10,000 Matching Annotations
  1. Jul 2018
    1. On 2017 Sep 22, Jan Tunér commented:

      The parameters here are unclear but with the assistance of the laser manufacturer, the following calculation is made: 1. IR Source 905 nm pulsed (pulse duration = 200 ns, adjustable frequency, peak power, according to the frequency of the nominal value (45 W) 2. Continuous visible source 650 nm (output power 70 mW) The peak power (45 W nominal power) depends on the set frequency and it decreases when the frequency increases. The frequency used in the article of 30 kHz (30,000 Hz) is of about 34 Watt. The energetic value reported on the article (48.6 joule) is given from the sum of the contribution of the 2 sources: 1. Source contribution IR 905nm: 34 W200 ns30000 Hz180 sec ≈ 36 joule 2. Source contribution Visible 650nm: 0.07 W180sec = 12.6 joule The weight of a Wistar rat of 5 weeks of age is around 200 g, so a child of 10 years weighting 15 kg, in the need of PBM for the investigated condition would then receive more than 75 times 48.6 J = 3645 J. This, applied seven times during a period of two weeks, would end up in a total applied energy of 25515 J. The relevance of the reported results need to be put into that perspective.


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    1. 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 originating journal article. The ID given is NCT0029779. We believe the correct ID, which we have found by hand searching, is NCT00297791.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 PMID: 27056367

      * 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


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    1. On 2014 Nov 26, Harri Hemila commented:

      Lee HK, 2014 include in their meta-analysis the RCT by Chubak J, 2006, although serious problems in that study have been pointed out in Hemilä H, 2007; which is freely available as a manuscript version Handle. In addition, Lee et al. did not refer a large cohort study by Hemilä H, 2003, which found that physical activity at work and at leisure had no association with common cold risk; freely available as a manuscript version Handle.

      A comment on the Lee et al. meta-analysis is also available at Korean J Fam Med.


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    1. On 2016 Aug 23, Traolach S Brugha commented:

      We are grateful to J Stone for this PubMed Commons comment of 2016 Aug 16 10:53 a.m. Detailed scrutiny of the methods used in this unique epidemiological research on autism in adulthood (cited reference 1 Brugha TS, 2011) is in the best interests of people with autism, their carers and the research community and is therefore of great importance.

      The author’s assertion that the statistics published by us have been downgraded to the status of experimental statistics is mistaken. He should read the references cited by him (4, 5) more carefully. Furthermore this research has been published in world leading psychiatric journals (Cited reference 1 Brugha TS, 2011; additional references: Brugha et al 2012, and 2016).

      The author refers to the study (cited reference 1 Brugha TS, 2011; and Brugha et al, cited reference 2) derived from a 2009 NHS publication (cited reference 3) to further assert that criticism of the methodology includes questions over five issues. But the author does not provide the five questions or reference their source. However the points listed can be addressed very briefly.

      Interested readers will find more information on the basis for the scoring of the diagnostic autism test ADOS-4 and evaluation of its use in a validation study published since (Brugha et al 2012). This additional research was required because the original scoring of the diagnostic autism test ADOS-4, at that time, had only been tested in teen age and young adult patients attending specialist US autism clinics; it had never been validated in the survey population, a random sample of adults and elderly people living in private households throughout England. The resulting validated scoring was different. We plan to publish more details of this.

      The author then questions the ‘transparency of the weighting method used in the APMS 2007 survey’. A description of the methods is available at: http://www.hscic.gov.uk/catalogue/PUB02931/adul-psyc-morb-res-hou-sur-eng-2007-rep.pdf and at: http://www.hscic.gov.uk/catalogue/PUB01131/aut-sp-dis-adu-liv-ho-a-p-m-sur-eng-2007-rep.pdf. The assertion that that the work inflated 19 "cases" to 72 is also mistaken (table 1, cited reference (1) Brugha TS, 2011).

      The ‘substitution of the category "Autistic Spectrum Disorder" for "Asperger Syndrome" between the publication of the original 2007 psychiatric morbidity survey (cited reference 7) and its appendix (cited reference 3) in 2009’ will be unsurprising to readers of the 5th Revision of the Diagnostic and Statistical Manual (2013). The term ‘asperger’ is no longer justified officially.

      The author refers to ethical issues. Ethical approval for the study was obtained from the Royal Free Medical School Research Ethics Committee, London, England (cited reference 1). The ethical approval application clearly states the purpose of the research including: “…The main objective of the survey is to collect data on the mental health of adults...” More specifically, “... the survey will aim to estimate the levels of psychiatric disorder according to diagnostic category among the population aged 16 and over living in England…”

      And finally the author makes the point that ‘the survey published by the NHS and funded by the Department of Health was claimed by the NHS at the time to be evidence that measles, mumps, rubella vaccine (MMR) had not affected the rate of autism, citing a newspaper article (cited reference 6). Further discussion of possible relevance to the context of this point may be of interest to the reader: http://www.bmj.com/content/342/bmj.c7452/rr/635992.

      Additional references referred to in this response:

      American Psychiatric Association (2013). Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5™). American Psychiatric Press, Washington DC.

      Brugha TS, McManus S, Smith J, Scott FJ, Meltzer H, Purdon S, et al. Validating two survey methods for identifying cases of autism spectrum disorder among adults in the community. Psychol Med 2012 Mar;42(3):647-56 Brugha TS, 2012.

      Brugha,T.S., Spiers,N., Bankart,J., Cooper,S.A., McManus,S., Scott,F.J., Smith,J. & Tyrer,F. (2016). Epidemiology of autism in adults across age groups and ability levels. Br.J Psychiatry. Brugha TS, 2016. DOI: 10.1192/bjp.bp.115.174649.


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    2. On 2016 Aug 16, J Stone commented:

      The data in the study cited (1) by Brugha et al (2) is derived from a 2009 NHS publication which was published as National Statistics (3). However, according to government documents published on line in May 2016 (4, 5) the UK Statistics Authority have downgraded these statistics to the status of "experimental statistics". The survey published by the NHS and funded by the Department of Health was claimed by the NHS at the time to be evidence that measles, mumps, rubella vaccine (MMR) had not affected the rate of autism (6).

      Apart from the political context of its publication, criticism of the methodology include questions over:

      • the correct scoring of the diagnostic autism test ADOS-4

      • ADOS-4 was used incorrectly as a stand-alone test

      • a non-transparent weighting method was used that inflated 19 "cases" to 72

      • the substitution of the category "Autistic Spectrum Disorder" for "Asperger Syndrome" between the publication of the original 2007 psychiatric morbidity survey (7) and its appendix (3) in 2009

        • the ethical issue of whether members of public were told that they were to be assessed for "morbid" conditions.

      (1) Brugha TS, McManus S, Bankart J, Scott F, Purdon S, Smith J, Bebbington P, Jenkins R, Meltzer H. Epidemiology of autism spectrum disorders in adults in the community in England. Arch Gen Psychiatry 2011 May;68(5):459-65. (2) Brugha TS, McManus S, Bankart J, Jenkins R, Smith J, Scott F, The proportion of true cases of autism is not changing. BMJ. 2014 Jun 11;348:g3774. doi: 10.1136/bmj.g3774. (3) Brugha TS, McManus S, Meltzer H, Smith J, Scott FJ, Purdon S, Harris J, Bankart J, Autistic Spectrum Disorders in adults living in households throughout England: Report from the Adult Psychiatric Morbidity Survey 2007, http://digital.nhs.uk/catalogue/PUB01131/aut-sp-dis-adu-liv-ho-a-p-m-sur-eng-2007-rep.pdf (4) Letter from Ed Humpherson to Clifford Miller, https://www.statisticsauthority.gov.uk/wp-content/uploads/2016/05/Letter-from-Ed-Humpherson-to-Mr-Miller-230616-1.pdf (5) UK Statistics Authority, Assesment of the compliance with the code of practice for official statistics:, National Study of health and Wellbeing: Adult psychiatric morbidity survey 2007. (6) Sarah Boseley, Autism is just as common in adults, so MMR is off the hook, https://www.theguardian.com/society/2009/sep/22/autism-rate-mmr-vaccine (7) Bebbington P, Brugha T, Wessely S etc. Adult psychiatric morbidity in England, 2007, http://digital.nhs.uk/catalogue/PUB02931/adul-psyc-morb-res-hou-sur-eng-2007-rep.pdf


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    1. On 2014 Aug 12, David Reardon commented:

      The association between PTSD and preterm birth revealed by Yonkers et al<sup>1</sup> is unfortunately marred by the failure to control for a common risk factor for both PTSD and pre-term birth: induced abortion.

      For example, a recent systematic review and meta-analysis of 37 qualifying studies found that the risk of preterm birth rose 36% after a single induced abortion and 93% after two or more induced abortions.^2  The risk of low birth weight deliveries also rose 35% after a single abortion and 72% after two or more abortions.
      
      Regarding PTSD, a study of 155 women presenting for abortion found that the presence of PTSD symptoms had increased 61 percent at three month post-abortion evaluation.^3   Yet another study, interviewing women a few hours after their abortions and again six weeks later, reported that 38% of the women had PTSD symptomatology.^4   Another study which interviewed 217 American women seeking general health care found that 65 percent reported multiple symptoms of PTSD which they self-attributed to their abortions, with slightly over 14 percent reporting all the symptoms necessary for a clinical diagnosis of PTSD.^5
      

      In light of these other studies, Yonker's finding of some correlation between PTSD and preterm births is not surprising. But lacking any segregation of results relative to history of induced abortion, this study fails to tease out whether PTSD itself contributes to the risk of premature birth or whether PTSD is simply a marker for a history of abortion which may have contributed to physiological changes that increase the risk of preterm birth.

      The above concerns were submitted as a letter to the editor of JAMA Psychiatry but it was rejected because it "did not receive a high enough priority rating for publication."

      I also contacted the lead author, Dr. Yonkers, by email inquiring whether prior pregnancy loss information had been collected, suggesting it may have in impact on her results. In her reply she stated that the history of induced abortions and spontaneous miscarriages had been collected, but that they had chosen to not use that data in their analysis. I replied with citations to the studies listed below showing that abortion is associated with both PTSD and preterm births and urged her to conduct an additional analysis to stratify the into these four categories: (1) no reported prior pregnancy loss; (2) 1 miscarriage, 0 abortion; (3) 0 miscarriage, 1 abortion; (4)more than one reported pregnancy loss.

      Whether Dr. Yonkers bothered to take a look at what the data might show is unknown. But her response, in full was "Please stop emailing me. Abortion is safe and legal." That suggests that even if she did look at the data as I had requested, she is not going to share the results with us . . . especially if they are in agreement with the trend in the studies I have indicated.

      Unfortunately, the passions surrounding the abortion issue appear to limit how deeply some researchers are willing to look at the data. Dr. Yonkers is not unique in this regard. Other researchers have similarly rejected requests for reanalysis considering pregnancy loss history, and especially any stratification of results relative to pregnancy loss.<sup>6</sup> Given the trend already seen in the few studies that do so, there is ample reason to be concerned that many researchers are afraid that publishing results that might be seen as "criticizing" abortion may either lead to these results being exploited by "anti-choice zealots" or may expose the researcher to being accused of such zealotry. The possibility that this chilling effect is so strong that researchers will refuse to consider additional analyses when studies, like those I cited herein, clearly support the need for doing so is deeply concerning.

      If we allow the political and emotional gravitas surrounding the word "abortion" to become a barrier to simply analyzing our data from every direction, then we are choosing to give priority to ideologies rather than scientific inquiry. Analyses should be done to show what the data reveals however it is sliced. Interpretations of those results may be disputed, or tentative, or subject to reconsideration based on future research findings. But future research cannot even be defined if we refuse to publish analyses regarding the data that is already at hand.

      In my view, every study which deals with the overlap between reproductive health and mental health should show results that are stratified relative to women's exposure to both natural pregnancy losses and induced pregnancy losses. Only in this way can we begin to more clearly distinguish the roles that may be played by psychological causes, physiological states, or both.

      References

      1) Yonkers KA, Smith MV, Forray A, Epperson CN, Costello D, Lin H, Belanger K. Pregnant Women With Posttraumatic Stress Disorder and Risk of Preterm Birth. JAMA Psychiatry. 2014 Jun 11. doi: 10.1001/jamapsychiatry.2014.558.

      2) Shah PS, Zao J. Induced termination of pregnancy and low birthweight and preterm birth: a systematic review and meta-analysis. BJOG 2009;116:1425-1442.

      3) Sharain Suliman et. al., “Comparison of pain, cortisol levels, and psychological distress in women undergoing surgical termination of pregnancy under local anaesthesia versus intravenous sedation,” BMC Psychiatry 2007, 7:24.

      4) Rousset, C. Brulfert, N. Séjourné, N. Goutaudier & H. Chabrol Posttraumatic Stress Disorder and psychological distress following medical and surgical abortion. C. Journal of Reproductive and Infant Psychology, (2011) Volume 29(5), 506-517.

      5) Rue VM, Coleman PK, Rue JJ, Reardon DC. Induced abortion and traumatic stress: A preliminary comparison of American and Russian women. Med Sci Monit, 2004 10(10): SR5-16.

      6) Munk-Olsen T, Gasse C, Laursen TM. Prevalence of antidepressant use and contacts with psychiatrists and psychologists in pregnant and postpartum women. Acta Psychiatr Scand. 2011 Nov 25. doi: 10.1111/j.1600-0447.2011.01784.x.


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    1. On 2014 Jun 26, Jackie Marchington commented:

      Ghostwriting is neither common nor current

      We, the members of the Global Alliance for Publication Professionals, are concerned by the implication in Gabriel and Goldberg’s article that ghostwriting is a common and current practice in pharmaceutical industry-sponsored research reporting.

      We wholeheartedly agree that ghostwriting – undisclosed writing support, of any kind – is dishonest and unethical. We understand that the thrust of Gabriel and Goldberg’s article is not about ghostwriting, but casual references to ghostwriting in the present tense and use of anecdotal and popularised stories about its frequency are not supported by published evidence. We appreciate why Gabriel and Goldberg (and others) have the perception that ghostwriting is common, given the lack of critical analysis of early reports of ghostwriting and the traction that this perception has had in the literature, despite subsequent research that refutes it. The prevalence of ghostwriting is small (0.16%) and decreasing.[1] Indeed, the first systematic review on the prevalence of ghostwriting (Stretton S; accepted for publication in BMJ Open) documents how early estimates of ghostwriting have been poorly interpreted, incorrectly cited, and published without critical review.

      In contrast to ghostwriters, professional medical writers are transparent about their contributions, work within ethical guidelines and ensure that authors control the content at every step of the process.[2–4] In addition, articles written with professional medical writing assistance are more likely to comply with reporting standards[5,6] and are less likely to be retracted for misconduct.[7]

      The World Association of Medical Editors (WAME) Editorial Policy Committee statement quoted by Gabriel and Goldberg goes on to state that professional medical writers can be legitimate contributors to an article as long as their roles, affiliations and funding are described in the manuscript,[8] as do the recently revised International Committee of Medical Journal Editors’ (ICMJE) recommendations for the conduct, reporting, editing, and publication of scholarly work in medical journals.[9]

      Gabriel and Goldberg also mention that reform efforts in the US are underway, but make no reference to any of the steps taken internationally by the pharmaceutical industry and by publication professionals to create best practice guidelines relating to ethical and transparent publication development. [10–13] The recently published Global Publication Survey of publication professionals shows that these guidelines are routinely followed by over 90% of pharmaceutical industry, medical communications agency and contract research organization (CRO) respondents, and that acknowledgement of medical writing support by authors working with publication professionals was almost universal (96% industry, 99% agency, 100% CRO).[14]

      Gabriel and Goldberg discuss a range of activities they describe as “...dubious practices that should be significantly curtailed if not entirely eliminated”. As previously stated, we wholeheartedly agree that ghostwriting should be curtailed and eliminated, and we believe the publications we have cited demonstrate the commitment and progress of professional medical writers – not ghostwriters – towards this goal.

      Authors and affiliations Jackie Marchington PhD CMPP,a Art Gertel MS,b Cindy W. Hamilton PharmD,c Adam Jacobs PhD,d Karen L. Woolley PhD CMPPe (Global Alliance of Publication Professionals; www.gappteam.org) a. Director of Operations, Caudex Medical, UK. b. Principal Consultant, MedSciCom, LLC c. Assistant Clinical Professor, Virginia Commonwealth University School of Pharmacy; Principal, Hamilton House, USA. d. Director, Dianthus Medical Limited, UK. e. Divisional Lead. ProScribe – Envision Pharma Group; Adjunct Professor, University of the Sunshine Coast, Australia; Adjunct Professor, University of Queensland, Australia; Director, Sunshine Coast Hospital and Health Service. Disclosure: All authors declare that: 1) we have provided or do provide ethical medical writing services to academic, biotechnology, or pharmaceutical clients, 2) KW’s husband is also an employee of Proscribe – Envision Pharma Group; all other authors’ spouses, partners, or children have no financial relationships that may be relevant to the submitted work; and 3) we are active in national and international not-for-profit associations that encourage ethical medical writing practices. No external sponsors were involved in the preparation of this comment, and no external funding was used.

      References 1. Wislar JS, 2011 2. International Society for Medical Publication Professionals. Code of Ethics. Available: http://www.ismpp.org/ismpp-code-of-ethics. Accessed 14 April 2014. 3. American Medical Writers Association. AMWA Code of ethics. Available: http://www.amwa.org/amwa_ethics. Accessed 14 April 2014. 4. Jacobs A, 2005 5. Global Alliance of Publication Professionals (GAPP):., 2012 6. Jacobs A (2010) Adherence to the CONSORT guideline in papers written by professional medical writers. Med Writ 19: 196–200. 7. Woolley KL, 2011 8. WAME Editorial Policy Committee (2005) Policy Statements: #Ghost Writing. Available: <http://www.wame.org/about/policy-statements#Ghost Writing>. Accessed 23 June 2014. 9. International Committee of Medical Journal Editors. Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly work in Medical Journals. Available: http://www.icmje.org/recommendations/. Accessed 14 April 2014. 10. Wager E, 2003 11. Graf C, 2009 12. Chipperfield L, 2010 13. Clark J, 2010 14. Wager E, 2014


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    1. On 2016 Jan 27, Sergio Alonso commented:

      Very interesting article clarifying several histopathologic characteristics of FCCTX. I think there is an inconsistency between the third paragraph of results "FCCTX CRCs were more commonly poorly differentiated compared with LS/non-AC1" while the table 1 shows that FCCTX tumors are less frequently poorly differentiated (11%) than LS (22%) or non-AC1 (15%).


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    1. On 2016 Aug 24, Ben Goldacre commented:

      One of the trials in this article has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0198539. We believe the correct ID, which we have found by hand searching, is NCT01098539.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 PMID: 27056367

      * 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


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    1. On 2014 Jul 20, Johan van Schalkwyk commented:

      Within Ingelfinger’s thorough review[1] of elevated blood pressure (EBP) in adolescents and children lies a paradox that will likely increase costs and diminish putative benefits of diagnosis and treatment of EBP. If EBP is defined as a sustained increase in pressure over the 90th percentile, why should teen rates be 12.3–19%,1 and not the expected 10%?

      The answer must lie in the diagnostic criteria used. With diagnosis based on elevated levels on three or more occasions[1,2] rather than an average of all values taken on many occasions, random variation in blood pressure predisposes to spurious identification of EBP.[3] More lax criteria, as commonly used,[4] will cause higher error rates.

      Without application of consistent, appropriate diagnostic criteria, many completely normal teens will be subjected to basic laboratory tests, renal ultrasonography, left ventricular mass assessment, eye examination and other tests,[1] and even unnecessary treatment.

      [1] Ingelfinger JR. The Child or Adolescent with Elevated Blood Pressure. N Engl J Med. 2014; 370:2316-2325.

      [2] National High Blood Pressure Education Program Working Group on High Blood Pressure in Children and Adolescents. The fourth report on the diagnosis, evaluation, and treatment of high blood pressure in children and adolescents. Pediatrics 2004;114:Suppl:555-76.

      [3] van Schalkwyk JM, Turner MJ. Diagnosing hypertension in children and adolescents. JAMA. 2008;299:168.

      [4] Feber J, Ahmed M. Hypertension in children: new trends and challenges. Clin Sci (Lond) 2010;119:151-61.

      (Note: Publication of the above comment was declined by the NEJM editors)


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    1. On 2017 Sep 07, Donald Forsdyke commented:

      REFERENCE WITHDRAWN

      Reference 7 in this paper (de Oliveira MF, 2011) has been retracted by the Editors Human Neuroscience Editorial Office., 2016. The discovery of the problem was made in 2015 by Ondrej Havlicek and announced in the Neurosceptic section of Discover Magazine Here, which was reviewing one of my papers on the topic. In an End-Note (Oct 2012) to an earlier paper on my web-pages Forsdyke DR, 2009 Here, I had juxtaposed the figure of Feuillet et al. (2007) with the one from the paper of Oliviera et al. (2011). With hindsight, it is easy to see that the photographs for the patient of Feuillet et al. are reproduced in Oliviera et al., without appropriate acknowledgement.

      .<br> However, the fact that the third repetition of an observation does not withstand scrutiny, in no way implies a similar problem with the first two reports, one by Lorber, and one by Oliviera et al. (2007). While many, like myself, remain sceptical, we await further independent reports (such as that provided by Rosie Raveis in the Neurosceptic blog), and post-mortem verifications of the patients described in the first two reports.


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    1. On 2015 Jun 02, thomas samaras commented:

      Many facts challenge the thesis that taller people have an inherent advantage in relation to coronary heart disease (CHD) or cardiovascular disease (CVD). Some of these facts follow: (See references 1-3).

      1. The World Cancer Research Fund reported that during industrialization, height and CHD increased.

      2. Taller northern Europeans had a 40% higher CHD mortality vs. shorter southern Europeans.

      3. Many short populations (< 5” to 5’4”) had no evidence of CHD or stroke.

      4. US Asians had the lowest CHD death rate compared to taller ethnic groups. (Based on about 8 million deaths.)

      5. Osika and Montgomery found that among low income people, taller adults had a 39% higher risk of CHD vs. shorter adults.

      6. Based on over 1 million WW I recruits, taller recruits had more heart problems.

      7. A study found Sicilian centenarians were short and free of CVD risk factors.
        
      8. WHO reported Europeans and Americans had low CHD in the early 1900s. They were also shorter than
        today by 2 to 4 inches.
        
      9. A large Chinese study found that shorter rural Chinese had lower CHD risk compared to taller
        rural men and women.
        
      10. Great Danes have 70 times the risk of heart failure compared to shorter miniature Dachshunds.
        
      11. I have found 15 biological factors that favor shorter height and proportionately lower weight. (Assumes similar lifestyle and environment.) These include longer telomeres, lower left ventricular mass, lower blood pressure, higher HDL, lower pulse wave velocity, lower homocysteine, higher sex hormone binding globulin, and lower C-reactive protein. All of these are related to cardiovascular disease.

      Recent longevity papers also support the preceding material.See references 4-7.

      References

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

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

      3 Samaras TT (Ed): Human Body Size and the Laws of Scaling: Physiological Performance, Growth, Longevity and Ecological Ramifications. New York: Nova Science Pub; 2007.

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

      5 He Q, Morris BJ, Grove JS, Petrovitch H, Ross W, Masaki KH, et al. Shorter men live longer: Association of height with longevity and FOXO3 genotype in American men of Japanese ancestry. 2014. Plos ONE 9(5): e94385. doi:10.1371/journal.pone.0094385.

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

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


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    1. On 2014 Jun 25, Ryan Radecki commented:

      Post-publication commentary:

      "Stroke MRI in 6-Minutes or Your Money Back"

      Despite the advances of modern medicine, the non-contrast CT of the brain is a crude tool. It is especially poor in the setting of acute stroke – infrequently providing helpful diagnostic information, while serving primarily to rule out intracranial hemorrhage....

      http://www.emlitofnote.com/2014/06/a-possible-6-minute-mri-protocol.html


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    1. On 2014 Nov 21, Irina M Conboy commented:

      Thank you for the positive and constructive comment on our manuscript. We agree in general terms that it would be premature to start prescribing oxtocin to people who suffer from muscle wasting and many of your points suggested to be addressed before the clinical trials are actually being performed or are planned as near future work in our laboratory.

      1) How does the short half-life of OT (3-5 minutes) impact the utility of it being a therapeutic agent for sarcopenia? Short half-life does not signify a lack of activity particularly for hormones with physiological short life; and in animal studies once a day single injection of oxytocin sufficed for the enhanced regeneration of old muscle after less than 2 weeks of administration.

      2) Could systemic administration of OT suppress appetite and actually exacerbate muscle wasting in the elderly? There is a known problem with obesity in general and in the elderly; obesity exacerbates the lack of mobility (leading to decline in muscle health) and obesity also leads to and aggravates metabolic disorders, which in turn promote muscle wasting. Therefore, suppression of appetite by oxytocin might be actually therapeutic for obese individuals. For those who are frail or have poor appetite due to old age or disease, there should be of course, a caution in recommending oxytocin.

      3) What would their dose be when expressed as a human equivalent dose, and how does this relate to what we already know about the maximum safe dose for OT? The therapeutic safe for humans doses of oxytocin will be determined experimentally and this is in our plans. The path to this is well developed and many commercial as well as UC Berkeley services are available. The current clinical use of oxytocin facilitates the development of its use for additional therapeutic applications.

      Lastly, similar to many other basic science studies, the authors suggest that OT could impact ‘muscle strength and agility’, but have done no functional or behavioral measurements. As we, and others, have pointed out, the age-related loss of muscle strength is only partially explained by the reduction in muscle mass, as many other neural and muscular factors are involved in age-related muscle weakness (as well as motor function outcomes, such as agility). In fact, a number of papers indicate that an increase in muscle mass does not increase strength in both rodents and humans. Our ongoing work is promising in suggesting that animal strength and agility indeed rely (at least in part) on oxytocin and healthy muscle that regenerates well is obviously innervated/re-innervated better. With respect to experimentally induced increase in muscle mass, e.g. by decrease in tissue remodeling, such unbalanced non-physiological interventions would be predicted not to have sustainable functional improvement in tissue health. In contrast, restoring physiological levels of a hormone that is important for muscle tissue maintenance and declines with age is predicted to lead to successful restoration of both regeneration and function of skeletal muscle. This will be examined in the necessary pre-clinical work, which is in our plans. Of important note, in all single gene KO studies, the age and gender matched littermates provide the necessary controls; as such, premature sacropenia in oxytocin KO mice as compared to the wt littermates (established in our work) signifies that oxytocin is needed not only for muscle regeneration, but also for the maintenance of muscle mass and fiber size.


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    2. On 2014 Nov 07, Brian Clark commented:

      Oxytocin as a treatment for sarcopenia?

      ARISING FROM C. Elabd, W. Cousin, P. Upadhyayula, R.Y. Chen, M.S. Chooljian, J. Li, S. Kung, K.P. Jiang, and I.M. Conboy Nature Communications 5:4082 (2014)

      In a very elegant series of experiments Elabd et al. have introduced the intriguing possibility that oxytocin, known for its effects on the reproductive system and more recently on social behaviors, may prove to be useful in treating age-related muscle wasting (i.e., sarcopenia) through an effect on satellite cells [1]. They conclude that “oxytocin (OT) and oxytocin receptor (OTR) agonists might be potentially used as systemically applicable and sustainable molecules for combating the deterioration of muscle mass, strength and agility in the elderly”. Since OT is already approved for use by the FDA, it may be tempting for clinicians to use this conclusion to justify the use of OT in elderly patients suffering from sarcopenia. Caution, however, is needed.

      Elabd et al. show convincingly that OT administration in old mice promotes recovery from cardiotoxin-induced muscle injury through an effect on satellite cells. However, they fail to present evidence indicating that OT (or OTR agonist) administration increases muscle mass or muscle function in their older male mice or the OT-KO mice. That is, they did not perform the basic efficacy experiment for such a conclusion to provide proof-of-concept evidence to rationalize translation of this work directly to human application or trials. Additionally, there are a number of issues that must be addressed to support this translation to humans. For example, 1) How does the short half-life of OT (3-5 minutes) impact the utility of it being a therapeutic agent for sarcopenia?; 2) Could systemic administration of OT suppress appetite [2, 3] and actually exacerbate muscle wasting in the elderly?; and 3) What would their dose be when expressed as a human equivalent dose [4], and how does this relate to what we already know about the maximum safe dose for OT? Lastly, similar to many other basic science studies, the authors suggest that OT could impact ‘muscle strength and agility’, but have done no functional or behavioral measurements. As we, and others, have pointed out, the age-related loss of muscle strength is only partially explained by the reduction in muscle mass, as many other neural and muscular factors are involved in age-related muscle weakness (as well as motor function outcomes, such as agility) [5, 6]. In fact, a number of papers indicate that an increase in muscle mass does not increase strength in both rodents [7] and humans [8].

      The results of the Elabd et al. study are important because they may open a new area of research, but it is also important that our concerns are recognized in order to prevent OT, which is already approved by the FDA, from being hastily prescribed off-label in an attempt to combat muscle wasting, weakness and/or mobility disability in the elderly.


      Brian C. Clark1,2,3, David W. Russ1,4, John N. Howell1,2Anne B. Loucks1,5, Timothy D. Law1,6, Leatha A. Clark1, Kentaro Oki1, Shinichi Amano1, Niladri K. Mahato1, S. Lee Hong1,2,3, Todd M. Manini7

      1Ohio Musculoskeletal and Neurological Institute (OMNI), 2Department of Biomedical Sciences, 3Department of Geriatric Medicine, 4School of Rehabilitation and Communication Sciences, 5Department of Biological Sciences, 6Department of Family Medicine at Ohio University, Athens, OH, USA; 7Insnstitute on Aging and Department of Aging and Geriatric Research, University of Florida, Gainesville, FL, USA

      Correspondence: Brian C. Clark, Ph.D. Ohio University Ohio Musculoskeletal and Neurological Institute (OMNI), 250 Irvine Hall Athens, OH 45701 740-593-2354 (O) 740-597-2778 clarkb2@ohio.edu

      REFERENCES

      1. 1. Elabd, C., et al., Oxytocin is an age-specific circulating hormone that is necessary for muscle maintenance and regeneration. Nat Commun, 2014. 5: p. 4082.
      2. 2. Sabatier, N., G. Leng, and J. Menzies, Oxytocin, feeding, and satiety. Front Endocrinol (Lausanne), 2013. 4: p. 35.
      3. 3. Morton, G.J., et al., Peripheral oxytocin suppresses food intake and causes weight loss in diet-induced obese rats. Am J Physiol Endocrinol Metab, 2012. 302(1): p. E134-44.
      4. 4. Guidance for Industry: Estimating the Maximum Safe Starting Dose in Initial Clinical Trials for Therapeutics in Adult Healthy Volunteers, U.S.D.o.H.a.H. Services., Editor 2005, Food and Drug Adminstration. Center for Drug Evaluation and Research.: Rockville, MD. p. 1-30.
      5. 5. Clark, B.C. and T.M. Manini, Sarcopenia =/= dynapenia. J Gerontol A Biol Sci Med Sci, 2008. 63(8): p. 829-34.
      6. 6. Russ, D.W., et al., Evolving concepts on the age-related changes in "muscle quality". Journal of cachexia, sarcopenia and muscle, 2012.
      7. 7. Personius, K.E., et al., Grip force, EDL contractile properties, and voluntary wheel running after postdevelopmental myostatin depletion in mice. J Appl Physiol (1985), 2010. 109(3): p. 886-94.
      8. 8. Delmonico, M.J., et al., Longitudinal study of muscle strength, quality, and adipose tissue infiltration. Am J Clin Nutr, 2009. 90(6): p. 1579-85.


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    1. On 2016 Jan 08, Tom Kindlon commented:

      "Trial By Error, Continued: Did the PACE Trial Really Prove that Graded Exercise Is Safe?"

      By two science journalists: (i) Julie Rehmeyer is a journalist and Ted Scripps Environmental Journalism Fellow at the University of Colorado, Boulder, who has written extensively about ME/CFS and (ii) David Tuller DrPH is academic coordinator of the concurrent masters degree program in public health and journalism at the University of California, Berkeley.

      I am quoted in it.

      http://www.virology.ws/2016/01/07/trial-by-error-continued-did-the-pace-trial-really-prove-that-graded-exercise-is-safe/


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    1. On 2014 Jul 16, David Keller commented:

      Beta-asarone, derived from the herb Acorus tatarinowii Schott, has demonstrated neuro-protection against cerebral ischemia in rats (1). Now, this study raises the possibility that beta-asarone might be co-administered with levodopa to increase brain levels of dopamine by a different mechanism than benserazide or (in the U.S.) carbidopa.

      Co-administration of beta-asarone could thereby allow reduction of the dose of carbidopa/levodopa required to achieve symptom control in PD. High doses of carbidopa/levodopa are thought to deplete vitamin B6, increasing the risk of peripheral neuropathy and seizures (2,3,4,5).

      References

      1: Yang YX, Chen YT, Zhou XJ, Hong CL, Li CY, Guo JY. Beta-asarone, a major component of Acorus tatarinowii Schott, attenuates focal cerebral ischemia induced by middle cerebral artery occlusion in rats. BMC Complement Altern Med. 2013 Sep 25;13:236. doi: 10.1186/1472-6882-13-236. PubMed PMID: 24066702; PubMed Central PMCID: PMC3853232

      2: Skodda S, Müller T. Refractory epileptic seizures due to vitamin B6 deficiency in a patient with Parkinson's disease under duodopa® therapy. J Neural Transm. 2013 Feb;120(2):315-8. doi: 10.1007/s00702-012-0856-1. Epub 2012 Jul 14. PubMed PMID: 22798026.

      3: Bamford CR, Highkin DJ, Sandyk R, Travis T, Lee S, Torres F, Auerbach G. Serial epilepsy caused by levodopa/carbidopa administration in two patients on hemodialysis. Int J Neurosci. 1990 Feb;50(3-4):209-14. PubMed PMID: 2265898.

      4: Das Gupta V, Gupta A. Effect of pyridoxal 5-phosphate on carbidopa and decarboxylation of levodopa. J Pharm Sci. 1980 Oct;69(10):1145-8. PubMed PMID: 7420279.

      5: Müller T, van Laar T, Cornblath DR, Odin P, Klostermann F, Grandas FJ, Ebersbach G, Urban PP, Valldeoriola F, Antonini A. Peripheral neuropathy in Parkinson's disease: levodopa exposure and implications for duodenal delivery. Parkinsonism Relat Disord. 2013 May;19(5):501-7 ; discussion 501. doi: 10.1016/j.parkreldis.2013.02.006. Epub 2013 Feb 27. Review. PubMed PMID: 23453891.


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    1. On 2014 Oct 02, Morgan Price commented:

      The authors predict that 36% of bacteria cannot synthesize phenylalanine, but many (most?) of these predictions are erroneous. I looked over the predictions, which were graciously provided by Dr. Kost, and noticed the following errors. First, many cyanobacteria are predicted auxotrophs (i.e., Synechococcus elongatus PCC 6301, and members of the genera Prochlorococcus, Anabaena, Cyanothece, Nostoc, and Gloeobacter) . However cyanobacteria are normally grown in a mineral medium with no organic carbon. Second, our group studies the sulfate-reducing bacteria Desulfovibrio alaskensis G20 and D. vulgaris Miyazaki F, which grow in a defined minimal medium without any amino acids, yet these are predicted to be phenylalanine auxotrophs. Third, Caulobacter crescentus CB15 is predicted to be a phenylalanine auxotroph, but it can grow at very low nutrient levels, including in defined mineral media with a small amount of sugar added.


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    1. On 2015 May 29, David Reardon commented:

      In previous studies of the intersection of reproductive health and mental health, Munk-Olsen's team has failed to control for the impact of prior pregnancy losses (miscarriage and induced abortion). See for example Munk-Olsen T, 2012, Munk-Olsen T, 2012, Munk-Olsen T, 2011 and my comments on each entry with requests for additional analyses to address these oversights . . . all of which have been refused.

      In this case, once again, Munk-Olsen's examination of psychiatric disorders following fetal death is flawed by her decision to disclose the effects of induced abortions on the analyses. She reports that IRR were adjusted for "age, calendar period, parity status, induced abortion status and family history of formerly treated psychiatric disorders" but she chose not to report on how each of these factors contributed to psychiatric illness. This appears to be selective reporting to avoid publication of data that contradicts her previous claims that abortion does not contribute to mental health problems.

      Numerous other researchers, in many countries using many different methodologies, have found that both natural miscarriage and induced abortion have distinct effects on subsequent mental health, especially during and after subsequent pregnancies. Below is a list of such studies.

      I once again ask Munk-Olsen to address these oversights by publishing analyses which compare outcomes relative to the full reproductive history of women, including segregated results showing the outcome relative to no prior pregnancy loss, one or more miscarriages, one or more induced abortions, and for women with a history of at least one induced abortion and one miscarriage.

      See for example:

      • Giannandrea SA, 2013 Increased risk for postpartum psychiatric disorders among women with past pregnancy loss. Giannandrea SA, Cerulli C, Anson E, Chaudron LH. J Womens Health (Larchmt). 2013 Sep;22(9):760-8. doi: 10.1089/jwh.2012.4011.

      • Gong X, 2013 Pregnancy loss and anxiety and depression during subsequent pregnancies: data from the C-ABC study. Eur J Obstet Gynecol Reprod Biol. 2013 Jan;166(1):30-6. doi: 10.1016/j.ejogrb.2012.09.024. Epub 2012 Nov 10.Source School of Public Health, Anhui Medical University, Hefei, Anhui, China.

      • Coleman PK, 2002 History of induced abortion in relation to substance abuse during subsequent pregnancies carried to term. Am J Obstet Gynecol 187: 1673-1678, 2002.

      • Coleman PK, 2005 Substance use among pregnant women in the context of previous reproductive loss and desire for current pregnancy. Br J Health Psychol 2005; 10: 255–68.

      • Reardon DC, 2003 Psychiatric admissions of low income women following abortion and childbirth. Can Med Assoc J. 2003; 168(10):1253-7

      • Coleman PK, 2002 State-funded abortions vs. deliveries: A comparison of outpatient mental health claims over five years. American Journal of Orthopsychiatry, 2002; 72(1):141–52.

      • H David et al, "Postabortion or Postpartum Psychotic Reactions," Family Planning Perspectives 13(2): 892, 1981

      • Ronald Somers, "Risk of Admission to Psychiatric Institutions among Danish Women Who Experienced Induced Abortion: An Analysis Based on A National Record Linkage," Dissertation Abstracts Int'l, Public Health 2621-B, 1979.


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    1. On 2014 Sep 05, M Felix Freshwater commented:

      This study has a few unanswered questions concerning the relevant variables obesity and ADM. Obesity was not defined. Was BMI recorded and some cutoff used or was there some other definition. If so, did the authors find a cutoff for BMI? The study intimates that ADM was used after 2005. No data are provided for complications as a function of time. Perhaps ADM is a proxy for this and rather than there being a protective effect from ADM, the "benefit" was in fact the learning curve that the group experienced? I hope the authors can provide answers.


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    1. On 2014 Jul 28, Amanda Capes-Davis commented:

      The title says that this work looks at laryngeal carcinoma. Unfortunately the cell line used, HEp-2, is not a laryngeal carcinoma cell line. HEp-2 is cross-contaminated with HeLa and is actually cervical adenocarcinoma. For a database of known cross-contaminated cell lines, please see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Jun 08, Christopher Southan commented:

      Given the commercial availabilty of at least some close anologues of Triptofordin B1 https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5322125 it seems odd that neither the editor nor the referees for this paper recomended the relatively simple step of experimental verification of predicted inhibitory activity, without which this modeling study is largely meaningless


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    1. On 2014 Oct 15, Amanda Capes-Davis commented:

      The suggestion here that Tan IIA might be an anticancer agent for oral cancer relies on a single cell line - KB. Unfortunately, KB has been shown to be cross-contaminated by HeLa and so is a misidentified cell line. KB cells are actually from cervical cancer, not oral cancer.

      For a list of known misidentified cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Jun 06, Gwinyai Masukume commented:

      In this review article on pregnancy and infection, highlighting infections which can be more severe during the pregnant compared to the non-pregnant state, genital warts caused by human papilloma virus are omitted.

      It is known that genital warts in general worsen during pregnancy Ghaemmaghami F, 2007. In addition, genital warts have a high economic and humanistic cost Raymakers AJ, 2012. Their previous article on the same topic Sappenfield E, 2013 also omits human papilloma virus associated conditions.


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    1. On 2016 Jun 03, David C. Norris commented:

      The ‘spam’ clinical messaging applications advanced by Schneeweiss will be Medicine’s just deserts for adopting “analytic approaches that embrace the data turmoil”<sup>1</sup> of a routine clinical practice which eschews scientific method. Only scientific practice, capturing in computable form exquisite clinical observation together with detailed clinical reasoning, holds the promise of individualized care within a true learning system.<sup>2</sup> Whatever obstacles Medicine presents to scientific reform, equally fearsome technical and social-engineering problems bedevil ‘big data’.

      These problems arise from Judea Pearl’s “golden rule of causal analysis: No causal claim can be established by a purely statistical method, be it propensity scores, regression, stratification, or any other distribution-based design.”<sup>3(p350)</sup> Sound causal inference in non-experimental settings apparently requires graphical methods to support correct reasoning about confounding.<sup>4</sup> When deconfounding variables are missing—surely typical wherever inference relies on ‘big data’ scavenged from the waste bins of routine clinical practice—then quantitative bias analysis<sup>5</sup> becomes essential for credibly evaluating the uncertainty engendered by residual confounding. Would the software automation Schneeweiss envisions be grounded in such methods? If so, will “users with little training”<sup>1</sup> adopt methods at which most professionals balk?

      [1] Schneeweiss S, 2014

      [2] Weed LL, Weed L. Medicine in Denial. Charleston, SC: CreateSpace; 2011.

      [3] Pearl, J. Causality: Models, Reasoning and Inference. 2nd edition. New York: Cambridge University Press, 2009.

      [4] Howards PP, 2012

      [5] Greenland, S. Multiple-Bias Modelling for Analysis of Observational Data (with Discussion). Journal of the Royal Statistical Society: Series A (Statistics in Society) 168, no. 2 (March 2005): 267–306.


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    1. On 2015 Feb 27, Geriatric Medicine Journal Club commented:

      This systematic review and meta-analysis of pre-operative indicators for mortality following hip fracture surgery was discussed at the December 2014 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full transcript of the discussion can be found here: http://gerimedjc.blogspot.com/2014/12/gerimedjc-december-19-2014.html?spref=tw The question of whether this article changes management was raised.


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    1. On 2017 Jun 25, Thomas Heston commented:

      This study performs a meta-analysis in the right way, by following the recommendations from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement. Computer aided diagnosis has been used for many years in radiology prior to the advent of computerized provider order entry incorporation in electronic medical records. Computer aided diagnosis in radiology has consistently been shown to increase diagnostic accuracy and consistency. Computerized provider order entry (CPOE) takes computer assistance beyond diagnosis, and into therapy. The next step for CPOE beyond assistance in medication prescribing, is applying CPOE to order sets. This is commonly done as of 2017. For example, a sepsis protocol order set in the CPOE may generate a dozen or so physician orders. These order sets can decrease further errors that occur when hand writing out orders. The order sets can also decrease errors that occur when the provider has to selecting orders individually from the electronic medical record. What is critically important now is to extend computer aided diagnosis beyond medical imaging into clinical areas. For example, a computerized progam, acting as a digital doctor, could continually survey a hospital's entire electronic medical record database of active patients. This computer program would look at lab results, vital signs, and additional quantitative objective data. These digital doctor programs could then quickly and perhaps more accurately identify significant medical conditions. When a clear diagnosis is identified, the digitial doctor could even initiate order sets automatically. Such a system of computer aided diagnosis in clinical medicine would not only decrease morbidity and mortality, but also decrease healthcare costs. Having common computerized terminology for the variables would allow implementation via a blockchain that would increase interoperability and widespread distribution of these smart applications running on top of electronic medical record systems.


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    1. On 2015 Nov 12, Lydia Maniatis commented:

      This article confirms that lightness within a subregion of a visual image is roughly based on a ratio rule comparing a target surface luminance with the luminances of surrounding surfaces. It exploits previous researchers' insights on transparency to apply, post hoc, a manipulation that gives a reasonable fit to their data. There is nothing new here.

      In addition to data-fitting based on previously known principles, the authors go through the motions of comparing different models of lightness; but this is only pro forma, since, as they explain, they really had no idea how to apply these alternative (and very incomplete) “models:” “Again, an interpretation of the predictions based on anchoring and edge integration theory is difficult because we simply utilized numerical parameters that were derived with very different experimental stimuli.” (A third model was completely unrealistic). Why bother with these pseudo-comparisons if model application is crude and results uninterpretable?

      The authors also make a confession: “The important piece of information that is still missing, and which we secretly inserted, was the knowledge about regions of different contrast range. Here we simply used the values that we knew to originate from the checks within the regions corresponding to plain view, shadow, or transparent media, but for a model to be applicable to any image this segmentation step still needs to be elucidated.”

      It is an amazing fact that contemporary lightness researchers are happily going about their business, ignoring the key factor mediating lightness perception, i.e. the factor of shape. The principles guiding the segmentation of the field into regions of figure and ground – whether that figure is opaque, transparent, shadowy, cloudy, etc – have been largely elucidated. Yet, these researchers prefer either “sneak it in” or to use stimuli (like checkerboards) in which it can be ignored (but not really – see discussion on Radonjic and Gilchrist( 2014)). To the extent that understanding of perceptual organisation is incomplete, it will limit progress in lightness – the problem it cannot be circumvented by ignoring structure.

      Unfortunately, the authors don't seem to appreciate this: “It remains a task for future experiments to put the normalized contrast computation under scrutiny by systematically manipulating the contrast range in different regions of illumination and testing the effects of varying the luminance (image) or the reflectance contrast (real world surfaces).” You can manipulate the “contrast range” and “reflectance contrast” ad infinitum, but if you don't explicitly take structure into account – if you keep having to “sneak it in” to fit each individual stimulus, you will get nowhere.

      Like other lightness/color researchers (e.g. Radonjic, Cottaris, Brainard (2015); see comments) Maertens and Zeiner (2014) use very vague descriptors for their stimuli: “relatively naturalistic;” “stimuli of moderate photometric and geometric complexity;” “a relatively naturalistic luminance range.” The possible stimulus characteristics to which such terms could apply are infinite, and thus they are uninformative and cannot constitute the premises of a serious experimental study. The questions and the methods of a study are closely linked; if the method is vague and ambiguous, so is the question; and if the question is vague and ambiguous, so are the conclusions bound to be. Perception research was not always like this, and doesn't need to be.

      (Needless to say, the technobabble is not worth bothering with).


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    1. On 2014 Jun 18, Ryan Radecki commented:

      Post-publication commentary:

      "Conclusively Settling Azithromycin’s Cardiac Toxicity Forever"

      We’ve been obsessed with azithromycin’s cardiovascular effects for quite some time – with some studies showing an increase in events, and other studies using azithromycin as the active agent to decrease coronary events. Why is it such an issue? Mostly because azithromycin has become the nonsensical cure-all of eager-to-please primary care physicians for self-limited or viral conditions, let alone the mainstay of treatment for pneumonia....

      http://www.emlitofnote.com/2014/06/conclusively-settling-azithromycins_11.html


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    1. On 2014 Jun 23, James Lane commented:

      James makes an interesting and important point in this article, that withdrawal relief must be considered when assessing the effects of common drugs in habitual users by means of a placebo-control comparison condition. He raises this issue about caffeine research, but it is important as well for studies of nicotine effects in smokers and research into the chronic effects of other drugs in habitual users. More attention should be paid to this problem.


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    1. On 2015 Oct 10, Peter Good commented:

      Baron-Cohen and colleagues here present “the first direct evidence of elevated fetal steroidogenic activity in autism” – primarily elevated androgenic hormones of the Δ4 pathway androstenedione and testosterone. They propose that high fetal testosterone explains the “extreme male brain” of autism [Baron-Cohen S, 2005] – why these children appear to be extreme versions of normal male intelligence, as Asperger noted many years ago [Frith 1991].

      But high fetal testosterone does NOT readily explain why autistic children are often anxious, even timid, in the presence of others. Markram and colleagues pointed out that Kanner (1943) observed abnormal anxiety and phobias in these children, as other researchers have since [Markram K, 2010]. Melvin Konner noted that early pioneers of autism research Niko and Elisabeth Tinbergen detected signs of fear in these children in social situations, and “reasoned that exceptionally timid children might be at risk for developing the disorder if they grew up in a sufficiently threatening – or perhaps for them, merely a very intrusive – social environment.”[Konner 1982] Since testesterone allays fear [Konner], why are autistic children timid?

      One explanation may be androstenedione, which the present study also found at higher than normal levels in amniotic fluid of these children. Androstenedione is a weak androgen precursor of testosterone, estrone, and estradiol, the primary estrogen. However, Taylor and colleagues concluded that its effects on rat sexual behavior reveal that androstenedione leaves “behavioral footprints” different from testosterone [Taylor GT, 2012]. Jacklin and colleagues assessed timidity in infants by their reaction to fear-provoking toys. Low timidity in boys was associated with higher levels of testosterone at birth – but not androstenedione [Jacklin CN, 1983]. Ward pointed out prenatal stress “causes an increase in the weak adrenal androgen, androstenedione, from the maternal or fetal adrenal cortices, or from both, and a concurrent decrease in the potent gonadal androgen, testosterone.”[Ward IL, 1972] This happens because release of androstenedione and testosterone from the testes is triggered by luteinizing hormone (LH) from the pituitary; high adrenal androstenedione suppresses LH release by negative feedback.” Do high levels of androstenedione differentiate the brain of a male fetus BEFORE they turn to testosterone and estrogen?

      A second challenge to high prenatal testosterone is the certainty the brain overgrowth of autism happens after birth, not before. Courchesne and colleagues found that children with autism have smaller heads at birth, then a sudden excessive increase in head size beginning a few months after birth and lasting six to 14 months: “[O]ur study found evidence of neonatal brain undergrowth followed by rapid and excessive postnatal brain growth beginning in the first few months that precedes the clinical behavioral onset of autism.”[Courchesne E, 2003] This sounds like postnatal catch-up growth in infants born prematurely or whose fetal head growth was restrained for any reason [Cockerill J, 2006]. Or was it due to the usual postnatal testosterone surge in male infants within a few months of birth [Swaab DF, 2007]? Courchesne et al. didn’t mention the surge; some of the infants they studied were girls.

      Herbert reviewed the pathology of these large brains in ASD: disproportionate proliferation of white matter, yet diminished connectivity, and neuroinflammation and astrogliosis [Herbert MR, 2005]. She and her colleagues previously found the increased brain volume was confined to the subcortical white matter, especially in the frontal lobes, and did not include the deep white matter, e.g. corpus callosum: “This lack of expected association between radiate compartment and corpus callosum volume suggests that the white matter volume increase predominantly involves short and medium-range corticocortical connections within hemispheres, with less, if any, involvement of connections between hemispheres.” [Herbert MR, 2004] Intrahemispheric white-matter tracts are testosterone-dependent; interhemispheric white-matter tracts estrogen-dependent [Baron-Cohen S, 2005]. If postnatal brain overgrowth in ASD is catch-up growth, overgrowth of testosterone-dependent structures implies prenatal undergrowth of the structures. Yet insufficient estradiol might also explain smaller brains at birth. But then why doesn’t postnatal brain overgrowth favor estrogen-dependent structures?

      These arguments have also been posted online in my paper Chronic neurochemical cerebral asymmetry and dysconnection in autism. Implications of a personal trial of oral citrulline + taurine at: http://www.autismstudies.net

      references

      Baron-Cohen S, Knickmeyer RC, Belmonte MK. Sex differences in the brain: implications for explaining autism. Science 2005;310: 819–823.

      Cockerill J, Uthaya S, Doré CJ, Modi N. Accelerated postnatal head growth follows preterm birth. Arch Dis Child Fetal Neonatal Ed 2006;91:F184–F187.

      Courchesne E, Carper R, Akshoomoff N. Evidence of brain overgrowth in the first year of life in autism. JAMA 2003;290(3):337–344.

      Frith U. Autism and Asperger Syndrome. Cambridge, England: Cambridge University Press; 1991.

      Herbert MR, Ziegler DA, Makris N, Filipek PA. Kemper TL. Localization of white matter volume increase in autism and developmental language disorder. Ann Neurol 2004;55:530–540.

      Herbert MR. Large brains in autism: the challenge of pervasive abnormality. Neuroscientist 2005;11:417–440.

      Jacklin CN, Maccoby EE, Doering CH. Neonatal sex-steroid hormones and timidity in 6-to-18-month-old boys and girls. Dev Psychobiol 1983;16:163–168.

      Konner M. The Tangled Wing. Biological Constraints on the Human Spirit. New York: Holt, Rinehart and Winston; 1982.

      Markram K, Markram H. The intense world theory – a unifying theory of the neurobiology of autism. Front Hum Neurosci 2010;4:224.

      Swaab DF. Sexual differentiation of the brain and behavior. Best Pract Res Clin Endocrinol Metab 2007;21:431–444.

      Taylor GT, Dearborn JT, Maloney SE. Adrenal steroids uniquely influence sexual motivation behavior in male rats. Behav Sci 2012;2:195–206.

      Ward IL. Prenatal stress feminizes and demasculinizes the behavior of males. Science 1972;175:82–84.


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    1. On 2014 Jun 03, David Keller commented:

      Two large, well-designed randomized trials agree: Multivitamins reduce cancer risk in men

      Guallar and colleagues dismiss the clinical trial data demonstrating that multivitamin and mineral supplements (MVM’s) reduce cancer risk in men, stating: “ Because the observed possible benefits were limited to men, were modest (as in PHS II), or were evident only in subgroup analyses (as in the SU.VI.MAX study) and did not consistently extend to reductions in mortality, these findings are only weak signals compatible with small or no benefit.” (1)

      I will challenge each clause of their compound statement separately, but first, for the record, I quote the abstract of the Su.Vi.Max study (2):

      "However, a significant interaction between sex and group effects on cancer incidence was found (P = .004). Sex-stratified analysis showed a protective effect of antioxidants in men (relative risk, 0.69 [95% confidence interval {CI}, 0.53-0.91]) but not in women (relative risk, 1.04 [95% CI, 0.85-1.29]). A similar trend was observed for all-cause mortality (relative risk, 0.63 [95% CI, 0.42-0.93] in men vs 1.03 [95% CI, 0.64-1.63] in women; P = .11 for interaction)."

      Simply stated: Men who took multivitamins had significantly fewer cancers and a lower overall death rate than men who did not. These were not small effects: the cancer rate for men was reduced by 31% and the overall death rate by 37%.

      First, let us discuss the fact that these benefits “were evident only in subgroup analyses”. Multiple post-hoc subgroup analyses are frowned on because they can be used to dredge the data for statistical flukes, such as finding that the tested intervention benefits only persons born under a certain astrological sign, or some other biologically implausible subgroup. The criteria for an acceptable subgroup analysis are: the subgroup should be rational, predefined in the experimental protocol, based on pre-randomization patient characteristics, large enough to retain statistical power, one of only a small number of such analyses, and the subgroup effect should be evident in other studies (3,4). The Su.vi.max subgroup analysis met these requirements; it was conducted on men, a large, natural subgroup which derived benefits in another study and was pre-specified in the study protocol. This rigorous analysis for the male subgroup yielded unambiguous results, the integrity of which withstands methodological scrutiny.

      Guallar and colleagues also cast doubt on the data because the benefits of MVM’s were limited to men. The Su.vi.max investigators explained this by noting that women generally have better nutritional status than men; they are both more likely to eat fruits and vegetables, and also more likely to take MVM’s at baseline. Women, with good baseline nutrition, have less to gain by taking MVM’s and therefore exhibit no benefit in these studies.

      There are many differences between men and women, both biological and cultural, which result, for one thing, in the fact that women outlive men by several years on average. The Su.vi.max and PHS-II study results indicate that relative dietary deficiencies of micro-nutrients may help explain the premature mortality of the male half of the population, as compared with the female.

      As I pointed out in another comment (5), the five antioxidants included in the Su.vi.max supplement were a subset of the 30 nutrients in Centrum Silver, but at significantly higher doses. Thus, there was a dose-response effect evident for these antioxidants, with the PHS-II men who took MVM’s displaying a small but significant reduction in cancer rates, and the Su.vi.max men exhibiting a larger reduction in cancer rates, plus a decrease in all-cause mortality, consistent with the higher nutrient levels in the Su.vi.max supplement. The dose-response effect explains why the men in Su.vi.max had lower cancer rates compared with the men in PHS-II, and a significant reduction in overall mortality: they were taking higher doses of the beneficial micronutrients. Guallar’s complaint that the reduction in mortality was “not consistent” is thus refuted.

      The USPSTF update again gave MVM supplements a grade of “I” (insufficient evidence to make a recommendation for the general population) for cancer prevention. However, NIH regulations mandate that clinical studies be analyzed separately for men and women when the response to an intervention differs by sex (6). Given the quality of the data supporting MVM use for men, USPSTF should change their rating of MVM supplements to at least a “C” level recommendation for men - meaning that men should discuss MVM supplements with their doctors in the context of their individual diet quality and nutritional status.

      Unless they are consuming a diet rich in fruits and vegetables, men should consider adding a standard multivitamin & mineral supplement to reduce their risk of cancer, according to the best available evidence from two large, prospective randomized trials.

      References:

      1: Guallar E. Enough Is Enough, Annals of Int Med. June 3 2014; Vol 160, No. 9

      2: Hercberg S, Galan P, Preziosi P, Bertrais S, Mennen L, Malvy D, et al. The SU.VI.MAX Study: a randomized, placebo-controlled trial of the health effects of antioxidant vitamins and minerals. Arch Intern Med. 2004; 164:2335-42.

      3: Wittes J. On Looking at Subgroups. Circulation.2009; 119: 912-915 doi: 10.1161/CIRCULATIONAHA.108.836601

      4: Dijkman B, et al. How to work with a subgroup analysis. Can J Surg. Dec 2009; 52(6): 515–522. PMCID: PMC2792383

      5: Keller DL. Open letter to the USPSTF: the evidence shows multivitamins reduce cancers in men, PubMed Commons, accessed on 6/3/2014 http://www.ncbi.nlm.nih.gov/pubmed/24566474#cm24566474_4093

      6: NIH website, accessed on 6/29/2014 http://grants.nih.gov/grants/funding/women_min/guidelines_update.htm


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    1. On 2014 Jun 20, Erik Hess commented:

      Thank you for these insightful comments. This is Dr. Erik Hess, the PI on this multicenter trial. What is not necessarily intuitive and may not be immediately apparent to the reader is the how the process of decision aid development determines the content selected for inclusion. The main factor that determines what information is included in the decision aid is how the information facilitates a conversation between the clinician and the patient and what information the end-users find relevant to the decision at hand (not what insights seem to make good theoretical sense outside the context of the clinical encounter). In the process of decision aid development we used prototypes of the tool in real ED encounters and, with each use, elicited feedback from both the clinician and the patient regarding the clarity, usefulness, and relevance of the information to the discussion and whether the decision aid was a distractor (brought undue focus on itself) or facilitated a conversation. In one of the earlier iterations of the tool (there were over 15 iterations) the patient and stakeholder advisory group did make a similar comment -- that more information comparing the test characteristics, degree of radiation exposure, and cost of each of the diagnostic modalities and the risks and benefits of the follow-up options might be helpful. However, when we included this information on the DA and tested it in clinical encounters we were told by the clinicians and patients who used it in practice that the information was not needed for decision making, brought undue focus on the decision aid itself rather than promoting a conversation, and was confusing (information overload when used in real time). Note that as a compromise a reference to the different stress testing modalities and some of their key differences are referred to as a footnote on the bottom left of the decision aid but we reduced the amount of information, chose a smaller font, and put the information in a footnote so as to not distract from the conversation. In addition, though the test characteristics between CTA and the various stress testing modalities differ, there is no difference in the relative risk of MI between each of these modalities, as they are diagnostic modalities, not treatments. At best, they further refine prognosis but do not change it.

      See the responses and related blog conversation at http://www.emlitofnote.com/2014/06/a-shared-decision-making-trial-but.html


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    2. On 2014 Jun 18, Ryan Radecki commented:

      Post-publication critique:

      A Shared Decision-Making Trial … But Fatally Flawed?

      Shared decision-making is developing as the proposed solution to many of the problems with resource utilization today. Rather than embrace “zero miss” practice without properly involving patients as the decision-makers, we are now encouraged to offer the patient choices regarding their diagnostic and treatment decisions. By sharing the decision – and the risk – I find patients quite amenable to forgoing much low-yield testing....

      http://www.emlitofnote.com/2014/06/a-shared-decision-making-trial-but.html


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    1. On 2014 Jun 05, Alexis Verger commented:

      Would like to point to a related study by the Gang Cai's lab http://www.ncbi.nlm.nih.gov/pubmed/24810298 and a blog post I wrote about these 2 important papers that completly revisit the Mediator complex architecture - http://aninfinityofhypotheses.wordpress.com/2014/06/03/the-topsy-turvy-mediator-complex/


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    1. On 2014 Jun 28, M Felix Freshwater commented:

      This "clarification" discloses a heretofore undisclosed fact. The authors now claim: "We then asked the patients whether they preferred a medical drug treatment that could decrease the libido and cause liver problems or whether they preferred to eliminate from their diet products that contained yeast, such as bread, beer, pizza, etc. The patients preferred the diet. We assert that a proposed diet does not require informed consent." The original paper made no mention of this choice. Did the authors ignore the facts that they were doing a clinical trial comparing treatment A and B, which required ethics approval or, despite their assertion that this was a prospective study, perhaps it was not. Unless the authors respond, readers will have to reach their own conclusions.


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    1. On 2014 Nov 17, Raphael Levy commented:

      Jackson et al 2004 Jackson AM, 2004 observed that the same particles (MPA/OT) "avoid non-specific adsorption of proteins [...] because of the unique subnanometre-ordered repetition of hydrophobic and hydrophilic regions on the particles' ligand shell." No data were shown, but this scheme was provided: http://www.nature.com/nmat/journal/v3/n5/fig_tab/nmat1116_F5.html

      It would be nice if the apparent discrepancy between Jackson et al and Huang et al were discussed?

      More broadly, the article belongs to the “stripy nanoparticles” series. The evidence behind the structure and special properties of these nanoparticles has been challenged by Cesbron Y, 2012. The publication in 2012 of Cesbron Y, 2012 took three years and has been followed by post-publication peer review of the various existing and new stripy articles on my blog, PubPeer, etc.

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


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    1. On 2014 Jun 06, Amanda Capes-Davis commented:

      The authors note that HSG cells are a standard reference cell line from human salivary gland. Please be aware that HSG is known to be cross-contaminated with HeLa (cervical carcinoma). It is possible that some authentic stocks exist; authentication testing using short tandem repeat (STR) profiling will allow the authors to compare their stocks to others held at Biological Resource Centers worldwide. For a database of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Jul 07, Ryan Radecki commented:

      Post-publication commentary:

      "How Much Money Is Wasted By Endovascular Treatment for Stroke?"

      If you recall, last year was a bumper crop of prospective, randomized, controlled trials testing the efficacy of endovascular devices versus tPA alone for acute ischemic stroke. These trials – SYNTHESIS, MR-RESCUE, and IMS-III – were unified by demonstrating no additive benefit. Of course, these trials proved nothing to proponents of endovascular therapy, owing to the “outdated” devices used....

      http://www.emlitofnote.com/2014/07/how-much-money-is-wasted-by.html


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    1. On 2014 Jun 05, Bruce Hope commented:

      I expect that different afferents carry different types of information to the accumbens shell. Some brain areas can carry concrete information that does not vary too much between the two environmental contexts used in the above experiments (e.g., many physical attributes are relatively similar), so you might expect similar ensembles to be activated in these brain areas. Meanwhile other brain areas such as vmPFC may carry the more abstract 'meaning' of the context, which is not as dependent on the overall similarity of the concrete physical attributes but important for deciding to lever press, so you might expect very different ensembles to be activated in these brain areas. Overall its an empirical question and based on the literature, the hippocampus would be an interesting place to use Daun02 in the context-induced reinstatement model.


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    1. On 2014 Jul 30, Christopher Southan commented:

      As was pointed out in http://www.ncbi.nlm.nih.gov/pubmed/15174140 it is incumbent on those proposing novel/alternative ORFs, on whatever evidence basis, to try to collaboratively progress these into "mainstream" protein entries (i.e. as fully expert annoted RefSeq and Swiss-Prot entries). As hitherto, this requires at least the submission of independantly sequenced transcripts with a CDS to the INSDC. UniProt can also then hook-in corroborative MS data via PRIDE (but promotion to Swiss-Prot may require a supporting PubMed citation). As XR points out, bringing verified AltORFs from data limbo land into the cannonical protein fold may need adaptions and expansions to the RefSeq and UniProt criteria (e.g. inclusion of specific antibody data, mass-spec SRM, the promotion of TPA entries ect. See relevant comments at http://cdsouthan.blogspot.se/2011/06/so-is-it-or-isnt-it-protein.html


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    2. On 2014 Jul 15, Xavier Roucou commented:

      Among several significant contributions in this work, the discovery of 44 novel protein-coding open reading frames (ORFs) illustrates the complexity of the human proteome. Recently, we reported the discovery of 83,886 previously undescribed ORFs termed alternative ORFs (AltORFs) Vanderperre B, 2013. AltORFs are defined as ORFs present in the transcriptome that are different from annotated ORFs. We detected 1,259 proteins translated from AltORFs in human biological samples Vanderperre B, 2013. While the role and importance of this “alternative proteome” will require substantial further validation, there can be no doubt that a comprehensive description of the human proteome must include the distinct possibility of a vastly greater number of functional proteins than has been traditionally considered. Given the existence of the alternative proteome, it is not surprising that Kim et al. found that nearly 50% of the 35 million MS/MS spectra of human proteins did not match proteins in the NCBI’s RefSeq human protein sequence database. In an attempt to identify these novel proteins, the authors translated the human reference genome, RefSeq transcript sequences, non-coding RNAs, and pseudogenes. Among the 193 newly identified proteins, 44 were translated from novel uORFs, ORFs located in an alternate reading frame within coding regions of annotated genes, or ORFs located in 3’-UTRs. The astonishing failure to have detected the alternative proteome years ago results from the fact that MS-based proteomic methods rely on existing protein sequence databases that are far from complete and therefore do not allow the assignment of all MS/MS spectra. Recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals Ingolia NT, 2011 Lee S, 2012 Michel AM, 2012, and these alternative proteins should have been detected. In order to better define the human proteome, we generated a new database of alternative ORFs (AltORFs) present in NCBI’s RefSeq human mRNA sequence database. AltORFs overlap the annotated or reference protein coding ORF (RefORF) in an alternate reading frame, are located in the 5′- and 3′-UTR regions of an mRNA, or partially overlap with both the RefORF and an UTR region. This approach led to the discovery of 83,886 unique AltORFs with a minimum size of 40 codons Vanderperre B, 2013. The majority of mRNAs (87%) have at least one predicted AltORF, with an average of 3.88 AltORFs per mRNA. Additionally, the evolutionary conservation of many of these reading frames suggests functional importance. These AltORFs were translated in silico and included in an alternative protein database we used to interpret unmatched MS/MS spectra. So far, we and others have identified nearly 1300 alternative proteins in different human cell lines and tissues Vanderperre B, 2013, Klemke M, 2001 Oyama M, 2004 Vanderperre B, 2011 Bergeron D, 2013 Slavoff SA, 2013 Menschaert G, 2013, including certain of the 44 new proteins mentioned in the Kim et al. study: the alternative protein translated from the AltORFs mapping to the 5’-UTR of the SLC35A4 gene (or AltSLC35A4), was detected in Hela cells and lung tissue; the AltC11orf48 was detected in Hela cells, colon, lung and ovary tissues; and the AltCHTF8 was detected in Hela cells Vanderperre B, 2013. Twenty four of the 44 novel ORFs detected by Kim et al. were, in fact, already present in our AltORF database, and 9 of the 44 proteins translated from these novel ORFs were previously detected: AltASNSD1, AltSLC35A4, AltMKKS, AltSMCR7L, AltCHTF8, AltRPP14, AltSF1, AltC110rf48, AltHNRNPUL12. In this sense, Kim et al.`s study strongly supports the existence of the alternative proteome. Clearly, the alternative proteins detected by Kim et al. and by our team are the proverbial tip of the iceberg. A full map of the human proteome is thus still years away, and will require several important changes in our current thinking concerning the proteome and the concept that each mature mRNA only codes for one protein.


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    3. On 2014 Jun 22, Pavel Baranov commented:

      This is a wonderful work and the resource is very useful. Regrettably references to a "novel" protein coding transcript in C11ORF48 locus are missing. Its protein coding properties were identified with ribosome profiling and analyzed using phylogenetic approaches, see Michel AM, 2012. The corresponding N-terminal peptide was detected with mass spectrometry even earlier, see Oyama M, 2007.


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    1. On 2014 Jun 18, Ryan Radecki commented:

      Post-publication commentary:

      "SIRS is Rarely Sepsis"

      You already knew this – but that hasn’t stopped your hospital from purchasing the “Sepsis Alert” tool for your electronic health record. Now, you and your nurses get blasted with computerized interruptions every time a patient is tachycardic and has an elevated WBC count. And, you ignore it – because it’s 1) wrong, or 2) you placed a central line and admitted the patient to the ICU half an hour ago....

      http://www.emlitofnote.com/2014/06/sirs-is-rarely-sepsis.html


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    1. On 2014 Jun 02, Gaetano Santulli commented:

      In this article, Ribeiro and colleagues report that β2-adrenergic receptor (β2AR) knockout (KO) mice exhibit altered glucose homeostasis (1). Albeit surprisingly not reported by the Authors, the notion that deletion of the β2AR has profound effects on glucose metabolism is a consolidated acquisition. Indeed, we recently demonstrated that the deletion of β2AR impairs insulin release ultimately leading to glucose intolerance (2). Previously, Muzzin and colleagues had found that the lack of βARs associates with glucose intolerance (3). Findings from several groups support such a molecular mechanism (4-6). Equally important, in the clinical scenario, a mechanistic role for β2AR in the regulation of insulin secretion had been also suggested by the evidence of a decreased number of β2AR in type I diabetes mellitus patients (7-9). Nevertheless, the Authors fail to discuss previous relevant literature describing the alterations in glucose metabolism observed in β2AR KO mice and do not accurately circumstantiate their findings. In fact, they state that “available animal models indicate only a minor metabolic role” for β2AR. Moreover, despite insulin signaling has been shown to play a key role in the regulation of thermogenesis, as recently verified by Ron Kahn and colleagues (10), the Authors just show baseline serum insulin levels without providing any measurement (not even in isolated islets) following glucose challenge. We believe that for the sake of scientific appropriateness the Readers will appreciate a clarification by the Authors and the Editors, in particular regarding the fact that pertinent literature in the field has been overlooked.

      References:

      1. Fernandes GW, Ueta CB, Fonseca TL, Gouveia CH, Lancellotti CL, Brum PC, Christoffolete MA, Bianco AC, Ribeiro MO 2014 Inactivation of the adrenergic receptor beta2 disrupts glucose homeostasis in mice. The Journal of endocrinology 221:381-390
      2. Santulli G, Lombardi A, Sorriento D, Anastasio A, Del Giudice C, Formisano P, Beguinot F, Trimarco B, Miele C, Iaccarino G 2012 Age-related impairment in insulin release: the essential role of beta(2)-adrenergic receptor. Diabetes 61:692-701
      3. Asensio C, Jimenez M, Kuhne F, Rohner-Jeanrenaud F, Muzzin P 2005 The lack of beta-adrenoceptors results in enhanced insulin sensitivity in mice exhibiting increased adiposity and glucose intolerance. Diabetes 54:3490-3495
      4. Panagiotidis G, Stenstrom A, Lundquist I 1993 Influence of beta 2-adrenoceptor stimulation and glucose on islet monoamine oxidase activity and insulin secretory response in the mouse. Pancreas 8:368-374
      5. Ahren B, Jarhult J, Lundquist I 1981 Insulin secretion induced by glucose and by stimulation of beta 2 -adrenoceptors in the rat. Different sensitivity to somatostatin. Acta physiologica Scandinavica 112:421-426
      6. Loubatieres A, Mariani MM, Sorel G, Savi L 1971 The action of beta-adrenergic blocking and stimulating agents on insulin secretion. Characterization of the type of beta receptor. Diabetologia 7:127-132
      7. Schwab KO, Bartels H, Martin C, Leichtenschlag EM 1993 Decreased beta 2-adrenoceptor density and decreased isoproterenol induced c-AMP increase in juvenile type I diabetes mellitus: an additional cause of severe hypoglycaemia in childhood diabetes? European journal of pediatrics 152:797-801
      8. Noji T, Tashiro M, Yagi H, Nagashima K, Suzuki S, Kuroume T 1986 Adaptive regulation of beta-adrenergic receptors in children with insulin dependent diabetes mellitus. Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et metabolisme 18:604-606
      9. Santulli G, Iaccarino G 2013 Pinpointing beta adrenergic receptor in ageing pathophysiology: victim or executioner? Evidence from crime scenes. Immunity & ageing : I & A 10:10
      10. Boucher J, Mori MA, Lee KY, Smyth G, Liew CW, Macotela Y, Rourk M, Bluher M, Russell SJ, Kahn CR 2012 Impaired thermogenesis and adipose tissue development in mice with fat-specific disruption of insulin and IGF-1 signalling. Nature communications 3:902

      Gaetano Santulli MD, PhD (1,2) and Guido Iaccarino MD, PhD (3,4)

      From the (1) College of Physicians & Surgeons, Columbia University Medical Center, New York, NY, USA; (2) Departments of Translational Medical Sciences and Advanced Biomedical Sciences, “Federico II” University, Naples Italy; (3) Department of Medicine and Surgery, University of Salerno, Salerno, Italy; (4) IRCCS Multimedica, Milan, Italy.


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    1. On 2014 May 29, Amanda Capes-Davis commented:

      It is important to point out that HEp-2 cells do not come from laryngeal squamous cell carcinoma. The cell line is known to be cross-contaminated and is actually HeLa (cervical carcinoma). A list of known misidentified cell lines can be found at http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Dec 10, Mohammad Saeid Rezaee-Zavareh commented:

      This is a great study about treatment of chronic hepatitis c infection (CHC). As we know occult HCV infection (OCI) is a new defined type of CHC that we should consider it in screening of high risk groups like hemodialysis patients and etc. Also it’s very important to determine a place for OCI in the treatment approach of CHC. It is said that a treatment with pegylated interferon plus ribavirin might be useful for OCI patients. However OCI eradication cannot be achieved in all cases. Hence OCI needs more attention in the treatment approach.

      References: Rezaee-Zavareh MS, Einollahi B. Treatment of occult hepatitis C virus infection: does it need special attention? Hepatitis monthly. 2014;14(7):e16665. Epub 2014/07/30. Rezaee-Zavareh MS, Ramezani Binabaj M, Alavian SM. Screening for occult hepatitis C virus infection, does it need special attention? Hepatology (Baltimore, Md). 2014. Epub 2014/12/06.


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    1. On 2014 Jun 25, Ryan Radecki commented:

      Post-publication commentary:

      "Guideline Recommendations Are Written in Dry Erase Marker, Not Stone."

      Medicine is filled with guidelines, professional recommendations and expert consensus statements. These documents guide clinical practice. In Emergency Medicine, we often rely on non-EM specialty guidelines. For instance, we often state that a patient in whom you consider ACS should get evocative testing (i.e. stress test) within 72 hours of presentation according to the American College of Cardiology/American Heart Association (ACC/AHA) guidelines. As more guidelines and subsequent revisions are released a number of questions arise. Should we adopt the guidelines immediately? If so, which pieces are ready for immediate incorporation into clinical care? At the heart of these questions is the strength and durability of the recommendations....

      http://www.emlitofnote.com/2014/06/guideline-recommendations-are-written.html


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    1. On 2014 Sep 16, Anders von Heijne commented:

      It would be extremely valuable if the exact locations of the presumed occult fractures were to be reported. At what vertebral levels? In what parts of the vertebrae? Body? Facett joints? Posterior arch? There also must be an excellent opportunity to correlate the SPECT findings with MRI since all patients also were part of an earlier reported MRI study (Kongsted A 2008).It also seems likely that a majority of these patients have undergone acute CT of the cervical spine after the trauma - another opportunity for imaging correlations


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    1. On 2014 May 30, Lane Rasberry commented:

      As a Wikipedia contributor I appreciate this paper greatly. Questions about complementary and alternative medicine are among the most popular questions asked on Wikipedia, and by extension, I believe that this sorts of questions are among the most popular health questions asked generally.

      Wikipedia has a long history of restricting discussion about CAM to separate explanations of its cultural impact and what is reported in academic literature as evidence based medicine coming from review articles or other secondary sources. While anyone familiar with the societal practice of CAM is encouraged to present non-medical claims as they like with whatever reliable sources they can cite, as this article says - Wikipedia articles on CAM get a lot of traffic and the public's demand for summarized results of medical research on CAM is not being met in Wikipedia. I feel this is because there are as many health professionals in CAM doing educational outreach as there are in other sectors of health.

      As a Wikipedia community anecdote, I would also like to share that Wikipedia founder Jimbo Wales also expressed a need for more evidence based reporting on Wikipedia about CAM, as he said in 2014 in response to a petition to include non-evidence based medical information on Wikipedia.


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    1. On 2014 May 29, Amanda Capes-Davis commented:

      This study focuses on P. gingivalis and its effect on endothelial cells. Please be aware however that ECV-304 is not an endothelial cell line. ECV-304 is known to be cross-contaminated and is actually T-24 (bladder carcinoma). A list of known misidentified cell lines can be found at http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 May 30, Amanda Capes-Davis commented:

      Scientists working in this area may not be aware that many cell lines are cross-contaminated (overgrown by other cell lines) and no longer correspond to the expected cell type. The KB cell line is cross-contaminated with HeLa (cervical cancer) and is not oral cancer. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Jul 08, Swapnil Hiremath commented:

      The POSEIDON trial was discussed on June 18th 2014 on the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available at the NephJC website. It was a fascinating discussion, with participation from nephrologists, clinical pharmacologists, internists, and cardiologists. The conversation also touched upon other aspects of contrast-induced acute kidney injury. A transcript and three different curated (i.e. Storified) versions of the tweetchat are available at the same NephJC link.

      On July 1st 2014, there was a video interview of principal investigator of the POSIEDON trial, Somjot Brar, which can be viewed on Youtube. Many important insights into the design and interpretation of the trial were provided by Dr Brar, and readers are encouraged to check out the video.

      The highlights of the tweetchat and the hangout were:

      1. The investigators should be commended for planning and executing this trial so meticulously. Also, the funding agency (Kaiser Permanente) for supporting this important trial.

      2. The intervention (based on LVEDP measurement to guide fluid administration) was designed to identify patients in whom it would be safe to give higher volumes of saline.

      3. This trial provides critical evidence that preventing contrast-induced acute kidney injury protects the patient from future negative, extra-renal adverse events, a finding that previously had been seen in observational and retrospective cohorts but had been absent from prospective trials.

      Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.


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    1. On 2015 Jan 30, NephJC - Nephrology Journal Club commented:

      This review was discussed on January 6th and 7th in the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available at the NephJC website. It was a fascinating discussion, which served to help understand the physiology and functions of the distal convoluted tubule. It had more than 70 participants, including nephrologists, physiologists, basic scientists and nephrology fellows. The first author, Arohan ‘Ro’ Subramanya, and the section editor, Melanie Hoenig also joined in the discussion. A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website.

      The CJASN should be commended for commissioning  this series, and moreover, for making it freely available. It will remain an extremely useful resource for providing understanding of basic renal physiology, at the same time providing a glimpse into the ongoing cutting edge research in this field.  

      Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.


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    1. On 2014 Oct 01, Preben Berthelsen commented:

      Platelet transfusions are not innocuous. Furthermore, they do not reliably prevent bleeding connected with mishaps during central venous catheterisation via an internal jugular or subclavian vein.

      Central venous access via an external jugular vein is successful in more than 95% of patients if the external jugular vein can be visualised and cannulated. (Berthelsen et al. Acta Anaesthesiol Scand 1986;30:470-. Kato et al. J Invest Surg 2014;27(3):176-)

      If access via an external jugular vein is chosen, there is no need to check or modify the patient’s coagulation status before central venous access is attempted. P.G.Berthelsen. Charlottenlund. Denmark


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    1. On 2015 Nov 05, ALEXANDER TSAI commented:

      Please be advised there are two errors in the abstract.

      The abstract currently reads: "The pooled prevalence of probable depression was 29.5% [95% confidence interval (CI): 20.5 to 39.4], whereas the pooled prevalence of major depressive disorder was 13.9% (95% CI: 9.7 to 18.6)."

      The abstract should read: "The pooled prevalence of probable depression was 30.2% [95% confidence interval (CI): 19.7–41.8], whereas the pooled prevalence of major depressive disorder was 14.5% (95% CI, 8.9–21.2)."

      The numbers in the text of the article are correct. I am grateful to Charlotte Bernard of VIH, Cancer and Global Health in Africa, INSERM U897, ISPED, University of Bordeaux, for pointing out the error. On November 5, 2015, I contacted the journal editors about issuing an erratum and will update this post with more information as it comes available. As of November 30 I have not heard a response.


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    1. On 2014 May 26, Jonathan Eisen commented:

      This paper received a lot of press coverage. Unfortunately a lot of the reporting has included some comments or claims that are not supported by the evidence. I have written a detailed blog post with responses to the reporting. See http://phylogenomics.blogspot.com/2014/05/overselling-microbiome-award-many-for.html.


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    1. On 2014 May 26, Serge Ahmed commented:

      This clever study shows that responding for cocaine-associated cues can be entirely and persistently abolished by canceling out cocaine-induced long-term plasticity at hippocampal and cortical synaptic inputs to D1R-expressing neurons in the nucleus accumbens. Importantly, the latter feat was achieved by acutely co-opting endogenous mechanisms of synaptic plasticity using astute optogenetic-based LTD protocols.

      The efficacy of these LTD protocols was specific to responding for cocaine-associated cues and had no impact on responding for sucrose or sucrose-associated cues - which were both notably more intense and more robust than responding for cocaine-associated cues.

      One may regret that the authors did not test whether and to what extent the same LTD protocol that acutely abolished responding for cocaine-associated cues would also affect the maintenance of responding for cocaine itself and/or the ability of other well-known factors to trigger “relapse.” These additional experiments would have been helpful to better define what has exactly been erased by the LTD protocols. It would also be important to know whether the same efficacy could be achieved after more prolonged exposure to cocaine self-administration.

      Finally, this study paradoxically shows that endogenous mechanisms of synaptic plasticity are apparently largely intact in cocaine-exposed animals and can be co-opted to reverse, persistently and rather easily, cocaine-induced synaptic plasticity. One may then wonder whether and to what extent similar mechanisms could be self-recruited by people who successfully quit cocaine.


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    1. On 2015 Feb 27, Geriatric Medicine Journal Club commented:

      This trial of physical therapy on pain and physical function in patients with hip osteoarthritis was discussed at the October 2014 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full transcript can be found at: http://gerimedjc.blogspot.com/2014/11/gerimedjc-october-31-2014.html?spref=tw Highlights include whether physiotherapy is just a sham in hip osteoarthritis?


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    1. On 2014 May 28, David Keller commented:

      Bravo - PSA screening guidelines should be issued by urologists & prostate cancer experts

      According to the USPSTF website, their volunteer members devote an average of 200 hours per year to their unpaid duties on that committee, and those 200 hours are divided between consideration of several separate and vastly different issues. In addition, the USPSTF includes specialists who do not treat or screen for prostate cancer, such as pediatricians and gynecologists. Contrast that with professors of urology, who have devoted their careers to study of the complex issues related to prostate cancer screening. As a primary care physician, I place far more credence in the recommendations of urology professors when it comes to PSA screening, than to (let us say) a USPSTF gynecologist who has spent (let us say) 100 hours studying the topic, and has never examined a prostate as an attending physician. I predict that future evidence will force the USPSTF to retract their "D" recommendation against PSA screening. The harms done, though, will not be easy to retract.

      The AUA guidelines suggest increasing the routine PSA screening interval to 2 years (instead of annual screening) in order to "reduce the harms of screening". However, PSA is a noisy signal, and decreasing the rate at which it is sampled will lower the effective signal-to-noise ratio and decrease the accuracy of the PSA measurement. Further, increasing the interval between PSA samples will reduce the bandwidth of PSA signal we can detect. In other words, we may miss the opportunity to detect prostate cancers with high Gleason scores and fast doubling times while they are still confined to the prostate. Increasing the gap between PSA samples to 2 years will reduce our ability to cure the most aggressive cancers with prostatectomy.

      One of the oft-cited "harms" of screening is false positive PSA results triggering too many unnecessary biopsies. But none of the clinical trials used even the most basic PSA signal processing techniques to improve specificity, such as simply waiting a week and repeating the PSA before rushing to biopsy. This eliminates a great many false-positive PSA spikes. Another technique which seems likely to improve the validity of PSA screening is to include PSA velocity (the rate of increase of PSA) into biopsy decisions (1). For example, a man whose PSA has been stable at 4.0 for one year seems less likely to have a threatening prostate malignancy than a man whose PSA has tripled from 1.0 to 3.0 during that same year. Yet, every major study has relied on static PSA biopsy thresholds which would biopsy the patient with the stable PSA of 4.0 but not the man whose PSA tripled.

      Other oft-cited harms of screening, such as patient anxiety, are easily overcome by physician reassurances regarding the benign nature of most spikes and glitches in the PSA, and the indolent nature of most prostate cancers.

      The PSA test gives us information; it does not require a reflex response. More information is usually better, and information cannot hurt us unless we misuse it.

      Reference

      1: Bjurlin MA, Loeb S. PSA Velocity in Risk Stratification of Prostate Cancer. Rev Urol. 2013;15(4):204-6. Review. PubMed PMID: 24659919; PubMed Central PMCID: PMC3922327.


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    1. On 2014 May 31, David Keller commented:

      Can Directional DBS be combined with Adaptive DBS to further optimize therapeutic effects?

      Directional DBS was shown to provide a therapeutic window 41.3% wider than for standard omnidirectional DBS, and to achieve this with a smaller electrode; this new technique seems to offer significant improvements over standard DBS.

      Standard DBS is observed to cause a syndrome of mild loss of verbal fluency due to the small amount of brain damage caused by the placement of the leads. Does the smaller lead size employed for directional DBS reduce this adverse side effect compared with standard lead placement surgery?

      Because it requires a new electrode, patients with pre-existing omnidirectional DBS will likely require repeat stereotactic neurosurgery to replace their brain leads when and if they need an upgrade to directional DBS. Waiting for directional DBS to be approved may be a reasonable choice for patients who can defer DBS.

      Recently, another new technique known as adaptive DBS (aDBS) was also demonstrated to provide meaningful improvements over standard DBS (1). aDBS involves using feedback from a pathological brain electrical signal to modulate the applied DBS signal, and it also serves to reduce the required electrical signal to achieve therapeutic effects.

      An obvious question arises: can we combine directional DBS with adaptive DBS, in order to more fully optimize their therapeutic effects? The answer to that question, according to Peter Brown, Professor of Experimental Neurology at University of Oxford, and principal investigator on the team which developed aDBS, is "I agree that the two could be usefully combined in the future" (2). I invite the scientists who developed dDBS to add their assessment of the utility of combining these 2 techniques, and to consider a collaborative effort with Dr. Brown to do so.

      Reference

      1: Little S, Pogosyan A, Neal S, Zavala B, Zrinzo L, Hariz M, Foltynie T, Limousin P, Ashkan K, FitzGerald J, Green AL, Aziz TZ, Brown P. Adaptive deep brain stimulation in advanced Parkinson disease. Ann Neurol. 2013 Sep;74(3):449-57. doi: 10.1002/ana.23951. Epub 2013 Jul 12. PubMed PMID: 23852650; PubMed Central PMCID: PMC3886292.

      2: Brown P, private correspondence, June 1, 2014


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    1. On 2015 Jan 28, JAMES STIVERS commented:

      In this study, Yin et al use photo-induced electron transfer diffusion-decelerated fluorescence correlation spectroscopy (PET-ddFCS) to investigate spontaneous opening of a mismatched T-G base pair DNA (Yin Y, 2014). This elegant and potentially useful method involves electron transfer between a guanine and the singlet excited state of a tetramethylrhodamine fluorophore (TMR) that is attached via a linker to the exocyclic 4-amino group of dC in the sequence context 5´-CC<sup>TMR</sup> TCC-3´. The results are interpreted in terms of the rate of spontaneous exposure of the guanine base opposite to T in the mismatch (“base flipping”). The measured exposure rates are ~10<sup>4-fold</sup> less than previous T-G opening rates measured by the NMR imino exchange method (Moe JG, 1992), from which the authors conclude that PET-ddFCS measures “true” base flipping rates that are relevant for mismatched detection by base flipping DNA repair enzymes (Friedman JI, 2010), and that the NMR measurements “are irrelevant to (the) significant enzymatic base flipping”.

      In this work, the authors mischaracterize the implications of previous NMR DNA imino proton exchange measurements and also the general role of dynamics in specific biomolecular recognition. The authors argue that the imino exchange measurements are irrelevant to the process of enzymatic base flipping because exchange occurs during a state when the base has not yet rotated completely from the DNA base stack [see references cited in (Friedman JI, 2010)]. Using this criterion, which is narrowly centered on the amplitude of the motion, nearly all spontaneous dynamic motions of biomolecules would be deemed irrelevant for molecular recognition.

      The appropriate way of viewing the problem is to ask whether damaged or mismatched DNA base pairs have kinetically competent motions that fall on the pathway of enzymatic base flipping (Friedman JI, 2010). The kinetic competence requirement is addressed by comparing base pair opening rates with the measured rates of enzymatic base flipping [(Cao C, 2006) and references therein], and the on-pathway requirement is addressed by obtaining structures of the early stages of base flipping on enzymes (Cao C, 2006). For uracil DNA glycosylase (hUNG)(Cao C, 2006), both the kinetic and structural requirements for productive dynamic motions have been rigorously met. In contrast, the base flipping rate for the T-G mismatch measured by PET-ddFCS is ~10<sup>4-fold</sup> too slow to account for U-A base flipping by hUNG. Assuming the authors interpretation of the measured opening rates by PET-ddFCS, their rates fail the kinetic competence criterion, requiring that enzymes actively lower the kinetic barrier for large amplitude rotations of bases from the DNA. This essential role of these enzymes has never been disputed by anyone to my knowledge.

      Finally, these PET-ddFCS studies would be strengthened by further controls that would help validate the author’s interpretations. First, the approach simply measures the proximity of TMR to guanine, which could occur by any plausible mechanism such as transient intercalation into a site that is induced by the increased flexibility of a mismatched duplex. Further, the DNA construct used in this work had multiple G’s near the mismatch, any of which might be involved in electron transfer. Third, the author’s interpretation assumes that the rate-limiting step is guanine exposure, but they do not consider that many opening events may occur before a productive ET complex forms. Finally, the authors should report imino proton NMR spectra of a TMR modified duplex to confirm that this non-trivial modification does not perturb the dynamic behavior.


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    1. On 2014 Nov 17, Raphael Levy commented:

      Various aspects of this article are questioned at PubPeer, in particular the evidence for cytosolic localisation of striped nanoparticles. It is also worth noting that the article contains no experimental evidence for the existence of the stripes: not a single figure of Scanning Tunnelling Microscopy or other morphological characterization of the surface organisation of the nanoparticles neither in the paper, nor in the 47 pages SI.

      The article belongs to the “stripy nanoparticles” series. The evidence behind the structure and special properties of these nanoparticles has been challenged by Cesbron Y, 2012. The publication in 2012 of Cesbron Y, 2012 took three years and has been followed by post-publication peer review of the various existing and new stripy articles on my blog, PubPeer, etc.

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


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    1. On 2014 May 24, John B Furness commented:

      Thanks for your comment. These cells have multiple receptors for luminal nutrients(e.g. Furness, Nature gastroenterology 2013). I imagine that different nutrient receptors may be coupled to the selective release of hormones, perhaps through selective receptor - second messenger - Ca release - vesicular store microdomains.


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    1. On 2014 Jun 03, Salvatore Chirumbolo commented:

      This thorough review on the chemopreventive action exhibited by several natural components in human daily diet, should have addressed the possibility of a toxic activity by herbal remedies and phytochemicals, besides their claimed protective potential (Banerjee et al., Phytother Res 2003, 17(2):97). Many phenolic and aromatic derivatives, working as active components, often show a bimodal, “Janus-like” behaviour in the organism, what causes scientific challenge to be continued (Lee and Park, Mutat Res 2003; 523:265). For example, toxicity of garlic was addressed since past reports (Abraham and Kesavan, Mutat Res 1984, 36(1):85; Joseph et al, Ind J Exp Biol, 1989; 27(11):977)and may be an important debating issue in cancer research and chemoprevention. Garlic (Allium sativum L.) contains an active form of arsenic (Sousa-Ferreira H et al., Food Anal Methods, 2011; 4:411). Intake of garlic, as a chemopreventive raw food, involves a complex mechanism of raw food treatment, adsorption, pharmacokinetics and bioavailability (Amagase et al., J Nutr 2001, 131:955S), which were not yet addressed in the review. Evidence was reported showing that different people might have a different response to garlic, and thus garlic may be more beneficial for some specific groups. Garlic-derived compounds may work synergistically to produce various effects, but, because of garlic's chemical complexity, processing methods yield preparations with differing efficacy and safety, and this is a critical issue to ascertain garlic property against cancer. For example thiosulfinates (Amagase, J Nutr 2006, 136:716S), such as allicin, have been long misunderstood to be active compounds due to their characteristic odor, but some paper reported that it is not necessary for garlic preparations to contain such odorous compounds to be effective, as they decompose and disappear during any processing. Therefore, concluding remarks about the molecular activity of specific phytochemicals in daily food, should be reviewed by taking into account the role of ancillary molecules in raw sources and in vivo or clinical research.


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    1. On 2015 Feb 18, Radboudumc Psycho-Oncology Journal Club commented:

      This study examines a uniquely large cohort of breast cancer survivors after a long follow-up period (median 6.3 years post-diagnosis). Since severe postcancer fatigue becomes a chronic condition in approximately 25% of breast cancer survivors*, we believe it is important to identify predictors of long-term fatigue. During the plenary discussion of this paper in our Journal club, the following questions were raised:

      1) We would like to know how fatigue scores develop in course of time. What are the mean fatigue scores and how many patients in your cohort are severely fatigued?

      2) Misinterpretation of the 0-10 fatigue rating scale was reason for exclusion of cases with high pre-diagnosis fatigue levels. We wonder how you assessed if this rating scale was misinterpreted?

      3) You have reported interesting outcomes on the predictors of long-term fatigue in breast cancer survivors. We are curious about your recommendations on these outcomes for future research and clinical practice.

      *Servaes P, 2007


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    1. On 2014 May 21, Amanda Capes-Davis commented:

      Tissue specificity is important for this study, so the identity of the cell line used is critical. Unfortunately HEp-2 cells do not come from laryngeal squamous cancer; HEp-2 is cross-contaminated with HeLa, a cervical carcinoma cell line. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2016 Aug 30, Ben Goldacre commented:

      This trial has the wrong trial registry ID associated with it on PubMed. The ID given is NCT0040951 - the correct ID, which we found within the text of the article itself, is NCT00470951.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 in PubMed.

      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 PMID: 27056367

      * 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


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    1. On 2014 May 25, Daniel Mietchen commented:

      The choice of two pop songs for the musical examples seems unfortunate here, since these pieces are copyrighted the classical way, which precludes the sharing of the audio and video files under the Creative Commons Attribution 4.0 License that the article was published under.

      For the purposes of this research, this was completely unnecessary, and compatibly licensed sound samples suitable for this study can easily be found, e.g., on Soundcloud.


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    1. On 2014 Jul 24, Ryan Radecki commented:

      Post-publication commentary:

      "End-Tidal CO2 Monitoring Unhelpful in Sedation"

      Capnography during procedural sedation has rapidly become standard practice in the interests of “safety” – despite decades of Emergency Medicine experience safely performing sedation without. The theory: earlier detection of inadequate ventilation allows for intervention and prevention of hypoxemic episodes. In the most prominent randomized trial, there was a 17% absolute reduction in transient hypoxemic events. Critics appropriately point out, however, that transient events are hardly a meaningful patient-oriented outcome....

      http://www.emlitofnote.com/2014/07/end-tidal-co2-monitoring-unhelpful-in.html


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    1. On 2017 Sep 28, Jacob H. Hanna commented:

      Follow-up papers from Hanna group further critique this study: http://www.biorxiv.org/content/early/2017/09/07/184135

      Jacob (Yaqub) Hanna M.D. Ph.D.

      Department of Molecular Genetics

      Weizmann Institute of Science | 234 Herzl St, Rehovot 7610001, Israel

      Email: jacob.hanna@weizmann.ac.il

      Lab website: http://hannalabweb.weizmann.ac.il/

      Twitter: @Jacob_Hanna


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    2. On 2016 Jan 23, Jacob H. Hanna commented:

      A critique of this paper is available on bioRxiv: http://dx.doi.org/10.1101/013961

      We copy below the most important section indicating that the entire findings by Dos Santos et al. claiming that Mbd3 facilitates epigenetic reprogramming can be trivially explained by inducing cell proliferation block as a result of 100% ablation of Mbd3 early in the process:

      "Complete depletion of Mbd3 blocks somatic cell proliferation and viability"

      In Rais et al. Nature 2013 clearly indicated that near 100% complete inhibition of Mbd3 in somatic cells or EPiSCs results leads to abrupt decrease in cell proliferation and viability. As such we greatly focused on using hypomorphic Mbd3flox/- cell lines and compared them to Mbd3+/+ WT cells. In cases where we achieved high reprogramming efficiency of Mbd3-/- cells (Rais et al, Figure1-2, Extended Data Figure 3B,C), we always started with Mbd3flox/- cells (and NOT Mbd3-/- cells as used in Dos Santos et al.) in order to ensure low and residual Mbd3 protein levels already during the first 48 hours of OSKM induction. Afterwards, 2i was supplemented with tamoxifen to achieve complete ablation of Mbd3. This is a critical point that was highlighted in our paper - Rais et al Nature 2013:

      “Mbd3-/- MEFs (but not pluripotent cells) experience accelerated senescence and proliferation capacity loss, and thus Mbd3-/- somatic cells were reprogrammed by applying tamoxifen on Mbd3flox/- cells only after 48 h of OSKM induction”. (A direct quote from Rais et al. Nature 20131 Methods section)

      The results presented by Dos Santos et al. systematically used different conditions where they did either one of the following:

      1) Dos Santos et al.2 used Mbd3-/- cells that were maintained for multiple passages as null cells and only afterwards OSKM were introduced. As we had previously indicated1, these cells dramatically lose their proliferation capacity, and indeed all growth proliferations curves shown in Dos Santos et al. validate this result (even though they were carried for 4 days only). Therefore the entire findings by Dos Santos et al. claiming that Mbd3 facilitates epigenetic reprogramming can be TRIVIALLY explained by inducing cell proliferation block, and in our opinion, has nothing to do per se with epigenetic reprogramming. Further, the latter decrease in cell proliferation occurs even without OSKM induction, further supporting the notion that the inhibition of reprogramming results from simply hampering cell proliferation in donor cells, rather than epigenetic reprogramming per se.

      2) For Tamoxifen induced deletion experiments, Dos Santos et al.2 used Mbd3flox/flox cells (and not Mbd3flox/- cells), and applied tamoxifen at different time points. However, these experiments lead to complete deletion of Mbd3, and not during the critical window of early reprogramming, which we highlighted as critical1.

      3) Finally, Dos Santos et al. did not compare WT vs. Mbd3flox/- cells as starting somatic donors for reprogramming, which is the most relevant comparison and the most robust comparative one presented in Rais et al. Nature 2013.

      In summary, our findings in fact are consistent with Dos Santos et al, as they use conditions that ensure either complete inhibition of Mbd3 and block cell proliferation, or avoid optimal depletion of Mbd3/NuRD activity during a critical early reprogramming window, which we previously highlighted1 as critical determinants for capturing the beneficial effect of Mbd3/NuRD depletion on iPSC reprogramming.

      For full version of our critiques you are invited to read bioRxiv preprint: http://dx.doi.org/10.1101/013961

      Jacob (Yaqub) Hanna M.D. Ph.D.

      Department of Molecular Genetics

      Weizmann Institute of Science | 234 Herzl St, Rehovot 7610001, Israel

      Email: jacob.hanna@weizmann.ac.il

      Lab website: http://hannalabweb.weizmann.ac.il/

      Twitter: @Jacob_Hanna


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    1. On 2014 May 21, Amanda Capes-Davis commented:

      BG-1 is not from ovarian cancer; it is known to be cross-contaminated by breast carcinoma cell line MCF-7. A database of known cross-contaminated cell lines can be found at http://iclac.org/databases/cross-contaminations/. Having said that, it's possible that a lab may have authentic stock for a known cross-contaminated cell line. If you have STR profiling data to support the existence of authentic stock, please let us know (http://iclac.org/contact-us/).


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    1. On 2014 Jul 29, Amanda Capes-Davis commented:

      The authors use 7T cells for their work, which are derived from HEp-2. Please be aware that HEp-2 cells (and thus 7T) are not from laryngeal carcinoma. HEp-2 is cross-contaminated with HeLa and is actually cervical adenocarcinoma. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2015 Oct 21, James C Coyne commented:

      I am delighted that your group has formed a PubMed Commons Journal Club and you have selected our article for comment. Hopefully my colleagues will respond as well, but here are my reactions.

      Our study grew out of an ambitious dissertation project in which the PhD student sought to implement best practices for recruiting a consecutive sample. Rather than obtaining the anticipated sample size, her effort stands as a cautionary note for anyone who would consider mounting such a randomized trial as part of a PhD effort without a lot of resources that are typically available.

      I would now suggest that if a PhD student wishes to conduct an evaluation of an intervention largely on their own, they should stick to evaluating the feasibility and acceptability, not expecting to accrue enough patience for an adequately powered estimate of effect size. We have far too many underpowered studies claiming to produce effect sizes that, in the end, are not reliable.

      Because recruitment for our study was not part of routine care, assent had to be obtained for approaching patients.

      The Dutch practice of talking to every patient who wants a discussion is admirable, butit is not screening. Throughout medical practice, screening involves making decisions about who will have a further discussion based on their obtaining a score above a cutpoint. Indeed, if taken seriously and literally, the widely touted international standards for screening threaten an excellent, well-established Dutch practice.

      I think that your comments, like a lot of the conventional understanding of cancer patients' interest in psychotherapy, reflect an overoptimism about their uptake. Our experience is actually quite consistent with other data that suggest interest in psychotherapy or counseling is a lot lower than generally assumed.

      With more resources, perhaps we could have relied on touchscreen assessments, but I doubt the yield would be much better than what we obtained.

      There is no evidence that systematic and routine screening for distress of cancer patients produces are better outcome than simply allowing patients access to services without the intervening screening. However, a large number of studies demonstrate that most patients who are interested in psychological services are not distressed enough to register an effect of receipt of those services. That is quite a dilemma.


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    2. On 2015 Sep 17, Radboudumc Psycho-Oncology Journal Club commented:

      This interesting study which has important implications for psychosocial oncology researchers was discussed by our Journal Club on 16th September, 2015 and generated a lively discussion. This study reports on difficulties associated with using distress screening to identify patients for randomisation to psychological therapy intervention trials. The authors conclude that although distress screening of consecutive patients to determine psychological trial entry is recommended by guidelines, it may be an inefficient use of resources and introduced bias.

      During the plenary discussion of this paper our journal club raised the following points:

      • 1) In this study nurses distributed screening instruments at Time 1 but the results of those questionnaires were mailed back to the researcher. At Time 2 all screening questionnaires were conducted by the researcher via the mail with a follow-up phone by the researcher. Our group discussed that this scenario does not reflect how screening is (or should) be used in most clinical settings. To ensure the maximum benefits of screening we believe it is important for clinical staff responsible for screening to discuss the results with patients and offer services (or studies) according to identified needs. We wondered whether the uptake of the PST intervention study may have been higher if this approach had been adopted?
      • 2) This study also raises some broader issues about patient perceptions of psychological therapies and how best to explain what is offered in psychological intervention trials to patients. We noted with interest that need for help was explored with a rather general question “Would you like to talk to a care provider about your situation?” however, what was ultimately offered to the patient was the opportunity to speak with a psychologist. Our group felt an important component of trial uptake is ensuring a good match between what is screened and the services ultimately offered.
      • 3) The authors identify that a large component of the 17 hours calculated to recruit one patients to the study was taken up by data management issues. They recommend that automated methods may be more efficient. We are wondering if the authors have a sense of the efficiency gains offered by automated screening and whether using automated methods makes the process of distress screening for trial entry efficient?
      • 4) We note with interest the current dilemma that although it may be inefficient the screening of consecutive patients for trial entry is currently a required component of best practice guidelines on the conduct of randomised controlled trials (eg. CONSORT). Do the authors have any suggestions for what can be done to address this problem if distress screening for trial entry indeed introduces bias and threatens external validity?


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    1. On 2014 Jul 29, Shunichi Nakamura commented:

      "Author Response"

      Spiegel confounded the results in pulmonary embolism (PE), including massive and submassive PE, with the results in submassive PE only. Our meta-analysis selected randomized trials that enrolled patients with submassive PE only, whereas the meta-analysis published in the JAMA explored the effects of thrombolysis in patients with PE, including the massive, submassive, and non-massive types. The researchers who conducted the meta-analysis evaluated the efficacy of thrombolysis in submassive PE as a subanalysis. The number of enrolled patients in their meta-analysis was slightly larger than that enrolled in our meta-analysis (1755 patients [8 trials] vs. 1510 patients [6 trials]). The mortality risk reduction rate among the patients with submassive PE was 52% in the published met-analysis and 28% in our meta-analysis. This difference can be explained by the following reasons. We are concerned that an important selection bias might have existed in the meta-analysis published in the JAMA. First, the ULTIMA trial was designed to prove that the ultrasound-accelerated strategy was superior to anticoagulation with heparin alone in patients with submassive PE; therefore, the trial was not conducted purely to compare between thrombolysis and heparin-only therapy, and this technology is considered to influence the overall results. Second, as for the study selection, the MOPPET trial should not have been selected in their meta-analysis because its inclusion criteria were simply determined by the extent of disturbed pulmonary blood flow irrespective of the existence of RV dysfunction or myocardial injury, and this condition and submassive PE are not equivalent. Consequently, the ULTIMA and MOPPET trials influenced the overall result of their meta-analysis because of the larger risk-reduction impact of the two trials. Third, the subjects included by Goldhaber (1993) included patients with massive pulmonary embolism. The corrected number was 18 in their study, as well as in our meta-analysis. Fourth, in the meta-analysis previously published in the JAMA, although the odds ratio was calculated as an analysis method, we think that the risk ratio should be used in the meta-analysis of randomized controlled studies. Based on these issues, we believe that our article more specifically demonstrated the efficacy of thrombolytic therapy in submassive PE. Recent registry studies report that the 30-day mortality rate in patients with submassive PE was 3.0%, which is in line with our result. These results also suggest that if compared with heparin-only therapy, an adjunctive thrombolytic therapy reduces the risk of mortality in patients with submassive PE by about 30%, which is similar to the result from our meta-analysis (28%), then the size effect of this treatment is only about 1%. This could explain why the survival benefit of adjunctive thrombolytic therapy has been difficult to demonstrate in patients with submassive PE. In the two meta-analyses, a significant increase in the risk of intracranial bleeding was observed with thrombolytic therapy compared with heparin alone. Therefore, our major argument was that the harmful effects such as intracranial bleeding might be the trade-off for the benefit of a reduction in clinical deterioration, not the ineffectiveness of thrombolysis for difficult cases of submassive PE. Thus, risk stratification of patients with submassive PE is of great clinical importance. New agents also need to be developed to reduce the incidence of intracranial bleeding and replace the thrombolytic agents used in the previous studies. Moreover, we suggest the use of half-dose thrombolysis in further studies.


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    2. On 2014 Jul 24, Ryan Radecki commented:

      Post-publication commentary:

      "Dueling PE Meta-Analyses"

      Nothing sparks controversy quite like a discussion on the utility of thrombolytics. No sooner had the wave of debate brought on by the publication of the PEITHO trial and its finding of no overall mortality benefit died down, did JAMA stoke these flames with the publication of a meta-analysis including the entirety of the literature on thrombolytic use for pulmonary embolism. Examining 16 trials, the authors found a statistically significant absolute mortality benefit of 1.12% or an NNT of 59 patients. This benefit was offset by the increase in major bleeding events observed in those given thrombolytics (9.24% vs 3.42%) with a 1.27% absolute increase in ICH.

...

      http://www.emlitofnote.com/2014/07/dueling-pe-meta-analyses.html


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    1. On 2014 Aug 06, Xudong Fu commented:

      Thanks for your comments. It is really interesting. I hope I could explain why I don't think alpha-ketoglutarate works as an antioxidant to extend lifespan.

      It has been shown that α-ketoglutarate is an antioxidant. However, antioxidants are not necessarily able to extend lifespan. Actually, the relationship between ROS and lifespan has not been established. Increase of ROS may contribute to lifespan extention potenially through downstream defensim activation and overexpression of antioxidant enzyme is not able to extend lifespan in mice (http://www.sciencedirect.com/science/article/pii/S0092867413006454, http://onlinelibrary.wiley.com/doi/10.1111/j.1474-9726.2008.00449.x/full).

      Our paper discovers that α-ketoglutarate can bind and inhibit ATP synthase and extend lifespan in C. elegans. The inhibition of ATP synthase is actually likely to generate more ROS. It has been shown that oligomycin, a known ATP synthase inhibitor, could induce ROS in vivo. In our hand, we also find that α-ketoglutarate could induce ROS (by DCFDA dye measurement) both in C. elegans and cells. That suggest α-ketoglutarate is unlikely to increase lifespan simply through antioxidant function. It's more likely α-KG regulates lifespan through induction of ROS instead. We actually have explained why we don't think ROS plays a major role in the life extension effect for α-ketoglutarate; see Supplementary Information (http://www.nature.com/nature/journal/v510/n7505/extref/nature13264-s1.pdf). Briefly speaking, although α-ketoglutarate could induce ROS, additional antioxidants does not decrease the lifespan extension effect of α-KG in our hands. In addition, ROS has been suggested to activate TOR but we observed α-ketoglutarate decrease TOR.

      In terms of the dosage we used, it has been known that α-KG is not highly membrane permeable. To solve this issue, we made octyl α-KG, an ester form of α-KG which is more membrane permeable. After octyl α-KG goes into the membrane, it gets hydrolyzed and releases free α-KG. Most of the assays in Fig. 2 were done with octyl α-ketoglutarate instead of original α-KG. That's the main reason we don't need to use 8mM dose for Fig. 2 assays. We also tried octyl α-KG in lifespan assays (see Extended Data Table 2). It only required micromolar scale of octyl α-KG instead of millimolar for us to observe the lifespan extension. In addition, after treatment of 400 uM of octyl α-KG on cells or after treatment of 8mM α-KG on C. elegans, the in vivo concentration of α-kG increased comparably around 50-100%. That suggest 50-100% increase of endogenous α-KG could inhibit ATP synthase and extend lifespan, nonetheless the different forms or concentration of α-KG we used, consolidating our hypothesis that α-KG extend lifespan through direct ATP synthase inhibition. Also, because the endogenous increase of α-KG is only 50-100%, this concentration does not seem to be in line with the concentration suitable for non-enzymatic reaction.


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    2. On 2014 Aug 04, Paul Brookes commented:

      This is an interesting result, but I believe there's a fundamental mechanism that may have been overlooked, and is especially prescient given the high concentration of alpha-ketoglutarate that was required for this effect (8mM).

      Like all alpha-keto acids, a-KG is an antioxidant. It can react freely with H2O2 (the products being succinate and CO2). Such oxidative decarboxylation has been widely studied (e.g. http://www.ncbi.nlm.nih.gov/pubmed/16781453), and essentially amounts to a short-cut in the TCA cycle (see our editorial on Fedotcheva's paper - http://www.ncbi.nlm.nih.gov/pubmed/16781451). This is why such acids exhibit short half-lives in vitro. For example if you keep a solution of pyruvate on ice it'll all be decarboxylated to acetate within a few hours.

      Bottom line, letting worms swim around in an 8mM solution of an antioxidant MIGHT give rise to some effects on lifespan that are completely independent of any of the claimed mechanisms herein.


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    1. On 2015 Mar 22, Richard Jahan-Tigh commented:

      I think this is probably just a Becker's nevus with breast hypoplasia. A nontender,non-pruritic brownish patch evolving over 2 years (probably when puberty started for her) and continuing to be asymptomatic for 3 more years afterwards doesn't really describe morphea. Morphea characteristically spares the nipple and doesn't prevent the breast from completely forming as in this case.


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    1. On 2014 May 21, Amanda Capes-Davis commented:

      In regard to the cell line used here: HSG is cross-contaminated with HeLa and so is from cervical carcinoma, not salivary gland tumor. A list of known cross-contaminated cell lines can be found at http://iclac.org/databases/cross-contaminations/. It is possible that a lab may have authentic stocks for a known cross-contaminated cell line. If the lab has STR profiling to support that assertion, please contact us via the website.


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    1. On 2014 May 21, David Keller commented:

      Red wine and the French Paradox: another beautiful theory murdered by the ugly facts

      The French paradox is the presence of low coronary heart disease (CHD) death rates in France, despite high levels of cholesterol and saturated fat in the French diet. This has been explained partially by a number of factors, including: French doctors under-reporting CHD on death certificates (this accounted for 20% of the paradox in one study); the fact that the French ingest ethanol in moderate doses continuously all day, every day, compared with other countries where most ethanol is consumed in binges on one or two days per week (ethanol binges produce less increase in HDL and inconsistent anti-platelet effects); the French eat large amounts of saturated fat from animal sources, compared with Americans who consume slightly less saturated fat overall, but much more of it is hydrogenated trans fat, which is thought to be more atherogenic; a time-lag effect whereby the CHD rates of today reflect fat consumption levels 30 or more years ago, when the French diet was less fatty compared with the U.S.; consumption of possibly protective fruits and vegetables is also higher in France than in the U.S.(1) French serum lipid levels do not explain the paradox: they have been shown to be very similar to levels in countries with lower fat consumption and higher CHD rates (2). The most widely touted theory has been that the French regularly consume red wine, which has antioxidants and anti-inflammatory components, such as polyphenols and resveratrol, which confer greater protection against atherosclerosis than the ethanol in wine can account for. This study provides observational evidence that red wine consumption (for which urinary resveratrol is an accurate marker) does not correlate with lower rates of CHD. A placebo-controlled double-blinded interventional study of pharmacological doses of resveratrol would be more conclusive, but might be hard to justify given these findings. The source of protection enjoyed by French hearts remains debatable.

      References

      1: Ferrières J, The French paradox: lessons for other countries. Heart. Jan 2004; 90(1): 107–111. PMCID: PMC1768013

      2: Law M and Wald N. Why heart disease mortality is low in France: the time lag explanation BMJ. May 29, 1999; 318(7196): 1471–1480. PMCID: PMC1115846


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    2. On 2014 May 16, Juan Carlos Espin commented:

      This study demonstrates that (normal) dietary resveratrol levels are not correlated with all-cause mortality. And this is very logical. Why? Because resveratrol content in the diet is almost negligible. What is the effect of something that is hardly present in the diet? These results do not change the current evidence for resveratrol. Resveratrol is a component whose contribution in the diet is very low and unpredictable (even in wine drinkers) and despite the common belief, resveratrol does not explain the so-called ‘French Paradox’. In addition, resveratrol metabolism is very fast and a few hours are enough to detect resveratrol metabolites in urine. This means that the detection of resveratrol metabolites in urine is not a consequence of 'constant resveratrol intake for years'.

      Taking into account the above, to claim that resveratrol does not have influence on the all-cause of mortality would require the follow-up for 9 years of a cohort with 'normal' resveratrol levels (very low and unpredictable) versus another cohort with a standardized resveratrol supplementation.

      For more information: Resveratrol in primary and secondary prevention of cardiovascular disease: a dietary and clinical perspective. Tomé-Carneiro J, Gonzálvez M, Larrosa M, Yáñez-Gascón MJ, García-Almagro FJ, Ruiz-Ros JA, Tomás-Barberán FA, García-Conesa MT, Espín JC. Ann N Y Acad Sci. 2013 Jul;1290:37-51. doi: 10.1111/nyas.12150. Review. PMID: 23855464

      Resveratrol and clinical trials: the crossroad from in vitro studies to human evidence. Tomé-Carneiro J, Larrosa M, González-Sarrías A, Tomás-Barberán FA, García-Conesa MT, Espín JC. Curr Pharm Des. 2013;19(34):6064-93. Review. PMID: 23448440


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    1. On 2016 Sep 10, Morten Oksvold commented:

      Before reading or citing this article, please read the conclusion from the expert group for misconduct at the Central Ethical review Board which finds Paolo Macchiarini guilty of scientific misconduct:

      http://ki.se/en/news/macchiarini

      The specific report fromt the synthetic trachea transplantations:

      http://www.sll.se/Global/Verksamhet/Hälsa och vård/Nyhet bilaga/The Macchiarini Case Summary (eng).pdf


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    1. On 2016 Jan 29, Darko Lavrencic commented:

      I have a comment in regard to the following statement in the article: “However, the novel concepts are also challenged mainly by the lack of validated supporting data. For example, Klarica et al. failed to reproduce the historical experiments of Dandy, since no circulation of CSF was found along a plastic cannula introduced into the aqueduct of cats.«

      In the article by Dandy and Blackfan, which you cite, it is said »a piece of cotton in a small gelatin capsule … into the aqueduct of Sylvius, where it is deposited. « In the article by Oreskovic, Klarica and Vukic ( here I would like to point out the correct order of authors as opposed to “Klarica, Oreskovic and Vukic” used in the article), which you cite, it is said “A plastic cannula was introduced into the aqueduct of Sylvius through the vermis cerebelli and the outflow of CSF from the cannula was used as the CSF formation and circulation index” (also described in other similar articles by the above authors).

      Dandy and Blackfan blocked CSF flow in the aqueduct of Sylvius, while Oreskovic, Klarica and Vukic allowed CSF flow in the aqueduct of Sylvius through cannula. Can we assume that both experimental methods are the same? If the release of freshly actively formatted CSF happens during diastole when brain and choroid plexus shrink and create relative negative pressure in brain ventricles, this could explain hydrocephalus in Dandy and Blackfan experiment. For the comment on Oreskovic, Klarica and Vukic experiment, please see my on-line comment (Lavrencic 2013).

      References: Lavrencic, D. D. (2013). “During which phase of cardiac cycle is freshly actively formatted (FAF) cerebrospinal fluid (CSF) released into the brain ventricles: systole or diastole?”. Retrieved 30 April 2013, from http://www.med-lavrencic.si/download/Lavrencic_CSF_release_cardiac_cycle.pdf


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    2. On 2014 Sep 18, Thomas Brinker commented:

      We greatly appreciate your comments. However, the primary message of our review is that both experimental and clinical in-vivo observations must correspond to morphological and physiological findings. Regarding the perivascular space (PVS) it is unfortunate that, in humans, it is primarily still considered to be an optional rather than physiologically significant space. This view, based on morphological examination of human brain tissue, seems to contradict our mutual observations as well as those of others, i.e. the recent findings of the group of Needergard. We have discussed this point in our review and believe that substantial research efforts are warranted to clarify whether the PVS in humans is functionally significant.


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    3. On 2014 Sep 15, Andrew Tarnaris commented:

      Corresponding author: Andrew Tarnaris University Hospitals Birmingham Foundation NHS Trust Department of Neurosurgery Queen Elizabeth Medical Centre, Birmingham B15 2TH, United Kingdom.

      Email: andrewtarnaris@gmail.com

      I have read with interest the review article by Brinker et al. titled "A new look at cerebrospinal fluid circulation" published in Fluids Barriers CNS, 2014 May. The authors discuss key developments regarding cerebral cerebrospinal fluid (CSF) circulation including of production and absorption touching particularly among others the Virchow-Robin space (VRS) circulation.

      The significance of VRS in hydrocephalus in general has not been thus far well investigated [1]. Our group first attempted to examine the significance of VRS circulation in idiopathic normal pressure hydrocephalus (iNPH), and in particular investigate whether they could represent a surrogate imaging marker for coexisitng microvascular disease which is known to co-exist in a subset of patients with iNPH [2]. In that preliminary study we concluded that there may be a higher incidence of VRS in patients with iNPH, when compared with normal patients of similar age, however we could not prove with that initial study that there was any correlation with microvascular co-morbidities. We suggested that our data should be followed in a larger set of patients.

      We thus followed with a second study that was first presented in Hydrocephalus 2012 in Kyoto Japan entitled “In vivo study of the relationship of CSF dynamics and Virchow-Robin spaces in idiopathic normal pressure hydrocephalus “ (1OS-A2-05). We presented data from 17 patients with a diagnosis of iNPH and correlated the frequency of VRS with physiological data from lumbar infusion studies. Lumbar infusion studies can give unique information about the state of CSF dynamics in an individual. In summary we noted a lower compensatory reserve being associated with more intense perivascular CSF absorption, that resulting in a decrease in global outflow resistance. In that larger study (data submitted elsewhere) we confirmed that the incidence of VRS does not differ in normal population with the same risk factors for microvascular disease and proposed that VRS in iNPH may have a different pathophysiological origin representing impaired CSF circulation [3].

      We are glad that the concept of our previous work is now acknowledged in this excellent review and hope that other groups will investigate the role of VRS in iNPH or hydrocephalus in general with modern imaging or by employing other experimental models.

      References

      [1] Gideon P, Thomsen C, Gjerris F, Sørensen PS, Henriksen O. Increased self-diffusion of brain water in hydrocephalus measured by MR imaging. Acta Radiologica. 1994;35(6):514-9.

      [2] Tarnaris A, Tamangani J, Fayeye O, Kombogiorgas D, Murphy H, Gan YC, et al. Virchow-Robin Spaces in Idiopathic Normal Pressure Hydrocephalus: A Surrogate Imaging Marker for Coexisting Microvascular Disease? Hydrocephalus.33-7.

      [3] W.A. Mohamed, A. Tarnaris, H. Murphy, M. Csoznyka, Flint G. In vivo study of the relationship of CSF dynamics and Virchow – Robin spaces in idiopathic normal pressure hydrocephalus. Society of British Neurological Surgeons; 2012 October 2012; Leeds: British Journal of Neurosurgery; 2012. p. 596-629.


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    1. On 2017 Sep 29, Elena Gavrilova commented:

      The detailed answers on all E.V. Dueva’s comments regarding this article have been already published on the PLOS One page. Anyway, I am, as an author, glad that the article attracts the attention of the readers – it is in line with authors purpose to draw readers for a broad discussion of a new subject we have been working on. Here below the short answers on some comments are represented. The article provides all the details and data and it has been written as openly and clearly as possible. The nature of the posted comments confirms that the article is fully transparent for the readers so they have an opportunity to familiarize themselves with these results and arrive at their own opinion. The principal E.V. Dueva’s statement is incorrect since the product described in the article is not homeopathic. The technology used in some steps of the released-active forms of antibodies production is similar to the one used in the preparation of homeopathic products. This is obvious and indicated in papers and patents about these products. At the same time it should be highlighted that homeopathy therapy principle is the similarity principle, which is the basis for special approaches for the homeopathic drug investigation and application in practice. Quite the reverse, products containing released-active forms of antibodies have all the necessary attributes of standard pharmacological medicine. In addition, I would like to emphasize that the article is dedicated not to the investigation of basic features of released-active products, but the possibility to expand the use of ELISA as a method of activity assessment of RA forms of antibodies to interferon-gamma (RA forms of Abs to IFNg). The fact that RA forms of Abs to IFNg are the Active Pharmaceutical Ingredient of commercially available drug product ‘Anaferon for children’ was not in any way concealed from the readers as it is clearly stated in the article (section ‘Materials and Methods’, subsection ‘Preparation of anti-IFN-gamma release-active dilutions’). The article clearly states the purpose of the study, namely to assess the ELISA approach as the assay for the detection of RA forms of Abs to IFNg. Design of the study and conducted work have fully addressed its purpose.


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    2. On 2017 Sep 15, Evgenia V Dueva commented:

      This is an article about homeopathy, although the word «homeopathy» is never explicitly mentioned. The authors state: «RA forms of Abs to IFN-gamma contain release-active dilutions of antibodies to IFN-gamma consisting of a mixture of C12+C30+C50 final dilutions».

      Here the object of the study is described using homeopathic terminology. When translated this means the following: a mixture of rabbit polyclonal antibodies to recombinant human interferon gamma diluted to the power of 10<sup>-24,</sup> 10<sup>-60</sup> and 10<sup>-100.</sup> Or in other words: containing no measurable quantities of antibodies. Even the 10<sup>-24</sup> dilution is indistinguishable from zero. Note that these preparations were eventually diluted even further (at least to ~10<sup>-28)</sup> during the actual experiments. The claim that dilutions of substances beyond Avogadro’s limit have specific effects is a homeopathic claim.

      The authors, including Oleg Epstein – CEO of OOO "NPF "MATERIA MEDICA HOLDING" – a Russian Company that markets a number of drugs which contain active ingredients diluted beyond Avogadro’s limit, are not telling the truth when they state that «There are no patents, products in development or marketed products to declare».

      In fact, «RA forms of Abs to IFN-gamma» are the claimed «active ingredient» of one of the Company’s products called «Anaferon for Children». The article by Gavrilova et al. is listed on the Company’s website in the section called «Anaferon for Children», subheading «Articles, Preclinical» http://materiamedica.ru/en/stat/articles/. It is also actively self-cited by the Company in contexts such as «Data obtained using ELISA and piezoelectric immunosensors evidences that anaferon is able to modify IFNγ affinity to specific antibodies to IFNγ» https://medi.ru/info/11531/ and even in statements that the main mechanism of action for «Anaferon» is to improve ligand to receptor binding affinity.

      We revealed critical flaws in the key assumptions and conclusions made by the authors. One can find our critical comment on this article at PLOS One page.

      Considering that the actual data consists of just four ELISA runs, one cannot conclude that sufficient effort has been made to investigate such an extraordinary claim as the measurable biological effects of ultra-low homeopathic dilutions beyond Avogadro’s limit.


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    1. On 2014 Aug 13, Janet Kern commented:

      The following studies that showed an association between Thimerosal and the risk of autism were not included in the Taylor et al. (2014) meta-analysis even though they were published within the same time frame as the studies that were included.

      Gallagher CM, Goodman MS. Hepatitis B vaccination of male neonates and autism diagnosis, NHIS 1997-2002. J Toxicol Environ Health A 2010;73(24):1665-1677.

      Geier DA, Hooker BS, Kern JK, King PG, Sykes LK, Geier MR. A two-phase study evaluating the relationship between Thimerosal-containing vaccine administration and the risk for an autism spectrum disorder in the United States. Transl Neurodegener 2013;2(1):25.

      Young HA, Geier DA, Geier MR. Thimerosal exposure in infants and neurodevelopmental disorders: an assessment of computerized medical records in the Vaccine Safety Datalink. J Neurol Sci 2008;271(1-2):110-118.

      Geier DA, Geier MR. An evaluation of the effects of Thimerosal on neurodevelopmental disorders reported following DTP and Hib vaccines in comparison to DTPH vaccine in the United States. J Toxicol Environ Health A. 2006;69(15):1481-95.


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    1. On 2014 May 15, Andreas R Gruber commented:

      The fact that CFIm25 is a broad repressor of proximal poly(A) site usage and that knock-down of CFIm25 leads to a transcriptome-wide shortening of 3' UTRs is not novel and was first reported here:

      Gruber AR, Martin G, Keller W, Zavolan M. Cleavage factor Im is a key regulator of 3' UTR length. RNA Biol. 2012 9(12):1405-12. doi: 10.4161/rna.22570

      The study by Gruber et al. uses a high-quality 3'-end sequencing approach that allows direct inference of polyadenylation sites and not indirectly from less sensitive, standard RNA-seq data. The data set is publicly available in NCBI GEO: GSE40137.


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    1. On 2015 Feb 14, Martine Crasnier-Mednansky commented:

      Data are fully supported by previous studies by Kao KC, 2004 aimed at the determination of Transcription Factor Activities (TFAs) and gene expression profiles, particularly after a transition from glucose to acetate. Thus the level of CRP-cAMP was shown to peak within the first hour of transition and gradually reduce after an hour. The gene expression profile of pckA indicated a similar time scale, pckA being down-regulated within the first hour (after 5 minutes of the transition) and up-regulated gradually after an hour. This 'Cyclic AMP Responsive Switching' is particularly interesting as it bears consequences for analyzing the drastic downshift from glucose to acetate.


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    1. On 2014 Aug 06, Matthew Toth commented:

      This paper is a wonderful example of how understanding the pathophysiology of a rare disease can lead to specific treatments and how this can increase our knowledge of cellular biology and metabolism. It is a very dense paper that presents a lot of data including a unique visual example of one of the symptoms of this rare disease. I encourage all who are interested in Barth syndrome to visit the BSF website (www.barthsyndrome.org) and read the paper in its full length.


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    1. On 2014 Nov 13, Madhusudana Girija Sanal commented:

      The paper from Rosenberg's group titled 'Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer' (1) raises a lot of questions.

      • The exact tumor volumes observed in the single patient mentioned in this report are not provided in this paper. Tumor volume details in lungs, liver and other places. This is very important because the entire success story is built on tumor volumes of the lungs and liver.

      • Usually more than one T-cell is involved in killing a cancer cell. Even if we assume one T-cell is involved in killing one cancer cell, the amount of cells infused into the patient is not sufficient for the clearance of the tumor mass which should be large (from the description it is clear that the patient is in the advanced stage of her disease).

      • Solid tumors are not well perfused and it is not clear how the T-cells managed to get into the solid nodules in sufficient numbers to cause a very significant reduction in tumor volume.

      • Solid tumors also suffer from hypoxia. It is well known that hypoxia can impair anti-cancer immunity by altering the function of innate and adaptive immune cells (for example by inhibition of proliferation and induction of cell death) and/or by increasing the intrinsic resistance of tumor cells to the cytolytic activity of immune effectors.

      • The mutant protein (note that there is only one amino acid difference) is degraded and processed like any other protein to be displayed on the cancer cell surface by the class one MHC complex. What is the probability that the right epitope of the mutated protein is displayed on a significant proportion of cancer cells to attract immune mediated destruction of the whole cell? Is there any evidence that the mutated protein is over-expressed in this cancer?

      • In many cancers class one MHC is down-regulated as a mechanism to evade immunity. Is the scenario very different in this patient?

      • If the transfused cells are clearing the tumor cells by recruiting other cells, why didn’t the authors study the changes in the number, distribution and re-activity and cytokine responses of other members of the leukocytes-at least by FACS analysis of circulating immune cells-an easy to do experiment?

      • Cancer is a very dynamic process which involves continuous evolution and natural selection. There exists high tumor variability- (cellular, genetic, epigenetic and immunological)-especially in advanced disease-such as a relapse after a few courses of radiotherapy and chemotherapy. How can an immune mediated killing overcome such heterogeneity (of epitopes evolved)?

      Reference

      1) Tran E et al. Science. 2014 May 9;344(6184):641-5.


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    1. On 2015 May 21, ALEXANDER TSAI commented:

      The measures of n-3 and n-6 PUFA intake used in this study have well documented construct validity, as supported by moderate-to-strong correlations with fatty acids measured in plasma and erythrocytes and adipose tissue, and by their ability to predict the incidence of relevant conditions such as coronary heart disease, type 2 diabetes, and macular degeneration. The experimental evidence for the use of n-3 in the treatment of depression is not conclusive. In the meta-analysis by Bloch & Hannestad (Mol Psych 2012;17:1272–1282), the estimated treatment effect was small in magnitude and not statistically significant. Even if one accepts the criticisms that were published in response to that study, the reanalyses (Mol Psych 2012;17:1163–1167) did not change the fundamental conclusion that any possible measurable effect of n-3 on depression is small and likely explained by publication bias.


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    2. On 2015 Mar 12, Dennis Embry commented:

      One should consider this finding in the context of self-report on diet versus the studies using biological markers such the study by Lewis et al. http://www.ncbi.nlm.nih.gov/pubmed/21903029.

      The correct conclusion ought not to imply that there is no "…evidence that intake of n-3 PUFAs or fish lowered the risk of completed suicide." One of the reasons that the questionnaire presents a grave difficulty is the ubiquity of n6 in American foods that people have no idea about—even nurses. Few people realize for example that virtually all packaged baked goods in grocery stores contain significant n6. And snacks like a 1oz bag of any chip-type product are about about 3/4's by weight n6.

      The issue here is that present food questionnaires may be too course and insensitive to n3 and n6 ratios in any, which is the issue. Yes, the study has large numbers but larger numbers with insensitive instrumentation may be just large numbers. This null finding is not dispositive, given other data such as the military studies that have much finer analyses, plus the experimental studies that show considerable impact on the layers of impulsive, depressive and aggressive behaviors associated with n3 deficit and n6 surplus.


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    1. On 2014 May 14, Jim Woodgett commented:

      Interesting paper but the evidence that the effect is selectively mediated through GSK-3beta is questionable. In support of the contention is that a band of ~45kDa was found (figure 5A) with a phospho-Akt substrate antibody. However, there's another band ~4kDa above it. In figure 6, an inhibitor to GSK-3 was used: "glucose uptake and lactate production were measured in the presence or absence of the Gsk-3β inhibitor SB 216763". This inhibitor is equally effective in blocking the 51kDa isoform, GSK-3alpha (no small molecule inhibitors are isoform selective - I am a scratched record). Moreover, Akt/PKB phosphorylates GSK-3alpha at serine 21 and GSK-3beta at serine 9. As far as I am aware, there are no published data to suggest that Akt differentiates between the two GSK-3 isoforms and since they are ubiquitously expressed, both are very likely phosphorylated and inhibited upon phosphatidylinositol 3' kinase activation. Hence, I'd recommend modifying the title and conclusions to: "Insulin Receptor Substrate-2 Mediated Phosphatidylinositol 3-kinase Signaling Selectively Inhibits Glycogen Synthase Kinase-3 to Regulate Aerobic Glycolysis" as this more accurately reflects the actual experimental data and tools used. This mistake is frequent in the literature (assumptive assignment of effects to GSK-3β). In the majority of cases, the experimental evidence presented does not exclude GSK-3alpha.


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    1. On 2014 Aug 27, Ryan Radecki commented:

      Post-publication commentary:

      "Failing Our Profession Through Futile Care"

      It is not always feasible to serve all masters in medicine. From a resource utilization standpoint, unfortunately, one missed opportunity is with regard to how we approach futile care. We have all experienced the care of a patient who, regardless of testing and therapy, has zero chance of meaningful recovery. To terminate care for these patients sometimes requires difficult conversations, and can snowball out of control with adverse legal and public relations consequences.

      But, as this report from UCLA and RAND details, our failures to properly address futile care and end-of-life issues result in direct downstream harms to other patients....

      http://www.emlitofnote.com/2014/08/failing-our-profession-through-futile.html


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    1. On 2014 May 11, Hilda Bastian commented:

      An important reminder that multiple publication bias - which can lead to double-counting of patients - in meta-analysis has not disappeared (PMC full text). Choi and colleagues point to a recent study suggesting the incidence of duplicate publication in the field of otolaryngology didn't change over 10 years (Cheung VW, 2014), although it may have reduced in some other fields.

      Systematic reviewers weed out most duplicate reporting, but as this new study shows, some still slip through. In a meta-analysis, the magnification of events can tip the balance of evidence. A study a decade ago showed that authorship was an unreliable criterion for detecting duplicate publication of trial data (von Elm E, 2004), and the publications don't cross-reference each other, either. Choi and colleagues don't raise the issue of the importance of clinical trial registration here: Antes and Dickersin pointed to this as a key strategy to address this problem (Antes G, 2004).

      There is also duplicate registration of trials in different registers, though (Zarin DA, 2007, Califf RM, 2012). ClinicalTrials.gov aims to identify and resolve duplicate registration of trials (Zarin DA, 2007), and most registered trials are included there. Consistent citation of trial registration numbers, especially the ClinicalTrials.gov identification (NCT number), in all systematic reviews of trials would be useful for readers and those trying to identify studies. It might help reduce reviewers' workload in weeding out duplicate reports, too.

      (I work on projects related to systematic reviews at NCBI (National Center for Biotechnology Information, U.S. National Library of Medicine), which is also responsible for ClinicalTrials.gov.)


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    1. On 2014 Jun 10, Robert M Flight commented:

      How we forgot to put these links in the abstract, I'll never know.

      The software is available as a Bioconductor package

      A development version is available on Github, this is also where issues should be filed if you have any problems using the software.

      The code used for the analysis presented in the Paper is on Github as well


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    1. On 2014 May 21, Amanda Capes-Davis commented:

      You would think a cell line named "Chang liver" is hepatic - but unfortunately this is not the case. Chang liver cells are cross-contaminated with HeLa, a cervical carcinoma cell line. For a database of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2016 Aug 27, David Keller commented:

      Risk of other dementias may be exacerbated by lower aluminum levels than are required to cause dialysis encephalopathy

      I thank Lidsky for his comment, and I understand his point that dialysis encephalopathy requires serum aluminum levels too high to occur in persons with normal renal function. However, this does not answer the crucial question: does chronic aluminum ingestion increase the risk of dementia in persons with normal renal function? It is possible that other dementing processes might be exacerbated by the lower levels of aluminum found in patients with normal renal function who chronically ingest aluminum. The fact that dialysis encephalopathy cannot occur in patients with normal renal function does not preclude the possibility that the risk of dementia is indeed increased by environmental exposure to aluminum.


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    2. On 2016 Aug 07, David Keller commented:

      Dementia caused by elevated aluminum levels in dialysis is not Alzheimer's disease: a distinction without a difference

      Lidsky points out that the clinical presentation of dementia caused by elevated aluminum levels in dialysis patients is clearly distinct from that of true Alzheimer-type dementia. He also debunks the rumor that elevated aluminum levels cause the neurofibrillary tangles in the human brain which are pathognomonic for Alzheimer disease, noting that the neurofibrillary tangles caused by aluminum exhibit a distinctly different pattern when examined carefully under immunofluorescence, proving once and for all that this form of brain damage caused by aluminum is definitely not Alzheimer disease.

      These findings are noted, but are of little comfort if they merely imply that aluminum ingestion causes brain damage and dementia which cannot be classified as Alzheimer type. As a primary-care physician who must answer patients' questions about the risks of dietary aluminum, that distinction truly makes no difference to patients or to myself.


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    1. On 2014 May 24, Carl Blackman commented:

      In the last century where were a series of publications with first authors: R Adey, S Bawin, A Sheppard, C Blackman and S Dutta, who showed that radiofrequency radiation at 50, 147, 450 and 980 MHz could cause biological changes, primarily in calcium ion releases from nervous system tissues/cells, when the carrier wave was amplitude modulated at low frequency between approximately 9-20 Hz, and again at 50 Hz. Based on these reports, it would appear the authors of the Nature report have substantial work to do to unfold the underlying critical mechanisms of action.

      More recently, B Pasche and colleagues have reported potential therapeutic used of 27 MHz fields when they are amplitude modulated at specific low frequencies.

      Of course, when discovery research is done, if it is productive it should immediately cause more questions to be asked than it can answer; thus the need for multidisciplinary teams (and of course resources).


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    2. On 2014 May 10, Madhusudana Girija Sanal commented:

      I am skeptical about the observations and conclusions presented in this paper on the effect of radio waves on spacial position sensing in birds. The paper raises more questions than answers. This paper needs scrutiny. Metal wire meshes are used to block electromagnetic waves (depending on the frequency). I did not understand how electric grounding attenuated electromagnetic noise and it came back when the circuit was open (see the accompanying video). Why the birds are sensitive to AM frequency range 50 kHz to 5 MHz? What is the evolutionary logic by which birds are sensitive to electromagnetic waves at this frequency? The earth has a magnetic field, but how it generates electromagnetic waves in this frequency range? To my knowledge there is something called "Schumann resonances" but it is unlikely that birds will evolve a mechanism to use this to sense directions. The main background in this Schumann spectrum, beginning at 3 Hz and extend to 60 Hz, and peaks at extremely low frequencies 7.83 (fundamental), 14.3, 20.8, 27.3 and 33.8 Hz. The solar radiation and its effect on the earth's atmosphere is another source of naturally occurring electromagnetic interference besides the lightning. It is also not clear in the paper about the orientation of the huts with respect to the earth's magnetic field and the position with reference to the sun. However the authors seem to admit that the previous efforts to show the influence of electromagnetic noise (excluding heat and visible light!) were not reproducible. How much electromagnetic energy (in radio frequency) was received by these birds during the procedure?


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    1. On 2015 Feb 27, Geriatric Medicine Journal Club commented:

      This study of frailty to predict postoperative mortality risk was critically appraised at the first Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter) in August 2014. A full transcript of the discussion can be found here http://gerimedjc.blogspot.com/2014/08/first-gerimedjc.html?spref=tw. Highlights of the discussion include how to move from assessment of frailty to improving outcomes in the frail undergoing surgery.


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    1. On 2015 Apr 11, Takanori Eguchi commented:

      This is an interesting work. Here is the very important first report of MMP function for transcriptional control. Eguchi T, Kubota S, Kawata K, Mukudai Y, Uehara J, Ohgawara T, Ibaragi S, Sasaki A, Kuboki T, Takigawa M. Novel transcription-factor-like function of human matrix metalloproteinase 3 regulating the CTGF/CCN2 gene. Mol Cell Biol. 2008 Apr;28(7):2391-413.


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    1. On 2014 Aug 03, Swapnil Hiremath commented:

      This review article was discussed on July 8th 2014 in the open online nephrology journal club, #NephJC, on twitter. Introductory comments are available at the PBFluids blog and at the NephJC website. It was a fascinating discussion, with participation from nephrologists around the world including the center of the epidemic in Central and South America. A transcript and a curated (i.e. Storified) version of the tweetchat are available from the NephJC website. The highlights of the tweetchat were:

      • Mesoamerican nephropathy (or CKD of unknown etiology, CKDu) is increasingly recognized as an epidemic in Central American countries.
      • Dr Johnson and colleagues present a very intriguing and novel hypothesis, based on repeated episodes of dehydration driving kidney damage, mediated by increased production of sorbitol, its conversion to fructose and downstream effects of fructose.
      • The tweetchat participants found the hypothesis very interesting and physiologically fascinating. However, given past experience (notably with Balkan nephropathy), they felt an elusive toxin should still be entertained as a possibility. Further research efforts are urgently needed to confirm Dr Johnson's hypothesis and/or pinpoint the actual cause of this entity.

      Interested individuals can track and join in the conversation by following @NephJC or #NephJC, or visit the webpage at NephJC.com.


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    1. On 2015 Feb 27, Geriatric Medicine Journal Club commented:

      This study was discussed at the January 2015 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). The full transcript of the discussion can be found here: http://gerimedjc.blogspot.com/2015/01/gerimedjc-january-30-2015.html?spref=tw Highlights include links to Osteoporosis Canada's interpretation of prolonged bisphosphonate use and implications for campaigns such as Choosing Wisely.


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    1. On 2014 May 27, G L Francis commented:

      This editorial makes many pertinent points about the continuing frustration with the IGF-I Receptor as a cancer target for a number of therapeutic drugs of different classes directed at either the receptor extracellular domain or its intracellular tyrosine kinase domain. The only comment I wish to make on this excellent update of the field is a question in relation to the following statement “Although mutated IGF-IR has not been identified in any cancer, IGF-IR does appear to be up regulated in alveolar rhabdomyosarcoma, its signalling is required for survival of Ewing sarcoma cell lines, and the growth of osteosarcoma and desmoplastic small round cell turmors can be inhibited by IGF-IR blockade’’; and specifically, concerning the first part declaring the absence of any reports of receptor mutations in cancer.

      This is not quite the case as a paper published earlier this year, Hum Pathol. 2014 Jun;45(6):1162-8. doi: 10.1016/j.humpath.2014.01.010. Epub 2014 Jan 31. ‘’Insulin-like growth factor 1 pathway mutations and protein expression in resected non-small cell lung cancer.’’ PMID: 24745618. http://www.ncbi.nlm.nih.gov/pubmed/24745618. wherein analysis of samples from 304 patients found a silent mutation in exon 16 and 3 mutations in introns of the IGF-I Receptor gene intracellular tyrosine kinase domain.

      A further publication in Sarcoma. 2013;2013:450478. doi: 10.1155/2013/450478. Epub 2013 Jan 28 ‘’Insulin-like growth factor 1 receptor as a therapeutic target in ewing sarcoma: lack of consistent upregulation or recurrent mutation and a review of the clinical trial literature.”. http://www.ncbi.nlm.nih.gov/pubmed/23431249 in an analysis of 47 tumors identified only one mutation, a nonsynchronous change, R1353H, in a region with predicted low functional impact.

      Moreover, these limited observations suggest that considerable work needs to be undertaken to redefine the approach to the IGF-I receptor as a therapeutic target – a point very well made by the author in this editorial statement.


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    1. On 2014 May 21, Amanda Capes-Davis commented:

      This study demonstrates low toxicity against WISH cells. However, it is important to note that WISH comes from tumor tissue; it is cross-contaminated with HeLa, a cervical carcinoma cell line. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 Aug 04, Ryan Radecki commented:

      Post-publication commentary:

      "The Glucose-Insulin-Potassium in ACS (IMMEDIATE) Revisited"

      There are a few folks persistently enamored with the use of glucose-insulin-potassium cocktails in the setting of acute coronary syndrome. Two years ago, I reported on the initial results of the IMMEDIATE trial, published in JAMA. At the time, I boggled that such a small, underpowered study – and one that changed their enrollment target and primary endpoint during the trial – would ultimately be accepted into JAMA. It was also subsequently picked up and promoted by ACEPNow as a "promising therapy" that "slashes death risk" (Tweet still visible, site content since deleted)....

      http://www.emlitofnote.com/2014/07/the-glucose-insulin-potassium-in-acs.html


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    1. On 2014 Jul 01, Frank Twisk commented:

      A definition of recovery in myalgic encephalomyelitis and chronic fatigue syndrome should be based upon objective measures. Qual Life Res. 2014 Jun 17. doi: 10.1007/s11136-014-0737-1. Twisk FNM.

      Abstract

      Introduction

      Adamowicz and colleagues recently proposed to use "a consistent definition of recovery that captures a broad-based return to health with assessments of both fatigue and function as well as the patients' perceptions of his/her recovery status" for patients with chronic fatigue syndrome (CFS).

      Methods

      A qualitative analysis of case definitions for Myalgic encephalomyelitis (ME) and CFS and methods to assess the symptoms and clinical status of ME and CFS patients objectively.

      Results

      The criteria of CFS define a heterogeneous disorder. ME, often used interchangeably with CFS, is principally defined by muscle weakness, cognitive impairment etc., but above all post-exertional "malaise": a long-lasting increase in symptoms, e.g. muscle pain and cognitive deficits, after a minor exertion.

      The principle symptom of CFS however is "chronic fatigue". Since post-exertional "malaise" is not obligatory for CFS, only part of the CFS patients meet the diagnostic criteria for ME, while not all ME patients qualify as CFS patients.

      There are several accepted methods to assess characteristic symptoms and the clinical status of ME and CFS patients using objective measures, e.g. (repeated) cardiopulmonary exercise tests.

      Conclusion

      To resolve the debate about the clinical status, proposed effectiveness of therapies and recovery in ME and CFS, it is crucial to accurately diagnose patients using well-defined criteria for ME and CFS and an objective assessment of various typical symptoms, since subjective measures such as "fatigue" will perpetuate the debate.


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    2. On 2014 Jun 04, Joan Crawford commented:

      Part 2

      I’d have liked to have seen this article proposing solid, objective measures be used in the future – ones that have face validity with patients and doctors. Moreover, future trials need to decide if the researchers are aiming at recovery from ill health to as near/close to pre-morbid health (as in like how you’d recover from a severe, debilitating infection) or if they are aim at improving functioning/quality of life as a goal in its own right. This difference ideally should be clearly identified.

      The omission of the obvious mathematical/statistical flaws with the use of SF36 PF scale was notable. They miss that using 1SD below mean is not an OK thing to do to compare HC and patients. Doing this is a statistical nonsense. The HC data is massively skewed with a ceiling effect. The bulk of HCs score the max score of 100. (Bowling, 1999, Figure 1). The HC data is not normally distributed so using the mean is not terribly helpful here when comparing and setting standards for recovery. I think using the mode (the value that appears most often in the data sets) would be much more meaningful in this context. Similar will be true of the fatigue scores. There was also no mention of the lowering of the SF36 PF scale outcome measure cut off level in the PACE trial (White et al., 2011). There may well be good reasons for doing so but there was no critical review as to whether the reasons given by White et al were good enough to justify the changes between the proposed pre-trial paper measures (White et al 2007) and the final Lancet one. I notice that White was a co-author of the Knoop (2007) paper that selected a SF36 PF score of -1SD as recovered but in a later trial (White et al., 2011) this was reduced to 60 (-2SD). This is quite a leap by the same investigator.

      I particularly do not like their pathologisation/speculation of the role of pre-morbid patient functioning. Action prone nonsense. No one can or are they ever likely to prove objectively that pwME/CFS were overactive/overambitious/action prone before getting ill. I hear people mourning the loss of activities, relationships and careers they cherished and enjoyed immensely. So now they cannot even talk about their pre-illness time without feeling psychologised? To not take a more critical view of this is a real let down for me. It’s subjective, speculative nonsense that is unprovable. Patients have a right to get annoyed when they are psychologised in this manner. It should be rather obvious that patients have ex-work colleagues and friends who worked as hard (or harder, longer, faster) than them who are still employed, with families, fit and well with fulfilling lives. PwME/CFS cannot do this because they are sick. Not because they overdid it a bit. That is burnout, not ME/CFS. I thought it remiss to not see the other side regarding how the impact of this speculation might affect patients. Moreover, there are plenty of not especially ambitious, couch potatoes who are ill!

      How recovery in ME/CFS is operationalised in the future requires more critical thought and this must take into account how the patients define recovery and must be able to be demonstrated objectively (Haywood et al., 2011).

      References:

      Anthony, W. A. (1993) Recovery from mental illness: the guiding vision of the mental health service system in the 1990s. Psychosocial Rehabilitation Journal, 16, 11-23.

      Bowling A., Bond, M., Jenkinson, C., & Lamping, D.L. (1999). Short Form 36 (SF-36) Health Survey questionnaire: which normative data should be used? Comparisons between the norms provided by the Omnibus Survey in Britain, the Health Survey for England and the Oxford Healthy Life Survey. Journal of Public Health Medicine. 21(3):255-70.

      Haywood, K.L., Staniszewska, S., & Chapman, S. (2011). Quality and acceptability of patient-reported outcome measures used in chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME): A systematic review. Quality of Life Research, In press.

      Knoop, H., Bleijenberg, G., Gielissen, M. F. M., van der Meer, J.W. M., & White, P. D. (2007). Is a full recovery possible after cognitive behavioral therapy for chronic fatigue syndrome? Psychotherapy and Psychosomatics, 76, 171–176.

      Lester, H., & Gask, L. (2006). Delivering medical care for patients with serious mental illness or promoting a collaborative model of recovery. British Journal of Psychiatry, 188, 401–402.

      White, P.D., Sharpe, M.C., Chalder, T., DeCesare, J.C., Walwyn, R; on behalf of the PACE trial group. (2007). Protocol for the PACE trial: a randomised controlled trial of adaptive pacing, cognitive behaviour therapy, and graded exercise, as supplements to standardised specialist medical care versus standardised specialist medical care alone for patients with the chronic fatigue syndrome/myalgic encephalomyelitis or encephalopathy. BioMed Cent Neurology, 7:6.

      White, P.D., Goldsmith, K.A., Johnson, A.L., Potts, L., Walwyn, R., DeCesare, J.C., et al. (2011). Comparison of adaptive pacing therapy, cognitive behaviour therapy, graded exercise therapy, and specialist medical care for chronic fatigue syndrome (PACE): A randomised trial. Lancet, 5, 377(9768), 823-836.


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    3. On 2014 Jun 04, Joan Crawford commented:

      Part 1

      This paper has a great description of the differences between ‘recovery’ versus ‘adaptation/feeling better’. As a patient I describe this as the difference between ‘feeling better’ and ‘being better’ (i.e. recovered to point comparable with pre-existing health given age increase with ability to return to work/social life without the presence of limiting symptoms). These things appear to get muddled in many clinical trials. I suspect anyone feeling poorly will feel a bit or a lot better after a psychological intervention with a concerned, empathic individual, however, whether this has any impact on their underlying condition or activity levels needs to be shown by objective measures.

      It was a disappointment that in this paper there was no push for more objective measures of patient functioning to be used in future research work. For example, pedometers, actigraphy, neuropsychological tests, 2 day exercise testing (if well enough at baseline), using simple dynamometers taking readings over 2 days, return to work/school (or ability to do if the person wished), move from incapacity/sickness welfare payments to job seeking benefits and so on. I’m perplexed when researchers claim that patients are recovered if they continue to receive incapacity/ill health payments. Perhaps in this condition it might be worth measuring whether saliva cortisol levels and NK cell functioning normalise. At a push even the simple 6 minute walking test could be helpful. Objective measures need not be expensive. Simple, reliable and cheap equipment such as pedometers are available for around $30 and can show really well if a patient who is doing better over time. This could be used quite simply to get around the issue of is the patient feeling better because they are actually doing less that is discussed in the review. It’s a shame that straightforward solutions like this were not suggested.

      Within the paper the authors refer to Lester & Gask (2006), which includes a popular definition of recovery from within mental health context by William Anthony as: “‘a way of living a satisfying, hopeful and contributing life even with the limitations caused by illness. Recovery involves the development of a new meaning and purpose in one’s life as one grows beyond the catastrophic effects of mental illness’ (Antony, 1993: p. 21). I had not seen this definition before for recovery so it was educating to be made aware that this was a widely used concept. To me that defines adaptation, not recovery. I would not be happy with researchers who decided that that was a good place to start defining recovery from ME/CFS. I’d want the goal to be at a minimum to not feel ill or sick or debilitated and able to be free of disease symptoms and normal functioning for the patient for their age.

      References and Part 2 above


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    1. On 2015 Feb 03, Ashray Gunjur commented:

      Thank you Gabe (RG) Boldt for the useful comment. A well designed search strategy is indeed essential for a systematic review to 'net' all relevant studies and thus not represent incomplete or biased results.

      Our search strategy for the above systematic review was constructed using the advanced PubMed search engine of the MEDLINE database. All MeSH Terms are as suggested by the PubMed search engine, and were selected by authors as best aligning with our aim- to systematically review the literature on the treatment of adrenal metastases with stereotactic ablative body radiotherapy (SABR), adrenalectomy or percutaneous catheter ablation (PCA) techniques.

      We preferred MeSH term searches given the heterogeneity of terminology around therapeutic modalities. For example, SABR is also referred to as stereotactic body radiotherapy (SBRT) and fractionated stereotactic radiation therapy (FSRT). An extensive manual secondary search of bibliographies was completed for all netted manuscripts for inclusion. This resulted in a further 10 relevant articles being found. This thus proves that our original search strategy was not 100% sensitive in 'netting' all relevant articles, however we believe this was accounted for by our extensive secondary search.

      Once again, thank you for your comment.


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    2. On 2015 Jan 22, Gabe (RG) Boldt commented:

      The quality of the literature search in this systematic review is highly suspect!

      For example, "body radiotherapies, stereotactic[MeSH Terms]" is not a MeSH. The correct MeSH is radiosurgery[mh].<br> "Ablation, radiofrequency catheter[MeSH Terms]" is not a MeSH. The correct MeSH is Catheter Ablation[mh]. "Adrenal cancer[MeSH Terms] is not a MeSH. The correct MeSH is Adrenal Gland Neoplasms[mh]. Aside from these crucial errors of using the wrong indexed terms, the boolean logic in the search string is confusing, and the nesting of terms in the brackets does not make sense. If you are not searching with the proper Medical Subject Headings and using boolean logic correctly then you are not going to get proper results and this will effect how many research papers you find for your systematic review. Systematic reviews must be conducted with the assistance of a medical librarian who understands the functionality of the databases being searched and can help develop effective search strategies for the systematic review process.


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    1. On 2014 Jun 06, Amanda Capes-Davis commented:

      The authors very correctly use a panel of different cell lines to assess in vitro cytotoxic activity. Two cell lines do not come from the tissues listed; these two cell lines, HEp-2 and KB, were cross-contaminated during establishment and are actually HeLa. It is important to test cell lines for authenticity using a technique such as short tandem repeat (STR) profiling. For a list of known cross-contaminated cell lines, see http://iclac.org/databases/cross-contaminations/.


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    1. On 2014 May 07, Stefan Pokall commented:

      I wonder about the title since the answer is given by the clinical course and the chyle output. What this article adds is a late presentation with 3 months of age without a prenatal or perinatal history. The conclusion that pleuroperitoneal shunt is the first procedure to perform in children is not supported in literature, rather a TDL as demonstrated in cardiothoracic studies by Cleveland K 2009 and Nath DS 2009 and even Azizkhan recommends it secondary to pleurodesis (textbook ziegler/azizkhan/weber Fig.41-5).


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    1. On 2015 Jul 04, David Keller commented:

      A large, well-designed controlled study is needed to settle this debate

      Dr. Morgentaler argues persuasively in favor of the safety and benefits of prescribing testosterone therapy for widened indications, especially in aging men. The FDA warning on testosterone therapy, however, states: "The benefit and safety of these medications have not been established for the treatment of low testosterone levels due to aging, even if a man’s symptoms seem related to low testosterone" based on "a possible increased risk of heart attacks and strokes in patients taking testosterone." (1)

      We have seen prior cases where faint signals of cardiovascular harm were later verified in larger studies, and led to the withdrawal or restriction of drugs (e.g. Vioxx, Avandia, PremPro). My primary duty to my patients is to do no harm. We need a large, well-designed, controlled study of testosterone therapy to prove its safety and benefits for each proposed indication for which it is not currently approved. Until such proof is available, we should not widen our prescribing practices for this powerful steroid sex hormone, which has so many pleiotropic effects.

      Reference:

      1: FDA Drug Safety website, accessed on 7/4/2015, http://www.fda.gov/Drugs/DrugSafety/ucm436259.htm


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    1. On 2015 Apr 21, Bernard J Crespi commented:

      We are happy to clarify some points regarding our article, and reply to the issues raised in the comment from Dr. Bishop.

      First, we would consider the title of our article to be accurate, as it simply refers to mediation of schizotypy and handedness by the LRRTM1 gene, and does not, as the comment indicates, make any statements about SNPs in relation to handedness. We consider epigenetic phenomena, such as the methylation that we measured for LRRTM1, to be important mediators of a gene's functional effects. For example, Brucato et al. (2014) have recently linked methylation of LRRTM1 with risk of schizophrenia.

      Second, we used a measure of strength of handedness, which is compatible with Francks et al. (2007) only in being a continuous measure. We apologize in that we could have worded the relevant sentence more precisely. We did not use a specific measure that, like that of Francks et al. (2007), may confound handedness direction with handedness strength, because these two variables, direction and strength, appear to exhibit independent genetic underpinnings (e. g., Ocklenberg et al. 2014). Moreover, schizophrenia and schizotypy show associations predominantly with handedness strength, not direction, from previous work (e. g., Chapman et al. 2011).

      Third, we found a significant association at P = 0.026 (r = -0.375, product-moment correlation) for an association of PC1 (a composite methylation score) with handedness for our full sample, based on our predictions. We also provided the results for males and females separately, because of extensive evidence of gender differences for cognitive and psychiatric phenotypes such as those analyzed here. Considered separately, only the results for females were statistically significant (at r = -0.469, P = 0.032). Higher statistical significance would always be more compelling, of course.

      We welcome insightful comments and constructive criticism, and we hope that our results regarding LRRTM1 will motivate further research into the effects of genetic and epigenetic variation in this fascinating gene.

      References

      Brucato N, DeLisi LE, Fisher SE, Francks C. Hypomethylation of the paternally inherited LRRTM1 promoter linked to schizophrenia. Am J Med Genet B Neuropsychiatr Genet. 2014 Oct;165B(7):555-63.

      Chapman HL, Grimshaw GM, Nicholls ME. Going beyond students: an association between mixed-hand preference and schizotypy subscales in a general population. Psychiatry Res. 2011 May 15;187(1-2):89-93.

      Francks C, Maegawa S, Laurén J, … Monaco AP. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Mol Psychiatry. 2007 Dec;12(12):1129-39, 1057.

      Ocklenburg S, Beste C, Arning L. Handedness genetics: considering the phenotype. Front Psychol. 2014 Nov 11;5:1300.


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    2. On 2015 Apr 19, Dorothy V M Bishop commented:

      The genetics of handedness is a topic where there seems to be a considerable mismatch between conventional wisdom, where handedness is regarded as a highly heritable trait, and research, which has struggled to find evidence of significant heritability. I am aware that a meta-analysis of twin studies by Medland and colleagues reported heritability of around .25, but a subsequent study by Armour et al (2014) with N = 3940 failed to find any locus that reached genome-wide significance. I also appreciate that this does not rule out genetic influences with small effect sizes, especially when the picture is made more complex by potential imprinting.

      I think, though, that the title of this paper does rather overstate the case in claiming that LRRTM1 mediates schizotypy and handedness. (My focus is solely on the claims regarding handedness).

      I appreciate that researchers in this area have some major problems to grapple with. One is that there is no agreement about how to define the phenotype of handedness. Most studies rely on handedness questionnaires, but these have only an imperfect relationship with measures of relative hand skill. In the absence of an adequate underlying model of etiology of handedness, almost any kind of measure can be justified: a binary distinction between left and right, a distinction between left, mixed and right, a continuous, quantitative scale, or a distinction between consistent (left or right) vs inconsistent (mixed) handers. As I argued many years ago, such flexibility is dangerous, because it almost always possible to find some handedness measure that will show an apparently meaningful relationship with a criterion measure (Bishop, 1990).

      In this study, the handedness measure was strength of handedness, assessed by "taking the absolute value of the handedness score such that values near zero represent mixed handedness and values near 64 represent strong handedness (right or left)." It is stated that this was done to be consistent with the previous study on LRRTM1 by Francks et al (2007). However, my impression was that Francks et al used a continuous quantitative phenotype that represented relative hand skill, with R>L at one end and L>R at the other. Thus the raw laterality quotient (-64 to +64) from the Waterloo Handedness Questionnaire would seem conceptually closer to the measure used by Francks et al than the absolute measure. It's possible I have misunderstood this (Francks et al is an exceedingly complex paper), but I'd be grateful for clarification.

      I find the title misleading because in the current paper the LRRTM1 SNPs were not associated with the absolute handedness measure used with this sample. (This cannot be regarded as a failure to replicate Francks et al, since parent-of-origin effect were not analyzed and the measurement of handedness appears to have been different). The reference in the title to the gene mediating handedness presumably refers to the significant correlation between methylation in CpG sites and absolute handedness. However, this result does not survive correction for multiple comparisons. I therefore would suggest that the evidence for an association between LRRTM1 and handedness in this study is not compelling.

      References

      Armour, J. A. L., Davison, A., & McManus, I. C. (2014). Genome-wide association study of handedness excludes simple genetic models. Heredity, 112(3), 221-225. doi: 10.1038/hdy.2013.93

      Bishop, D. V. M. (1990). How to increase your chances of obtaining a significant association between handedness and disorder. Journal of Clinical and Experimental Ñeuropsychology, 12, 786-790.

      Francks, C., Maegawa, S., Lauren, J., Abrahams, B. S., Velayos-Baeza, A., Medland, S. E., . . . Monaco, A. P. (2007). LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Molecular Psychiatry, 12(12), 1129-1139.

      Medland, S. E., Duffy, D. L., Wright, M. J., Geffen, G. M., Hay, D. A., Levy, F., . . . Boomsma, D. I. (2009). Genetic influences on handedness: Data from 25,732 Australian and Dutch twin families. Neuropsychologia, 47(2), 330-337. doi: 10.1016/j.neuropsychologia.2008.09.005


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    1. On 2016 Aug 24, 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 originating journal article. The ID given is NCT5327714500. We believe the correct ID, which we have found by hand searching, is NCT01994005.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 PMID: 27056367

      * 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


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    1. On 2014 Jul 23, Qiyong Gong commented:

      Dear Dr. Castellanos,

      Thanks for your interest, and yes, we were using the Stroop Color-Word test rather than the numerical version of the Stroop. Those "numbers" were actually referring to the numbers of words rather than numerical numbers. For instance, "right numbers" denotes the number of answers for correctly identifying the objects, and vice versa, "error numbers" for the number of mistakes. Hope this helps.

      Best regards, Qiyong Gong


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    1. On 2014 Jun 19, Alexander Kordyuk commented:

      Dear Colleagues, the technique which you call "our new technique for detecting the nonlinearity" is exactly what we have suggested in Phys. Rev. B 85, 075414 (2012), which you cite as Ref.9, by the way. Look at Fig.8 and APPENDIX B there and compare to your Fig.1 and Fug.4. Have I missed something?


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    1. On 2015 Apr 11, Takanori Eguchi commented:

      This is an interesting work. Here is the very important first report of MMP function for transcriptional control. Eguchi T, Kubota S, Kawata K, Mukudai Y, Uehara J, Ohgawara T, Ibaragi S, Sasaki A, Kuboki T, Takigawa M. Novel transcription-factor-like function of human matrix metalloproteinase 3 regulating the CTGF/CCN2 gene. Mol Cell Biol. 2008 Apr;28(7):2391-413.


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    2. On 2015 Jan 14, Richard Schulz commented:

      This interesting paper challenges the traditional and widely held view of matrix metalloproteinases (MMPs) as secreted proteases which cleave extracellular proteins after activation in the pericellular space by the proteolytic removal of their inhibitory propeptide. It adds another novel entry to the growing number of intracellular functions performed by this family of 23 human enzymes [1,2].

      Yet some important findings regarding MMP localization, activation mechanisms and nuclear targets have been overlooked in this report. For example, Marchant et al wrote that “the intracellular transport and nuclear targeting mechanisms of these proteins are unknown, as are their intracellular roles”. However, MMP-2 does possess a canonical nuclear localization sequence [3], and MMP-2 and MMP-9 were identified a decade ago in purified nuclear fractions from heart and liver extracts, and visualized in the nuclei of cardiomyocytes by immunogold electron microscopy [3]. Furthermore, the nuclear proteins PARP1 [3] and XRCC1 [4] have both been shown to be proteolysed by MMPs.

      This paper ascribed the nuclear localization of MMP-12 to an unknown mechanism where it is secreted by macrophages and then taken up by the target cell and enters the nucleus. In contrast, there are at least 3 bona fide intracellular isoforms of MMP-2 [5,6]. MMP-2 has an N-terminal signal sequence that only inefficiently targets it to the secretory pathway, resulting in approximately half of it being retained in the cytosol [5]. In addition, two MMP-2 isoforms lacking the signal sequence (and hence non-secreted) are expressed in cardiomyocytes [5,6]. Intracellular MMP-2 [7] and other MMPs [8] can be activated by post-translational modifications triggered by oxidants such as peroxynitrite, without proteolytic removal of the inhibitory propeptide. Regarding these supposedly unknown “intracellular roles”, one pathological role of intracellular MMP-2 in cardiomyocytes is its cleavage of specific sarcomeric proteins such as troponin I, which results in acute contractile dysfunction in ischemia-reperfusion injury [1,2,9].

      In addition to MMP-12 and MMP-2, at least 6 other nuclear MMPs have already been reported [2]. Unbiased high throughput screens to identify putative MMP targets [2] suggest that several more nuclear protein targets will come to light, and unveil, as reported by Marchant et al for MMP-12, more nuclear functions for these proteases. In this respect, it is worth noting that the authors did not directly assess the potential contribution of MMP-12 to the transcription of endogenous genes but instead measured gene products (mRNA and protein). This is notable because the localization that they observe in HeLa cells reveals several large foci located in chromatin-depleted regions of the nucleus, which is not typical for a protein that binds to chromatin or regulates RNA polymerase II transcription, but shows some similarity to proteins involved in mRNA processing [10].

      A better understanding of how MMPs act within the cell will be key to the development of better targeted MMP inhibitors for the treatment of viral infections, cancer, inflammation and heart disease.

      This comment was written as a collaboration by Bryan G. Hughes, Sabina Baghirova, Michael J. Hendzel and Richard Schulz

      References

      1.Schulz R. Intracellular Targets of Matrix Metalloproteinase-2 in Cardiac Disease: Rationale and Therapeutic Approaches. Annual Review of Pharmacology and Toxicology 2007;47:211-242. Schulz R, 2007

      2.Cauwe B, Opdenakker G. Intracellular substrate cleavage: a novel dimension in the biochemistry, biology and pathology of matrix metalloproteinases. Crit Rev Biochem Mol Biol 2010;45:351-423.<br> Cauwe B, 2010

      3.Kwan JA, Schulze CJ, Wang W, Leon H, Sariahmetoglu M, Sung M, Sawicka J, Sims DE, Sawicki G, Schulz R. Matrix metalloproteinase-2 (MMP-2) is present in the nucleus of cardiac myocytes and is capable of cleaving poly (ADP-ribose) polymerase (PARP) in vitro. The FASEB Journal 2004;18:690-692.<br> Kwan JA, 2004

      4.Yang Y, Candelario-Jalil E, Thompson JF, Cuadrado E, Estrada EY, Rosell A, Montaner J, Rosenberg GA. Increased intranuclear matrix metalloproteinase activity in neurons interferes with oxidative DNA repair in focal cerebral ischemia. Journal of Neurochemistry 2010;112:134-149.<br> Yang Y, 2010

      5.Ali MAM, Chow AK, Kandasamy AD, Fan X, West LJ, Crawford BD, Simmen T, Schulz R. Mechanisms of cytosolic targeting of matrix metalloproteinase-2. Journal of Cellular Physiology 2012;227:3397-3404.<br> Ali MA, 2012

      6.Lovett DH, Mahimkar R, Raffai RL, Cape L, Maklashina E, Cecchini G, Karliner JS. A Novel Intracellular Isoform of Matrix Metalloproteinase-2 Induced by Oxidative Stress Activates Innate Immunity. PLoS One 2012;7:e34177.<br> Lovett DH, 2012

      7.Viappiani S, Nicolescu AC, Holt A, Sawicki G, Crawford BD, León H, van Mulligen T, Schulz R. Activation and modulation of 72 kDa matrix metalloproteinase-2 by peroxynitrite and glutathione. Biochemical Pharmacology 2009;77:826-834.<br> Viappiani S, 2009

      8.Okamoto T, Akaike T, Sawa T, Miyamoto Y, van der Vliet A, Maeda H. Activation of Matrix Metalloproteinases by Peroxynitrite-induced Protein S-Glutathiolation via Disulfide S-Oxide Formation. Journal of Biological Chemistry 2001;276:29596-29602.<br> Okamoto T, 2001

      9.Wang W, Schulze CJ, Suarez-Pinzon WL, Dyck JRB, Sawicki G, Schulz R. Intracellular Action of Matrix Metalloproteinase-2 Accounts for Acute Myocardial Ischemia and Reperfusion Injury. Circulation 2002;106:1543-1549.<br> Wang W, 2002

      10.Hendzel MJ, Kruhlak MJ, Bazett-Jones DP. Organization of Highly Acetylated Chromatin around Sites of Heterogeneous Nuclear RNA Accumulation. Molecular Biology of the Cell 1998;9:2491-2507.<br> Hendzel MJ, 1998


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    1. On 2016 Jun 02, David C. Norris commented:

      Drs Goitein<sup>1</sup> and Lee<sup>2</sup> agree that debate over the proper role of physicians in controlling costs languishes in unsatisfactory condition. Goitein objects to the evasiveness of policy statements that advocate such a role; Lee derides the debate's stubborn persistence and sheer bulk. Against the Hegelian dialectics Lee alarmingly invokes as a remedy, I advocate instead the clarity of thought and expression rendered by a simple economic concept.

      Goitein's premise is that physicians' bedside preferences over quality and cost should be, as economists say, lexicographic. That is, just as dictionaries rank 'azygous' lexically before 'baa', physicians should rank treatment options first on quality, and then — only within strata of equivalent quality — on questions of cost. Objecting that maximizing 'value' defined as "the ratio of quality to cost" violates this principle, Goitein recapitulates the theorem that a real-valued utility function is incompatible with lexicographic preferences. Lee for his part, although neither affirming nor denying Goitein's normative premise, clearly advances the corresponding positive claim: despite value-based incentives, physicians retain lexicographic preferences over quality and cost. In supporting this claim by citing "powerful counter-balancing forces"<sup>2</sup> of opprobrium against bedside rationing, Lee recapitulates the theorem that lexicographic preferences are attained in the limit where one good (reputation) is worth infinitely more than another (incentives).

      Formulated thus, the debate comes into focus as a broad expanse of potential consensus, punctuated by disputes over a few, scientifically testable propositions. The formulation also shows promise as a means for holding debate accountable to logic. It shines withering light, for example, upon a conflicted notion of 'value' about which its very architect says both "value [is] defined as the health outcomes achieved per dollar spent"<sup>3</sup> and "Value, as I define it, is created only when health outcomes are not compromised; lower costs are value-creating only when corresponding outcomes are unchanged or improved."<sup>4</sup> We may in all fairness ask Lee to which of these incompatible definitions he subscribes, a Hegelian dialectical synthesis being mathematically debarred.

      Perhaps the best contribution this economic concept makes is to abstract away the coarsest features of debate, along with their attendant trivialities (said theorems), thereby redirecting our attention to the substantive considerations on which a genuinely productive discourse can progress. Chief among these will be embarrassments to the classical economic conceit of 'perfect information', inasmuch as "there is no evidence to suggest"<sup>5</sup> remains enthroned as arbiter of equivalent quality in the face of uncertain comparative effectiveness.

      [1] Goitein L, 2014

      [2] Lee TH, 2014

      [3] Porter ME, 2010

      [4] Porter, ME. What is value in health care? NEJM. 2011;364:e26

      [5] Braithwaite RS, 2013


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    1. On 2014 May 04, Jim Woodgett commented:

      The somewhat surprising finding here is the apparent cytotoxicity induced by BIO which we and others haven't observed (as noted by the authors) since the original publication by Sato et al (PMID: 14702635 - ref 26). The lack of effects of BIO on Wnt in this paper are largely due to the authors having to use much lower concentrations of BIO (0.5 micromolar) than for the CHIR compounds (5 micromolar) due to the observed cytotoxicity. In our hands, and other studies (e.g. PMID 21295277), there is a strong correlation between induction of beta-catenin, inhibition of GSK-3 and maintenance of pluripotency of ES cells. We'd argue that any selective inhibitors of GSK-3 will activate the canonical Wnt pathway (as well as other pathways negatively regulated by this kinase) but that since greater than 80-90% of total GSK-3 activity must be blocked to observe effects, choice of inhibitors for this purpose will be largely determined by off-target effects. As an aside, lithium is a very poor inhibitor of GSK-3 (ki = 2-3 mM) but is perfectly able to induce beta-catenin signalling and maintain pluripotency. It's also considerably cheaper than most small molecules.


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    1. On 2014 May 23, Morgan Price commented:

      The claim that cross-feeding of amino acids is common is based on auxotroph predictions, but I suspect that most of the auxotroph predictions are incorrect. For example, I examined the IMG pages for four bacteria that my colleagues have been working with -- Shewanella oneidensis MR-1, Zymomonas mobilis ZM4, Desulfovibrio alaskensis G20, and Pseudomonas stutzeri RCH2. All of them grow in defined media without any added amino acids, and yet the IMG web site predicts that each is auxotrophic for 5 or more different amino acids.


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    1. On 2014 Oct 06, Paul Vaucher commented:

      False conclusions drawn about the level of evidence of factual statements drawn from Wikipedia

      Paul Vaucher, PhD, DiO<sup>1,</sup> Jean Gabriel Jeannot, MD<sup>2,</sup> Reto Auer, MD, MAS<sup>2</sup>

      1 University Center of Legal Medicine Lausanne-Geneva, University Hospital of Lausanne (CHUV), Lausanne, Switzerland

      2 Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland

      We believe Hastly et al's study (Hasty RT, 2014) to be misleading and that their paper should not be made available to the scientific community without serious revision. Apparently, it has passed unnoticed that the methodology and statistical analysis they used had little to do with their stated hypothesis and that their interpretation of the statistics was erroneous. Authors concluded Wikipedia to be an unreliable source of health information when an alternate interpretation of the presented results would in contrary point towards considering Wikipedia as a trusted source of information, provided rigorous reanalysis and reinterpretation. There conclusions were therefore in contradiction with other studies on the subject (Archambault PM, 2013, Kräenbring J, 2014) that tend to show that for topics for which health workers contribute, such as for drugs, Wikipedia’s information as trustworthy as those from textbooks. These discrepancies can be explained by major statistical and methodological errors in Hastly et al’s publication.

      The correct interpretation of the McNemar statistic suggests that the concordance for diabetes and back pain are significantly better than for concussion, and not the reverse, as stated by the authors. Using data provided in Table 3, for factual statements identified by both reviewers (two first columns of Table 3), for diabetes mellitus and back pain, the authors found that up to 94% of assertions on Wikipedia were verified (respectively 72 out of 75 statement and 63 out of 67, p<0.001 for NcNemar statistic). In contrast, for concussion, only 65% were verified (66 out of 98, p=0.888 for NcNemar statistic ). The McNemar statistic tests whether the proportion of factual statements from both reviewers, classified as concordant or discordant by the authors, are above what would be expected by chance alone (i.e. 50%). The interpretation for diabetes mellitus, if McNemar’s test should be used at all, is that we would fail to reject the null hypothesis of a proportion of concordance of 50% in < 1% of the cases. McNemar statistic thus suggests that the concordance for diabetes and back pain are significantly better than for concussion, and not the reverse, as stated by the authors. The calculation is based on the number of discordant results on the diagonals (i.e. 34 vs 1 for diabetes mellitus). It does by no means test the discordance between Wikipedia statements and existing guidelines. To test their hypothesis, it would appear more relevant to simply report the pooled average proportion of correct statements with their confidence intervals. On a technical note, McNemar statistic should not be used when there are different numbers of assertions assessed between reviewers. McNemar is also known to be highly dependent on the number of factual statements within each article. Article with higher number of statements would reach the level of significance with higher proportion of ungrounded factual statements.

      Second, the article falsely leads readers to believe that all factual statements (assertions) from 10 Wikipedia articles were identified and independently assessed by two internist to see whether they were concordant or not. Using two reviewers is a recognized method for increasing precision of a measure. However, the authors did not to provide statistics allowing readers to assess the between-reviewers variability in the identification of assertions. Table 3 suggests that over a third of assertions were reported by only one of the two reviewers. Authors did not find a method to then resolve these dissimilarities (to use their definition in Table 2) and clearly define which assertions were factual statements and which were not. They then did not to define a method of agreement to define which assertions were supported by evidence and which were not. Analysed results therefore only tend to show that for certain topics, internists have difficulties in detecting factual statements from Wikipedia and knowing whether they are grounded or not.

      Hastly et al’s findings suggest that while there might be some discrepancies in the quality of articles between topics, some appear of very high quality, such as diabetes mellitus and back pain. Given the unnoticed errors included in their article and the importance on the interpretation of the results, Hastly et al.’s published article reveals that peer reviewed misleading information can also be made available to the public.

      Conflicts of interest : Reto Auer and Jean-Gabriel Jeannot are advocates of the use of Wikipedia as a communication mean to inform the population on health issues. Paul Vaucher is an important contributor to the French Wikipedia page dedicated to osteopathic medicine.


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    2. On 2014 May 28, Lane Rasberry commented:

      I participate in WikiProject Medicine, the community which develops health content on English Wikipedia. We discuss most publications which review our content, but this paper for whatever reason was picked up by popular media.

      Anyone who wishes to learn more about Wikipedia's health content is invited to say hello at WikiProject Medicine. There really is no way to understand Wikipedia without talking to some of the people who make it.

      Here are some links to discussions about this paper:

      +Poor paper on Wikipedia, the WikiProject Medicine discussion about this on 30 April

      +r/science discussion May 27 on reddit, with 2000 comments

      +Don’t Trust Wikipedia When It Comes to Your Health, Study Says, Time magazine

      +Trust your doctor, not Wikipedia, say scientists, BBC

      Online search will show 10 other news sources reviewing the paper. In my opinion journalists covering this academic article interpret it in various ways, none of which I would expect to be the interpretation which the authors would want people to have.

      What a fascinating paper, and what an overwhelming public response to it!


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    1. On 2016 Mar 01, Jeffrey S Mogil commented:

      In fact, stress is well known to produce both hypersensitivity to pain (see Imbe et al., Front. Biosci. 11:2179-2192, 2006) or inhibition of pain (see Butler & Finn, Prog. Neurobiol. 88:184-202, 2009), depending on the parameters of the stress. In our study, stress produced stress-induced analgesia. This is not a confound; it's the entire finding.


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    2. On 2016 Feb 22, Alireza Gharib commented:

      Dear Editor I enjoyed studding your paper. However, I have a question. As an accepted fact “higher levels of stress induces pain”; yet, I suppose the results in this paper showed an inconsistent fact in support of other related literature “reduced pain response after stress exposure”. Maybe you just wanted to rule out stress as an intervening factor that may cause bias. I will be grateful if you could explain more. Best


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    1. On 2014 Nov 24, Guillaume Filion commented:

      This article is one of the "CISCOM meta-analyses", which are very similar papers written by different authors. For more information about the CISCOM meta-analyses, check the blog post "A flurry of copycast on PubMed" at the following link http://blog.thegrandlocus.com/2014/10/a-flurry-of-copycats-on-pubmed


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    1. On 2017 Feb 24, Ahmet Selçuk Can commented:

      Correction: Evaluation of leptin and insulin resistance in patients with cholelithiasis

      We would like to correct our mistakes in the above paper<sup>1</sup> (Atamer A, 2013) titled “Evaluation of leptin and insulin resistance in patients with cholelithiasis” published in the Indian Journal of Biochemistry & Biophysics. We tried to contact the Editor of the Indian Journal of Biochemistry & Biophysics via e-mail on September 15th 2015 and via surface mail on February 16th 2016, but we did not get a response. The reason probably is that the Indian Journal of Biochemistry & Biophysics is not active and its last issue was published in April 2015, before our effort to contact the Editor. There are errors in the abstract, text and Table 1 of the manuscript. We apologize for these errors. These errors were also present in another publication of Atamer et al.<sup>2</sup> (Atamer A, 2014) that derived data from the same subject group. We were alerted by a correspondence by Agilli et al.<sup>3</sup> (Agilli M, 2014) that pointed to these errors. Those errors were addressed and corrected in a previously published letter<sup>4</sup> (Atamer A, 2016) submitted by us. We now address our mistakes in the above paper<sup>1</sup> (Atamer A, 2013). Table 1 has the following errors. The mean age of the controls was 56.93 years and was significantly higher than subjects with cholelithiasis (p=0.016). There was an error in the calculation of LDL by the Friedewald formula in healthy controls; the correct calculation of LDL-C is 100.86 mg/dl for the healthy control group. AST level for the healthy control group was 30.00 IU/L. AST level for the cholelithiasis group was 25.48 IU/L. The mean AST level of control subjects was significantly higher than subjects with cholelithiasis (p<0.001). The mean GGT level for the healthy control group was correct and was 41.70 IU/L, but the mean GGT level of cholelithiasis subjects was 35.81 IU/L. The mean GGT level of control subjects was significantly higher than subjects with cholelithiasis (p=0.002). The following corrections need to be done in the text of the manuscript that pertains to the erroneous Table 1. The third sentence of the Abstract should be “The control group included 25 women (62.5%) and 15 men (37.5%) with a mean age of 56.93 ± 11.73 yrs.” The first two sentences of the Results Section should be as follows: “There were 55 women (68.8%) and 25 men (31.3%) with a mean age and standard deviation (SD) of 50.56 ± 14.28 yrs in the cholelithiasis group and 25 women (62.5%) and 15 men (37.5%) with a mean age and SD of 56.93 ± 11.73 yrs in the control group. There were no significant differences in terms of BMI, fasting blood glucose, TG, CRP and ALT levels between two groups (p>0.05), but control subjects were older and had higher AST and GGT levels compared to cholelithiasis subjects (p<0.05).” Biochemical parameters and ultrasound studies subsection under Materials and Methods Section, Results Section, Table 1 and Table 2 should indicate that CRP was measured as highly sensitive CRP (hsCRP). An Acknowledgements section should be added and should mention that part of the data was submitted to a different journal<sup>2</sup> Atamer A, 2014 and acknowledge the editing and submission assistance by Ahmet Selçuk Can (the third author of this letter). Aytaç Atamer and Yıldız Atamer are responsible from the integrity of the published data<sup>1,2</sup> Atamer A, 2013, Atamer A, 2014. Ahmet Selçuk Can is responsible from editing and submission of the previously published manuscripts<sup>1,2</sup> Atamer A, 2013, Atamer A, 2014 and writing and submission of this correspondence. We concur with Agilli et al.<sup>3</sup> Agilli M, 2014 and accept that several errors make the previously published studies<sup>1,2</sup> Atamer A, 2013, Atamer A, 2014 unreliable<sup>4</sup> Atamer A, 2016.

      Aytaç Atamer<sup>1,2</sup> , Yıldız Atamer<sup>1</sup> and Ahmet Selçuk Can<sup>1*</sup>

      <sup>1</sup> Termal Vocational School, Yalova University, Kışla Caddesi, Gökçedere Mahallesi, Nergis Sokak, No: 23, Termal, Yalova, 77200, Turkey

      <sup>2</sup> Formerly from the Division of Gastroenterology, Department of Internal Medicine, Republic of Turkey, Ministry of Health Haydarpaşa Numune Training and Research Hospital, Istanbul, Turkey

      *Corresponding Author E-mail: selcukcan@endokrinoloji.com

      References

      1) Atamer A, Ovunc AO, Yesil A, Atamer Y. Evaluation of leptin and insulin resistance in patients with cholelithiasis. Indian J Biochem Biophys 2013;50:266-72.

      2) Atamer A, Kurdas-Ovunc AO, Yesil A, Atamer Y. Evaluation of paraoxonase, malondialdehyde, and lipoprotein levels in patients with asymptomatic cholelithiasis. Saudi J Gastroenterol 2014;20:66-73.

      3) Agilli M, Aydin FN, Aydin I. Serum paraoxonase and malondialdehyde levels in asymptomatic cholelithiasis. Saudi J Gastroenterol 2014;20:203-4.

      4) Atamer A, Atamer Y, Can AS. Response to: Serum paraoxonase and malondialdehyde levels in asymptomatic cholelithiasis. Saudi J Gastroenterol 2016;22:84-5.


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    1. On 2015 Jan 21, John Cannell commented:

      How was the abuse "documented"? By a Child Abuse Committee? By Child Protective Services (CPS)? By the courts? How were the caregivers judged to be guilty? Without witnessed abuse or free and un-coerced confessions by caregivers, you have no way of knowing how many innocent caregivers were included in the "guilty" group.

      Therefore, selection bias makes studies similar to Darling et al's practically useless. What percent of studies of “guilty” cases involve CPS telling innocent parents if they admit to the abuse - and take parenting classes - they can immediately get their infant back and avoid further costly litigation? What percentage of “guilty” cases involves CPS allowing innocent parents to plead "guilty" to the lesser charge of neglect to get their infant returned and avoid further litigation?

      In what percentage of “guilty” cases does the district attorney or CPS give a mother the “Sophie’s Choice” of not being prosecuted and getting her infant back if she will testify against her innocent husband? What percent of “guilty” cases involve an innocent parent accepting a plea bargain after the defense attorney concludes a trial will result in conviction?

      For these reasons studies on infantile child abuse such as Darling et al have selection bias and, in my opinion, include an unknown number of innocent caregivers in the "guilty" group, making the studies scientifically unreliable.


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    1. On 2014 Apr 29, Gwinyai Masukume commented:

      “Data from WHO [World Health Organization] suggest that nearly half of all births in China were delivered by caesarean section in 2007–08 …”; in the article that the author’s cite to support their statement it is written, “The results, especially rates of caesarean section, should not be regarded as representative rates and outcomes for entire countries or regions.” [1]

      The authors claim that the caesarean section rate in China (42% in 2010) is the highest in the world; however this does not seem true; the Chinese rate could be around 26% (still a high rate) but the rate is certainly not the highest in the world [2].

      The authors also state that WHO recommends a 15% proportion of births by caesarean section, but they give no reference. WHO states, “Both very low and very high rates of caesarean section can be dangerous, but the optimum rate is unknown.” - the 15% proportion has its origins in 1985 [3].

      References

      [1] Lumbiganon P, Laopaiboon M, Gülmezoglu AM, Souza JP, Taneepanichskul S, Ruyan P, et al. Method of delivery and pregnancy outcomes in Asia: the WHO global survey on maternal and perinatal health 2007-08. Lancet. 2010; 375(9713):490-9. Lumbiganon P, 2010

      [2] Gibbons L, Belizán JM, Lauer JA, Betrán AP, Merialdi M, Althabe F. The Global Numbers and Costs of Additionally Needed and Unnecessary Caesarean Sections Performed per Year: Overuse as a Barrier to Universal Coverage. World Health Report, Background Paper, 30. [Internet] 2010. [cited 25 April 2014]. Available from: http://www.who.int/healthsystems/topics/financing/healthreport/30C-sectioncosts.pdf

      [3] Monitoring emergency obstetric care – a handbook. [Internet] 2009. [cited 25 April 2014]. Available from: http://whqlibdoc.who.int/publications/2009/9789241547734_eng.pdf


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    1. On 2016 Aug 24, 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 originating journal article. The ID given is NCT00123456. We believe the correct ID, which we have found by hand searching, is NCT00403767.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 PMID: 27056367

      * 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


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    1. On 2016 Aug 30, 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 originating journal article. The ID given is NCT001747. We have contacted the corresponding author, who has told us that this trial was not registered.

      This comment is being posted as part of the OpenTrials.net project<sup>[1]</sup> , 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 PMID: 27056367

      * 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


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    1. On 2014 Aug 16, Melissa A Farmer commented:

      Dear Dennis,

      Thank you for your interest in our methods, and we are pleased to address your questions.

      The first question raised is related to the amount of solution injected. For estradiol and progesterone, the mice received injections of 0.1 mL of each solution under the scruff of the neck. We found that the mice could easily tolerate this volume (no scratching or visual discomfort), provided that injections were limited to once per week (thereby limiting frequency of mating). We chose this volume due to the sensitivity of our scale, which constrained the concentration of stock solutions we could make. Lesser volumes with appropriately adjusted dilutions would work, as well.

      The second issue is related to optimizing copulation/female receptivity in novel couples. On one hand, the probability of a novel couple mating can be enhanced by providing the male with prior sexual experience with other receptive females (“stimulus” females). This prior learning will increase the frequency with which he approaches the novel female, which in turn increases probability that copulation will occur.

      A complementary strategy is to optimize hormonal and environmental factors that can facilitate female receptivity in virgin mice, independent of the actions of the male. Sexually mature female mice should be used (> 6 weeks age). Based on our experience, the timing of the progesterone injection is the most important factor that optimizes a female’s behavioral response during testing. Unfortunately the mouse mating literature is older and authors infrequently reported the timing of progesterone administration in females (hence the Jones et al. reference). In pilot experiments, we varied progesterone injections from 4-6 hours pre-test, and in our hands, 5.5 hours produced the most consistent behavioral results. To further optimize behavioral receptivity, we scheduled testing towards the beginning of the dark cycle when mice would be most physically active. Even though mice were maintained in an artificially-lit vivarium, we noticed seasonal variation in the onset of dark cycle physical activity, and so we shifted the timing of testing (and therefore progesterone injections) accordingly, with a later testing time during winter. Also note that more complicated mating environments, like a paced mating boxes, require repeated habituation to reduce novelty effects.


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    2. On 2014 Aug 14, Dennis Eckmeier commented:

      Dear authors,

      A really interesting paper!

      I have a question according to methods:

      You write "Sexual receptivity was induced in ovariectomized females with subcutaneous (s.c.) injections of estradiol benzoate (5 μg/0.1 ml in sesame oil; Sigma-Aldrich) given 48 h pretest, and progesterone (500 μg/0.1 ml in sesame oil) 5.5 h pretest. These parameters are known to induce a state of optimal sexual receptivity, comparable to the estrus phase (Jones et al., 2013)."

      What amount of drug solutions did you administer?

      You determined that some pairs of treated ovariectomized females and males would indeed mate, so no doubt it worked for your study. However, a study I am planning doesn't allow previous encounters between the stimulus female and the male. The paper you cite (Jones et al., 2013) is about rats. Did you somehow determine whether your treatment induces optimal sexual receptivity in mice?


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    1. On 2014 Apr 28, Jim Woodgett commented:

      SB415286 inhibits both the GSK-3alpha and GSK-3beta isoforms (encoded by different genes) with similar potency. Beta-catenin is only stabilized when Axin-associated GSK-3 (a mixture of both alpha and beta isoforms) is disrupted following Wnt receptor binding - causing association with of Axin with LRP5/6 (PMID 22682247). Knocking out GSK-3 alpha or GSK-3beta typically has no measurable effect on beta-catenin levels as only 5-10% of cellular GSK-3 is bound to Axin and each isoform fully compensates for the other in this pathway (e.g. PMID 17543867). Hence, the observed effects are likely (in the case of the drug) not GSK-3beta specific and in the case of the KO, likely reflect increased sensitivity of the residual GSK-3alpha to an endogenous signal (presumably Wnt).


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    1. On 2015 Jan 29, Wichor Bramer commented:

      I found a rather lage error in the search strategy as presented in this article, resulting in the retrieval of 26 times more irrelevant than relevant terms. When creating a complex search strategy it is very important to have the parentheses correct. The authors developed a search strategy in which they plan to search for P AND (I OR C) AND O, which is a god way (albeit maybe a bit too much elements). However the search string as shown on page 53 is constructed as (P) AND (I) OR (C) AND (O). PubMed alike other databases does not have a preset preference for Boolean operators, but just adds new elements in the order given. Constructed like this PubMed will retrieve all articles on Music Therapy and the desired outcomes, but not related to dementia. When using this search strategy in PubMed it currently retrieves 8000 references. When the parentheses are corrected only 300 articles remain, containing much more relevant references. Do watch closely when creating more complex searches that parentheses are placed correctly. Always fill them in yourself, and don't let PubMed decide that!


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    1. On 2014 Apr 28, Daniel Macqueen commented:

      Firstly, congratulations to these authors for being the first to publish a salmonid genome sequence. This is a major achievement and an important landmark for salmonid biologists and fish biologists generally. I find many of the analyses in the paper to be interesting and novel.

      With that said, readers of this paper should be aware that the timing of the salmonid genome duplication (i.e. ‘Ss4r’) was already demonstrated in an earlier article that (surprisingly) was not cited by Berthelot et al. (Macqueen and Johnston 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. R. Soc. B. 281: 20132881). See Macqueen and Johnston's earlier paper here http://rspb.royalsocietypublishing.org/content/281/1778/20132881.short?rss=1

      In short, Macqueen and Johnston (2014) performed a Bayesian relaxed molecular clock and phylogenetic analysis, calibrated by the fossil record, to estimate that Ss4r occurred 88-103 Mya. The Berthelot et al. estimate (90-102 Mya) was achieved using a more basic method, but nevertheless, is strikingly consistent with our earlier independent result.

      I would also like to comment on some text from Berthelot et al:

      We first use the rainbow trout genome to refine the timing of the Ss4R and we dated this event around 96 Mya (±5.5 Mya), a timing in the upper range of the previous 25–100 Mya estimation<sup>11<sup>.</sup></sup> This result is in striking contrast with the age of the Salmonidae family, which has been estimated as 50–60 Mya <sup>4,16<sup>,</sup></sup> suggesting that the Ss4R occurred long before the last common ancestor of extant salmonids.

      Again, Macqueen and Johnston (2014) reported this result already. From the abstract: “Our results suggest that the event [WGD] occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the [salmonid] subfamilies diverged”.

      These comments were made by Dr Dan Macqueen from the Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom. Email: daniel.macqueen@abdn.ac.uk


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    1. On 2014 Nov 23, Stephen Wood commented:

      We feel the authors should consider the possibility that their key finding, that Large for Gestational Age (LGA) birth weight is a risk factor for stillbirth, was an artifact of sampling. We note that 50% of the stillbirths in your study occurred at <28 weeks gestation yet < 1% of the live birth controls were <28 weeks and only 1% <32 weeks. This may have been appropriate for the analysis that determined LGA using population norms but error may have been introduced when using the ultrasound (Hadlock) or indvidualized norms. In developing these norms Hadlock et al assessed only 392 subjects and although they had ultrasounds at a range of gestational ages the accuracy of the estimates was only reported for deliveries > 36 weeks. Therefore, it is uncertain how accurate they would be for preterm fetuses. The individualized norms are also prone to similar error as they are as essentially slightly adjusted Hadlock ultrasound norms. As your controls were a population based sample not matched by gestational age then this error could have been important. To investigate this possibility we analyzed data from our provincial perinatal database. For the years 1992-2009 there were 727693 singleton births at 23 weeks or greater gestation, we excluded 11 with gestational age>45 weeks and 3216 with missing birth weights. In the first analysis all stillbirths were matched with the next two live births (population based controls). The gestational age distribution of live birth controls was similar to your study with only 1.1% delivering <28 weeks. Using the same population norms as your study (Alexander) we observed similar results to those you reported; SGA was associated with stillbirth using both population and ultrasound norms but LGA only increased the risk of stillbirth using the Hadlock ultrasound norms. In fact using the population norms it was protective.

      Hadlock U/S norms SGA (small for gestational age) OR 6.38 (5.77, 7.06) AGA (appropriate for gestational age) Reference LGA (large for gestational age) OR 1.91 (1.64, 2.22)

      Alexander Population norms SGA OR 6.43 (5.74, 7.21) AGA Reference LGA OR 0.61 (0.51, 0.74)

      To evaluate the possible effect of sampling we then matched all stillbirths to the next two live births with the same gestational age.

      Hadlock (ultrasound norms) SGA OR 4.77 (4.32, 5.26) AGA Reference LGA OR 0.98 (0.85, 1.13)

      Alexander (population norms) SGA OR 6.47 (5.78, 7.24) AGA Reference LGA OR 0.83 (0.69, 1.01)

      The results as you see are quite different. While SGA is still strongly associated with stillbirth LGA is not using either population or ultrasound norms. This suggests that the increase in risk of LGA observed in your study was an artifact of sampling. This almost certainly applies to the results using the "individualized norms" as they essentially modification of the ultrasound norms. We suggest that you do a similar analysis on your own data with gestational age matched controls to ensure the increase risk of stillbirth you observed with LGA is robust to changes in the control population.


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