On 2016 Dec 20, Claudiu Bandea commented:

The etiology of Parkinson's disease is not an enigma

In a recent expert review article entitled “How close are we to revealing the etiology of Parkinson's disease?” (1), Kurt Jellinger concluded: “Although major advances have been made in our understanding of the etiology (and pathogenesis) of PD (and related synucleinopathies) over the last 20 years, it remains as much an enigma as when James Parkinson first described its clinical features” (italics added).

It remains to be seen if the study by Sampson et al. (2) will join the growing list of “major advances” in the field of Parkinson’s, which have revealed numerous contributing factors, including environmental (e.g. toxins), microbial (e.g. various bacteria and viruses), physiological (e.g. oxidative stress) and genetic (e. g. mutations) in addition to the main risk factor - aging.

But what if the etiology of Parkinson’s has remained an enigma primarily because of these “major advances”? What if, by promoting a multitude of different causes and pathogenic mechanisms, each supported by strong data and observations, these “major advances” have led to confusion and have constrained progress? What if Parkinson’s enigma is a classic case of ‘not seeing the forest because of the trees’?

Contrary to the conventional thinking in the field, I recently proposed that the existing data and observations, including those in Sampson et al. (2) and other “major advances”, when integrated in a comprehensive conceptual framework that makes biological and evolutionary sense, point towards a sensible solution to Parkinson’s enigma (3, 4; for recent additional evidence see Ref. 5):

(i) α-synuclein (aSyn), the primary protein implicated in Parkinson’s and related synucleinopathies, is a member of the innate immune system;

(ii) The assembly of αSyn into various oligomers and fibers is not a protein misfolding event as currently defined, nor is it a prion-like replication/propagation activity, but it is an integral part of its biological function in innate immunity;

(iii) The activities associated with the immune function of αSyn lead to Parkinson’s and other synucleinopathies, which are innate autoimmune disorders.

Sampson et al. (2) performed a series of ingenious experiments evaluating the impact of gut microbiota and some of their metabolites on the aggregation of αSyn, activation of microglia, and motor and gut motility deficits in a transgenic mouse model for Parkinson’s that expresses high levels of human αSyn. Similar to other studies showing a strong influence of enteric microbiota on the immune and nervous systems, the results showed that, compared to germ-free transgenic mice, mice carrying complex gut microbiota had increased αSyn associated pathology and microglia activation in the brain and displayed progressive deficit in motor functions and gut motility. The study would have benefited from parallel experiments in mice with disrupted vagal nerve, likely the main portal for αSyn aggregates (as well as for neurotropic microbial/viral pathogens) to the brain, particularly in the light of the finding that the administration of a mixture of short-chain fatty acids, which can reach the brain via the blood circulatory system, simulates the effects of gut microbiota. Perhaps the most intriguing finding reported by Sampson et al. was that the gut microbiota transferred from patients with Parkinson’s enhanced motor impairments, whereas the microbiota from healthy human donors did not, which suggested that the effects might be induced by specific Parkinson’s associated microbial taxa; however, I suggest an additional putative mechanism: the impairment was initiated by ‘αSyn oligomeric seeds’ that were transferred from the patients with Parkinson’s.

As interesting and valuable the results reported Sampson et al. (2) are, the authors have failed to make sense of them in context of the other “major advances” in the field, thereby adding to the enigma (i.e. confusion) regarding the etiology of Parkinson’s and related synucleinopathies.

For example, given that the ‘prion’ concept has been one of the major emerging paradigms in the field of Parkinson’s and other neurodegenerative diseases, including Alzheimer’s, Huntington’s, and ALS (e.g. 5-10), it is highly surprising that Sampson et al. have only mentioned it in the following statement: “Braak’s hypothesis posits that aberrant αSyn accumulation initiates in the gut and propagates via the vagus nerve to the brain in a prion-like fashion (Del Tredici and Braak, 2008)” (italics added). It appears that “Del Tredici and Braak, 2008” reference is a technical error as it doesn’t present a “Braak’s hypothesis”; possibly, Sampson et al. intended to refer to the ‘dual-hit hypothesis’, first presented in 2007 and re-published by the same authors two years later (11). Nevertheless, as I have previously discussed (3,4,12), the ‘prion hypothesis’ is probably flawed, so I commend Sampson et al. for omitting it, but I doubt that the authors were motivated by the same perspective.

I end this brief essay on Sampson et al. (2) by outlining its major weakness, which it is shared with most studies addressing the role of αSyn: the failure to consider the physiological function of αSyn when exploring its pathogenic mechanisms and the etiology of Parkinson’s and related synucleinopathies. Unfortunately, the prion hypothesis and the associated ‘protein misfolding’ paradigm have conceptually uncoupled the pathogenic mechanisms associated with αSyn, as well as with the other main proteins implicated in neurodegeneration (e.g. APP/amyloid-β, tau, huntingtin, TDP-43, prion protein), from their evolutionarily selected biological function (3,4). As recently suggested, the paths toward understanding neurodegeneration must be re-evaluated (13), and this should start with assessing the scientific foundation of the prion hypothesis and protein misfolding paradigm, which are questionable.

References:

(1) Jellinger KA. 2015. How close are we to revealing the etiology of Parkinson's disease? Expert Rev Neurother. 15(10):1105-7. Jellinger KA, 2015

(2) Sampson et al. 2016. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Cell. 167(6):1469-80. Sampson TR, 2016

(3) Bandea CI. 2013. Aβ, tau, α-synuclein, huntingtin, TDP-43, PrP and AA are members of the innate immune system: a unifying hypothesis on the etiology of AD, PD, HD, ALS, CJD and RSA as innate immunity disorders. bioRxiv. doi: 10.1101/000604; http://biorxiv.org/content/early/2013/11/18/000604

(4) Bandea CI. 2009. Endogenous viral etiology of prion diseases. Nature Precedings. http://precedings.nature.com/documents/3887/version/1/files/npre20093887-1.pdf

(5) Beatman et al. 2015. Alpha-Synuclein Expression Restricts RNA Viral Infections in the Brain. J Virol. 90(6):2767-82; Beatman EL, 2015

(6) Miller G. 2009. Neurodegeneration. Could they all be prion diseases? Science. 326(5958):1337-9. Miller G, 2009

(7) Goedert M, Clavaguera F, Tolnay M. 2010. The propagation of prion-like protein inclusions in neurodegenerative diseases. Trends Neurosci. 33(7):317-25. Goedert M, 2010

(8) Angot et al. 2010. Are synucleinopathies prion-like disorders? Lancet Neurol. 9(11):1128-38. Angot E, 2010

(9) Jucker M, Walker LC. 2013. Self-propagation of pathogenic protein aggregates in neurodegenerative diseases. Nature. 501(7465):45-51. Jucker M, 2013

(10) Prusiner SB. 2013. Biology and genetics of prions causing neurodegeneration. Annu Rev Genet. 47:601-23. Prusiner SB, 2013

(11) Hawkes CH, Del Tredici K, Braak H. 2009. Parkinson's disease: the dual hit theory revisited. Ann N Y Acad Sci. 1170:615-22. Hawkes CH, 2009

(12) Bandea CI. 1986. From prions to prionic viruses. Med Hypotheses. 20(2):139-42. Bândea CI, 1986

(13) Kosik et al. 2016. A path toward understanding neurodegeneration. Science. 353(6302):872-3. Kosik KS, 2016

On 2017 Jul 31, George McNamara commented:

Western (blot) misconduct paper: not perfect, but worth reading and thinking about. I'll also add that: * in this era of NGS (next generation sequencing), any RNAseq or single cell RNAseq that does not pass all the filters/gates, is going to be ignored ... enabling the authors to "prove their hypothesis (again and again)". * More NGS = fewer Northern blots. Of course Northern blots are just as susceptible to cropping = misconduct as Western blots. * the article mentions insulin, but came out sooner than this paper: https://www.ncbi.nlm.nih.gov/pubmed/28263308 Kracht et al 2017 Autoimmunity against a defective ribosomal insulin gene product in type 1 diabetes. Nature Medicine ... insulin alternative reading frame mRNA results in "a highly immunogenic polypeptide" targeted by cytolytic CD8 T-cells.

On 2016 Dec 16, Kevin Kavanagh commented:

We have ongoing concerns regarding several of the questions posed in our previous letter(1) along with the authors’ response.(2) The major concern is that we are still not able to reconcile the data presented in the author’s reply letter with those presented in the manuscript. Thus, we feel there may be an over-statement of the efficacy of the intervention. In addition, we have ongoing concerns regarding the reporting of conflicts-of-interests.

1. The most important stated outcome of this study is the 42% decrease in hospital-onset MRSA infections.

This outcome has been widely disseminated in the media and even appeared in the headline of a major infectious disease news outlet, Infection Control Today: “Hospital Reduces MRSA Rates by 42% with electronic hand hygiene measurement.”(3) However, the pre and post-intervention rates (baseline rate of 0.381 infections per 1000 days, reduction of 0.114 infections per 1000 days and post-intervention of rate of 0.267 infections per 1000 days) of MRSA that Kelly, et al. (2) gave in their letter showed only a 30% reduction:

0.114 / 0.381 = 0.299 or 29.9%

In their letter, Kelly, et al.(2) questioned our calculation of the baseline rate. Our calculation was based upon the data given in their manuscript of a 42% reduction which corresponded to a reduction in MRSA infections of 0.114 per 1000 patient days. Using algebra, the baseline and post-intervention rates can then be calculated:

If the reduction is 0.114 and corresponds to 42%, then the baseline rate equals:<br> 0.114 / ( 0.42 ) = 0.271

If the baseline rate is 0.271 and the reduction 0.114, then the post-intervention rate equals: 0.271 – 0.114 = 0.157

We feel the authors should explain or correct this discrepancy in their study’s outcome. As we stated, our calculated post-intervention rate (0.157) appeared to be even better than that reported by Jain, et al.(4) We agree that the authors’ reported post-intervention rate in their letter (0.267) is in accordance with that reported by Jain, et al, but appears to be different from the results reported in their manuscript.

2. The authors’ explanation of the conflict-of-interest (COI)

The authors’ statement regarding the original statement of conflicts-of-interest was given as follows: “The conflict of interest statement was inadvertently left off the prepublication galley proof, but was included in the final publication.” Since the publisher is the one which initially creates the galley poof, we feel this may give the impression it was a publisher’s error.

According to PubMed, the original date of online publication (Epub) for Kelly, et al.(5), was June 23, 2016. The Journal has a website designation for articles in this stage as “In Press Corrected Proof”. As of July 25, 2016, the article, which we received from the University of Kentucky Library, had a COI statement of “None to report.” The August 2016 print publication of the article and article’s current PDF both have the same DOI number as the June 23, 2016 e-published “In Press Corrected Proof”. These latter manuscripts have the revised COI statement.

In addition, the final publication is often considered the e-publication (Epub.), which is assigned a Digital Optic Identifier (DOI) when the article “is published”(6), and is available to libraries and/or PubMed. Some journals do not even publish a printed version of an article. At this stage author corrections are often time stamped or if major, accomplished by a letter or erratum.

Finally, the COI issue is not only with potential industrial funding but also with potential COIs involving the authors. According to Infection Control Today: “Connie Steed, MSN, RN, CIC, director of infection prevention at GHS and a MRSA study co-author, has been working with DebMed for the past seven years.”(3) The start of this relationship appears to have preceded the study start date by several years and we feel should have been either declared or explained. We also feel a COI statement from all authors should also accompany the publication of this and every article.

Summary: It is not the purpose of this communication to establish the efficacy of a device which monitors hand hygiene compliance but to express our concern that the Kelly, et al. study(5) should be viewed with caution when entering it in to a body of evidence to establish standards for patient care.

References

(1) Kavanagh KT, Saman DM. Comment Regarding: Electronic hand hygiene monitoring as a tool for reducing health care–associated methicillin-resistant Staphylococcus aureus infection. American Journal of infection Control. December 01 2016 http://www.ajicjournal.org/article/S0196-6553(16)30904-X/fulltext Kavanagh KT, 2016

(2) Kelly WJ, Blackhurst D, McAtee W, Steen C., Response to Letter Regarding Manuscript “Electronic Hand Hygiene Monitoring as a Tool for Reducing Nosocomial Methicillin-resistant Staphylococcus aureus Infection” American Journal of infection Control. December 01 2016 http://www.ajicjournal.org/article/S0196-6553(16)30812-4/fulltext

(3) Hospital Reduces MRSA Rates by 42% with electronic hand hygiene measurement. Infection Control Today. July 8, 2016. http://www.infectioncontroltoday.com/news/2016/07/hospital-reduces-mrsa-rates-by-42-with-electronic-hand-hygiene-measurement.aspx

(4) Jain R, Kralovic SM, Evans NE, Ambrose M, Simbartl LA, Obrosky DS, Render ML, Freyberg RW, Jernigan JA, Muder RR , Miller LJ, Roselle GA. Veterans Affairs Initiative to Prevent Methicillin-resistant Staphyloccus aureus Infections . NEJM Apr 2011:364:1419-1430 Retrieved From: http://www.nejm.org/doi/full/10.1056/NEJMoa1007474

(5) Kelly JW, Blackhurst D, McAtee W, Steed C. Electronic hand hygiene monitoring as a tool for reducing health care-associated methicillin-resistant Staphylococcus aureus infection. Am J Infect Control. 2016 Jun 23. pii: S0196-6553(16)30340-6. doi: 10.1016/j.ajic.2016.04.215. [Epub ahead of print] Kelly JW, 2016

(6) What is a digital object identifier, or DOI? APA Style. American Psychological Association. Last accessed on Dec. 3, 2016 from http://www.apastyle.org/learn/faqs/what-is-doi.aspx

Kevin T. Kavanagh, MD, MS Daniel M. Saman, DrPh, MPH

On 2017 May 04, Ralph Brinks commented:

One of the key methods used in this paper is not appropriate. Note the comment about a similar paper authored from the same group: Hoyer A, 2017

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 Mar 17, Sin Hang Lee commented:

"In science you don't need to be polite, you merely have to be right."- Winston Churchill.

On 2017 Feb 22, Marcia Herman-giddens commented:

Please explain for what reason this comment was removed.

On 2017 Feb 19, Sin Hang Lee commented:

None

On 2017 Feb 19, Sin Hang Lee commented:

None

On 2017 Feb 14, Mark Schiffman commented:

Prophylactic HPV vaccines consist of the major coat protein L1 assembled into macromolecular structures – virus like particles (VLPs) that mimic the geometry and morphology of the wild type virus coat or capsid but do not contain full length HPV DNA genomes. VLPs, with their repeat crystalline array of L1 pentamers as in the wild type virus, are intrinsically immunogenic(1) eliciting high antibody titres with or without adjuvant(2). The safety profile of the licensed vaccines was assessed extensively in randomized clinical trials (RCTs)(3-5). In the 10 years since the first 2 commercial vaccines Gardasil and Cervarix were licensed, the safety profile has been intensively monitored in the post-licensure setting by robust pharmacovigilance using both passive and active surveillance (3, 6). These studies, which collectively have included millions of subjects, provide no evidence whatsoever to support the speculation that HPV vaccines by virtue of their protein content, adjuvants or any other element within the formulation –could induce, trigger or exacerbate auto-immune disorders, thromboembolic events, demyelinating diseases or other chronic conditions.<br> The Global Advisory Committee on Vaccine Safety of the World Health Organisation has reviewed the safety data for HPV vaccines on several occasions http://www.who.int/vaccine_safety/committee/topics/hpv/en/ GACVS stated in 2014: “In summary, the GACVS continues to closely monitor the safety of HPV vaccines and, based on a careful examination of the available evidence, continues to affirm that its benefit-risk profile remains favorable. The Committee is concerned, however, by the claims of harm that are being raised on the basis of anecdotal observations and reports in the absence of biological or epidemiological substantiation. While the reporting of adverse events following immunization by the public and health care providers should be encouraged and remains the cornerstone of safety surveillance, their interpretation requires due diligence and great care. As stated before, allegations of harm from vaccination based on weak evidence can lead to real harm when, as a result, safe and effective vaccines cease to be used. To date, there is no scientific evidence that aluminium-containing vaccines cause harm, that the presence of aluminium at the injection site (the MMF “tattoo”) is related to any autoimmune syndrome, and that HPV DNA fragments are responsible for inflammation, cerebral vasculitis or other immune-mediated phenomena.” http://www.who.int/vaccine_safety/committee/topics/hpv/GACVS_Statement_HPV_12_Mar_2014.pdf Efficacy against vaccine type high grade cervical intraepithelial neoplasia CIN3 (the well-established precursor of cervical cancer(7)) has been demonstrated for the vaccines in the relevant RCTs (8-10). Cervical cancer cannot be used for ethical reasons as an end point in clinical trials (7). With regard to screening, contrary to the misleading comments by Dr. Lee, there is a large and authoritative body of evidence (including many RCTs) showing that any of the approved HPV tests is substantially more sensitive for detection of CIN2, CIN3, or cancer than cytology (11). The figure he quotes of 58% sensitivity is the result of a controversial application of “verification bias adjustment” in detection of CIN2 or worse, in a single trial. Large systematic reviews have consistently reported much higher sensitivity of HPV testing compared to cytology (12). The sensitivity of HPV testing is not at issue; rather specificity is a concern. As we emphasized in the article, HPV testing does require a secondary triage method to identify persistent infection and cancer precursors that require treatment, because HPV is very common and most infections “clear”. There are several choice of triage strategy prior to treatment; HPV typing and cytology or its analogues are most often proposed. Automated methods will soon be available. Carcinogenic human papillomavirus infections are a global public health problem, >80 % of the annual ≥530,000 cervical cancer cases occur in resource poor countries in which the disease is often incurable (13). Whatever preventive measures are adopted, evaluating the impact of interventions to control infection and disease requires a global perspective; from this perspective the promise of HPV vaccination and HPV testing are overwhelmingly supported by highly credible data. • Mark Schiffman • , John Doorbar • , Nicolas Wentzensen • , Silvia de Sanjosé • , Carole Fakhry • , Bradley J. Monk • , Margaret A. Stanley • & Silvia Franceschi  

1. Bachmann MF, Zinkernagel RM. The influence of virus structure on antibody responses and virus serotype formation. Immunology today. 1996;17(12):553-8.
2. Harro CD, Pang YY, Roden RB, Hildesheim A, Wang Z, Reynolds MJ, et al. Safety and immunogenicity trial in adult volunteers of a human papillomavirus 16 L1 virus-like particle vaccine. J Natl Cancer Inst. 2001;93(Feb 21. 4): 284-492.
3. Vichnin M, Bonanni P, Klein NP, Garland SM, Block SL, Kjaer SK, et al. An Overview of Quadrivalent Human Papillomavirus Vaccine Safety: 2006 to 2015. Pediatr Infect Dis J. 2015;34(9):983-91.
4. Moreira ED, Jr., Block SL, Ferris D, Giuliano AR, Iversen OE, Joura EA, et al. Safety Profile of the 9-Valent HPV Vaccine: A Combined Analysis of 7 Phase III Clinical Trials. Pediatrics. 2016.
5. Descamps D, Hardt K, Spiessens B, Izurieta P, Verstraeten T, Breuer T, et al. Safety of human papillomavirus (HPV)-16/18 AS04-adjuvanted vaccine for cervical cancer prevention: A pooled analysis of 11 clinical trials. Hum Vaccin. 2009;5(5).
6. Angelo MG, Zima J, Tavares Da Silva F, Baril L, Arellano F. Post-licensure safety surveillance for human papillomavirus-16/18-AS04-adjuvanted vaccine: more than 4 years of experience. Pharmacoepidemiol Drug Saf. 2014;23(5):456-65.
7. Pagliusi SR, Teresa Aguado M. Efficacy and other milestones for human papillomavirus vaccine introduction. Vaccine. 2004;23(Dec 16. 5):569-78.
8. Future II Study Group. Quadrivalent vaccine against human papillomavirus to prevent high-grade cervical lesions. The New England journal of medicine. 2007;356(19):1915-27.
9. Lehtinen M, Paavonen J, Wheeler CM, Jaisamrarn U, Garland SM, Castellsague X, et al. Overall efficacy of HPV-16/18 AS04-adjuvanted vaccine against grade 3 or greater cervical intraepithelial neoplasia: 4-year end-of-study analysis of the randomised, double-blind PATRICIA trial. Lancet Oncol. 2012;13(1):89-99.
10. Joura EA, Giuliano AR, Iversen OE, Bouchard C, Mao C, Mehlsen J, et al. A 9-valent HPV vaccine against infection and intraepithelial neoplasia in women. The New England journal of medicine. 2015;372(8):711-23.
11. Ronco G, Dillner J, Elfström KM, Tunesi S, Snijders PJ, Arbyn M, Kitchener H, Segnan N, Gilham C, Giorgi-Rossi P, Berkhof J, Peto J, Meijer CJ; International HPV screening working group.. Efficacy of HPV-based screening for prevention of invasive cervical cancer: follow-up of four European randomised controlled trials. Lancet. 2014 Feb 8;383(9916):524-32. Erratum in: Lancet. 2015 Oct 10;386(10002):1446.<br>
12. Arbyn M, Ronco G, Anttila A, Meijer CJLM, Poljak M, Ogilvie G et al. Evidence Regarding Human Papillomavirus Testing in Secondary Prevention of Cervical Cancer. Vaccine. 2012; 30 Suppl 5:F88-99.
13. Plummer M, de Martel C, Vignat J, Ferlay J, Bray F, Franceschi S. Global burden of cancers attributable to infections in 2012: a synthetic analysis. Lancet Glob Health. 2016 Sep;4(9):e609-16. doi: 10.1016/S2214-109X(16)30143-7.

On 2017 Jan 19, Sin Hang Lee commented:

None

On 2017 Apr 06, Randi Pechacek commented:

Holly Bik, new faculty addition to UC Riverside and 1st author of this paper, wrote a blog describing the background for this research on microBEnet. Read about it here

On 2016 Dec 08, NephJC - Nephrology Journal Club commented:

This commentary on CKD staging and Precision Medicine was discussed on December 6th and 7th in the open online nephrology journal club, #NephJC, on twitter. Introductory comments written by Tom Oates and Kevin Fowler are available at the NephJC website here and here. The journal also kindly made the commentary free to access for this month. The discussion was quite detailed, with over 100 participants, including nephrologists, fellows and patients as well as author Jonathan Himmelfarb. The highlights of the tweetchat were:

• The authors have written a richly referenced, thoughtful and though-provoking commentary, which is a must-read for anyone interested in gaining a perspective in this area.

• The advent of eGFR reporting and CKD staging have resulted in many advances, including improved recognition and diagnosis, planning therapy, epidemiological estimates and public messaging. Nonetheless, the categorical staging system is not perfect (groups together diverse diseases) though opinion was sharply divided on the issue of CKD in the elderly being a true phenomenon versus an ageing effect.

• The section on precision medicine in kidney disease was also quite nuanced, with a lot of optimism and ideas discussed, such as new trial designs and personalized care.

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 2016 Dec 07, Katherine S Button commented:

Thanks Erick H Turner this reference and the others you provide are very helpful.

On 2016 Dec 03, Erick H Turner commented:

Please see... Turner EH. Publication bias, with a focus on psychiatry: causes and solutions. CNS Drugs 2013;27:457–68. doi:10.1007/s40263-013-0067-9 ...which cited earlier proposals along this line. My article proposed a related approach, but it differs in that the subject of the review is the study protocol, which is written before--not after--the study results are known.

On 2016 Dec 03, Lydia Maniatis commented:

Could the authors please provide a citation(s) for the following introductory comments?

"Over much of the dynamic range of human cone-mediated vision, light adaptation obeys Weber's law. Raw light intensity is transformed into a neural response that is proportional to contrast...where ϕW is the physiological response to a flash of intensity ΔI, and I is the light level to which the system is preadapted. Put another way, the cone visual system takes the physical flash intensity ΔI as input and applies to this input the multiplicative Weber gain factor to produce the neural response (Equation 1). This transformation begins in the cones themselves and is well suited to support color constancy when the illumination level varies."

Does this statement, assuming relevant though missing citations, apply in general, or is it a description of results collected under very narrow and special conditions, and if so, what are they?

As in many psychophysical studies, a very small number of subjects included an author. In experiments 1 and 2, one of two observers was an author. Why isn't this considered a problem with respect to bias?

Also similar to many other psychophysical papers, the "hypothesis" being tested is the tip of a bundle of casually-made, rather complex, rather vague, undefended assumptions which the experiments do not, in fact, test. For example:

1. "As our working hypothesis, we assume that the observer’s signal-to-noise ratio for discriminating trials in which an adapting field is presented alone from trials with a superimposed small, brief flash is [equation].

2. "The assumption that visual sensitivity is limited by such multiplied Poisson noise has been previously proposed (Reeves, Wu, & Schirillo, 1998) as an explanation of why visual sensitivity is less than would be expected if threshold was limited by the photon fluctuations from the adapting field (Denton & Pirenne, 1954; Graham & Hood, 1992)."

I note that the mere fact that Reeves, Wu and Schirillo proposed an assumption does not amount to an argument.

Roughly, what researchers are doing is similar to this:

Let's assume that how quickly a substance burns is a function of the amount of (assumed) phlogiston (possessing a number of assumed characteristics) it contains. So I burn substance "a", and I burn substance "b", and conclude that, since the former burns faster than the latter, it also contains more assumed phlogiston having the assumed characteristics. The phlogiston assumptions (and the authors here bundle together layers of assumptions) get a free ride, and they shouldn't. The title of this paper is tantamount to "Substance "a" contains more phlogiston than substance "b." It can only be valid if all of the underlying assumptions based on which the data was interpreted are valid, and that's unknown at best. We can even make the predictions a little more specific, and thus appear to test among competing models (which I think is actually what is going on here). For example, one model might predict a faster burn function than another, allowing us to "decide" between two different phlogiston models neither of which will actually have been tested. (Helping to avoid this type of fruitless diversion is what Popper's epistemology was designed to accomplish.)

Also, it seems odd for the authors to be testing a tentative theory from the 1940's, which was clearly premature and inadequate, and apparently choosing to test a less-informed version of it:

"In presenting the theory in this way, we have adhered more closely to the original presentation of Rose—an engineer who was interested in both biological and machine vision—than to that of de Vries, who was a physiologist and who introduced supplementary assumptions about the spatiotemporal summation parameters in human rod vision. We adopt Rose’s approach because the relevant neural parameters are still not well understood, and we wish to clearly distinguish between the absolute limits on threshold set by physics and the still incompletely understood neural mechanisms."

In addition, the authors seem to have adopted the attitude that various selected contents of perception can be directly correlated with the activity of cells at any chosen level of the visual system (even when the neural parameters are still not well understood!), and that the rest of the activity leading to the conscious percept can be ignored, and that percepts that can't be directly correlated with the activity of the chosen cells can be ignored, via casual assumptions such as N. Graham's "the brain becomes transparent" under certain conditions.

On 2017 Mar 10, Jose M. Moran commented:

I think that authors have not correctly addressed the analysis of their results. They have correctly performed intragroup comparisons, but fail to analyze the between groups results. At the final time point, there are no statistically significant differences P=0.366 for LSS and P=0.641 for IDATE-state, between G1 (massasage+rest) and G2 (massage+reiki) so no effect of reiki intervention was detected at all in this study. Again the size effects measured also do not differ between G1 and G2 for both LSS IDATE-STATE, authors have failed in the analysis of the CI95% for the calculated Cohen’s d that are completely overlapped. Obviosly both G1 and G2 significantly differ from the G3 group (no intervention) but both in the same amount.

On 2017 Aug 12, Nikhil Meena commented:

In our experience, Patients who don't appear to be candidates for a pleuroscopy may also be poor candidates for sclerosant therpay. http://journals.sagepub.com/doi/10.1177/1753465817721146

Abstract BACKGROUND: Indwelling tunneled pleural catheters (TPCs) are increasingly being used to treat recurrent pleural effusions. There is also an increased interest in early pleurodesis in order to prevent infectious complications. We studied the time to removal and other outcomes for all the TPCs placed at our institution. METHODS: After institutional review board approval, records of patients who had had a TPC placed between July 2009 and June 2016 were reviewed; the catheters were placed in an endoscopy suite or during pleuroscopy with or without a sclerosant. The catheters were drained daily or less frequently and were removed after three drainages of less than 50 ml. RESULTS: During the study period 193 TPCs were placed. Of these 45 (23%) were placed for benign diseases. The commonest malignancy was lung cancer 70 (36%). Drainage 2-3 times a week without a sclerosant ( n = 100) lead to pleurodesis at 57 ± 78 days, while daily drainage after TPC + pleuroscopy + talc ( n = 41) achieved the same result in 14 ± 8 days ( p < 0.001). TPC + talc + daily protocol achieved pleurodesis in 19 ± 7 days, TPC + rapid protocol achieved the same result in 28 ± 19 days ( p = 0.013). The TPCs + sclerosant had an odds ratio of 6.01 (95% confidence interval: 2.1-17.2) of having a complication versus TPC without sclerosant. CONCLUSIONS: It is clear that TPCs when placed with a sclerosant had a significantly shorter dwell time; However, they were associated with higher odds of complications. One must be aware of these possibilities when offering what is essentially a palliative therapy.

On 2017 Sep 08, Koene Van Dijk commented:

CAUTION: Something went terribly wrong during the peer-review process of this manuscript

The study by Molfino et al., (2017, 10.1002/jcsm.12156) included extremely small samples (n=9 and n=4 for patient groups and n=2 for the control group).

According to the text of the manuscript, BOLD fMRI data that was collected did not undergo any pre-processing to remove noise but raw values from a hand-drawn region of interest were exported from the Siemens scanner console and imported into Microsoft Excel.

No statistical analysis was applied to measure contrast between different conditions, but raw BOLD values before (during time frames 0-50), during (time frames 51-261), and after (single time frame 262) nutritional ingestion values were calculated/extracted.

I recommend the authors and readers who want to learn more about BOLD fMRI data collection and analyses to read "Handbook of Functional MRI Data Analysis" by Poldrack, Mumford, and Nichols.

DISCLAIMER: I am an employee of Pfizer. The statements or opinions expressed on this site are my own and do not necessarily represent those of Pfizer.

On 2016 Dec 01, Ricardo Pujol-Borrell commented:

This confirms the rare but interesting nature of autoimmune hypophysitis

On 2017 Jan 26, Janet Kern commented:

Bonferroni is a 'multiple comparisons adjustment' for reducing the risk of false-positive findings when engaging in statistical 'fishing expeditions' among many unrelated associations. It is appropriate only when any of the following are true: 1. those associations are equally important, likely, and expected to be zero (absent) based on external (a priori) considerations; 2. the cost of any false negative is minor compared to the cost of any false positive; and 3. the associations are independent (unrelated) to one another. In return for the reduce risk of false positives, multiple comparison adjustments, like Bonferroni, dramatically increase the risk of missing real associations (false negatives). So, even if there were no other objections, Bonferroni as used by the authors (with N = 8) is simply erroneous. Using Bonferroni in this study was wrong for several other reasons: First, the authors specifically wanted to test if influenza vaccination during pregnancy was a risk factor for ASD—this was not a 'fishing expedition" as assumed by Bonferroni (violating '1' above). Second, the overall association of influenza vaccination anytime during pregnancy depends completely on the associations within each trimester, so violates the Bonferroni assumption of independence (violates '3' above). Third, the first trimester is expected to be the period of greatest vulnerability for the developing fetus, and so is a pre-specified hypothesis. (In other words, before the study, the stakeholders expected (a priori) an association, which also violates '1') Finally, we need to be confident that vaccines are safe: the costs of wrongly concluding that the influenza vaccine is safe rivals the costs of wrongly concluding that it causes harm, which violates the Bonferroni assumption ('2') that wrongly concluding harm is more costly than wrongly concluding safety.

On 2016 Nov 30, Lydia Maniatis commented:

Do you know what "p-hacking" means? I think that's what you're labelling as "data-driven." Are you aware that there have been six news reports amplifying the uncorroborated claims in your title? Sorry, but your title should have been, "We collected a lot of data."

On 2016 Nov 30, Antoine Coutrot commented:

Dear Lydia,

thank you for highlighting our limitation section, it is indeed quite important. You are absolutely right, our method is too confounded to allow us to draw any general conclusion. As are all experiments in cognitive science. They are all limited by the sample size, by the participant profile, by the task... But we try and do our best. For instance we collected 400+ participants from 58 nationalities, more than any eye-tracking experiment ever published. The main points of the paper are 1- gaze contains a wealth of information about the observer 2- with a big and diverse eye database it is possible to capture in a data-driven fashion what demographics explain different gaze patterns. Here, it happens to be the gender, hence the title.

On 2016 Nov 29, Lydia Maniatis commented:

Anyone familiar with the vision science literature should know by now that the best place to start reading a published paper is the section at the tail end titled “Limitations of the study.” This is where we can see whether the titular claims have any connection to what the study is actually entitled to report in terms of findings.

Compare, for example, the title of this study with its “limitations” section, quoted below in full (caps mine):

“The authors would like to make clear that THIS STUDY DOES NOT DEMONSTRATE THAT GENDER IS THE VARIABLE THAT MOST INFLUENCES GAZE PATTERNS DURING FACE EXPLORATION in general. [i.e. our method is too confounded to allow us to draw any such conclusion in principle].Many aspects of the experimental design might have influenced the results presented in this paper. The actors we used were all Caucasian between 20 and 40 years old with a neutral expression and did not speak—all factors that could have influenced observers' strategies (Coutrot & Guyader, 2014; Schurgin et al., 2014; Wheeler et al., 2011). Even the initial gaze position has been shown to have a significant impact on the following scanpaths (Arizpe et al., 2012; Arizpe et al., 2015). In particular, the task given to the participants—rating the level of comfort they felt with the actor's duration of direct gaze—would certainly bias participants' attention toward actors' eyes. One of the first eye-tracking experiments in history suggested that gaze patterns are strongly modulated by different task demands (Yarbus, 1965). This result has since been replicated and extended: More recent studies showed that the task at hand can even be inferred using gaze-based classifiers (Boisvert & Bruce, 2016; Borji & Itti, 2014; Haji-Abolhassani & Clark, 2014; Kanan et al., 2015). Here, gender appears to be the variable that produces the strongest differences between participants. But one could legitimately hypothesize that if the task had been to determine the emotion displayed by the actors' face, the culture of the observer could have played a more important role as it has been shown that the way we perceive facial expression is not universal (Jack, Blais, Scheepers, Schyns, & Caldara, 2009). Considering the above, the key message of this paper is that our method allows capturing systematic differences between groups of observers in a data-driven fashion.”

In other words, this is not a research paper, but a preliminary application of a method that might be useful for a research study. As far as the reported results go, it is an exercise in p-hacking. The title is purely cosmetic. As such it seems to have been rather effective, insofar as the article has already been the subject of six news stories, including reports in the Daily Mail and Le Monde.

On 2017 Mar 11, Christopher Southan commented:

While cogently reported and as Open Access, the Journal has allowed the publication of an irreproducible study. This is because of the non-disclosure of the key inhibitor structure, DCC-3014 from Deciphera (it might be exemplified in WO2014145023, or 025 or 029)

On 2017 Jan 05, Yuwei Fan commented:

To analyze Zr using EDS, the specimen should not be sputter coated with gold. Result in Fig. 7 seems to be questionable.

On 2016 Dec 02, Alessandro Rasman commented:

The problem in this study comes in using a percentage for veins rather than an absolute area as a measure of physiological flow problems in veins. Please read this article (http://www.pagepressjournals.org/index.php/vl/article/view/5012) and Figure 3.

On 2016 Nov 30, Monica Green commented:

It is useful for Pařízek and colleagues to have presented this hypothetical scenario of an alleged Caesarean section. It was surprising, however, that the study did not engage with the other published literature on the medieval history of C-section (a bibliography is available here: https://www.academia.edu/30089387/Bibliography_on_Caesarean_Section_in_the_Middle_Ages). There is also considerable literature on the history of surgery in medieval Europe and the history of anesthesia.

What is puzzling about this study is that it is nothing but a hypothetical scenario. The authors have found no testimony contemporary with Beatrice herself to confirm that she had any complications at all with the birth, let alone that it ended in a C-section. The only hint they have found that anything was amiss is her (or her scribe's) use of the phrase salva incolumitate in referring to herself after the birth. Incolumis (and derivative forms) is not a common word in medieval medical texts, but it is not at all rare in diplomatic documents. In my searches (DuCange's Glossarium, http://www.uni-mannheim.de/mateo/camenaref/ducange.html; the Epistolae collection of medieval women's letters: https://epistolae.ccnmtl.columbia.edu/), the phrase comes up commonly simply to confirm one's general health and fitness for office. In other words, there is nothing at all unusual here. Given that obstetrical mishaps were common in the Middle Ages (Green MH, 2008), the principle of lex parsimoniae would have asked that analysis be given first to other complications. Given Beatrice's age at the time of the birth (19), obstetric fistula would likely be high on that list.

It is a separate question why a legend surrounding Wenceslaus' birth arose, which this study has traced back no further than the 15th century, nearly 100 years after the birth itself. Stories of Caesar were very popular in royal circles at that time, and his birth (by C-section, allegedly, because of a medieval misunderstanding of classical sources) was often depicted in quite elaborately decorated manuscripts. A more interesting question, therefore, is why the legend arose, and why the vernacular histories of the Caesars might have been so influential in this imaginary.

Finally, it may be important for readers of this post to note that most work in the history of medicine is never registered in the PubMed database. Most historians publish in Humanities venues, and those are not indexed here. So please remember to look beyond PubMed if you are researching historical questions.

On 2017 Dec 19, Stuart RAY commented:

Not noted on this PubMed entry (yet, perhaps), this paper has been retracted. Of particular note, the retraction statement makes an excellent case for the authors' dedication to data sharing - it was reanalysis of the raw data by another group of scientists that revealed an unexpected finding. Without data sharing it would have been very difficult to discover the problem of mixed species in the sample. Kudos to the authors, and data sharing for reliable science!

On 2016 Dec 08, NephJC - Nephrology Journal Club commented:

This trial on early steroid tapering was discussed on November 29th and 30th 2016 in the open online nephrology journal club, #NephJC, on twitter. Introductory comments written by Hector Madariaga and Kevin Fowler are available at the NephJC website here and here.

The discussion was quite detailed, with over 60 participants, including general and transplant nephrologists, fellows and patients. The highlights of the tweetchat were:

• The authors should be commended for designing and conducting this important trial, with funding received from the industry.

• The trial results generated a lot of discussion, though it was thought to be underpowered for the outcome of biopsy proven acute rejection, given the small difference observed (9.9% in ATG versus 10.6 to 11.2% in basiliximab arms) relative to the generous sample size assumptions (6.7and 17% respectively). The high rate of new onset diabetes observed overall (compared to lower rates in other trials such as SYMPHONY) were explained on the basis of explicit evaluation on the basis of glucose tolerance tests.

• Overall, the trial did not change any opinions amongst the discussants: practitioners favoring steroid-free regimens were comforted with these results, but others would like to see stronger data with long term graft outcomes before embracing steroid-free regimens.

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 Jul 31, Robin P Clarke commented:

Nutrient deficiencies being factors in autism causation was predicted by the antiinnatia theory of autism (Clarke, 1993; Clarke, 2016), which stated that autism is caused by a high level of "antiinnatia factors" (factors tending to cause a sort of "general" reduction of gene-expression).

It was stated therein that "Gene-expression depends on processes that have many possibilities for malfunction, with many common factors underlying (for instance) all transcription from DNA, all being dependent on, for example, supply of nutrients....".<br> And that thus the autism-causing antiinnatia would tend to result from nutrient deficiencies (though of course nutrient deficits would also produce their own specific symptoms such as bone problems in respect of vit D).

The extent to which supplementation later in life can reverse the effects of deficiency in earlier developmental periods would depend on to what extent irreversible effects have been caused, such as perhaps neurons not migrating in neurotypical ways, or learning processes delayed too long.

Future studies should perhaps look for the possibility that the supplementation has more effect on younger children and less (or no) effect on older ones. It would further be expected that the improvements would be relatively permanent rather than ceasing on discontinuation of the supplementation.

Clarke RP (1993) A theory of general impairment of gene-expression manifesting as autism. Personality and Individual Differences 14,465-482.

Clarke RP (2016) (Updated presentation of preceding) - (PDF-file:) A theory of evolution-biased reduction of gene-expression manifesting as autism.

On 2016 Nov 21, Donald Forsdyke commented:

THE RNA WORLD AND DARRYL REANNEY

The title of historian Neeraja Sankaran's paper in a "special historical issue" of the Journal of Molecular Evolution implies that the RNA world idea was formulated 30 years ago (i.e. 1986) by a single author, Walter Gilbert (1). Yet the paper traces the story to authors who wrote at earlier times. Missing from the author list is Darryl Reanney who, like Gilbert, documented a "genes in pieces" hypothesis in February 1978 and went on to explore the RNA world idea with the imperative that error-correcting mechanisms must have evolved at a very early stage (2). Much of Reanney's work is now supported (3).

However, Sankaran cites the video of a US National Library of Medicine meeting organized by historian Nathaniel Comfort on 17th March 2016 (4). Here W. F. Doolittle, who had consistently cited Reanney, discusses the evolutionary speculation triggered by the discovery of introns in 1977, declaring that "several things came together at that time," things that "a guy named Darryl Reanney had been articulating before that." Furthermore, "it occurred to several of us simultaneously and to Darryl Reanney a bit before – before me anyway – that you could just recast the whole theory in terms of the RNA world."

Gilbert himself thought that "most molecular biologists did not seriously read the evolution literature; probably still don’t." Indeed, contemporary molecular biologists writing on "the origin of the RNA world," do not mention Reanney (5). Thus, we look to historians to put the record straight.

1.Sankaran N (2016) The RNA world at thirty: a look back with its author. J Mol Evol DOI 10.1007/s00239-016-9767-3 Sankaran N, 2016

2.Reanney DC (1987) Genetic error and genome design. Cold Spring Harb Symp Quant Biol 52:751-757

3.Forsdyke DR (2013) Introns first. Biological Theory 7:196-203 Paper here

4.Comfort N (2016) The origins of the RNA world. Library of Congress Webcast. NLM Webcast

5.Robertson MP, Joyce GF (2012) The origins of the RNA world. Cold Spring Harb Perspect Biol 4:a003608. Robertson MP, 2012

On 2016 Nov 21, Erik Shapiro commented:

Interesting work! It may be a subtle detail, but did you use iron pentacarbonyl or iron acac as the starting material? In the list of chemicals, you say iron pentacarbonyl, and in the methods you say iron acac. It is somewhat important because the synthesis of iron oxide using the two different starting materials is often different; one being a hot-injection method (pentacarbonyl) the other being what you described (iron acac).

On 2017 May 11, Jean-Pierre Bayley commented:

Should we screen carriers of maternally inherited SDHD mutations?

Jean-Pierre Bayley (1), Jeroen C Jansen (2), Eleonora P M Corssmit (3) and Frederik J Hes (4) 1. Department of Human Genetics, 2. Department of Otorhinolaryngology, 3. Department of Endocrinology and Metabolic Diseases, 4. Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands

We wish to comment on the above paper by Burnichon and colleagues: Burnichon N, et al. Risk assessment of maternally inherited SDHD paraganglioma and phaeochromocytoma. J Med Genet. 2017; 54:125-133. 3

In this paper a prospective study is presented that identified and described development of pheochromocytoma in a carrier of an SDHD mutation. Although at first sight not an uncommon occurrence in carriers of these mutations, this case is unusual because the mutation was inherited via the maternal line. This is now only the third reported case of confirmed phaeochromocytoma development following maternal transmission of an SDHD mutation. (1-3) The patient in question was identified amongst a cohort of 20 maternal mutation carriers who underwent imaging surveillance. Based on the identification of one patient in this cohort (5%), the authors make recommendations for the clinical care of carriers of a maternally inherited SDHD mutation. They advise targeted familial genetic testing from the age of 18 in families with SDHD mutations, and that identified carriers undergo imaging and biochemical workup to detect asymptomatic tumours. If the first workup is negative, the authors suggest that patients be informed about paraganglioma-phaeochromocytoma (PPGL) symptoms and recommend an annual clinical examination and blood pressure measurement, with a new workup indicated in case of symptoms suggestive of PPGL. Although this paper is a meaningful contribution to the literature, we are concerned that the authors base their subsequent clinical recommendations on a relatively small cohort. In a recent study, we described one confirmed case of maternal transmission and concluded that “we consider the increase in risk represented by these reports to be negligible.” (2)

Two reasons underlie this statement. Firstly, the somatic rearrangements underlying the maternal cases identified to date are far more complex (loss of the paternal wild-type SDHD allele by mitotic recombination, followed by loss of the recombined paternal chromosome containing the paternal 11q23 region and the maternal 11p15 region) than the molecular events seen in paternal cases (loss of whole chromosome 11). Secondly, our conclusions were based, implicitly, on many previous studies at our centre over the past three decades in which we described various aspects of the large SDHD cohort collected by us over that period. Genetic aspects of this cohort, and 601 patients with paternally transmitted SDHD mutations, were described by Hensen and co-workers in 2012. (4) As all previous studies suggest that mutations are equally transmissible via the paternal or maternal line, our identification of a single maternal case amongst this cohort suggests that the penetrance of maternally transmitted mutations is very low. Using the calculation employed by Burnichon and colleagues and assuming that at least 600 maternal mutation carriers are alive in the Netherlands, we arrive at an estimate of 0.17% (1/601 = 0.17%), rather than their figure of 5%. In addition to our own cohort, 1000’s of SDHD mutation carriers have been identified world-wide. Assuming that 1 in 20 maternally transmitted mutations result in tumours, many more maternally inherited cases would have come to our attention, even without surveillance.

In our opinion the question of management of maternally inherited SDHD mutations comes down to a risk-benefit analysis. The most obvious implication of the recommendations made by Burnichon and colleagues in our patient population would be the institution of surveillance, with all the attendant practical, financial and psychological burdens for 600 carriers of maternally inherited SDHD mutations in order to identify a single case. Furthermore, SDHD-associated PPGL mortality rates and survival in a Dutch cohort of SDHD variant carriers was not substantially increased compared with the general population. (5) In practice, carriers of maternally inherited SDHD mutations at our centre are not advised to undergo surveillance. Instead, we reassure them that their risk of developing PPGL is exceptionally low (described three times worldwide), but that they should be aware, more so than the general population, of symptoms that are suggestive of paraganglioma or phaeochromocytoma. Many families have been in our care for over 25 years and in that time we have found no evidence to suggest that this policy should be revised.

NB. A version of this comment has been posted on the Journal of Medical Genetics website and has been commented on in turn by Burnichon and colleagues.

References

1.Yeap PM, Tobias ES, Mavraki E, Fletcher A, Bradshaw N, Freel EM, Cooke A, Murday VA, Davidson HR, Perry CG, Lindsay RS. Molecular analysis of pheochromocytoma after maternal transmission of SDHD mutation elucidates mechanism of parent-of-origin effect. J Clin Endocrinol Metab 2011;96:E2009-E2013.

2.Bayley JP, Oldenburg RA, Nuk J, Hoekstra AS, van der Meer CA, Korpershoek E, McGillivray B, Corssmit EP, Dinjens WN, de Krijger RR, Devilee P, Jansen JC, Hes FJ. Paraganglioma and pheochromocytoma upon maternal transmission of SDHD mutations. BMC Med Genet 2014;15:111.

3.Burnichon N, Mazzella JM, Drui D, Amar L, Bertherat J, Coupier I, Delemer B, Guilhem I, Herman P, Kerlan V, Tabarin A, Wion N, Lahlou-Laforet K, Favier J, Gimenez-Roqueplo AP. Risk assessment of maternally inherited SDHD paraganglioma and phaeochromocytoma. J Med Genet 2017;54:125-33.

4.Hensen EF, van DN, Jansen JC, Corssmit EP, Tops CM, Romijn JA, Vriends AH, Van Der Mey AG, Cornelisse CJ, Devilee P, Bayley JP. High prevalence of founder mutations of the succinate dehydrogenase genes in the Netherlands. Clin Genet 2012;81:284-8.

5.van Hulsteijn LT, Heesterman B, Jansen JC, Bayley JP, Hes FJ, Corssmit EP, Dekkers OM. No evidence for increased mortality in SDHD variant carriers compared with the general population. Eur J Hum Genet 2015;23:1713-6.

On 2017 Apr 18, Darko Lavrencic commented:

I believe that implantable systems for continuous liquorpheresis and CSF replacement could be successfully used also for intracranial hypotension-hypovolemia syndrome as it could be caused by decreased CSF formation. See: http://www.med-lavrencic.si/research/correspondence/

On date unavailable, commented:

None

On 2017 Aug 01, Daniel Quintana commented:

We thank Dr. Grossman for his comments on our manuscript. We are cognisant of the study’s limitations, which we highlighted in our original manuscript. Despite these limitations, we believe our conclusions are still valid but also understand that Dr. Grossman may not agree with our interpretation.

We will now address Dr. Grossman’s two comments in turn, which we have reprinted for clarity:

• Comment 1 from Dr. Grossman: The authors report respiration frequency as the peak frequency in a band range between 0.15-0.40 Hz. Resting respiration rate (i.e. frequency), however, is rarely a constant phenomenon for most people within a resting period of several minutes: some breaths are longer, some are shorter, and the peak frequency does not necessarily reflect average breathing rate; in fact, there are very likely to be different peaks, and only the highest peak would have been used to estimate (or misestimate) average respiratory frequency. Spectral frequency analysis, therefore, is a highly imprecise method to calculate mean breathing frequency (perhaps, the difference in relations found between mentally ill vs. healthy people were merely due to increased variability of respiratory frequency among the ill individuals; see Fig. 1F). In any case, this may be be sufficient to disqualify the main conclusions of the study.

Response: We recognize that spectral frequency may not be an optimal method to calculate mean respiration frequency given the intraindividual variation of respiration rate. However, Levene's Test of Equality of Variances shows that the variances in the clinical and healthy groups are not significantly different [F(1,202) = 1.6, p = 0.21], which suggests that we cannot discard our null hypothesis that the group variances are equal. Thus, variability in mean respiration rates between the groups are unlikely to have confounded our results.

• Comment 2 from Dr. Grossman: However, there is may be even a more serious problem that invalidates the conclusions of this investigation. As already mentioned, the authors examined respiration frequencies only between 0.15-0.40 Hz; this corresponds to a range between 9 and 24 breaths/minute. Already in 1992, we demonstrated among a group of healthy participants that a sizable proportion of participants manifest substantial proportions of resting breathing cycles below 9 cycles per minute: among 16 healthy individuals carefully assessed for respiration rate during a 10-minute resting period, we found that half of the participants showed 1/5 of their total breathing cycles to be slower than 9 cycles/minute (cpm); over 60% of participants showed >10% of their cycles to be slower than 9 cpm (also very likely thqat a substantial proportion of breaths occurred beyond 24 cpm). Thus, accurate estimation of mean resting respiration frequency is also seriously compromised by the insufficient range of frequencies included in the analysis. See Grossman (1992, Fig. 5): Grossman, P. Biological Psychology 34 (1992) 131 -161

Response: To confirm that mean respiration the frequency was not missed or misattributed to non-respiratory frequencies, we re-analysed the data including participants that we originally excluded as they fell outside the 0.15-0.4 Hz range. In total, 2 participants (both from the patient group) had a mean respiratory frequency < 0.15Hz and 4 participants (3 from the patient group and 1 from the healthy control group) had a mean respiratory frequency > 0.4Hz. We also re-analysed absolute high frequency HRV and adjusted the frequency bands accordingly (0.1Hz – 0.4Hz for the 2 participants with a lower than average respiratory rate and, 0.15Hz-0.5Hz for the 4 participants with a higher than average respiratory rate).

We found that including these participants did not change the overall conclusions of the study. While we reported an estimated correlation (p) of −0.29 between HF-HRV and respiration in the patient group [95% CI (−0.53, −0.03)], our updated analysis demonstrated a slightly stronger estimated association -0.47 [95% CI (−0.66, −0.26)]. For the healthy controls, we originally reported an estimated correlation (p) of −0.04 between HF-HRV and respiration in the patient group [95% CI (−0.21, 0.12)]. Our updated analyses demonstrated a close to equivalent estimated association of -0.04 [95% CI (−0.20, −0.12)]. We also originally reported that computing the posterior difference of p between these two tests revealed a 94.1% probability that p was more negative in the clinical group compared to the control group. Running this analysis modestly increased this probability to 99.7%.

Daniel S. Quintana (on behalf of study co-authors)

On 2017 Apr 25, Paul Grossman commented:

Quintana et al. (2016) suggest that individual difference in respiration rate is only correlated with high-frequency heart-rate variability (HF-HRV), i.e. respiratory sinus arrhythmia (RSA) among seriously mentally ill people, but not among healthy individuals. The data presented has several methodological problems that seem very likely to severely compromise the authors' conclusions:

1. The authors report respiration frequency as the peak frequency in a band range between 0.15-0.40 Hz. Resting respiration rate (i.e. frequency), however, is rarely a constant phenomenon for most people within a resting period of several minutes: some breaths are longer, some are shorter, and the peak frequency does not necessarily reflect average breathing rate; in fact, there are very likely to be different peaks, and only the highest peak would have been used to estimate (or misestimate) average respiratory frequency. Spectral frequency analysis, therefore, is a highly imprecise method to calculate mean breathing frequency (perhaps, the difference in relations found between mentally ill vs. healthy people were merely due to increased variability of respiratory frequency among the ill individuals; see Fig. 1F). In any case, this may be be sufficient to disqualify the main conclusions of the study.

2. However, there is may be even a more serious problem that invalidates the conclusions of this investigation. As already mentioned, the authors examined respiration frequencies only between 0.15-0.40 Hz; this corresponds to a range between 9 and 24 breaths/minute. Already in 1992, we demonstrated among a group of healthy participants that a sizable proportion of participants manifest substantial proportions of resting breathing cycles below 9 cycles per minute: among 16 healthy individuals carefully assessed for respiration rate during a 10-minute resting period, we found that half of the participants showed 1/5 of their total breathing cycles to be slower than 9 cycles/minute (cpm); over 60% of participants showed >10% of their cycles to be slower than 9 cpm (also very likely thqat a substantial proportion of breaths occurred beyond 24 cpm). Thus, accurate estimation of mean resting respiration frequency is also seriously compromised by the insufficient range of frequencies included in the analysis. See Grossman (1992, Fig. 5): Grossman, P. Biological Psychology 34 (1992) 131 -161

https://www.researchgate.net/profile/Paul_Grossman2/publication/21689110_Respiratory_and_cardiac_rhythms_as_windows_to_central_and_autonomic_biobehavioral_regulation_Selection_of_window_frames_keeping_the_panes_clean_and_viewing_the_neural_topography/links/5731a22708ae6cca19a2d221/Respiratory-and-cardiac-rhythms-as-windows-to-central-and-autonomic-biobehavioral-regulation-Selection-of-window-frames-keeping-the-panes-clean-and-viewing-the-neural-topography.pdf?origin=publication_detail&ev=pub_int_prw_xdl&msrp=vu97U8y7CNd-ip3iK-qeQgkeqfmS6EwOYfT0BMazIWb4K9Weys1ta4uRS9rdGDRYEbtODvNOG_dr7MWpJIsjJrRkt_z8sTfSS4XmxvaEPMo.DabVyZLtsNb0XPkl_aRXgRYPgmzZVGFb4rchSD_o4vKn98sRTVYBXvo7RQOTYFxDbL7VMx9qNlfuFZvJNy8-9g.kd_GECHVk8wJ18QwWTmSdS3htJncx0qJ0Okn_km-wIHEkyXmPXbXIO-Rb_KUvz_72b5WrLKh7otlmZ6awszetQ.c3eR_WnqJ55XOex_Q4-EHpow-8RGg-Oi87AAPSljLLDtjYimkEgJ99Lu9lmclW4kkI11Jzzp2mkQ4pKenDt6BA

It is also unfortunate that the authors merely cited a single investigation that unusually showed no relation between individual differences in respiration frequency and RSA magnitude (i.e. Denver et al., 2007), but none of the many studies that have found correlations in the range of r's= 0.3-0.5; e.g. https://www.researchgate.net/publication/279615441_Respiratory_Sinus_Arrhythmia_and_Parasympathetic_Cardiac_Control_Some_Basic_Issues_Concerning_Quantification_Applications_and_Implications

http://journal.frontiersin.org/article/10.3389/fphys.2016.00356/Fülle

https://pdfs.semanticscholar.org/6e44/e75dd2061a43cc69a4354171540e8a98e6a5.pdf

The Denver et al. study, additionally, used the same methods inaccurately to calculate respiration rate.

Paul Grossman Pgrossman0@gmail.com

On 2017 Apr 24, Paul Grossman commented:

None

On 2017 Mar 15, KEVIN BLACK commented:

We proposed that "the most likely cause for the" excess prevalence of depression in PD was "that both syndromes arise from similar causes, with either appearing first in a given individual. ... [O]ne may reasonably search for such shared causative factors among the known risk factors for" either disease, "such as genes (probably plural), aging, chemical toxins, or psychologically stressful life events" (Black KJ, Pandya A. Depression in Parkinson disease. Pp. 199-237 in Gilliam F, Kanner AM, Sheline YI: Depression and Brain Dysfunction. New York: Taylor & Francis, 2006, at pp. 216-217).

Arabia and colleagues (2007) found that depressive and anxious disorders were much more likely in first-degree relatives of PD patients than of controls (doi: 10.1001/archpsyc.64.12.1385). One gene that may contribute to that finding is the serotonin transporter, discussed in the review cited above. Cagni et al here identify an additional gene that may also be a shared risk factor: the G/G phenotype of the Val66Met polymorphism of the BDNF gene.

Studies such as these may contribute useful information not only to the etiology of depression and anxiety but also to the etiology of Parkinson disease.

On 2016 Dec 04, Lydia Maniatis commented:

Let's say we ask the proverbial “man in the street” the following question: Do you think chickens will be better at discriminating between the colors of tiled food containers if the tiles are many or large, or if they are few or small?

I think that most, without too much thought, would answer the former. “More and bigger” of anything is generally more salient then “Fewer and smaller.” Would those who made correct guesses be licensed to claim that their pet theory about chicken vision had been corroborated? It should be obvious that predictable predictions do not constitute rigorous tests of any hypothesis. This is the type of hypothesis-testing Olsson et al (2017) engage in in this study.

Furthermore, the hypothesis that the authors are supposed to be testing doesn’t consist of a straightforward, coherent, intelligible set of assumptions, but of a hodgepodge of uncorroborated assumptions and models spanning over fifty years. The “success” of the authors’ simple experiment implies corroboration of all of these subsidiary models and assumptions. Obviously, the experiments are being tasked with far too much heavy-lifting, and the conclusions that hinge on them are not credible.

Here is a sampling of the assumptions and models that chickens greater sensitivity to “more and bigger” are presumed to corroborate:

The main hypothesis: “Chickens use spatial summation to maintain color discrimination in low light intensities.”

Supporting models/assumptions: “Color differences delta S in the unit of just-noticeable differences (JND) were calculated using the receptor noise limited (RNL) model (Vorobyev and Osorio, 1998) as….” I.e. the RNL model is assumed to be valid.

“Spectral sensitivities, R, were derived by fitting a template (Govardovskii, Fyhrquist, Reuter, Kuzmin, & Donne, 2000)…” I.e. the model template is assumed to be valid.

“We assumed the same standard deviation of noise for all cone types such that the Weber fraction for the L channel was 0.06, based on the color discrimination thresholds measured in a previous study (Olsson et al 2015)” Note that, according to a Pubmed Commons comment by the lead author, Olsson et al (2015) “figure out the equivalent Weber fraction which describe these limits. Whether that is actually caused by noise or not we can not say from our experiment..." Yet the main hypothesis of Olsson et al (2017) uncritically assumes a “noisy” process.

“The same simple model (SM) of calculating the absolute quantum catch as in a previous study (Olsson et al 2015)” Again, the authors cannot say that the results of that previous study were “actually caused by noise or not”, i.e that the “simple model” is actually modeling what they are claiming.

“We modeled increasing levels of spatial summation, assuming that absolute quantum catches….are summed linearly…” Should we even ask why?

“From ….cone densities in the dorso-temporal retina of chickens (Kram et al, 2010) we estimated the number of cones that viewed a single color tile of a stimulus.” This last assumption obviously doesn’t consider the fact of chicken eye movements, which would make the number of cones involved much larger. The idea of simple pooling is also problematic from the point of view that chickens do exhibit constancy under varying illumination, so in the context of sunshine and shadow, pooling across an illumination boundary would arguably produce unreliable estimates that would undermine constancy.

“We derived intensity thresholds by fitting a logistic psychometric function to the choice data of each experimental group of chickens and individual chickes using the Matlab toolbox palamedes (Prins & Kingdom, 2009).” We assume that Prins and Kingdom’s hypothesized quantitative link between choice and thresholds, as well as all of those authors’ underlying assumptions, e.g. that signal detection theory is an appropriate model for vision, are valid.

I would note, finally, that the authors’ current description of the findings of Olsson, Lind and Kelber (2015) differs significantly from those implied by the title of the latter publication (“Bird color vision: behavioral thresholds reveal receptor noise”). As mentioned above, the lead author of that study has acknowledged that the title goes further than was licensed by experiment. Here, the Olsson et al (2015) study is described as having shown that “the intensity threshold for color discrimination in chickens depends on the chromatic contrast between the stimuli and on stimulus brightness.” This result, i.e. that “higher contrast, brighter = more salient”, is, if anything, even more predictable than the prediction of Olson et al (2017).

On 2017 Nov 01, Trevor Bell commented:

The source code of the pipeline described in this paper is now available online at the following address:

https://github.com/DrTrevorBell/CuratedGenBank

On 2017 Jul 25, Trevor Bell commented:

Multiple sequence alignments containing only full-length sequences, for each genotype, are now also available for download from the alignments page. These sequences are a subset of the alignments already available.

On 2017 Jan 26, Trevor Bell commented:

A comma character has inadvertantly been added to the query provided under the "GenBank download" section during post-production of this article. The comma in the number "99,999" should be deleted, so that the number reads "99999".

On 2017 Jan 26, Trevor Bell commented:

The authors would like to clarify a point made in the abstract. Although multiple sequence alignments of HBV are publicly available, as far as we are aware, ours is the first to include both full length and subgenomic fragments of HBV in the same alignment.

On 2017 Apr 08, Raha Pazoki commented:

Supplementary Table 6 of this article is supposed to provide GERA results for previously identified blood pressure loci. This table is however exactly the same as Supplementary Table 3 and does not include SNPs flagged as "P" for previously identified in Supplementary Table 4.

On 2016 Nov 14, David Mage commented:

The Sudden Infant Death Syndrome (SIDS) and other causes of human respiratory failures appear to be X-linked (PMID 27188625). OMIM shows human TASK-1 to be autosomal, that would imply if Task-1 is involved in SIDS that an interaction with an X-linkage might also be considered.

On 2016 Nov 14, Pavel Nesmiyanov commented:

What strain and what waas the exact procedure for the microbiological assessment? Disc diffusion method is not the most accurate method. Authors should have used standard strains and dilution method for MIC.

On 2016 Nov 20, Alessandro Rasman commented:

Bernhard HJ. Juurlink MD, Dario Alpini MD, Giampiero Avruscio MD, Miro Denislic MD, Attilio Guazzoni MD, Laura Mendozzi MD, Raffaello Pagani MD, Adnan Siddiqui MD, PierluigI Stimamiglio MD, Pierfrancesco Veroux MD snd Pietro Maria Bavera MD

We read with interest the consensus statement titled "The central vein sign and its clinical evaluation for the diagnosis of multiple sclerosis: a consensus statement from the North American Imaging in Multiple Sclerosis Cooperative" (1). We wonder why the authors haven't cited in the notes any paper of Dr. Paolo Zamboni from University of Ferrara, Italy. Particulary, his oldest paper titled "The big idea: iron-dependent inflammation in venous disease and proposed parallels in multiple sclerosis" published in November 2006 (2). In that paper he readily showed the histology of the CVS, and explicitly reported the possibility to image it by the means of MR, as well.

References: 1) Sati, Pascal, et al. "The central vein sign and its clinical evaluation for the diagnosis of multiple sclerosis: a consensus statement from the North American Imaging in Multiple Sclerosis Cooperative." Nature Reviews Neurology (2016). 2) Zamboni, Paolo. "The big idea: iron-dependent inflammation in venous disease and proposed parallels in multiple sclerosis." Journal of the Royal Society of Medicine 99.11 (2006): 589-593.

On 2017 May 13, Kiyoshi Ezawa commented:

None

On 2017 Apr 24, Kiyoshi Ezawa commented:

[Alert by the author]

The web-page (or XML) version of this Erratum (at the BMC Bioinformatics web-site: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1282-4) contained errors during two periods: one from its initial publication on Nov 10th, 2016 till around Nov 18th, 2016, and the other from around March 3rd, 2017 till the release of the latest version on April 7th, 2017. The latest version does not contain these errors.

In consequence, the Erratum at the PubMed Central web-page (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105235/) also contained the same errors, since its initial release till around April 13th, 2017, when it was updated.

(It should be noted that, since its initial publication, the PDF version of the Erratum has been nearly error-free, containing at most one relatively harmless error in Eq.(R4.6) before the correction.)

Therefore, if you visited the Erratum only around any of the aforementioned periods but did not download its PDF, I strongly urge you to re-visit the Erratum, and hopefully to download the PDF.

And I would be grateful if you could inform your colleagues of the release of the new version of this Erratum, so that these errors in its previous versions will be eradicated eventually.

Incidentally, most of the errors discussed in this Erratum apply only to the web-page (or XML) version of the original article (PMID: 27638547; DOI: 10.1186/s12859-016-1105-7).

There are only two exceptions: one is the error in Eq.(R5.4), and the other is the update on the reference information (reference [2] in the Erratum, or PMID: 27677569); they apply to both the XML and the PDF.

(In the proofreading process, I was allowed to proofread only the PDF but not the web-page version. Therefore, I had no control over those errors in the web-page that were not in the PDF.)

Kiyoshi Ezawa, Ph.D, the author of the Erratum (PMID: 27832741).

On 2017 Feb 24, Atanas G. Atanasov commented:

Excellent overview, I have featured it at: http://healthandscienceportal.blogspot.co.at/2017/02/ageing-neurodegeneration-and-brain.html

On 2016 Nov 24, Lydia Maniatis commented:

As should be evident from the corresponding PubPeer discussion, I have to disagree with all of Guy’s claims. I think logic and evidence are on my side. Not only is there not “considerable evidence that humans acquire knowledge of how depth cues work from experience,” the evidence and logic are all on the opposite side. The naïve use of the term “object” and reference to how objects change “as we approach or touch them and learn about how they change in size, aerial perspective, linear perspective etc” indicates a failure to understand the fundamental problem of perception, i.e. how the proximal stimulus, which does not consist objects of any size or shape, is metamorphosed into a shaped 3D percept. Perceiving 3D shape presupposes depth perception. As Gilchrist (2003) points out in a critical Nature review of Purves and Lotto’s book, “Why we see what we do:” “Infant habituation studies show that size and shape are perceived correctly on the first day of life. The baby regards a small nearby object and a distant larger object as different even when they make the same retinal image. But newborns can recognize an object placed at two different distances as the same object, despite the different retinal size, or the same rectangle placed at different slants. How can the newborn learn something so sophisticated in matter of hours?” Gilchrist also addresses the logical problems of the “learning” perspective (caps mine): “In the 18th C, George Berkeley argued that touch educates vision. However, this merely displaces the problem. Tactile stimulation is even more ambiguous than retinal stimulation, and the weight of the evidence show that vision educates touch, not vice versa. Purves and Lotto speak of what the ambiguous stimulus “turned out to signify in past experience.” But exactly how did it turn out thus? WHAT IS THE SOURCE OF FEEDBACK THAT RESOLVES THE AMBIGUITY?” “Learning” proponents consistently fail to acknowledge, let alone attempt to answer, this last question. As I point out on PubPeer, if touch helps us to learn to see, then the wide use of touchscreens by children should presumably compromise 3D perception, since the tactile feedback is presumably indicative of flatness at all times.

The confusion is evident in Guy’s reference to the “trusted cue – occlusion implying depth.” Again, there is a naïve use of the term “occlusion.” Obviously, the image observers see on the screen isn’t occluded, it’s just a pattern of colored points. With respect to both the screen and the retinal stimulation, there is no occlusion because there are no objects. Occlusion is a perceptual, not a physical, fact as far as the proximal stimulus is concerned. So the cue itself is an inferred construct intimately linked to object perception. So we’re forced to ask, what cued the cue…and so on, ad infinitum. Ultimately, we’re forced to go back to brass tacks, to tackle figure ground organization via general principles of organization. Even if we accepted that there could (somehow) be unambiguous cues, we would still have the problem that each retinal image is unique, so we would need a different cue - and thus an infinite number of cues- to handle all of the ambiguity. Which makes the use of “cues” redundant.

So the notion that “one might not need much to allow a self-organising system of cue to rapidly ‘boot-strap’itself into a robust system in which myriad sensory cues are integrated optimally” is clearly untenable if we try to actually work through what it implies. The concept of ‘cue recruitment’ throws up a lot of concerns only because even its provisional acceptance requires that we accept unacceptable assumptions.

On 2016 Nov 21, Guy M Wallis commented:

Lydia raises an important question. Surely we can't learn everything! We need something to hang our perceptual hat on to get the ball rolling. After all, in the experiments described in our paper, Ben and I relied on the presence of a trusted cue - occlusion implying depth - to allow the observer to harness the new cue which we imposed - arm movement. But where did knowledge of the trusted depth cue come from? Did we have to learn that too? Well there is considerable empirical evidence that humans do acquire knowledge of how depth cues work from experience. We observe objects as we approach or touch them and learn about how they change in size, aerial perspective, linear perspective etc. But it also seems likely that some cues have been acquired in phylogentic time due to their reliability and utility. The apparently in-built assumption that lighting in a scene comes from above and the left may be an example of this. In the end though, one might not need much to allow a self-organising system of cues to rapidly 'boot-strap' itself into a robust system in which myriad sensory cues are integrated optimally.

Lydia and my co-author, Benjamin Backus, have been engaged in a lively and informative exchange on PubPeer which I recommend to those interested in this debate. The concept of cue recruitment throws up a lot of concerns and queries.

https://pubpeer.com/publications/2622B45C885243AFCB5C604CB0638B

On 2016 Nov 12, Lydia Maniatis commented:

It occurs to me that the "cue recruitment theory" is susceptible to the problem of infinite regress. If percepts are by their nature ambiguous, and require "cues" to disambiguate, then aren't the cues, which are also perceptual articles, also in need of disambiguation? Don't we need to cue the cue? And so on....

On 2016 Nov 12, Lydia Maniatis commented:

Two (probably) final points regarding the authors' conclusion quoted below:

"In conclusion, the present study presents evidence that a voluntary action (arm movement) can influence visual perceptual processes. We suggest that this relationship may develop through an already functional link between motor behavior and the visual system (Cisek & Kalaska, 2010; Fagioli et al., 2007; Wohlschläger & Wohlschläger, 1998). Through the associative learning paradigm used here, this relationship can be modified to enable arbitrary relationships between limb movement and perceived motion of a perceptually ambiguous stimulus. "

First, most stimuli are not perceptually ambiguous (i.e. they are not bistable or multistable), so the relevance of this putative finding is questionable in practice, and would require much more development in theory.

Second, the claim that it is possible to construct "arbitrary relationships between limb movement and perceived motion of a perceptually ambiguous stimulus" is a radical behaviorist claim, of a type that has consistently been falsified both logically and empirically.

On 2016 Nov 12, Lydia Maniatis commented:

The degree of uncertainty incorporated into this study in the form of confounds means that the claims at the front end carry no weight.

Essentially, the authors apparently are employing a forced choice paradigm. (They don’t refer to it as such, but rather as a “dichotomous perceptual decision.” Their stimulus is bistable, unstable, briefly presented, temporally decaying and the response relies on memory as it occurs after the image has left the screen. Their training procedure likely produces expectations that may bias outcomes.

The highly unstable nature of the Necker cube, even in static form, is self-evident. I don’t know if this is mitigated by motion, but I doubt it. I would expect the uncertainty to be even greater when the square face of the figure isn’t in a vertical/horizontal orientation.

In their discussion, the authors address the possibility of response bias in their study: “Firestone and Scholl (in press)…include a section on action-based influences on perception. The authors argue that much of this literature is polluted with response bias and that suitable control studies have undermined many of the earlier findings.”

Wallis and Backus counter this possibility with a straw man. “If participants were trying to respond in a manner they thought we might expect, there is no reason why they would not have done so in the passive conditions…”

However, the question isn’t only whether participants were trying to meet investigator expectations, but whether they had developed expectations of their own based on the “training” procedures.

In the so-called passive training condition, an arrow, either congruent or incongruent, was associated with the rotation of a disambiguated Necker cube. However, in this condition observers have no incentive to pay attention to this peripheral form and its connection with the area of interest. In the active condition, in contrast, it is necessary attend the arrows and to act on them. This obligation to act on the arrows while observing the figure ensures that attention is paid to their connection with cube rotation.

The conceptual and methodological uncertainty is compounded by the fact that the authors themselves can’t explain (though they presumably expected it) the failure of the arrows alone to produce a perceptual bias. As with the previous issue, they dispense too casually with the problem:

“So why did the participants in the passive conditions show little or no cue recruitment? As mentioned in the Introduction, Orhan et al. (2010) have argued that there must be a mechanism for determining which cues can be combined to create a meaningful interpretation of the sensory array. In the context of this study it would appear that passive viewing of the rotating object and the contingent arrows, does not satisfy this mechanism's requirements. This is perhaps because the arrows are regarded as extrinsic to the stimulus and hence unfavored for recruitment (Jain et al., 2014).

This is as weak and evasive an argument as could possibly be made in a scientific paper. The authors as why the arrow “cue” itself didn’t have an effect. They answer that it didn’t have an effect because it doesn’t satisfy the unknown requirements of an unknown mechanism that is nevertheless presumed to exist. So if a putative cue “works,” it proves the mechanism exists, and if a putative cue doesn’t work, it shows the mechanism is uninterested in it. Thus the cue theory is a classic case of an unfalsifiable, untestable proposition. It is merely assumed and data uncritically interpreted in that light.

The bottom line here is that the failure of the arrows to act as “cues” contradicts the investigators predictions, and they don’t know why. Which begs the question of why they planned an experiment containing what at the beginning they must have considered a serious confound? The failure of the arrows to cue the percept constitutes a serious challenge to their underlying assumptions, and needs to be addressed.

The authors’ further rationalization, that “This is perhaps because the arrows are regarded as extrinsic to the stimulus and hence unfavored for recruitment” begs the question, regarded as extrinsic by whom? The conscious observer? This leads, again, to the possibility of response bias.

But Wallis and Backus have their own response bias to the suggestion of response bias in their subjects: “We regard cue-recruitment as a cognitively impenetrable, bottom-up process….”

Thinking this is one thing, corroborating it another. The use of perceptually unstable stimuli producing temporally limited effects reliant on memory and forced choice responses isn’t a method designed to guard against potential response bias, but rather one that offers fertile ground for it. The convenience of dichotomous responses for data analysis can’t offset these disadvantages.

Short version: The possibility of response bias has in no way been excluded.

On 2016 Dec 01, Amy Donahue commented:

None

On 2016 Dec 01, Amy Donahue commented:

Using the information in this article for a presentation on assisted reproduction technology, it's very helpful. Appreciate that it's open access, too! But as a medical librarian, I couldn't help but note that the search strategy could be improved. Even excluding articles published after 8/1/16, this strategy retrieves more articles than the authors noted finding:

((("Oocytes"[Majr] OR oocyte*[tiab])) AND ("Cryopreservation"[Majr] OR freez*[tiab] OR "Vitrification"[Majr] OR vitrif*[tiab])) AND ("Pregnancy"[Mesh] OR pregnan*[tiab] OR survival[tiab] OR birth[tiab] OR "quality embryo"[tiab] OR "quality embryos"[tiab] OR "embryo quality"[tiab] OR "viable embryo"[tiab] OR "viable embryos"[tiab])

Not limiting to humans (which is helpful, but does limit to only Medline articles; maybe that was the authors' intent) yields roughly 1500; limiting to humans (which does exclude some human studies that just aren't indexed as such) brings it down to almost 1,000.

Additionally, searches should probably be done in other databases, not just PubMed (and note that Medline is the subset of articles in PubMed that are indexed with MeSH terms), for the sake of being comprehensive, although that certainly adds time and effort to screening and deduplicating the results (but librarians can also help with that). There should be librarians at some of the authors' institutions, if not all - getting some search help next time would make your work even stronger.

On 2017 Aug 08, Christopher Tench commented:

Could you possibly provide the coordinates analysed otherwise it is difficult to interpret the results.

On 2017 Jan 18, Jack Gilbert commented:

We have been following some of the comments about this paper and accept that the wording of parts of our paper could be interpreted in ways we did not intend and that do not reflect the work performed.  We want to make it clear that for this paper we made predictions about nitrate, etc based on analysis of rRNA amplicon sequences and matching them to known genomes.  We did not directly measure these genes involved in nitrate metabolism (nitrate reductase, nitrite reductase, etc.), or know for certain that the strains present in the samples have such functions (although they are widely distributed in the matching phylogenetic groups).  Some of the wording (e.g., of the title in the abstract) did not come across as we intended, and could be interpreted as implying that we made direct measurements.  We want to note that we believe the predictions we made are useful, but acknowledge that they have limitations. We also want to stress that to test these hypotheses and advance clinical practice, we would need to perform extensive validation through intervention studies in carefully controlled clinical populations, which is obviously considered beyond the scope of the Observation format. However, we are currently performing ongoing studies that we believe will advance this research including some work based on public comments made about the lack of validation of the specific claims of the paper.

On 2016 Dec 28, Lydia Maniatis commented:

Cherniawsky and Mullen’s (2016) article lies well within the perimeter of a school of thought that, despite its obvious intellectual and empirical absurdity, is popular within the vision science community.

The school persists, and is relentlessly prolific, because it has insulated itself from the possibility of falsification, mainly by ignoring both fact and reason.

Explanatory schemes are concocted with respect to a narrow set of stimuli and conditions. Data generated under this narrow set of conditions are always interpreted in terms of the narrow scheme of assumptions, via permissive post hoc modeling. When, as here, results contradict expectation, additional ad hoc assumptions are made with reference to the specific, narrow type of stimuli used, which then, of course, may subsequently be corroborated, more or less, using those same stimuli or mild variants thereof.

The process continues ad infinitum via the same ad hoc route. This is the reason that, as Kingdom (2011) has noted, the study of lightness, brightness and transparency (and I would add, vision science in general) is divided into camps “each with its own preferred stimuli and methodology” and characterized by “ideological divides.“ The term “ideological” is highly appropriate here, as it indicates a refusal to face facts and arguments that contradict or challenge the preferred view. It is obviously antithetical to the scientific attitude and, unfortunately, very typical of virtually all of contemporary vision science.

The title of this paper ”The whole is other than the sum...” indicates that a prediction of “summation” failed even under the gentle treatment it received. The authors don’t quite know what to make of their results, but a conclusion of “other” is enough by today’s standards.

The ideological camp to which this article belongs is a scandal on many counts. First, it adopts the view that there are certain figures whose retinal projections trigger visual processes such that the ultimate percept directly reflects local “low-level” processes. More specifically, it reflects “low-level” processes as they are currently (and crudely) understood. The figures supposed to have this quality are those for which the appropriate “low-level” story du jour has been concocted.

The success of the method is well-described by Graham (1997, discussed in PubPeer), who notes that countless experiments were "consistent" with the behavior of V1 neurons at a time when V1 had only begun to be explored and when researchers were unaware not only of the complexities of V1 but also of the many hierarchically higher-level and processes that intervene between retina and percept. This amazing success is rationalized (if we may use the term loosely) by Graham, who with magical thinking reckons that under certain conditions the brain becomes “transparent” down to the initial processing levels. Teller (1984) had earlier (to no apparent effect) described such a view as “the nothing mucks it up proviso,” and pointed out the obvious logical problems.

Cherniawsky and Mullen premise their article on this view with their opening sentence: “Two-dimensional orthogonal gratings (plaids) are a useful tool in the study of complex form perception, as early spatial vision is well described by responses to simple one-dimensional sinusoidal gratings…” In fact, the “one-dimensional sinusoidal gratings” in question typically produce 3D percepts of light and shadow, and the authors’ plaids in Figure 1 appear curved and partially obscured by a foggy overlay. So as illogical as the transparent brain hypothesis is to begin with, the stimuli supposed to tap into lower level processes aren’t even consistent with a strictly “low-level” interpretive process.

The uninitiated might wonder why the authors use the term “spatial vision.” It is because they have uncritically adopted the partner of the transparent brain hypothesis, the view that the early visual processes perform a Fourier analysis on the retinal projection. It is not clear that this is at all realistic at the physiological level, but there is also no apparent functional reason for such a challenging process, as it would in no way further the achievement of the goal of organizing the incoming light into figures and grounds as the basis for further interpretation leading to a (usually) veridical representation of the environment. The Fourier conceit is, of course, maintained by employing sinusoidal gratings while ignoring their actual perceptual effects. That is, the sinusoidal gratings and combinations thereof are said to tap into the low-level frequency channels, which then determine contrast via summation, inhibition, etc, (whatever post hoc interpretation the data of any particular experiment seem to require). These contrast impressions, though experienced in the context of, e.g. impressions of partially-shadowed tubes, are never considered with respect to these complex 3D percepts. Lacking necessary interpretive assumptions, investigators are reduced to describing their results in terms of “other,” precisely described, but theoretically unintelligible and tangled effects.

The idea that “summation” of local neural activities can explain perception is contradicted by a million cases, and counting, including the much-loved sinusoidal gratings and their shape-from-shading effects. But ideology is stronger and, apparently, good enough for vision science today.

Finally, the notion of “detectors” is a staple of this school and the authors’ discussion; for a discussion of why this concept is untenable, please see Teller (1984).

p.s. As usual, I’ll ask why its ok for an author to be one of a small number of subjects, the rest of whom are described as “naïve.” If it’s important to be naïve, then…

Also, why use forced choices, and thus inject more uncertainty than necessary into the results? It’s theoretically possible that observers never see what you think they’re seeing…Obviously, if you’re committed to interpreting results a certain way, it’s convenient to force the data to look a certain way…

Also, no explanation is given for methodological choices, e.g. the (very brief) presentation times.

On 2017 May 25, Christopher Miller commented:

The clonEvol package has changed slightly, requiring an update to the "run.R" example script contained in Additional File 2. The updated script can be found here: https://gist.github.com/chrisamiller/f4eae5618ec2985e105d05e3032ae674

On 2016 Dec 11, Martin Mayer commented:

Cut the fat: Putting the risks of hypertriglyceridemia into context

A brief response to “Nonfasting mild-to-moderate hypertriglyceridemia and risk of acute pancreatitis”

In their article, Pedersen and colleagues present findings from their prospective cohort study on hypertriglyceridemia and its association with both acute pancreatitis and myocardial infarction.¹ With a median follow-up of 6.7 years (interquartile range, 4.0 to 9.4 years) among 116,550 "white individuals of Danish descent from the Danish general population"^1(p1835) selected randomly from two similar prospective studies (the Copenhagen City Heart Study and the Copenhagen General Population Study), this is a sizable study with respectable follow-up, even if generalizability of the findings might be at least somewhat limited. They rightly note “there is no consensus on a clear threshold above which triglycerides are associated with acute pancreatitis,”^1(p1835) and others have highlighted important issues with the evidence base.² Pedersen and colleagues also cite a review³ on triglycerides and cardiovascular disease, but here too the evidence is not entirely clear; the review only concludes evidence “is increasing”^3(p633) and recommends high-intensity statin therapy. The review also considers the future potential of add-on triglyceride-lowering therapy for those already on a statin, pointing to two ongoing trials of ω-3 fatty acids (REDUCE-IT and STRENGTH). However, the currently-available evidence - particularly that with patient-relevant outcomes - does not support such a strategy for ω-3 fatty acids or other agents that can substantially lower triglycerides (such as fibrates and niacin).^2,4,5

Even if their study reflects an underlying truth, Pedersen and colleagues unfortunately demonstrate a relative inattention to absolute risks and the implications thereof. They devote a small amount of text to absolute risks and report absolute numbers in the figures, but they repeatedly state their findings show “high risk” for acute pancreatitis, a perspective seemingly driven by the magnitude of the hazard ratios (HRs). In their concluding statements, they even remark: “Mild-to-moderate hypertriglyceridemia at 177 mg/dL (2 mmol/L) and above is associated with high risk of acute pancreatitis in the general population, with HRs higher than for myocardial infarction.”^1(p1841)

When caring for individual patients, relative metrics such as HRs are most useful when appropriately applied to corresponding baseline absolute risks. Conversely, disproportionate focus on relative metrics or failure to adequately contextualize relative metrics with corresponding absolute risks is considerably less informative and can contribute to a distorted sense of reality. Even if one accepts research findings as being likely reflective of an underlying truth, one must always carefully appraise absolute risks to gain a finer appreciation of the quantitative implications of the research findings. This practice is still useful even if one finds weaknesses in methodology, as one can simply consider the estimates increasingly uncertain in a manner qualitatively proportional to the weaknesses in methodology. A tool customized for this study is available here (TinyURL: http://tinyurl.com/JAMAIMhypertrigcalctool).

According to their own data, comparing the lowest triglyceride level group (<89 mg/dL or <1 mmol/L) to the highest triglyceride level group (≥443 mg/dL or ≥5 mmol/L), one finds an absolute risk difference (ARD) for acute pancreatitis of 0.93% over 10 years if using the absolute numbers reported in Figure 1 to estimate absolute risks, and an ARD of 2.05% over 10 years (95% confidence interval [CI], 0.73% to 4.99%) if using the absolute risk in the lowest triglyceride level group and the multivariable-adjusted HR estimate for the highest triglyceride level group (HR 8.7; 95% CI, 3.7 to 20). Repeating this for myocardial infarction, one finds an ARD of 5.6% over 10 years or an ARD of 5.08% (95% CI, 3.00% to 7.73%) over 10 years. This demonstrates at least one reason why it is important to put relative metrics into context: Although the HRs for acute pancreatitis may be “higher than for myocardial infarction”,^1(p1841) the absolute risks and absolute risk differences are higher for myocardial infarction. Additionally, it is more informative to provide risk estimates in absolute terms than in relative terms. Indeed, as aforementioned, absolute risks give better insight into what research might mean for a patient if one accepts the findings as being reflective of an underlying truth. Unfortunately, The New York Times' coverage of the study exacerbates the issue, with the only attempt to contextualize the relative metrics being a quote from one of the study’s authors. (Such mishandling of evidence is not uncommon in the media, but that is not the focus of this commentary. Including The New York Times’ coverage is not meant to single them out as uniquely bad or good in this regard; it simply serves as an example.) It is ultimately a disservice to say the risk of pancreatitis was 770% higher in patients with triglycerides ≥443 mg/dL (≥5 mmol/L) compared to patients with triglycerides <89 mg/dL (<1 mmol/L) without contextualizing such a metric with absolute risks. More technically, and as discussed in the tool, HRs are also not quite the same as relative risks.

Lastly, while management was not a focus Pedersen and colleagues’ article, sensible lifestyle changes should be emphasized wherever poor lifestyle factors exist. As for interventions beyond lifestyle changes, a medication that can reduce cardiovascular risk – such as a statin – might be instituted after shared decision-making concerning a person’s cardiovascular risk estimate; importantly, however, a person’s cardiovascular risk estimate is not dependent on triglyceride levels, and pharmaceutical intervention targeted at lowering triglycerides per se is not clearly supported by currently-available evidence examining cardiovascular, pancreatic, or other patient-relevant outcomes.  

References

(1) Pedersen SB, Langsted A, Nordestgaard BG. Nonfasting mild-to-moderate hypertriglyceridemia and risk of acute pancreatitis. JAMA Intern Med. 2016 Dec 1;176(12):1834-1842. doi: 10.1001/jamainternmed.2016.6875.

(2) Lederle FA, Bloomfield HE. Drug treatment of asymptomatic hypertriglyceridemia to prevent pancreatitis: where is the evidence? Ann Intern Med. 2012 Nov 6;157(9):662-664. doi: 10.7326/0003-4819-157-9-201211060-00011.

(3) Nordestgaard BG, Varbo A. Triglycerides and cardiovascular disease. Lancet. 2014;384(9943):626-635.

(4) Rizos EC, Ntzani EE, Bika E, Kostapanos MS, Elisaf MS. Association between omega-3 fatty acid supplementation and risk of major cardiovascular disease events: a systematic review and meta-analysis. JAMA. 2012 Sep 12;308(10):1024-1033. doi: 10.1001/2012.jama.11374.

(5) Keene D, Price C, Shun-Shin MJ, Francis DP. Effect on cardiovascular risk of high density lipoprotein targeted drug treatments niacin, fibrates, and CETP inhibitors: meta-analysis of randomised controlled trials including 117,411 patients. BMJ. 2014 Jul 18;349:g4379. doi: 10.1136/bmj.g4379. (Note about this reference: Although the title implies focus on HDL as a therapeutic target, this study nevertheless provides meaningful insight into whether there is any cardiovascular or mortality benefit from adding either niacin or a fibrate to statin therapy, and both these agents can substantially lower triglycerides.)

On 2017 May 26, Su-Fang Lin commented:

None

On 2017 May 26, Su-Fang Lin commented:

Now the link in Oncotarget is back.

On 2017 Jan 18, Stephen Maher commented:

Comments for this article in PubPeer (https://pubpeer.com/publications/27816970) suggest that the statistical data and some of the figures in this article are exactly the same and therefore unsubstantiated. As of late November 2016, the article can no longer be found on the Oncotarget website. No retraction has been reported.

On 2016 Nov 08, Peter Hajek commented:

One problem with interpretation is that in these studies, very few if any people actually stopped smoking. The provision of stop smoking treatments (as opposed to actually stopping smoking) does not seem to undermine concurrent substance use treatments, but the question of whether actually stopping smoking helps with or undermines concurrent efforts to stop using other drugs, and whether sequential treatments yield better results than doing this concurrently, have not been well answered so far.

On 2017 Jan 23, Harri Hemila commented:

Vitamin E may increase and decrease all-cause mortality in subgroups of males

Galli F, 2017 claimed that supplementation with vitamin E may have no effect on all-cause mortality even at supra-nutritional doses. They did not consider the strong evidence from the ATBC Study, which indicates that the effects of vitamin E on all-cause mortality appear to be heterogeneous.

The ATBC Study investigated 29 133 male smokers, and Hemilä H, 2009 showed that the effect of vitamin E on all-cause mortality was simultaneously modified by age and dietary vitamin C intake with P = 0.0005 for the test of heterogeneity. Vitamin E had no influence on mortality in males who had a low dietary intake of vitamin C. However, among males who had a high intake of vitamin C, supplementation with vitamin E increased mortality by 19% among those who were 50-62 years at the baseline of the trial, whereas it decreased mortality by 41% among those who were 66 years and older. The decrease in mortality amongst the oldest participants suggested that vitamin E might increase life span, and indeed, men that were administered vitamin E lived for half a year longer at the upper end of the follow-up age range, see Hemilä H, 2011.

Galli F, 2017 further also claimed that vitamin E intake is unlikely to affect mortality regardless of dose, and they referred to the Bayesian meta-analysis on vitamin E by Berry D, 2009. However, Galli et al. overlooked that the Bayesian meta-analysis was based on between-trial analysis, whereas the evidence for heterogeneity in vitamin E effect in the ATBC Study was based on individual participant level analysis, a much more reliable analysis Hemilä H, 2009. Between-study analysis may suffer from ecological fallacy. Galli et al. also disregarded other detailed criticisms of the Berry et al. meta-analysis on vitamin E by Greenland S, 2009 and Miller ER 3rd, 2009.

Galli F, 2017 concluded that since an indiscriminate vitamin E supplementation is not supported by the available evidence, future efforts are necessary to establish biomarkers and selection criteria to predict who is likely to benefit from vitamin E supplementation. However, the ATBC Study analyses indicate that age and responses to life style questionnaires may characterize people who benefit of vitamin E administration. It seems illogical therefore that the variables already identified in the ATBC Study analyses were not considered in the review by Galli et al.

On 2016 Nov 18, Mohamed Fahmy commented:

not commonly recognised, but significantly important anomalies.

On 2017 May 09, Yang K Xiang commented:

In the their commentary, Dr. Santulli has noted the differences in glucose tolerance tests between two studies (1, 2). In our study, 5-6 week old WT and β2AR -/- were fed a high fat diet (60% fat) for 6 months; both strains develop diabetes and glucose intolerance when compared to animals of same genotypes fed with a control chow (10% fat). We did not observe differences in glucose homeostasis between WT and β2AR -/- fed with the control chow. This contrasts with the Santulli study, in which β2AR -/- strain used in their studies develop diabetes and glucose intolerance at 6-months of age when fed a chow diet. Several factors may contribute to the differences in diabetic phenotypes observed.

1. In the Stanlulli study, β2AR -/- were backcrossed to the C57Bl6/N strain. In our study, the β2AR -/- is backcrossed into the C57Bl6/J strain.
2. Our study used a defined control chow with 10% fat whose composition with the exception of fat and sucrose content matched that of the high-fat diet. The possibility therefore exists that the “chow” diet in the Santulli study, whose composition is not described in detail could contribute in part to some of the metabolic changes observed. In addition, our study does not exclude that β2AR -/- mice may have metabolic issues relative to WT after feeding with the defined control chow.

The primary focus of our work was to understand the cardiac response to obesity and long-term hyperinsulinemia. In this regard the β2AR -/- mice on a high fat diet developed hyperglycemia and hyperinsulinemia, which therefore enabled us to determine if the absence of β2ARs in the heart could modulate the cardiac maladaptation that develops in wild type animals. We reported fasted insulin concentrations to demonstrate the existence of hyperinsulinemia in response to high fat feeding. However, we did observe in data not presented in the manuscript that insulin concentrations in β2AR -/- mice after intraperitoneal administration glucose were statistically lower than those in high fat fed WT, suggesting a reduced insulin release from islets, consistent with the conclusions of the in Santulli study. The Muzzin study, mentioned in the commentary is an animal with complete absence of all three β adrenergic receptors and as such caution is advised in comparing that model to mice with selective loss of the β2AR.

A study published by Jiang and colleagues was also discussed, which reported that β2AR -/- mice display a diabetic retinopathy phenotype. Although the authors of this study did not provide background information of glucose and insulin levels, they suggest that β adrenergic signaling is essential for maintaining retinal muller cell viability. Thus the observed retinopathy might not be related to diabetes per se. Taken together, these data suggest that β2AR signaling is associated with glucose metabolism and complications that may be modulated in a tissue-specific manner in different tissues in diabetes. Ultimately, transgenic approaches with tissue-specific deletion of β2AR may offer more insight into the underlying mechanism of these tissue-specific phenotypes.

Reference

1) Inhibiting Insulin-Mediated β2-Adrenergic Receptor Activation Prevents Diabetes-Associated Cardiac Dysfunction. Circulation. 2017;135:73-88.

2) Age-related impairment in insulin release: the essential role of β2-adrenergic receptor. Diabetes. 2012;61:692-701.

On 2017 Apr 28, Gaetano Santulli commented:

In the present article, Wang, Liu, Fu and colleagues report that β2-adrenergic receptor (β2AR) plays a key role in hyperinsulinemia-induced cardiac dysfunction (1). Overall, the data are very interesting and compelling. However, we noticed that in this paper β2AR-/- mice do not exhibit glucose intolerance; in fact, they seem to have a response to intraperitoneal glucose that is even better than wild-type mice (though a statistical analysis comparing these two groups is not provided). Although surprisingly not reported by the Authors, mounting evidence indicates that the deletion of β2AR has detrimental effects on glucose metabolism (2-4). Indeed, we have demonstrated that β2AR-/- mice display impaired insulin release and significant glucose intolerance (2). Muzzin and colleagues found that the ablation of βARs mechanistically underlies impaired glucose homeostasis (3). Other groups have confirmed these results, also showing that β2AR-/- mice develop diabetic-related microvascular complications (i.e. retinopathy)(4). Nonetheless, the Authors fail to at least discuss previous relevant literature describing the alterations in glucose metabolism observed in β2AR-/- mice and do not accurately circumstantiate their findings. Furthermore, the Authors do not provide any measurement (not in vivo nor in isolated islets) of insulin levels following glucose challenge, showing just baseline serum levels. We believe that for the sake of scientific appropriateness the Readers of Circulation will appreciate a clarification, in particular regarding the fact that pertinent literature in the field has been overlooked.

A formal e-Letter has been published by Circulation.

Competing Interests: None.

References 1) Inhibiting Insulin-Mediated beta2-Adrenergic Receptor Activation Prevents Diabetes-Associated Cardiac Dysfunction. Circulation. 2017;135:73-88.

2) Age-related impairment in insulin release: the essential role of β2-adrenergic receptor. Diabetes. 2012;61:692-701.

3) The lack of beta-adrenoceptors results in enhanced insulin sensitivity in mice exhibiting increased adiposity and glucose intolerance. Diabetes. 2005;54:3490-5.

4) Beta2-adrenergic receptor knockout mice exhibit a diabetic retinopathy phenotype. PLoS One. 2013;8:e70555.

On 2017 Aug 09, Serina Stretton commented:

Prasad and Rajkumar’s editorial on conflicts of interest (COI) published in the Blood Cancer Journal [1] explores how management of financial COI in academic oncology influences treatment decisions away from best patient care. We share Prasad and Rajkumar’s concerns about the potential negative influence of COI, irrespective of its source, but disagree that banning industry-funded PMWs is a reasonable or practical solution.

This year (2017) three leading professional organizations, the International Society for Medical Publication Professionals (ISMPP), the American Medical Writers Association (AMWA), and the European Medical Writers Association (EMWA), released a joint position statement reaffirming PMWs’ obligations to be transparent about their contributions and sources of funding, and to clearly delineate the respective roles of authors and PMWs [2]. Prasad and Rajkumar claim that publications written with assistance from industry-funded PMWs may not reflect authors’ views and that authors may feel unable to challenge inappropriate sponsor influence. These statements undermine the clear responsibilities and accountability that authors should uphold when publishing clinical data [3,4]. For example. as required by the International Committee of Medical Journal Editors [3] and upheld by the AMWA-EMWA-ISMPP joint position statement, authors must provide all of the following: early intellectual input to a publication, be involved in the drafting, approve the final version for publication, and agree to be accountable for all aspects of the work. It is the latter two requirements that counter Prasad and Rajkumar’s premise that authors have little opportunity to control the content of the manuscript. In contrast, PMWs who often do not meet authorship criteria, assist authors to disclose findings from clinical studies in a timely, ethical, and accurate manner; ensure that authors and sponsors are aware of their obligations; and document author contributions to the development of a publication [2,4]. To contribute value in these roles, PMWs regularly receive mandatory training on ethical publication practices from their employers and industry funders [5-7].

Of concern, Prasad and Rajkumar’s present misleading data to support their arguments for banning industry-funded PMWs. First, they state that “writing assistance” is common, citing prevalence data from a survey of honorary or ghost authorship by Wislar et al [8]. Honorary or ghost authorship occurs when an individual who merits authorship is excluded from the author byline. This is quite distinct from medical writers who not meet authorship criteria and (i) declare their involvement in the acknowledgements (PMWs) [3] or (ii) keep their involvement hidden (ghostwriters) [9]. Indeed, the prevalence of ghostwriting in the Wislar et al survey was 0.2% of articles, far lower than the 21% cited by Prasad and Rajkumar for ghost authorship. Second, Prasad and Rajkumar state that ghost authorship in industry-funded trials is far worse, citing a study by Gøtzsche et al [10]. However, Gøtzsche et al used a nonstandard definition of ghost authorship by extending the definition to undeclared contributions (either as authors or in the acknowledgments) from individuals who wrote the trial protocol and those who conducted the statistical analyses.

As acknowledged by Prasad and Rajkumar, there are multiple benefits to engaging a PMW in terms of time and readability [1]. More importantly, publications involving PMWs are of higher quality – they have a shorter acceptance time [11], are more compliant with international reporting guidelines [12, 13], contain significantly fewer non-prespecified outcomes [14], and have a lower rate of retraction due to misconduct [15] than publications without PMWs or with those that are not funded by industry. As such, it is entirely unreasonable to exclude PMWs as an option on the basis of their funding. We strongly advocate that PMWs are selected on the basis of a proven track record and commitment to ethical and transparent publication practices. In addition, we strongly recommend that authors become familiar with reporting guidelines and be aware of, and fully comply with their obligations and roles as authors.

The Global Alliance of Publication Professionals (www.gappteam.org)

Serina Stretton, ProScribe – Envision Pharma Group, Sydney, NSW, Australia; Jackie Marchington, Caudex – McCann Complete Medical Ltd, Oxford, UK; Cindy W. Hamilton Virginia Commonwealth University School of Pharmacy, Richmond; Hamilton House Medical and Scientific Communications, Virginia Beach, VA, USA; Art Gertel, MedSciCom, LLC, Lebanon, NJ, USA

GAPP is a group of independent individuals who volunteer their time and receive no funding (other than website hosting fees from the International Society for Medical Publication Professionals). All GAPP members have held, or do hold, leadership positions at associations representing professional medical writers (eg, AMWA, EMWA, DIA, ISMPP, ARCS), but do not speak on behalf of those organisations. GAPP members have, or do provide, professional medical writing services to not-for-profit and for-profit clients.

REFERENCES [1] Prasad V, Rajkumar SV. Blood Cancer J 2016;6:e489 [2] www.ismpp.org/assets/docs/Inititives/amwa-emwa-ismpp joint position statement on the role of professional medical writersjanuary 2017.pdf 2017 [accessed 08.06.17] [3] www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html; 2016 [accessed 08.06.17] [4] Battisti WP et al. International Society for Medical Publication Professionals. Good Publication Practice for communicating company-sponsored medical research: GPP3. Ann Intern Med. 2015;163(6):461-4 [5] www.ismpp.org/ismpp-code-of-ethics [accessed 08.06.17] [6] www.amwa.org/page/Codeof_Ethics [accessed 08.06.17] [7] Wager E et al. BMJ Open. 2014;4(4):e004780 [8] Wislar JS et al. BMJ 2011;343:d6128.4-7 [9] Stretton S. BMJ Open 2014;4(7): e004777. [10] Gøtzsche PC et al. PLoS Med 2007;4:0047-52 [11] Bailey, M. AMWA J 2011;26(4):147-152 [12] Gattrell W et al. BMJ Open. 2016;6:e010329 [13] Jacobs A. Write Stuff 2010;19(3):196-200 [14] Gattrell W et al. ISMPP EU Annual Meeting 2017 [15] Woolley KL et al. Curr Med Res Opin 2011;27(6)1175-82

On 2017 Jan 28, Robert West commented:

This is a very useful article that will be of value to those working in other disciplines and interdicisplinary fields such as addiction. We are just at the beginning of a era in which we use ontologies and AI to build behavioural science. The Human Behaviour Change Project (www.humanbehaviourchange.org) is an ambitious attempt to take this forward, headed up by Prof Susan Michie with collaboration of IBM, computer and information scientists at UCL, and behavioural scientists in the Universities of Aberdeen and Cambridge.

On 2016 Nov 10, Lydia Maniatis commented:

The authors assert that their findings: “support the idea that there are density-selective channels in the visual system, and that perceived density is in part based on a comparison of these channel responses across space. “

Looking at the stimuli, I would suggest another interpretation. The areas with more closely grouped dots tend to be seen as figure, and the more dilute ones as ground. This is my impression. If this is the case, we should expect the dense areas to appear even denser, and the less dense areas to appear even less dense because: It has been understood since Rubin that figure appears more dense and ground less so: “According to Rubin (1915/1921), figures…adhere or cling together (are compact)…In comparison, the ground…has a “loose” structure....” (Wertheimer/Spillman Ed. 2012 On perceived motion and figural organization, MIT Press).

There is no obvious functional rationale for positing “density channels” that compare the densities (how is this evaluated?) of adjacent or overlapping surfaces.

On 2016 Dec 04, Alessandro Rasman commented:

Increased levels of coagulation factors in Multiple Sclerosis: a defending mechanism from microbleedings?

On 2016 Nov 12, Martine Crasnier-Mednansky commented:

The statement by Vincent Detours "Our interest, as scientists and citizens, is to reject the totalitarian reduction of human activities to numbers, and adopt policies acknowledging the diversity of human talents and promoting individuals’ autonomy." is echoing the statement by Lewis Mumford "The test of maturity, for nations as well as individuals, is not the increase in power, but the increase of self-understanding, self-control, self-direction, and self-transcendence. For in a mature society, man himself and not his machines or his organizations is the chief work of art."

On 2016 Nov 09, Donald Forsdyke commented:

Marketing in science

In it ironic that Vincent Detours insightful analysis of the "managers" who outdo the "competent" comes at a time when the triumph of marketing over ability is so evident on the political scene. For any who might think this could not happen in science, two accounts of the career of Niels Jerne will perhaps provide helpful reading (1, 2).

1.Soderqvist T (2003) Science as Autobiograph: the Troubled Life of Niels Jerne (Yale Univ. Press, New Haven).

2.Eichmann K (2008) The Network Collective: Rise and Fall of a Scientific Paradigm (Birkhauser, Berlin).

On 2016 Nov 07, Vincent Detours commented:

Who wants to be a number?

Sinatra et al. present another metrics to predict scientific impact. Like their predecessors, they fail to discuss the wider consequences of (i) equating impact and scientific quality, and (ii) reducing scientists' activity to a number.

The number of times a paper is cited—the basic quantity behind impact metrics—is by essence a measure of popularity, not a direct measure of truth and novelty. Intelligent thinking together with the availability of resources required to work, effective communication and access to high circulation venues all contribute to popularity. Building impact often means less work in the lab and more networking with those in charge of science funding and dissemination, presence on social media, etc. In this context, the form of communication increasingly takes precedence over its content, aggravating the current reproducibility crisis.

Impact metrics routinely guide hiring and funding. It spares decision makers the hurdle and risk of exerting sound scientific judgment: they simply promote the most popular folks. It conveniently shortens debates arising from diverse expert viewpoints. And who can argue against it? Aren’t the winners ‘elected’ by the community? As a result, scientifically unremarkable managers gain control at the expense of competent active scientists and, incidentally, the riches get richer. Yet, the vast majority of scientists are loosing control over resources and over their own destiny, being herded to the same 'high-impact' topics, for example.

The proliferation of impact metrics, social networks ‘likes’ and other audience measures fuel the increasing tyranny of rankings in society. While alienating and isolating individuals in narcissism and permanent competition, rankings ultimately benefit those who aggregate information and control communication. Our interest, as scientists and citizens, is to reject the totalitarian reduction of human activities to numbers, and adopt policies acknowledging the diversity of human talents and promoting individuals’ autonomy.

On 2017 May 25, Lydia Maniatis commented:

"A simple alternative model is developed that is consistent with the results."

I.e. an ad hoc, data-fitted proposal is submitted that, as such, is experimentally uncorroborated and carries no theoretical weight. This is because experimental conditions must always be informed by theoretical assumptions (which they are supposed to test), so that the experiment can select which variables to hold constant, and which to allow to vary so as to test their hypothesized role, Post hoc explanations cannot distinguish between causal variables and confounds, and thus the experiments which they are evaluating in hindsight cannot serve as tests of a hypothesis so-derived.

I suppose the authors will test their proposal in the future, but at the the present stage it was not worth reporting. Testing it would, of course, require much more extensive and detailed conceptual development, precisely so that anyone wanting to test it could exercise the necessary experimental control over the presumed causal variables, and minimize researcher degrees of freedom, i.e. the degree of uncertainty, in interpreting results.

On 2017 Feb 08, Seung Gyu Yun commented:

First, I agree with your opinion, such as definition of saliva. We seem to have misrepresented a saliva that was confused it with the oral fluid.

ASAP, I will request a correction to JCM.

Second, we don't exaclty know that the levels of virus in oral fluid would be sufficient to cause infection. Because we did not test virus culture test in oral fluid. However, we generally found that virus in oral fluid had low level. Perhaps your opinion is correct, but unfortunately I have not found accurate data about resiratory viral culture in oral fluid

Thank for your comment.

On 2017 Jan 26, Ronald Eccles commented:

Dear Authors

I was very pleased to read your recent article in Virology- a very interesting project.

I am often asked if saliva can be a source of common cold and influenza infections and I usually reply NO

The respiratory viruses such as rhinovirus and influenza replicate in the respiratory epithelium of nose, larynx and trachea and do not replicate in the oral mucosa.

However, your study clearly demonstrates that these respiratory viruses can be found in fluid samples taken from the oral cavity- I say fluid samples because saliva in the mouth may be contaminated with respiratory mucus on sneezing an coughing. The fluid you samples in the mouth was not pure saliva.

I agree that adenoviruses may replicate in the oral cavity but the respiratory viruses by definition do not.

I believe that the levels of virus you have detected in oral fluid with your very sensitive pcr technique demonstrate the presence of viruses in oral fluid rather than saliva- it is a fine point but in order to get pure saliva you would need to cannulate the parotid duct and I doubt if you would find any respiratory viruses in this pure saliva.

I found your research very interesting and congratulate you on a very important project.

One final point- do you believe the levels of virus you found in oral fluid would be sufficient to cause infection? I am doubtful as your pcr technique would detect very small amounts of RNA or DNA and the viral titre of infectious particles would be very low

I would be interested in your comments

Kind Regards

Professor Ron Eccles Director Common Cold Centre & Healthcare Clinical Trials Cardiff School of Biosciences Sir Martin Evans building Cardiff University Museum Avenue Cardiff CF10 3AX United Kingdom

Ronald Eccles Cyfarwyddwr Treialon Gofal lechyd a Chanolfan Anywyd Caerdydd Ffordd yr Amgueddfa Caerrdydd CF10 3AX

On 2017 Mar 19, Harri Hemila commented:

Shortcomings in the meta-analysis on vitamin C and atrial fibrillation

In their meta-analysis on vitamin C and postoperative atrial fibrillation (POAF), Baker WL, 2016 stated that they restricted to randomized trials; however, they included the Carnes CA, 2001 study which was not randomized. Furthermore, their meta-analysis did not include data for three US trials, two of which were substantially larger than the included POAF trials, see Hemilä H, 2017.

The conclusion by Baker WL, 2016 that vitamin C does have effects on POAF is reasonable, yet their analysis did not reveal the significant heterogeneity in the effects. Although 5 trials studies in the USA found no benefit, several studies in less wealthy countries have found significant benefit of vitamin C against POAF indicating that further research should be carried in less wealthy countries, see Hemilä H, 2017.

On 2016 Dec 07, Peter Hajek commented:

There was no significant association between respiratory symptoms and current vaping when controlling for smoking status, and this is the key analysis which should have been reported, rather than unadjusted results that reflect the fact that most vapers are smokers.

Past experimentation with vaping remained linked to some symptoms but it also significantly reduced wheezing. With the absence of any effects of current vaping, these links are likely to be flukes as there is no obvious mechanism for them. Here is a link to a more detailed critique of the way these findings were reported: http://www.ecigarette-research.org/research/index.php/whats-new/whatsnew-2016/248-bronch

On 2016 Nov 21, MICHAEL SIEGEL commented:

None

On 2017 Sep 19, Helmi BEN SAAD commented:

The correct name of the last author is: "Ben Saad H".

On 2016 Nov 24, Helmi BEN SAAD commented:

None

On 2017 Sep 30, Yuichi Hongoh commented:

Dear Dr.Price, your comment is very helpful to us. I agree with your suggestions. Thank you very much.

On 2017 Sep 25, Morgan Price commented:

The authors suggest that D. trichonymphae cannot synthesize threonine or methionine, but I think pathways for synthesizing both amino acids are present. First, the only gap in threonine synthesis appears to be a missing homoserine kinase. In Desulfivibrio vulgaris Miyazaki F, a misannotated shikimate kinase (DvMF_0971) provides the missing homoserine kinase activity (https://www.biorxiv.org/content/early/2017/09/23/192971). RSDT_0983 from D. trichonymphae is over 50% identical to DvMF_0971 and is also probably a homoserine kinase. Second, I found plausible candidates for all steps in methionine synthesis. D. trichonymphae has putative genes converting aspartate to homoserine (RSDT_0709, RSDT_1035, RSDT_0549), for activating homoserine (RSDT_0485), for sulfhydrylation of the activated homoserine (RSDT_0816), and for B12-dependent methionine synthase (RSDT_0316). Thus, D. trichonymphae contains the genes to synthesize threonine and methionine.

On 2017 Oct 06, Christopher Southan commented:

The structure mapping analysis, including SciFinder intersects, has now been updated, one year on https://cdsouthan.blogspot.se/2017/09/osm-antimalarial-series-1-findability.html

On 2016 Nov 02, Christopher Southan commented:

Blog post on PubChem mappings for the structures https://cdsouthan.blogspot.se/2016/09/series-1-antimalarials-publication.html

On 2017 Jun 23, Joshua L Cherry commented:

NO EVIDENCE THAT SELECTION DRIVES SWITCHING

This article claims that “the great majority of codon set switches proceed by two consecutive nucleotide substitutions…and are driven by selection”. The data in fact support a predominance of simultaneous switches that are not driven by selection. Even if we assume that sequential switches predominate, the implication that selection increases their rate by a factor of ~50 is unjustified. Moreover, selection against the non-serine intermediate is expected to decrease the rate of sequential switches, not to drive them. The authors’ argument to the contrary is analogous to arguing that a mountain range between two locations speeds the journey between them because it accelerates the downhill portion of the trip.

Inappropriate standard of comparsion

The usual way to establish that an evolutionary process is driven by selection is show that it is faster than some process that is largely unaffected by selection. The authors instead made comparisons to “expectations” derived from nonsynonymous substitution rates, which are greatly decreased by selection. This comparison cannot establish that switching is driven by selection, and would greatly overestimate any such effect.

A more appropriate comparison would be to expectations derived from synonymous rates. These are several-fold higher than nonsynonymous rates, and “expectations” involve products of two rates. Thus, the claimed acceleration by selection mostly or entirely disappears with a proper standard of comparison.

Unjustified rejection of simultaneous switching

The authors reject a significant role for simultaneous double mutation in switching because the rate of switching is higher than the rate of analogous double changes in noncoding sequences by a factor of 5-10. This argument would be valid if non-coding regions were evolving nearly neutrally, but this is far from the case: rates of non-coding transversions (Fig. 3) are comparable to the rates of some nonsynonymous transversions (Fig 2).

I have determined that the rates of the relevant synonymous transversions are higher than the corresponding single-base non-coding changes by a factor of >5. This presumably reflects purifying selection in non-coding regions. The effect of selection on simultaneous tandem changes is expected to be larger. Thus, the excess of serine switches over non-coding tandem changes can easily be explained by selection in non-coding regions. Put differently, we can estimate a lower limit on the rate of simultaneous serine switches, and it corresponds to the majority of the observed switches.

Slow- vs. fast-evolving genes

The article claims to have shown that the rate of switching is “higher in conserved genes than in nonconserved genes in full agreement with the selection hypothesis”. The results (Fig. 6) in fact demonstrate just the opposite: the rate of switching in “nonconserved” genes (0.0032 or 0.0022) is about three times higher than that in “conserved” genes (0.0010 or 0.0008).

The authors considered the ratio of the switching rate to a sum of products of nonsynonymous rates. This ratio is higher in “conserved” genes only because the nonsynonymous rates are lower in “conserved” genes. This is true almost by the definition of “conserved” (low dN/dS), and has nothing to do with serine codon switches.

Theoretical expectation

Under the simple selection scheme considered by the authors, selection will actually decrease the rate of sequential switching. After fixation of a deleterious Ser->Thr or Ser->Cys mutant, selection will indeed increase the fixation probability of a mutant that restores Ser. However, selection always decreases the fixation probability of the initial deleterious mutant by a larger factor. As illustrated here, the product of the two relative fixation probabilities, and hence the relative probability of a switch during a short interval, is always less than one (selection slows switching) for nonzero s, and it decreases monotonically and approaches zero as the strength of selection (|Nes|) increases.

The above implicitly assumes weak mutation, but the same conclusion holds outside of this regime (Kimura, 1985).

Conclusion

Neither the data nor the authors’ model supports the claim that serine codon switching is driven by selection or has an especially “high frequency”. In fact, both data and theory point to the opposite conclusion.

References

Kimura, M (1985) The role of compensatory neutral mutations in molecular evolution. Journal of Genetics 64(1):7-19.

On 2016 Nov 03, Donald Forsdyke commented:

CONSIDERATION OF NUCLEIC ACID LEVEL SELECTION?

The authors set out "to investigate the evolutionary factors that affect serine codon set switches" (i.e. between TCN and AGY). Their "findings imply unexpectedly high levels of selection" (1). Indeed, the data strongly support the conclusion that codon mutations "are driven by selection." It is conjectured that the codon mutation "switch would involve as an intermediate either threonine ACN or cysteine TGY, amino acid residues with properties substantially different from those of serine, so that such changes are unlikely to be tolerated at critical functional or structural sites of a protein."

However, it does not follow that the unsuitability of the interim amino acids drove the rapid tandem substitutions. Choice of "coincident codons" has long been seen as influenced by pressures acting at the nucleic acid level (2-4). These pressures evolve in parallel with, and sometimes dominate, protein pressures. One example is purine-loading pressure (3). If this cannot be satisfied by changes at third codon positions, then sometimes the organism must accept a less favorable amino acid. With serine codons, a change from TCN to AGY (i.e. first and second codon positions) can increase purine-loading pressure without compromising the amino acid that is encoded see Ref. 3.

1.Rogozin IB, Belinky F, Pavlenko V, Shabilina SA, Kristensen DM, Koonin EV (2016) Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci USA www.pnas.org/cgi/doi/10.1073/pnas.1615832113 Rogozin IB, 2016

2.Bains W. (1987) Codon distribution in vertebrate genes may be used to predict gene length. J Mol Biol 197:379-388. Bains W, 1987

3.Mortimer JR, Forsdyke DR (2003) Comparison of responses by bacteriophage and bacteria to pressures on the base composition of open reading frames. Appl Bioinf 2: 47-62. Mortimer JR, 2003

4.Forsdyke DR (2016) Evolutionary Bioinformatics, 3rd edition (Springer, New York).

On 2017 Apr 15, Darko Lavrencic commented:

There are three levels of research on intracraniospinal anatomy and fluids:

1) Research at the basic level: intracraniospinal anatomy, cells, barriers, biochemical fluids exchange, flow patterns, composition, etc.

2) Physiological intracraniospinal hydrodynamics

3) Pathological hydrodynamic changes and anatomic adaptations

Contemporary stage of research is predominantly still at the first level. The problems of the first level limit the solutions to the second and the third level.

Hypothesis "The Intracraniovertebral Volumes, the Cerebrospinal Fluid Flow and the Cerebrospinal Fluid Pressure, Their Homeostasis and Its Physical Regulation" is at the second level of research: http://www.med-lavrencic.si/research/the-intracraniovertebral-volumes/.

On 2016 Dec 20, Natalie Clairoux commented:

Free version of this article available at https://papyrus.bib.umontreal.ca/xmlui/handle/1866/16349

On 2016 Nov 18, David Mage commented:

Any candidate model for SIDS causation must explain the 50% male excess in SIDS and its 4-parameter lognormal age distribution. OMIM shows orexin, pPERK and ATF4 are all autosomal with no X-linkage involved. Therefore this line of research appears to be "barking up the wrong tree." Do the authors have any other explanation for the universal 0.61 male fraction of SIDS other than a recessive X-linkage or pure happenstance?

On 2017 Jun 27, Louise B Andrew MD JD commented:

Medscape has published a synopsis of this article at www.medscape.com/viewarticle/869777. The principal author of this study has more recently published a formal study of licensure application questions which is Open Access, and can be found at https://www.ncbi.nlm.nih.gov/pubmed/28633174 They should really be read together. I have written a comprehensive article on Physician Suicide for Medscape http://emedicine.medscape.com/article/806779. Medscape requires a free subscription. However, all materials and many more resources can be accessed freely through www.Physiciansuicide.com. If you care about mental health and physicians, please learn more and help to publicize and address it.<br> A doctor a day (in the US alone) is too many to lose to an eminently treatable disease.

On 2016 Nov 10, Egon Willighagen commented:

The SPLASH methods used in the paper is now described in this Nature Biotech paper: http://dx.doi.org/10.1038/nbt.3689

On 2017 Jan 11, Tania M O Abe commented:

After reviewing the entire paper, we noticed an error in data of the last column of Table 2. During the registration of information in Table 2, the last column mistakenly recorded incorrect monthly number of deaths for myocardial infarction. The correction will be done this week. Once this is an government data, it can be found in http://tabnet.datasus.gov.br/cgi/tabcgi.exe?sim/cnv/obt10SP.def

On 2016 Dec 27, Clive Bates commented:

The reporting of this study is highly misleading. The abstract confidently asserts:

RESULTS: We observed a reduction in mortality rate (-11.9% in the first 17 months after the law) and in hospital admission rate (-5.4% in the first 3 months after the law) for myocardial infarction after the implementation of the smoking ban law.

In fact, those with access to the full study will not find these observed reductions anywhere. Both myocardial infarction (heart attack) deaths and hospital admissions increased substantially after the smoking ban came into effect in August 2009. See graphs of the study data for myocardial infarction deaths and hospital admissions courtesy of Chris Snowden's blog post on these findings: Brazilian Smoking Ban Miracle.

The supposed 'decrease' emerges from modelling that adjusts for other factors that may influence heart attacks to create a counterfactual (what would have been expected to happen without the smoking ban). These factors give predicted rates of heart attack deaths and hospital admissions over the period studied. But why would the predicted rates suddenly shoot up to levels unprecedented in the dataset and so high that the observed large observed increases represent a decline compared to the even-higher prediction?

The explanation given in the paper is as follows:

The Autoregressive Integrated Moving Average with exogenous variables (ARIMAX) method was used to analyse the effect of the smoking ban law, modelled as a dummy variable, in the mortality rate and hospital admission rate data for myocardial infarction. The ARIMAX models were also adjusted to other parameters, including ‘total hospital admission’, CO, minimum temperature and air relative humidity. The ARIMAX method allows to estimate lag effects of input series and to forecast output series, as a function of a linear filter of the input series (transfer function) and of the noise (ARIMA filter) and by controlling for the autocorrelations. It enables us to compare the predicted rate of hospital admission and mortality with the real observed rate.

But how these corrections are made and whether they are valid is barely justified in the paper - they are buried in the black-box model used and reported uncritically. Given that these adjustments reverse the observed effects - turning a sharp rise into a decline - then surely the authors should have asked themselves harder questions and not just trusted the model and their choice of inputs to it. However, they don't even remark on this change of the sign of the effect in the paper as if the actual observations are an embarrassment to be ignored rather than discussed. Yet this is the most striking feature of the paper. Had the authors wished to explain their work transparently, they could have plotted the counterfactual (the predicted values for deaths and admissions with no ban) and the actual emissions and shown the decrease that way. But that would have begged the question: what is causing the very steep predicted rise? Or raised the possibility of modelling error or rogue assumptions.

Surely, confronted with this highly counterintuitive result, the editors and peer-reviewers should have demanded more explanation for the choice of confounding variables, a sensitivity analysis to flex whatever opaque assumptions have been made, publication of the data used to make adjustments, and a plausible narrative to explain the reversal of an increase to a decrease and the implicit massive underlying increase in background hospital admission and MI mortality rate that apparently coincided with the smoking ban. Finally, whatever the methodology, it is highly misleading to report these adjusted figures as an observed reduction in the abstract, especially with the faux precision of one decimal point.

I would like to suggest the following rewording of the results for inclusion a revised abstract:

RESULTS: We observed a substantial increase in mortality and hospital admissions for myocardial infarction after the implementation of the smoking ban law in Sao Paulo in August 2009. However, it is possible that other factors are responsible for this increase. After hand-picking a small number of possible confounding variables, and applying opaque statistical adjustments to account for their effect though without providing the data necessary for verification, we have been able to demonstrate that these increases could represent a modelled reduction in mortality attributable the smoking ban (−11.9% in the first 17 months after the law) and in hospital admission rate (−5.4% in the first 3 months after the law).

CONCLUSIONS: Hospital admissions and mortality rate for myocardial infarction were increased in the first months after the comprehensive smoking ban law was implemented. However, it is possible that factors other than the smoking ban accounted for some or all of this.

One must be concerned about the role of the journal Tobacco Control. Is this journal really an easy conduit for admitting studies of dubious quality to the peer-reviewed literature simply because the findings appear to provide support for certain tobacco control policies? I would welcome the editors' comments as well as that of the authors.

Please see original commentary from Dr Michael Siegel, Professor in the Department of Community Health Sciences, Boston University School of Public Health on his blog here and here.

On 2017 Aug 17, José L Oliver commented:

We are glad to announce that, after correcting the serious problem suffered by the backend on the past weeks, NGSmethDB is now running again: http://bioinfo2.ugr.es/NGSmethDB. Sorry by the inconveniences the downtime may have caused.

On 2017 Aug 11, José L Oliver commented:

The main backend of NGSmethDB, a no-SQL database coupled to an API-server, has suffered a serious, and by the moment unrecoverable, problem, being therefore currently unavailable. Sorry by the inconveniences this may cause. We follow applying our best efforts to recover it as soon as possible.

In the meantime, we want to remember that NGSmethDB implemented a second mode to access the data: the NGSmethDB track hubs at UCSC, which are fully operative these days: http://bioinfo2.ugr.es:8080/NGSmethDB/data-access/ Track hubs, together with the coupled Table Browser and Data Integrator tools, provide standard and efficient ways for visualizing, retrieving, combine and compare NGSmethDB data to any other third-part annotation.

On 2017 Aug 03, Julia Romanowska commented:

The link seems to lead to an unexisting page. Is it just a short maintenance issue?

On 2016 Nov 03, Darren L Dahly commented:

Because BMC has not actually linked the original reviews to this paper on their site, I have posted my original review here. Some but not all of my concerns were addressed in the final manuscript.

Major Compulsory Revisions

The paper is entirely exploratory and this should be emphasized by the authors. There are no specific hypotheses being tested here, nor are there any theory based predictions that the observed results can be compared against. While exploratory analyses can of course be helpful, the utility here is seriously limited by the observational nature of the data, the crudeness with which key covariates are measured (by survey) and represented (by dichotomization), and the use of modelling technique that will be unfamiliar to most readers. Consequently, almost any result obtained from this analysis could be explained, or explained away, fairly easily. Given the results obtained, the authors claim the research can inform out understanding of the aetiology and prevention of obesity, but notably fail to provide even one concrete example of how.

My concerns are amplified in light of how the modelling of BMI SD scores has been reported in the paper. First and foremost, the paper doesn’t report the exact form of the growth mixture model (i.e. exactly what is the set of parameters being estimated), or the values of any of the estimates obtained (nor any indication of the uncertainly in these estimates). It is thus not possible to fully evaluate the work that has been done, and this must be corrected before any final decision on the paper could be made.

Based on what I can infer about the model from the text, I have some additional concerns for the authors that I hope are useful. The authors only state that the variances of the latent growth factors are “fixed.” This could mean they are fixed to any specific value, or that they are estimated but fixed to be equal across classes. Based on the text, I will assume they were fixed as zero. This means that 100% of the variance in BMI SD scores is explained by group membership, and the final model reported includes two groups, each with similar intercepts but different slopes (one increasing and one decreasing). The model being reported (assuming I am correctly guessing the exact form of the model) precludes any variation in the degree of these changes. Thus, if the model was a faithful, complete representation of how these children are growing, then the exact same grouping could be discovered by simply dividing the sample into children with increasing BMI SDs and those with decreasing scores. I find this hard to believe. Ironically, to justify the use of growth mixture modelling, the authors state that it is useful for better understanding heterogeneity in growth – but they then go on to describe a model that describes all of that heterogeneity with a binary classification. I predict that the variability in the BMI SD scores at any single time point is more informative than the binary classification resulting from the “complex” model being reported.

The authors should report how differences in the exact ages of measurement were handled. There are several options. The authors might have assumed everyone was measured at the same age at times 1, 2, and 3, which could be a considerable source of error depending on the variances of the ages of measurement. It seems more likely they have used the Mplus time-scores option, and if so, this needs to be described along with other details of the model. The authors might have also smoothed the individual curves prior to modelling, in which case the details of the procedure used should be reported.

The use of BMI SDs scores could be problematic. One the one hand, it has the advantage of normalising the BMI measures and simplifying the functional form of the growth curve (though BMI change is fairly linear from the age of 4 years anyway). However, it introduces a new challenge to interpreting the result, as it’s hard to distinguish the degree to which the model is describing changes in BMI within children over time, and differences between the observed sample and the reference population.

The 2 stage modelling process employed is sub-optimal. It ignores the uncertainty inherent in the classification and thus subsequent standard errors of the estimated relationships between class memberships and other covariates are artificially reduced. Mplus is very capable of estimating the models being reported here in a single model that avoids this limitation (and has several other options for relating class membership to covariates that are also likely more appropriate).

The authors state that the “clinical interpretation” of the models was an important factor in determining the number of classes included in the final, reported models, but give no indication or example of what this term means in this specific context. This should be clarified.

There are some serious limitations, independent of the growth mixture modelling, that bear consideration by the authors. The first is that there is no consideration of the role of puberty, or recognition of the distinction between developmental time vs calendar time. Second, there is no consideration of the children’s heights, and even if BMI is defined as a measure of mass that is roughly independent of height, it’s hard to say anything useful about a child’s growth while ignorant of how tall he/she is.

The description of how missing data was handled is insufficient and I would point the authors to several guidelines that I hope they find helpful (doi 10.1186/1471-2288-12-96).

The sample is not described in sufficient detail. At the very least, the overall response rate should be provided. I would suggest that the authors refer to an established reporting guideline (e.g. STROBE) to help avoid this kind of reporting error.

The paper overemphasizes the novelty of this analysis based solely on the use of growth mixture models. There the hundreds of existing population based studies of BMI in children and no reason to think this particular analysis is more informative than many/most of these.

The term “confounding” is found nowhere in the paper. To have any utility regarding identified risk factors, the authors should have something to say about the exchangeability of groups being compared.

On 2017 Feb 10, Richard Holliday commented:

As highlighted by the previous comments there are several weaknesses with this study. I would like to add a few further observations:

-There is inadequate choice of e-liquids and controls. The cells were exposed to three conditions: air control, e-liquid [tobacco, 16mg] and e-liquid [menthol, 0mg nicotine]. There are two variables here (nicotine concentration and flavour) making any analysis of the results impossible.

-In the methods, a menthol, 13-16 mg nicotine e-liquid is mentioned but this is not mentioned anywhere else in the paper, nor presented in the results.

-The main conclusion of this paper is that ‘flavoured e-cigs’ gave a ‘greater response’. As there was no unflavoured control this conclusion is invalid. Likewise, if the authors are trying to say ‘menthol flavour’ gave a greater response than ‘tobacco flavour’ this is again invalid as nicotine concentration is a confounding factor in their study design.

The UK E-cigarette Research Forum (an initiative developed by Cancer Research UK in partnership with Public Health England and the UK Centre for Tobacco and Alcohol Studies) recently reviewed this paper. The full review can be found here (see review 5 with further comments in the final paragraph of the overview).

On 2016 Dec 27, Clive Bates commented:

There are several weaknesses in this paper and the surrounding commentary, and it caused unwarranted alarmist news coverage, which has not been corrected: New e-cigarettes alert as experts warn that the exposure to chemicals could trigger severe gum disease and even increase the risk of mouth cancer, Daily Mail, 17 December 2016.

Comparators. The study lacks adequate comparators - for example, coffee and/or cigarette smoke could have been used. That would have allowed these observations to be placed in a meaningful comparative context. Given that the vast majority of users or potential users are smokers, the comparison with smoking is most relevant. Further, if the effect of vaping is no different to that arising from an everyday habit like drinking coffee then we would be correspondingly reassured.

Interpretation of cell study. These effects on cells in vitro will not necessarily translate into material oral health risks in live subjects and the authors do not show evidence that the effects observed at the magnitudes measured are a realistic proxy for human gum disease risk. If human cells are exposed to any aversive environment, some effect is likely. But it is heroic to interpolate that to a human disease risk associated with normal use of the product. Ames (Ames BN, 2000) explains why:

Humans have many natural defenses that buffer against normal exposures to toxins and these are usually general, rather than tailored for each specific chemical. Thus they work against both natural and synthetic chemicals. Examples of general defenses include the continuous shedding of cells exposed to toxins. The surface layers of the mouth, esophagus, stomach, intestine, colon, skin and lungs are discarded every few days; DNA repair enzymes, which repair DNA that was damaged from many different sources; and detoxification enzymes of the liver and other organs which generally target classes of chemicals rather than individual chemicals.

Professor Brad Rodu elaborates further: Imaginary Hobgoblins From E-Cigarette Liquid Lab Tests, February 2016.

Methodology The lead author's commentary speaks of 'burning' e-liquid and 'smoking' e-cigarettes. This does not inspire much confidence that the authors understand this non-combustible technology or that they have operated the device in realistic conditions for humans. There have been other studies where the devices have been operated at higher temperature than would be possible for human users, and then measurements of unrealistic levels of thermal decomposition products reported - see for example, Jensen RP, 2015. The authors provide little reassurance that have not fallen into the same methodological pit. The discussion of the methodology followed is thin and insufficient to allow replication.

Overpromoting results. So in the absence of useful comparators and no link from these observations to disease risk it hard to see what this study adds. Further, it is unclear how it justifies the alarmist over-confident commentary First-ever Study Shows E-cigarettes Cause Damage to Gum Tissue that accompanied it and led to the news coverage cited above. This promotes the implicit claim (in the absence of an explicit caveat) that e-cigarette use would damage the gums in the mouth of a living person.

Failure to provide a rounded view when communicating with the public. Other studies suggest that switching from smoking to vaping has a beneficial effect on oral health. For example, see Tatullo M, 2016:

At the end of the study, we registered a progressive improvement in the periodontal indexes, as well as in the general health perception. Finally, many patients reported an interesting reduction in the need to smoke.In the light of this pilot study, the e-cigarette can be considered as a valuable alternative to tobacco cigarettes, but with a positive impact on periodontal and general health status.

And this study, Wadia R, 2016 which found an increase in gingival inflammation when tobacco smokers switched from smoking to vaping for two weeks but noted that this was similar to the effects observed when people quit smoking:

The clinical findings from the current study are similar to those that occur following verified smoking cessation. For example, during a successful period of quitting smoking, gingival bleeding doubled from 16% to 32% in a group of 27 smokers followed for 4–6 weeks, even though there were some improvements in the subjects’ plaque control. Results from this study are also consistent with studies that suggest a fairly rapid recovery of the inflammatory response following smoking cessation. (emphases added)

The benefits of switching from smoking to vaping are pervasive and include improvements in oral health.

On 2017 Jul 09, Lydia Maniatis commented:

"The former observation was expected, as human vision prioritizes processing as a function of distance from fixation (23⇓–25). "

Reference 25 is to Rovamo & Virsu (1979) "An estimation and application of the human cortical magnification factor. Exp Brain Res 37(3):495–510.. ." The authors seem to be making a statement of fact, based on this and two other references, that "human vision prioritizes processing as a function of distance from fixation."

However, according to Strasburger, Rentschler and Juttner, (2011):

"The strong, all-embracing hypothesis put forward by Rovamo & Virsu (1979) is hardly, if ever, satisfied." In other words, to the extent that it rests on the Rovamo citation, the first statement quoted above appears to me to be false. At best, it requires qualification. I don't know how reliable the other two citations are, I haven't checked.

On 2017 Apr 12, Konstantinos Fountoulakis commented:

None

On 2017 Apr 12, Konstantinos Fountoulakis commented:

This is a study on 70 patients suggesting that depressed people exposed to high early life stress (ELS) had a greater likelihood of remission when their amygdala showed hyperreactivity to socially rewarding stimuli, whereas for those with low-ELS exposure, amygdala hyporeactivity to both rewarding and threat-related stimuli predicted remission (1) The main problem with this study is that the data are uncontrolled. It is important to note that depressed patients have a high placebo response rate (up to 40%) in the short term (2) We also know that acute response to placebo is equal to up to 80% or more to the response to active drugs (3, 4), meaning that if we accept the additivity hypothesis (this is of course a matter of debate) (5, 6), most patient who acutely responded to active drug might be in reality placebo responders. Therefore the results of the study under discussion should not be accepted without caution. Adding to the above concerns is the report the STAR-D study, that one third of patients who remitted after step 1 will relapse within 4-5 months, while up to 50% will relapse from later steps (7). It is unknown what these patients stand for, however one could argue that at least some of them are patients unresponsive to antidepressants who however manifested a placebo response. Additional problems are that the patients included had low depression severity (mean HDRS=21) and low dosages of antidepressants used (on average 10 mg of escitalopram, 50-62.5 mg of sertraline and 87.5-90.8 mg of venlafaxine). Also, of prime importance is that the determining of early life stress (ELF) with the use of a self-report questionnaire alone could be misleading, since many depressed patients especially with character pathology might tend to over-report such events.<br> These problems exist mainly because the study under discussion tries to elucidate an issue concerning a mechanism of action without using an adequately controlling methodology. What that study suggests is that patients who acutely remit (no matter the reason) might present with the characteristics reported, but any inference concerning the role of pharmacotherapy per se is problematic.

References

1. Goldstein-Piekarski A, et al. (2016) Human amygdala engagement moderated by early life stress exposure is a biobehavioral target for predicting recovery on antidepressants. PNAS.
2. Furukawa TA, et al. (2016) Placebo response rates in antidepressant trials: a systematic review of published and unpublished double-blind randomised controlled studies. The lancet. Psychiatry.
3. Khan A, Leventhal RM, Khan SR, & Brown WA (2002) Severity of depression and response to antidepressants and placebo: an analysis of the Food and Drug Administration database. Journal of clinical psychopharmacology 22(1):40-45.
4. Gibbons RD, Hur K, Brown CH, Davis JM, & Mann JJ (2012) Benefits from antidepressants: synthesis of 6-week patient-level outcomes from double-blind placebo-controlled randomized trials of fluoxetine and venlafaxine. Archives of general psychiatry 69(6):572-579.
5. Yang H, Novick SJ, & Zhao W (2015) Testing drug additivity based on monotherapies. Pharmaceutical statistics 14(4):332-340.
6. Lund K, Vase L, Petersen GL, Jensen TS, & Finnerup NB (2014) Randomised controlled trials may underestimate drug effects: balanced placebo trial design. PloS one 9(1):e84104.
7. Rush AJ, et al. (2006) Acute and longer-term outcomes in depressed outpatients requiring one or several treatment steps: a STAR*D report. The American journal of psychiatry 163(11):1905-1917.

On 2017 May 30, Lydia Maniatis commented:

Comment 3: The speciousness of the interpretation may perhaps be better grasped if we imagine that the centroids contained patches differing in ways other than color. If, for example, some had been shaped like rectangles and others stars, would we have been justified in concluding that we were measuring the activities of rectangle and star "filters"? Or if some had been x's and some had been o's...etc. Color might seem like a simpler property than shape, but given that it is wholly mediated by the organization of the visual field and the resulting shape properties, this intuition is in error (the tendency of vision science publications to refer to color as a "low-level" property notwithstanding.)

In fact, while we're talking about shape, there can be little doubt that the arrangement (e.g. symmetrical vs asymmetrical) of the differently colored patches in the present type of experiment will affect the accuracy of the responses. The effects might, perhaps, be averaged out, but this doesn't mean that these "high-level" effects of organization aren't mediating the purportedly "low-level" effects of color at all times.

On 2017 May 29, Lydia Maniatis commented:

Comment 2:

There seems to have been a kind of natural selection in vision science (and of course not only vision science) in which the following practice has come to dominate: The results of ad hoc measurements made under arbitrary (poorly rationalized) conditions and fitted to “models” with the help of ad hoc post hoc mathematical adjustments are treated as though they amounted to, or could amount to, functional principles.

Thus, here, the data generated by a particular task are reified; the data patterns are labelled “attention filters,” and the latter are treated as though they corresponded to a fundamental principle of visual processing. But principles have generality, while the "attention filter" moniker is here applied in a strictly ad hoc fashion:

First, the model is based on an arbitrary definition of color in terms of isolated ""colors" on a "neutral" background (i.e. conditions producing the perception of particular color patches on a neutral background), whose attributes we are told are “fully described by the relative stimulation of long, medium and short wavelength sensitive retinal cones.” These conditions and, thus, the specific patterns of stimulation correlated with them, constitute only one of an infinite number of possible conditions and thus of patterns of stimulation. (The naive equating of cone activity with color perception is a manifestation of the conceptual problems discussed in my earlier comment.)

Second, the model is ad hoc (“particularized”); “The inference process is illustrated by the model of selective attention illustrated in Fig. 1B particularized for the present experiments.” What would the generalized form of the model look like?

Third, the results only apply to individual subject/context combinations: “The model’s optimally predictive filter fk(i)fk(i) is called the observed attention filter. It typically is a very good [post hoc] predictor of a subject’s observed centroid judgments.† Therefore, we say for short that fk(i)fk(i) is the subject’s attention filter for attending to color CkCk in that context.”

It is the case that different colors vary in their salience. We could perform any number of experiments under any number of conditions with any number of observers, and generate various numbers that reflected this fact. Our experiments would, hopefully, succeed in reproducing the general facts, but the actual numbers would differ. Unless underpinned by potentially informative rationalizations guiding experimental conditions, none of these quantifications would carry any more theoretical weight than any of the others (the value-added via quantification would be zero). There is, in other words, nothing special about the numbers generated by Sun et al (2017). They make no testable claims; their specific "predictions" are all post hoc. Their results are entirely self-referential.

On 2017 May 27, Lydia Maniatis commented:

"The visual images in the eyes contain much more information than the brain can process. An important selection mechanism is feature-based attention (FBA)."

There is something very wrong here. There are no visual images in the eyes, if by images we mean organized percepts - shaped figures with features such as colors, relative locations, etc. Such things are the products of the whole perceptual process, i.e. the products of a process that begins with the effects of the point stimulation of light striking photoreceptors on the retina, setting into motion dynamic interactions of the integrated neural elements of the visual system, ultimately leading to conscious percepts.

Thus, the mechanism being referenced (if it exists) is selecting from features of the conscious products of these perceptual processes, not from the initial point information or early stages of processing in the retina.

"...a color-attention filter describes the relative effectiveness with which each color in the retinal input ultimately influences performance."

Again, there are no colors in the retinal input, color being a perceptual property of the organized output. So we are missing a retinal-state-based description of what the proposed "filters" are supposed to be attending to. This is a problem since, as is well-known, the physical (wavelength) correlate of any perceived color can have pretty much any composition, because what is perceived locally is contingent on the global context.

The use of the term filter here seems inappropriate, its misuse linked to the failure to distinguish between the proximal stimulation and perceptual facts. The implication seems to be that we are dealing with a constraint on what will be perceived, whereas on the contrary we are dealing with selection from available perceptual facts, .

The theoretical significance of measuring jnd's is not clear, as they are known to be condition-sensitive in a way not predictable on the basis of available theory. The failure to discriminate between physical/perceptual facts also means it isn't clear which of these potential differences is being referred to.

On 2016 Dec 17, Matthew Romo commented:

In their article, Kelling and colleagues identified clinical preventive services recommended by the US Preventive Services Task Force (USPSTF) that can be offered by community pharmacists, including folic acid supplementation, smoking cessation, and screening for osteoporosis and HIV (1). Clinical services are typically thought of in the context of individual patient-provider interaction, but adapting a population-level approach is particularly important for pharmacy-based preventive care services. Specifically, pharmacies located in high poverty areas have a tremendous opportunity to not only meet their communities’ public health needs, but to also reduce health disparities.

New York City exemplifies the need for this type of population-level thinking because health differs greatly by neighborhoods, which often have both poverty and racial/ethnic distinctions. For example, there are major disparities in HIV incidence, with a median annual HIV diagnosis rate of 75.6 per 100,000 population in the highest poverty neighborhoods vs. 13.7 per 100,000 population in the lowest poverty neighborhoods (2). Pharmacy-based HIV testing is indeed feasible in the city (3) and could be a service targeted to residents of high-risk neighborhoods. Nonprescription syringe sales by pharmacies to injection drug users present a propitious opportunity to promote screening for HIV.

Smoking prevalence in the highest poverty neighborhoods of New York City is more than double that of the lowest poverty neighborhoods (29.7% vs. 14.3%) (4). Availability of tobacco in pharmacies is germane if community pharmacies are to be regarded by the public as health promoting institutions. Tobacco bans in pharmacies are, of course, strongly advisable but do not appear to have a real impact on tobacco availability in poorer neighborhoods where smoking prevalence is highest. In an analysis of 240 census tracts in Rhode Island (5), tobacco retail outlet density was positively associated with neighborhood poverty and when excluding pharmacies as tobacco retailers, this association did not change. Of course, the availability of nicotine replacement therapy on pharmacy shelves allows pharmacists to counsel patients on their use. However, as mentioned by Kelling and colleagues, simple frameworks like “Ask, Advise, Refer” can help pharmacists connect patients to a telephone quitline, which can provide counseling and linkage to programs offering free or low cost nicotine replacement therapy and medication. Linkage to quitlines could be coupled with existing services, such as administering seasonal influenza vaccines or screening for drug-tobacco interactions (which are numerous). These opportunities could give a non-intrusive opportunity to “ask” and “advise.”

Pharmacy services, like other healthcare services, can differ by neighborhood. In New York City, higher poverty neighborhoods are characterized as having significantly more independent (vs. chain) pharmacies and pharmacies that are more likely to have medications out of stock (6). Nevertheless, it appears that community pharmacists support providing clinical preventive services, regardless of the neighborhood poverty level where their pharmacy is located. This was suggested by a study assessing New York City pharmacists’ attitudes about providing vaccinations to their patients when state legislation was passed allowing them to do so (7).

As highlighted by Kelling and colleagues, community pharmacists are highly accessible (and often underutilized) healthcare professionals who are clearly capable of implementing USPSTF recommendations, among others. Pharmacies are also attractive conduits for improving public health, as demonstrated by successes in immunization uptake and most recently with expansion of non-prescription naloxone access. Because of their focus on population health, local health departments should partner with community pharmacists and pharmacy owners, if they are not doing so already, to better meet the public health needs of their communities. Community pharmacists not only have the potential to positively impact public health, but because of where they work in the community, they are ideally positioned to reduce health disparities.

Matthew L. Romo, PharmD, MPH

Department of Epidemiology and Biostatistics, CUNY Graduate School of Public Health and Health Policy; CUNY Institute for Implementation Science in Population Health; matthew.romo@sph.cuny.edu

REFERENCES 1. Kelling SE, Rondon-Begazo A, DiPietro Mager NA, Murphy BL, Bright DR. Provision of clinical preventive services by community pharmacists. Prev Chronic Dis 2016;13:160232. DOI: http://dx.doi.org/10.5888/pcd13.160232. 2. Wiewel EW, Bocour A, Kersanske LS, Bodach SD, Xia Q, Braunstein SL. The association between neighborhood poverty and HIV diagnoses among males and females in New York City, 2010-2011. Public Health Rep. 2016;131(2):290-302. 3. Amesty S, Crawford ND, Nandi V, Perez-Figueroa R, Rivera A, Sutton M, et al. Evaluation of pharmacy-based HIV testing in a high-risk New York City community. AIDS Patient Care STDS. 2015;29(8):437-44. 4. Perlman SE, Chernov C, Farley SM, Greene CM, Aldous KM, Freeman A, et al. Exposure to secondhand smoke among nonsmokers in New York City in the context of recent tobacco control policies: Current status, changes over the past decade, and national comparisons. Nicotine Tob Res. 2016;18(11):2065-74. 5. Tucker-Seeley RD, Bezold CP, James P, Miller M, Wallington SF. Retail pharmacy policy to end the sale of tobacco products: What is the impact on disparity in neighborhood density of tobacco outlets? Cancer Epidemiol Biomarkers Prev. 2016;25(9):1305-10. 6. Amstislavski P, Matthews A, Sheffield S, Maroko AR, Weedon J. Medication deserts: survey of neighborhood disparities in availability of prescription medications. Int J Health Geogr. 2012;11:48. 7. Crawford ND, Blaney S, Amesty S, Rivera AV, Turner AK, Ompad DC, et al. Individual- and neighborhood-level characteristics associated with support of in-pharmacy vaccination among ESAP-registered pharmacies: pharmacists' role in reducing racial/ethnic disparities in influenza vaccinations in New York City. J Urban Health. 2011;88(1):176-85.

On 2017 Aug 15, Victoria MacBean commented:

Plain English summary:

Parasternal intercostal electromyography (EMGpara) is a method used to measure breathing function by monitoring signals sent from the brain, to the parasternal intercostal muscles (muscles between the ribs). These muscles, together with the diaphragm (a thin muscle under the lungs) and some others, move together to control your breathing. EMGpara can be used to measure a person's neural respiratory drive (NRD), which is an indication of the strength of the respiratory (breathing) muscles under a certain amount of strain (how hard the muscles may have to work when they are coping with different diseases or environments). This method is an alternative to other more traditional practices that, for example, may involve the use of needles. Therefore, EMGpara is less invasive and ideal for monitoring the breathing muscles in many groups of people.

In the case of this study EMGpara was measured in healthy adults in order to discover what factors determine normal EMGpara readings. The participants were over the age of 18, and were of different body types and sexes.

In preparation for the EMGpara tests, each participant's body size, shape and composition was measured – this included taking note of their height, weight, hip and waist size, body fat percentage and body mass index – as well as tests to confirm that each person had normally functioning lungs.

Electrode stickers were placed on the chest to measure the EMGpara signals as the subjects breathed normally and effortfully. The tests were repeated at a later date to make sure the results could be reproduced, thereby checking that the EMGpara technique is consistent.

The study suggests that sex is the most important factor in determining EMGpara; a higher value for EMGpara was observed in the women who took part. This may be because in general, woman have smaller lungs and narrower airways compared to men and their respiratory muscles are usually not as strong. Age did not seem to have a significant effect on the readings; however this could have been because the average age of those involved was only 31, and those who were older were quite athletic, meaning their respiratory health was very good.

The results of this study can be used as a reference for what a normal EMGpara reading is, and therefore they can be used when assessing patients in the future. The study included many people from different backgrounds, so it is quite representative of the population. The study was also important in working out which methods and techniques are best for measuring EMGpara, as well as for highlighting possible areas of further research for future studies.

This summary was produced by Djenné Oseitwum-Parris, Year 12 student from Burntwood School, London, UK, as part of the authors' departmental educational outreach programme.

On 2017 Jan 18, Martin Hofmeister commented:

Physical activity is an underestimated modifiable factor

I thank Wat et al. for their very interesting review article "Associations between diabetic retinopathy and systemic risk factors" in the December 2016 issue of the Hong Kong Medical Journal. I agree with the authors but there is one lifestyle aspect worth mentioning. Recent studies suggest that regular physical activity can be a protective factor for the development of diabetic retinopathy (DR) and microvascular diabetes-related complications [1-6]. Physical activity and exercise is characterized by a simultaneous antihyperglycemic (reduction in haemoglobin A1c of -0.6%), antihyperlipidemic, antihypertensive, antioxidative, anti-inflammatory, and cardioprotective effects.

An example of neurobiological adaptations to exercise is the increased expression of neuroprotective factors such as brain-derived neurotrophic factor (BDNF) in the brain, blood, and muscles. Decreased plasma levels of BDNF were detected as an independent risk factor for DR and vision-threatening DR in Chinese type 2 diabetic patients [7-8]. The downregulation of BDNF probably has an important role in the complex and multifactorial pathogenesis of DR [9].

In a first study, Loprinzi also observed a positive association between sedentary behavior and DR [10]. The American Diabetes Association has recently updated its evidence-based recommendations on physical activity and exercise for diabetic patients. The main innovation is that diabetics should minimize the total amount of daily sedentary time. Prolonged sitting time should be interrupted every 30 min with brief (≤5 min) bouts of standing or light activity to improve the glycemic control [11].

In the case of severe nonproliferative and unstable proliferative retinopathy, it is recommended that vigorous-intensity activities be avoided [11].

REFERENCES

1) Dirani M, Crowston JG, van Wijngaarden P. Physical inactivity as a risk factor for diabetic retinopathy? A review. Clin Exp Ophthalmol 2014;42(6):574-81. Dirani M, 2014

2) Loprinzi PD, Brodowicz GR, Sengupta S, Solomon SD, Ramulu PY. Accelerometer-assessed physical activity and diabetic retinopathy in the United States. JAMA Ophthalmol 2014;132(8):1017-9. Loprinzi PD, 2014

3) Gutiérrez Manzanedo JV, Carral San Laureano F, García Domínguez G, Ayala Ortega C, Jiménez Carmona S, Aguilar Diosdado M. High prevalence of inactivity among young patients with type 1 diabetes in south Spain. Nutr Hosp. 2014;29(4):922-8. Gutiérrez Manzanedo JV, 2014

4) Loprinzi PD. Concurrent healthy behavior adoption and diabetic retinopathy in the United States. Prev Med Rep. 2015;2:591-4. Loprinzi PD, 2015

5) Li Y, Wu QH, Jiao ML, Fan XH, Hu Q, Hao YH, Liu RH, Zhang W, Cui Y, Han LY. Gene-environment interaction between adiponectin gene polymorphisms and environmental factors on the risk of diabetic retinopathy. J Diabetes Investig. 2015;6(1):56-66. Li Y, 2015

6) Praidou A, Harris M, Niakas D, Labiris G. Physical activity and its correlation to diabetic retinopathy. J Diabetes Complications. 2016 Jun 29. pii: S1056-8727(16)30256-2. doi: 10.1016/j.jdiacomp.2016.06.027. [Epub ahead of print]. Praidou A, 2017

7) Liu SY, Du XF, Ma X, Guo JL, Lu JM, Ma LS. Low plasma levels of brain derived neurotrophic factor are potential risk factors for diabetic retinopathy in Chinese type 2 diabetic patients. Mol Cell Endocrinol 2016;420:152-8. Liu SY, 2016

8) Guo M, Liu H, Li SS, Jiang FL, Xu JM, Tang YY. LOW SERUM BRAIN-DERIVED NEUROTROPHIC FACTOR BUT NOT BRAIN-DERIVED NEUROTROPHIC FACTOR GENE VAL66MET POLYMORPHISM IS ASSOCIATED WITH DIABETIC RETINOPATHY IN CHINESE TYPE 2 DIABETIC PATIENTS. Retina. 2016 Jun 27. [Epub ahead of print]. Guo M, 2017

9) Behl T, Kotwani A. Downregulated Brain-Derived Neurotrophic Factor-Induced Oxidative Stress in the Pathophysiology of Diabetic Retinopathy. Can J Diabetes. 2016 Nov 29. pii: S1499-2671(16)30079-X. doi: 10.1016/j.jcjd.2016.08.228. [Epub ahead of print]. Behl T, 2017

10) Loprinzi PD. Association of Accelerometer-Assessed Sedentary Behavior With Diabetic Retinopathy in the United States. JAMA Ophthalmol 2016;134(10):1197-8. Loprinzi PD, 2016

11) Colberg SR, Sigal RJ, Yardley JE, Riddell MC, Dunstan DW, Dempsey PC, Horton ES, Castorino K, Tate DF. Physical activity/exercise and diabetes: a position statement of the American Diabetes Association. Diabetes Care 2016; 39(11): 2065-79. Colberg SR, 2016

On 2016 Oct 26, Ian Dworkin commented:

Links to the dataset and scripts can be found here: https://github.com/DworkinLab/HaberDworkin_Evolution2016

and on DRYAD http://www.datadryad.org/resource/doi:10.5061/dryad.3b426

On 2016 Dec 04, Alessandro Rasman commented:

Increased levels of coagulation factors in Multiple Sclerosis: a defending mechanism from microbleedings?

On 2016 Nov 08, P P Wolkow commented:

It is true that culture negative blood samples are difficult to work with and the interpretation of the obtained results is not easy. We believe that we have taken every care to avoid contamination and to analyze our data accordingly. However, we understand that you might not fully concur with our results.

Indeed NTC and blood samples contain the same taxa as viewed on Fig. 3a. However based on this sole statement, one cannot claim that these samples are similar. In fact they are different, what can be seen below based on following examples at the Order level. Bifidobacteriales in the healthy blood constituted 73.0% of reads vs. 12.8% in NTC samples (p = 2.76 x 10-7). In our opinion this level of significance confirms that the groups are different. Few other examples based on Figure 4 data: healthy vs NTC vs sepsis: Actinomycetales: 2.0% vs 7.7% vs 30.9%- p=0.04; Pseudomonadales: 6.7% vs 0.0% vs 4.4% - p=0.006; Sphingomonadales: 0.2% vs 11.4% vs 7.3%-p=3 x 10-7.

It is true that NTC samples cluster with clinical samples in PCoA analysis, however they cluster with septic samples but not with healthy ones. Clustering with the latter could potentially mean that the results for the healthy people are untrue due to sequencing a contamination only. Please note that only 3 out of 5 NTC samples passed the analytical threshold and only these are depicted on Fig. 2. In the two NTC samples filtered out from further analysis, the numbers of reads were very low, 480 and 73, respectively. Also, contamination of simultaneously processed NTC samples should result in similar abundance of phyla in these samples, which is not the case (Fig. 3).

PCR conditions are provided in Table 1. Negative control procedure was exactly the same for all samples analyzed and should have no impact on the results. All samples were prepared in one batch so we did not expect a batching effect.

An idea of retrospective contaminant read removal is in our opinion controversial. There are deep inter-individual differences between the NTC samples. Removal of the reads based on mean number of reads would lead to skewed results and negative read numbers in some samples.

We expected that results depicted on Fig. 5 would be self-explanatory. However, we admit that providing qPCR data would be superior. We are grateful for drawing our attention to this issue which will have implications for our future work.

On 2016 Oct 27, Susannah Salter commented:

The paper by Gosiewski et al (PMID27771780) draws strange conclusions from the data. Culture-negative blood samples are certainly difficult to work with as they are more susceptible to the influence of DNA contamination.

In the text attention is drawn to the sequenced controls (water) but some assertions are patently untrue: for example stating that Bifidobacterales were a noteworthy constituent of healthy blood when it also makes up >10% proportion of the negative controls (Fig 4), or stating that the control profiles are "completely different" to the blood samples despite appearing to contain most of the same taxa (Fig 4) and clustering with the clinical samples on PCoA (Fig 2).

The authors provide no detailed information about the number of PCR cycles, the negative control procedure, kit batching of samples, retrospective contaminant read removal etc, which would lend confidence that the described patterns are not artefacts of sample processing. qPCR would also help to clarify the background contaminant DNA levels and allow more robust conclusions to be drawn.

The supplemental figure has the most potentially interesting information but unfortunately it is not labelled or described in text. If the contaminant taxa are removed, there may be some nice signals hiding in there.

On 2016 Dec 20, Natalie Clairoux commented:

Free version of this article available after 2017-10-19 at https://papyrus.bib.umontreal.ca/xmlui/handle/1866/16350