On 2013 Nov 15, George McNamara commented:

The direct link to the supplemental files is http://bloodjournal.hematologylibrary.org/content/107/7/2643/suppl/DC1 The supplemental files includes two movies. My rule of thumb is you should make popcorn before watching movies.

An additional movie from this project is available at http://works.bepress.com/gmcnamara/21/ Shows a triplet cell division. That is, a cell that divided three ways. I have discussed this with other researchers, a few of whom have observed triplet cell divisions as well.

Several of the authors have moved from City of Hope - Mike Jensen is in Seattle. I am with Laurence Cooper at M.D. Anderson Cancer Center in Houston.

On 2015 Feb 23, Ivan Oransky commented:

None

On 2015 Feb 23, Ivan Oransky commented:

Although this paper has been retracted, it has been cited 52 times since, with only two of those citations mentioning the retraction: http://retractionwatch.com/2015/02/18/evidence-scientists-continue-cite-retracted-papers/

(Deleted first of these comments as they posted twice.)

On 2014 Feb 21, Tom Kindlon commented:

MDDm should be resolved for more than 5 years before a CFS diagnosis can be given

(This was originally posted here http://www.biomedcentral.com/1741-7015/3/19/comments#285572 but the formatting has gone from that page)

In this paper, it says: "Following recommendations of the International CFS Study Group, only current MDDm was considered exclusionary for CFS." However, part of the specific recommendations of the International CFS Study Group [1] was that MDDm had to have been resolved for more than 5 years: "The 1994 case definition stated that any past or current diagnosis of major depressive disorder with psychotic or melancholic features, anorexia nervosa, or bulimia permanently excluded a subject from the classification of CFS ... we now recommend that if these conditions have been resolved for more than 5 years before the onset of the current chronically fatiguing illness, they should not be considered exclusionary." It might not be important to point this out for definitions for some illnesses: however if one looks at table 2, 6 of the 16 who are said to have CFS using the "current classification" of CFS, had been diagnosed with MDDm at a previous assessment which suggests it is important in this context.

Reference:

[1] Reeves WC, Lloyd A, Vernon SD, Klimas N, Jason LA, Bleijenberg G, Evengard B, White PD, Nisenbaum R, Unger ER, International Chronic Fatigue Syndrome Study Group: Identification of ambiguities in the 1994 chronic fatigue syndrome research case definition and recommendations for resolution.BMC Health Services Research 2003, 3:25. http://dx.doi.org/10.1186/1472-6963-3-25

On 2014 Feb 21, Tom Kindlon commented:

Data from another population study found scores on the RE subscale are similar in CFS patients to those found in healthy controls

(This was originally posted here http://www.biomedcentral.com/1741-7015/3/19/comments#285575 but the formatting has gone from that page)

I previously said that I questioned the value of using the Role Emotional (RE) subscale to satisfy functional impairment criteria (http://www.biomedcentral.com/1741-7015/3/19/comments#284561). Researchers deciding whether to follow the method of operationalizing the Fukuda [1] used in this study, might be interested at looking at Table 2 in Jason et al [2].

The subjects were also obtained from a random-digit population study. Here is what the authors said in the text on this part of the results: "A MANCOVA for the Medical Outcomes Study SF-36 Health Survey (controlling for the effects of work status) revealed significant differences in gradations of disability across the diagnostic categories of CFS only, MCS only, FM only, more than one diagnosis, and no diagnosis on seven of the eight subscales (F(4,208) = 1.82, p < .05). The role-emotional scale was the only scale that did not reveal significant differences between the groups (see Table 2). Significant post hoc tests revealed that individuals with CFS demonstrated greater disability than those with no diagnosis on the role-physical; bodily pain; vitality; and social functioning scales. Individuals with MCS demonstrated greater disability than the no diagnosis group on the physical functioning; role-physical; bodily pain; general health; vitality; social functioning; and mental health scales. Individuals with FM demonstrated greater disability than the no diagnosis group on the physical functioning; role-physical; bodily pain; and social functioning scales. In addition, individuals with more than one diagnosis demonstrated greater disability than those in the no diagnosis group on the physical functioning; role-physical; bodily pain; vitality; and social functioning scales. Means for each of the Medical Outcomes Study subscales are reported in Table 2."

This issue of how the Fukuda criteria [1] are operationalized is not a trivial matter. Using the previous method of operationalizing the criteria, a CDC team found a prevalence for CFS of 235 per 100,000 [3]. Using the method of operationalizing the criteria outlined in this study, the prevalence rate for CFS was found to be 2.54% or 2540 per 100,000 [4] or 10.81 times the previous prevalence rate!

References

[1] Fukuda, K., Straus, S.E., Hickie, I., Sharpe, M.C., Dobbins, J.G., & Komaroff, A. (1994). The chronic fatigue syndrome: A comprehensive approach to its definition and study. Annals of Internal Medicine, 121 (12):953-959. http://www.annals.org/cgi/content/full/121/12/953

[2] Jason, L.E., Taylor, R.R., & Kennedy, C.L. "Chronic Fatigue Syndrome, Fibromyalgia, and Multiple Chemical Sensitivities in a Community-Based Sample of Persons With Chronic Fatigue Syndrome-Like Symptoms." Psychosomatic Medicine 62:655-663 (2000). http://www.psychosomaticmedicine.org/cgi/reprint/62/5/655

[3] Reyes M, Nisenbaum R, Hoaglin DC, Unger ER, Emmons C, Randall B, Stewart JA, Abbey S, Jones JF, Gantz N. Prevalence and incidence of chronic fatigue syndrome in Wichita, Kansas. Arch Intern Med. 2003;163:1530–1536. doi: 10.1001/archinte.163.13.1530.

[4] 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. Population Health Metrics 2007, 5:5 doi:10.1186/1478-7954-5-5

On 2014 Feb 28, Tom Kindlon commented:

This may not be a representative group of those who would be diagnosed in a random sample using the "standardized clinically empirical criteria"

(This was originally posted here http://www.biomedcentral.com/1741-7015/3/19/comments#290587 but the formatting has gone from that page)

This "empirical" method of operationalizing the CDC 1994 CFS criteria[1] has subsequently been used in a population study[2]. It found a prevalence rate for CFS of 2540 per 100,000 persons 18 to 59 years of age[2].

This is considerably higher than the prevalence rates found in earlier studies.

For example, a previous study using this cohort using a "previous" method of operationalizing the CDC 1994 CFS criteria[1] found a prevalence rate of 235 per 100,000[3]. Given the way the cohort in this current study was drawn up, using 58 people who had previously been diagnosed using a "previous" method of operationalizing the CDC 1994 CFS criteria, the group satisfying the new method of operationalizing the CDC 1994 CFS criteria, the "empirical" criteria, in this study may well not be the same sort of people that would show up if the method was used on a random sample of the population. So for example the results in Table 6 may not be similar to the results one can get in a random sample.

Unfortunately the paper giving the prevalence rate for Georgia[2] does not give the same pieces of information as is in Table 6 in this study. However we do have a paper which uses a group from the Georgia cohort[4]. Table 1 of this study[4] includes similar data. Some of the numbers are somewhat similar. However one that particularly stands out is the Role Emotional score. It was 35.6 (95% CI: 26.3-44.8). That compares to the value in this paper of 55.8+/-42.2.

Perhaps other data will be published in time. The main point of this comment is to point out or remind people that the data presented in this paper may not be representative of those that would be diagnosed using the empirical criteria.

References:

[1] Fukuda K, Straus SE, Hickie I, Sharpe MC, Dobbins JG, & Komaroff A. (1994). The chronic fatigue syndrome: A comprehensive approach to its definition and study. Annals of Internal Medicine, 121 (12):953-959. http://www.annals.org/cgi/content/full/121/12/953

[2] 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. Population Health Metrics 2007, 5:5 doi:10.1186/1478-7954-5-5http://www.pophealthmetrics.com/content/5/1/5

[3] Reyes M, Nisenbaum R, Hoaglin DC, Unger ER, Emmons C, Randall B, Stewart JA, Abbey S, Jones JF, Gantz N, Minden S, Reeves WC: Prevalence and incidence of chronic fatigue syndrome in Wichita, Kansas. Arch Int Med 2003, 163:1530-1536.

[4] 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. 2007 Dec 26

On 2014 Feb 28, Tom Kindlon commented:

Why is this definition being referred to as an "empirical definition"?

(This was originally posted here http://www.biomedcentral.com/1741-7015/3/19/comments#301566 but the formatting has gone from that page)

I believe most people's understanding of "empirical criteria" or an "empirical definition" would be that the data would speak for itself; it "would decide" the cut-off points through methods such as cluster analysis (for example).

Indeed this would seem to have been William Reeves' understanding of an empirical definition. For example, in a presentation on the CDC's CFS research program (to a Task Force Meeting on the Epidemiology of Interstitial Cystitis)[1], he said: "The problem with the CFS criteria was that they were not specific enough and not empiric-based. For example, one of the criteria stated that the research subject must have at least four of eight symptoms, among them, impaired concentration or memory and postexertional worsening of physical or mental fatigue. "The accompanying symptoms need to be defined in and of themselves," Dr. Reeves said.

The 1994 International Study Group also hypothesized that fatigue led to patients' symptoms rather than the reverse. The CDC is currently conducting population studies to develop an empiric definition of CFS that is based on statistical modeling."At the inaugural meeting of the US Department of Health and Human Services' Chronic Fatigue Syndrome Advisory Committee (CFSAC), Dr Reeves said the CDC team of research would "derive an empirical case definition based on data".[2]

The definition presented here does not seem to have been based either on "statistical modeling" or "data". It seems to involve relatively arbitrary cut-off points; for example, of the 8 subscales of the SF-36, four are chosen and, for each of these, the 25th percentile of the published US population is chosen as a cut-off point. A patient is required to be in the bottom quartile for just one of these subscales to satisfy the criteria. Where did this cut-off point come from? There is no mention of it in the paper that suggested the use of the SF-36[3]; nor is there any mention that these particular subscales should be chosen or that one would be sufficient. One of the authors of the paper[3] has confirmed that cut-off points were never chosen nor was it decided which sub-scales would be used.

Given that the CDC's definition of CFS tends to go on to be used in numerous studies, would it not be better to investigate which thresholds give a "better" definition e.g. with a higher specificity and sensitivity - for example, for some of the SF-36 subscales, perhaps (say) the 13th, 15th, 20th or even 30th percentiles may be more appropriate.

The cut-off points suggested in this paper may or may not be useful. But is it really accurate to suggest that they are "empirically" derived?

References:

[1] Epidemiology of Interstitial Cystitis - Executive Committee Summary and Task Force Meeting Report October 29th, 2003. http://www.niddk.nih.gov/fund/reports/ic/task_force_summary.pdf

[2] US Department of Health and Human Services - Chronic Fatigue Syndrome Advisory Committee (CFSAC). Inaugural Meeting. September 29th, 2003Meeting Summary. http://www.hhs.gov/advcomcfs/CSFAC_mins_2003.09.29R.pdf

[3] Reeves WC, Lloyd A, Vernon SD, Klimas N, Jason LA, Bleijenberg G, Evengard B, White PD, Nisenbaum R, Unger ER, International Chronic Fatigue Syndrome Study Group: Identification of ambiguities in the 1994 chronic fatigue syndrome research case definition and recommendations for resolution. BMC Health Services Research 2003, 3:25

On 2014 Feb 28, Tom Kindlon commented:

Using two MFI scales ("General Fatigue" or "Reduced Activity") to ensure patients satisfying the definition have "severe fatigue"

(This was originally posted here http://www.biomedcentral.com/1741-7015/3/19/comments#304567 but the formatting has gone from that page)

Initially when I read this paper, where it says "we defined severe fatigue as >= medians of the MFI general fatigue (>=13) or reduced activity (>=10) scales", I thought this referred to medians of the general population.Hearing other people commenting on it, that's how some other people have been interpreting it also. It is probably somewhat natural to do this as the sentence before reads: "We defined substantial reduction in occupational, educational, social, or recreational activities as scores lower than the 25th percentile of published US population [11] on the physical function (<=70), or role physical (<=50), or social function (<=75), or role emotional (<=66.7) subscales of the SF-36."

However from looking at the scores for controls in other papers, these MFI scores do not look like medians for the whole US population but in fact are medians for this particular group of patients. This seems a strange way to set cut-off points for a CFS definition that is used for numerous studies into the illness, given the cohort that is being used as a basis: "This population-based case control study enrolled 227 adults identified from the population of Wichita with: (1) CFS (n = 58); (2) non-fatigued controls matched to CFS on sex, race, age and body mass index (n = 55); (3) persons with medically unexplained fatigue not CFS, which we term ISF (n = 59); (4) CFS accompanied by melancholic depression (n = 27); and (5) ISF plus melancholic depression (n= 28)." i.e. this is not a random sample of the US population but a group of people selected for a specific purpose (or purposes) (not necessarily to design a definition, but as a follow-up study of people previously diagnosed with CFS or given some other label).

Some of the groups are of different sizes - if the relative size of these groups had been changed, with relatively more people taken from some classification groups and less people taken from other groups, the median scores would likely have been different.

It should also be remembered that in this context the categories listed in the last paragraph refer to their classification when they evaluated years before (from 1997 to 2000), and not necessarily at the time when they were evaluated in this study (December 2002 to July 2003) (as is clear from the tables in this paper).

I thought it would be interesting to look at MFI scores in some other papers on CFS that did not use the "empirical definition".

I don't claim this is a definitive list but, at the same time, mean MFI scores with standard deviations only seem to be listed in a small percentage of papers. The papers use cohorts from a variety of locations: England [3], The Netherlands [4], Germany [5] and the USA (New Jersey) [6]. I did not see any ranges given which would be useful given the task at hand (selecting cut-off points for a definition).Unfortunately not all of the papers I found used the Fukuda [1] definition for CFS; some also used the Sharpe [2] definition for CFS. I indicate which definition is used in each case.

MFI: General Fatigue (i) Sample/(ii) Sample Size/(iii) Mean/(iv) SD/ (v) (Mean - 13)/SD/ (vi) Definition

Weatherley-Jones [3] 53 18.4 1.7 3.176470588 Sharpe (1991)

Vermeulen (Group 1) [4] 30 18.6 1.9 2.947368421 Fukuda (1994)

Vermeulen (Group 2) [4] 30 18.4 1.8 3 Fukuda (1994)

Vermeulen (Group 3) [4] 30 19.1 1.4 4.357142857 Fukuda (1994)

Gaab [5] 21 17.7 0.5 9.4 Sharpe (1991) and Fukuda (1994)

Brimacombe [6] 65 18.41 2.02 2.678217822 Fukuda (1994)Combining these give a sample of 229 patients with a mean "General Fatigue" score of 18.45655022.

This data suggests that a threshold of >=13 will have a very very high sensitivity. This would suggest that another measure would not be necessary (unless it was being used as an extra criterion to increase the specificity, which isn't done with this definition).

However for completeness, I'm including the "Reduced Activity" data from the same papers:Reduced activity (MFI) (i) Sample / (ii) Sample Size / (iii) Mean Score / (iv) SE (v) (Mean-10)/SD (vi) Definition

Weatherley-Jones [3] 53 16.1 3.1 1.967741935 Sharpe(1991)

Gaab [5] 21 15 0.7 8.714285714 Sharpe (1991) and Fukuda(1994)

Brimacombe [6] 65 15.93 4.55 1.340659341 Fukuda 1994

Combining these give a sample of 139 patients with a mean Reduced Activity score of 15.85431655.

Note: the Vermeulen paper[4] did not collect the MFI scores for Reduced Activity, just "the fatigue axes of the Multidimensional Fatigue Inventory" (which they defined as the MFI scores for General fatigue, Physical fatigue, Mental fatigue).

It seems strange in the definition of Chronic Fatigue Syndrome defined in this paper (i.e. Reeves et al) that the "severe fatigue" criterion can be satisfied by a patient having a low score on a subscale of the MFI testing activity levels (as opposed to one of the 3 subscales measuring fatigue), especially when the function of the SF-36 is to "measure functional impairment". Just because someone is inactive doesn't mean they have severe fatigue. Allowing patients to be included if they simply have a "Reduced Activity" score of 10 or more (without necessarily having a low score on one of the fatigue axes of the MFI) risks reducing the specificity of the definition.

References:

[1] 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.

[2] Sharpe MC, Archard LC, Banatvala JE, Borysiewicz LK, Clare AW, David A, Edwards RH, Hawton KE, Lambert HP, Lane RJ, et al. A report--chronic fatigue syndrome: guidelines for research. J R Soc Med. 1991 Feb;84(2):118-21.

[3] Weatherley-Jones, E., Nicholl, JP., Thomas, KJ., Parry, GJ., McKendrick, MW., Green, ST., Stanley, PJ and Lynch, SPJ. A randomised, controlled, triple-blind trial of the efficacy of homeopathic treatment for chronic fatigue syndrome. Journal of Psychosomatic Research, 2004, 56, 2, 189-197.

[4] Vermeulen, RCW and Scholte, HR. Exploratory open label, randomized study of acetyl- and propionylcarnitine in chronic fatigue syndrome. Psychosomatic Medicine, 2004, 66, 276-282.

[5] Gaab J, Hüster D, Peisen R, Engert V, Heitz V, Schad T, Schürmeyer TH, Ehlert U. Hypothalamic-pituitary-adrenal axis reactivity in chronic fatigue syndrome and health under psychological, physiological, and pharmacological stimulation.Psychosom Med. 2002 Nov-Dec;64(6):951-62.

[6] Brimacombe, Michael; Lange, Gudrun; Bisuchio, Kim; Ciccone, Donald S.; Natelson, Benjamin. Cognitive Function Index for Patients with Chronic Fatigue Syndrome Journal of Chronic Fatigue Syndrome, 2004, vol 12; number 4, pages 3-24

On 2016 Jul 21, Tom Kindlon commented:

Another study raises serious questions about the use of the role emotional subscale of the SF-36 in the diagnosis of CFS

A CDC group (Reeves et al (2005)) proposed a way to operationalise chronic fatigue syndrome (CFS) criteria including subscales of the SF-36[1,2]: "We defined substantial reduction in occupational, educational, social, or recreational activities as scores lower than the 25th percentile of published US population [] on the physical function (≤ 70), or role physical (≤ 50), or social function (≤ 75), or role emotional (≤ 66.7) subscales of the SF-36." This method has been used in numerous subsequent CDC CFS studies but not by external groups, apart from Leonard Jason and colleagues who have examined the effect of this operationalisation of the criteria.

A newly published study looked at using the SF 36 subscales to define reduced activity in CFS (and ME)[3]. Six of the 8 subscales (Physical Functioning, Role-Physical, Bodily Pain, General Health, Vitality and Social Functioning) correlated with the sum of current hours of activity. Two subscales did not correlate (Role-Emotional and Mental Health).

The same 6 subscales (negatively) correlated with percentage reduction in the total hours of activity. Again, two subscales did not correlate (Role-Emotional and Mental Health).

Also, a "ROC analysis was used to assess which of the SF-36 subscales best discriminated between patients with ME and CFS and healthy controls. The ROC analysis used a plot of sensitivity versus 1-specificity for scores on the SF-36. The area under the curve (AUC) assessed the degree to which each subscale was able to discriminate between patients and controls. The closer the AUC is to 1, the better discriminatory power that SF-36 subscale has." The same 6 subscales (Physical Functioning, Role-Physical, Bodily Pain, General Health, Vitality and Social Functioning) had AUCs of 0.89 or better. By comparison, the Mental Health Functioning subscale had a AUC of 0.59. The AUC for the Role Emotional subscale was even worse at 0.47.

Each of these results demonstrates that the Role Emotional subscale is not suitable to be used to operationalise criteria for CFS.

References:

[1] Reeves WC, Wagner D, Risenbaum R, et al. Chronic fatigue syndrome – a clinically empirical approach to its definition and study. BMC Med. 2005;3(19):1–9.

[2] Ware JE, Sherbourne CD. The MOS 36-item short-form health survey (SF-36): conceptual framework and item selection. Med Care. 1992;30:473–483

[3] Thorpe T, McManimen S, Gleason K, Stoothoff J, Newton J, Strand EB, Jason LA (2016). Assessing current functioning as a measure of significant reduction in activity level. Fatigue: Biomedicine, Health & Behavior. Published online: 19 Jul 2016 doi: 10.1080/21641846.2016.1206176

On 2014 Jun 01, Ivan Oransky commented:

This paper has been retracted: http://retractionwatch.com/2014/05/27/oncology-researcher-getzenberg-notches-seventh-retraction/

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 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 2014 Oct 12, EDWARD BERRY commented:

The structure of the 3NPA-Arg adduct proposed here has been confirmed in the case of E. coli fumarate reductase, and a mechanism for its formation has been proposed, by Tomasiak et al. (J Biol Chem. 2011 286:3047-56) Pubmed ID 21098488 . Correction: The heterocyclic ring of carboxin is modeled with the wrong orientation in 2fbw, shown in Figure 6 here. Ruprecht et al.(J Biol Chem. 2009 284:29836-46) PMID 19710024. have deposited a corrected structure as 2wqy. The original authors agree with this correction as indicated here. Edward A. Berry 21:52, 21 May 2014 (IDT)

On 2014 May 06, John Roger Andersen commented:

Green Open Access to the authors final version: click here.

On 2017 Dec 23, Adriano Aguzzi commented:

If anything, it should read "E uno plures".

On 2016 Mar 29, Jonathan Wren commented:

URL relocated: http://www.genenames.org/

On 2016 Dec 15, Jim Stewart commented:

Please note, this article has been retracted. The "full text" link will take you to the retraction notice.

On 2018 Jan 08, Alexander Kraev commented:

Please note that this is a peculiar case of retraction, since while there are indeed problems with certain images, the authors stated the following in the retraction notice: "Nevertheless, although we feel that the scientific conclusions of the paper (that loss of NNT impairs insulin secretion and impairs glucose tolerance in C57BL/6J mice) still stand, given the conclusion of scientific misconduct against the first author, the authors think the most responsible course is to retract the paper." It is important to understand that nuance especially in view that thousands of publications state that they used "C57BL6" without making a crucial distinction between C57BL/6J and C57BL/6N.

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 Jan 21, Anders von Heijne commented:

We have just seen a case (young woman;in Stockholm, Sweden) with the exakt same type of vascular malformation and no obvious etiology, but with episodes of left sided pleuritic pain.

On 2016 Nov 20, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2014 Jan 09, Andrew Brown commented:

This article was corrected in 2006, but does not appear to be linked in PubMed. Correction: Are fast food restaurants an environmental risk factor for obesity? http://www.ijbnpa.org/content/pdf/1479-5868-3-35.pdf

On 2015 Oct 27, Peter Gøtzsche commented:

This review concludes that, “The three cholinesterase inhibitors are efficacious for mild to moderate Alzheimer’s disease.” I believe these drugs don’t work. The improvement in cognitive function was 2.7 points, in the midrange of a 70-point scale. This is less than the 4 points the FDA considers the minimally relevant clinical chan¬ge (1). We can also compare with the smallest effect that can be per¬ceived on the Hamilton scale for depression, which is 5-6 (2), although the maximum on this scale is only 52.

The placebo controlled trials have not been effectively blinded, as cholinesterase inhibitors have conspicuous side effect. This lack of blinding can in itself easily have caused the very minor effect that was noted in the trials (3).

A long-term trial of 565 patients with mild to moderate Alz¬heimer’s disease that compared donepezil with placebo found no meaningful effects whatsoever, and the authors concluded that do¬nepezil isn’t cost-effective, with benefits below minimally relevant thresholds (4). In contrast to other trials, it was publicly funded. This trial was excluded from the Cochrane review, for no good reason, as far as I can see. The outcomes after three years were similar on drug and placebo with respect to institutionalisation, progression of disability, and behavioural and psychological symptoms.

The author of the Cochrane review wrote that “donepezil appears to have no serious or common side effects.” This sentence is highly misleading. The harms are both common and serious, and she documents in her review that 29% of the patients left the drug group on account of adverse events, as compared to only 18% in the placebo groups. The most common side effects of donepezil are nausea, diarrhoea, not sleeping well, vomiting, muscle cramps, feeling tired, and not wanting to eat. I believe this is not what we would want for an old person who might already have problems with not sleeping well, feeling tired, and not wanting to eat.

The list of frequent side effects in Pfizer’s product information for Aricept (donepezil) is very long (5). Hypotension and syncope occurs in more than 1% and when old people fall, there is a considerable risk that they break their hip and die. A large Canadian cohort study showed that people who took anti-dementia drugs had almost a doubled risk of hospitalisation for syncope compared to demented people who didn’t take these drugs, and they had more pacemakers inserted and more hip fractures (6). Most astonishingly, more than half the patients who were admitted to hospital for bradycardia were retreated with the drug.

There are many good reasons not to use anti-dementia drugs.

1 Molnar FJ, Man-Son-Hing M, Fergusson D. Systematic review of measures of clinical significance employed in randomized controlled trials of drugs for de¬mentia. J Am Geriatr Soc 2009;57:536-46.

2 Leucht S, Fennema H, Engel R, et al. What does the HAMD mean? J Affect Disord 2013;148:243-8.

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

4 Courtney C, Farrell D, Gray R, et al. Long-term donepezil treatment in 565 patients with Alzheimer’s disease (AD2000): randomised double-blind trial. Lancet 2004;363:2105-15.

5 ARICEPT ® (donepezil hydrochloride) tablets. http://labeling.pfizer.com/ShowLabeling.aspx?id=510.

6 Syncope with cholinesterase inhibitors. Rev Prescrire 2011;31:434.

On 2016 Feb 12, Daniel Schwartz commented:

This tool can be used online and in mobile apps here:

https://qxmd.com/calculate/mayo-early-screen-for-discharge-planning

Conflict of interest: Medical Director, QxMD

On 2016 Jan 05, Morten Oksvold commented:

Please note that this article contains fraudulent data, which was concluded from an investigation by the University of Alabama at Birmingham in 2009 (!):

http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issues

The case was recently discussed at Retraction Watch: http://retractionwatch.com/2016/01/04/nature-retracts-paper-six-years-after-it-was-flagged-for-fraud/

PNAS was informed about this case in 2009, but as far as I can see there has still not been published any retraction. In light of the fact that this single article has been cited more than 40 times since 2009, and all the wasted work and resources, correction of the literature is highly important.

On 2016 Feb 01, Raphael Levy commented:

I have written a blog post where I identify this influential article (cited 5000 times) as one that introduces the (misleading) idea that nanoparticles can "penetrate cell membrane". Comments very much welcome, here or at the blog:

NANOPARTICLES & CELL MEMBRANES: HISTORY OF A (SCIENCE) FICTION? https://raphazlab.wordpress.com/2016/02/01/nanoparticles-cell-membranes-history-of-a-science-fiction/

On 2014 Nov 23, Harri Hemila commented:

A comment on the study is available at: http://hdl.handle.net/10250/8081

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 2013 Nov 24, John Sotos commented:

The death of “Mr. Abbott” (*) whose overlooked aortic dissection was misdiagnosed as an acute coronary syndrome, illuminates more than just the demise of the physical examination. It also illustrates Goethe`s precept “What one knows, one sees” (1).

A patient writhing because of chest pain should immediately be suspected to have aortic dissection (2)(3). Patients with chest discomfort due to coronary events more characteristically lie motionless (3), as noted in older (4), but not newer (5) cardiology textbooks.

Today`s highly specific imaging and biochemical tests have changed the role of physical examination from hypothesis confirmation to hypothesis generation. However, these tests have not, in the words of Dr. Joseph Bell (the model for Sherlock Holmes), changed the obligation of each physician to know “the features of disease… as precisely as you know the features, the gait, the tricks of manner of your most intimate friend” (3).

(*) Jauhar S. The demise of the physical exam. N Engl J Med. 2006; 354: 548-551.

(1) DeGowin RL. DeGowin & DeGowin`s Bedside Diagnostic Examination. 5th ed. New York: Macmillan, 1987; 37.

(2) Slater EE. Aortic dissection: presentation and diagnosis. In: Doroghazi RM, Slater EE, Aortic Dissection. New York: McGraw-Hill, 1983; 62.

(3) Sotos JG. Zebra Cards. Philadelphia: American College of Physicians, 1989; page 19 and card HE-011.

(4) Pasternak RC, Braunwald E, Sobel BE. Acute myocardial infarction. In: Heart Disease. 3rd ed. Braunwald E (ed.). Philadelphia: WB Saunders, 1988; 1235.

(5) Antman EM, Braunwald E. Acute myocardial infarction. In: Heart Disease. 5th ed. Braunwald E (ed.). Philadelphia: WB Saunders, 1997; 1198.

On 2016 Jul 14, Pedro Reche commented:

This tool is now maintained at the Facultad de Medicina of the University Complutense of Madrid (http://imed.med.ucm.es/dachis/)

On 2014 Nov 14, Robert Eibl commented:

This was the very first report on VLA-1 / VCAM-1 interactions measured at the single-molecule level with AFM and at the same time between two living mammalian cells. Two later AFM reports on VLA-4/VCAM-1 lack citation and discussion of my original work, although they were clearly induced or even initiated by myself; interestingly, my years of initiating and pioniering such AFM experiments as independent and unpaid guest PI and exclusive sharing of know-how was neither acknowledged, nor cited in related reviews.

On 2014 Apr 24, Stuart RAY commented:

NOTE: Sequence features reported prominently in this report have been found in a subsequent report (http://www.ncbi.nlm.nih.gov/pubmed/21702696) to have been erroneous, due to alignment error and other issues.

On 2016 Aug 21, Morten Oksvold commented:

Please note that this article represents one of eleven publications which were found to contain false data, after an investigation led by ORI in 2015:

https://ori.hhs.gov/content/case-summary-dasmahapatra-girija

This article should therefor 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 2016 Jul 29, Noel O'Boyle commented:

I believe that the description of the structure as cyclo-(D-NMePhe-L-Leu-L-Ile-L-NMeTyr-L-Phe-NMeGly-L-Pro) is incorrect, as the convention is to write the residues from the N terminus to the C terminus. This is a cyclic peptide, and thus missing the terminii, but there is still a directionality from the N of a residue towards its carbonyl.

In short, to be consistent with the X-ray and structural depiction, I believe that it should be written instead as cyclo-(L-Pro-NMeGly-L-Phe-L-NMeTyr-L-Ile-L-Leu-D-NMePhe).

On 2015 Oct 29, Vinodh Srinivasasainagendra commented:

PowerAtlas web-application has a new URL http://poweratlas.ssg.uab.edu , which replaces our previous homepage http://www.poweratlas.org.

Thanks, PowerAtlas Team

On 2016 Nov 20, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2014 Sep 15, Dr Yasmin Momin commented:

a rare event --intresting

On 2016 Nov 20, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2016 Oct 19, Richard Kunert commented:

The central claim of this paper is not supported by the numbers reported in the paper.

p. 142:

Participants exhibited the core personality features of psychopathy (Factor 1) to a greater extent than the core behavioral features of psychopathy (Factor 2).

In contradiction to this central claim of the paper, Factor 2 scores at 7.1 (the behavioural features of psychopathy) are actually higher than the Factor 1 scores at 5.2 (the personality features of psychopathy). The numbers tell the exactly opposite story to the words.

The numbers are given twice in the paper making a typo unlikely (p. 138 and p. 139). Adjusting the scores for the maxima of the scales that they are from (factor 1 x/xmax = 0.352 < factor 2 x/xmax=0.394) or the sample maximum (factor 1 x/xmaxobtained = 0.433 < factor 2 x/xmaxobtained = 0.44375) makes no difference. No outlier rejection is mentioned in the paper.

In sum, it appears as if DeMatteo and his co-authors interpret their numbers in a way which makes intuitive sense but which is in direct contradiction to their own data.

This issue was first raised publicly on Brain's Idea. The first author (DeMatteo) and the editor of the journal (Ewing) have been invited to respond via e-mail on 12/8/2016. Now, more than two months later, there is still no response.

On 2016 Feb 18, Kristina Hanspers commented:

A version of the pathway in figure 6a is available in the "Open Access Publication" collection at WikiPathways: http://www.wikipathways.org/index.php/Pathway:WP2293. This pathway can be downloaded for use in network analysis tools such as Cytoscape and PathVisio.

On 2014 Nov 23, Harri Hemila commented:

A manuscript version is available at HDL

On 2013 Nov 18, Lior Pachter commented:

The GeneMapper software is no longer supported or maintained.

On 2014 Jan 09, Tom Kindlon commented:

Why is the 11-item bimodal Chalder Fatigue Scale being used as a primary outcome measure?

(This was originally posted here http://www.biomedcentral.com/1741-7015/4/9/comments in 2008)

Stouten [1] has analysed some commonly used fatigue scales in the CFS area: the Chalder Fatigue Scale, the Checklist Individual Strength and the Krupp Fatigue Severity. He calculated the lower bound for the number and percentage of items with the maximum score for several studies and found that "extreme scoring" was common in studies in the field using these instruments. What is clear from this analysis is that the bimodal Chalder Fatigue Scale comes out worst in this regard.

Two of the authors of the current study should have been "intimately" aware of this problem as they were involved in one [2] of the two studies examined by Stouten [1] that used the 11-item bimodal Chalder Fatigue Scale. Here is the data from that study[2]: Baseline assessment for four intervention groups: Mean (95% Confidence Interval): 10.6 (10.4 to 10.9); 10.4 (10.0 to 10.7); 9.9 (9.2 to 10.6); 10.2 (9.9 to 10.6).

In percentage terms, this means that the lower bounds for the number of items with the maximum score for intervention groups were: 96%;95%;90%;93%. One can also calculate a lower bound for the percentage of patients who scored a maximum of 11 out of 11 for the items in the four intervention groups: 60%; 40%; 0%; 20%.

It should be remembered that these are lower bounds and the actual figure is likely to be higher (unless the authors give this data one can't calculate it from the mean). This can be illustrated by calculating the lower bound for the percentage of maximum (11 out of 11) scores for one study of an outpatient clinic in London[3] and comparing it to the actually percentage with the maximum score that was given. The Mean Score on the 11-item bimodal Chalder Fatigue Scale was 9.9. This translates to a lower bound for the percentage of patients who scored a maximum of 11 out of 11 of 0% (this could be achieved, for example, by 90% of the patients scoring 10/11 and 10% scoring 9/11). However the actual percentage of patients who scored the maximum (11/11) was 58%.

This shows that the 11-item bimodal Chalder Fatigue Scale doesn't just have a low ceiling for each individual question but also for the total score when applied to Chronic Fatigue Syndrome patients. Why is this important? Well, as the authors point out, some surveys of patient groups have found patients reporting being made worse by interventions such as Graded Exercise Therapy and Cognitive Behavioural Therapy (CBT).

For example, the results of a large survey with 2338 respondents were published in a report for the Chief Medical Officer[4]: it found that, of 285 who had done Cognitive Behavioural Therapy, 26% reported being made worse by the program, compared to 7% who said they were helped and 67% who said it made no difference. Of 1214 people who had done a graded exercise program, 50% had been been made worse by it (compared to 34% who said it helped and 16% who said it made no difference).These are not once-off results. For example, a recently published report of 2763 patients with ME or CFS in the UK[5] which asked about people's experiences of treatments over the last three years, found that of 699 who said they'd tried Graded Exercise Therapy, 34% said they'd been made worse by it compared to 45% who said they'd been helped and 21% who said it made no difference. The contention that people would not have being made worse by a treatment if they had done the treatment under specialist supervision, is not backed up by the data from this study[5]. Patients were asked who provided the GET treatment. Of the 567 who answered this question, 181 (31.92%) said it had made them worse compared to 276 (48.68%) who said it helped and 110 (19.40%) who said it made no difference; these are very similar percentages to the subgroup of 335 patients who had done the management strategy under an "NHS specialist": 111 (31.27%) of this group said they'd been made worse compared to 162 (45.63%) who said they'd been helped and 82 (23.10%) who said it made no difference. Again these don't appear to be once-off figures. In 2003, Action for ME did a smaller survey of 550 members asking about their experiences of Treatments[6]. 354 (64%) replied. The numbers for this study were small but if you combined the data from those who had done GET under a Physiotherapist, Occupational Therapist, Doctor or Behavioural Therapist, the results are: Negative 22 (56.41%) Neutral 2 (5.13%) Positive 15 (38.46%). [These don't compare favorably to the small group who did GET under no professional: Negative 1 (8.33%), Neutral 4 (33%) and Positive 7 (58%)]. A large percentage of the patients also reported being made by made worse by CBT in this study. Of 55 who had done CBT under a CBT Therapist/psychologist, Doctor/Psychiatrist, CPN/Other Mental Health, Counsellor/Psychotherapist, OT or Nurse specialist, 19 (34.55%) said it had made them worse compared to 24 (43.64%) who had been helped and 12 (21.82%) who said it made no difference.

The reason this is important is that if somebody already has a score of 11/11, they can't come up on the 11-item bimodal Chalder Fatigue Scale as being made worse on the treatment. Indeed, once they improved on one item, it would be marked as an improvement overall even if they actually felt worse on one or more of the other 10 items. Of course, this doesn't just apply to patients who score 11 out of 11; a patient could score 10/11 (say), feel worse on several items they'd already scored the maximum but come out as an improver once they improved on one idea. Saying all that, it would be good if the authors reported how many patients in each branch of the study scored the maximum.

Some of the items on the 11-item Chalder Fatigue Scale may also not be good as a measure of severity of CFS or ME. For example, somebody could be severe but not answer positively to the question, 'do you feel sleepy or drowsy'. Similarly a patient could disimprove and still not answer positively to this question. So a patient who scores 11 may not necessarily be more severely affected on a patient scoring 10. Saying all this, the generally very high scores (i.e. close to 11 on average) found in previous studies in the field suggest that the Likert method (0,1,2,3) of scoring does appear preferable. However it too also suffers from a ceiling effect although not to the same extent[1]. Also as previously pointed out, because of questions such as 'do you feel sleepy or drowsy', (which many if not most would feel are not intrinsic to Chronic Fatigue Syndrome or ME), even the likert version of the Chalder Fatigue Scale is not ideal for measuring severity of the condition.

On 2014 Jan 09, Tom Kindlon commented:

Further comments on the outcome measures being used and suggestions for other outcome measures that could be useful in such trials

(This was originally posted here http://www.biomedcentral.com/1741-7015/4/9/comments in 2009)

In the protocol, the authors say the following: "A 2001 systematic review of all treatments for CFS/ME concluded that cognitive behaviour therapy (CBT) and graded exercise therapy (GET) were the most promising treatments for CFS/ME, but that owing to the small number of studies available for review, the generalisability of these results could not be assured [1]*. The authors recommended that further studies be carried out using standardised outcome measures."

They authors neglect to say that the authors of that review also recommended the use of more objective outcome measures: e.g. "Outcomes such as 'improvement,' in which participants were asked to rate themselves as better or worse than they were before the intervention began, were frequently reported. However, the person may feel better able to cope with daily activities because they have reduced their expectations of what they should achieve, rather than because they have made any recovery as a result of the intervention. A more objective measure of the effect of any intervention would be whether participants have increased their working hours, returned to work or school, or increased their physical activities."

It is very disappointing that the organisers of this trial have not taken this on board with this study. Given the cost of the trial (over £1m), the cost of some actometers (for example) would have virtually neglible.

Existing research has some interesting findings on the issue. For example, one study (on a single patient)[2] found "using a 26-session graded activity intervention involved gradual increases in physical activity" that "from baseline to treatment termination, the patient’s self-reported increase in walk time from 0 to 155 min a week contrasted with a surprising 10.6% decrease in mean weekly step counts."The authors of the current trial refer to the Prins (2001) study[3] as an example of a study which supposedly found that hospital-based hospital-based CBT was an "effective treatment" for CFS. Judging by some of the questionnaire data, it does look like CBT has had an effect. However the actometer data from this study subsequently became available[4) and the increases in activity were minimal. For instance, the baseline average for the group which received CBT was 67.9, which increased to 68.8 after treatment and to 72.2 at follow-up. About 4 points. Not unlike the medical care controls, who went from 64.9 to 68.7 in the same period.

One of the aims of CBT (for CFS) has been said to be "increased confidence in exercise and physical activity"[5]. Thus it may be the case that when asked questions about one's ability to do things, such as in the physical functioning subscale of SF-36 (one of the three primary outcome measures in the FINE Trial), the patients might say that they are "Limited A Little" or "Not Limited At All" but may be just as limited as patients in other arms of study who say "limited a lot".

The physical functioning subscale is the primary outcome measure that is also being used to measure "clinically significant improvement" ("An improvement of 50% or more on the SF-36 physical functioning scale, or a score of 75% or more on that scale, will be considered a clinically significant improvement"). It is not an objective instrument, particularly in a psychosocial trial.

In my two previous comments, I have criticised the use of the bimodal Chalder Fatigue Scale as an outcome measure in a trial of patients with "CFS/ME". Recently another trial[6] was published involving CFS patients in the UK. The mean score was not given but the median mark was 11. That is to say, at least 50% of the people scored the maximum mark before the intervention. These people can not "get worse" on the scale using the scale even if they feel worse.

The third and final primary outcome measure being used is a quality of life measure. Although it may be useful to measure the quality of life, the findings of a recent study[7] make for interesting reading. It used 73 patients, also with a diagnosis of CFS according to the Oxford criteria, from UK clinics. It involved using principal-component analysis to analyse various bits of questionnaire. The Principal-component analysis of all scale scores revealed 2 distinct components, explaining 53% of the total variance. The results are summarised in the following extract: "The perceived incapacity in fulfilling social and physical roles may be best captured by the subscales of the SF-36 on social and physical functioning. The scores on these subscales are associated with vitality and inversely with one of the defining symptoms of CFS, i.e. fatigue (Chalder Fatigue Scale, Fatigue Visual Analogue Scale). They are also associated with other physical symptoms (SDQ, SCL-90-R subscale ‘somatization’), but not with psychological symptoms such as depression (Beck Hopelessness Scale, SCL-90-R subscale ‘depression’) and anxiety (Spielberger Trait Anxiety Questionnaire, SCL-90-R subscale ‘anxiety’). These psychological symptoms are linked to a generic measure of quality of life (MANSA), reflecting satisfaction with life in general and life domains, and to emotional role functioning and mental health (SF-36, subscale)."

Of course, the instrument to measure quality of life is different in this study so the relevance of this study is unclear at this time. But like the other two outcome measures (Chalder Fatigue Scale and SF-36 PF), the Euroqol is subjective.

It is disappointing that there apart from checking for the presence or absence of the CDC criteria, there appears to be no measurement of other symptoms apart from fatigue. (And of course I've already pointed out the problems with using the bimodal Chalder Fatigue Scale e.g. it's hard for some patients to score "worse" scores using the scale). But most researchers do not think CFS = fatigue. Even if some patients have few other symptoms because the Oxford criteria is being used, this should not have mattered.

(contd.)

On 2014 Jan 09, Tom Kindlon commented:

Comment on the discussion of the effectiveness of interventions for CFS

(This was originally posted here http://www.biomedcentral.com/1741-7015/4/9/comments in 2009)

The authors state that, in this study, "effect sizes and confidence intervals will be reported for each group", which is to be welcomed. As well as giving the protocol for the FINE Trial, this paper also gives information and data from some previous studies in the area including saying some treatments have been shown to be "effective". However, it does not report effect sizes.

Readers of this paper may be interested to know about a recent meta-analysis of the efficacy of CBT for CFS[1]. The studies involved a total of 1371 patients. It involved calculating the size of an effect measure, the Cohen's d value. They calculated d using the following method: "Separate mean effect sizes were calculated for each category of outcome variable (e.g., fatigue self- rating) and for each type of outcome variable (mental, physical, and mixed mental and physical). Studies generally included multiple outcome measures. For all analyses except those that compared different categories or types of outcome variables, we used the mean effect size of all the relevant outcome variables of the study." d was calculated to be 0.48.

For anyone unfamiliar with Cohen's d values, they are not bounded by 1; also, the higher the score, the bigger the "effect size" i.e. the more "effective" a treatment was found to be. Cohen's d values are considered to be a small effect size at 0.2, a moderate effect size at 0.5, and a large effect size at 0.8[2]. CBT had a more general definition in this paper and included some papers on GET. For example, the current paper says that, "Graded exercise therapy has also been shown to be effective in randomised controlled trials with selected hospital patients[3] and in our own previous study with a more general sample of hospital patients[4]." Malouff et al[1] calculated the d value for these studies as 0.46 (95% CI: 0.03 -0.95) and 0.17 (95% CI: -0.30 - +0.65) respectively (For the latter study, Malouff et al calculated the figures by comparing drug (i.e. antidepressant) treatment plus CBT to drug treatment without CBT).

References:

[1] Malouff, J. M., et al., Efficacy of cognitive behavioral therapy for chronic fatigue syndrome: A meta-analysis. Clinical Psychology Review (2007), doi:10.1016/j.cpr.2007.10.004

[2] Cohen J: Statistical power analysis for the behavioural sciences. Edited by: 2. New Jersey: Lawrence Erlbaum; 1988.

[3] Fulcher KY, White PD: Randomised controlled trial of graded exercise in patients with the chronic fatigue syndrome. BMJ 1997, 314:1647-1652.

[4] Wearden, A. J., Morriss, R. K., Mullis, R., Strickland, P. L., Pearson, D. J., Appleby, L., et al. (1998). Randomised, double-blind, placebo-controlled treatment trial of fluoxetine and graded exercise for chronic fatigue syndrome. British Journal of Psychiatry, 172, 485?490.

On 2016 Oct 17, Arturo Martí-Carvajal commented:

Reading this abstract, I asked myself two questions:

1. What is the relation between title and conclusions of this RCT?
2. TWAUC cholesterol from week 4 decreased more in the pravastatin group (-0.8 +/- 1.0 versus -0.3 +/- 0.9 mmol/L/week; P = 0.04) Query: mean (SE) or (SD)?

Does somebody have the answer please? Arturo

On 2014 Feb 01, Ferenc Zsila commented:

None

On 2014 Feb 12, Ferenc Zsila commented:

This text is shown on the page 24, in the paper of Ma et al. (see above):

"Figure 2C shows the change in intensity of CD bands in the presence of 1.0 mol equiv of Cu²⁺ at 252, 312, and 514 nm. Relatively strong CD bands are often for d-d transitions of Cu²⁺ tetragonal complexes.²⁹ However, these complexes involve main-chain amide coordination as well as histidine coordination via the imidazole ring. In these cases, the dominant contribution to optical activity observed is due to the vicinal contributions resulting from the asymmetric alpha carbon held in a chelate ring between two chelating donor atoms, such as adjacent main-chain amides.⁴³ At physiological pH and below, the lack of optical activity from the d-d transition of the complex suggests that backbone amide coordination is absent. At pH 8.5 and above, amide proton is deprotonated, which promotes copper coordination by the main chain, resulting in a negative CD band appearing at 514 nm. Clearly, Aβ(1-16) forms a type II square-planar coordination geometry with Cu^2+, and the coordination geometry is 3N1O at pH 7.5. Both visible absorption and CD spectra indicate that the coordinating ligands are strongly pH dependent, a mixed species is present at physiological pH, and main-chain amide coordination is absent at lower pH values."

The following text is shown on the page 18171, in the paper of Syme et al. Syme CD, 2004:

"The insets in Fig. 2 show the change in the intensity of CD bands in the presence of 1 eq of Cu²⁺ at 252, 312, and 514 nm. Relatively strong CD bands are often observed for d-d transitions of Cu²⁺ tetragonal complexes (36, 37). However, these complexes involve main-chain amide coordination as well as histidine coordination via the imidazole ring. In these cases, the dominant contribution to optical activity observed is due to the vicinal contributions resulting when the asymmetric α-carbon is held in a chelate ring between two chelating donor atoms (e.g. adjacent main-chain amides) (38). At physiological pH and below, the lack of optical activity from the d-d transition of the Cu-Aβ complex suggests that backbone amide coordination is not taking place. It is likely that raising the pH above 8 promotes amide deprotonation and copper coordination by the main chain, resulting in a CD band being observed at 514 nm. In summary, it is clear that Aβ forms a TypeII square-planar coordination geometry with Cu^2+, and both EPR and CD measurements indicate that the coordinating ligands are highly pH-dependent, a mixed species is present at physiological pH, and main-chain amide coordination is not present at lower pH values."

[Syme CD, Nadal RC, Rigby SE, Viles JH. Copper binding to the amyloid-β (Aβ) peptide associated with Alzheimer's disease: folding, coordination geometry, pH dependence, stoichiometry, and affinity of Abeta-(1-28): insights from a range of complementary spectroscopic techniques. J. Biol. Chem. 2004 (279) 18169-18177.]

On 2014 Nov 23, Harri Hemila commented:

The comment is available at DOI

On 2016 Sep 21, Morten Oksvold commented:

The published erratum of this article does not mention that a committee at McGill University has completed an investigation and concluded that several articles, included this one, were subjected to research misconduct. More specifically they found that two figures in this study “were intentionally contrived and falsified,”.

Please see a discussion at Retraction Watch: http://retractionwatch.com/2013/01/25/mcgill-committee-says-nature-figures-were-intentionally-contrived-and-falsified/

More recently a study by Vande Walle et al. (Nature, Brief communication) is questioning the conclusions in this article.

Please follow link:

http://www.nature.com/nature/journal/v534/n7605/full/nature17649.html

On 2013 Oct 29, Hilda Bastian commented:

The results of this systematic review are contradicted by a more recent and more comprehensive analysis of the methodologically more rigorous trials of viscosupplementation of the knee (Rutjes AW, 2012). In that more recent review, Rutjes and colleagues identify significant publication bias as a contributing factor in previous over-estimations of the benefit of intra-articular injections.

Rutjes and colleagues conclude that the intervention has only a clinically irrelevant benefit on pain, no statistically significant effect on function and is associated with serious unexplained adverse events. They discourage the use of the intervention and suggest an individual patient data meta-analysis would be needed to explore the issue of adverse events.

Doubts about the potential for viscosupplementation of the knee to do more good than harm were also expressed in another systematic review published after that by Bellamy and colleagues (Samson DJ, 2007).

UPDATE: A network meta-analysis by Bannuru RR, 2015 was able to analyze intra-inarticular injections, intra-articular placebos, and oral placebos, as well as a range of active treatments. It found a clinically meaningful benefit from intra-articular hyaluronic acid injections, in large part attributable to the effects of intra-articular injections per se.

(I discussed the implications of the 2015 review in a February 2015 blog post.)

On 2016 May 02, Hiten Patel commented:

WAT. No other trials?

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 2013 Jun 28, Rafael Irizarry commented:

I highly recommend reading this paper. It presents the statistical motivation for the widely used limma package. Although originally developed for microarrays, I have used the ideas presented here for other high throughput data include next generation sequencing. Of particular importance is the idea of shrinking sample standard deviations before computing signal to noise summaries such as the t-test.

On 2016 Apr 20, Daniel Corcos commented:

There is a serious bias in this study, as the mutation status for the cases was determined after diagnosis, whereas the controls were at-risk women. The large majority of the cancers were not diagnosed by screening mammography, indicating that screening was not performed efficiently in this group. On the contrary, being at-risk implicates implementation of screening, and, as a consequence, more mammograms in this group.

On 2016 Nov 20, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2014 Aug 20, Peter Gøtzsche commented:

This meta-analysis, which was based on observational studies, found that a history of depression doubled the risk of developing Alzheimer’s disease later in life. The authors speculate that vascular disease and inflammation may be risk factors for both diseases. Nowhere in the paper do they alert their readers to the most obvious explanation. Virtually all people with a history of depression have been treated with antidepressant drugs and it might very well be the drugs that cause dementia.

We know for sure that antipsychotics cause permanent brain damage, and many of us suspect that this is also the case for other psychotropic drugs. Animal studies have been particularly worrying in this respect. However, the psychiatrists have learned from the drug industry never to blame the drug but always to blame the disease (1-4). There are countless studies in depression and countless statements by official bodies representing psychiatry about how dangerous untreated depression is, about visible deterioration on brain scans, etc, when in actual fact these opinions are built on studies of patients who were treated with antidepressant drugs (3). This makes no sense.

Peter C Gøtzsche Professor and Director, DrMedSci, MSc, MD Nordic Cochrane Centre Rigshospitalet Copenhagen

Conflicts of interest: none.

1. Healy D. Let Them Eat Prozac. New York: New York University Press; 2004.

2. Whitaker R. Anatomy of an Epidemic. New York: Broadway Paperbacks; 2010.

3. Raven M. Depression and antidepressants in Australia and beyond: A critical public health analysis. PhD thesis, University of Wollongong, Australia; 2012 (http://ro.uow.edu.au/theses/3686/, accessed 13 August 2014).

4. Gøtzsche PC. Deadly medicines and organised crime: How big pharma has corrupted health care. London: Radcliffe Publishing, 2013.

On 2016 Aug 29, Jaime A. Teixeira da Silva commented:

The listed authorship on PubMed is incorrect. It should be Esashi Y, Nagao M. The affiliation for Nagao is also missing, and should be: 2 Biological Institute, Faculty of Science, Tohoku University, Aobayama, Sendai, Japan

On 2015 Jul 08, Bill Cayley commented:

A good example of when "less" is "more": https://lessismoreebm.wordpress.com/2015/07/08/comparison-of-the-surgical-outcomes-of-punch-incision-and-elliptical-excision-in-treating-epidermal-inclusion-cysts-a-prospective-randomized-study/

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 2014 Nov 23, Harri Hemila commented:

A comment on the paper is available at: http://hdl.handle.net/10250/8080

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 2015 Mar 09, Salzman Lab Journal Club commented:

Interesting science! This paper provides the first evidence which suggests that the major RNA isoform produced by the muscleblind gene in Drosophila is a circular RNA that may be developmentally regulated.

On 2013 Dec 16, Andrew Davison commented:

Source code for the model described in this article is available at ModelDB with accession number 64261

On 2014 Jun 29, Ivan Oransky commented:

This paper has been retracted, one of three by the same group: http://retractionwatch.com/2014/06/23/cancer-genetics-group-retracts-three-papers-for-inappropriate-presentation-of-data/

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 May 27, Anne Niknejad commented:

Error in Table 2: pEGFP-N1 585.5 ± 2.5

Text reports ∼35% palmitic acid fold-increase, by comparing EGFP-BGR containing fractions and controls (COS-7 cells transfected with pEGFP-N1), so the value should be '58.5'

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 2013 Oct 22, Rafael Najmanovich commented:

Genome-wide metabolic reconstructions have numerous uses. One of which is predicting what would be the effect of knocking out one or more genes or inhibiting the function of the corresponding protein(s). Once a gene is deleted or the protein inhibited, matter flows around other available metabolic routes. Such rearrangements may drastically disrupt the production of biomass or altogether prevent it, signifying that the gene/protein is fundamental or essential. Such proteins represent potential therapeutic targets.

Flux Balance Analysis (FBA) is widely used to perform predictions of gene essentiality Orth JD, 2010. Wunderlich and Mirny introduce Synthetic Accessibility (SA) as an alternative method that is based solely on the topology of the metabolic network. The idea is derived from synthetic chemistry labs where the difficulty in creating a new molecule is measured as the number of synthetic steps necessary to produce the molecule starting from available starting materials. In the case of metabolic networks, the idea is to calculate the number of steps necessary to produce biomass compounds from input metabolites.

The validity of the SA approach in predicting essential genes was verified in E. coli and S. cerevisiae. When a gene is knocked out or its protein inhibited in silico, the SA will necessarily either remain unchanged or increase (even infinitely) reflecting the longer path (or the absence thereof) necessary to reach output compounds using alternate metabolic routes.

SA and FBA are equivalent in terms of accuracy, around 60% and 80% respectively for E. coli and S. cereviseae. We implemented both SA and FBA in our lab and independently verified these results. Furthermore we also tested B. subtilis where a metabolic network exists Oh YK, 2007 and the full list of essential genes is known Kobayashi K, 2003, obtaining a success rate of 92% with SA (equivalent to the 94% obtained by Oh et al. Oh YK, 2007 with FBA). Wunderlich and Mirny point that the equivalent success rates between FBA and SA suggests the success of the former should be attributed mainly to network topology.

Some advantages of SA over FBA involve the simplicity of the approach (in terms of implementation and execution), not requiring any knowledge of the stoichiometry of reactions (or initial ranges for reaction rates). The latter in my opinion is a very interesting aspect of SA that allows its application to mixed networks that integrate gene regulatory networks, metabolic networks and other cellular processes that are more difficult to define in terms of stoichiometry and reaction rates.

On 2017 Jun 06, Egon Willighagen commented:

A third paper about the CDK was published today in the J. Cheminform.: https://doi.org/10.1186/s13321-017-0220-4

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 26, Bill Cayley commented:

A good example of when less is more: https://lessismoreebm.wordpress.com/2015/06/26/improving-womens-experience-during-speculum-examinations-at-routine-gynaecological-visits-randomised-clinical-trial/

On 2016 Mar 04, Chris Del Mar commented:

Between 1 - 5/1,000 children aged <5 years in developed countries may need hospital admission each year because of influenza infections, (PMID: 26111238) -- much lower (e.g. 0.6/1,000 children when based on laboratory confirmation of influenza, (http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19365). The benefits of influenza vaccination in children are a NNTB of 28 to prevent one child age aged >6 years getting influenza, but there is no effect on any downstream consequences such as secondary infections, nor benefit for children aged <2 years, from a Cochrane review (PMID 22895945). This systematic review estimates a rate of fevers of 6-7%, and of febrile convulsions at ~1/1,000 from inactivated vaccine fever in children aged >6 years (NNTH of 16 and 1,000 respectively) -- in the same range as those who might be prevented from a post-influenza admission. This suggests the decision about influenza vaccination needs discussion with parents to balance benefits against harms, perhaps using shared decision making (patient decision aid might be ideal), rather than public health pronouncements. Peer Collingnon collignon.peter@gmail.com; Chris Del Mar cdelmar@bond.edu.au

On 2013 Nov 04, Jamie Horder commented:

In a conference abstract, Berl and colleagues suggested that the striking results presented in this paper may have been the result of an artifact, observed in some MRI DTI sequences.

They argued that although the vibration signal-loss artifact in question is best known as an issue on Siemens MRI scanners, GE scanners, such as the one used in the Voss study, are not immune.

Berl et al wrote:

"The artifact may be the basis for a clinical misinterpretation that has been cited as evidence to change policy and practice [i.e the Voss study]. The speed that this article was propagated was assisted by the inherent interest of the case details; however, it also illustrates the danger of premature clinical interpretation of DTI data.

We suggest that repositioning the patient by adjusting the roll would be a simple and practical method to determine if such findings were indeed axonal regrowth or artifact."

On 2014 Feb 14, Henning Voss commented:

We were aware of the possibility of artefacts in DTI at the time of publishing of [1], and therefore as noted in our study [1] we tested for increased residuals in the tensor fits, which would be a sign of the artefact described in [2] and [3]. We did not find increased residuals in the medial parietal occipital region or the cerebellar vermis. In particular for the vermis, later we also created plots corresponding to [3], Figure 2, on higher quality data of the same subject obtained with a headcoil unavailable at the time of first timepoint of study (not published) which showed the same effect. We did not find any hint for the artefact there, either. We also compared this case with 20 healthy control subjects scanned on the same equipment with the same protocol and the patient had the highest anisotropy in the medial parietal occipital region.

[1] Voss HU, Uluç AM, Dyke JP, Watts R, Kobylarz EJ, McCandliss BD, Heier LA, Beattie BJ, Hamacher KA, Vallabhajosula S, Goldsmith SJ, Ballon D, Giacino JT, Schiff ND. Possible axonal regrowth in late recovery from the minimally conscious state. J Clin Invest. 2006 Jul;116(7):2005-11. [2] Berl M, Walker L, Sarlls J, and Pierpaoli, C. Investigation of vibration induced artifacts in clinical diffusion weighted imaging of the brain. Proc. Intl. Soc. Mag. Reson. Med. 20, 3740 (2012). [3] Gallichan D, Scholz J, Bartsch A, Behrens TE, Robson MD, Miller KL. Addressing a systematic vibration artifact in diffusion-weighted MRI. Hum Brain Mapp. 2010 Feb;31(2):193-202.

H.U. Voss and N.D. Schiff

On 2016 Aug 19, Morten Oksvold commented:

Please note that this article has been retracted and should therefore not be cited in the future:

http://onlinelibrary.wiley.com/doi/10.1002/ijc.30268/full

On 2015 Jun 16, Bill Cayley commented:

A great example of when "Less" is more: https://lessismoreebm.wordpress.com/2015/06/16/written-action-plans-for-asthma-in-children/

On 2017 Jan 05, Robert Badgett commented:

A subsequent systematic review (Mathieson S, 2015) reports that the ID Pain using a cutoff of 2 or more to suggest neuropathic pain, "demonstrated satisfactory hypothesis testing and reliability" but sensitivity and specificity were not reported.

On 2017 May 15, Eric Yarnell commented:

Authors names are incorrect, being listed by their given names not their family names. Should be Bao XY, Wong CK, Li EKM, Tam LS, Leung PC, Yin YB, and Lam CWK.

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 2016 Nov 18, Morten Oksvold commented:

An investigation committee at Wayne State University (WSU) recommends that 42 articles from Fazlul Sarkar to be retracted (report finished August 31, 2015). This article represents one of them.

This information was published by Retraction Watch (November 17, 2016) and you can find a link to the full report here:

http://retractionwatch.com/2016/11/17/details-of-investigative-report-into-sarkar-released-by-aclu/

This article should therefore no longer be cited.

On 2014 Sep 28, Guillem Feixas commented:

Could anyone tell me whether fibromyalgia could be considered a NCD? Thanks.

On 2017 Jun 26, Guangcun Huang commented:

The third author's name, Guangcun Huang, has been incorrectly spelled as Quangcun Huang.

http://onlinelibrary.wiley.com/doi/10.1111/j.1872-034X.2007.00295_1.x/full

On 2016 Jun 11, Egon Willighagen commented:

The website is inaccessible. Is the database discontinued or is there a new website?

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 2016 Sep 06, Jakob Suckale commented:

PubSum: The stem cells that can generate our body's specialized cell types take cues from the stiffness of their environment to decide which cell to become; soft generates nerve-like cells, hard generates bone-like cells. To arrive at this hypothesis researchers grew human stem cells on surfaces of varying stiffness and analyzed how they changed over time.

On 2014 Jun 15, Jorge H Ramírez commented:

Related articles:

Ramírez JH, Palacios M, Tamayo O, et al. Acute and subacute toxicity of Salvia scutellarioides in mice and rats. J Ethnopharmacol 2007;109:348–53. URL: http://www.ncbi.nlm.nih.gov/pubmed/16978817 Full text article available in English

Ramírez JH, Palacios M, Gutiérrez O. Implementation of the isolated vascular tissue model as a device for the validation of medicinal plants: Study of the vasodilator activity of Salvia scutellarioides. Colomb. Med. 2007;38:28–39. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/471/480 Full text article available in English and Spanish.

Ramírez JH, Palacios M, Ocampo HH, et al. Lack of association between blood pressure, target organ damage and retinopathy in the L-NAME rat hypertension model: Are new animal models of hypertension required?. Colomb. Med. 2006;37:328–31. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/465/471 Full text article available in Spanish. Abstract available in English.

Ramírez JH, Palacios M, Gutiérrez O. Evaluation of the antihypertensive effect of Salvia scutellarioides in a rat model of hypertension. Colomb Med 2006; 37: 53-60. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/412/417 Full text article available in Spanish. Abstract available in English.

On 2014 Sep 14, Daniel Haft commented:

EpsH family proteins in bacteria are now called exosortase. Their very distant homologs in the archaea are termed archaeosortase. Exosortases and archaeosortases belong to an extended superfamily, exclusive to prokaryotes, whose members can be detected by TIGRFAMs model TIGR04178. An updated description of the superfamily occurs in PMID:22037399 (Haft, et al., 2012). The variety of archaeosortase and exosortase systems should recall the situation with sortases and their substrates, "An embarrassment of sortases - a richness of substrates?" (PMID:11239768, Pallen, et al. 2001).

The first characterized member of the extended family is archaeosortase A, ArtA, from Haloferax volcanii. Its primary target is the major cell surface glycoprotein, which forms the S-layer. This target has been a model for studying post-translational modification in the archaea. Knocking out ArtA blocks removal of the PGF-CTERM sorting signal and causes a variety of phenotypic differences include S-layer defects. See Abdul Halim, et al., 2013, PMID:23651326.

The work on archaeosortase suggests that both exosortases and archaeosortases may be transpeptidases. The S-layer glycoprotein was previously known to have a large prenyl-derived lipid, attached somewhere toward the C-terminus. Its purpose was unclear because the final C-terminal transmembrane helix seemed sufficient to anchor the protein to membrane. However, proof that the PGF-CTERM sorting signal is removed during maturation suggests that the lipid replaces it as the anchor. Transpeptidase activity would allow removal of the C-terminal sorting signal and attachment of the lipid to occur simultaneously.

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the body of the text of the article. The ID given is NCT00092791. We believe the correct ID, which we have found by hand searching, is NCT00092781.

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

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

On 2014 Nov 23, Harri Hemila commented:

The published version is available at DOI.

A manuscript version is available at https://helda.helsinki.fi/handle/10138/228095

On 2017 Jul 07, Morten Oksvold commented:

This article should have been retracted after an investigation by The University of Maryland found this article to contain "compromised" data (a total of 26 articles in 11 journals were affected). The journal Cancer Research was informed in August 2016, according to Retraction Watch.

http://retractionwatch.com/2017/04/26/university-asked-numerous-retractions-eight-months-later-three-journals-done-nothing/

On 2013 Nov 24, John Sotos commented:

The courageous effort by Emanuel to outline a new pre-medical and medical curriculum has one contradiction and two omissions.

First, after advocating a year of biochemistry in the pre-medical curriculum, he rightly states that knowledge of the Krebs cycle generally has no practical use at the bedside. This contradiction suggests that devoting a year to biochemistry is excessive.

Second, there is a fundamental, yet unspoken truth about medicine: as an intellectual endeavor, it is extremely easy. While the hard sciences require detailed understanding and nuanced application of difficult quantitative principles, medical textbooks simply demand memorization on a massive scale. One could argue that mnemonic training is the greatest omission in medical teaching and that, of all pre-medical requirements, organic chemistry is the greatest developer of memorization skills.

Finally, I wish there were some way to teach humility more effectively and more permanently. Any physician not cowed by their own ignorance should be drummed out of the profession.

(1) Emanuel EJ. Changing premed requirements and the medical curriculum. JAMA. 2006 Sep 6;296(9):1128-1131. Pubmed 16954492

On 2013 Jun 13, Robert Tibshirani commented:

The interested reader should be sure to look at the published comments to this paper:

http://www.ncbi.nlm.nih.gov/pubmed/17872427 http://www.ncbi.nlm.nih.gov/pubmed/17872429 http://www.ncbi.nlm.nih.gov/pubmed/17872428

All three groups found similar, serious flaws in the analyses

On 2013 Nov 15, George McNamara commented:

For fluorescence spectra data, please see the current PubSpectra download site at

http://works.bepress.com/gmcnamara/9/

For spectra graphing web sites, please see my comment in PubMed 16969821, McNamara et al 2006 Spectral imaging microscopy web sites and data. Cytometry A 69:863-871.

On 2013 Nov 15, George McNamara commented:

The PubSpectra dataset of over 2,000 fluorescence spectra is now (2013) downloadable in the Excel XLSX file inside a zip archive downloadable from

http://works.bepress.com/gmcnamara/9/

The Boswell spectra graphing site described in this paper is defunct and has been replaced by Urs Utzinger and Carl Boswell's University of Arizona Spectra site

http://www.spectra.arizona.edu/

Urs has added additional spectra - especially 2-photon excitation spectra - to his web site.

Several vendors have spectral graphing sites, including (but not limited to)

http://www.semrock.com/searchlight-welcome.aspx

http://www.chroma.com/spectra-viewer

LifeTech/Invitrogen/Molecular Probes http://www.lifetechnologies.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html instructions: http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/technical-notes-and-product-highlights/using-the-fluorescence-spectraviewer.html

Leica http://www.leica-microsystems.com/fluoscout/ (filter sets are from Chroma, so may be simpler to use Chroma’s web site)

BD Biosciences http://www.bdbiosciences.com/research/multicolor/spectrum_viewer/index.jsp

Most of the confocal microscope companies have spectral viewers in their software. Zeiss ZEN acknowledges PubSpectra as the source of data.

Re-using data: This 2006 paper includes a section,

Data Is Not Copyrightable During the course of developing this data, one of us had an epiphany while reading in Lessig (18) about a U.S. Supreme Court decision: data is not subject to copyright (14). Text and commentary about Feist can be found on many legal web sites by doing a Google search. Indeed, the broad availability of the text of Supreme Court decisions is because they are not subject to copyright. The Feist decision reaffirmed the U.S. Copyright act of 1976 that "there can be no copyright in facts". The basis for the Feist decision can be found in the U.S. Constitution. 14. Feist Publications, Inc. v. Rural Tel. Serv. Co. 1991;499 U.S. 340. 18. Lessig L. The Future of Ideas. New York: Random House; 2001. p 368. For those interested in reference 17, Multi-Probe Microscopy, it is available for download at http://works.bepress.com/gmcnamara/2/

Now in 2013, I want to reinforce in this PubMed Comment, that: 1. Data is not copyrightable (in the United States). 2. I encourage re-use of PubSpectra instead of you starting from scratch. 3. If anyone wants to "take over" adding data, please go ahead and do so. I would love for someone to find money and organizational skills to set up a village in India or China - or downtown Troy NY or Detroit MI - to hire people to unscan spectra graphs, and add it to "New PubSpectra".

On 2014 Jun 15, Jorge H Ramírez commented:

Related articles:

Ramírez JH, Palacios M, Gutiérrez O. Diuretic effect of an infusion of the herbal plant, Salvia scutellarioides, in rats. Biomedica 2006;26:145–9. URL: http://www.ncbi.nlm.nih.gov/pubmed/16929912 Full text article available in Spanish. Abstract available in English.

Ramírez JH, Palacios M, Gutiérrez O. Implementation of the isolated vascular tissue model as a device for the validation of medicinal plants: Study of the vasodilator activity of Salvia scutellarioides. Colomb. Med. 2007;38:28–39. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/471/480 Full text article available in English and Spanish.

Ramírez JH, Palacios M, Ocampo HH, et al. Lack of association between blood pressure, target organ damage and retinopathy in the L-NAME rat hypertension model: Are new animal models of hypertension required?. Colomb. Med. 2006;37:328–31. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/465/471 Full text article available in Spanish. Abstract available in English.

Ramírez JH, Palacios M, Gutiérrez O. Evaluation of the antihypertensive effect of Salvia scutellarioides in a rat model of hypertension. Colomb Med 2006; 37: 53-60. URL: http://colombiamedica.univalle.edu.co/index.php/comedica/article/view/412/417 Full text article available in Spanish. Abstract available in English.

On 2015 May 19, Stephen Maher commented:

According to Br J Radiol a retraction has been issued for this article. http://www.birpublications.org/doi/full/10.1259/bjr.20139004

On 2016 Aug 29, Jaime A. Teixeira da Silva commented:

The abstract describes the study as being about "rude" medicinal material. What is this? Also, the results describe tentacles being found in the rhizomes. At first glance, this sounds like a paper on octopii. Unable to view the full text, and presumably the full text being in Chinese, one wonders how this type of research has the luxury of being listed in PubMed. Such sloppily (botanically) written abstract call into question the rigor of peer review and the validity - at first glance - of the findings.

On 2013 Oct 23, Andrew R Kniss commented:

This paper (on which I am a co-author) was an early report based solely on greenhouse and laboratory studies. Glyphosate applied to glyphosate-resistant sugarbeet increased disease under greenhouse conditions in this work. Our conclusions with respect to field management of the disease went beyond what the limited data could support. Subsequent research has shown over five field seasons, two growing regions, and 6 sugarbeet cultivars that the effect presented here is unlikely to occur in the field. Based on evidence presented in these subsequent works (outlined below), it appears that adoption of glyphosate-resistant sugarbeet is likely to have had no impact, or possibly even a positive impact, on Rhizoctonia root and crown rot management in sugarbeet in the US.

In an M.S. thesis by Youdon (http://search.proquest.com/docview/899255899), field studies using 2 sugarbeet cultivars over 3 field seasons failed to find any significant effect of glyphosate on Rhizoctonia root and crown rot in sugarbeet. Youdon's work further showed that the timing of glyphosate application in relation to disease infection had no impact on disease severity or incidence. Similar to the Larson et al. paper, glyphosate increased Rhizoctonia root and crown rot under greenhouse conditions. However, conventional sugarbeet herbicides caused greater disease than glyphosate. Therefore even if it is true that glyphosate can increase sugarbeet susceptibility to this disease, the conventional herbicides that glyphosate replaced would likely have even greater impact. A conventional herbicide control was not used in the Larson et al. paper, and therefore the conclusions were not relevant to real-world growing conditions.

In preliminary greenhouse studies similar to those conducted in the Larson paper, Barnett et al. (2012) http://www.bioone.org/doi/abs/10.1614/WS-D-11-00027.1 observed mixed results; glyphosate increased Rhizoctonia in one sugarbeet cultivar, decreased Rhizoctonia in a different cultivar, and had no effect on a third cultivar. A second set of greenhouse studies using 4 commercial sugarbeet cultivars showed no effect of glyphosate on Rhizoctonia severity. Glyphosate treatments also had no observable effect on Rhizoctonia root and crown rot in any of four sugarbeet cultivars conducted over two years in field studies.

On 2016 Mar 15, Kristina Hanspers commented:

The pathway in figure 2 is available as a pathway in the Open Access Publication Collection at WikiPathways: http://wikipathways.org/index.php/Pathway:WP1591. These pathways are available for download in multiple formats and can be used for analysis and visualization in tools like PathVisio and Cytoscape.

On 2013 Jul 03, Jessie Tenenbaum commented:

This is such a seminal paper in this area, and Connectivity Map data has proven very valuable in many follow-on studies by other authors- a great model for how data sharing can work.

I remember being struck by this sentence when I first read this paper- "There is no standard approach for estimating the statistical significance of the connections observed." I wonder if the authors would revise that 6 years later? Have they developed, or seen work by others, any methods to advance this capabilities? Certainly this flavor of analysis has been done many times. FDR seems to be the statistic of choice, though often applied somewhat differently on a case by case basis.

On 2015 Jan 31, Stephen Jacobs commented:

8 Years after this publication, the prevailing autoimmune explanation of celiac disease still has not been fleshed out. We have known for 10 years that gluten fragments activate T cells, but there remains no explanation of why that should cause a localized failure of gut function (often within half an hour), nor of why that should cause substantial remodeling of the epithelium. The blocked recognition hypothesis explains the nature and timing of the celiac response to gluten in some detail, and remains consistent with newer results.

On 2014 Jun 18, Madhusudana Girija Sanal commented:

This paper in Nature Genetics - 38, 1323 – 1328, 2006 is rather "unique" in its findings. I wonder someone has made similar observations/reproduced these results in the past 8 years (2014)! Even the original observations by Briggs (Phili) and King (Bronx, New York) suggest nucleus from immature (less differentiated) cells are better for SCNT compared to more mature (or differentiated) cells. In their classic experiments in frogs they used nucleus from early embryonic cells to perform SCNT. Refer Briggs Robert, and King Thomas Joseph. “The transplantation of living nuclei from blastula cells into enucleated frogs’ eggs.” Proceedings of the National Academy of Sciences 38 (1952): 455–463. However later many tried with nucleus from more mature frog cells but failed. In 1958, Gurdon (Oxford,UK), successfully cloned a frog using intact nuclei from the somatic cells (gut epitheial cells) of a tadpole and won the Nobel prize together with Yamanaka. These experiments are well documented and part of the history. Going by logic one would think, reprogramming an immature cell is easier compared to a differentiated and mature cell which has undergone extensive epigenetic rearrangements and condensation of chromosomes. It is also reported that generating iPSC or embryonic cells through SCNT from older adults is more difficult compared to infants or children. Moreover, isolation, purification of haematopoietic stem cells by FACS or Magnetic beads (involving seven markers) might have damaged these cells more compared to granulocytes which were isolated by anti-Gr-1 and scatter. The abundance and ease of isolation of granulocytes might have contributed to this observation which was interpreted by the authors as suggested by the title "Differentiated cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer"!