On 2017 Jul 29, Christopher Southan commented:

BIA 10-2474 is now avaible from vendors (see https://cdsouthan.blogspot.se/2016/01/molecular-details-related-to-bia-10-2474.html). The experimental verification of the predictions in this paper are thus awaited with interest.

On 2016 Dec 29, Lydia Maniatis commented:

The title of this article indicates that the authors may have something to say about “lightness perception for surfaces moving through different illumination levels”, but leaves us in the dark what that might be.

The abstract isn’t much more illuminating. The somewhat vague message seems to be that the perceived lightness of a patch in the visual field depends on the structure of the “light field,” the “choice of fixation positions,” and whether the scene is viewed freely or not, and that “eye movements in [dynamic scenes and nonuniform light fields] are chosen to improve lightness constancy.”

Unfortunately and fatally absent from the terms of the discussion is any reference to shape. Yet, shape (i.e. the organization (segregation/unification, 3D interpretation), via the visual process, of the points in the retinal projection into perceived forms) is the only available means to the goal of creating percepts of lightness as well as relative illumination of surfaces. This is obvious with respect to the authors' sitmuli, which are images on a computer screen. The luminance structure of the light emitting points on that screen is the only information the visual system has to work with, and unless those points are grouped and boundaries and depth relations inferred there is no basis for designating continuous surfaces, their lightness, their relative illumination. Whether areas of the visual are interpreted as changing in reflectance or illumination is contingent on which parts of the field are eligible to be grouped into perceived physical units, with a homogeneous surface.

In other words: When the luminance of a surface in a part of the visual field changes, (e.g. from lighter to darker), the change may be interpreted as being due to a change in illumination of a surface in that location, a change in the color of the surface at that location, the presence of a fog overlying the surface at that location, etc., or a combination of these possibilities. How is the solution (the percept) arrived at? For example, at the lower left side of Toscani et al’s (2016) Figure 1, an edge between a dark area (the “wall)” and a lighter area (the “side of a cube”) to its right is perceived as a lightening in terms of both perceived illumination and perceived reflectance) while a change from same lighter area to a darker area to its right is seen as a change in illumination only. The reason is structural, based on the very principles of organization not mentioned by the authors.

The consequence of the failure to consider principles of organization in any study of lightness perception is that ANY resulting claims can be immediately falsified. It is impossible to predict how a surface will look when placed in any given location in the visual field by referring only to the distribution of incident illumination, since this information doesn’t in the least allow us to predict luminance structure. And a description of luminance structure doesn’t help us if we don’t consider visual principles of organization. The former fact should be particularly obvious to people using uniformly illuminated pictorial stimuli, whether on a page or on a screen, which produce impressions of non-uniform illumination. Like reflectance, the perception of illumination is constructed, it isn’t an independent variable for vision; so it makes no sense, in the context of perception experiments, to refer to it as though it is – as the authors do in the phrase “moving through different illumination levels” - especially if we aren’t even talking about actual illumination levels, but only visually-constructed ones! The perception of changing illumination levels is the flip side to the perception of unchanging surfaces, and vice versa. Like lightness, perceived illumination is dependent on principles of organization, starting with figure/ground segregation.

So, for example, when the authors say that the brightest parts of a (perceived) surface’s luminance distribution is “an efficient…heuristic for the visual system to achieve accurate…judgments of lightness,” we can counter (falsify) with the glare illusion (http://www.opticalillusion.net/optical-illusions/grey-glow-illusion-the-glare-effect/) in which the brightest area is not perceived as the plain view color of the surface, which appears black and obscured by a glare or bright fog.

With respect to eye movements and fixation: It seems to be the case that fixations are the product, not the cause, of perceptual solutions. For example, it has been shown that while viewing the Muller-Lyer illusion, eye movements trace a longer path when we’re looking at the apparently longer figure and vice versa. Another problem with the claim that eye movements have a causal role by sampling “more relevant” parts of the field is that all parts of the field are taken into account in the generation of a percept, e.g. in order for the visual system to conclude that a particular patch is the lightest part of a homogeneously-colored but differently-illuminated physical unit, rather than a differently colored patch on a different unit. Since the perceived relative lightness/illumination of that particular patch is related to the perceived lightness/illumination of the whole visual field, isolating that patch by fixation can’t be uniquely informative. As we know, reduction conditions can transform the perception of surfaces.

I would note that the emphasis on “lightness constancy” rather than “principles of lightness perception” is common but ill-conceived. With respect to understanding perception, understanding lightness constancy is no more informative than understanding lightness inconstancy. (For a great example, complete with movement, of lightness INconstancy, see https://www.youtube.com/watch?v=z9Sen1HTu5o). In either case, what is constant are the underlying perceptual principles; to understand one effect is to understand the other. This is another reason the claim that eye movements are chosen “to improve lightness constancy” is ill-conceived. Only an all-knowing homunculus can know, a priori, which areas of the visual field represent stimulation from physical surfaces with constant reflectance x, which represent physical surfaces obstructed by fog or in shadow, which areas represent physical surfaces that are actually changing in their light reflecting properties (a squid, for example - do we want to improve his or her constancy?), etc. The visual system has to go where the evidence goes, as interpreted via the evolved process. This process achieves veridicality – e.g. seeing surface properties as unchanging when they’re unchanging, and as changing when they’re changing - in typical conditions.

Ironically, observers in Toscani et al’s (2016) experiments are not perceiving surfaces veridically, since, for example, parts of the screen surface that are actually varying in their color are perceived as unchanging in that respect, while, correspondingly, they are seen (incorrectly) as experiencing changing illumination. So we’re actually talking about the converse of lightness constancy; the authors are equating a physical surface that is unchanging in its light-reflecting properties, but experiencing changing illumination, with a surface (a section of the screen) that is actually changing in its light reflecting/emitting properties independently of incident illumination, which is constant. In the former case, seeing the surface as unchanging parallels the physical situation, while in the latter case it is opposite to the physical situation. Calling both situations examples of “lightness constancy” only confuses the issue, which is: “Why does a retinal projection with a particular luminance structure result in patch x looking the way it does.” The question, again, cannot be answered reliably without invoking principles of organization, i.e. the consequences of that luminance structure for perceived shape.

Short version: Shape.

On 2017 Jan 04, Lydia Maniatis commented:

This article belongs to the popular "transparent brain" school of thought. (The label is inspired by Graham (1992) see comment https://pubpeer.com/publications/8F9314481736594E8D58E237D3C0D0).

That is, certain visual scenes selectively tap neurons at particular levels of the visual system, such that by analyzing the percept we can draw conclusions about the behavior of groups of neurons at that level.

Teller (1984) called this view the "nothing mucks it up proviso," referring to the fact that it assumes all other parts of the hierarchically-organized, complicatedly interconnected visual system play no role in the particular effect of interest.

The untenable transparent brain fiction is compromised even further by the "simple" stimuli that are supposed to enable the transparent view into V1 etc, as they actually elicit highly sophisticated 3D percepts including effects such as the perception of light and shadow and fog/transparency. OF course, these perceptual features are mediated by the activity of V1 (etc) neurons. But the factors the investigators reference - orientation here, often contrast - are somehow supposed to retain their power to reflect only the behavior of V1 (or whatever level particular investigators are claiming to isolate and "model.")

On 2017 Jan 23, Scott D Slotnick commented:

There has been a call for peer commentary on the Editorial/Discussion Paper (Slotnick SD, 2017) in the journal Cognitive Neuroscience (due February 13th, 2017). The Editorial/Discussion Paper, Commentaries, and an Author Response will be published in an issue of Cognitive Neuroscience later this year.

On 2017 Jan 04, Gerard Ridgway commented:

This editorial suggests that the problems identified by Eklund A, 2016 arise solely from the use of resting-state data in place of null data. It seems to overlook the fact that Eklund A, 2016 use randomly timed designs (two blocked designs and two event-related), meaning the unknown timecourse of default mode network activity cannot consistently give rise to design-synchronised activation (except perhaps in the special case of the initial transients, which is mentioned briefly in an article by Flandin and Friston, 2016, but probably warrants further investigation). On the other hand, the activity of the DMN could perhaps be contributing to non-Gaussianity of the residuals and/or a more complex spatial autocorrelation function (ACF) than is typically modelled, but these aspects seem not to be mentioned, or to be addressed in the author's recommended simulation approach (which seems to be very similar to the original AlphaSim from AFNI).

Regarding the spatial ACF in particular, but also the issue of the cluster-defining threshold (CDT), this article should be contrasted with Cox et al., 2016, which recommends a new long-tailed non-Gaussian ACF available in newer versions of AlphaSim, together with a CDT of 0.001 or below.

On 2017 Feb 08, Chris Del Mar commented:

Has this trial report hidden the results -- that symptomatic outcomes are clinically almost identical -- in plain sight? See this blog that plots the results more transparently:-

http://blogs.bmj.com/bmj/2017/02/08/how-to-hide-trial-results-in-plain-sight/?utm_campaign=shareaholic&utm_medium=twitter&utm_source=socialnetwork

Chris Del Mar cdelmar@bond.edu.au Paul Glasziou pglaszio@bond.edu.au

On 2017 Mar 24, Dorothy V M Bishop commented:

It is a pleasure to see this paper, which has the potential to transform the field of ERP research by setting new standards for reproducibility.

I have one suggestion to add to those already given for reducing the false discovery rate in this field, and that is to include dummy conditions where no effect is anticipated. This is exactly what the authors did in their demonstration example, but it can also be incorporated in an experiment. We started to do this in our research on mismatch negativity (MMN), inspired by a study by McGee et al 1997; they worked at a time when it was not unusual for the MMN to be identified by 'experts' – and what they showed was that experts were prone to identify MMNs when the standard and deviant stimuli were identical. We found this approach – inclusion of a 'dummy' mismatch – invaluable when attempting to study MMN in individuals (Hardiman and Bishop, 2010). It was particularly helpful, for instance, when validating an approach for identifying time periods of significant mismatch in the waveform.

Another suggestion is that the field could start to work more collaboratively to address these issues. As the authors note, replication is the best way to confirm that one has a real effect. Sometimes it may be possible to use an existing dataset to replicate a result, but data-sharing is not yet the norm for the field – journals could change that by requiring deposition of the data for published papers. But, more generally, if journals and/or funders started to require replications before work could be published, then one might see more reciprocal arrangements, whereby groups would agree to replicate each other's findings. Years ago, when I suggested this, I remember some people said you could not expect findings to replicate because everyone had different systems for data acquisition and processing. But if our data are specific to the lab that collected them, then surely we have a problem.

Finally, I have one request, which is that the authors make their simulation script available. My own experience is that working with simulations is the best way to persuade people that the problems you have highlighted are real and not just statistical quibbles, and we need to encourage researchers in this area to become familiar with this approach.

Bishop, D. V. M., & Hardiman, M. J. (2010). Measurement of mismatch negativity in individuals: a study using single-trial analysis. Psychophysiology, 47, 697-705 doi:10.1111/j.1469-8986.2009.00970.x

McGee, T., Kraus, N., & Nicol, T. (1997). Is it really a mismatch negativity? An assessment of methds for determining response validity in individual subjects. Electroencephalography and Clinical Neurophysiology, 104, 359-368.

On 2017 Jan 03, Daniel Schwartz commented:

The BC Cardiac Surgical Intensive Care Score is available online or via the Calculate mobile app for iOS, Android and Windows 10 at https://www.qxmd.com/calculate/calculator_36/bc-cardiac-surgical-intensive-care-score

Conflict of interest: Medical Director, QxMD

On 2016 Dec 23, Alessandro Rasman commented:

Bernhard HJ. Juurlink MD, Giovanni Battista Agus MD, Dario Alpini MD, Maria Amitrano MD, Giampiero Avruscio MD, Pietro Maria Bavera MD, Aldo Bruno MD, Pietro Cecconi MD, Elcio da Silveira Machado MD, Miro Denislic MD, Massimiliano Farina MD, Hector Ferral MD, Claude Franceschi MD, Massimo Lanza MD, Marcello Mancini MD, Donato Oreste MD, Raffaello Pagani MD, Fabio Pozzi Mucelli MD, Franz Schelling MD, Salvatore JA Sclafani MD, Adnan Siddiqui MD, PierluigI Stimamiglio MD, Arnaldo Toffon MD, Antonio Tori MD, Gianfranco Vettorello MD, Ivan Zuran MD and Pierfrancesco Veroux MD

We read with interest the study titled "Free serum haemoglobin is associated with brain atrophy in secondary progressive multiple sclerosis" (1). Dr. Zamboni first outlined the similarities between impaired venous drainage in the lower extremities and MS in 2006 in his "Big Idea" paper (2). Chronic venous insufficiency can cause a breakdown of red blood cells, leading to increased levels of free hemoglobin. Exactly what the London researchers saw 11 years later.

References: 1) Lewin, Alex, et al. "Free serum haemoglobin is associated with brain atrophy in secondary progressive multiple sclerosis" Wellcome open research 1-10 (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 Feb 27, Zvi Herzig commented:

Prolonged exposures of oropharyngeal tissue submerged in refill liquids are a poor comparison to brief exposures from accidents.

The constituents of EC liquids other than nicotine (glycerol, propylene glycol and food flavorings) are GRAS approved in relation to oral consumption. It's therefore unlikely that these would pose a particular hazard in relation to oral cancer.

Likewise, with regards to nicotine, epidemiology of prolonged oral exposure in relation to snus is not linked to oral cancer either Lee PN, 2011.

Thus none of the known e-liquid constituents are plausibly related to oral cancer. Which supports the above conclusion that the study's results unrelated to normal exposures.

On 2017 Jan 03, Christian Welz commented:

we discussed that issue in the publication: "Because most EC users refill their cartridges by themselves, and incidental or accidental contact is logical and described (Varelt et al., 2015; Vakkalanka et al., 2014) we intentionally used unvapored liquids for our experiments...."

On 2016 Dec 20, Zvi Herzig commented:

This study directly exposes cells to liquids, despite that fact that users are exposed to the vapor, not the liquid. This issue has been noted previously Hajek P, 2014, Farsalinos KE, 2014. The ~3 ml of liquid which EC users consume daily Farsalinos KE, 2014 is diluted by much air over hundreds of puffs. This is incomparable to the direct exposures to liquids in the present study.

On 2017 Jun 09, M Mangan commented:

There has now been an EFSA review of the paper, with an eye towards regulatory aspects in the EU. They describe the work as incomplete and with "severe shortcomings".

http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2017.EN-1249/abstract

On 2017 Jan 03, M Mangan commented:

There have now been some really good summaries of issues with this work.

Is GM corn really different to non-GM corn? http://sciblogs.co.nz/code-for-life/2016/12/31/gm-corn-really-different-non-gm-corn/

What are isogenic lines and why should they be used to study GE traits? http://themadvirologist.blogspot.com/2017/01/what-is-isogenic-line-and-why-should-it.html

Another: http://biobeef.faculty.ucdavis.edu/2017/01/03/i_would_appreciate_your_comments/

On 2016 Dec 22, M Mangan commented:

The top fold change showed in this paper turns out to be a plant pathogen protein, that might have been affecting the maize. http://www.uniprot.org/uniprot/W7LNM5

If that is the case, it may demonstrate the power of -omics in revealing that the claims of differences have to be evaluated very carefully. They may not be what the authors claim they are.

We await some explanation of this large difference between samples from the authors.

Edit to add: The author Mesnage asked me to post questions at the journal site, but is not coming over to answer them. Maybe the authors will find them here, so I'll also add them here as well.

There's a lot of nonsense drama below now, but I want to hear from the authors (Robin Mesnage asked me to post here, but I can't see if he's responding):

1. What is your explanation for the fact that top fold-change proteins in your data set are fungal proteins (and it's a known maize pathogen)?

2. Are you aware that fungal contamination could result in similar changes in regards to the pathway changes that you describe? Did you consider this at all? Why didn't you address this in your paper?

3. If you wish to dismiss your own top reported proteins, how can you stand by the importance of the fold-change claims you are making about other proteins?

Thanks for your guidance on this. It's very perplexing.

On 2017 Jan 10, Jesper M Kivelä commented:

The URL in the reference number 2 is invalid (i.e. html is missing in the end). This error slipped through my (evidently not so) pedantic eyes at proof stage.

On 2017 Mar 15, Sin Hang Lee commented:

Correspondence submitted to Nat.Rev.Dis.Primers

In their recent Primer [Lyme borreliosis. Nat. Rev. Dis. Primers 2, 16091 (2016)] Allen Steere and colleagues described Lyme borreliosis as an important emerging infectious disease [1]. The authors assert that the natural history of untreated Lyme borreliosis can be divided into stages 1, 2 and 3, and that the early stage 1 infections can be treated successfully with a 10–14 day course of antibiotics. However, the authors also stated that demonstration of borrelial infection by laboratory testing is required for reliable diagnosis of Lyme borreliosis, with the exception of erythema migrans and that serodiagnostic tests are insensitive during the first several weeks of infection. If not treated early, “within days to weeks, the strains of B. burgdorferi in the United States commonly disseminate from the site of the tick bite to other regions of the body”. In other words, the authors have affirmed that if reliably diagnosed at the early stage of the infection, Lyme borreliosis can be cured with timely, appropriate antibiotics to prevent deep tissue damage along with its associated clinical manifestations resulting from host immune response to various spirochetal products or components. In the Outlook Diagnostic tests section of the article, the authors failed to mention the fact that currently the diagnosis of emerging infectious diseases largely depends on finding evidence of the causative agent in the host by nucleic acid-based tests [2], not serodiagnostic tests which usually turn positive only during convalescence. The authors seem to advise the medical practitioners to not treat Lyme disease patients until the proliferating spirochetes in the host have elicited certain immune responses which can be confirmed by serologic tests. Such practice should not be accepted or continued for obvious reasons.

The authors stated “After being deposited in the skin, B. burgdorferi usually multiplies locally before spreading through tissues and into the blood or lymphatic system, which facilitates migration to distant sites.”. This statement acknowledges that spirochetemia is an early phase in the pathogenesis of Lyme borreliosis. But under the section of Diagnostic tests, polymerase chain reaction (PCR) test was only mentioned for synovial fluid of patients in late Lyme arthritis and for cerebrospinal fluid (CSF) of late neuroborreliosis. To refute the usefulness of DNA test for Lyme disease diagnosis, the authors cited a study which showed borrelial DNA was detected in synovial fluid of Lyme arthritis patients containing moribund or dead spirochetes [3]. However, the authors failed to discuss the significance of detection of borrelial DNA in the diagnosis of spirochetemia. The authors failed to acknowledge that even the finding of moribund or dead borrelial cells circulating in the blood is diagnostic of an active infection. Free foreign DNA is degraded and eliminated from the mammalian host’s blood within 48 hours [4]. Detection of any borrelial DNA validated by DNA sequencing is indicative of a recent presence of spirochetes, dead or alive, in the circulating blood which is evidence of an active infection beyond a reasonable doubt.

It seems unfortunate for many current Lyme disease patients that Lyme arthritis was described before the era of Sanger sequencing and PCR [5]. If Lyme borreliosis were discovered as an emerging infectious disease today, Lyme disease would probably be routinely diagnosed using a highly accurate nucleic acid amplification test, as reiterated by Dr. Tom Frieden, director of the Centers for Disease Control and Prevention (CDC) for Zika virus infection [6], or by the European Centre for Disease Prevention and Control for the case definition of Ebola virus infection [7]. Now there is evidence that clinical “Lyme disease” in the United States may be caused by B. miyamotoi [8-10], co-infection of B. burgdorferi and B. miyamotoi [9], a novel CDC strain (GenBank ID# KM052618) of unnamed borrelia [10], and a novel strain of B. burgdorferi with two homeologous 16S rRNA genes [11]. The Lyme disease patients infected with these less common strains of borreliae may have negative or non-diagnostic two-tiered serology test results. Neither erythema migrans nor serologic test is reliable for the diagnosis of Lyme disease. In one summer, the emergency room of a small hospital in Connecticut saw 7 DNA sequencing-proven B. burgdorferi spirochetemic patients. Only three of them (3/7) had a skin lesion and only one (1/7) had a positive two-tiered serologic Lyme test [12].

After a 40-year delay, the medical establishment should begin to diagnose “Lyme disease” as an emerging infectious disease by implementing nucleic acid-based diagnostic tests in the Lyme disease-endemic areas. A national proficiency test program to survey the competency of diagnostic laboratories in detecting various pathogenic borrelia species is urgently needed for stimulating diagnostic innovation. We should treat the borrelial infection of “Lyme disease” to reduce its autoimmune consequences, just like treating streptococcal infection early to reduce the incidence of rheumatic heart disease in the past.

Allen Steere and colleagues have written a prescription to treat Lyme borreliosis in their lengthy article raising numerous questions [1], but paid little attention to the issue of how to select the patients at the right time for the most effective treatment. For the physicians managing current and future Lyme disease patients, a sensitive and no-false positive molecular diagnostic test is a priority, also the most important issue for the patients that Allen Steere and his colleagues have simply glossed over.

Conflict of Interest: Sin Hang Lee is the director of Milford Molecular Diagnostics Laboratory specialized in developing DNA sequencing-based diagnostic tests for community hospital laboratories.

References 1. Steere, A.C. et al. Lyme borreliosis. Nat. Rev. Dis. Primers 2,16091 (2016). 2. Olano, J.P. & Walker, D.H. Diagnosing emerging and reemerging infectious diseases: the pivotal role of the pathologist. Arch. Pathol. Lab. Med. 135, 83-91 (2011). 3. Li, X. et al. Burden and viability of Borrelia burgdorferi in skin and joints of patients with erythema migrans or Lyme arthritis. Arthritis Rheum. 63, 2238–2247 (2011). 4. Schubbert, R. et al. Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA. Proc. Natl. Acad. Sci. U. S. A. 94, 961-966 (1997). 5. Steere, A. C. et al. Lyme arthritis: an epidemic of oligoarticular arthritis in children and adults in three connecticut communities. Arthritis Rheum. 20, 7–17 (1977). 6. Frieden T. Transcript for CDC Telebriefing: Zika Update. https://www.cdc.gov/media/releases/2016/t0617-zika.html (2016) 7. ECDC. Ebola virus disease case definition for reporting in EU. http://ecdc.europa.eu/en/healthtopics/ebola_marburg_fevers/EVDcasedefinition/Pages/default.aspx#sthash.LvKojQGu.wf5kwZDT.dpuf (2016 last accessed) 8. Jobe, D.A. et al. Borrelia miyamotoi Infection in Patients from Upper Midwestern United States, 2014-2015. Emerg. Infect. Dis. 22, 1471-1473 (2016). 9. Lee, S.H. et al. Detection of borreliae in archived sera from patients with clinically suspect Lyme disease. Int. J. Mol. Sci. 15, 4284-4298 (2014). 10. Lee, S.H. et al. DNA sequencing diagnosis of off-season spirochetemia with low bacterial density in Borrelia burgdorferi and Borrelia miyamotoi infections. Int. J. Mol. Sci. 15, 11364-11386 (2014). 11. Lee, S.H. Lyme disease caused by Borrelia burgdorferi with two homeologous 16S rRNA genes: a case report. Int. Med. Case Rep. J. 9,101-106 (2016). 12. Lee, S.H. et al. Early Lyme disease with spirochetemia - diagnosed by DNA sequencing. BMC Res. Notes. 3, 273 (2010).

On 2016 Dec 28, Marcia Herman-giddens commented:

While there are many aspects of this review paper by Steere, et al, which beg for comment, I focus on the erythema migrans rash (EM). Steere, et al, state that “erythema migrans is the presenting manifestation of Lyme borreliosis in ~80% of patients in the United States” based on their 2003 paper. It is unclear from that paper exactly how this figure was obtained. As far as I know, there has never been a well-designed study to examine this issue.

I was pleased to see Figure 5 showing photographs of EM rashes with their more accurate solid red appearance. Research has shown that, contrary to popular belief (likely because of the promotion of the so-called ‘target or bull’s-eye’ type of lesion), most EMs are solid red. As stated by Shapiro in 2014 in the NEJM, “Although reputed to have a bull’s-eye appearance, approximately two thirds of single erythema migrans lesions either are uniformly erythematous or have enhanced central erythema without clearing around it.” Later, some may have central clearing. The CDC estimates “70-80%” of Lyme disease patients have an EM rash and call the picture on their webpage “classic” even though it shows a bull’s-eye or target type lesion.

One outcome of this misrepresentation as a bull’s eye or target lesion, is that patients with the more common solid EM rash may not present to their medical provider in a timely manner thinking that it does not represent possible Lyme disease. I know of several cases where this happened and the patients went on to develop late Lyme disease. Aucott et al, in their 2012 paper, “Bull’s-Eye and Nontarget Skin Lesions of Lyme Disease: An Internet Survey of Identification of Erythema Migrans,” found that many of the general public participants were familiar with the classic target-type erythema migrans lesion but only 20.5% could correctly identify the nonclassic erythema migrans. In addition, many health care providers are not well trained in the recognition of EM rashes. In a case series by Aucott et al. in 2009, among Lyme disease patients presenting with a rash, the diagnosis of EM was initially missed by providers in 23%.

The well-known lack of sensitivity in the recommended two-tier test for diagnosis of Lyme disease in early infections and the probability that many EM rashes are misdiagnosed or missed, especially among people living alone or when the rash occurs in the hairline, etc. contribute to the lack of accurate data on the incidence of EM rashes following infection with B. burgdorferi. These factors and others affect the collection of accurate data on the proportion of patients newly infected with B. burgdorferi who do develop erythema migrans and suggest that the true incidence is likely lower than 70-80%.

Steere et al. Lyme borreliosis. Nat Rev Dis Primers. 2016 Dec 15;2:16090. doi: 10.1038/nrdp.2016.90. Steere AC, Sikand VK. The presenting manifestations of Lyme disease and the outcomes of treatment. New England Journal of Medicine. 2003 Jun 12;348(24):2472-4. Shapiro ED. Lyme disease. New England Journal of Medicine. 2014 May 1;370(18):1724-31. www.cdc.gov/lyme/signs_symptoms/ Aucott JN, Crowder LA, Yedlin V, Kortte KB. Bull’s-Eye and Nontarget Skin Lesions of Lyme Disease: An Internet Survey of Identification of Erythema Migrans. Dermatology research and practice. 2012 Oct 24;2012. Aucott J, Morrison C, Munoz B, Rowe PC, Schwarzwalder A, West SK. Diagnostic challenges of early Lyme disease: lessons from a community case series. BMC Infectious Diseases. 2009 Jun 1;9(1):1.

On 2016 Dec 25, Raphael Stricker commented:

Lyme Primer is Obsolete (Part 1)

Raphael B. Stricker, Union Square Medical Associates, San Francisco, CA; Lorraine Johnson, LymeDisease.org, Chico, CA. rstricker@usmamed.com; lbjohnson@lymedisease.org

The Lyme primer by Steere and colleagues presents an overview of the epidemiology, pathogenesis, diagnosis and treatment of Lyme disease. The authors adhere to the dogma and opinions of the Infectious Diseases Society of America (IDSA), and as a result the primer showcases the schizoid nature of the IDSA view of Lyme disease: while the pathogenesis of the disease is highly complex and worthy of a formidable infectious agent, the epidemiology, diagnosis and treatment of the disease is ridiculously simple and rather banal ("hard to catch and easy to cure"). As a result, the primer propagates the myths and misinformation about Lyme disease that have made the IDSA view obsolete and contributed to the unchecked spread of the tickborne disease epidemic around the world. The following points address significant flaws and deficiencies in the primer, with appropriate references.

There are two standards of care for Lyme disease. One is based on the guidelines of IDSA (Reference 101 in the primer) and the other is based on the guidelines of the International Lyme and Associated Diseases Society (ILADS) (1). The primer adheres to the IDSA guidelines, which are based largely on "expert opinion" (2,3) and were recently delisted by the National Guideline Clearinghouse (NGC) because they are obsolete and fail to meet methodological quality standards for guideline development set forth by the Institute of Medicine (IOM) (1). The NGC recognizes the ILADS guidelines, which were developed using the GRADE methodology endorsed by the IOM (1). Much of the clinical information in the primer is refuted by the ILADS guidelines, as outlined below.

In the Abstract, the primer states that "All manifestations of the infection can usually be treated successfully with appropriate antibiotic regimens, but the disease may be followed by post-infectious sequelae in some patients." Current evidence from "big data" analysis indicates that 36-63% of patients treated with IDSA-recommended short-course antibiotics may fail this therapy (4-6). The concept of "post-infectious sequelae" ignores the extensive literature on persistent Borrelia burgdorferi (Bb) infection despite antibiotic treatment (1,7).

The primer states that "Infection through alternate modes of transmission, including transfusion, sexual contact, semen, urine, or breast milk, has not been demonstrated." This is a very strong statement that ignores growing evidence of other modes of Bb transmission, especially via pregnancy and sexual contact (8-10). The primer states that Borrelia does not produce its own matrix degrading proteases. This statement ignores the description of a Bb aggrecanase that plays a role in tissue invasion by the spirochete and probably facilitates chronic infection as well (11,12).

Neurological syndromes associated with Bb infection are considered "controversial" by IDSA proponents because only hard neurological signs (Bell's palsy, meningoencephalitis) are accepted as significant by that group. In contrast, many Lyme patients have only soft neurological signs (cognitive and memory problems, severe fatigue, neuropathy), and these features of chronic Lyme disease are ignored by the primer authors despite supportive literature (13,14). The concept that neurological and cardiac involvement in Lyme disease resolves spontaneously, even without treatment, promotes a pet IDSA theme that Lyme disease is a trivial illness. This concept is not supported by recent literature that has documented cardiac deaths in untreated patients (15).

The primer repeats the discredited view that Lyme testing is "virtually 100%" positive after 4-8 weeks of untreated infection. This unreferenced statement ignores the fact that two-tier testing for persistent Bb infection has poor sensitivity (46%) despite excellent specificity (99%) (16,17). The studies that allegedly show high sensitivity of two tier testing used circular reasoning to arrive at this conclusion: patients were chosen because they had positive Lyme tests, and then they had positive Lyme tests (18). Thus the primer propagates one of the biggest myths about Lyme disease diagnosis instead of acknowledging the dreadful state of 30-year-old Lyme serology and the need for better testing, such as companion and molecular diagnostics.

On 2016 Dec 25, Raphael Stricker commented:

Lyme Primer is Obsolete (Part 2)

Raphael B. Stricker, Union Square Medical Associates, San Francisco, CA; Lorraine Johnson, LymeDisease.org, Chico, CA. rstricker@usmamed.com; lbjohnson@lymedisease.org

The primer states that a tick must usually be attached for more than 24 hours to transmit Bb, and that a single 200 mg dose of doxycycline can prevent transmission of Bb. The former statement is not supported by recent literature, especially when coinfecting agents are transmitted along with Bb (19). The latter statement is based on a flimsy study that has been attacked repeatedly for its many flaws (1).

The statement that there has been no evidence of Bb drug resistance ignores studies showing that resistance may occur (20-22). The issue of cyst forms that evade the immune system and antibiotic therapy is also ignored (6,23), and the primer disregards recent literature on antibiotic-tolerant persister organisms in Lyme disease (24-26). Once again the primer propagates the IDSA theme that Lyme disease is a trivial infection, with statements about quality of life after short-course treatment such as this: "Regardless of the disease manifestation, most patients with Lyme borreliosis respond well to antibiotic therapy and experience complete recovery." This statement whitewashes the significant morbidity associated with chronic Lyme disease symptoms (4,5). Approximately 42% of respondents in a survey of over 3,000 patients reported that they stopped working as a result of Lyme disease (with 24% reporting that they received disability as a result of chronic Lyme disease), while 25% reported having to reduce their work hours or change the nature of their work due to Lyme disease (4,5).

The unreferenced statement that two weeks of antibiotics cures Lyme carditis is not supported by the literature (1). The primer has limited the discussion of longer antibiotic treatment for post-treatment Lyme disease to studies by Klempner et al. and Berende et al. The authors ignore the positive studies of Krupp et al. and Fallon et al. showing benefit of longer antibiotic treatment, and they avoid discussion of the deep flaws in the negative Lyme treatment trials that lacked the size and power to yield meaningful results (27,28).

The primer calls the LYMErix(R) Lyme vaccine that was withdrawn from the market "safe and efficacious" and the authors blame Lyme advocacy groups for the vaccine failure. This mantra of "blaming the victims" has become a familiar excuse for the failed vaccine, which generated a class action lawsuit based on its lack of safety (29,30). Until vaccine developers come to grips with the very real potential hazards of Lyme vaccine constructs, a successful Lyme vaccine will remain out of reach.

Under "competing interests", there is no disclaimer by Paul Mead, who is an employee of the Centers for Disease Control and Prevention (CDC). Does this mean that Mead represents the CDC in endorsing this slanted and obsolete view of Lyme disease? If that is the case, it is disturbing that a government agency is shirking its responsibility to lead the battle against tickborne disease and instead endorses a regressive viewpoint that stunts science and harms patients.

References 1. Cameron et al, Expert Rev Anti Infect Ther. 2014;12:1103-35. 2. Johnson & Stricker, Philos Ethics Human Med 2010;5:9. 3. Johnson & Stricker, Clin Infect Dis. 2010;51:1108-9. 4. Johnson et al, Health Policy 2011;102:64- 71. 5. Johnson et al, PeerJ 2014;2:e322; DOI 10.7717/peerj.322. 6. Adrion et al, PLoS ONE 2015;10:e0116767. 7. Stricker & Johnson, Infect Drug Resist 2011:4:1-9. 8. Wright & Nielsen, Am J Vet Res. 1990;51:1980-7. 9. MacDonald, Rheum Dis Clin NA. 1989;15:657-677. 10. Stricker & Middelveen, Expert Rev Anti-Infect Ther. 2015;13:1303-6. 11. Russell and Johnson, Mol Microbiol. 2013;90:228-40. 12. Stricker & Johnson, Front Cell Infect Microbiol. 2013;3:40. 13. Cairns & Godwin, Int J Epidemiol. 2005;34:1340-5. 14. Fallon et al, Neurobiol Dis. 2010;37:534-41. 15. Muehlenbachs et al, Am J Pathol. 2016;186:1195-205. 16. Ang et al, Eur J Clin Microbiol Infect Dis. 2011;30:1027-32. 17. Stricker & Johnson, Minerva Med. 2010;101:419-25. 18. Stricker/PMC, Comment on Cook & Puri, Int J Gen Med. 2016;9:427-40. 19. Cook, Int J Gen Med. 2014;8:1-8. 20. Terekhova et al, Antimicrob Agents Chemother. 2002;46:3637-40. 21. Galbraith et al, Antimicrob Agents Chemother. 2005;49:4354-7. 22. Hunfeld & Brade, Wien Klin Wochenschr. 2006;118:659-68. 23. Merilainen et al, Microbiology. 2015;161:516-27. 24. Feng et al, Emerg Microbes Infect. 2014;3:e49. 25. Sharma et al, Antimicrob Agents Chemother. 2015;59:4616-24. 26. Hodzic, Bosn J Basic Med Sci. 2015;15:1-13. 27. Delong et al, Contemp Clin Trials 2012;33:1132-42. 28. Stricker/PMC, Comment on Berende et al, N Engl J Med. 2016;374:1209-20. 29. Marks, Int J Risk Saf Med. 2011;23:89-96. 30. Stricker & Johnson, Lancet Infect Dis. 2014;14:12. Disclosure: RBS and LJ are members of the International Lyme and Associated Diseases Society (ILADS) and directors of LymeDisease.org. They have no financial or other conflicts to declare.

On 2016 Dec 20, Sin Hang Lee commented:

None

On 2016 Dec 17, Lydia Maniatis commented:

While the title of this article refers to perception, the term is used loosely. The authors are not examining the process or principles via which a percept is formed, but, rather, how certain already-formed features of that percept are used to identify and label various substances whose general appearance is only one, and sometimes not even the most important, characteristic normally used to identify the substance. The question seems trivial and essentially non-perceptual.

An excerpt from the concluding paragraph of the paper may help convey the level of the conceptual discussion:

“…the name “chocolate” is assigned to all viscosities as long as the optical material is chocolate. This presumably reflects the fact that different concentrations and temperatures of chocolate yield a wide range of viscosities, but changes to the surface color and optical appearance are less common… The term “water” specifies a specific colorless transparent appearance and a specific (runny) viscosity. “

What does it mean to say that “the optical material is chocolate.” It seems like just a jargony way of saying “the name chocolate is assigned to anything that looks like chocolate” which begs the (trivial) question, and which isn’t even necessarily true, since the dispositive feature of chocolate is the flavor. Similarly, how do the authors distinguish between the label "water" and the labels "alcohol," "white vinegar," "salt solution" etc?

The distinction the authors are making between “optical” and “mechanical” properties indicates they haven’t understood the problem of perception. It’s not clear what distinction they are making between “optical appearance” and simply "appearance." In the category of “optical” characteristics they place color, transparency, gloss, etc. But color, transparency, gloss as experienced by observers are perceptual characteristics, and as such are in exactly the same category as perceived “mechanical” characteristics, among which the authors place perceived viscosity.

That the distinction they are making is a perceptual one is in no doubt as they are using images as stimuli, i.e. stimuli whose perceived "optical and mechanical" properties differ greatly from their physical properties. Even if they were using actual objects, the objection would be the same, as the actual stimulus would be the retinal projection, which contains neither color, viscosity, etc.

It is also inexplicable to me why the authors would refer to “optical appearance” as equivalent to “low-level image correlates.” Converting a retinal projection into a percept containing features such as transparency or color or gloss requires the very highest level of visual processes.

All in all, the article conveys conceptual confusion about the basic problem of perception, let alone how it is achieved, while the problem chosen for study doesn’t touch on any of these problems or solutions.

On 2016 Dec 22, William Davies commented:

I would like to congratulate the authors on their interesting study. We have recently shown that acute inhibition of the steroid sulfatase enzyme in new mouse mothers results in increased brain expression of the Nov/Ccn3 gene; as there is some evidence for the extracellular CCN3 protein interacting with integrin B1, I wondered whether the authors had, or had considered, looking at CCN3 levels in their cellular model?

On 2017 Mar 19, Harri Hemila commented:

Problems in study inclusions, in data extraction, and in the scales may bias the meta-analysis on vitamin C and post-operative atrial fibrillation (POAF)

Hu X, 2017 state in their methods that “studies that met the following criteria were included: (1) randomized controlled trials (RCTs) of adult patients who underwent cardiac surgery; (2) patients randomly assigned to receive vitamin C or placebo …”. However, Hu X, 2017 included the study by Carnes CA, 2001 although that was not an RCT, instead “an age- and gender-matched control group (not receiving ascorbic acid) was retrospectively selected”. In addition, the Hu X, 2017 meta-analysis did not include the data of 2 rather large US trials that found no effect of vitamin C against POAF and thus remained unpublished leading to publication bias, see Hemilä H, 2017. Furthermore, Hu X, 2017 claimed that “funnel plots showed no evidence of publication bias”, but the existence of the 2 unpublished US studies refutes that statement.

Furthermore, Altman DG, 1998 pointed out that “the odds ratio [OR] should not be interpreted as an approximate relative risk [RR] unless the events are rare in both groups (say, less than 20-30%)”. However, in the Fig. 2 of Hu X, 2017, the lowest incidence of POAF in the placebo groups was 19% and 6 out of 8 studies had incidence of POAF over 30% in their placebo groups. In such a case the OR does not properly approximate RR, and the authors should have calculated the effect on the RR scale instead.

In their Fig. 4, Hu X, 2017 state that the mean duration of intensive care unit (ICU) stay in the vitamin C group was 24.9 hours in Colby JA, 2011. However, Colby JA, 2011 reported in their Table 1 that the duration of ICU stay was 249.9 hours, i.e. 10 times greater. Evidently, such an error leads to bias in the pooled estimate of effect, but also leads to exaggeration of the heterogeneity between the included trials.

Hu X, 2017 calculated the effect of vitamin C on the duration of ICU stay and of hospital stay on the absolute scale, i.e. on days, although there were substantial variations in the placebo groups, and thus the relative scale would have been much more informative Hemilä H, 2016. As an illustration of this difference between the scales, Hemilä H, 2017 calculated that the effect of vitamin C on hospital stay in days was significantly heterogeneous with I² = 60% (P = 0.02). In contrast, the effect of vitamin C on hospital stay on the relative scale was not significantly heterogeneous with I² = 39% (P = 0.09). The lower heterogeneity on the relative scale is explained by the adjustment for the baseline variations in the studies.

Hu X, 2017 write “compared with placebo group, vitamin C administration was not associated with any length of stay, including in the ICU”. However, Hemilä H, 2017 calculated that there was strong evidence from 10 RCTs that vitamin C shortened ICU stay in the POAF trials by 7% (P = 0.002).

Hu X, 2017 also concluded that vitamin C did not shorten the duration of hospital stay, whereas Hemilä H, 2017 calculated that vitamin C shortened hospital stay in 11 POAF trials by 10% (P = 10^-7 ).

Although the general conclusion of Hu X, 2017 that vitamin C has effects against POAF seems reasonable, there is very strong evidence of heterogeneity in the effect. Five trials in the USA found no benefit, discouraging further research in the USA. However, positive findings in less wealthy countries suggest that the effect of vitamin C should be further studied in such countries, Hemilä H, 2017.

On 2017 Sep 24, Harri Hemila commented:

A manuscript version is available at HDL.

On 2017 Feb 21, Stuart RAY commented:

Here is the retraction: Finelli C, 2016

On 2016 Dec 14, Matthew Wargo commented:

While this report increases our understanding of SphR, many of the findings, including SphR direct transcriptional control of the neutral ceramidase (gene designation cerN (PA0845)), promoter mapping, and binding site determination were previously reported in LaBauve and Wargo 2014 (PMID 24465209)

On 2016 Dec 12, Lydia Maniatis commented:

It’s amazing how shy Agaoglu and Chung (2017) are in making their legitimate point, and how gently and casually they make it when they finally do get there (even giving credit where credit is not due). We can’t be sure, until we get to the very end (of the article not the abstract), what the authors think about the question posed, somewhat awkwardly, in their title: “Can (should) theories of crowding be unified?” The title begs the question, if they can be unified, then why shouldn’t they be? The explanation for the awkwardness, also saved for the end, is that the term “crowding” is conceptually vague, and has been used as a catch-all term for all manner of demonstrations of the fact that peripheral vision is not as good as central vision. “All in all, although we applaud the attempts at unifying various types of response errors in crowding studies, we think that without a better taxonomy of crowding—instead of calling everything crowding, perhaps introducing types of crowding (as in the masking literature)—unifying attempts will remain unsuccessful.” In other words, the issue of a unifying “theory of crowding” is moot given that we’re talking about a hodge-podge of poorly-understood phenomena.

What is also moot are the experiments reported in the article. While I think they have a lot of problems common to the field (layers of untested/untestable or even false, arbitrarily chosen assumptions), that doesn’t matter. As should be clear from the authors’ own discussion, no new experiments were needed to make the necessary theoretical point, which is that a clear conceptual understanding of phenomena needs to precede any attempt at a technical, causal explanation. Clearly, the experiments added by the authors do not make more acute the stated need for “a better taxonomy of crowding.” The redundancy of the study is reflected in the statement (caps mine) that “Our empirical data and modeling results ALSO [i.e. in addition to previous existing evidence] suggest that crowded percepts cannot be fully accounted for by a single mechanism (or model).” They continue to say that “The part of the problem is that many seemingly similar but mechanistically different phenomena tend to be categorized under the same umbrella in an effort to organize the knowledge in the field. Therefore, constraints for theoretical models become inflated.”

Agaoglu and Chung’s (2016) message, in short, is that the heterogeneous class of phenomena/conditions referred to as “crowding” are clearly not candidates for a common explanation or “model” as they routinely produce mutually conflicting experimental outcomes (one model works for this one but not that one, etc) and that there is a need for investigators to clarify more precisely what they are talking about when they use the term crowding. While, as mentioned, they could surely have made their argument without new experiments, they couldn’t have published it, as the rational argument in science has unfortunately been demoted and degraded in favor of uninterpretable, un-unifyable, premature p-values.

On 2016 Dec 13, Lydia Maniatis commented:

Witzel et al’s (2016) degree of ignorance of the fundamentals of their chosen topic is capable of disconcerting even the most jaded observer of the vision literature (me). Intentionally or not, it reflects the tenacious, subterranean grip of the behaviorist tradition (consideration only of simple signal (stimulus)/response paradigms) despite overwhelming evidence, both logical and empirical, of its inadequacy. That editors allow such products to pass into the literature is, I guess, also par for the course.

The problem here is that the authors simply ignore one of the most basic facts about color perception, though it is highly relevant to their problem of interest. It is not clear from the text whether they are even aware of this fact, i.e. that the color perceived at any given location in the visual field is contingent on the light reflected both from the local segment of the scene and the areas in the scene as a whole, (both adjacent and non-adjacent), and more specifically, to the structural relationships (and their implications) of the light-reflecting areas in question. These empirical facts are not in the least in question, yet for Witzel et al (2016) they might not as well exist. They acknowledge only local contrast and adaptation as possible reasons for why similar local “color signals” can produce different color experiences:

“To clarify the role of metamer mismatching in color constancy, we investigated whether metamer mismatching predicts the variation of performance in color constancy that cannot be attributed to adaptation and local contrast.”

“In the present study, we tested different high-level (color categories) and sensory factors (metamer mismatching, sensory singularities, and cone ratios) that are likely to affect performance in color constancy beyond what is predicted by adaptation [for some reason “contrast” has been dropped].”

“However, it is known that color appearance and color naming can be influenced by context, such as local contrast and adaptation (Hansen et al., 2007).” Their conclusion that “a considerable degree of uncertainty (about 50%) in judging colors across illuminations is explained by the size of metamer mismatch volumes” is meaningless since results are condition-sensitive and the authors have not considered the relevant confounds (e.g. figure-ground structure of the visual field).

Bizarrely, they speculate that the unexplained “50%” of the failures of color constancy “beyond what is predicted by adaptation…may be rather the result of linguistic categorization.” Anything but consider the alternative that is well-known and rather well-understood. (They also considered the bizarre notion of the role of “color singularities” i.e. that the visual system “maps the sensory signal that results from looking directly at the light of the illumination (illuminant signal).” Given that their stimuli are pictorial, I don’t even know how to interpret their use of the term color singularity. At any rate there is no such illumination signal, as has been proven both logically and empirically (it would, for example, eliminate the possibility of pictorial lighting effects).

The presence of such articles in the vision science literature is mind-boggling.

On 2016 Dec 13, Lydia Maniatis commented:

None

On 2017 Feb 17, Andrey Khlystov commented:

Gentlemen, The problem with your arguments is that Brand II, though being the “cleaner” of the three we tested, still produces very high aldehyde emissions. Three out of five V2 liquids that we tested exceeded the one time (one time!) exposure limits in a single puff. They also produced higher emissions than non-flavored liquids used in more powerful Brand I and III e-cigarettes. Surely you can check that. Please see our reply to Farsalinos et al. letter to ES&T – there are other studies that found even higher aldehyde concentrations than we did. High aldehyde emissions are not limited to a single study or a single liquid. We also demonstrate that “dry puff” arguments that Farsalinos et al. use to dismiss all high aldehyde studies have absolutely no factual basis. I doubt I can add anything else to this discussion except for reminding you that the strength of science is not only in reproducing results, but also in not cherry-picking studies and data that fit one’s theories or expectations. I do appreciate your efforts in clarifying the benefits and risks of e-cigarette use and whish you success in this endeavor.

On 2017 Feb 13, Peter Hajek commented:

Dr Khlystov, I understand that your laboratory has a good track record. Your findings are potentially important, but they do need to be replicated so a possibility that they were an artefact of some part of your procedure is ruled out The reason for wanting to test Brand 1 liquids is as follows. If other liquids show no alarming toxicant levels (which is possible because in previous studies where dry puffs were excluded, no such levels were found), the next level of explanation will be that the levels may be low in other liquids, but they were high in the liquid you tested. It is of course possible that your results will be replicated, but if not, this would necessitate another round of testing of the liquids you used. Testing your Brand 1 liquids straight away would remove this potential expense and delay in clarifying the issue. Providing information on which liquids you used, if this is available, should be simple and uncontroversial.

On 2017 Feb 11, Konstantinos Farsalinos commented:

Dr Khlystov mentions that there is information about 5 samples tested in their study. Unfortunately he refers to the samples with the lowest (by far) levels of carbonyl emissions. In fact, only one of these samples had high carbonyl emissions, unlike Brand I samples which showed very high levels of toxic emissions (especially for 3 of the samples, the levels found were extreme).

Liquids from different batches may not be the same, but finding almost 7000 ug/g of formaldehyde compared to < 0.65 ug/g from an unflavored sample can be easily reproduced with reasonable accuracy even with different batches. A replication study finding levels of carbonyl emissions lower by orders of magnitude cannot be attributed to different batches.

As i mentioned in my ES&T letter to the editor, the levels found by Khlystov and Samburova could only be explained by dry puffs, but this has been excluded because of the findings in unflavored liquids. Also, previous studies with verified realistic (i.e. no dry puff conditions) have found aldehyde levels orders of magnitude lower compared to their study. This creates a crucial need to replicate the samples with the highest levels of carbonyl emissions, despite the reassurance about the laboratory quality. Replication is the epitomy of science. But the authors are not providing the necessary information for these liquids.

On 2017 Feb 11, Andrey Khlystov commented:

Dr. Hajek,

You have not read the paper carefully. As I said earlier, our paper has information on 5 liquids that should be enough to get anybody started in replicating the data. They are from Brand II, which is V2 Standard (see Table 1). The brand is very easy to find (www.v2.com). The other liquids were from local vape shops, but this is of little consequence for the study, see below.

You seem to miss the point of our paper. Please let me briefly summarize its message: flavors, especially at higher concentrations, appear to dominate aldehyde production. To check generality of our observations, all one needs to do is take any flavored liquid and test it at different concentrations and/or against unflavored liquids and see what happens.

Contrary to what you suggest, there is little value in testing exactly the same liquids. Testing specific liquids or flavors was not the point of our study. We observed that a fairly wide variety of randomly selected flavored liquids produce significant aldehyde emissions, with aldehyde profiles varying among different flavors. If only PG or VG were responsible for the majority of aldehyde emissions, there would be no differences among liquids that have the same PG/VG composition. Yet, we observed significant differences among such liquids.

I also doubt that liquids from different batches are exactly the same, especially from small-time operations. At the time of writing the paper, we did not measure concentrations of liquid constituents. Having understood their role, we are controlling for liquid composition in our on-going study. As we mentioned in the letter to ES&T, we see appreciable aldehyde concentrations in both mainstream and secondary aerosols for a wide variety of e-cigarettes and liquids that users bring to our study. High aldehyde emissions are not limited to the 15 liquids and 3 e-cigarette brands we tested in our original study, it appears; the problem seems to be quite universal.

As we stated in our letter to ES&T, we are calling for checking findings of ANY e-cigarette study. I would like to note, however, that if one doubts our measurements, he or she needs to come up with a plausible mechanism, other than the effect of flavors, that explains why unflavored liquids produced significantly lower emissions than flavored ones or why a diluted flavored liquid was producing less than a more concentrated one. Please note, this was observed for the same e-cigarette, the same power output, and the same experimental setup. As of now and as far as I know, nobody came up with a single credible reason to doubt our results. I would also like to stress that aldehyde measurements are not trivial. We have over 20 years of experience in these measurements with a solid track record of QA/QC. Please rest assured - we stand by the quality of our data.

On 2017 Feb 09, Peter Hajek commented:

Your paper does not identify the actual products. Can you let others know the product name and the online address where it was purchased? There is no point trying to clarify your finding with different e-liquids.

On 2017 Feb 08, Andrey Khlystov commented:

Please read our paper carefully. There is information on 5 liquids that can be easily ordered online. Good luck with your experiments.

On 2017 Feb 08, Peter Hajek commented:

In their just published response to Farsalinos et al. comment on these unexpected results, the authors acknowledge that replications are needed. Could they please respond to repeated requests to specify which e-liquids they used so a replication can be performed?

On 2016 Dec 12, Peter Hajek commented:

The authors are correct that other studies are needed to check this phenomenon. Can they specify which e-liquids they tested so a replication is possible?

On 2017 Feb 06, Joe G. Gitchell commented:

In the brief report at the link, we have provided an update to include the 2015 NHIS data.

On 2017 Feb 21, Stuart RAY commented:

Definitely worth reading, a letter from one of the victims: Dansinger M, 2017

On 2017 Feb 14, Lydia Maniatis commented:

In this article, Felin et al (2016) mix up two different issues, which, like oil and water, intermingle but don’t mix. Put another way, the authors alternate between the two poles of a false dichotomy. On the one side is a truism, on the other an epistemological fallacy.

The latter involves the view expressed by Koenderink (2014) in an editorial called “The All-Seeing-Eye?” Here, he essentially makes the old argument that because all knowledge, and all perception, is indirect, inferential and selective, it makes no sense to posit a unique, real world. As I have pointed out in Maniatis (2015), the anti-realist position of Koenderink (2014) as well as Rogers (2014) and Hoffman (2009) and Purves et al (2014) (all of whom are cited in this respect by Felin et al (2016)) are paradoxical and inconsistently asserted. Rogers (2014), for example, describes the concept of “illusion” as invalid, while at the same time saying that “illusions” are useful). Inconsistency is inevitable if we want to make references to an objective world on the one hand (e.g. in making scientific statements), and at the same time claim that there is no unique, objective world.

It is clear from the text that Felin et al (2016) are not, in fact, adopting an anti-realist view. It has simply been inappropriately mixed into a critique of poor practices in the social sciences. These practices involve setting up situations in which participants make incorrect inferences, and treating this as an example of bias or irrationality. As the authors correctly discuss, this is pointless and inappropriate; the relevant question is how do organisms manage, most of the time, to make correct or useful inferences on the basis of information that is always inadequate and partial? What implicit assumptions allow them to fill in the gaps?

These are basic, fundamental points, but do not license a leap to irrationality; Arguing that it is not useful to treat a visual illusion, for example, as simply a mistake is not a reason to reject the distinction between veridical and non-veridical solutions, and this applies also to cognitive inferences about the world.

As the authors themselves note, their points are not new - despite the existence of researchers who have ignored or failed to understand them. So they seem to be giving themselves a little too much credit when they describe their views as “provocative” and a prescription for a “radically different, organism-specific understanding of nature, perception, and rationality.”

On 2017 Jun 14, Gregory Francis commented:

An analysis of the statistics reported in this paper suggest that the findings appear too good to be true. Details are published as an eLetter to the original article at

http://www.jneurosci.org/content/36/49/12448/tab-e-letters

On 2017 Jan 15, Ashraf Nabhan commented:

I thank the authors for this elegant work. The Results are reassuring regarding the risk of congenital malformations after ACE inhibitor exposure during the first trimester. The authors made a wise note to caregivers that women on ACE-I during reproductive years should have a transition off of these medications early in pregnancy to avoid the known adverse fetal effects associated with late pregnancy exposure. This wise note should have appeared in the abstract, since we know that most readers only read the abstract as many do not have access to the full text and some only focus on the authors' conclusion.

On 2016 Dec 13, Stuart RAY commented:

This finding is intriguing, but the reported findings seem inconclusive, for the following reasons: (1) figure 2a - the tree of sequences from Core/E1 region - has weak clustering with no significant bootstrap value to show confident clustering with subtype 3a, and no significant bootstrap value in genotype 1 to exclude the query sequence; (2) the nearly full-length sequence was cobbled together from 12 overlapping PCR amplifications, raising the possibility that this was a mixed infection with different regions amplified from different variants in the blood, rather than a single recombinant genome; and (3) the title says "not uncommon" but it appears that detailed study was only done for one specimen. It would be more convincing if a single longer amplicon, with phylogenetically-informative sequences on both sides of the breakpoint and showing a reproducible breakpoint, were recovered from separate blood aliquots (i.e. fully independent amplifications). Submission of the resulting sequence(s) to GenBank is a reasonable and important expectation of such studies. In addition, the title of the paper should not say "not uncommon" unless the prevalence can be estimated with some modicum of confidence.

On 2017 Jul 14, Randi Pechacek commented:

Russell Neches, first author of this paper, wrote a blog on microBEnet explaining the process and background of this experiment.

On 2016 Dec 07, Raphael Stricker commented:

Serological Test Sensitivity in Late Lyme Disease.

Raphael B. Stricker, MD<br> Union Square Medical Associates San Francisco, CA rstricker@usmamed.com

Cook and Puri have written an excellent review of the sorry state of commercial two-tier testing for Lyme disease (1). Unfortunately the authors failed to address the myth of high serological test sensitivity in late Lyme disease.

In the review, Figure 4 and Table 7 show a mean two-tier serological test sensitivity of 87.3-95.8% for late Lyme arthritis, neuroborreliosis and Lyme carditis. However, this apparently high sensitivity is based on circular reasoning: in order for patients to be diagnosed with these late conditions, they were required to have clinical symptoms AND POSITIVE SEROLOGICAL TESTING. Then guess what, they had positive serological testing! This spurious circular reasoning invalidates the high sensitivity rate and should have been pointed out by the authors of the review.

As an example, the study by Bacon et al. (2) contains the following language: "For late disease, the case definition requires at least one late manifestation AND LABORATORY CONFIRMATION OF INFECTION, and therefore the possibility of selection bias toward reactive samples cannot be discounted" (emphasis added). Other studies of late Lyme disease using spurious circular reasoning to prove high sensitivity of two-tier serological testing have been discussed elsewhere (3-5).

In the ongoing controversy over Lyme disease, it is important to avoid propagation of myths about the tickborne illness, and insightful analysis of flawed reasoning is the best way to accomplish this goal.

References 1. Cook MJ, Puri BK. Commercial test kits for detection of Lyme borreliosis: a meta-analysis of test accuracy. Int J Gen Med 2016;9:427–40. 2. Bacon RM, Biggerstaff BJ, Schriefer ME, et al. Serodiagnosis of Lyme disease by kinetic enzyme-linked immunosorbent assay using recombinant VlsE1 or peptide antigens of Borrelia burgdorferi compared with 2-tiered testing using whole-cell lysates. J Infect Dis. 2003;187:1187–99. 3. Stricker RB, Johnson L. Serologic tests for Lyme disease: More smoke and mirrors. Clin Infect Dis. 2008;47:1111-2. 4. Stricker RB, Johnson L. Lyme disease: the next decade. Infect Drug Resist. 2011;4:1–9. 5. Stricker RB, Johnson L. Circular reasoning in CDC Lyme disease test review. Pubmed Commons comment on: Moore A, Nelson C, Molins C, Mead P, Schriefer M. Current guidelines, common clinical pitfalls, and future directions for laboratory diagnosis of Lyme disease, United States. Emerg Infect Dis. 2016;22:1169-77.

Disclosure: RBS is a member of the International Lyme and Associated Diseases Society (ILADS) and a director of LymeDisease.org. He has no financial or other conflicts to declare.

On 2017 Nov 30, Alejandro Montenegro-Montero commented:

I read this very interesting review summarizing recent global studies aimed at characterizing circadian gene expression in mammals. It presents a nice summary of the different ways in which the clock can impact gene expression and additionally, briefly discusses various statistical methods currently used for the identification of rhythmic genes from global data sets. This is a very welcome review on the subject.

Readers might also be interested in our discussion of the relative contributions of the different stages of gene expression, in determining rhythmic profiles in eukaryotes. In our commentary, "In the Driver's Seat: The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes", we discuss several scenarios in which gene transcription (even when apparently arrhythmic) might play a much relevant role in determining oscillations in gene expression than currently estimated, regulating rhythms at downstream steps. Further, we argue that due to both biological and technical reasons, the jury is still out on the determination of the relative contributions of each of the different stages of gene expression in regulating output molecular rhythms.

We hope that reviews like the one by Mermet et al., and commentaries like the one presented in this post, stimulate further discussions on this exciting topic: there are still many important challenges ahead in the field of circadian gene regulation.

On 2016 Dec 08, Lydia Maniatis commented:

Part 2: 2. The terms “adaptation” and “aftereffects.” There is no way to discern the meaning of these terms in the context of this study. The authors seem to be using the term very loosely: “….many aspects of visual perception are adaptive, such that the appearance of a given stimulus may be affected by what has been seen before.” The example they give involves motion aftereffects, the cause of which, as far as I can discover, is still unknown. Continuing, they declare that “This perceptual bias is known as an aftereffect [last term italicized].”

This exposition conflates all possible effects of experience on subsequent perceptual impressions with the color aftereffects based on color opponency at the retinal level, and with the less well-understood motion aftereffects. In other words, we’re lumping together the phenomenon known as “perceptual set,” for example, with color aftereffects, as well as with motion aftereffects. In these latter cases, at least, it is intelligible to talk about aftereffects as being “opposite” to the original effects. In the case of motion, we are fairly straightforwardly talking about a percept of a motion in the opposite direction. In the case of color, the situation is not based on percepts having perceptually opposing characteristics; what makes green the opposite of red is more physiological then perceptual. So even with respect to what the authors refer to as “low-level” effects, ‘opposite’ means rather different things.

The vagueness of the ‘opposite’ concept as used by Burton et al (2016) is expressed in their placement of quotation marks around the term: “In the facial expression aftereffect, adaptation to a face with a particular expression will bias participants’ judgments of subsequent faces towards the “opposite” expression: The expression with visual characteristics opposite those of the adaptor, relative to the central tendency of expressions.”

All of the unexamined theoretical assumptions implicit in the terms ‘visual characteristics,’ ‘adaptor’ ‘central tendency’ and, therefore, ‘opposite’ are embedded in the uncritically-adopted procedure of Tiddeman et al (2001). While the example the authors give – “Where fear has raised eyebrows and an open mouth, anti-fear has lowered eyebrows and a closed mouth, and so on” may seem straightforward, neither it nor the procedure is as straightforward as we might assume. The devil is in the “and so on.” First, “lowered eyebrows” is a relative term; lowered in relation to what? Different faces have different relationships between eyebrows, eyes, nose, hairline, etc. And a closed mouth is a very general state. Second, this discrete, if vague, description doesn’t directly reference the technical procedure developed by Tiddeman et al (2001). When we are told by Burton et al (2016) that “anti-expressions were created by morphing along a trajectory that ran from one of the identity-neutral faces [they look like nothing?] through the average expression and beyond it to a point that differed from the average to the same extent as the original expression,” we have absolutely no way to interpret this without examining the assumptions and mathematics utilized by Tiddeman et al (2001). On a conceptual and practical level, readers and authors are blind as to the theoretical significance of this manipulation and the description of its products in terms of “opposites.”

In addition, there is no way to distinguish the authors’ description of adaptation from any possible effect of previous experience, e.g. to distinguish it from the previously-mentioned concept of “perceptual set,” or from the fact that we perceive things in relative terms; a baby tiger cub, for example, evokes an impression of smallness while a smaller but fully-grown cat large for its size might evoke the impression of largeness. Someone used to being around short people might find average-height people tall, and vice versa. Should we lump this with color, motion aftereffects and perceptual set effects? Maybe we should, but we need to make the case, we need a rationale.

1. Implications The authors say that their results indicate that “expression aftereffects” may have a significant impact on day-to-day expression perception, but given that they needed to train their observers to deliver adequate results, and given the very particular conditions that they chose (without explanation), this is not particularly convincing. Questions about the specifics of the design are always relevant in this type of studies, where stimuli are very briefly presented. Why, for example, did Burton et al (2016) use a 150 millisecond ISI, versus the 500 millisecond ISI used by Skinner and Benton (2010). With such tight conditions, such decisions can obviously influence results, so it’s important to rationalize them in the context of theory.

2. It should be obvious already, but the following statement, taken from the General discussion, is an apt demonstration of the general intellectual vagueness of the article: “Face aftereffects are often used to examine the visual representation of faces, with the assumption that these aftereffects tap the mechanisms of visual perception in the same way as lower level visual aftereffects.”

The phrase “in the same way…” is wholly without a referent; we don’t even know what level of analysis is being referred to. In the same way as (retinally-mediated, as far as we understand) color aftereffects? In the same (physiologically not well understood) way as motion aftereffects?” In the same way as the effects of perceptual set? In the same way as seeing size, or shape, or color, etc, in relative terms? What way is “the same way”?

On 2016 Dec 08, Lydia Maniatis commented:

Part 1: There seems to be a widespread misunderstanding in the vision sciences about the role of experiment in science. The value of experiment rests solely on the clarity, coherence, internal consistency, and respect for known facts of the underlying rationale, certain of whose predictions it is designed to test. The methodological choices made in conducting the experimental test are directly linked to this rationale. (For example, if I did a study on the heritability of a single (assumed) gene underlying nose size (plus “noise”), my results would be interpretable in the terms of my assumption (especially if “size” were not clearly defined), even if my assumption were false. This is why it’s important to take care in constructing our hypotheses and tests). If the underlying concepts are vague, or if the rationale lacks internal consistency, or if it lacks coherence, then the results of the experiment cannot be interpreted (in a scientific sense).

The problems of rationale and method are overwhelmingly on display here. Below, I enumerate and expand on various issues.

1. The stimuli The theory/method behind the (implicitly) theory-laden stimuli (averaged and morphed photos of faces having various expressions ) is briefly described as having been adapted from those used by Skinner and Benton (2010). (As the corresponding author has clarified to me, the stimuli are, in fact, the same ones used in that study.) The pre-morphed versions of those stimuli came from a database of 70 individual faces exhibiting various expressions collected by Lundqvist, Flykt & Ohman (1998). This reference is not cited by Burton et al (2016), which I feel is an oversight, and neither Bonner et al (2016) nor Skinner and Benton (2010) feel the need to address the sampling criteria used by Lundqvist et al (1998). Sampling methods are a science in themselves, and are always informed by the purpose and assumptions of a study.

However, we’ll assume the investigators evaluated Lundqvist et al’s (1998) sampling technique and found it acceptable, as it’s arguably less problematic than the theoretical problems glossed over in the morphing procedure. The only (non)description of this procedure provided by either Burton et al (2016) or Skinner and Benton (2010) is a single reference, to Tiddeman, Burt, & Perrett,( 2001). A cursory examination of the work reported on by those researchers reveals it to be a wholly inadequate basis for the use Burton et al (2016) make of it.

Tiddeman et al (2001) were interested in the problem of using morphing techniques to age faces. They were trying to improve the technique in comparison to previous attempts, with regard to this specific problem. They didn’t merely assume their computational solutions achieved the aim, but evaluated the results in empirical tests with observers. (However, they, too, fail to describe the source of the images on which they are basing their procedures; the reference to 70 original faces seems the only clue that we are dealing with the sample collected by Lundqvist et al (1998).) The study is clearly a preliminary step in the development of morphing techniques for a specific purpose: “We plan to use the new prototyping and transformation methods to investigate psychological theories of facial attraction related to aging….We’ll also investigate technical extensions to the texture processing algorithms. Our results show that previous statistical models of facial images in terms of shape and color are incomplete.”

The use of the computational methods being tentatively proposed by Tiddeman et al (2001) by Skinner and Benton (2010) and Burton et al (2016) for a very different purpose has been neither analyzed, rationalized nor validated by either group. Rather, the procedure is casually and thoughtlessly adopted to produce stimuli that the authors refer to as exhibiting “anti-expressions.” What this label means or implies at a theoretical level is completely opaque. I suspect the authors may not even know what the Tiddeman et al algorithm actually does. (Earlier work by Rhodes clearly shows the pitfalls of blind application of computational procedures to stimuli and labeling them on the basis of the pre-manipulation perception. I remember seeing pictures of morphed or averaged“faces” in studies on the perception of beauty that appeared grossly deformed and non-human.)

Averaging of things in general is dicey, as the average may be a completely unrealistic or meaningless value. If we mix all the colors of the rainbow, do we get an “average” color? All the more so when it comes to complex shapes. If we combined images of a pine tree and a palm tree, would the result be the average of the two? What would this mean? Complex structures are composed of multiple internal relationships and the significance of the products of a crude averaging process is difficult to evaluate and should be used with caution. Or not.

On 2016 Dec 12, David Mage commented:

Carlin and Moon have provided a very thorough review of risk factors for SIDS with one major flaw – a complete lack of recognition that SIDS have a male excess of 50% corresponding to a male fraction of 0.60, or 3 males for each 2 females. CDC (http://wonder.cdc.gov) reports for years 1968-2014 that for causes of death by SIDS, Unknown (UNK) and Accidental Suffocation and Strangulation in Bed (ASSB) there were 119,201 male and 79,629 female post-neonatal cases (28-364 days) for a male fraction of 0.600. Naeye et al. (PMID 5129451) were, to our knowledge, the first to claim that this 50% male excess in infant mortality must be X-linked. We agreed, and have proposed that an X-linked recessive allele with frequency q = 2/3 that is not protective against acute anoxic encephalopathy would place XY males at risk with frequency q = 2/3 and XX females at risk with frequency q*q = 4/9 (PMID 9076695, 15384886).

On 2017 Feb 22, Atanas G. Atanasov commented:

Dear Colleagues, thank you so much for the excellent collaborative work! Consumer Health Digest Scientific Abstract of this article is now available at: https://www.consumerhealthdigest.com/brain-health/protection-against-neurodegenerative-diseases.html

On 2017 Apr 13, Konstantinos Fountoulakis commented:

This paper compares CBT with short-term psychoanalytical therapy and versus a brief psychological intervention. The results of the paper suggest no difference between the three types of interventions and the conclusion is as follows: ‘Short-term psychoanalytical psychotherapy is as effective as CBT and, together with brief psychosocial intervention, offers an additional patient choice for psychological therapy, alongside CBT, for adolescents with moderate to severe depression who are attending routine specialist child and adolescent mental health service clinics’. Essentially this conclusion is misleading. The description of the ‘brief psychosocial intervention’ suggests it was something between a general psychoeducational approach and supportive psychotherapy, and it was delivered by the usual general staff of the setting without any specialized training in a treatment-as-usual approach. Therefore the interpretation of the results is either that the brief psychosocial intervention was a kind of placebo, and in this case the ‘active’ psychotherapies did not differ from a placebo condition (negative trial), or, if the brief psychosocial intervention is indeed efficacious, then the results do not support the added value of the more complex, demanding, expensive and time consuming CBT and psychoanalytical treatments applied by highly trained therapists versus simpler techniques applied by nurses. In my opinion, the results of this study do not support the applicability of cognitive and psychoanalytical theories in the treatment of adolescent depression but this is not entirely clear and it is debatable. What is clear, is that CBT and psychoanalytic therapy are not better than simpler and cheaper treatment-as-usual psychosocial interventions which are traditionally routinely applied in many clinical settings already.

On 2017 Mar 31, Krishnan Raghunathan commented:

"We would like to acknowledge the work of Dr. Ingela Parmyrd and colleagues (1) who have shown that in living cells, crosslinking of for instance CTxB induces ordered domain formation in an actin-dependent manner.

(1) Dinic, J., Ashrafzadeh, P., Parmryd, I. (2013) "Actin filaments attachment at the plasma membrane in live cells cause the formation of ordered lipid domains" Biochimica et Biophysica Acta - Biomembranes, 1828(3): 1102-1111"

On 2017 Jul 12, Bjarke M Klein commented:

Bjarke Mirner Klein, PhD, Director, Biometrics, Ferring Pharmaceuticals, Copenhagen, Denmark.

We thank the authors for their interest in our trial. This publication is the first reporting data from the ESTHER-1 trial and therefore presents the overall results at a high level. More publications presenting full details on different aspects of the data are in progress. In their comment, they raise the following three concerns: 1) the presentation of the number of oocytes retrieved, 2) the decision not to present the so-called ‘inverted’ responders, and 3) the possibility that the individualised dosing regimen may increase excessive response in low AMH patients. Each of these will be addressed in the following.

Concerning the presentation of the number of oocytes retrieved: Strict criteria for cycle cancellation due to poor or excessive response were specified in the trial protocol. Since a priori both scenarios were considered a possibility and since there is no consensus on how the number of oocytes retrieved should be imputed for each scenario it was decided to present the data as in Table 3. This is a transparent way of presenting the results since the reader can derive the numbers for all subjects using his/her own assumptions on how to impute the cycle cancellations. This is exactly what the two authors have done assuming that cycle cancellations due to poor response should be included as zero oocytes retrieved in the calculations. It should be noted that the treatment difference remains the same irrespective of method of display.

Concerning the ‘inverted’ responders: The terminology of ‘inverted’ ovarian response may be misunderstood, since it may suggest that e.g. a subject who would have <4 oocytes retrieved using a standard starting dose of follitropin alfa (GONAL-F) would have ≥20 oocytes retrieved with the individualised follitropin delta (REKOVELLE®) dose. This would indeed be a dramatic and surprising impact considering that the maximum daily dose of follitropin delta is 12 mcg and the starting dose of follitropin alfa is 150 IU (11 mcg). However, as illustrated on Figures 1A and 1B the consequences of the individualised follitropin delta (REKOVELLE®) dosing regimen dose are not that drastic. From these figures, it can be observed that the ovarian response in terms of number of oocyte retrieved is comparable for the mid-range AMH while the treatment differences are seen at the lower and higher AMH level.

Since the individualised dosing algorithm assigns the same daily dose of individualised follitropin delta (REKOVELLE®) to subjects with an AMH <15 pmol/L and gradually decreases the dose as a function of AMH for subjects with AMH ≥15 pmol/L it seems relevant to present the data by these subgroups. As can be seen from Table 3, the individualised follitropin delta (REKOVELLE®) dosing regimen shifts the distribution of oocytes retrieved upwards for subjects with AMH <15 pmol/L while it shifts the distribution downwards for subjects with AMH ≥15 pmol/L. Such a shift in the distribution obviously also affects the tails of the distribution, i.e. in this case the probability of either too low or too high number of oocytes retrieved. For the publication, it was considered relevant to focus on the risk of poor response in the subjects at risk of hypo-response and the risk of excessive response for the subjects at risk of hyper-response.

Concerning the possibility that the individualised dosing regimen may increase excessive response in low AMH patients: Relevant data on OHSS and preventive interventions is presented in Table 3 and the relationship to AMH is illustrated in Figure 1C. The authors are concerned that since excessive response is not presented for the potential hypo-responders (AMH <15 pmol/L) the overall safety of the individualised dosing is unclear. We take the opportunity to present the data for excessive response in the subjects at risk of hypo-response, where the observed incidence of having ≥15 oocytes retrieved among subjects with AMH <15 pmol/L was (6%) and (5%) in the follitropin delta and follitropin alfa groups, respectively.

On 2017 Jun 29, Jack Wilkinson commented:

Jack Wilkinson, Centre for Biostatistics,Institute of Population Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK.

Sarah Lensen, Department of Obstetrics and Gynaecology, University of Auckland, New Zealand.

Nyboe Andersen and colleagues (2017) present a large randomised study comparing follitropin delta, with dosing based on AMH and body weight, against follitropin alfa, with dose selection by conventional means. Stated key findings of the study include the fact that more women achieved a target response of 8-14 oocytes (43.3% vs 38.4%) in the follitropin delta group, and that fewer women had poor (< 4 oocytes) or excessive (>= 15 or >= 20 oocytes) responses compared to the follitropin alfa group. However, on close inspection of the published study, it is not clear that follitropin delta, administered using this dose selection algorithm, has been shown to be superior to the standard dose of follitropin alfa in relation to response to stimulation.

We note that calculations regarding number of oocytes obtained do not include women who were randomised but subsequently had their stimulation cycle cancelled for anticipated poor response (prior to hCG trigger). Indeed, there were more women with cycles cancelled for anticipated poor response in the follitropin delta group than the follitropin alfa group. The claim that poor response was lower in the follitropin delta arm then appears to be technically correct but potentially highly misleading. It would be preferable to include women with cancelled cycles in the numerator and denominator (they appeared in neither numerator nor denominator in the analysis presented by Nyboe Andersen and colleagues) by setting the number of oocytes recovered for women with cancelled stimulation cycles to be zero. This would rectify any bias resulting from differential cancellation rates between the study arms. It would also preserve the balance over confounding factors produced by randomisation, which is otherwise violated. When we include all patients in this way, the mean number of oocytes retrieved in the follitropin delta and follitropin alfa arms is 9.6 and 10.1, respectively, and the numbers achieving the target response are 275 (41%) and 247 (37%), which gives p=0.15 from a chi-squared test.

A second concern is the fact that the authors present the rate of poor response in the low AMH group and the rate of hyper response in the high AMH group, but do not present the rate of poor response in the high AMH group or the rate of hyper response in the low AMH group. If we refer to hyper responses in low AMH patients and poor responses in high AMH patients as ‘inverted’, then we can calculate the number of inverted responses in each group. In fact, the number of inverted responses are greater in the follitropin delta group (5% vs 4% using 15 oocytes as the threshold for hyper response, or 4% vs 2% using 20 oocytes):

Number Inverted <4 or >=15 is 34/640 (5%) in experimental arm and 25/643 (4%) in the control arm, p=0.233 from Fisher's exact test.<br> Number Inverted <4 or >=20 is 23/640 (4%) in experimental arm and 11/643 (2%) in the control arm, p=0.038 from Fisher’s exact test.

These calculations are conducted in patients achieving hCG trigger, as it does not appear to be possible to identify whether the women with cycles cancelled for poor response were in the high or low AMH stratum from the information presented. The number of hyper responses in the low AMH group is of particular interest, since this represents increased risk to the treated woman and any resulting offspring. Unfortunately, this information is obfuscated by the presentation in the manuscript. We also note that the decision to report the rates of hypo and hyper response only in these subgroups appears to be a departure from the clinicaltrials.gov record for the trial (https://clinicaltrials.gov/ct2/show/NCT01956110).

Given that the claim of the authors in relation to the effectiveness of treatment was one of non-inferiority, the matter of the safety of the individualised dosing regimen compared to standard dosing would appear to be of paramount importance. On the basis of the considerations outlined above, it is unclear that an advantage of the individualised follitropin delta regimen in relation to achieving target ovarian responses has been demonstrated. Moreover, the data leave open the possibility that the individualised regimen may increase excessive responses in low AMH patients. We would like to invite the authors to clarify this point.

A version of this comment has been posted on the journal's website.

References Nyboe Andersen, A., et al. (2017). "Individualized versus conventional ovarian stimulation for in vitro fertilization: a multicenter, randomized, controlled, assessor-blinded, phase 3 noninferiority trial." Fertil Steril 107(2): 387-396 e384.

Conflict of interest statement

JW is funded by a Doctoral Research Fellowship from the National Institute for Health Research (DRF-2014-07-050). The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health. JW also declares that publishing research is beneficial to his career. JW is a statistical editor for the Cochrane Gynaecology and Fertility Group, although the views expressed here are not necessarily those of the group.

On 2017 Jan 09, Gerhard Holt commented:

Intimate Cohabitants'Shared Microbiomes and Alpha-Synuclein Pathology

Sampson et al.'s findings on the role of gut microbiota on Alpha-synucleinopathies[1] raise considerable potential concern regarding the microbiome of intimate cohabitants of patients with Alpha-Synuclein pathology, since they are likely to have substantial exposure to a shared microbiome.

Do these intimate cohabitants develop more early Alpha-Synuclein pathology than non-cohabitant controls ?

Are they at greater risk for Parkinson's disease and other alpha-synucleinopathies ?

From an Infectious Disease perspective, this might be an important clinical study.

Perhaps some of the intimate cohabitants are more resistant to A-SYN pathology, SCFAs, or the underlying gut microbes than others - despite similar microbiome exposure ?

Perhaps differences in the interactions between their immune systems and their microbiome alter outcomes ?

This might be a fertile area for differential proteome studies.

Given the importance of Sampson et al.'s findings, hopefully a clinical trial of antibiotics followed by (healthy donor) fecal transplant for patients with Parkinson's Disease will soon follow - perhaps with a cross-over design.

Given the low risks of a potential treatment which uses well known medications and a well established procedure (Fecal Transplant), and given the grossly disproportionate potential benefit, hopefully this study will be expedited in humans.

It may be useful however to also study Alpha-Synuclein pathology in their intimate cohabitants relative to controls.

References :

[1] Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease Sampson, Timothy R. et al. Cell , Volume 167 , Issue 6 , 1469 - 1480.e12

  <www.cell.com/cell/pdf/S0092-8674(16)31590-2.pdf>

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.)