still powerful in the questions it reveals. To summarize, Shi and co-workers used a combination of selected reaction monitoring based proteomics and tandem mass tagging to identify and orthogonally validate 4 RPs as substoichiometric in tissue culture polysomes. We viewed this result as the major breakthrough in the field. The remainder of the paper looked more closely at two RPs, RPS25 and RPL10A, and their associated transcriptome. Interestingly, they found divergent enrichments within the Ribo-seq datasets associated with these proteins. We speculated, from the distinct transcriptome of these RPs, that cellular environment could play a large role in RP composition. However, instead of following up on these observations, the authors instread probe RPL10A’s function in IRES mediated translation. After performing multiple rounds of experiments with bicistronic constructs, they found this protein had the ability to interact with some - such as HCV, host-mRNAs - but not every IRES type. We discussed previous publications linking ribosomal proteins PMCID: PMC4243054 and RP PTMs PMCID: PMC2253395 to proper translation of HCV. Therefore, we found the observations in Fig 6 interesting but unsurprising and wondered how each observation pieced together in the larger picture of viral translation. This conversation brought us to the conclusion of the paper, with a noticeably short discussion section. We were left with two main unanswered questions: are these substochiometric differences ever combined or limited to one RP at a time; and does RP composition change with cell environment and location? This publication makes a big step towards answering these questions, especially with the quantitative lengths used to determine stoichiometric ratios of RPs, but we found the paper lacking in proposing a distinct in vivo role for these substoichiometric ribosomes and will look forward to follow-up publications leading to these answers.

On 2017 Jun 18, Hilda Bastian commented:

An assessment of a critical problem, with important conclusions. It would be helpful, though, if the scope of the 4 guidelines were shown. The inclusion criteria are not very specific on this matter, and the citations of the versions of the 4 included guidelines are not provided.

In addition to the scope, the dating of the guidelines' last search for evidence (if available) with respect to the dates of the systematic reviews would be valuable. Gauging to what extent systematic reviews were not included because of being out of scope, out of date, or not yet published is important to interpreting these findings. Given how quickly systematic reviews can go out of date (Shojania KG, 2007), the non-inclusion of older systematic reviews may have been deliberate.

The publisher of the article does not appear to have uploaded Appendix A, which includes the references to the systematic reviews. Further, confusion has been created by linking the citations of the first 44 systematic reviews to the references of the article's texts. The end result is that neither the 4 guidelines nor the 71 systematic reviews are identifiable. It would be helpful if the authors would post these 75 citations here.

Disclosure: I work on PubMed Health, the PubMed resource on systematic reviews and information based on them.

On 2017 Aug 06, Stuart Buck commented:

What bothers me most is the following statement from a study author: "Each of these increase LDL-cholesterol compared to carbohydrate and more so when compared to the unsaturated fats. This is sufficient to warn the public about anticipated adverse effects of coconut oil on CVD."

No, it is not. There are at least 5 treatments that lower LDL without lowering CVD, and sometimes even make CVD worse. See Table 1: http://www.nejm.org/doi/full/10.1056/NEJMp1508120?af=R&rss=currentIssue#t=article.

Nutritionists should not give advice based on trials about LDL while ignoring that LDL manipulation is often disconnected from or even directly contrary to CVD outcomes.

On date unavailable, commented:

None

On 2017 Aug 02, Hilda Bastian commented:

Thank you for the reply, Professor Sacks. However, the reply does not address the errors I pointed to, nor respond directly the key problems I raised. Much of it is directed to rebutting claims I did not make.

... (1) Lack of reporting on the processes for selecting evidence

My first point was that although the statement asserts that the totality of evidence and recent studies was reviewed, it does not report the process for identifying the systematic reviews it selected. No validated method for evaluating the systematic reviews is reported, and reasons for excluding each of the trials in the chosen systematic reviews are not reported either (with the exception of 6 trials, accounting for 10 trials in total). Hamley S, 2017, for example, lists 19 randomized trials on the question of replacing saturated with polyunsaturated fat, drawn from 8 systematic reviews/meta-analyses (Table 2). I stress that my point here is not related to the conclusions, but rather to the adequacy and transparency of the methodology.

The totality of evidence approach considering a variety of research types does not obviate the need to explain how the studies were sought, selected, and appraised (Institute of Medicine (US) Committee on Standards for Developing Trustworthy Clinical Practice Guidelines, 2011).

... (2) Singling out coconut oil

The reply reiterates a statement based on a single survey and people's beliefs about coconut oil. But there is no data to show that dietary coconut oil is consumed at levels that warrant this attention, whereas palm oil, for example, does not. I am not sure whether the data I could find on this is an accurate reflection or not (Bastian, June 2017). If it is, however, then the issue of replacing palm oil in commercially produced food would have warranted more attention than coconut oil. Given the very different standards applied to studies of coconut oil, the question of why it was addressed at all, when so much else in scope was not, remains a relevant one.

... (3) Inadequacy of Eyres L, 2016 as a basis for wide-ranging conclusions on health effects of coconut oil

I reiterate the point I made: the conclusions that clinical trials on the effects on CVD measures have not been reported, and that there are "no known offsetting favorable effects" would require a high-quality systematic review on the effects of coconut oil on both CVD and non-CVD health outcomes of dietary coconut oil. Eyres L, 2016 is not that review. Whichever of the validated and accepted methodologies for assessing the quality of a systematic review you would use (Pussegoda K, 2017), the Eyres review would not fare well. It does not include elements required for a high quality systematic review - such as reporting on the excluded studies and including a study-by-study assessment of the methodological characteristics and risk of bias of included studies. More importantly, its scope is too narrow.

I identified the 8 trials in the 7 papers I mention, in a quick search to test the adequacy of coverage of the Eyres review. I only included those on CVD outcomes. There are undoubtedly further relevant trials. That short search though, established the limits of scope of the Eyres review, even in CVD health.

This is how the authors of the Eyres characterize the evidence they found:

"Much of the research has important limitations that warrant caution when interpreting results, such as small sample size, biased samples, inadequate dietary assessment, and a strong likelihood of confounding. There is no robust evidence on disease outcomes, and most of the evidence is related to lipid profiles."

I agree with that assessment, and the reply offers no methodologically sound counter to this. Instead, the studies not in the Eyres review were critiqued. The reply cites these criteria for excluding all but 3 of the 8 studies as acceptable for consideration (presumably the 2 reported in a single paper were regarded as a single study):

[A]mong the 7 studies...4 would appropriately be excluded as result of being non-randomized, uncontrolled, using a very small amount, not including a control group or not even being a trial of coconut oil.

I don't really know what to make of "uncontrolled" and "not including a control group" as 2 criteria, given all these trials are controlled: the final 3 that aren't rejected don't make it clear to me either. No threshold is offered for what is a large enough dose, so I can't work with that either. However, I took the other 2 - randomized or not, and having a solely coconut oil arm as objective criteria I could apply to the 8 trials within Eyres and the 8 trials outside it (and extracted some additional data). This is reported in full on a blog post (Bastian, August 2017). In summary:

• The Eyres group has fewer randomized trials: 4/8 compared to 7/8 in the non-Eyres group (or 6/7 for non-Eyres after knocking out the trial with no separate coconut arm).
• There are fewer randomized participants in the Eyres group: 143 compared to 234 in 6 non-Eyres randomized trials with a separate coconut arm.
• All the trials in the Eyres group only look at blood lipid profiles whereas most in the non-Eyres group assess at least 1 non-blood-test outcome (5/8 or 4/7). That is in part because of the Eyres exclusion criteria (such as rejecting any trial in a specific population or clinical subgroup, such as overweight people).

The Eyres group cannot be regarded as an adequate or representative subset of trials. And the same level of critique has not been applied even-handedly.

... (4) Errors in representation of the Eyres findings on coconut oil versus other saturated fats

As this was not addressed in the reply, I'll reiterate it, with additional detail. This is what the Eyres review concludes on this question:

"In comparison with other fat sources, coconut oil did not raise total or LDL cholesterol to the same extent as butter in one of the studies by Cox et al., but it did increase both measures to a greater extent than did cis unsaturated vegetable oils...[W]hen the data from the 5 trials that directly compared coconut oil with another saturated fat are examined collectively, the results are largely inconsistent".

This is what the AHA writes:

"The authors also noted that the 7 trials did not find a difference in raising LDL cholesterol between coconut oil and other oils high in saturated fat such as butter, beef fat, or palm oil".

As there was no meta-analysis of these trials, there is no single estimate to discuss. Of the 5 that did include a comparison with saturated fats, there were differences among their results: the AHA had pointed out 1 of them just a few sentences previous to their "no difference" statement. This is objectively a mis-statement of the Eyres' review's findings, which results in an exaggeration of the strength of the evidence.

Nothing in the reply to my comment changes, for me, the conclusion I came to in my first blog post on this:

"On coconut oil, the AHA has taken a stand on very shaky ground with some major claims – as though they had a very strong systematic review of reliable research on all possible health consequences of dietary coconut oil. They don’t. The people arguing the opposite – that coconut oil is so healthy you should try to use it every day – are also on shaky ground".

Disclosure: I have no financial, livelihood, or intellectual conflicts of interest in relation to coconut or dietary fats. I discuss my personal, social, and professional biases in a blog post that discusses the AHA advisory on coconut oil in detail. (Bastian, August 2017). This PubMed Commons comment also contains some excerpts from that post.

On 2017 Jul 24, Frank M Sacks commented:

On behalf of the authors, I respond to comments by Hilda Bastian about the American Heart Association Presidential Advisory on Dietary Fats and Cardiovascular disease Sacks FM, 2017.

The comprehensive advisory includes, (i) Clinical trials that tested the effects of dietary saturated fat compared to unsaturated fat or carbohydrate on cardiovascular disease (CVD) events, e.g. heart attack, (ii) Clinical trials that tested the effects of dietary fats on lipid risk factors, e.g. LDL-cholesterol, (iii) Prospective epidemiological studies on dietary fats and carbohydrates and CVD, and (iv) Animal models of diet and atherosclerosis. Thus, it reflects the “totality of evidence”. The confluence of findings provides a very strong scientific case for the recommendation that dietary saturated fat be replaced with unsaturated fat, especially polyunsaturated fat.

Recent systematic reviews and meta-analyses Mozaffarian D, 2010, Chowdhury R, 2014, Hooper <PMID: 26068959 used well accepted methodologies, and included trials published up to 2009, 2013, and 2014. Only a small number of clinical trials evaluated direct effects of dietary fat on CVD. Most of these studies, and all that have an impact on the overall findings, were conducted years ago, and are well known. Contrary to the Bastian’s comments, there are no more recent trials on this topic. These 3 meta-analyses each confirm the beneficial effect of replacing saturated with polyunsaturated fat. The similarity of findings lends robustness to the overall conclusions of the report. The meta-analyses and all the individual trials are discussed critically in detail in the advisory.

Because the topic of the advisory is the effect of dietary fats on CVD, coconut oil is well within its scope. Coconut oil is currently rated as a healthy oil by 72% of the American public, despite its composition derived from 98% saturated fats, which increase the blood level of LDL-cholesterol, a cause of atherosclerosis and CVD. The meta-analysis by Mensink reports the quantitative effects on LDL-cholesterol of the saturated fats that are in coconut oil, mainly lauric, myristic, and palmitic acids. Each of these increase LDL-cholesterol compared to carbohydrate and more so when compared to the unsaturated fats. This is sufficient to warn the public about anticipated adverse effects of coconut oil on CVD.

Some studies tested coconut oil itself, and found that it increases LDL-cholesterol as would be predicted by its saturated fat content. These studies were identified and summarized in the systematic review by Eyres L, 2016 which used rigorous, well-accepted methodology. The criteria for inclusion of an article in the systematic review were well conceived. Eyres et al. concluded, “Overall, the weight of the evidence from intervention studies to date suggests that replacing coconut oil with cis unsaturated fats would alter blood lipid profiles in a manner consistent with a reduction in risk factors for cardiovascular disease.” Bastian implies that this systematic review is composed of weak studies and omitted several studies that would affect the conclusion of the advisory to avoid eating coconut oil. This is not true. Eyres et al. identified eight studies; all were controlled clinical trials that used valid nutritional protocols and statistical analyses. All reported higher LDL-C levels when coconut oil was consumed compared to unsaturated oils, including olive, corn and soybean oils, statistically significantly in 7 of them. Together, these trials included populations from the US, Sri Lanka, New Zealand, Pacific Islands, and Malaysia, demonstrating generalizability. There is no objective scientific reason to disparage them. The only substantive criticisms mentioned by Bastian are a short duration and small sample. These criticisms are unwarranted. Effects of diet on blood lipids, especially LDL-cholesterol, are established quickly, by 2 weeks. A small sample, with careful dietary control and execution, can yield a well-powered trial with valid results. In summary, the 8 trials in the Eyres et al. systematic review provide strong evidence that coconut oil increases LDL-C levels compared with unsaturated oils.

What about the 7 studies named by Bastian that were not included in the systematic review? McKenney JM, 1995 reported that coconut oil increased LDL-cholesterol significantly by 12% compared with canola oil in 11 patients with hypercholesterolemia. In a second study in 17 patients treated with lovastatin, LDL-C increased nonsignificantly in the coconut oil period. Thus, the results of this small study would add to the overall effects of coconut oil shown in the other studies to increase LDL-cholesterol. Ganji V, 1996 reported that coconut oil increased LDL-cholesterol compared to soybean oil in 10 normal participants. Assunção ML, 2009 reported no difference in the effects of coconut and soybean oils on LDL-cholesterol levels. However, LDL-cholesterol levels increased during the soybean oil period, clearly an anomolous result. Cardoso DA, 2015 conducted a nonrandomized study comparing coconut oil, 13 mL per day, with no supplemental oil. Because there is no control for the coconut oil, it is unclear how to interpret the lack of difference in LDL-cholesterol between the groups. de Paula Franco E, 2015 conducted a sequential study of a calorie-reduced diet followed by coconut flour, 26 g per day. This study was not randomized and did not have a control group. Enns reported in her Ph.D. degree dissertation at the University of Manitoba the results of a randomized trial that compared a 2:1:1 mix of butter, coconut oil, and high-linoleic safflower oil, 25 g per day, with canola oil, 25 g per day. This trial did not claim to be a study on the effects of coconut oil. Finally, Shedden reported in her M.S. degree thesis at Arizona State University the results of a placebo-controlled randomized trial of coconut oil, 2 g per day. This miniscule amount of coconut oil did not affect LDL-cholesterol. In summary, among the 7 studies cited by Bastian not in the Eyers review, 4 would appropriately be excluded as result of being non-randomized, uncontrolled, using a very small amount, not including a control group or not even being a trial of coconut oil. Among the 3 randomized trials, McKenney et al., Ganji et al. and Assuncao et al., the first two found that coconut oil increased LDL-cholesterol levels. The trial of Assuncao et al. would likely fail an outlier test because it is the only one among 12 studies in which LDL-C levels is lower on coconut than soybean oil. Given the differences in study designs, populations, and localities, the results of coconut oil trials are remarkably uniform showing that it increases LDL-cholesterol levels, an established cause of cardiovascular disease.

Bastian employs a tactic in common with some other critics of good nutritional science, namely, to a) disparage and misrepresent high quality studies that show harmful effects of saturated fat; b) promote and misrepresent seriously flawed and irrelevant studies that report the opposite; and c) cite meta-analyses with faulty designs often based on inclusion of flawed studies. We offer a challenge to those who assert health benefits to coconut oil, or saturated fat, in general. Produce well-designed and executed studies that show that there are beneficial effects on a bona fide health outcome or a recognized surrogate, e.g., LDL-cholesterol.

Frank M. Sacks, for the authors.

On 2017 Jun 30, Hilda Bastian commented:

The authors state that this advisory "reviews and discusses the scientific evidence, including the most recent studies", and that its primary recommendation is made, "taking into consideration the totality of the scientific evidence, satisfying rigorous criteria for causality". They do not report what evidence was sought and how, or the basis upon which it was selected. There is little in this report to suggest that "the totality of scientific evidence" was considered.

For example, four reviews of trials are referred to:

• Mozaffarian D, 2010 (date of last search June 2009)
• Chowdhury R, 2014 (date of last search July 2013)
• Hooper L, 2015 (Cochrane Collaboration) (date of last search March 2014)
• Mensink, 2016 (WHO) (date of last search December 2013)

However, the more recent systematic review and meta-analysis within Ramsden CE, 2016 (date of last search March 2015) was not mentioned. Nor are, for example, these systematic reviews: Skeaff CM, 2009; Stroster, 2013; National Clinical Guideline Centre (UK), 2014; Schwingshackl L, 2014; Pimpin L, 2016.

The AHA advisory includes sections reviewing two specific sources of saturated fat, dairy and coconut oil. Dairy products are a major source of dietary saturated fats. However, no basis for singling out coconut oil is offered, or for not addressing evidence about other, and larger, sources of saturated fats in Americans' diets. The section concludes: "we advise against the use of coconut oil".

There are three conclusions/statements leading to that recommendation:

• Eyres L, 2016 "noted that the 7 trials did not find a difference in raising LDL cholesterol between coconut oil and other oils high in saturated fat such as butter, beef fat, or palm oil."
• "Clinical trials that compared direct effects on CVD of coconut oil and other dietary oils have not been reported."
• Coconut oil increases LDL cholesterol "and has no known offsetting favorable effects".

The only studies of coconut oil cited by the advisory to support these conclusions are one review (Eyres L, 2016) - reasonably described as a narrative, not systematic, review by its authors - and 7 of the 8 studies included in that review. The date of search of this study was the end of 2013 (with an apparently abbreviated update search, not fully reported, in 2015). Not only is that too long ago to be reasonably certain there are no recent studies, the review's inclusion and exclusion criteria are too narrow to support broad conclusions about coconut oil and CVD or other health effects.

The AHA's first statement - that Eyres et al noted no difference between 7 trials comparing coconut oil with other saturated fats - is not correct. Only 5 small trials included such comparisons, and their results were inconsistent (with 2 of the 3 randomized trials finding a difference). There was no meta-analysis, so there was no single summative finding. The trials in question are very small, none lasting longer than eight weeks, and have a range of methodological quality issues. The authors of the Eyres review caution about interpreting conclusions based on the methodologically limited evidence in their paper. In accepting these trials as a reliable basis for a strong recommendation, the AHA has not applied as rigorous a standard of proof as they did for the trials they designated as "non-core" and rejected for their meta-analysis on replacing dietary saturated fat with polyunsaturated fat.

Further, even a rapid, unsystematic search shows that there are more participants in relevant randomized trials not included in the Eyres review than there are randomized participants within it. For example: McKenney JM, 1995; Ganji V, 1996; Assunção ML, 2009; Cardoso DA, 2015; de Paula Franco E, 2015; and Enns, 2015 (as well as another published since the AHA's panel finished its work, Shedden, 2017).

The conclusions of the coconut oil section of the AHA advisory are not supported by the evidence it cites. A high quality systematic review that minimizes bias is required to draw any conclusion about the health effects of coconut oil.

Disclosure: I have no financial, livelihood, or intellectual conflicts of interest in relation to coconut or dietary fats. I discuss my personal, social, and professional biases in a blog post that discusses the AHA advisory on coconut oil in detail (Bastian, June 2017).

On 2017 Jul 07, JEANNIE LEE commented:

Authors: John E. Froberg,* Chen-Yu Wang,* Roy Blum, Yesu Jeon, and Jeannie T. Lee**

equal contribution * corresponding author **

We appreciate the response of Chen et al. to our Technical Comment. However, we do not believe the response satisfies our concerns regarding the genotypes of the cells used in Chen et al. We outline our critique below and invite commentary from the community:

1. Chen et al. continued to maintain that ∆LBS is a true deletion and stated that they confirmed ∆LBS by Sanger sequencing. They should provide FASTA files containing the Sanger sequence data from the same clone used in the study.

2. Chen et al. erroneously stated that our idea of an LBS inversion was based on the presence of discordant reads within the Xist locus. The “inversion reads” are a specific subset of discordant reads with one end mapped within the LBS region and the other just outside and where both reads align to the same strand. Whereas discordant reads can indeed be found outside of the LBS region in both WT and ∆LBS cells, such inversion reads can only be detected in ∆LBS and ∆LBS rescue, but not in WT, LBR knockdown, and SHARP knockdown samples. Thus, “inversion reads” are specific to ∆LBS and ∆LBS rescue and not simply an artifact of the discordant RAP reads.

3. In Figure 2, Chen et al. proposed that the discordant reads that suggest an inversion are simply an artifact of sequencing the RAP capture probes. This cannot be the case. The inversion reads were also found in input samples for both ∆LBS and ∆LBS rescue. The input was set aside before addition of capture probes, therefore the presence of inversion reads in input cannot be explained by sequencing the probes. Thus, the inversion reads likely arose from a genuine inverted sequence at the endogenous locus, not from capture probe contamination.

4. To explain why we were able to align many reads to the LBS region, Chen et al. proposed that LBS inserted into a repetitive region of chromosome 12 (and that the region was not flipped in situ). The authors provided no data to support this. We were also unable to see an enrichment of chr12 (or any other autosome) among the discordant reads. The authors must provide the inverse PCR Sanger sequence data and confirmation of a chr12 insertion by FISH, southern blot, or other means.

5. Chen at al. stated that our analysis of the LBS deletion is flawed because we used the wrong coordinates for ∆LBS. We used chrX:100676777-100677593 (mm9). These coordinates completely overlap and are nearly identical to the ∆LBS mm9 coordinates provided by Chen et al. (chrX: 100676791-100677575). Thus, the coordinates are essentially the same and cannot explain our differences.

6. We raised the major concern that the authors’ CLIP data lacked crossover reads that must be present if a deletion is present. In response, Chen et al. suggested that there were 4 crossover reads. We dispute that these 4 reads cross over the deleted region. Read 1 (1928049) could potentially cross over “∆LBS”, but showed deletions and mismatches that gave the read a poor alignment score (right side pair cigar: 21M3D14M). Read 2 (4677231) could also potentially cross over, but its quality score was also so low that it was filtered out by our pipeline. Read 3 (1928051) does not cross over at all, and was also filtered out due to a low quality score. Read 4 (4677228) also does not cross over and instead aligned upstream of the LBS region. Thus, the 4 reads do not qualify as crossovers, leaving unanswered why the CLIP data failed to reveal a deletion, inversion, or intact sequence.

7. The RNA FISH experiment in Figure 1F the authors use to argue against inversion may not have worked. Chen et al. argued that the absence of RNA FISH signal with probes antisense to LBS to argue that LBS is deleted and not inverted. The antisense probe should have produced one pinpoint spot in wild-type cells due to Tsix transcription. However, there is no pinpoint spot in wild-type cells.

8. The ∆A cell line they used for RAP does not have a Repeat A deletion, at least at the endogenous locus. Chen et al. admitted that they used the wrong cell line and published an incorrect dataset. They should provide full characterization of the cells actually used in the published experiment and explain how the data coincidentally supported their conclusions.

9. Chen et al. claimed that our RAP analysis is different from theirs because we did not properly account for probe sequences. This suggestion fails to explain the differences between our analyses. First, Chen et al. did not describe how they “account for probe sequences”. Second, our RAP patterns were derived after excluding discordant reads. This means that we already excluded the reads Chen et al. claim cause the discrepancy between our RAP patterns and theirs. Finally, excluding probe sequences will not change the global X-chromosomal RAP pattern because probe sequences are only found within Xist.

10. We question how Chen et al. scaled RAP coverage tracks when comparing different RAP samples. As our analysis showed that, excepting the WT RAP, all RAP experiments showed very limited coverage on the X outside of the Xist locus — thereby strongly indicating a failure of RAP experiments. These observation are not consistent with the continued assertion of Chen et al. that reduced Xist binding is found in ∆LBS and ∆A HPRT (even though they admittedly used the wrong cell line), but not in ∆LBS rescue. It remains unclear how they scaled and normalized different RAPs and how they arrived at these conclusions.

11. Furthermore, the possibility that the observed phenotypes arise from experimental variability cannot be excluded. Chen et al. argue that the fact that multiple Xist mutants (LBR KD, ∆LBR, an un-described ∆A line) all show the same phenotype eliminates the necessity of replicates. This is simply not true; it is possible that all mutants show a Xist localization defect because all of the mutant RAPs failed. The authors also argue that replicates aren’t necessary since they compare average profiles across all active vs. inactive regions of the chromosome. However, this comparison does not take into account RAP efficiency, and comparing RAP signal between active vs. inactive regions in an inefficient RAP is not biologically meaningful. Biological replicates of the same mutants in parallel with wild-type are absolutely essential for evaluating RAP phenotypes.

12. Chen et al. utilized FISH to show that perturbing LBR-Xist interaction abolishes the ability of Xist to internalize active genes into the Xist cloud (Chen et al. 2016), a phenotype similar to the ΔA Xist mutants (Chaumeil et al. 2006). Strikingly, the distance from X-linked genes to the ΔA or ΔLBS Xist clouds measured by Chen et al. spanned ~ ½ nuclear radius, far greater than what was described in Chaumeil et al. This very large nuclear distance calls into question the specificity of the FISH experiments.

13. In the final paragraph, the authors questioned the nucleation site model. However, no evidence was provided. The references they cited in connection to this statement are not relevant to the role of YY1 or to the Repeat F region for Xist nucleation. In fact, the original LBR study of Chen et al. argued that the nucleation site (a.k.a. “LBS region”) is needed for proper Xist spreading. This argument (notwithstanding the questionable genotypes) would be entirely consistent with the original findings of Jeon & Lee in 2011, which reported that deleting this region of Xist inhibits Xist spreading as a consequence of failed nucleation.

On 2017 Jul 07, Cicely Saunders Institute Journal Club commented:

The Cicely Saunders Institute journal club reviewed this paper on Wednesday 5th July 2017. We enjoyed discussing this paper and felt that the authors had addressed an important area, especially with the increasing importance on how we coordinate services at the end-of-life. The authors provided detailed information about the settings, which was useful in understanding the context in which the data was collected. Additionally, the authors provide an allied health professional perspective, highlighting the difference that can be made by changes to the environment and equipment.

We felt that the authors could have applied a theoretical framework to strengthen understanding of the proposed topic and their findings, such as Andersen’s healthcare utilisation model. We were interested in their focus on patient, carer and professional views, but felt that these could have benefitted from triangulation in the narrative of the paper.

The authors highlighted many interesting aspects (tipping points for carers, how patients will manage increased risk to be able to stay home), we would have liked supplementary materials to explore these further, as the authors collected such a wealth of data from both interviews and observations.

Commentary by Sophie Pask and Dr Catherine Evans

On 2018 Feb 04, Sin Hang Lee commented:

The medical profession, including medical schools and hospitals, is now a part of the health care industry, and implementation of editorial policies of medical journals is commonly biased in favor of business interests. PubMed Commons has offered the only, albeit constrained, open forum to air dissenting research and opinions in science-based language. Discontinuation of PubMed Commons will silence any questioning of the industry-sponsored promotional publications indexed in PubMed.

On 2017 Jun 23, Samuel Shor commented:

Marzec, et al (1) described 5 cases of treated chronic Lyme disease that resulted in poor outcomes We are concerned about 3 conclusions: 1. Characterization of chronic Lyme disease as an invalid nebulous condition 2 “…..evidence that the recommended two-tiered serologic testing is actually more sensitive the longer B. burgdeorferi infection has been present” 3. “Studies have not shown that such treatments lead to substantial long-term improvements for patients.” We too are concerned about any individual whose outcomes represent complications to well-intentioned intervention. However, there is substantive support in the literature for the existence of 1. Chronic Lyme disease-Our perspective is that this represents the clinical manifestations of ongoing active infection by Borrelia burgdorferi (Bb) sensu latu complex in the setting of either chronic untreated or inadequately treated individuals. The lilkihood of undiagnosed acute Lyme is increased by the infrequency of patients recalling tick bites. In one study representing CDC criteria diagnosed Lyme disease, only 14% had that recollection. (2) Not all cases of acute Lyme are associated with an erythema (EM) rash. Over 15 years, 31% of the reported surveillance cases lacked an EM rash. (3) The ILADS guidelines (4) describe the Lyme post treatment "….persistence of B. burgdorferi in specific individuals and animal models." The 2012 Embers (5) nonhuman primate and 2014 Hodzic (6) murine studies provide evidence of persistence of Bb infection after MBC adequate courses of antimicrobials. Additional animal and human studies support this concept (7-10). We want to emphasize that other etiologies may be causal, but that a cohort of these patients likely have a perpetuation of chronic signs and symptoms due to an active Bb infection. 2. Sensitivity of two tiered testing in late Lyme: Based upon a 2008 study by Steere et al (11) “the sensitivity of 2-tier testing in patients with later manifestations of Lyme disease was 100%, and the specificity was 99%” Entrance criteria for late stage Lyme: “In all patients with neurologic, cardiac, or joint involvement, a serologic result positive for B. burgdorferi by ELISA and Western blot was required for case inclusion….” “Because the entrance criteria for the aforementioned analysis REQUIRED positive serologies … by definition, all patients with disseminated or persistent Lyme disease were required to have a positive serologic test result. It is disingenuous to define a condition by a positive test result and then state that the test has 100% sensitivity…” (12) By extension, the concept of seronegativity is well-documented in cases of chronic Lyme disease (13-15) In a study, patients with a positive culture and/or PCR results and active late Lyme disease, 63.5% were not two-tier positive. (16) A second study of pcr positive late Lyme patients found that 56.3% were seronegative. (17) 3. “Studies have not shown that such treatments lead to substantial long-term improvements for patients.” A number of studies discount this claim. In 2 of the 4 NIH supported prospective human trials by Fallon (18) and Krupp (19), sub-cohort analysis showed statistically significant benefit to retreatment. In the former study 37 patients who were suspected of having active neuroborreliosis, and were treated with 10 weeks of 2gms/day IV Ceftriaxone. Pain and physical functioning improved at 12 and was sustained at 24 weeks. The authors indicated that “these benefits were felt to be independent of carefully assessed placebo effects.” In the latter study 55 patients who were felt to have active infection by Bb, with persistent severe fatigue of 6 or more months received 28 days of IV Ceftriaxone. A significant improvement in fatigue was sustained at 6 months. Other prospective trials of prolonged antimicrobial treatment were employed that revealed statistically significant improved outcomes. (20-22) In summary, as unfortunate are the 5 cases reported by Marzec, it is this author’s belief that they should not be used to discount a real entity, chronic Lyme disease. Whether due to the lack of timely diagnosis or adequacy of intervention, the literature supports the concept of chronic active Bb infection. That the diagnostic sensitivity of the 2 tiered paradigm is flawed, and seronegative active Bb infection exists. That emphasis should be made to generate a careful differential diagnosis, proactive management with probiotics and careful monitoring in the selective utility of long term antibiotics. As such, these often disabled individuals will more readily have access to the care they deserve, with compassion and empathetic oversight. Samuel Shor, MD, FACP President ILADS [International Lyme and Associated Diseases Society] Associate Clinical Professor George Washington University Health Care Sciences 1. Marzec NS, 2017 2. Berger BW, 1989 3. Bacon RM, 2008 4. Cameron DJ, 2014 5. Embers ME, 2012 6. Hodzic E, 2014 7. Treib J, 1998 8. Steere AC, 1990 9. Dvoráková J, 2004 10. Berglund J, 2002 11. Steere AC, 2008 12. Stricker RB, 2008 13. Breier F, 2001 14. Dejmková H, 2002 15. Schutzer SE, 1990 16. Oksi J, 1995 17. Chmielewski T, 2003 18. Fallon BA, 2008 19. Krupp LB, 2003 20. Cameron D, 2008 21. Wahlberg P, 1994 22. Oksi J, 1998

On 2017 Jun 20, Sin Hang Lee commented:

Dear L Ide: I have stopped reading NEJM since its Publisher fired Dr. Jerome Kassirer as the editor in chief. If you have published an article in the NEJM against intravenous or prolonged antibiotic treatment of SBE cases, please list the reference here. Then I will try to read it. What is elispot anyway? Have you used it? I was talking about using borrelial gene sequencing to diagnose chronic Lyme disease. Please write more if you have any objections.

On 2017 Jun 19, L Ide commented:

Sin Hang Lee, please read the NEJM. Longterm antibiotics are rubbish. I hope you 're not in favor of the not evidence-based test elispot? Thank you Marzec et al. for your article.

On 2017 Jun 19, Sin Hang Lee commented:

Marzec and colleagues presented five “chronic Lyme disease” patients who did not benefit from additional antibiotic treatment when the diagnoses of “chronic Lyme disease” were made on the basis of clinical symptoms and signs (www.cdc.gov/lyme/diagnosistesting/) or by unvalidated tests. The authors have not presented evidence to show that chronic Lyme disease patients with borrelial spirochetemia proven by culture or by gene sequencing do not benefit from additional antibiotic treatment. In medicine, certain chronic infections, such as subacute bacterial endocarditis, may require intravenous or prolonged antibiotic treatment [1] in spite of its potential side effects.

The CDC should give the practitioners a case definition of Lyme disease, as for Ebola and Zika.

Conflicts of Interest: Sin Hang Lee, MD is the director of Milford Molecular Diagnostics Laboratory specialized in developing DNA sequencing-based diagnostic tests.

References 1. Hoen B. Epidemiology and antibiotic treatment of infective endocarditis: an update. Heart 2006 ;92 :1694-700. Review.

On 2017 Jun 18, Raphael Stricker commented:

Chronic Lyme Disease Treatment: Science versus Anecdotes.

Lorraine Johnson, Raphael B. Stricker, MD.

Lymedisease.org, PO Box 1352, Chico, CA 95927; ILADS, PO Box 341461, Bethesda, MD 20827

lorrainejohnson@outlook.com; rstricker@usmamed.com

The article by Marzec et al. published in MMWR purports to show the dangers of treatment in patients diagnosed with chronic Lyme disease (1). Recent reports from the Centers for Disease Control and Prevention (CDC) indicate that more than 300,000 new cases of Lyme disease are diagnosed each year in the USA (2). The MMWR article from the CDC describes five anecdotal cases of treatment complications in these patients while ignoring the significant morbidity related to denial of treatment for chronic Lyme disease (2,3). The resultant biased report raises scientific and ethical issues about the CDC's role in promoting the best care for patients with tickborne diseases.

The MMWR piece resulted from anecdotal reports gathered by Dr. Christina Nelson of the CDC. The article notes that the information was gathered because “clinicians and state health departments periodically contact CDC concerning patients who have acquired serious bacterial infections during treatments for chronic Lyme disease.” However, an ethics complaint filed against Dr. Nelson by the Lyme disease patient advocacy group LymeDisease.org suggests that these adverse event reports were in fact specifically solicited by Dr. Nelson via emails distributed in 2014 (4). Dr. Nelson asked clinicians from the Infectious Diseases Society of America (IDSA) to provide anecdotal evidence of harm to patients from intravenous antibiotic therapy related to Lyme disease, and she apparently offered coauthorship of her article as an incentive to describe these adverse events. She did not ask for consequences of failing to treat these patients, nor did she solicit commentary from practitioners who treat chronic Lyme disease according to the guidelines of the International Lyme and Associated Diseases Society (ILADS).

The risk of any medical treatment is extremely context-sensitive. A crucial question is whether the risks of treatment are warranted given the potential benefits, the availability of other treatment options, the severity of the patient's presentation, and the risk tolerance of the individual patient. By asking for an assessment of treatment risks only, Dr. Nelson is framing the issue in a manner that excludes the other half of the equation in a risk/benefit assessment. She is also ignoring an issue that is critical to patients who suffer a profoundly diminished quality of life due to their illness, namely the risk of not treating (5,6). Moreover, by failing to mention that these adverse event reports were rare and specifically solicited, she implies that these rare occurrences are a common concern. In reality, studies of the risks and benefits associated with intravenous antibiotic treatment for Lyme disease indicate that the risks of adverse events are no greater than the risks of intravenous therapy in other unrelated diseases (7,8).

By asking the question only of those on one side of the controversy, Dr. Nelson is further demonstrating favoritism and a lack of impartiality on the part of the CDC. Accordingly, Dr. Nelson's solicitation of anecdotal adverse events for case studies of Lyme disease is a highly inappropriate partisan act of favoritism toward the IDSA viewpoint at the expense of critical stakeholders - Lyme disease patients and their treating physicians - and an attack on the ILADS viewpoints.

References 1. Marzec NS, Nelson C, Waldron PR, et al. Serious bacterial infections acquired during treatment of patients given a diagnosis of chronic Lyme disease - United States. MMWR Morb Mortal Wkly Rep. 2017 Jun 16;66(23):607-609. 2. Stricker RB, Johnson L. Lyme disease: Call for a ‘‘Manhattan Project’’ to combat the epidemic. PLoS Pathog. 2014;10(1): e1003796. 3. Stricker RB, Fesler MC. Chronic Lyme disease: A working case definition. Chronic Dis Int. 2017; 4(1): 1025. 4. Leland DK. TOUCHED BY LYME: CDC ignores ethics, attacks “chronic Lyme”. Available at https://www.lymedisease.org/touchedbylyme-cdc-ignores-ethics/. Accessed June 16, 2017. 5. Johnson L, Aylward A, Stricker RB. Healthcare access and burden of care for patients with Lyme disease: a large United States survey. Health Policy. 2011;102: 64–71. 6. Johnson L, Wilcox S, Mankoff J, Stricker RB. Severity of chronic Lyme disease compared to other chronic conditions: a quality of life survey. Peer J. 2014;2:e322. 7. Stricker RB, Green CL, Savely VR, Chamallas SN, Johnson L. Safety of intravenous antibiotic therapy in patients referred for treatment of neurologic Lyme disease. Minerva Med. 2010;101:1–7. 8. Stricker RB, Delong AK, Green CL, et al. Benefit of intravenous antibiotic therapy in patients referred for treatment of neurologic Lyme disease. Int J Gen Med. 2011; 4: 639–646. 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 2017 Sep 02, Lise Bankir commented:

After we published the paper above " Relationship between Sodium Intake and Water Intake: The False and the True", we rediscovered a publication that we should have mentioned in this paper because it is one more study showing no change in urine volume (= water excretion) in normal subjects in response to marked changes in sodium intake (leading to corresponding changes in sodium excretion). The reference of this paper is : Hormonal responses to gradual changes in dietary sodium intake in humans. Sagnella GA, Markandu ND, Buckley MG, Miller MA, Singer DR, MacGregor GA. Am J Physiol. 1989 Jun;256(6 Pt 2):R1171-5. PMID: 2525347

Table 1 shows urine volumes in six normal subjects submitted to increasing sodium intakes. After 4 days on a very low sodium intake (12 mmol/24h), sodium intake was increased gradually by 50 mmol/day on successive days. For sodium intakes of 10, 50, 100, 150, 200, 300, 350, 350 mmol/day, urine volumes were 1.43, 1.40, 1.23, 1.38, 1.47, 1.96, 1.69, 1.53 L/24h, respectively. No comment is made in the paper about this relatively stable urine volume.

This study, like several others cited in our paper, confirms that urine volume, and thus probably fluid intake, do not increase with increasing sodium intake without other changes, when studied in healthy young subjects.

This observation in 1989 is at variance with the results of an experimental study reported by the same group in 2001, in hypertensive patients (off their usual treatment for 3 months). Effect of salt intake on renal excretion of water in humans. He FJ, Markandu ND, Sagnella GA, MacGregor GA. Hypertension. 2001 Sep;38(3):317-20. PMID: 11566897

After a few days on a 350 mmol/day salt intake, these hypertensive patients were switched to a low salt intake of 10-20 mmol/day. Urine volume fell significantly from 2.2 ± 0.09 to 1.3 ± 0.05 L/day. The difference between the two studies can possibly be explained by the fact that the 1989 study was conducted in healthy young subjects (age range 19-21 y) whereas the 2001 study concerned hypertensive patients (mean age 48 y, range 19-70).

On 2017 Jul 29, Alex Vasquez commented:

As a researcher, author, clinician, and recent (2015) reviewer for PLOS One, I am writing with great concern about the editorial quality and review process of this previously esteemed journal, particularly with regard to the article discussed below. This Letter was sent to the PLOS One Editor by email on 20 July 2017 with receipt acknowledged on 21 July 2017; the response that "We encourage you to contact the corresponding authors of the article directly" is absurd as it will not address either the 1) lack of editorial quality, 2) the defects in the review process, or 3) the [in my opinion] erroneous publication of this article. Oddly, PLOS One does not publish letters and therefore provides no means for the archived biomedical record (e.g., in Pubmed, PubMed Central, Europe PMC, etc) to be corrected. Thus, given the aforementioned lackluster response and nearly nonexistent channels to correct and critique this PLOS One article, this critique is published online publicly https://www.academia.edu/34072801 and also via Pubmed Commons.

In their 4-week open trial with no control group, no laboratory testing, and which relied on participant-reported "data" for every aspect of treatment compliance and treatment effect, the Lawrence and Hyde [1] prescribed a program of psychosocial support (conference call with in-person/online contact with healthcare provider and support group) and dietary improvements (including avoidance of sugar, alcohol, grains and refined carbohydrates) and then attributed the purported health benefits (including self-reported weight loss and subjective improvements in digestion, cognition, physical and emotional wellbeing) to changes in the participants’ gut microbiome. Participants were a self-selected “convenience sample of people seeking the services of a nutritional therapist. The majority of participants’ primary goal was therefore weight-loss, with several additionally aiming to improve digestive symptoms (chronic acid reflux, bloating, constipation, loose stools, wind), plus energy, and pain issues.” Without providing any data to support their conclusion that the intervention changed a single microbe or metabolite from the gut microbiota, the authors assert that, “This dietary microbiome intervention has the potential to improve physical and emotional wellbeing in the general population but also to be investigated as a treatment option for individuals with conditions as diverse as IBS, anxiety, depression and Alzheimer’s disease.” Similarly and without evidence showing that the intervention modified any parameter of the gut microbiome, the authors assert, “Taken together with our findings, these results suggest that dietary interventions to optimise gut bacteria may have a role to play both in the treatment of Alzheimer’s disease but also in optimising cognitive functioning in non-clinical populations.” The most remarkable aspect of this research is the attribution of the mechanism of action of their diet intervention to gut microbiomal modification without a single original data point of evidence; indeed, the authors acknowledge that the effect of the “diet on the health and diversity of the microbiome has not been directly tested.” The authors utilized a participant-completed medical screening questionnaire which they acknowledge “was not selected specifically for the purpose of research, and is lacking in detailed information relating to its reliability and validity compared to scales used more specifically for research.”

Therefore in summary, this “research article” has the following attributes: 1. No objective data on health outcomes was collected; the study presents only participant-reported subjective data, 2. No objective data on treatment compliance was collected; we do not know if the participants followed the diet nor to what extent, 3. No objective data on treatment effect/mechanisms: The authors claim that the intervention changes the gut microbiome but failed to measure even a single parameter, microbe, molecule, or metabolite. 4. Participants were a positively self-selected “convenience sample” ripe and ready for a placebo response given their demonstrated positive expectations. 5. Impossible attribution, especially to the gut microbiome: With no control group, no-one knows if the supposed "improvements" were due to the psychosocial intervention, the diet, the season, the natural history the non-disease being non-studied, chance; the attribution of supposed benefit to a mechanism involving the gut microbiome is not supported by any data in this publication. 6. Short duration with no durability of effect: No demonstrated durability to the supposed benefits; the study was of notably short duration (4 weeks), 7. Wild attribution without any shred of evidence: The treatment included 1) diet intervention and 2) psychosocial support and then the authors attributed (without any supporting data whatsoever) the subjective/undocumented/purported benefits to 3) changes in the gut microbiotal composition. 8. Unreliable methods: The authors note that their use of the Functional Medicine Medical Symptoms Questionnaire “was not selected specifically for the purpose of research, and is lacking in detailed information relating to its reliability and validity compared to scales used more specifically for research” and that 9. No previous validation, as the diet plan “has not been directly tested” for its effect on the “health and diversity of the microbiome.” If this had been a follow-up survey or symptom assessment based on previous research, then such a publication might be reasonable; however, such is not the case with this publication. 10. The financial and self-promotional conflict of interest and the prominent mention of their proprietary book not fewer than 16 times in the manuscript. Does PLOS One now publish thinly veiled infomercials—masquerading as clinical research—for proprietary products? Given all these confounding variables and lack of objective data including zero data showing changes in the gut microbiome, a reasonable reviewer and reader can ask “What—if any—scientific value does this article provide?”

To be sure, we as researchers and clinicians have increasingly appreciated the role of the body-wide microbiome in health and disease, and we appreciate that diet potently shapes the gut microbiome [2,3]. However, to ascribe health benefits to changes in the microbiome from uncontrolled positively-selected participant-collected data following diet modification and psychosocial intervention is premature at best, unscientific at worst; the authors failed to collect even a single data point showing change in any microbe, molecule, or metabolite related to the gut microbiome, and yet the published title of the article is “Microbiome restoration diet.” Studies attributing therapeutic benefit to microbiome improvements should provide evidence supporting their hypothesis via the quantitative correlation of direct microbial analysis (or at the very least via surrogate markers such as serum endotoxin levels or serum 16SrRNA, both of which are also influenced by other factors such as intestinal permeability) with mostly objective data from biochemical markers and reliable tests of neurocognitive and emotional status. The financial and self-promotional conflict of interest and the prominent mention of their proprietary book not fewer than 16 times in the manuscript further calls into question the motive and actual value of this publication in a scientific journal.

Citations: 1. Lawrence K, Hyde J. PLoS One 2017 Jun:e0179017. 2. Vasquez A. Nutritional and Botanical Treatments against Silent Infections and Gastrointestinal Dysbiosis. Nutr Perspect 2006 Jan https://www.academia.edu/3862817. 3. Vasquez A. Human Microbiome and Dysbiosis in Clinical Disease, Volume 1. Barcelona: International College of Human Nutrition and Functional Medicine; 2015. ISBN13: 978-0990620419

On 2017 Jun 30, DANIEL BROWN commented:

Mycobacterium is not the same thing as Mycoplasma. Never has been, never will be.

On 2017 Jul 05, Suzy Chapman commented:

As mentioned in my previous comment, in the literature one observes frequent instances where the term "bodily distress disorder" has been used when what is actually being discussed within the paper or editorial is the Fink et al. (2010) "bodily distress syndrome (BDS)" disorder construct.

For example, "bodily distress disorder" is used interchangeably with "bodily distress syndrome" in the editorial (Creed et al. 2010): Is there a better term than "medically unexplained symptoms"? [1].

In this (Rief and Isaac 2014) editorial: The future of somatoform disorders: somatic symptom disorder, bodily distress disorder or functional syndromes? the authors are using the term, "bodily distress disorder" while clearly discussing the Fink et al. (2010) BDS construct [2].

The ICD-11 S3DWG sub working group's proposed term is seen, here, as "Bodily distress disorder (Fink and Schroder 2010)" in Slide #3 of the symposium presentation: An introduction to "medically unexplained" persistent physical symptoms. (Professor Trudie Chalder, Department of Psychological Medicine, King’s Health Partners, 2014) [3].

This paper: Medium- and long-term prognostic validity of competing classification proposals for the former somatoform disorders (Schumacher et al. 2017) compares prognostic validity of DSM-5 "somatic symptom disorder (SSD)" with "bodily distress disorder (BDD)" and "polysymptomatic distress disorder (PSDD)" and discusses their potential as alternatives to SSD for the replacement of the somatoform disorders for the forthcoming ICD-11 [4].

The authors state, "the current draft of the WHO group is based on the BDD proposal." But the authors have confirmed that for their study, they had operationalized "Bodily distress disorder based on Fink et al. 2007" [5].

In the (Fink et al. 2007) paper: Symptoms and syndromes of bodily distress: an exploratory study of 978 internal medical, neurological, and primary care patients, the authors conclude: "We identified a general, distinct, bodily distress syndrome or disorder that seems to encompass the various functional syndromes advanced by different medical specialties as well as somatization disorder and related diagnoses of the psychiatric classification."

There are other examples in research literature, publications [6] and in the field.

But these examples above suffice to demonstrate that the term, "bodily distress disorder" is already used synonymously with disorder term "bodily distress syndrome (BDS)" and that many researchers and clinicians do not differentiate between the two.

These examples also serve to demonstrate that the "bodily distress disorder" term is already being used outside ICD-11 Beta draft to describe a diagnostic construct that subsumes CFS, ME, IBS and FM under a single, unifying disorder construct - which does not correspond with how ICD Revision has defined "BDD" for the ICD-11 core edition, in which these categories remain discretely classified in chapters outside the Mental, behavioural or neurodevelopmental disorders chapter.

Since researchers/clinicians do not differentiate between "bodily distress syndrome" and "bodily distress disorder" (and in some cases, one also observes the conflations, "bodily distress syndrome or disorder" and "bodily distress syndrome/disorder"), ICD Revision needs to give urgent consideration to the difficulties and implications for maintaining the discrete identity of its proposed disorder, once ICD-11 is released and in the hands of its end users – clinicians, allied health professionals and coders, and to urgently review its current choice of nomenclature.

1 Creed F, Guthrie E, Fink P, Henningsen P, Rief W, Sharpe M, White P. Is there a better term than "medically unexplained symptoms"? J Psychosom Res. 2010 Jan;68(1):5-8. doi:10.1016/j.jpsychores.2009.09.004. [PMID: 20004295]

2 Rief W, Isaac M. The future of somatoform disorders: somatic symptom disorder, bodily distress disorder or functional syndromes? Curr Opin Psychiatry September 2014 – Volume 27 – Issue 5 – p315–319. [PMID: 25023885]

3 Chalder, T. An introduction to "medically unexplained" persistent physical symptoms. Presentation, Department of Psychological Medicine, King’s Health Partners, 2014. [Accessed 27 February 2017]

4 Schumacher S, Rief W, Klaus K, Brähler E, Mewes R. Medium- and long-term prognostic validity of competing classification proposals for the former somatoform disorders. Psychol Med. 2017 Feb 9:1-14. doi: 10.1017/S0033291717000149. [PMID: 28179046]

5 Fink P, Toft T, Hansen MS, Ornbol E, Olesen F. Symptoms and syndromes of bodily distress: an exploratory study of 978 internal medical, neurological, and primary care patients. Psychosom Med. 2007 Jan;69(1):30-9. [PMID: 17244846]

6 Medically Unexplained Symptoms, Somatisation and Bodily Distress: Developing Better Clinical Services, Francis Creed, Peter Henningsen, Per Fink (Eds), Cambridge University Press, 2011.

On 2017 Jul 05, Suzy Chapman commented:

In his lecture, Prof Fink discusses DSM-5's "somatic symptom disorder (SSD)" and its alignment with the proposed new diagnostic category, "bodily distress disorder (BDD)", as defined and characterized for the core edition of ICD-11 [1].

Prof Fink notes that SSD is a diagnosis mainly based on psychological and behavioural characteristics, with a very low symptom threshold - only one chronic, disturbing symptom required to meet the criteria, which may or may not be associated with a general medical condition - and suggests this will include most patients seen in both primary and secondary care.

That DSM-5's SSD (and the similarly conceptualized BDD, as defined by ICD-11) risk mislabelling millions of patients with an inappropriate mental disorder diagnosis was identified in 2013 by Frances & Chapman [2] and Frances [3][4].

Prof Fink is rightly concerned that ICD-11's proposed new single category replacement for the ICD-10 somatoform disorders will share the problems inherent in the DSM-5 SSD diagnosis.

However, Prof Fink omits from his lecture a crucial consideration concerning proposed nomenclature.

Since at least 2007, the term "bodily distress disorder" is frequently seen in the literature, at symposia and in presentations being used interchangeably with the term "bodily distress syndrome (BDS)" - the diagnostic construct developed by Prof Fink and his colleagues, which he confirms has been rejected by ICD Revision for inclusion in the ICD-11 core edition.

To the best of my knowledge, no clinician or researcher has published on the potential for confusion and conflation between the two disorder constructs or the implications for maintaining disorder integrity within and beyond ICD-11 - if ICD Revision names its differently conceptualized construct, with its very different criteria set and which potentially captures a different patient population, "bodily distress disorder."

Thus far, ICD Revision has provided no rationale for re-purposing a disorder term that is already closely associated with the Fink et al (2010) disorder construct and criteria set.

There is no justification for introducing a new disorder category into ICD-11 that has greater conceptual alignment with the DSM-5 SSD construct but is proposed to be assigned a disorder name that is closely associated with a divergent (and operationalized) construct/criteria set, that is already in use in research and clinical settings in Denmark and beyond.

This is unsafe and unsound classificatory practice and a very obvious flaw in their recommendations that remains unaddressed.

It is disappointing, then, that whilst having identified problems with clinical utility and given some consideration to the implications for patients for a diagnosis of SSD or its ICD-11 sister diagnosis, the author misses the opportunity to alert his audience to the potential for disorder conflation between ICD-11's proposed "BDD" and his own divergent, "BDS" diagnostic construct.

Comment from the author on this specific issue of nomenclature would be welcomed.

Secondly, there have been two working groups making recommendations to ICD Revision for the revision of the somatoform disorders.

Within his lecture, Prof Fink also refers to the proposals of the ICD-11 Primary Care Consultation Group (PCCG), that is chaired by Prof Sir David Goldberg.

The 28 mental disorders proposed for inclusion in the abridged primary care version (ICD-11 PHC) will require a corresponding category within the core edition. However, the PCCG considers that the "BDD" construct, as defined and characterized for the ICD-11 core edition, lacks utility in primary care settings.

The PCCG's recommendation is for an alternative construct for use in the primary care version which is a modification of the Fink et al (2010) BDS diagnostic construct and criteria set.

Prof Fink states that the PCCG is recommending the name "bodily stress disorder (BSD)" for the new disorder category which it proposes as the replacement for the ICD-10 PHC "F45 Unexplained somatic complaints" category rather than use the name "bodily distress syndrome (BDS)."

But according to Goldberg et al (2017), the PCCG would appear to continue to recommend the term "bodily stress syndrome (BSS)" for their modification - not "bodily stress disorder (BSD)" as Prof Fink has reported [4]. It would be helpful to have this apparent anomaly clarified.

If the PCCG's proposals for the abridged primary care version are approved by WHO/ICD Revision, there will be a lack of correspondence between the ICD-11 core edition replacement for the ICD-10 somatoform disorders and the primary care version.

A lack of consistency between the two editions risks confusion and conflation between the "BSS" BDS modification, the Fink et al (2010) unmodified BDS and the ICD-11 core edition defined BDD, resulting in loss of disorder definition integrity, lack of clarity over which patient populations these constructs are intended to capture, potential misapplication, confusion between different diagnoses across primary care and specialty settings, and will hamper statistical analyses.

Furthermore, and crucially, there appear to be no exclusions or differential diagnoses within the PCCG's proposed "BSS" criteria for CFS, ME, IBS and FM - diagnostic categories that are discretely classified within ICD-11 under chapters outside the mental, behavioural or neurodevelopmental disorders chapter.

This issue is still unaddressed by ICD Revision.

With only a few months left before the Beta draft needs to be finalized, the revision of the somatoform disorders for ICD-11 and ICD-11 PHC remains an indigestible alphabet soup.

1 Gureje O, Reed GM. Bodily distress disorder in ICD-11: problems and prospects. World Psychiatry. 2016 Oct;15(3):291-292. doi: 10.1002/wps.20353. [PMID: 27717252]

2 Allen Frances¹, Suzy Chapman². DSM-5 somatic symptom disorder mislabels medical illness as mental disorder. 1 Department of Psychiatry, Duke University 2 DxRevisionWatch.com Aust N Z J Psychiatry. 2013 May;47(5):483-4.[PMID: 23653063]

3 Frances A. DSM-5 Somatic Symptom Disorder. J Nerv Ment Dis. 2013 Jun;201(6):530-1. doi: 10.1097/NMD.0b013e318294827c [PMID: 23719325]

4 Frances A. The new somatic symptom disorder in DSM-5 risks mislabeling many people as mentally ill. BMJ. 2013 Mar 18;346:f1580. doi: 10.1136/bmj.f1580. [PMID: 23511949] 5 Primary care physicians' use of the proposed classification of common mental disorders for ICD-11. Goldberg et al. Fam Pract. 2017 May 4. doi: 10.1093/fampra/cmx033. [PMID: 28475675]

On 2017 Aug 20, NephJC - Nephrology Journal Club commented:

The exciting paper “Canagliflozin and Cardiovascular and Renal Events in Type 2 Diabetes” was discussed on June 27th and 28th 2017 on #NephJC, the open online nephrology journal club.

Introductory comments written by Swapnil Hiremath are available at the NephJC website here

Nearly 200 people participated in the discussion with over 1000 tweets. One of the authors, Vlado Perkovic also kindly joined the journal club

The highlights of the tweetchat were:

• There has been very heterogenous use of SGLT2 inhibitors (SGLT2i) across the globe to date. They tend to be more commonly started by endocrinologists. There have been some cases of euglycemic DKA noted.

• The studies were felt to be well-designed followed FDA guidance for non-inferiority meticulously. According to the authors, unexpected effects made it difficult to proceed to larger study without understanding cardiovascular safety in detail – hence CANVAS-R.

• It was unusual that such a high percentage (70%) of the group had normoalbuminuria.

• It would be interesting to determine what weight loss was calorific and what was diuretic effect.

• The excess of amputations and fractures in the canagliflozin group was surprising. Postulated mechanisms for this included expression of SGLT2i elsewhere in the body and differential effects on oxidative phosphorylation.

• Overall there were promising composite renal endpoints but there is still some concern about the potential adverse events revealed here which time may better delineate the extent of.

Transcripts of the tweetchats, and curated versions as storify are available from the NephJC website.

Interested individuals can track and join in the conversation by following @NephJC or #NephJC on twitter, liking @NephJC on facebook, signing up for the mailing list, or just visit the webpage at NephJC.com.

On 2017 Jun 18, Thomas Heston commented:

This trial basically shows that treating diabetes helps decrease cardiovascular morbidity, which is not a new finding. To determine if canagliflozin has a unique property in decreasing cardiovascular events beyond simply lowering blood sugar, the analysis would have had to match patients by their hemoglobin A1c, then compare outcomes of placebo vs canagliflozin. Amazingly, this was not done. They did not look at cardiovascular events after correcting for hemoglobin A1c levels. Note that this was a pharmaceutical company funded research project, and the conclusion heavily implies that canagliflozin (as opposed to any agent that lowers blood sugar) has a unique quality of lowering cardiovascular events in diabetics. The authors did not prove that canagliflozin had any unique cardiovascular protective properties [Heston TF, 2017]. By not separating out the potential unique effects of canagliflozin beyond just lowering blood sugar, the results regarding a unique cardiovascular effect are basically meaningless and even worse, misleading.

On 2017 Jun 14, Kay Tye commented:

We would like to make a clarification regarding the following sentences addressing the impact of previous social experience or social history on DRN DA dynamics across multiple stimuli:

In reference to the fiber photometry signals in response to a number of stimuli, Cho and colleagues stated that “These findings did not vary with subject social history, as similar patterns of DRNDA activation were seen in group-housed mice (Figures S2J–S2L)” and “DRNDA activation by a wide variety of rewarding and aversive stimuli, both social and non-social, occurred irrespective of the subject’s social history, as the stimulus-evoked change in DRNDA fluorescence was not influenced by chronic separation from cage-mates (Figures S2J–S2M).”

However, with respect to the presentation of a social stimulus, Cho and colleagues report a similar trend as Matthews and colleagues, albeit one that was not statistically significant:

In Matthews et al., Cell (2016) the experiments in Figure 2 showed a significantly greater DRN DA fiber photometry signal (GCaMP6m in TH::Cre male mice) in response to a juvenile male when subjects were acutely (24 hours) single-housed than when group-housed (n=9, within-subject comparison). PMID: 26871628

In Cho et al., Neuron (2017) the experiments in Figure S2J showed a non-significant trend reflecting a greater mean DRN DA fiber photometry signal (GCaMP6f in TH::Cre male mice) in response to an adult female when subjects were chronically single-housed (at least 4 weeks, standard for sleep studies; n=7) versus group-housed mice(n=4, between-subjects comparison).

Examining the impact of social stimuli on DRN DA activity was not the focus of the study by Cho and colleagues. Further, as stated in the discussion of Cho and colleagues, a number of experimental parameters such as the nature of social target (male exposed to juvenile vs. female), isolation paradigms (acute vs. chronic) and optical fiber tip location differed between these studies (please see the publications for details). Nonetheless, the experiments related to social behavior in these two studies produce largely consistent results.

This post was composed by Kay M. Tye, a corresponding author of the Matthews and colleagues study, following discussion with and approval from Viviana Gradinaru, the corresponding author of the Cho and colleagues study.

On 2018 Jan 04, Marilyn Tirard commented:

We have published a response to the comment by Wilkinson et al, which can be found with the online version of the original article: https://elifesciences.org/articles/26338#annotations:1fKgOgXREei5NxuiEWEQ0w

On 2017 Sep 20, Kevin Wilkinson commented:

Is the His6-HA-SUMO1 knock-in mouse a valid model system to study protein SUMOylation?

K.A. Wilkinson^1* , S. Martin² , S.K. Tyagarajan³ , O Arancio⁴ , T.J. Craig⁵ , C. Guo⁶ , P.E. Fraser⁷ , S.A.N. Goldstein⁸ , J.M. Henley^1* .

¹ School of Biochemistry, Centre for Synaptic Plasticity, University of Bristol, Bristol, UK. ² Université Côte d’Azur, INSERM, CNRS, IPMC, France. ³ Institute of Pharmacology and Toxicology, University of Zurich, Switzerland. ⁴ Taub Institute & Dept of Pathology and Cell Biology, Columbia University, New York, NY, USA. ⁵ Centre for Research in Biosciences, University of the West of England, Bristol, UK. ⁶ Department of Biomedical Science, University of Sheffield, Sheffield, UK. ⁷ Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Canada. ⁸ Stritch School of Medicine, Loyola University, Chicago, USA.

*Address for correspondence: kevin.wilkinson@bristol.ac.uk or J.M.Henley@bristol.ac.uk.

Introduction

There is a large and growing literature on protein SUMOylation in neurons and other cell types. While there is a consensus that most protein SUMOylation occurs within the nucleus, SUMOylation of many classes of extranuclear proteins has been identified and, importantly, functionally validated. Notably, in neurons these include neurotransmitter receptors, transporters, sodium and potassium channels, mitochondrial proteins, and numerous key pre- and post-synaptic proteins (for reviews see Henley JM, 2014, Wasik U, 2014, Peng J, 2016, Martin S, 2007, Luo J, 2013, Craig TJ, 2012, Scheschonka A, 2007, Guo C, 2014, Wu H, 2016, Schorova L, 2016). Furthermore, several groups have reported SUMO1-ylated proteins in synaptic fractions using biochemical subcellular fractionation approaches, using a range of different validated anti-SUMO1 antibodies (Martin S, 2007, Feligioni M, 2009, Marcelli S, 2017, Loriol C, 2012) and many studies have independently observed colocalisation of SUMO1 immunoreactivity with synaptic markers (Konopacki FA, 2011, Ghosh H, 2016, Gwizdek C, 2013, Jaafari N, 2013, Hasegawa Y, 2014). Tirard and co-workers (Daniel JA, 2017) directly challenge this wealth of compelling evidence. Primarily using a His6-HA-SUMO1 knock-in (KI) mouse the authors contest any significant involvement of post-translational modification by SUMO1 in the function of synaptic proteins.

On what basis do Daniel et al. argue against synaptic SUMOylation?

Most of the experiments reported by Daniel et al. use a knock-in (KI) mouse that expresses His6-HA-SUMO1 in place of endogenous SUMO1. Using tissue from these mice, followed by immunoprecipitation experiments, they fail to biochemically identify SUMOylation of the previously validated SUMO targets synapsin1a (Tang LT, 2015), gephyrin (Ghosh H, 2016), GluK2 (Martin S, 2007, Konopacki FA, 2011, Chamberlain SE, 2012, Zhu QJ, 2012), syntaxin1a (Craig TJ, 2015), RIM1α (Girach F, 2013), mGluR7 (Wilkinson KA, 2011, Choi JH, 2016), and synaptotagmin1 (Matsuzaki S, 2015). Moreover, by staining and subcellular fractionation, they also fail to detect protein SUMOylation in synaptic fractions or colocalisation of specific anti-SUMO1 signal with synaptic markers. On this basis, they conclude there is essentially no functionally relevant SUMOylation of synaptic proteins.

What are the reasons for these discrepancies?

• Inefficiency of His6-HA-SUMO1 conjugation and compensation by SUMO2/3

A major cause for concern is that there is 20-30% less SUMO1-ylation in His6-HA-SUMO1 KI mice than in wild-type (WT) mice (Daniel JA, 2017, Tirard M, 2012). Moreover, in the paper initially characterising these KI mice, Tirard et al. showed that while total protein SUMO1-ylation is reduced, total SUMO2/3-ylation is correspondingly increased (Tirard M, 2012). Thus, His6-HA-SUMO1 conjugation is significantly impaired and most likely compensated for by increased conjugation by SUMO2/3. Crucially, however, Daniel et al. do not examine modification by SUMO2/3 at any point in their recent study.<br> Given that SUMO modification is notoriously difficult to detect the 20-30% reduction in His6-HA-SUMO1 compared to wild-type SUMO1 conjugation will make it even more technically challenging. Moreover, this deficit in SUMO1-ylation may well be offset by an increase in SUMO2/3-ylation of individual proteins, but this likely compensation was not tested. Since these deficits alone could explain why Daniel et al. failed to detect SUMO1 modification of the previously characterised synaptic substrate proteins it is surprising that they did not attempt to recapitulate SUMO1-ylation of the target proteins under the endogenous conditions in wild-type systems used in the original papers.

• Lack of functional studies on the substrates they examine

Daniel et al. confine their studies to immunoblotting and immunolabelling. However, these techniques address only one aspect of validating a bone fide SUMO substrate. It is at least as important to examine the effects of target protein SUMOylation in functional assays. Function-based approaches such as electrophysiology or neurotransmitter release assays are not reported or even discussed by Daniel et al. This is an extremely important omission. We argue that simply because SUMO1-ylation of a protein is beneath the detection sensitivity in a model system that exhibits sub-endogenous levels of SUMO1-ylation, does not mean that protein is not a functionally important and physiologically relevant SUMO1 substrate.

• Insensitivity or inadequate use of assay systems

Failure to detect GluK2 SUMOylation

GluK2 is a prototypic synaptic SUMO1 substrate that has been validated in exogenous expression systems, neuronal cultures and rat brain (Martin S, 2007, Konopacki FA, 2011, Chamberlain SE, 2012, Zhu QJ, 2012). Daniel et al. attempt to detect SUMOylation of GluK2 using immunoprecipitation experiments from the His6-HA-SUMO1 KI mice. However, a key flaw in this experiment is that the C-terminal anti-GluK2 monoclonal rabbit antibody used does not recognise SUMOylated GluK2 because its epitope is masked by SUMO conjugation. Thus, due to technical reasons, the experiment shown could not possibly detect SUMOylated GluK2 whether or not it occurs in the KI mice.

Subcellular fractionation and immunolabelling

Daniel et al. perform subcellular fractionation and anti-SUMO1 Western blots to compare His6-HA-SUMO1 KI and SUMO1 knockout (KO) mice. In the KI mice they fail to detect SUMO1-ylated proteins in synaptic fractions. Importantly, however, they do not address what happens in WT mice, which, unlike the KI mice, exhibit normal levels of SUMO1-ylation. While the authors provide beautiful images of SUMO1 immunolabelling in neurons cultured from WT, His6-HA-SUMO1 KI mice and SUMO1 KO mice, in stark contrast to previous reports using rat cultures (Martin S, 2007, Konopacki FA, 2011, Gwizdek C, 2013, Jaafari N, 2013), they detect no specific synaptic SUMO1 immunoreactivity in neurons prepared from WT mice. We note, however, that the nuclear SUMO1 staining in neurons from His6-HA-SUMO1 KI mice is weak, and even weaker in WT neurons. Given that a very large proportion of SUMO1 staining is nuclear, these low detection levels would almost certainly rule out visualisation of the far less abundant, but nonetheless functionally important, extranuclear SUMO1 immunoreactivity.

In conclusion

Given these caveats we suggest that the failure of Daniel et al. to detect synaptic protein SUMO1-ylation in His6-HA-SUMO1 KI mice is due to intrinsic deficiencies in this model system that prevent it from reporting the low, yet physiologically relevant, levels of synaptic protein modification by endogenous SUMO1. In consequence, we question the conclusions reached and the usefulness of this model for investigation of previously identified and novel SUMO1 substrates.

On 2017 Jun 29, David Keller commented:

Were serum cholesterol levels adequately controlled for?

Low LDL cholesterol, and low total cholesterol, have been associated with higher risk of Parkinson disease (PD) in recent studies [1]. Consumption of lowfat dairy products, by displacing full-fat dairy products from the diet, certainly leads to lower serum cholesterol levels. Were serum cholesterol levels adequately controlled for? Does a person who consumes a lot of low fat dairy food run a higher risk of PD than a person with the same lipid levels who does not consume low fat dairy?

Reference

1: Huang X, Alonso A, Guo X, Umbach DM, Lichtenstein ML, Ballantyne CM, Mailman RB, Mosley TH, Chen H. Statins, plasma cholesterol, and risk of Parkinson's disease: a prospective study. Mov Disord. 2015 Apr;30(4):552-9. doi: 10.1002/mds.26152. Epub 2015 Jan 14. PubMed PMID: 25639598; PubMed Central PMCID: PMC4390443.

On 2017 Jun 21, Lydia Maniatis commented:

This paper seems to hinge on a notion that makes no functional sense, has never been corroborated, and has led to an absurd claim by one of its main proponents attempting to salvage it.

The notion is that the visual system performs a Fourier analysis on the "image" via "spatial frequency filters." As far as I can see, the reasons for the adoption of this functionally absurd notion were an ill-conceived analogy to hearing and the Fourier analysis that happens in the inner ear, combined with a gross over-interpretaion of the early findings of Hubel and Wiesel on the striate cortex of the cat. Psychophysicists were fabulously successful at corroborating the notion, accumulating heaps of evidence in its favor. Unfortunately, as Graham (2011) points out, the evidence generated had been interpreted in terms of a visual system that consisted solely of V1 (which was supposed to contain the orientation/frequency detectors) while it was later understood to be far more complex. The sitmuli that had been interpreted as tapping into V1 had somehow been ignored by neurons in V2, V3, V4, etc.! In these circumstances, Graham considers the "success" of the psychophysical program as something akin to "magic," and decides to explain it by arguing that, in the case of very simple stimuli, the brain becomes "transparent" down to the lower levels. Earlier, Teller (1984) had censured such attitudes as examples of an untenable "nothing mucks it up proviso." Below is the relevant passage from Graham (2011):

"The simple multiple-analyzers model shown in the top panel of Fig. 1 was and is a very good account, qualitatively and quantitatively, of the results of psychophysical experiments using near-threshold contrasts . And by 1985 there were hundreds of published papers each typically with many such experiments. It was quite clear by that time, however, that area V1 was only one of 10 or more different areas in the cortex devoted to vision. ...The success of this simple multiple-analyzers model seemed almost magical therefore. How could a model account for so many experimental results when it represented most areas of the visual cortex and the whole rest of the brain by a simple decision rule? One possible explanation of the magic is this: In response to near-threshold patterns, only a small proportion of the analyzers are being stimulated above their baseline. Perhaps this sparseness of information going upstream limits the kinds of processing that thehigher levels can do, and limits them to being described by simple decision rules because such rules may be close to optimal given the sparseness. It is as if the near-threshold experiments made all higher levels of visual processing transparent, therefore allowing the properties of the low-level analyzers to be seen." Or, as is well-known, it's always possible to arrange experiments, including employing a very restricted set of stimuli, so as to achieve consistency with any hypothesis.

I guess the fairly brief exposures used in the present experiment are supposed to qualify then for transparency status, unless the authors have their own views about the anatomical loci of the supposed spatial frequency filters, but all of this really should be discussed and defended explicitly.

The idea that the visual system performs a Fourier analysis i.e. analyzes the visual stimulation into spatial frequency patterns, is absurd for a number of reasons. First, the retinal stimulation is initially point stimulation, a mosaic of points (photoreceptors) whose activities at any given moment depend on the intensity/wavelength of the photons striking them. Therefore, to organize this mosaic into a set of images based on spatial frequency is not first a problem of detection, but of organization. The spatial frequency kind of organization in no way furthers, but rather impedes, the task that the visual system has to achieve, which is to group points of the mosaic such that the boundaries of those groups correspond to the boundaries of the objects in the visual field. So it is not only incredibly difficult (no mechanism has been proposed), it is a pointless diversion. Even if this were not the case, the requirement for a 'transparency hypothesis" renders it absurd on that basis alone. There is no credible evidence in its favor.

Other seemingly absurd claims include the statement that: "it recently has been shown that the availability of horizontal structure underlies the face-specific N170 response...." Is there such a thing as an image lacking "horizontal structure," or lacking structure in any direction? In other words, can we test this statement by controlling for "horizontal structure"? The term is too general to serve as a substitute for the much more specific and theoretically baseless image manipulation to which it refers.

Another problem I have is the problem of sampling. With complex stimuli, the number of potential confounds is large. Not only is the sample of stimuli used here small; in addition, the authors don't indicate that they were randomly selected, only that they were "selected." On what basis? It seems to me that faces with well-defined eyebrows, for example, would be more likely to produce the desired results, given that the vertical filters seem to make them disappear in the sample provided in the article.

I agree that familiarity makes perceptual tasks easier, and even that we notice relationships across the vertical axis more easily than across the horizontal, but the present experiment has nothing to do with that.

On 2017 Jun 22, Lydia Maniatis commented:

This study is an exercise in generating and crunching numbers following a 50-year-old recipe containing many untested and implausible assumptions, i.e. Green and Swets (1966) analogizing of perception to signal detection. I've commented on this issue in detail in a number of PubPeer/PubMedCommons on other articles.

I'll just make one additional comment here. In the Appendix, we're casually informed, as a preliminary, that:

"All targets were assumed to be known to the ideal observer."

In what sense is this omniscient-homunculus-assumption related to human perception? What is the neuroscientific theory behind it, and what is the relationship of this homunculus to the processes doing the "detecting and discriminating?" In other words, what is the relevance of the "ideal observer model" other than to provide an arbitrary value with which to compare the human data?

(Also, what does it mean, exactly, that the targets were "known" to the ideal observer? What does this knowing consist of?)

On 2017 Sep 22, Clive Bates commented:

I am struggling to see any useful purpose in this paper.

It seems to consist of finding alcohol flavours in tobacco product and e-liquids by looking on the internet. There is no data on volumes or any age-related information about sales or appeal. The authors have done nothing to show an effect that requires a regulatory intervention or anything to justify their policy conclusion.

The widespread availability of alcohol-flavoured tobacco products illustrates the need to regulate characterising flavours on all tobacco products.

No so. The widespread availability of a product is not in itself a problem. Nor is the widespread use of a product, unless its use can be linked to a harm - which the authors have not done here, other than by just asserting it. It is likely and certainly plausible that these flavours are beneficial by encouraging adults to switch from smoking to vaping and that a regulatory intervention would cause more harm than good. It is also possible that if young people were attracted to such flavours, they may be diverted from smoking to vaping, which is a benefit. Needless to say, the authors do not consider such real-world possibilities.

On 2017 Jun 23, Dorothy V M Bishop commented:

There is some evidence for diagnostic substitution from developmental language disorder to autism. I suspect, unfortunately, that this might be harder to quantify in public data than the substitution from intellectual disability, unless states have been consistent in terminology used for language disorder. Our study on this topic was just based on an adult follow-up of a small sample of children who had been diagnosed with language disorder, but it was striking how some cases who were identified as cases of language disorder (or specific language impairment) 20-30 yr earlier would nowadays been seen as clearcut cases of ASD - not because of any change in their profiles, but rather because of less restrictive diagnostic criteria for autism. Autism and diagnostic substitution: evidence from a study of adults with a history of developmental language disorder By: Bishop, Dorothy V. M.; Whitehouse, Andrew J. O.; Watt, Helen J.; et al. DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY Volume: 50 Issue: 5 Pages: 341-345 Published: MAY 2008