On 2015 Dec 28, Lydia Maniatis commented:

Part 2. THE HYPOTHESIS IS LAMARCKIAN The hypothesis does not appear consistent with the principles of evolution on the basis of natural selection. Unless I misunderstand, it seems to require not only that stimulus frequency information be accumulated throughout the lifetime of each organism, but also that this knowledge be passed on genetically - which is a form of Lamarckism. Natural selection doesn't work that way – mutations are random, lucky shots in the dark, not the result of accumulated, recorded luminance or responses to luminance – experience only comes into play after the fact, in the sense that if they happen to be adaptive, they undergo positive selection.

In addition, the hypothesis would seem to predict that populations living in highly different environments - one living, for example, in the arctic, the other in the dark jungle – would have different lightness codes. But even fish, for example, appear to possess color perception mechanisms similar to that of humans.

There is also a more subtle problem with the proposal; it purports to explain the production of particular qualia (light, dark) but doesn't actually doesn't touch on this problem at all. The luminance/lightness connection proposed is physically arbitrary, an accident of experience. Why should there be adaptive pressure to code physical conditions on the basis of the chance frequency with which they are encountered, rather than on the basis of features and factors directly relevant to survival and reproduction (a rare event might have more powerful effects)?

THE HYPOTHESIS IS NEITHER NECESSARY NOR SUFFICIENT AND LEAVES MANY QUESTIONS UNANSWERED The hypothesis proposes to explain why two surfaces of equal luminance, in a very limited number and type of displays, produce slightly different percepts; it does not try to explain the quite regular, in many contexts, relationship between luminance and lightness, specifically that the latter rises of falls with the other under certain describable conditions (when the structure of the pattern indicates an area under homogeneous illumination). In other words, although it is the case that the two equal target luminances in the simultaneous contrast demo differ in appearance, it is also the case that continuously increasing the luminance of either one will cause a continuous increase in its lightness. Thus, the hypothesis implies that, for any given context, the frequency of the target/context combination increases with increasing luminance of the target.

The authors seem to realize this when they state that: “by definition, the percentile of target luminance for the lowest luminance value within any contextual light pattern is 0% and corresponds to the perception of maximum darkness, the percentile for the highest luminance ...is 100% [?] and corresponds to the maximum perceivable brightness.” But they seem to be confusing prediction, definition and fact. We know as a matter of FACT – from empirical experience, not definition, not hypothesis - that increasing luminance of a patch in any given setting tends to increase its lightness. But this is not a logical implication of the frequency hypothesis (and certainly not an a priori “definition.”) Even assuming it is possible, methodologically, to show that the “percentiles” coincide with this straightforward luminance/lightness relationship, the “frequency hypothesis,” lacking any discernible rationale, would not seem to possess a logical advantage over the hypothesis that there is simply an adaptive value to a regular coding of lightness and relative luminance, i.e. to coding higher luminance with higher lightness values, with corrections for the sake of accurately separating perception of surfaces and perception of apparent illumination. The authors seem to imply that their proposal is superior to such accounts because it does not require a direct relationship between luminance and lightness – but no serious alternative could require any such thing.

Given that the fairly straightforward within -context luminance/lightness relationship, the hypothesis reduces to the idea that a change in the luminance of the background of a target can change the range of the target lightness values arising in perception. Why should this be? If the entire range for a “context” is shifted upwards, for example, should we assume that that context has a higher percentile than the lower-range-producing context, and that, again, the correspondingly regular luminance/lightness relationship within that range is a coincidence of frequency? And, finally, why does the frequency argument not apply to the apparent lightness of the background? Or does it? In this case, what happens if a low-frequency target/context combination occurs on a high-frequency context? Would the frequency of a single-luminance context equal the frequency of that luminance? Do some luminances occur more frequently than others? Or would we have to evaluate the frequency of each “context” given its own various possible contexts? And what about the fact that a more global changes are known to be able to affect local lightness (rendering any particular cut-off of “context” arbitrary and uninformative).

WHAT DOES IT MEAN THAT THE PROJECTION HAS “HIGHLY-STRUCTURED STATISTICS?” The authors make a mystifying claim about the nature of the retinal projection. We are told that it consists of 2D patterns of light intensity with “highly structured statistics.” What does this mean? How can one collect and evaluate the “structured statistics” in the pattern?

One thing is certain – the pattern of light intensities in the projection is wholly unpredictable, as is the pattern of light intensities in the environment. The light reflected to the eye depends on both the characteristics of surfaces and on the light falling on them. Both change from location to location, but the latter is also unstable within locales, shadows depending on chance locations and orientations of objects, on their shapes and relative locations, the location of the sun, the presence of clouds, etc. Given that the order of the shapes, and the shapes appearing with any given glance, is also unpredictable, it is difficult to see what the authors are talking about when they refer to “highly structured statistics.” They need to explain what they mean.

Methodological problems LACK OF TESTABILITY Even if we ignore the logical, practical and theoretical problems with the hypothesis, it seems impossible to test. Even if our sole interest were the classic simultaneous contrast illusion, and even if such configurations appeared as such in nature (which they do not), how could we develop a database for which frequencies of any target luminance on any background luminance (let alone all of them) falling on the retinas of all of the individuals forming the lineage of our species (until the process is supposed to have stopped (see above)), across all of the days and environments traversed, morning, noon and night, in the sea and on the land? The hypothesis does not entail any principled relationship between luminance and lightness, unless this relationship were in turn entailed by the luminance/frequency relationship for all possible contexts; thus, it is not clear what the criteria might be for obtaining a valid sample for testing. As it is, the notion has not been properly tested even for the narrow framing of this article, because the methods for choosing samples (the details of which are relegated to supplementary, online material) is too vague, arbitrary and opaque at key points to allow any attempts at replication.

On 2015 Dec 28, Lydia Maniatis commented:

Part 1. I have criticized Purves and colleagues' various iterations of the “wholly empirical” account of visual perception in various comments on PubMed Commons and on PubPeer. Here, I want to present a more comprehensive and organized critique, focussing on a study that has served as a centerpiece of these accounts. I think it is important to clarify the fact that the story is profoundly inadequate at both the conceptual and the methodological levels, and fails to meet fundamental criteria of empirical science (logical consistency and testability). Such criticism (which is not welcome in the published literature) is important, because if “anything goes” in published research at even the most elite journals, then this literature cannot help to construct the conceptual infrastructure necessary for progress in the visual sciences.

Conceptual problems LACK OF THEORETICAL MOTIVATION The hypothesis that the authors claim to have tested is effectively conjured out of thin air, subsequent to an exposition that is inaccurate, inadequate, and incoherent.

The phenomenon to be explained is inadequately described. We are told, first, that the luminance of a “visual target” elicits a “brightness” percept that can vary according to “context.”

The term brightness, here, is being used to refer to the impression of white-gray-black that a surface may elicit (and which is currently referred to by researchers as its “lightness.”) However, surfaces do not necessarily, or even usually, elicit a unitary percept; they often produce the impression of double layers, e.g. a shadow overlying a solid surface. Both the shadow and the surface have a perceptual valence, a “brightness.” Indeed, it is under conditions where one “target” appears to lie within the confines of a double layer, and the other does not, that the most extreme apparent differences between equiluminant targets arise.

The logic is simple: If a surface appears to lie under a shadow, then it will appear lighter than an equiluminant target that appears to lie outside of the shadow, because a target that emits the same amount of light under a lower illumination as one under stronger illumination must have a higher light-reflecting tendency (and this is what the visual system labels using the white-gray-black code.). The phenomenon and logic of double layers is not even intimated at by these Yang and Purves (2004); rather, the impression created is that the relationship between “brightnesses” under different “contexts” is not in the least understood or even amenable to rational analysis. (In addition, the achromatic conditions being considered are rare or even non-existent in natural, daytime conditions; but the more complex phenomenon of chromatic contrast is not mentioned.)

After this casual attempt to convince readers that vision science is completely in the dark on the subject of “brightness,” the authors assert that “A growing body of evidence has shown that the visual system uses the statistics of stimulus features in natural environments to generate visual percepts of the physical world.” No empirical studies are cited or described to clarify or support this rather opaque assertion. The only citation is of a book containing, not evidence, but “models” of brain function. The authors go on to state that “if so, the visual system must incorporate these statistics as a central feature of processing relevant to brightness and other visual qualia.” (It should be noted that the terms “statistics” and “features” here contain no concrete information. The authors could be counting the stones on Brighton beach.)

Even if we gave the authors the latitude to define “statistics” and “features” any way they wish, the following sentence would still come out of the blue: “Accordingly, we propose that the perceived brightness elicited by the luminance of a target in any given context is based on the value of the target luminance in the probability distribution function of the possible values that co-occur with that contextual luminance experienced during evolution. In particular, whenever the target luminance in a given context corresponds to a higher value in the probability distribution function of the possible luminance values in that context, the brightness of the target will be greater than the brightness elicited by the same luminance in contexts in which that luminance has a lower value in the probability distribution function.”

This frequency-percept correlation, in combination with the claim that it has come about on the basis of evolution by natural selection, is the working hypothesis. It is a pure guess; it does not follow naturally from anything that has come before, nor, for that matter, from the principles of natural selection (see below). It is, frankly, bizarre. If it could be corroborated, it would be a result in need of an explanation. As it is, it has not been corroborated, or even tested, nor is it amenable to testing (see below).

THE HYPOTHESIS The hypothesis offered is said to “explain” a narrow set of lightness demonstrations. Each consists of two displays, both containing a surface of luminance x; despite being equiluminant, these surfaces differ in their appearance, one appearing lighter than the other.

The claim is as follows: The visual system has evolved to represent as lighter those surfaces that appear more frequently in one “context” than in another. Thus, in each display, the surface that appears lighter must have been encountered more often in that particular “context” during the course of evolution. It is because seeing the higher-frequency target/context combination as lighter was “optimal” this situation arose. More specifically, it is because the response “lighter” to a target in one “context” and “darker” to a target in another context, and so on for contexts in-between, has had, over evolutionary time, positive adaptive effects, that these percepts have become instantiated in the visual process.

DO ORGANISMS TRACK ABSOLUTE AND RELATIVE LIGHT INTENSITY OVER MOMENTS, HOURS, DAYS, EONS, AT ALL POINTS IN THE RETINAL IMAGE, AND WHEN DID THEY STOP DOING THIS? The hypothesis would appear to presuppose that organisms can discriminate between, and keep track of, the absolute luminances of various “targets” in various “contexts,” as they have been encountered with every glance, of every individual (or at least the ancestors of every individual), at every point in the visual image, every moment, hour, day, across the evolutionary trajectory of the species. There is no suggestion as to how these absolute luminances might be tracked, even “in effect.” Not only is it difficult to imagine what mechanism (other than a miracle) might allow such (species-wide) data collection (or its equivalent) to arise, it runs contrary to the physiology of the visual system, in which inhibitory mechanisms ensure that relative, not absolute, luminance information, is coded even at the lowest levels of the nervous system. Furthermore, given that lightness perception does not change across an individual's lifetime, nor depend on their particular visual experience, it would seem that this process of statistical accumulation must have stopped at some point during our evolution. So we have to ask, when do the authors suppose this (impossible) process to have stopped, why did it stop, and what were the relevant environments at that time and previously? (The logical assumption that the authors suppose the process has, in fact, stopped is reinforced when they refer to “instantiated” rather than developing “statistical structures.”)

On 2015 Nov 02, R Andrew Moore commented:

Peter raises so many points that it is difficult to respond in detail to all of them. But they are all misdirected, and some of his contentions are plain wrong. As an example, yes, we do use examine randomisation and blinding in assessing quality, because being randomised and double blind is a minimum entry requirement in pain studies.

There are deficiencies in trial reporting – and that on adverse events in nothing new, as we reported some time ago (J Pain Symptom Manage 1999;18:427-37). Large observational studies have examined serious rare adverse events with topical NSAIDs, perhaps more appropriate given the modest numbers in RCTs. We have to work with what is available and comment on deficiencies.

Indirect comparisons have been shown to be as good if not better than direct, given available data. The fact that Peter found no effect of topical NSAIDs in his Clinical Evidence review is in direct contrast to our reviews, updated several times since our original review of topical analgesics in 1998, most recently in 2015. We are unaware of other reviews that agree with Peter’s analysis, and the results of recent reviews have been incorporated into a number of guidelines.

Peter’s attitude to the pharmaceutical industry is well known. The research group behind this review uncovered duplicate publication by industry (BMJ. 1997;315:635-40) and what some would see as the scandal of inappropriate statistical handling of missing data (Pain. 2012;153:265-8), as well as highlighting academic fraud, inter alia (Anaesthesia. 2010;65:327-30). We have tested the impact of possible industry bias in pain trials and found none in studies that compared like with like (Pain. 2006;121:207-18). We have worked with industry to obtain clinical trial reports, previously unpublished data, and individual patient level data. We have a simple rule – only do it if there is no bar to publication. Peter’s suggestion that we are in some way beholden to industry is beneath him.

On 2015 Oct 24, Peter Gøtzsche commented:

This meta-analysis is not reliable. It is not appropriate to pool all trials when small trials yield a considerably larger effect than large trials (P=0.001). The authors used rating scales for scoring the quality of trials and trial validity, but such scales have important weaknesses and should not be used (see JAMA 1999; 282: 1054-60 and the Cochrane Reviewers’ Handbook (www.cochrane.org). By using such scales, the authors rated far too many trials as being of acceptable quality. The authors are not clear about whether the trials that compared topical with oral NSAIDs compared the same or different drugs, and their finding that the old drug indomethacin was not significantly better than placebo is irrelevant since the P value depends on the sample size, and in fact, the effect obtained with indomethacin was similar to those of several of the other drugs that had significant effects. The trials reported insuffiently on harms; 56 of a total of 70 systemic adverse events occurred in a single trial, which raises the question whether this trial was more reliable than the others. The authors have consulted for various pharmaceutical companies but do not say which ones, which is an important omission, as they somewhat surprisingly report that one NSAID was better than the others. Their comparisons are questionable, however, as they were indirect, based on studies comparing active drug with placebo. In contrast to the authors, I did not find that any topical NSAID has a true effect (see London: BMJ Publications, Clinical Evidence, 2005; 14: 1498-1505). In contrast to the authors, I have no conflicts of interest and I believe that authors with financial conflicts of interest should not be authors on systematic reviews.

On 2015 May 17, Prof.Dr.Jogenananda Pramanik commented:

Invited co-authors: Dr.Myo Wint Zaw,Dr.Lwin Lwin Cho,and Dato'Dr. Mehmood bin Abu Yusoff, Universiti College UCSA,Kuantan,Pahang,Malaysia.

Improvement in health care facilities in resource poor setting needs high moral,determination and dedicated approach. Financial constraints obviously hinder progress.However, right kind of attitude and organized human approach may overcome obstacles and will definitely show results(1). Several health care teams are working 24/7 with minimum resources to save lives at recurrent earth quakes ridden Nepal. However, lack of team based organized approach, farsighted leadership and many other man-made barriers exist to hinder improvement in health care in both developing and developed countries alike. "we believe now that the duty to help the world's poor nations is everyone's. we wish our own nation were in the lead, and someday maybe it will be. Meanwhile, we can deepen our commitments. Our limited but consistent experience shows that we will meet in the developing world a level of will, skill, and constancy that may put ours to shame. We may well find ourselves not the teachers we thought we were, but students of those who simply will not be stopped under circumstances that would have stopped us long ago".(2) References: 1.Berwick DM: BMJ. 2004 May 8;328(7448):1124-9.Lessons from developing nations on improving health care. 2. Donald M Berwick, BMJ. 2004 May 8; 328(7448): 1124–1129.doi: 10.1136/bmj.328.7448.1124,PMCID: PMC406330; Lessons from developing nations on improving health care,

On 2014 Nov 09, Gary Ward commented:

We reported in this paper that the enhancers of invasion and motility identified in the screen do not stimulate an increase in parasite intracellular calcium levels. This conclusion was based on semiquantitative microscopy-based measurements of the fluorescence intensity of the calcium reporter Fluo-4 in individual parasites, before and after treatment with enhancer. More recent quantitative experiments on populations of parasites using the ratiometric calcium reporter Fura-2 showed that treatment with three of the four enhancers tested does in fact stimulate an increase in parasite intracellular calcium levels (Tang Q, 2014); results with the fourth were inconclusive due to spectral overlap between the compound and indicator.

The discovery that some, and perhaps all, of the enhancers identified in the screen increase parasite intracellular calcium levels provides a rationale for how this group of structurally diverse compounds can cause the same set of phenotypes, i.e, enhanced invasion, microneme secretion and motility.

On 2014 Nov 17, Raphael Levy commented:

This article is the first in the "stripy nanoparticle" series. It has been followed by over 35 articles, yet it is based on a scanning tunneling microscopy artefact.

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

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

On 2013 Nov 27, Neil Saunders commented:

Unfortunately, this database is no longer on line. I am first author and the server was not maintained after I left the University of New South Wales.

The methods described in the article have largely been supplanted by the use of NGS to sequence gut metagenomes. However, if time permits, I will release code/data on Github and update the comments here.

UPDATE 2014-07-22: now at Github - https://github.com/neilfws/archaeaEST.

On 2014 Nov 02, Ivan Oransky commented:

The first author of this paper, which was retracted in 2007, was found by the Office of Research Integrity to have falsely manipulated images: http://retractionwatch.com/2014/10/31/former-nih-lab-director-faked-findings-in-three-papers-ori/

On 2017 Nov 29, Anne Niknejad commented:

erroneous link in the reference list:

↵ Zhang, H., Yang, Z., Shen, Y. & Tong, L. (2003) Science 299 , 2064–2067. Abstract/FREE Full Text

the correct link is

http://science.sciencemag.org/content/299/5615/2064.long

On 2013 Nov 04, ANDREW SU commented:

!MOVED http://biogps.org

The URL in the original paper has now been retired. This data set (together with other gene expression data sets) are now hosted at http://biogps.org.

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2015 Jul 18, Jan Tunér commented:

Unfortunately, this study cannot be evaluated since the documentation of the actual laser parameters is poor. The only information given about these essential facts is "The LILT device had a wavelength of 905 nm and an average power of 0-60 mW. All LILT treatments were for 5 min per site." Which output was actually used? Pulse repetition rate? Dose? Power density?

On 2015 Jun 02, thomas samaras commented:

Additional information on height, CHD and longevity is available from these publications.

Samaras TT. Shorter height is related to lower cardiovascular disease risk—A narrative review. Indian Heart Journal 2013; 65: 66-71.

Samaras TT. Evidence from eight different types of studies showing that smaller body size is related to greater longevity. Journal of Scientific Research & Reports. 2014: 3 (16): 2150-2160, 2014; article no. JSRR.2014.16.003.

Samaras TT. Human Scaling and Body Mass Index. In: Samaras TT (ed): Human Body Size and the Laws of Scaling: Physiological Performance, Growth, Longevity and Ecological Ramifications. New York: Nova Science Pub; 2007: pp 17-32.

He Q, Morris BJ, Grove JS, Petrovitch H, Ross W, Masaki KH, et al. Shorter men live longer: Association of height with longevity and FOXO3 genotype in American men of Japanese ancestry. Plos ONE 9(5): e94385. doi:10.1371/journal.pone.0094385.

Salaris L, Poulain M, Samaras TT. Height and survival at older ages among men born in an inland village in Sardinia (Italy), 1866-2006. Biodemography and Social Biology, 58:1, 1-13.

Bartke A. Healthy Aging: Is Smaller better? A mini-review. Gerontology 2012; 58:337-43.

On 2013 Oct 23, Albert Erives commented:

This paper describes an example of what I have been calling an equivalence class of transcriptional enhancers. This is compared with other such sets in this short collection of slides: How to best approach transcriptional enhancers?. Albert Erives. figshare. http://dx.doi.org/10.6084/m9.figshare.829049

What is not well-described in this paper is how their common site organization was found based on a subset of "specialized sites" within homotypic site clusters. A specialized site is defined mathematically as a sequence matching a binding motif descriptor that identifies a single unique site within each member of a set of homotypic binding site clusters. In other words, specialized sites are identifiable and distinguishable by the existence of any motif that matches them as single components of each homotypic site cluster belonging to a set of mechanistically-equivalent enhancers. A motif that describes more than a single site in each cluster is therefore not a specialized motif. Okay, that's not the easiest thing to get across even today, but this method led to the identification of the so-called D-alpha site, which turned out to be a Su(H) binding site that had evolved over a relic Dorsal binding site, and the so-called D-beta site, which turned out to be the closest Dorsal-binding-like site to the Twist site, the distance to which we later found to encode a large component of the response to the Dorsal morphogen gradient. (See here Crocker J, 2008 and here Crocker J, 2010.) For me, the major significance of this method is that it works well in distinguishing functional sites from relic (pseudogenized), fast-evolving sequences.

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2014 Nov 23, Harri Hemila commented:

A comment is available at: http://hdl.handle.net/10250/7981

On 2014 Nov 08, Sean Barrett commented:

In my view, this paper should be considered to be a seminal contribution to the entire nicotine/tobacco research field.

On 2015 Jun 08, Michael Eisen commented:

Readers interested in this article should read the following blog post by Lior Pachter and associated comments:

https://liorpachter.wordpress.com/2015/05/26/pachters-p-value-prize/

The analyses presented there cast serious doubt on the claim made in the last paper, and highlighted in the last sentence of the abstract that "95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions".

On 2015 Oct 07, Bill Cayley commented:

One of many examples showing simpler care of lacerations is just as good or better: https://lessismoreebm.wordpress.com/?s=lacerat

On 2015 Jan 10, Tom Kindlon commented:

Important typo in abstract:

"After pregnancy, there was no change in CFS symptoms in 21 (30%), an improvement of symptoms in 14 (20%), and a worsening of symptoms in 35 (20%) of the subjects."

should say:

"After pregnancy, there was no change in CFS symptoms in 21 (30%), an improvement of symptoms in 14 (20%), and a worsening of symptoms in 35 (50%) of the subjects."

I checked this with the full text which says: "After pregnancy, there was no change in 30%, an improvement in 20%, and a worsening in 50% of patients."

On 2017 Jun 21, Gary Goldman commented:

It is well established that in Japan, where only 1 in 5 children received varicella vaccination, that those vaccinated maintained protective immunity for 20 years. This was largely due to the vacinees' receiving exogenous exposures to children with natural or wild-type varicella that boosted cell-mediated immunity to varicella zoster virus. During the majority of the study by Kuter et al., varicella vaccine receipients were likewise being boosted through exposure to individuals with wild-type varicella--especially during annual epidemics of varicella. This had the effect of artifically elevating vaccine effectiveness because of the shedding of varicella zoster virus in the community. In communities with widespread varicella vaccination, once oppotunities for exogenous boosts became rare, single-dose varicella vaccination efficacy declined to less than 50% five years after vaccination.Goldman GS, 2005

On 2015 Dec 11, Harri Hemila commented:

Available at DOI.

On 2013 Nov 24, John Sotos commented:

Dr. Schwartz dates the first description of hemoglobinuria (as black urine) to the 13th century AD (1).

About 400 BC, however, Hippocrates described urinary quantity, color, consistency, or sediment in 41 of 42 case reports in his Book of Epidemics (2). Twelve case reports mention black urine, a frequency so high that one wonders if glucose-6-phosphate dehydrogenase deficiency (3) and/or fava bean ingestion could have predisposed this population to hemolysis.

Inspection of the urine was important in ancient Greek medicine, but has been recently dismissed as “mostly nonsense” (4). Yet, the approach taken by Hippocrates was remarkably modern. In several patients having pigmented urine, Hippocrates checked for the appearance of a sediment after allowing the urine to sit — a maneuver that would have allowed him to distinguish hematuria from hemoglobinuria and myoglobinuria.

Such insights from Hippocrates are not surprising. As Garrison has remarked, “All that a man of genius could do for internal medicine, with no other instrument of precision than his own open mind and keen senses, he accomplished” (5).

(1) Schwartz RS. Black mornings, yellow sunsets — a day with paroxysmal nocturnal hemoglobinuria. N Engl J Med. 2004;350:537-538.

(2) Adams F. The Genuine Works of Hippocrates. Huntington, NY: Robert E. Krieger, 1972; 110-141.

(3) Tran TH, Day NP, Ly VC, Nguyen TH, Pham PL, Nguyen HP, Bethell DB, Dihn XS, Tran TH, White NJ. Blackwater fever in southern Vietnam: a prospective descriptive study of 50 cases. Clin Infect Dis. 1996;23:1274-1281.

(4) Majno G. The Healing Hand: Man and Wound in the Ancient World. Cambridge, MA: Harvard University Press, 197; 494 note 159.

(5) Garrison FH. An Introduction to the History of Medicine. 4th ed. Philadelphia: WB Saunders, 1929: 94.

On 2017 Jun 08, Egon Willighagen commented:

Happy to see the PubMed record was updated :)

On 2017 Feb 13, Egon Willighagen commented:

The correct DOI is 10.1042/bst0320083

On 2014 Oct 19, David Mage commented:

The authors have done an outstanding and excellent study. However, they seem to have failed to notice here that, in Table 2, their reported male fraction of SIDS (0.612) in 260 cases (excluding matched sets) is identical to the male fraction of SIDS reported by Mage and Donner (PMID 9076695) of 41,238 male and 26,140 female in 36 SIDS data sets giving a male fraction of 0.6120. This is important to note because the consistancy of the male fraction of SIDS throughout time and among various countries supports a recessive X-linkage of susceptibility to SIDS that seems to be ignored inspite of the early conclusion of Naeye et al. in PMID 5129451, that male susceptibility to infant death "must" be X-linked.

On 2016 Mar 29, Jonathan Wren commented:

URL relocated to: http://ppdb.tc.cornell.edu/

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2015 Jun 02, thomas samaras commented:

Additional information on birthweight, height, CHD, and longevity is available from these recent publications.

Samaras TT. Shorter height is related to lower cardiovascular disease risk—A narrative review. Indian Heart Journal 2013; 65: 66-71.

Samaras, TT. Is short height really a risk factor for coronary heart disease and stroke mortality? A review. Med Sci Monit 2004; 10(4): RA63-76.

Samaras TT. Evidence from eight different types of studies showing that smaller body size is related to greater longevity. Journal of Scientific Research & Reports. 2014: 3 (16): 2150-2160, 2014; article no. JSRR.2014.16.003.

Samaras TT. Human Scaling and Body Mass Index. In: Samaras TT (ed): Human Body Size and the Laws of Scaling: Physiological Performance, Growth, Longevity and Ecological Ramifications. New York: Nova Science Pub; 2007: pp 17-32.

He Q, Morris BJ, Grove JS, Petrovitch H, Ross W, Masaki KH, et al. Shorter men live longer: Association of height with longevity and FOXO3 genotype in American men of Japanese ancestry. Plos ONE 9(5): e94385. doi:10.1371/journal.pone.0094385.

Salaris L, Poulain M, Samaras TT. Height and survival at older ages among men born in an inland village in Sardinia (Italy), 1866-2006. Biodemography and Social Biology, 58:1, 1-13.

Bartke A. Healthy Aging: Is Smaller better? A mini-review. Gerontology 2012; 58:337-43.

On 2014 Feb 05, Tom Kindlon commented:

A CFS study which raises questions about the use of the Role Emotional (RE) subscale of the SF-36 to define CFS

(This was originally posted here: http://www.biomedcentral.com/1472-6963/3/25/comments but the formatting has been lost and some people may read the paper on PubMed Central)

As I mentioned in the previous comment, this paper recommends, amongst other questionnaires, the use of the SF-36 questionnaire but does not specify which subscales should be used.

One group of researchers[1] have decided to use the physical function, role physical, social function and role emotional subscales of the SF-36 to define disability, with a low score on just one of these subscales being sufficient to satisfy the criteria (i.e. there didn't need to be more than one low scores).

Since then, this definition has gone on to be used in numerous papers (such as [2-5]) as the CDC are using it as the definition they're using for their CFS studies in the US, and they probably have the largest CFS research program in the world. It was used to give the prevalence rate of 2.54% for CFS in the adult population[6]. Most recently, it was used to investigate the prevalence of the reporting of childhoold trauma in this cohort[7].

A study by Fulcher and White (2000)[8] raises questions about the use of the Role Emotional (RE) subscale of the SF-36 to select patients with CFS. The study involved 66 patients with CFS without a current psychiatric disorder, 30 healthy but sedentary controls, and 15 patients with a current major depressive disorder.

It found, amongst other things, that "the two patient groups were significantly more incapacitated than the sedentary controls on all SF-36 measures (p<0.001), except that the patients with CFS were not significantly different in emotional or mental function." Also, "the depressed subjects were significantly more incapacitated in emotional and mental functioning than the patients with CFS p<0.001)."

These results suggest that low scores on the emotional and mental functioning subscales of the SF-36 do not seem to be an intrinsic part of CFS (if they're found, they could be related to comorbid psychiatric issues). They also points out the risks of using the RE subscale alone [especially given CFS shares some characteristics with depression and so some people with depression (but not CFS) could potentially score the required 25 points on the Symptom Inventory] i.e. one could inadvertently include some people who have depression but not CFS, as CFS patients.

References

[1] Reeves WC, Wagner D, Nisenbaum R, Jones JF, Gurbaxani B, Solomon L, Papanicolaou DA, Unger ER, Vernon SD, Heim C. Chronic Fatigue Syndrome – A clinically empirical approach to its definition and study. BMC Medicine 2005, 3:19<br><br>

[2] Raison CL, Lin JM, Reeves WC. Association of peripheral inflammatory markers with chronic fatigue in a population-based sample. Brain Behav Immun. 2008 Dec 11.

[3] Welberg LA, Capuron L, Miller AH, Pagnoni G, Reeves WC. Neuropsychological performance in persons with chronic fatigue syndrome: results from a population-based study.Majer M, Psychosom Med. 2008 Sep;70(7):829-36.

[4] Nater UM, Youngblood LS, Jones JF, Unger ER, Miller AH, Reeves WC, Heim C. Alterations in diurnal salivary cortisol rhythm in a population-based sample of cases with chronic fatigue syndrome. Psychosom Med. 2008 Apr;70(3):298-305.

[5] Nater UM, Maloney E, Boneva RS, Gurbaxani BM, Lin JM, Jones JF, Reeves WC, Heim C. Attenuated morning salivary cortisol concentrations in a population-based study of persons with chronic fatigue syndrome and well controls. J Clin Endocrinol Metab. 2008 Mar;93(3):703-9.

[6] Reeves WC, Jones JF, Maloney E, Heim C, Hoaglin DC, Boneva RS, Morrissey M, Devlin R. Prevalence of chronic fatigue syndrome in metropolitan, urban, and rural Georgia. Popul Health Metr. 2007 Jun 8;5:5.

[7] Heim C, Nater UM, Maloney E, Boneva R, Jones JF, Reeves WC. Childhood trauma and risk for chronic fatigue syndrome: association with neuroendocrine dysfunction. Arch Gen Psychiatry. 2009 Jan;66(1):72-80.

[8] Fulcher KY, White PD. Strength and physiological response to exercise in patients with chronic fatigue syndrome. J Neurol Neurosurg Psychiatry. 2000 Sep;69(3):302-7.

On 2014 Feb 03, Tom Kindlon commented:

Which subscales of the SF-36 should be used? Results from a study in Fibromyalgia patients

(This was originally posted here: http://www.biomedcentral.com/1472-6963/3/25/comments but the formatting has been lost and some people may read the paper on PubMed Central)

This paper recommends, amongst other questionnaires, the use of the SF-36 questionnaire. But which subscales should be used? One group of researchers[1] decided to use the physical function, role physical, social function and role emotional subscales of the SF-36 to define disability, with a low score on just one of these subscales being sufficient to satisfy the criteria (i.e. there didn't need to be more than one low scores). Since then, this definition[1] has gone on to be used in numerous papers (for example, 2-5).

But is this a good way of using the SF-36 given the Fukuda definition for CFS[6] requires that there be a "substantial reduction in previous levels of occupational, educational, social, or personal activities".

Fibromyalgia patients share many similarities with CFS patients and many researchers use CFS and FMS patients together in their studies (for example [7-10]).

One study[11] recently assessed Fibromyalgia Syndrome (FS) patients using the SF-36 questionnaire. It found that patients could be broken down into two groups using the SF-36 subscales looking at mental well-being (social functioning, role limitation due to emotional health problems, and mental health). "One group demonstrated psychological dysfunction, whereas the other showed normal psychological scores. Physical well-being scores (physical functioning, role limitation due to physical health problems, bodily pain, general health, and vitality) did not differ between FS patients but were altogether below the normal range."

If this was found to be the same in other populations, it would suggest that perhaps including patients who solely have low scores on subscales assessing mental well-being such as the role emotional and social functioning subscales of SF-36, which is all the CFS definition prepared by Reeves[1] requires, would select a group of people with psychological dysfunction but not necessarily greater physical disability.

References:

[1] Reeves WC, Wagner D, Nisenbaum R, Jones JF, Gurbaxani B, Solomon L, Papanicolaou DA, Unger ER, Vernon SD, Heim C. Chronic Fatigue Syndrome – A clinically empirical approach to its definition and study. BMC Medicine 2005, 3:19

[2] Reeves WC, Heim C, Maloney EM, Youngblood LS, Unger ER, Decker MJ, Jones JF, Rye DB. Sleep characteristics of persons with chronic fatigue syndrome and non-fatigued controls: results from a population-based study. BMC Neurology 2006, 6:41

[3] Majer M, Jones JF, Unger ER, Youngblood LS, Decker MJ, Gurbaxani B, Heim C, Reeves WC. Perception versus polysomnographic assessment of sleep in CFS and non-fatigued control subjects: results from a population-based study. BMC Neurology 2007, 7:40

[4] Jones JF, Maloney EM, Boneva RS, Jones AB, Reeves WC. Complementary and alternative medical therapy utilization by people with chronic fatiguing illnesses in the United States. BMC Complementary and Alternative Medicine 2007, 7:12

[5] Reeves WC, Jones JF, Maloney E, Heim C, Hoaglin DC, Boneva RS, Morrissey M, Devlin R.Prevalence of chronic fatigue syndrome in metropolitan, urban, and rural Georgia. Popul Health Metr. 2007 Jun 8;5:5.

[6] Fukuda K, Straus SE, Hickie I, Sharpe MC, Dobbins JG, Komaroff A: The chronic fatigue syndrome; a comprehensive approach to its definition and study. Ann Int Med 1994, 121:953-959.

[7] Teitelbaum JE, Johnson C, St Cyr J. The use of D-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study. J Altern Complement Med. 2006 Nov;12(9):857-62.

[8] Glass JM. Cognitive dysfunction in fibromyalgia and chronic fatigue syndrome: new trends and future directions. Curr Rheumatol Rep. 2006 Dec;8(6):425-9.

[9] Zachrisson O, Regland B, Jahreskog M, Jonsson M, Kron M, Gottfries CG. Treatment with staphylococcus toxoid in fibromyalgia/chronic fatigue syndrome--a randomised controlled trial. Eur J Pain. 2002;6(6):455-66.

[10] Zachrisson O, Regland B, Jahreskog M, Kron M, Gottfries CG. A rating scale for fibromyalgia and chronic fatigue syndrome (the FibroFatigue scale). J Psychosom Res. 2002 Jun;52(6):501-9.

[11] Oswald J, Salemi S, Michel BA, Sprott H. Use of the Short-Form-36 Health Survey to detect a subgroup of fibromyalgia patients with psychological dysfunction. Clin Rheumatol. 2008 Apr 1

On 2015 Nov 25, S A Ostroumov commented:

I have studied this species of plants also. It was also a factor to remove some metals from water. It is a useful paper, congratulations to the authors!

On 2013 Oct 28, DAVID SANDERS commented:

See the earlier articles "Sulfhydryl involvement in fusion mechanisms" [2000]Sanders DA, 2000 and "Ancient viruses in the fight against HIV" [2003] Sanders DA, 2003 for the prediction of the results published here.

On 2014 Nov 02, Ivan Oransky commented:

The first author of this paper, which was retracted in 2007, was found by the Office of Research Integrity to have falsely manipulated images: http://retractionwatch.com/2014/10/31/former-nih-lab-director-faked-findings-in-three-papers-ori/

On 2017 Apr 23, Md. Shahidul Islam commented:

In human beta cells TRPM5 is almost absent while its closest relative TRPM4 is abundant. Marabita F, and Islam MS. Pancreas. 2017 Jan;46(1):97-101. Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells. PMID: 27464700 DOI: 10.1097/MPA.0000000000000685

On 2016 Aug 30, Stephen Strum commented:

This is an excellent article providing an in-depth review of c-Met and its relation to hepatocyte growth factor (HGF). Authors discuss various targets of therapy (TOT) involving this receptor (c-Met) + ligand (HGF) pathway. I highly recommend spending the time to read this article.

On 2014 Jun 23, Chandra Boosani commented:

This article doesn't exist in the journals website as on June 23rd 2014. http://www.invasivecardiology.com/issue/30?page=1

On 2014 Nov 23, Harri Hemila commented:

A manuscript version is available at handle

On 2015 Dec 02, S A Ostroumov commented:

This article was among TOP FULL-TEXT DOWNLOADS in 2014-2015. 67 downloads from ResearchGate, 669 views, 9 bookmarks by 26.01.2015. Full text online free: https://www.researchgate.net/publication/200594244; Full title of the journal: Rivista di Biologia / Biology Forum. 2003 (May). 96: 327-332. Abstracts in Eng. and Italian (p. 332).

Additional KEY WORDS: priorities, fundamentals, environmental sciences, biospheric sciences, life sciences, biomedical sciences, geosciences, ecosystems, biosphere, organisms, levels of life systems, man-made impact, anthropogenic, effects, terrestrial, aquatic, research topics;

On 2013 Jul 17, Toby Gibson commented:

Chk1 is an important DNA damage checkpoint protein kinase. Biochemical evidence suggests that the sites most vigorously phosphorylated by the Chk1/2 kinases match or are close to the pattern (LF)xRxx(pST)(LF). See, for example, these articles (PMID: 10648819; 10761933; 11821419; 12711320). If only one of the three specificity determining positions are lost, the kinases may still phosphorylate, but at reduced activity. This gradation in activity might have biological significance and also means that it is difficult to define motif patterns for Chk kinase substrate sites. Currently we are trying to do this for the ELM protein motif resource (http://elm.eu.org/).

In the paper that I would like to comment on here, the reported phosphorylation site at Ser47 of p73 - VgGtd(pS)S - lacks all of the strong specificity determinants (capitalised positions). It has been confounding our attempt to define a Chk phosphorylation site pattern for ELM. However, based on a close examination of the figures in the paper, we have now decided to exclude this p73 site from further consideration.

The MCB paper is open access and high resolution figures are available at both the MCB site and through PubMed.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC262369/figure/f2/

Fig. 2A lower left gel. Lanes 3-4 are the same as lanes 5-6. Note also the inconsistent gap length between band pairs. This gel appears to be a bounded grey box into which band pairs have been pasted.

Fig. 2B upper left gel. This appears to be a bounded grey box in which the + lanes have been pasted in. These have vertical edges that do not correspond to the edges of the bands. The - lanes are just smooth, grey blanks.

Fig. 2B lower left gel. The band in lane 4 is the same as in lane 5. Associated dots and shadows are diagnostic despite a slight size difference.

Fig. 2B lower right gel. This is a bounded grey box into which three bands have been pasted. The band in lane 1 has been pasted over the edge line! The band in lane 3 has also been pasted over the edge line!

Fig. 2C Lower left gel. The band in lane 2 has been pasted over the edge line! This is another grey box into which bands have been pasted.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC262369/figure/f3/

Fig. 3A upper gel. Bands in lanes 1-4, 6-7, 10 are identical. Maximum resolution is required to see this unambiguously.

Fig. 3B upper gel. Bands in lanes 4, 6, 9-10 are identical. Maximum resolution is required to see this.

Fig. 3B middle gel. Bands in lanes 2,4 and probably 3 are the same. Bands in lanes 6,7,9 are the same.

Fig. 3D upper right gel slice. All eight bands are identical. Maximum resolution is required to see this (it is not clear from the pdf download of the whole paper). Also these bands might be elongated versions of the reused bands listed for Fig. 3A.

Fig. 3 D lower left gel slice. Lanes 2-7 are identical to lanes labelled 8-13 of the lower right gel slice. According to the labelling above each lane, these are certainly to be understood as different experiments.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC262369/figure/f4/

Fig. 4A Upper right slice. Band pair in lanes 1-2 are the same as 7-8. Band in lane 4 is the same as band in lane 6.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC262369/figure/f5/

Fig. 5D lower panel. Bands 1-3 are the same as bands 6-8, except that they are the mirror image.

The paper is ten years old. Therefore it is unlikely that the raw data used to assemble these figures still exists, though it would be fascinating to make comparisons if any original data can be found.

On 2017 Aug 05, Fernando Castro-Chavez commented:

Dear Reader, This is where it all started, when I moved from Mexico to the U.S., at the Baylor College of Medicine (BCM), within the Texas Medical Center; we had Perilipin knock out mice able to eat as much fat and carbohydrates as they wanted, never getting obese, but remaining slender, so, we were able to determine the basic biochemical profile of these organisms, which had over expressed the pathways of Beta Oxidation, and of the Respiratory Chain, and also of the Krebs Cycle, while they had down regulated the pathways of the Unsaturation of Fats, and of the production of Cholesterol. Sincerely, Fernando Castro-Chavez.

On 2013 Nov 24, John Sotos commented:

The discussion of how to manage Mrs. P, a 60 year old woman with atrial fibrillation (1), nicely reprised Sir William Osler’s 1907 advice: “Too much stress should not be laid upon arrhythmia per se in the absence of organic disease” (2).

As presented, however, Mrs. P’s evaluation did not adequately exclude organic disease: neither her body mass index nor a general description of her habitus was provided. Although her physicians obviously had access to this information, its omission from the case record suggests that an emerging correlate of atrial fibrillation, obstructive sleep apnea (OSA), was not considered as a potential exacerbating factor in her illness.

The prevalence of OSA in American adults is estimated as 20%, most of it undiagnosed, and most of it related to obesity (3). Hypothyroidism and alcohol ingestion, both of which Mrs. P had, are two of several additional risk factors.

As recently reviewed in JAMA, the role of OSA in cardiac disorders is receiving increasing attention, in part because OSA “frequently coexists undiagnosed in patients with cardiovascular disease” (4). Several physiological mechanisms plausibly link OSA and atrial fibrillation (4), but few studies have examined their clinical links. Of highest relevance for Mrs. P, however, Kanagala et al (5) found that untreated sleep apnea doubles the likelihood of atrial fibrillation recurring within 12 months of cardioversion, when compared to OSA patients receiving positive pressure treatment.

The effectiveness, and, therefore, cost-effectiveness, of testing for OSA in patients with atrial fibrillation is unknown. However, given that OSA is itself common, serious, and treatable, a case can be made for testing patients such as Mrs. P for sleep apnea, especially if they are obese, before consigning them to a lifetime of perhaps unnecessary warfarin therapy. Certainly a stronger case can be made for taking a sleep history in all patients with atrial fibrillation.

(1) Singer DE. A 60-year-old woman with atrial fibrillation. JAMA. 2003;290:2182-9.

(2) Osler W. The Principles and Practice of Medicine. 6th ed., revised. New York: D. Appleton, 1907;835.

(3) Young T, Peppard PE, Gottlieb DJ. Epidemiology of obstructive sleep apnea: a population health perspective. Am J Respir Crit Care Med. 2002;165:1217-39.

(4) Shamsuzzaman AS, Gersh BJ, Somers VK. Obstructive sleep apnea: implications for cardiac and vascular disease. JAMA. 2003;290:1906-14.

(5) Kanagala R, Murali NS, Friedman PA, Ammash NM, Gersh BJ, Ballman KV, Shamsuzzaman AS, Somers VK. Obstructive sleep apnea and the recurrence of atrial fibrillation. Circulation. 2003;107:2589-94.

On 2016 Jul 23, Lydia Maniatis commented:

Part three: Here's an instant update: It seems that, a few years after this publication, the "merged models" were tested. They failed. This is to be expected with ad hoc models, but at least it shows that the authors were sincere in their attempts, though this doesn't excue sloppy reasoning at that level. They also seem inclined to continue in the same style ("adding components" to the failed models rather than rethinking their ideas). The transparency-requiring low-level channel assumptions are apparently untouchable, non-negotiable. I know it's a cliche, but it's a recipe for misguided Ptolemaic solar system-level complexity, as the authors demonstrate.

The article is "Probed-sinewave paradigm: a test of models of light-adaptation dynamics. Hood DC1, Graham N, von Wiegand TE, Chase VM" and its authors frankly acknowledge the utter failure of their hypothesis:

"Our purpose here was to explore a relatively unused paradigm, the probed-sinewave paradigm, as a vehicle for distinguishing among candidate models of light adaptation. The paradigm produced orderly data with clear features. The candidate light-adaptation models, however, were unable to predict these features and our attempts to rescue them by changing parameter values and the decision rule were unsuccessful. While it is plausible that other modifications would produce predictions closer to the data, it is hard to believe these models can be rescued without adding additional components. For discussion, we divide these possible components into those that seem to require an additional channel vs those components that can be added to the single-channel of the models in Fig. 6."

"While this discussion suggests a number of plausible directions for future work, it is not at all clear which direction or model will ultimately prove most successful. We started with a paradigm we thought would be a strong test of existing models; the test turned out to be even stronger than we expected."

So pretty much starting at zero, after all that. Performing a strong test was the right move. The wrong move was not realizing, on the basis of solid reasoning, that the theoretical foundation of the model was flimsy and that models with such flimsy foundations are bound to fail unless you are extraordinarily lucky.

Let me add that all models eventually fail, but it is the case of well-reasoned ones that these failures are informative, and necessary.

On 2016 Jul 23, Lydia Maniatis commented:

Part two: Popper has discussed traditions such as those described and illustrated above, and concluded that they are not the kind of traditions that endow scientific activity with its progressive character. He suggested that we choose not to immunize our hypotheses with the tactics discussed above, e.g. leaving problems for the future and piling ad hoc model on top of ad hoc model, and having tolerance for logical inconsistencies. But that's a harder way than the vagueness, sloppiness and special pleading masked in technical complexity that has come to dominate contemporary vision science and in fact almost the whole of science today.

On 2016 Jul 23, Lydia Maniatis commented:

This article is illustrative of the degradation of theory and practice in vision science. The article is not new (but compare with, e.g. Graham, 2011), but many of its assumptions and the style of argument - tolerance for layers upon layers of uncorroborated assumptions and inadequate, ad hoc models - are still very current and underpin a broad swath of contemporary (arguably pseudoscientific) activity. Below are quotes from the article and my comments.

The abstract: "Light adaptation has been studied using both aperiodic and periodic stimuli. Two well-documented phenomena are described: the background-onset effect (from an aperiodic-stimulus tradition) and high-temporal-frequency linearity (from the periodic-stimulus tradition). These phenomena have been explained within two different theoretical frameworks. Here we briefly review those frameworks. We then show that the models developed to predict the phenomenon from one tradition cannot predict the phenomenon from the other tradition, but that the models from the two traditions can be merged into a class of models that predicts both phenomena."

Comment: One wonders whether the merger was ultimately successful, and whether falsifying phenomena from yet other traditions could be merged with these two, to expand the ever-expanding ad hoc circle of tradition.

Note that the piecemeal "merger" philosophy expressed by Graham and Hood seems to preclude falsification. Falsifying phenomena from another "tradition" simply lead to the summing of individual ad hoc models into a compound ad hoc model, and so on. The complexity but not the information content of the models will thus increase. (This will also likely produce internal inconsistencies that not be noticed because they will not be looked for.) The question of whether these models correspond with the facts that they are supposedly trying to explain never really arises.

All this can be garnered from the abstract: If anything, the text is even worse.

"None of the parts of the merged models, however, is necessarily correct in detail. Many modifications or substitutes would clearly work just as well at this qualitative level. …Also, one could certainly expand the model to include more parts. …Similarly, the initial gain-controlling process might be composed of several processes having somewhat different properties"

Comment: The models are arbitrary, ad hoc, incomplete on their own terms, and there is no rational criterion for choosing among an infinite number of alternatives.

"No attempt was made to fine-tune either model to predict all the details in any one set of psychophysical data…much less in all the other psychophysical results that such a model might bear on…To attempt such a project in the future might be worthwhile...particularly if the experimental results were all collected on the same subjects..."

Comment: In other words, because the models are ad hoc they may only explain the results to which they were tailored. It may (or may not??) be worth checking to see whether this is the case. I.e. testing models for correspondence with the phenomena is optional. The effects in question are too fragile and too little understood to be tested across subjects with varying methods.

"The more vaguely-stated possibility suggested by this observation, however, is that any decision rule of the kind considered here may be in principle inadequate for the suprathreshold-discrimination case. It may be impossible to explain suprathreshold discriminations without more explicit modeling of higher-level of higher-level visual processes than is necessary to explain detection (where detection is a discrimination between a stimulus and a neutral stimulus.)... Thus a simple decision rule may be suitable in the detection case simply because all the higher-level processes are reduced to such simple action THAT THEY BECOME TRANSPARENT." [caps mine].

Comment: The idea that there are certain experimental conditions in which the conscious percept consists in the reading off of the activity of "low-level" neurons (as though there was a direct qualitative correspondence between neural firing and seeing, e.g., a blank screen!) is patently absurd and has been criticized in depth and from different angles by Teller (1984).

Pretending that we take it seriously, we could refute it by noting that the presumably simplest of all stimuli - a white surface free of any imperfections - produces the perception of a three-dimensional fog. Other experiments have also shown that organizational processes are engaged even at threshold conditions, and that, indeed, they influence thresholds.

The "transparency theory" is repeated by Graham (2011) in an article in Vision Research: "It is as if the near-threshold experiments made all higher levels of visual processing transparent, therefore allowing the properties of the low-level analyzers to be seen."

This casually proposed "transparency" theory of near-threshold stimulation is apparently the basis of the widespread belief in spatial frequency channels and the extraordinary elaboration of associated assumptions. Without the transparency theory, it is not clear that even cherry-picked evidence can support this popular field of research. (If you've ever wondered at the widespread use of "Gabor patches" in vision research, this is the root cause - they are considered elemental due to the transparency theory-supported low-level neuron spatial frequency sensitivity hypothesis. I suspect many of the people using then don't even know why).

Graham and Hood (1992) also go into a little finer detail about the putative basis of transparency: " In the suprathreshold discrimination case, the observer is trying to discriminate between two sets of neural responses…both of which sets contain many non-baseline responses. In the detection case…the observer is simply trying to detect some non-baseline responses in either set (since that is the set most likely to be the non-blank stimulus). Thus a simple decision rule may be suitable in the detection case simply because all the higher-level processes are reduced to such simple action that they become transparent."

Comment: The suggestion that investigators are managing to set their low-level visual neurons at baseline at the start of experiments also seems implausible. I certainly don't think this has been explicitly discussed from the point of view of method. "However, at this moment in time, we seem to be able to explain background onset with a subtractive process…Thus, we can just leave as a marker for the future – should troubles in fully explaining the data arise – the possibility that the background-onset effect in particular (and perhaps all the results) will not be explained in detail without including more about higher-level visual processing."

Comment: Translation: We'll accept our ad hoc hypo thesis for now, but it's probably wrong. But we'll worry about that later, if and when anyone makes trouble by bothering with actual tests. Because there's always a (zero) chance that it will be corroborated.

Finally, the article also provides a good example of misleading use of references: "Quantal noise exists in the visual stimulus, as is well known (see Pelli for a current discussion.)"

Comment: From Pelli, 1990: "It will be important to test the model…For gratings in dynamic white noise, this [model] prediction has been confirmed by Pelli (1981), disconfirmed by Kersten (1984) and reconfirmed by Thomas (1985). More work is needed." But we don't need to wait for evidence to firmly believe in "quantal noise."

On 2016 Mar 15, Kristina Hanspers commented:

The gene regulation depicted in Fig 2 is available as a pathway in the Open Access Publication Collection at WikiPathways: http://wikipathways.org/index.php/Pathway:WP410. These pathways can be downloaded in several formats and can be used for analysis and visualization in tools like PathVisio and Cytoscape.

On 2016 Sep 09, Pavel Nesmiyanov commented:

That is an interesting observation. Oligofructose-enriched inulin however even increased acetaldehyde production by microbiota.

1. Joossens M, de Preter V, Ballet V, Verbeke K, Rutgeerts P, Vermeire S. Effect of oligofructose-enriched inulin (OF-IN) on bacterial composition and disease activity of patients with Crohn's disease: results from a double-blinded randomised controlled trial. Gut 2012; 61: 958.
2. Joossens M, de Preter V, Ballet V, Verbeke K, Rutgeerts P, Vermeire S. Effect of oligofructose-enriched inulin (OF-IN) on bacterial composition and disease activity of patients with Crohn's disease: results from a double-blinded randomised controlled trial. Gut 2012; 61: 958.

On 2014 Nov 23, Harri Hemila commented:

A manuscript version of the comment is available at the University of Helsinki institutional repository: http://hdl.handle.net/10250/7977 and the final version from DOI

On 2014 Jan 08, Brett Snodgrass commented:

Dear Reader,

This article provides an image of a well-preserved section of the the heart that exhibits a vessel of Wearn.

For additional commentary on the normal anatomy (http://bit.ly/JTWearn) and the presentation in pathologic conditions, please see https://twitter.com/BrettSnodgrass1/status/392016004928131072

I would like to thank Elsevier for making the article by Wearn open access.

Comments and suggestions are welcome.

Thank you kindly.

On 2014 Nov 30, Harri Hemila commented:

A scanned version of this paper is available at: http://www.mv.helsinki.fi/home/hemila/CT/Chakrabarti_1955_ch.pdf

On 2017 May 21, Stuart RAY commented:

doi:10.1001/jama.1964.03070160046009

On 2016 Jan 03, Sergio Dueñas commented:

How i can a found the paper abstract

On 2015 Aug 15, Abdul-Aleem Khan commented:

ok

On 2015 Aug 15, Abdul-Aleem Khan commented:

I wish to see this article

On 2014 Jan 08, Brett Snodgrass commented:

Dear Reader,

The myocardial sinusoids connect to the vasa Wearn, which connect to a coronary artery.

Please see http://bit.ly/JTWearn

For additional commentary, please see. https://twitter.com/BrettSnodgrass1/status/412195032486014976

Please share if you agree or disagree with the previously proposed nomenclature and why.

Thank you kindly.

On 2016 Aug 17, R Relevo commented:

the citation has a typo the volume is actually 278, not 2

On 2014 Oct 28, Harri Hemila commented:

English translation of this paper is available at: http://www.mv.helsinki.fi/home/hemila/T2.pdf

On 2014 Dec 03, Harri Hemila commented:

Fulltext is available at http://dx.doi.org/10.1016/0952-0600(92)90016-A

On 2014 Oct 28, Harri Hemila commented:

English translation of this paper is available at: http://www.mv.helsinki.fi/home/hemila/T3.pdf

On 2015 Dec 11, Harri Hemila commented:

Available at http://dx.doi.org/10.1016/0168-1656(92)90010-7

On 2015 Feb 20, Jaime A. Teixeira da Silva commented:

The authors developed some alternative methods for cryopreserving a single chrysanthemum cultivar ‘Escort’ while developing an ultra-rapid freezing protocol for nine chrysanthemum cultivars. In the controlled rate freezing protocol, the authors do not indicate how many shoot tips are placed into each cryovial nor for how long explants are maintained in LN. The same lack of detailed information exists for the encapsulation-dehydration (ED) protocol. In the vitrification protocol, the authors claim that shoot tips were added to a small drop of PVS2 on a sheet of aluminium that was then placed in cryovials and then plunged into LN. However, what was the function of adding the aluminium foil to cryovials? Only for the vitrification protocol do the authors state that “The vials were cooled from underneath to liquid nitrogen temperature to prevent boiling of the liquid nitrogen in the vials.” But it is not clear if such caution was exercised in the other cryopreservation protocols. The density or ratio of explants to medium is never indicated for any protocol. The commercial source of the cryovials and the reagents and equipment is also not described thus the experiment cannot be reliably reproduced. Throughout the manuscript, the authors use two terms, shoot tips and apical shoots to describe the exact same experimental explant, which could be confusing to amateur readers. Much of the description of the protocols is very repetitive and poorly written, and most of the “noise” in the protocol caused by this overlapping information could have been considerably reduced had the authors used suitable acronyms, e.g., SIM for shoot induction medium rather than defining all constituents every time. Fig. 1 legend contains a mistake: it should indicate –1°C but instead it is written as –0.1°C. In Fig. 2 legend, the claim that “There were no statistically significant differences between the different preculture procedures” might be incorrect, considering the wide span between 31% and ~45%. No statistical analyses were conducted on data in Table 1 and Fig. 3, so there is an inconsistent use of statistics and thus interpretation of the data set. All data is represented as only shoot % regeneration, which is not very informative. Shoot numbers would have also been useful. Even though the authors claimed to assess shoot % regeneration from shoot tips after 4 weeks or from callus after 8 weeks, none of the figures or tables indicate the source of the shoots (i.e., from callus or from shoot tips?). Each figure represents different sample sizes, with no apparent explanation, and there is absolutely no discussion about shoot regeneration from callus, which is an undesirable form of clonal propagation for chrysanthemum and could result in somaclonal variation.

On 2015 Dec 11, Harri Hemila commented:

Available at DOI

On 2015 Dec 11, Harri Hemila commented:

Available at DOI

On 2014 Dec 03, Harri Hemila commented:

Fulltext is available at DOI

On 2015 Dec 21, Stephen Strum commented:

This is a critical paper that has been lost in the shuffle of time.

On 2013 Oct 30, Jamie Horder commented:

This 1957 paper contains the observations of Leo Kanner and his colleague Leon Eisenberg, based on 120 autistic children seen at John Hopkins since Kanner defined the syndrome of "autism" in 1943.

Notably, the authors in this paper suggested that the emotional 'coldness' often seen in parents of autistic children played some causal role in the development of the disorder - though only in conjunction with an 'inborn disturbance of affective contact', i.e. what would today be called a gene x environment interaction.

This idea, taken further, later became notorious as the 'refrigerator mother' psychodynamic theory of autism, associated with the now-discredited Bruno Bettelheim.

By 1971, Kanner denied advocating any kind of psychogenic hypothesis of autism: Kanner L, 1971. However such ideas are certainly evident in this paper.

On 2014 Jan 13, Brett Snodgrass commented:

Dear Reader,

Please provide your kind consideration to the following excerpt from page 502

"There were thrombi in the Thebesian vessels (including the Thebesian veins, the myocardial sinusoids, arterio-luminal and arteriosinusoidal vessels)"

The authors astutely document the various connections in the heart that were described by 1. Thebesius (Thebesian veins) http://bit.ly/vasaThebesii

and the structures described by Joseph T. Wearn

 1. myocardial sinusoids   and the

vessels of Wearn:

 2. arterio-luminal (arterioluminal) 


3. arteriosinusoidal vessels

http://bit.ly/JTWearn

Referring to the vessels of Wearn as Thebesian vessels is problematic as the former are strictly arterial in nature. The vessels described by Thebesius were venular in nature.

Reportedly, Thebesius only studied the veins. In addition, Thebesius neither defined nor studied the "myocardial sinusoids," "arterio-luminal (arteioluminal)," or "arteriosinusoidal" vessels.

Those were defined utilizing serial histologic sections by Wearn et al. The myocardial sinusoids have not been included as strict components of the "vessels of Wearn" as they have been noted to connect with many structures, and Wearn reported that they have a "meandering course."

Therefore, the arterial-cameral connections that bypass the capillary bed are probably best referred to as vessels of Wearn.

The venular-cameral connections that bypass the capillary bed are probably best referred to as any of the synonyms, 1. Thebesian veins (personally preferred term) 2. vessels of Thebesius 3. vasa Thebesii

At least one article uses the terms "Thebesian vessels" and "Thebesian veins" synonymously, (please ask for reference), and I agree that they are synonyms.

However, using the term "Thebesian vessels" to apply to all of the aformentioned connections is both inaccurate and has probably resulted in much confusion in the literature. Therefore, the use of the term "Thebesian vessels," as used in this article, is probably not accurate.

My opinion is that accurate anatomic terminology is a basic principle underlying good medical science, and I ask others to consider whether the aforementioned definitions are appropriate. If this comment is not helpful, please let me know how it might be improved.

Comments and suggestions are welcome.

Thank you very much.

On 2014 Dec 02, Harri Hemila commented:

Fulltext is available at DOI

On 2017 Apr 25, Guy Plunkett commented:

When this paper was published journals did not host supplementary material on their own servers, and those links in the paper are no longer valid, having suffered the consequences of site death as individuals retired or moved on. In January 2014, Dr. Gerdes reached out to me, and since then we have been hosting a full copy of the Supplemental Data at https://www.genome.wisc.edu/Gerdes2003/

On 2017 Nov 10, Thomas Heston commented:

This concept has stood the test of time. More and more research is showing beneficial effects of sauna bathing. An update of this topic is Sauna Bathing and the Cardiovascular System Int J Sci Res. 2017 Nov; 6(11) 569-570.

On 2014 Jan 08, Brett Snodgrass commented:

Dear Authors,

Thank you for the excellent article.

Might the pathogenesis of this case be explained by a vessel of Wearn that disrupted vasculogenesis?

The following linked image contains notes and references related to the probable pathogenesis in this case. https://twitter.com/BrettSnodgrass1/status/415991920104452096

Comments, disagreements, and suggestions are welcome.

Thank you kindly.

On 2015 Aug 27, Bernard Friedenson commented:

For more information please see the article entitled "Mutations in Breast Cancer Exome Sequences Predict Susceptibility to Infection and Converge on the Same Signaling Pathways" This article is available at http://la-press.com/article.php?article_id=5029

On 2016 Jan 04, S A Ostroumov commented:

Rotifers: Rotifers are an important part of the freshwater zooplankton, being a major foodsource and with many species also contributing to the decomposition of soil organic matter. Most rotifers are around 0.1–0.5 mm long, and are common in freshwater environments throughout the world. The word "rotifer" is derived from a Latin word meaning "wheel-bearer", due to the corona around the mouth that in concerted sequential motion resembles a wheel (though the organ does not actually rotate). The coronal cilia create a current that sweeps food into the mouth. Rotifers eat particulate organic detritus, dead bacteria, algae, and protozoans. They eat particles up to 10 micrometres in size. Like crustaceans, rotifers contribute to nutrient recycling. For this reason, they are used in fish tanks to help clean the water, to prevent clouds of waste matter.(Wikipedia was used).

On 2016 Jan 04, S A Ostroumov commented:

ABSTRACT: This paper discovered new type of toxicity of the cationic surfactant tetradecyltrimethylammonium bromide (TDTMA); a new toxic effect of this chemical was discovered: inhibition of water filtration by rotifers. This chemical exemplifies a new type of hazardous contaminants (pollutants) of water.

On 2016 Jan 04, S A Ostroumov commented:

EXPLANATION of and comment on TERMINOLOGY: cationic amphiphilic compound = cationic surfactant, Surface-Active Agent, in this paper it is the cationic surfactant tetradecyltrimethylammonium bromide (TDTMA); surfactants are a new class of water-polluting chemicals.

On 2015 Dec 06, S A Ostroumov commented:

FULL TEXT ONLINE FREE, ALSO, THE ABSTRACT: https://www.researchgate.net/publication/200578650

On 2015 Dec 16, Farrel Buchinsky commented:

This study reports that HPV 16 or 18 was detected in 24 out of 35 papilloma specimens. Absent carcinoma, no other study has reported such a high incidence of HPV 16 or 18 in benign recurrent respiratory papillomatosis. Therefore such a claim would require extraordinary evidence. It is possible that their primers had non-specific binding to DNA from other HPV types.

On 2013 Jun 20, Robert Tibshirani commented:

This is an important paper, introducing the RMA method for normalizing Affymetrix probe-level data. RMA is now widely used in the R package and other software environments.

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2015 Dec 15, S A Ostroumov commented:

Review (WorldCatalog) of the paper: Synecological Approach to the Problem of Eutrophication (new solution to the problem) https://www.researchgate.net/publication/286921503

On 2015 Dec 04, S A Ostroumov commented:

FULL TEXT ONLINE FREE: The synecological approach to the problem of eutrophication. https://www.researchgate.net/publication/10614405;

On 2015 Nov 30, S A Ostroumov commented:

Abstract of this paper, with some comment. ** The content of the article in short: A new solution to eutrophication. New concept of eutrophication control. Rating of this paper: In the top 25% of all articles scored by Altmetric. ** A new way of eutrophication control was suggested in the paper. The author suggested a new component of the measures against eutrophication: reducing the input of the chemical pollutants that weaken the potential of the filter-feeders for removing planktonic algae. The suggested way of controlling eutrophication is applicable to both freshwater and marine ecosystems. The article proposed a new idea, a new way of controlling eutrophication. The article is based on a series of the author's experiments with aquatic organisms (filter-feeders) that discovered and quantified relevant toxic effects of organic pollutants at sublethal concetrations. This article presented some new data to continue this line of research that is essential to the new solution to eutrophication. Among new facts that were reported in the paper, in addition to a substantial amount of relevant, related data previously obtained by the author: The liquid detergent (exemplified by the dish washing liquid, Fairy) 2 mg/L inhibited filtration by the bivalve mollusks, marine mussels (Mytilus galloprovincialis) within 2-23 min after addition, at temperature 22.5 ºС. This species of bivalve mollusks is one of key species in marine benthic ecosystems; it is one of ecological engineers that make a great impact on water quality. This is only one new fact that adds to many other facts (on how chemical pollutants can inhibit water filtration) discovered and reported by the author in other publications (papers and the book, Biological Effects of Surfactants). The paper presents a new approach to combat eutrophication.

On 2016 Jan 09, S A Ostroumov commented:

DOI: 10.1023/A:1012348127085; 'two-level synergism' is a new scientific term suggested by the author, it is explained in the text of the article.

On 2015 Dec 04, S A Ostroumov commented:

Abstract: The author identified a new type of ecological hazard of anthropogenic impact (using chemical pollution as an example), which he proposed to term “synecological summation” or “synergistic summation” of anthropogenic effects on organisms of two adjacent trophic levels. ** NEW FACTS: in the study reported in the paper, the following new type of environmental hazards was found. It was shown that even some relatively mild influences on organisms of two adjacent trophic levels may eventually produce a synergistic, pronounced and definitely undesirable effect which will lead to an abnormal increase in the abundance of organisms of one of the trophic levels. The concrete examples of that type of synergism were found when anthropogenic impacts affected the organisms of two adjacent trophic levels (bivalves and algae). Some new bioeffects of the action of the synthetic detergent (exemplified by the laundry detergent, namely, the detergent 'Vesna') (1 mg/l) on the bivalves, oysters Crassostrea gigas were described. Also, some new effects of the detergent (exemplified by the laundry detergent, namely, the detegent 'IXI') (10 mg/l) on the marine mussels Mytilus galloprovincialis, were found; also, new effects of the detergent (exemplified by the laundry detergent, namely the detergent 'Tide-Lemon') (50 mg/l) on M. galloprovincialis were discovered. ** CONCLUSION: The hazard of simultaneous influence of contamination of environment (e.g., by detergents) on organisms of the two trophic levels may occur when the polluting chemicals produce effects on algae and bivalves that are filter-feeders. It means that a new type of environmental hazards was discovered. [MAIK Nauka/Interperiodica, distributed by Springer Science+Business Media LLC.; ISSN 0012-4966 (Print) 1608-3105 (Online)]; DOI 10.1023/A:1012348127085;

On 2015 Dec 04, S A Ostroumov commented:

FULL TEXT OF THIS ARTICLE ONLINE FREE: (TITLE: The hazard of a two-level synergism of synecological summation of anthropogenic effects); https://www.researchgate.net/publication/10614388

On 2016 Apr 15, S A Ostroumov commented:

Unio is one of the most common freshwater bivalve mollusks. This species has a huge importance to water quality in rivers.

On 2016 Jan 09, S A Ostroumov commented:

DOI 10.1023/A:1012344026176. Full text is available on ResearchGate.

On 2015 Dec 04, S A Ostroumov commented:

Abstract: Responses of the freshwater bivalve Unio tumidus to mixed chemical preparations and the hazard of synecological summation of anthropogenic effects. - Doklady Biological Sciences, 2001, Volume 380, p. 492-495. ISSN 0012-4966 (Print) 1608-3105 (Online). DOI 10.1023/A:1012344026176. The author introduced a new concept and term, “the synecological summation of the effects of anthropogenic factors on organisms”. In the new author’s experiments, the effects of commercial detergents, which are chemical mixtures, on bivalves (e.g. effects of the laundry detergent OMO on the freshwater mussels Unio tumidus) were discovered and studied. Detergents exert two types of hazardous effects on organisms and ecosystems: the phosphorus-induced stimulation of phytoplankton growth and surfactant-induced inhibition of filter-feeders. Because filter-feeders are an effective natural factor of control of unicellular plankton populations, the two types of the detergent-induced effects on ecosystem facilitate the growth of phytoplankton populations. Therefore, these effects sum together, thereby increasing the hazard of the man-made impact on the ecosystem. The results contribute to a better understanding of the potential ecological danger of pollutants for integral functions of ecosystems. It is the synecological summation of the effects of anthropogenic factors on plankton populations and filter-feeders that is of particular concern. The interaction between populations of plankton organisms and filter-feeders that feed on plankton should be taken into consideration in the studies on the ecological effects of synthetic detergents on these populations. Situations of man-made impact should be analyzed with using the synecological approach to the problem. http://sites.google.com/site/2001dbs380p492unio/; www.springerlink.com/index/L33309208H28L87R.pdf; DOI 10.1023/A:1012344026176;

On 2015 Dec 04, S A Ostroumov commented:

ANOTHER LINK, THE FULL TEXT OF THIS ARTICLE ONLINE FREE: https://www.researchgate.net/publication/10614386 ; [Dokl. Biol. Sci. 2001;380:492-495. Responses of Unio tumidus to mixed chemical preparations and the hazard of synecological summation of anthropogenic effects.]

On 2015 Dec 04, S A Ostroumov commented:

This article ranked 1st among all papers in the journal, Doklady Biological Sciences; (Altmetrics) (on 26.01.2015). Article was published in a peer reviewed journal.

On 2015 Dec 04, S A Ostroumov commented:

FULL TEXT OF THIS ARTICLE FREE, AVAILABLE ONLINE (Responses of Unio tumidus to mixed chemical preparations and the hazard of synecological summation of anthropogenic effects): https://www.researchgate.net/publication/259579828

On 2015 Dec 14, S A Ostroumov commented:

WorldCat review of the article: Pellets of Some Mollusks in the Biogeochemical Flows of C, N, P, Si, and Al. https://www.researchgate.net/publication/286780426

On 2015 Dec 13, S A Ostroumov commented:

Explanation of methodology (some details on the choice of the biological species and chemicals to study). Why the great pond snail and freshwater mussels were studied in this reseach project: they are among the most common benthic species of invertebrates in water habitats of Eurasia. Their biomass is one of the biggest, or just the biggest, among aquatic invertebrates in Eurasia and other parts of the world. Why the plant species, Nuphar lutea (Yellow Water-lily) , was used in this research project: it is one of the most common aquatic plant species in the freshwater habitats of Eurasia. Why the plant species, Taraxacum officinale, was used in this research project: it is a common laboratory practice to feed the great pond snail with leaves of this higher plant. Why the synthetic surfactants ТDТМА (tetradecyltrimethylammonium bromide) and SDS (sodium dodecyl sulfate) were used: they are representatives of the two major classes of synthetic surfactants, namely, cationic surfactants, and anionic surfactants. These two chemicals were studied in many other publications of Dr. Sergei Ostroumov, so that lots of data to compare toxic effects of these chemicals on organisms are available. A detailed explanation of methodology was also published in the book Biological Effects of Surfactants (Ostroumov, 2005, https://www.researchgate.net/publication/200637626)

On 2015 Dec 13, S A Ostroumov commented:

Comment on the biological species that were studied in this paper: the great pond snail is a species of large air-breathing freshwater snail, an aquatic pulmonate gastropod mollusk in the family Lymnaeidae. Range Description: A widespread species distributed in Asia (central, north and south and southeast), north America, north Africa and New Zealand. The great pond snail has a shiny yellowish brown shell.

Nuphar lutea (Yellow Water-lily) is an aquatic plant of the family Nymphaeaceae, native to temperate regions of Europe, northwest Africa, and western Asia.

Unio is a genus of medium-sized freshwater mussels, aquatic bivalve mollusks in the family Unionidae, the river mussels. Unio is the type genus of the family Unionidae. About this family: The range of distribution for this family is world-wide. It is at its most diverse in North America, with about 297 recognised taxa, but China and Southeast Asia also support very diverse faunas. Freshwater mussels occupy a wide range of habitats, but most often occupy lotic waters, i.e. flowing water such as rivers, streams and creeks.

On 2015 Dec 13, S A Ostroumov commented:

Explanation of terminology: pellets are the particles of the undigested organic matter (mainly biomass of undigested food) that the aquatic mollusks (snails and freshwater mussels) excrete so that these mollusks function as engines that drive the transfer of a significant amount of the organic matter through aqautic ecosystems.

On 2015 Dec 05, S A Ostroumov commented:

ABSTRACT AND FULL TEXT ONLINE FREE: https://www.researchgate.net/publication/259579605

On 2016 Jan 09, S A Ostroumov commented:

DOI: 10.1023/a:1011600213221. This paper proved that even chemical pollutants that are not toxic to phytoplankton can influence abundance of the phytoplankton. It is intereting that some chemical pollutants (which are not nutrients) can finally stimulate the abundance of phytoplankton. How? See the article.

On 2015 Dec 18, S A Ostroumov commented:

DOI of this article. DOI: 10.1023/a:1011600213221;

On 2015 Dec 18, S A Ostroumov commented:

today: increase in rating of the article: Imbalance of Factors Providing Control of Unicellular Plankton Populations Exposed to Anthropogenic Impact; In the top 25% of all research publications; http://5bio5.blogspot.com/2015/12/today-increase-in-rating-of-article.html

On 2015 Dec 05, S A Ostroumov commented:

ABSTRACT AND FULL TEXT ONLINE FREE: Imbalance of Factors Providing Control of Unicellular Plankton Populations Exposed to Anthropogenic Impact. https://www.researchgate.net/publication/10614342

On 2016 Jan 12, S A Ostroumov commented:

Tags: surfactants, chemical mixtures, detergents, water, filtering, activity, oysters, Crassostrea gigas, aquaculture,

On 2016 Jan 12, S A Ostroumov commented:

DOI: 10.1023/A:1019270825775

On 2015 Dec 05, S A Ostroumov commented:

Full text of this ARTICLE free, and ABSTRACT: https://www.researchgate.net/publication/10614314; Explanation of some technical terminology: amphiphilic chemicals = synthetic surfactants, detergents that are potential pollutants;

On 2016 Feb 01, Morten Oksvold commented:

Please note that this article is 1 out of 15 publications for which an independent investigation initiated by the University of Copenhagen has found suspicion of scientific dishonesty. The conclusion from the report was published July 23, 2012:

http://news.ku.dk/all_news/2012/2012.8/indications_of_fraud_in_penkowas_early_research/

This articles should therefore not be cited.

On 2014 Dec 10, Kath Wright commented:

Other search filters are available from the InterTASC Information Specialists' Sub-Group Search Filter Resource at https://sites.google.com/a/york.ac.uk/issg-search-filters-resource/home

On 2015 Dec 02, S A Ostroumov commented:

Availability online of this article: Ostroumov S. A. Anthropogenic effects on the biota: towards a new system of principles and criteria for analysis of ecological hazards. Rivista di Biologia / Biology Forum. 2003. 96: 159-170. [ISSN 0035-6050] The full text: https://www.researchgate.net/publication/200581960; and: https://www.researchgate.net/publication/10669691;

https://www.researchgate.net/publication/10669691_Anthropogenic_effects_on_the_biota_towards_a_new_system_of_principles_and_criteria_for_analysis_of_ecological_hazards;

On 2013 Nov 18, Lior Pachter commented:

This software and server is no longer being supported. I recommend using FSA instead http://orangutan.math.berkeley.edu/fsa/

On 2013 Nov 18, Lior Pachter commented:

The SLAM software is no longer being supported or maintained.

On 2015 Jan 19, Paul Korir commented:

This paper claims that in about half (49%) of transcription units with multiple splice forms it appeared that usage of an alternative TSS was accompanied by alternative splicing of the initial exon. The authors therefore conclude that this might imply that alternative TSS may induce alternative splicing. However, if a transcription unit has a 50-50 chance of exhibiting this behaviour that would be the last conclusion that one could make. There are no positive epistemic implications that can be derived from a 50-50 chance; in fact, this is state with the maximal entropy and by extension the most uncertainty.

On 2014 Nov 24, Ivan Oransky commented:

The first author of this paper has agreed to retract it and five others following a finding of misconduct by the Office of Research Integrity: http://retractionwatch.com/2014/11/20/former-vanderbilt-scientist-faked-nearly-70-images-will-retract-6-papers-ori/

On 2015 Oct 28, Peter Gøtzsche commented:

The authors write that "approximately 50-60% of patients are thought to improve clinically as a consequence of antidepressant treatment." This is not correct. About 50% of the patients get better on an antidepressant and 40% on placebo, ie. only a 10% difference, and according to the patients’ own judgments, the drugs don’t work (1,2). Furthermore, these trials were not effectively blinded, and if atropine is put in the placebo to blind the trials better, even the psychiatrists cannot find any effect (3).

The authors write that, "Currently there is no evidence to suggest that ECT causes any kind of brain damage, although temporary cognitive impairment is frequently reported" and that "ECT seems to be a safe procedure". This is not the case. ECT is highly controversial (4), patients report permanent memory problems (5), and there seems to be a death rate of about 1 per 1000 (6).

Only one RCT met the inclusion criteria and that trial was a post-hoc analysis of data in elderly people who participated in the Nottingham trial. It would be of interest to readers to know what the Nottingham trial showed.

1 Laughren TP. Overview for December 13 Meeting of Psychopharmacologic Drugs Advisory Committee (PDAC). 2006 Nov 16. Available online at: www.fda.gov/ohrms/dockets/ac/06/briefi ng/2006-4272b1-01-FDA.pdf (accessed 22 October 2012).

2 Gøtzsche PC. Deadly psychiatry and organised denial. Copenhagen: People’s Press; 2015.

3 Moncrieff J, Wessely S, Hardy R. Active placebos versus antidepressants for depression. Cochrane Database Systematic Reviews 2004;1:CD003012.

4 Carney S, Geddes J. Electroconvulsive therapy. BMJ 2003;326:1343-4.

5 Rose D, Wykes T, Leese M, Bindman J, Fleischmann P. Patients perspectives on electroconvulsive therapy: systematic review. BMJ 2003;326:1363-5.

6 Read J, Bentall R. The effectiveness of electroconvulsive therapy: a literature review. Epidemiol Psichiatr Soc 2010 Oct-Dec;19:333-47.

On 2016 Feb 01, Morten Oksvold commented:

Please note that this article is 1 out of 15 publications for which an independent investigation initiated by the University of Copenhagen has found suspicion of scientific dishonesty. The conclusion from the report was published July 23, 2012:

http://news.ku.dk/all_news/2012/2012.8/indications_of_fraud_in_penkowas_early_research/

This articles should therefore not be cited.