On 2014 May 30, Alejandro Higuera-Matas commented:

A really interesting piece of work, I wonder what the results would be like if the same experiment was performed in the hippocampus.

On 2015 Mar 12, Zhibin Ning commented:

The database created in this paper is awesome.

On 2014 Aug 08, Pavel Baranov commented:

The number of protein coding ORFs in the human transcriptome is likely to vary greatly depending on what we set as the minimal lenghth of such ORFs. Counting genes in the genomes may turn to be unproductive, the term gene is in an existential crisis.

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

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.

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.

On 2014 Oct 09, Michael Hoffman commented:

The correct date of publication is 2014 Apr 16. See doi:10.11646/zootaxa.3790.1.9 for this article, including link to full text with correct date.

[The PubMed record now has the correct date.]

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

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.

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/.

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.

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

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

On 2017 Jul 13, Randi Pechacek commented:

Ameet Pinto, first author of this paper, wrote a blog post on microBEnet providing some background.

On 2014 Jun 09, Jake Chen commented:

this article shows how to use protein interaction iteratively to identify key biomarker proteins in a network of significant candidate proteins identified.

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.

On 2014 Sep 04, Justin Hensley commented:

Post publication commentary: Well written with good suggestions in the absence of Level 1 evidence. http://ebmgonewild.com/big-cats/

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/.

On 2014 Dec 17, Sean Ekins commented:

The story behind this paper http://www.collabchem.com/2014/04/09/publishing-on-rare-diseases-with-f1000research/

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/.

On 2014 Jun 02, Claudio Gil Araújo commented:

Not being an oncologist but rather an exercise/sports physician, I found the paper excellent, brief and bringing updated information. Particularly interesting it was to note that the text starts by emphasizing lifestyle issues, those that are unfortunately often undervalued

On 2014 May 28, GRAHAM COLDITZ commented:

For related online patient prevention materials, visit: http://tinyurl.com/l4a4g2j

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.

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.

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

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.

On 2014 May 23, Kamel Hamzaoui commented:

This paper should be very interesting if there is comparison with other cancer

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.

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.

On 2015 Jan 16, Cornelia de Moor commented:

Lovely paper! However, why do the authors not use the official protein name for this enzyme, and why has the journal not insisted that they do this? It took me ages to realize this was GPD2, and the paper doesn't show up in a search for this gene.

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?

On 2016 Feb 24, Sudheendra Rao commented:

Link out error. Correct Link is here. http://www.ias.ac.in/article/fulltext/jbsc/039/03/0537-0541

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.

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

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^TMR 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 ~10^4-fold 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 ~10^4-fold 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.

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.”

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.

On 2014 May 22, Art Beyder commented:

very cool. i wonder then how do the cells know which organelles to release?

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.

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

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/.

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

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.

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

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

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

On 2015 Mar 07, Jacob H. Hanna commented:

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

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

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/).

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/.

On 2014 Jun 05, Seung Y Rhee commented:

Dear George: Thank you for noticing and commenting. Science has corrected this typo on the online and PDF versions of the article. We will contact PUBMED to correct it in the abstract and make a link to the correct version of the full text at Science.

On 2014 Jun 05, Seung Y Rhee commented:

None

On 2014 May 30, George McNamara commented:

"flourescent" appears in both the abstract and the main text. Did any of the 30 authors, reviewers or editors spell check this manuscript?

On 2014 Jul 29, Amanda Capes-Davis commented:

Unfortunately HEp-2 cells are not from laryngeal cancer. The HEp-2 cell line is known to be 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/.

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.

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?

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.

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

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.

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.

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.

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.

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

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

On 2014 May 15, Bill Sardi commented:

None

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

On 2014 Aug 12, Daniele Marinazzo commented:

Could this effect be related to the MRI induced nystagmus as described here?

http://www.ncbi.nlm.nih.gov/pubmed/21945276

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

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.

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.

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.

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^-24, 10^-60 and 10^-100. Or in other words: containing no measurable quantities of antibodies. Even the 10^-24 dilution is indistinguishable from zero. Note that these preparations were eventually diluted even further (at least to ~10^-28) 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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.)

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

On 2015 Aug 22, Arnaud Chiolero MD PhD commented:

A fantastic review addressing the issue of cancer overdiagnosis and suggesting several solutions.

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/.

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.

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.

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).

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?

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.

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.

On 2014 May 12, Attila Csordas commented:

dataset available via PRIDE/ProteomeXchange http://www.ebi.ac.uk/pride/archive/projects/PXD000681 and http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD000681

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.

On 2016 Jun 22, Kristina Hanspers commented:

Figure 8 is available as a pathway model at WikiPathways: http://www.wikipathways.org/index.php/Pathway:WP2868. These models can be used for data analysis in Cytoscape, PathVisio and other network analysis tools, and can be downloaded in a variety of formats.

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.

On 2015 Dec 19, W Tröger commented:

Treatment option published in PMID: 25142075

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.

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/.

On 2016 Sep 10, Morten Oksvold commented:

Before reading or citing this article, please read reports regarding the Macchiarini case from Karolinska Institute:

http://ki.se/sites/default/files/karolinska_institutet_and_the_macchiarini_case_summary_in_english_and_swedish.pdf

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

http://ki.se/en/news/external-inquiry-finds-paolo-macchiarini-guilty-of-misconduct

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

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.

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.

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

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.

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.

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/.

On 2015 Sep 30, Jan Egger commented:

This article is related to: http://www.springerplus.com/content/2/1/395

Best wishes, Jan

On 2013 Oct 25, DAVID SANDERS commented:

Please see Monica K, 1990 "Our results show that small Mr G proteins are widely expressed in lymphoid cells and that Bcl-2 is not a novel member of this GTP-binding protein family."

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).

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

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.

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

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

Many thanks,

Jessica Fleminger, Ben Goldacre*

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

On 2014 Aug 01, Francisco Xavier Castellanos commented:

Many thanks