On 2015 Nov 06, Kenneth Witwer commented:

The figures in this article appear to have been previously published by another group (Tian Q, 2012) in the context of a different miRNA, miR-550a. The miRNA sequence in Figure 2 is also the sequence of miR-550a, not miR-1246 as labeled.

On date unavailable, commented:

None

On 2015 Aug 05, Roger H Reeves commented:

Response to Benoit Bruneau (Bruneau’s comments in italics)

Bruneau: The paper by Polk et al purports to demonstrate a genetic interaction between Tbx5 and Ts65Dn. I have a number of comments and questions related to the data used to reach this conclusion. First, the reduced amount of Tbx5 in the Ts65Dn is interesting, but puzzling is the almost complete absence in the Ts65Dn;Tbx5+/- embryos: based on previous investigations, this level of Tbx5 mRNA (almost zero) should result in extremely severe defects in heart formation, which are not observed.

Response: We show a qPCR analysis at a single developmental time point, the E12.5 heart. Although continuous low Tbx5 levels beginning earlier in heart development would result in severe heart defects as Bruneau suggests, the ramifications of diminished expression at E12.5 are unclear. Perhaps the increased lethality in Ts65Dn;Tbx5+/- mice is related to this observation. In an unnecessary ad homonym attack, Bruneau intimates that we are incapable of using qPCR appropriately (“This brings into question the quantitation of the mRNA levels”). Instead, it is Bruneau’s supposition that our observation at E12.5 could only be accurate if severe heart malformations were observed which is incorrect.

Bruneau: Data are presented only for 2 of the 4 genotypes that would be necessary to derive any conclusion [about genetic association]. In table 3, WT and Ts65Dn genotypes are not present. In Figure 2, only the compound heterozygote Ts65Dn;Tbx5+/- and WT are shown.

Response: The expected frequencies for these defects in wt and Ts65Dn mice have been published multiple times by us and others and three relevant studies are cited [1-3] showing that in a sample of this size, we would expect to see <1 ASD, <1 VSD, 0 AVSD and 0 OA in the same genetic background as this study. That is, we would expect to observe few or no defects and the same for wt. Perhaps we could have made a more concrete reference to the cited studies with regard to this specific point; however, neither we nor the reviewers found our presentation to be problematic. Even for those who missed the reference, we disagree with the statement that there is “no evidence [in Table 3] for genetic interaction.” The combination of genotypes unequivocally changes the phenotype; what forces not involving genetics might be responsible?

Bruneau: The same genotypes are missing from Fig 4.

Reponse: Fig. 4 is a histological representation. Since the defects don’t occur and such controls in the same genetic background have already been published, we choose to cite them rather than reproduce them here.

Bruneau: The in situ hybridization in Fig 4 suggests a reduction in Pitx2 expression in Ts65Dn;Tbx5+/- hearts; despite a very weak signal, this may be true, but this in no way indicates that the mice have atrial isomerism nor that the left-right pathway is involved in the defects shown.

Response: Here Bruneau overstates our conclusions about left-right patterning in order to criticize them (straw man argument). We show that OA incidence increases in Tbx5;Ts65Dn mice (Tbl. 3) – Bruneau tacitly agrees. We show that Pitx2 expression is lower in LA of Ts65Dn – Bruneau agrees with this as well. We discuss our findings in the context of the literature on OA where one finds frequent references to the relationship between OA and left-right development of the heart (see 12 references to the relationship between OA, Pitx2 and left-right signaling, 2nd paragraph of the Discussion). We point out the established link between altered patterns of Pitx2 expression, left-right isomerism and OA as a justification for doing this experiment in Fig 4 with the results shown. However, we do not state that OA is due to atrial isomerism, nor do we state that any of these mice have atrial isomerism. Bruneau has misstated our conclusion.

Bruneau: The atria of the mutant mice (in Fig 4) clearly have their normal morphology

Response: We note that it is not possible to correctly deduce complex pathological relationships from a single histological image. Regardless, it is irrelevant, as we do not assert that left-right isomerism is observed; that is a straw man of Bruneau’s invention.

Bruneau: I look forward to reading the authors' responses to these issues.

Response: We expect differences of opinion in interpretation by experts as a useful and necessary part of the scientific enterprise. Here, however, Bruneau has offered a superficial and needlessly aggressive critique replete with mischaracterization of our stated conclusions. We trust that objective readers interested in the complex phenomena resulting in heart defects in Down syndrome will consider our data for its intrinsic value and not mischaracterize our qualified speculations in the Discussion as conclusions.

Signed: Roger Reeves, Renita Polk, Peter Gergics, Ivan Modkowitz and Sally Camper

1. Moore CS (2006) Postnatal lethality and cardiac anomalies in the Ts65Dn Down syndrome mouse model. Mamm Genome 17: 1005-1012.
2. Williams AD, Mjaatvedt CH, Moore CS (2008) Characterization of the cardiac phenotype in neonatal Ts65Dn mice. Dev Dyn 237: 426-435.
3. Li H, Cherry S, Klinedinst D, DeLeon V, Redig J, et al. (2012) Genetic modifiers predisposing to congenital heart disease in the sensitized Down syndrome population. Circ Cardiovasc Genet 5: 301-308.

On 2015 Jul 29, Benoit Bruneau commented:

The paper by Polk et al purports to demonstrate a genetic interaction between Tbx5 and Ts65Dn. I have a number of comments and questions related to the data used to reach this conclusion. First, the reduced amount of Tbx5 in the Ts65Dn is interesting, but puzzling is the almost complete absence in the Ts65Dn;Tbx5+/- embryos: based on previous investigations, this level of Tbx5 mRNA (almost zero) should result in extremely severe defects in heart formation, which are not observed. This brings into question the quantitation of the mRNA levels. This is very minor point compared to the presentation of the data: data are presented only for 2 of the 4 genotypes that would be necessary to derive any conclusion. In table 3, WT and Ts65Dn genotypes are not present. In Figure 2, only the compound heterozygote Ts65Dn;Tbx5+/- and WT are shown; how can one judge any genetic interaction if the individual genotypes (Ts65Dn and Tbx5+/-) are not shown? In certain genetic backgrounds we see such defects occasionally in Tbx5+/- neonates, therefore the conclusions proposed by the authors cannot be reached with the data provided. The same genotypes are missing from Fig 4. The in situ hybridization in Fig 4 suggests a reduction in Pitx2 expression in Ts65Dn;Tbx5+/- hearts; despite a very weak signal, this may be true, but this in no way indicates that the mice have atrial isomerism nor that the left-right pathway is involved in the defects shown. The atria of the mutant mice clearly have their normal morphology, and there is no evidence presented of isomerism (e.g. ectopic or missing sinoatrial node, abnormal venous valve connections), not are any left-right pathway components (upstream or downstream of Pitx2) explored. The authors' conclusions regarding overriding aorta as a product of defective LR asymmetry, especially that of the atria, is particularly puzzling, as these are opposite poles of the heart. Therefore the conclusions related to disruption of left-right pathways in this genotype is not at all supported. I look forward to reading the authors' responses to these issues.

On 2016 Oct 27, Andy Collings commented:

Jawdat Al-Bassam's comment on this article (https://elifesciences.org/content/4/e08811#comment-2953448767) is reproduced below:

Negative stain EM 3D-reconstruction and consequent interpretations are often ambiguous due to their low resolution and rely on biochemical data for substantiation as provided in our manuscript. During the past year, we have used different 3D-reconstruction strategies to re-analyze negative stain data and obtain structures. From this re-analysis, we observed some changes in the features of 3D-reconstructions in Figures 5 and 7 in a program-dependent manner, which could result in changes to the fitted models described in Figures 5 and 7. As such, we would like the community to be aware that there are possible ambiguities and alternative interpretations of the published reconstructions, which likely arose from complex heterogeneity due to different conformational states or deformations from the negative staining process. However, these potential reconstruction differences do not change the general conclusions made in the manuscript regarding the overall organization of the complexes and the sites of binding for tubulin and tubulin cofactor C at low resolution. In addition, we deposited our raw data several months ago (EMPAIR-10034, 10035) and welcome suggestions and input from the community. We are currently focused on high-resolution structural studies using cryo-electron microscopy that will allow us to determine the de novo structure for the Tubulin cofactors-D-E with Arl2 assembly in complex with Tubulin dimer and Tubulin cofactor C.

Jawdat Al-Bassam (jawdat@ucdavis.edu)

On 2016 Nov 09, NLM Trainees’ Data Science Journal Club commented:

This is a preliminary study examining the discoverability of and access to biomedical datasets generated by research funded by the U.S. National Institutes of Health (NIH). More specifically, it focuses on datasets not deposited in a known repository and considered “invisible.” Analysis of the NIH-funded journal articles shows that only 12% explicitly mention deposition of datasets in known repositories, leaving a surprising 88% that are invisible datasets. The authors suggest that approximately 200,000 to 235,000 invisible datasets are generated from NIH-funded research published in one year alone. The study identifies issues to improve discoverability and access to research data: definition of a dataset, determining which data should be preserved and archived, and better methods for calculating the number of datasets of interest.

Our group had the honor of having two of the authors in attendance – Betsy Humphreys and Lou Knecht – to provide personal insights into the study. Betsy pointed out one the article’s strength – the opportunity to share this surprising discovery that has potential practical benefits to the research community. The study has received a fair amount of positive feedback, and Betsy mentioned that Clifford Lynch from the Coalition for Networked Information (CNI) has distributed this paper and calling for more studies on this subject. She also recognized the study’s weakness of not holding up as a model of research methodology and lack of consensus among the annotators on the definition of a dataset.

There was a lively discussion from the group on what constitute “invisible” dataset – are links to scientist or institutional websites considered invisible and how to detect visibility with better JATS tagging. For clinical researchers, personal domain self-archiving is the norm and considered invisible. Everyone agreed that it would be a priority to define visible and invisible for future research. Another interesting part of the discussion focused on having dataset be “in context” i.e., datasets are meaningful only when considered along with the published paper. It was surprising to learn that a large part of the formal repository name mentioned in the full text did not turn out to be in the context of an actual deposit. We discussed that it would be helpful to have guidelines and a consistent way to label the information – database name, date of deposit, accession number – in the acknowledgement for easier discoverability and preservation. We were pleased to see this preliminary study published because it brought light to the large problem of invisible dataset, and look forward to seeing more research in this area.

On 2015 Jul 25, Irving I. Gottesman commented:

This experimental confirmation of a "rumor" about pain insensitivity in patients with schizophrenia is a welcome one. If (when) it is noticed by schizophrenia researchers, the finding could be extended to testing the first degree relatives of patients for such decreased pain sensitivity.

On 2016 Dec 21, Daniel Corcos commented:

It is surprising that in situ cancer cumulative incidence after 7 years in the intervention group is only twice that in the control group, as these cancers are usually detected by screening, and a 4-fold difference would be expected instead.

On 2016 Apr 18, Duke RNA Biology Journal Club commented:

This comment is the summary of a discussion from our journal club meeting.

General Impressions: An impressively thorough paper which uses a combination of cell biology, biochemistry and high-throughput sequencing approaches to first identify lncRNAs associated with repressed chromatin, determine what genes a model lncRNA regulates and, finally, identify a specific structural mechanism by which this occurs. This paper lays the groundwork for future identification and characterization of chromatin associated lncRNAs. One overarching criticism with this work is it reads as two separate papers - one identifying the biological role that MEG3 plays in transcription regulation and a second developing the triple helix method of regulation.

Specific Points:<br> A technique, ChRIP-seq, was used to determine the global lncRNA environment of repressive chromatin. The design of the RIP protocol using two different proteins associated with repressed chromatin greatly simplified the final analysis by narrowing the pool of lncRNA targets to 70 unique lncRNAs. However, it was interesting that, even though both RIPs used 4SU crosslinking, the enrichment seen for T-to-C (or A-to-G) conversions was within the EZH2 pulldown and not the H3K27me3 pulldown. What are the 440 RNAs that specifically interacted with H3K27me3 but not EZH2 and why don’t they show crosslinking to the protein over input levels? While this was an interesting puzzle, the comparison that was done between the EZH2 crosslinked enriched RNAs and the chromatin enriched RNAs to provide a list of only 70 lncRNAs, was a clever way of finding chromatin associated RNAs that specifically bound to the PRC2 complex.

From the list of 70 candidate lncRNAs to study, MEG3 was selected. Even though the focus is on one lncRNA, a similar characterization pipeline could be used for the other RNAs identified through this technique. The cross-links identified through the T-to-C transitions were used as a starting point to identify a clear binding site to the protein. Luckily for them, the 4SU labeling, which usually over-crosslinks to its targets, shows only two identifiable clusters of crosslinks. Starting with crosslinks in the more conserved exon 3, they identified 9 bases that abolish ~50% of binding to EZH2 in vitro and in vivo, however, this would also imply there are separate sites on MEG3 that facilitate the other 50% of the binding. Additionally, the non-conserved sequences in MEG3 could fine-tune the binding to various proteins, including EZH2, in different tissues or organisms. Neither of these points is discussed further in the article but would be interesting to delve into if the ChRIP-seq analysis could be modified and applied to tissue samples.

After identifying MEG3’s putative site of binding to EZH2, the group did the obvious experiment and made knockdowns of both EZH2 and MEG3 to determine which genes were affected by RNA-seq experiments. An interesting addition might have been to use complete knockdown cells and a “rescue” with the mutant MEG3 from Fig 2 to provide insight into what genes that binding site specifically affects. They determine that both knockdowns show overlap for the TGF-beta pathway. This is further validated by using an orthogonal assay called ChOP-seq.<br> To explore the intricacies of the MEG3:TGF-beta gene interaction, Mondal and co-workers looked for sequence motifs within the MEG3-binding regions of the genome and discovered a GA-rich sequence motif. Interestingly, they also found GA-rich sequence motifs in the genomic binding locations of rox2 and HOTAIR, two well studied lncRNA known to bind the genome. This information suggests that GA-rich motifs are important for lncRNA localization across the genome.

Several previous studies explored the possibility that lncRNA form triple-helix structures with their target genome binding site using a combination of computational and experimental techniques; Mondal and co-workers used the Triplexator software, which is based on the binding rules needed for triple helix formation, as well as RNAse digestion assays. The Triplexator software identified several regions in MEG3 with high probability of forming triple helices, and those with the highest probability were GA-rich sequences. The assays combined GA-rich dsDNA probes and a target GA-rich segment of MEG3. After incubation, these solutions were separately treated with RNase A and RNase H. RNase A does not degrade ssDNA or dsDNA while RNase H degrades only ssRNA. The solution was sensitive to RNase A digestion, but resisted RNase H digestion. This indicates that the RNA present is not single stranded; however, the authors assume that a triple-helix structure is forming. Because they are not directly observing the structure, it is potentially possible that the RNA is displacing one of the DNA strands and forming an RNA:DNA double-helix. Mondal and co-workers use an anti- triplex dA.2rU antibody for their in vivo assays to confirm the presence of triple-helices, but there is no indication that this antibody was purchased from a commercial source, nor do they explain the method of raising the antibody in-house.

While this information indicates a RNA:DNA triple-helix structure, direct observation is necessary to confirm. Numerous methods could be used to assess the triple-helix structure: X-ray crystallography, nuclear magnetic resonance (NMR), small-angle x-ray or neutron scattering (SAXS/SANS), cryoelectron-microscopy (cryo-EM). As initially stated, we believe this work would have benefitted from splitting into two separate papers: one exploring the genomic binding of MEG3 to the TGF-beta pathway genes, and the other exploring the potential role of triple-helix formation in lncRNA binding.

On 2015 Sep 10, Holly G Prigerson commented:

Data appear to confirm that in some (most?) cases, less chemo is more QoL

On 2015 Aug 20, Bill Cayley commented:

A good example of when "less" is "more" - for more examples, see: https://lessismoreebm.wordpress.com/

On 2017 Feb 05, Stuart RAY commented:

I appreciate Prof Pybus' response, and have no objection to this use of the "Simplot" name; I was just providing context.

On 2017 Feb 01, Oliver Pybus commented:

I named the method "Deep Simplot" in homage to the very popular Simplot program. I apologise to Prof Ray and his colleagues for (i) not seeking their permission to use this term and (ii) not citing the original Simplot paper. To avoid confusion I recommend that, in future, the method described by our paper is referred to as "deep divergence plotting". My thanks to Prof Ray for bringing this issue to my attention.

On 2017 Jan 31, Stuart RAY commented:

As the author of Simplot (Lole KS, 1999) I infer that the "Deep Simplot" method described was named after Simplot; it also shares characteristic display elements (as seen in figure 3b). Of course, the bootscanning approach that I implemented in Simplot was pioneered by Mika Salminen et al (Salminen MO, 1995, which is cited by Iles et al.).

On 2015 Aug 12, Víctor M. Baizabal-Aguirre commented:

The PLKO1-GSK3beta1 and PLKO1-GSK3beta2 vectors used in our work were successfully used in a previous report by Yoeli-Lerner et al. (2009). As in our study, these authors were also able to fully silence the GSK3beta isoform (PMID: 19258413, see Figures 1A and 3A). Most of the studies on GSK3-dependent regulation of beta-catenin have used unspecific inhibitors that affect both GSK3 isoforms. Therefore, the contribution of GSK3alpha and GSK3beta to the regulation of beta-catenin is an issue that remains open. In this regard, Yu et al. (2003) reported that specific gene silencing of GSK3alpha or beta by siRNA expression vectors induces the stabilization of beta-catenin in P19 mouse embryonic carcinoma cells (PMID: 12597911, see Figure 5). As to the effect of GSK3 silencing on beta-catenin, results published in 2009 by Mamaghani et al., demonstrated that GSK3alpha or beta inhibition by siRNA increased the stabilization of beta-catenin in pancreatic cancer cells (PMID: 19405981, see Figure 3A). In contrast, Ryu et al., (2012) reported that specific GSK3alpha inhibition by siRNA decreased beta-catenin levels in human gastric cancer cells (PMID: 22328534, see Figure 3E). These findings indicate that complete removal of GSK3alpha or GSK3beta, as in our work, affect the relative abundance of beta-catenin and that GSK3alpha and GSK3beta alter in different ways the stabilization of beta–catenin, depending on the type of cell.

On 2015 Aug 04, Jim Woodgett commented:

Figure 3 appears to be missing panel B (beta-catenin blot).

The RNAi knockdowns here are remarkably efficient and it looks from the legend as though only one siRNA was used (although in the methods 3 alpha sequences and 2 beta sequences are listed). Figure 5 shows essentially complete removal. Blowing up the figure reveals some image artifacts. Typically, even complete inhibition of either GSK-3alpha or GSK-3beta has no effect on beta-catenin as the other isoform compensates fully (Axin is present at far lower concentrations that either isoform of GSK-3 and is the limiting factor in beta-catenin phosphorylation).

On 2016 Oct 24, Sean Ekins commented:

A poster based on this work from ACS in 2015 http://www.slideshare.net/ekinssean/mobile-apps-for-transporter-drugdrug-interaction-prediction-a-tool-of-the-future-now

On 2015 Dec 21, Will Rowe commented:

SEAR is now available for use as an App on the BaseSpace platform (Illumina).

This iteration of SEAR has been updated, changes include:

• The use of the open source VSEARCH (instead of USEARCH).

• New result output.

Please try it at:

https://basespace.illumina.com/apps/2083081/SEAR-Antibiotic-Resistance

Finally, the SEAR source code (for the App, Docker container image and original code) is available on GitHub:

https://github.com/wpmr2/SEAR

On 2016 Dec 05, Anne Carpenter commented:

As senior author on this paper, I report an error on page 10: the words "after cell fixation with 16% paraformaldehyde" should be replaced by "after cell fixation with 3.2% formaldehyde".

On 2015 Jul 25, David Keller commented:

This just in: pioglitazone proved futile for slowing the progression of Parkinson's disease

A large double-blind placebo-controlled randomized phase II study has proved pioglitazone futile for slowing the progression of early Parkinson's disease [1]. Pioglitazone is the only widely-prescribed thiazolidinedione ("glitazone") since the FDA placed safety restrictions on the use rosiglitazone (Avandia).

Glitazones now join the ranks of disproved neuro-protectants, including creatine, co-enzyme Q10, vitamin E and minocycline. Back to the laboratory....

Reference:

1: NINDS Exploratory Trials in Parkinson Disease (NET-PD) FS-ZONE Investigators. Pioglitazone in early Parkinson's disease: a phase 2, multicentre, double-blind, randomised trial. Lancet Neurol. 2015 Aug;14(8):795-803. doi: 10.1016/S1474-4422(15)00144-1. Epub 2015 Jun 23. PubMed PMID: 26116315.

On 2015 Jul 23, David Keller commented:

Exenatide, a different kind of diabetes drug, also exhibits activity against Parkinson's disease

The type-2 diabetes drug exenatide is in the category of incretin mimetics, and is not a thiazolidinedione ("glitazone") like the drugs in this study by Brauer and colleagues. Exenatide lowers blood sugar by raising levels of endogenous insulin, among other effects. It also has exhibited symptomatic benefits in Parkinson's disease, in a prospective randomized interventional trial [1], with persistent motor and cognitive benefits which suggest possible disease modification. Exenatide can be used concomitantly with glitazones, and such use should be accounted for in this glitazone study, to avoid skewed results. For example, if the percentage of glitazone patients taking exenatide was higher than the percentage of placebo patients taking exenatide, then the apparent benefits of glitazone use may have been all or partly due to this imbalance in the use of exenatide. Was this possibility controlled for?

Reference:

1: Aviles-Olmos I, Dickson J, Kefalopoulou Z, Djamshidian A, Kahan J, Ell P, Whitton P, Wyse R, Isaacs T, Lees A, Limousin P, Foltynie T. Motor and cognitive advantages persist 12 months after exenatide exposure in Parkinson's disease. J Parkinsons Dis. 2014;4(3):337-44. doi: 10.3233/JPD-140364. PubMed PMID: 24662192.

On 2017 Jun 28, Raphael Levy commented:

A response from Chad Mirkin. Well, nearly: a section of William Briley's PhD which starts with: "Though the endosomal escape of SNA nanostructures such as the Nanoflare and stickyflare is evident based upon their ability to provide sequence-specific information regarding RNA levels and locations within cells, one researcher [That’s me!] has concluded that SNAs cannot escape from endosomes.[75] That researcher is ignoring the many papers now that use such architectures for sequence-specific cell-sorting experiments." More here

On 2015 Nov 17, Raphael Levy commented:

David Mason and myself submitted a letter to the Editor of PNAS regarding that article. It was however deemed not to "contribute significantly to the discussion of this paper" by the editorial board, and therefore publication was declined. I leave it to the readers of PubMed Commons to decide: the letter was published as a PrePrint on bioRxiv. Our article argues that Briley et al own data show that the Sticky-Flare remain in endosome where they get degraded by nucleases (and therefore cannot report on RNA level and localisation).

On 2015 Nov 17, Raphael Levy commented:

The PNAS article itself includes a sentence which could be interpreted as SmartFlare advertising: "As a result, the Nanoflare has grown into a powerful and prolific tool in biology and medical diagnostics, with ∼1,600 unique forms commercially available today (sold under the SmartFlare trade name)." Furthermore, there is a Sticky-Flare patent which was published around a month before the communication of the PNAS article.

On 2015 Sep 28, George McNamara commented:

I posted this on PubPeer, https://pubpeer.com/publications/25CC01C366B9593D1686A78B52461F#fb36935

The Briley et al 2015 paper is deficient in methods - what is the length of the new product? what are the design criteria for specificity? how are the spherical nucleic acids constructed? Is there a mechanism by which the flare gets kicked off the SNA? I suggest PNAS explicitly require self contained full methods and materials in manuscripts they accept. The details can be in the supplemental file, and can both provide full details and cite -- or even quote -- earlier work.

The Briley COI statement states: "The authors declare no conflict of interest.". The authors and their University previously commercialized NanoFlare/SmartFlare - is PNAS sure they have not submitted patent applications for Sticky-Flare and intent to make money from it = financial interest. I am fine with commercialization of products, but if this is an advertisement for a future product, the authors should be honest in their COI an PNAS should mark the paper as an advertisement.

Citation for commercialization: "NanoFlares have been very useful for researchers that operate in the arena of quantifying gene expression. AuraSense, Inc., a biotechnology company that licensed the NanoFlare technology from Northwestern University, and EMD-Millipore, another biotech company, have commercialized NanoFlares. There are now more than 1,700 commercial forms of NanoFlares sold under the SmartFlare name in more than 230 countries." http://www.northwestern.edu/newscenter/stories/2015/07/new-tool-for-investigating-rna-gone-awry.html#sthash.GwI4hbRx.dpuf

One of their patents is US8507200B2 https://patents.google.com/patent/US8507200B2/en?q=mirkin&q=nanoflare

On 2017 Mar 27, Christopher Southan commented:

There was tutorial on this theme at the 2017 International Conference on Trends for Scientific Information (ICIC) https://www.slideshare.net/Haxel/icic-2017-tutorial-digging-bioactive-chemistry-out-of-patents-using-open-resources/1

On 2016 Jan 25, Dimitrios Tzalis commented:

The ELF Public Compound Collection (PCC) is a very unique collection of compounds that are already synthesized and available for screening within ELF Screening Campaign. The goal of the paper was to compare the PCC with other compounds that are available for biological screening or that were actually screened. That is why, with a full awareness, we have analyzed the PCC against part of the PubChem collection called MLP of NIH, commercially available Maybridge and already tested compounds represented by ChEMBL. It might be interesting to collate the PCC and the 15 millions of patent-extracted compounds, in respect to broadly understood novelty, but we wanted to avoid the contamination of our comparison with theoretical compounds. In such a way the work is much more consistent. Nevertheless, thank you for your valuable comment and we can think of extending our novelty check also in respect to theoretical compounds in the future analysis since our collection is still growing. We believe that by focusing on exploring underrepresented chemical space of spiro-compounds and saturated, fused hetero rings we are offering a very competitive and unprecedented collection.

On 2015 Jul 22, Christopher Southan commented:

This is part of a special issue "From chemistry to biology database curation" http://www.sciencedirect.com/science/journal/17406749/14/supp/C. The PubMed ID series is 26194580-6.

On 2015 Aug 03, Maria A. Landin commented:

Gratulere med ny artikkel Rivan :)

On 2015 Jul 22, Ellen M Goudsmit commented:

As one of the main authors, I note that the PACE trial could not have used the London criteria for ME, as often claimed, as there should have been at least one difference between the groups, and this was not reported. Ergo, they did not use the criteria for ME correctly and the results from the trial can not be extrapolated to this population. The attitude of the authors towards ME and the scientists who specialise in this disease is disappointing.

On 2015 Oct 03, Seyed Moayed Alavian commented:

Dear All, I would like to declare that receiving the medical services may be an important risk factor for acquiring the HCV and HBV infections in Middle East Countries. Yours Alavian SM

On 2016 Jan 14, Noman Shahzad commented:

The article is the highest level of evidence available on the topic. Reading the article, I am interested in knowing more about those who developed hernia. Like group wise details of how many of them were symptomatic, how many required surgical repair. Was there any statistical difference in detection method used to diagnose hernia? Was there difference in Quality of Life of those who developed hernia in traditional vs small suture group? This information will help in understanding the impact of change in technique from patient perspective. Clustering leading to increased risk of alfa error is a frequent problem of multicentric trials, it will be informative if information could be provided if adjustment was made for clustering in statistical analysis.

On 2016 Jan 10, Noman Shahzad commented:

None

On 2015 Jul 24, Jay Kaufman commented:

Etsuji Suzuki of Okayama University, Japan contacted the authors to note that on page 3 of the article, the text states that that conditioning on CVD in Figure 1c opens four paths that bias the effect of obesity on mortality. However, the first of these paths that is listed in the text (obesity <- smoking -> CVD -> mortality) does not in fact contain a collider on the path, since no nodes are entered and exited through arrowheads. Therefore, the text should state that there are three such paths, not four. This error in the exposition of the problem changes neither the quantitative results nor the conclusions of the paper.

On 2015 Dec 11, Mark Johnston commented:

Interactive protocols from this article are freely available at protocols.io.

On 2015 Sep 29, George McNamara commented:

Why does this paper's authorship section state:

Conflict-of-interest disclosure: The authors declare no competing financial interests.

when one of the authors works for the company that supplied the CB-839 drug feature in the abstract and key points?

http://www.calithera.com/programs/cb-839/

Genetically mandated alterations in the fundamental metabolic pathways of tumors often cause a dramatic rise in the uptake of the nutrients glucose and glutamine. Removal of glutamine leads to a substantial reduction in cell growth or induces cell death in certain types of cancer cells, indicating that these cells are dependent on, or “addicted” to, glutamine. Normal cells do not show this pronounced dependence on glutamine. The enzyme glutaminase, which converts glutamine to glutamate, has been identified as a critical choke point in the utilization of glutamine by cancer cells. CB-839 is a potent, selective, reversible and orally bioavailable inhibitor of human glutaminase.

On 2015 Oct 24, Geriatric Medicine Journal Club commented:

This article was critically appraised at the October 2015 Geriatric Medicine Journal Club (follow #GeriMedJC on Twitter). One of the study authors was also present for the tweet chat discussion! The full discussion can be found at: http://gerimedjc.blogspot.com/2015/10/october-2015-gerimedjc.html?spref=tw This is a very interesting study which separates common beliefs about older people in general as different from older patients in health care settings. This will help inform policies and education strategies to improve care for older adults.

On 2015 Aug 16, Xiang Ming commented:

Thanks very much for Murtaugh’s careful review. According to your comment, we make following explanations. 1. The pancreas photos on the first row of Fig.5A showed that the surgical removal of tissues do not include intestine. After being photographed, the tissues were embedded in paraffin, so we could ensure that all sections assessed in this paper are from pancreas. 2. As you said “the treatment might have induced cancers of an intestine-like pathology”, we should explain that a great quantity of non-tumor components existed in pancreatic cancer including stromal cells and lymphocytes. The immunohistochemical analysis in Figure.5 was consistent with this pathological characteristic which was similar to intestine-like pathology. 3. In our study, the malignant cell could secrete a small amount of amylase (Fig.5A). This also prove that the treatment didn’t induce cancers of an intestine-like pathology. On the other hand, the Ki67 is mainly expressed in the malignant acinar cell nucleus, so high levels of Ki67 expression could support our conclusion that Reg3g could promote proliferation in acinar cells

On 2015 Jul 30, L Charles Murtaugh commented:

While this is an interesting study, and the role of REG genes in pancreatic cancer is arguably understudied, the conclusions of this paper are tempered by irregularities in the histological analysis. Only one study group developed pancreatic cancer in this study, namely the high-dose pReg3g + DMBA treatment, referred to as HA10R. Inspection of the histology data presented for the HA10R group (Fig. 5A) reveals that several of the most relevant images (H&E staining, Ki67 and cytokeratin-19), for this group specifically, appear to be taken from sections of the intestine rather than the pancreas. While, in principal, the treatment might have induced cancers of an intestine-like pathology, this would not explain the clear organization of proliferative crypts and non-dividing villi, apparent from Ki67 staining. This raises doubts about the quantitative analysis of these and other variables, in Fig. 5B, as well as about the overall conclusion that treated mice developed cancer of the pancreas.

On 2015 Dec 05, David Keller commented:

Patient-oriented result: response rate to magnetic stimulation was the same as to placebo

This study of repetitive transcranial magnetic stimulation (rTMS) was designed to test the hypothesis that rTMS would result in a "statistically significantly greater percentage of responders to treatment in an active rTMS group compared with a placebo rTMS group" [1]. A relatively new metric called the Tinnitus Functional Index (TFI) was used to measure response to treatment. The TFI rated 18 of the 32 subjects actively treated with rTMS as responders to treatment (56%), while only 7 of the 32 subjects treated with sham therapy were rated as responders (22%). These two rates differed significantly, which was pre-specified in the Objectives section as defining a successful outcome.

However, 7 of the 18 treated subjects rated as "responders to therapy" using the TFI scale nevertheless believed they had received sham therapy, implying that they did not perceive any treatment benefit beyond the placebo effect. When a subject states that his treatments seemed like sham therapy, providing only placebo-strength benefit, this is important information. Since it is a direct expression of the subject's assessment of the efficacy of rTMS therapy, it has more validity than a contrived metric like the TFI, from a patient-oriented perspective.

The data in e-Table 12 indicate that, of the 32 subjects who received active rTMS treatments, only 11 correctly guessed they had received active therapy at the end of the last treatment, which implies that only 11 out of 32 actively-treated subjects (about 34%) noted perceptible improvement in their tinnitus symptoms. Coincidentally, 11 of the 32 placebo-treated subjects (also 34%) guessed that they had received active rTMS therapy, which equals the placebo effect. Thus, active rTMS treatments had the same response rate as sham therapy, equal to the placebo effect of 34%.

Conclusion: rTMS is no more effective than placebo for treating tinnitus, when assessed by subjects after a full course of treatments, based on their perception of whether they received active or sham therapy. The advantage of this assessment is that it eliminates uncertainty about the accuracy and clinical relevance of the TFI metric, because the assessment of treatment benefit came directly from the subjects themselves.

Reference

1: Folmer RL, Theodoroff SM, Casiana L, Shi Y, Griest S, Vachhani J. Repetitive Transcranial Magnetic Stimulation Treatment for Chronic Tinnitus: A Randomized Clinical Trial. JAMA Otolaryngol Head Neck Surg. 2015 Aug;141(8):716-22. doi: 10.1001/jamaoto.2015.1219. PubMed PMID: 26181507.

On 2015 Nov 29, David Keller commented:

38% of the reported "responders to therapy" thought they had been randomized to placebo & reply by author

At the end of this study, only 11 of the 32 subjects who received active treatment for tinnitus guessed that they had received active treatment. The remaining 21 subjects who were actively treated guessed that they had received placebo (sham treatments).

18 of the 32 actively treated subjects were rated as "responders" to therapy by Folmer et al. Thus, 7 of the actively treated subjects, who were rated as "responders" to therapy, thought they had received sham treatments. Bottom line: 7 of the 18 tinnitus sufferers (38%) who were reported to be "responders to therapy" actually did not perceive any benefit.

Tinnitus is a subjective phenomenon. I contend that, by definition, a responder to tinnitus therapy cannot believe that he received sham therapy. If a subject thinks he was treated with sham therapy, he did not perceive any benefit, and he cannot be a reported to be a "responder to therapy". This is the essence of my criticism of this study, and it has not been addressed.

Addendum (12/4/2015): Yesterday, in reply to the above comment, Dr. Folmer issued the following statement (start of quotation):

In our study, participants were categorized as "responders" or “non-responders” to TMS treatment based solely on the change in their TFI score from baseline to post-TMS assessment – this is stated in the article.

The definition of "responders" or “non-responders” we used had nothing to do with

1. Whether or not study participants “perceived” any benefit if that was based on anything else but their TFI score
   

2. Study participants’ guesses that they received active or placebo rTMS  
   

These are separate issues. You can debate, discuss or disagree with them, but they remain separate issues and definitions as specified in the article.

--Robert L. Folmer, Ph.D. (end of quotation)

On 2015 Oct 05, Eiko Fried commented:

A recent study published in Nature by the CONVERGE consortium [1] identified two Single Nucleotide Polymorphisms (SNPs) for Major Depressive Disorder (MDD) that replicated across two samples of Han-Chinese women with recurrent depression. The report was accompanied by an editorial [2] that hailed the findings as biologically and diagnostically relevant, suggesting that large-scale exploratory genome-wide studies offer enticing prospects towards aiding diagnosis and the development of new drugs.

We disagree with the editorial’s interpretation (and most of the media coverage) of these CONVERGE results, which also contrast with the careful phrasing of the authors themselves. Although the two SNPs discovered in the comparatively homogenous CONVERGE sample did replicate in a similarly ascertained group, the editorial fails to mention that they did not in the more heterogeneous Psychiatric Genomics Consortium (PGC) data also examined by the authors. Moreover, in polygenic risk score analysis, the genetic signal in the PGC sample explained less than 0.1% of disease risk in the CONVERGE data, implying a fundamental lack of overlap in genetic risk signal across samples.

The laudable effort of the CONVERGE consortium to ensure genetically and phenotypically homogenous samples confirms the elusiveness of the genetics of MDD. Hailing the results as robust insights into the biology of depression detracts from the true scientific relevance of the study: genetic effects for MDD are, even in large homogenous samples, small and do not generalize.

Given the hitherto negative results of genetic MDD studies [4,5], slogging along on this current road of ever-larger samples and discovering at best small effects is not an alluring prospect, especially so considering that these effects are likely not specific to MDD [6]. Instead, we suggest revising complex psychiatric phenotypes such as MDD that were transferred unquestioningly from psychiatry to genetics. Incorporating recently proposed network models [7], symptom- rather than syndrome-level analyses [8], and the development of new instruments that tap variation along the entire continuum [9,10] (i.e., in both "cases" and "controls") offer promising ways forward.

References

• 1.Cai, N. et al. Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature 523, 588–91 (2015).

• 2.Ledford, H. First robust genetic links to depression emerge. Nature 523, 268–269 (2015).

• 3.Keener, A. B. Genetic Variants Linked to Depression. Sci. (2015).

• 4.Hek, K., Demirkan, A., Lahti, J. & Terracciano, A. A Genome-Wide Association Study of Depressive Symptoms. Biol. Psychiatry 73(7), 667–78 (2013).

• 5.Daly, J. et al. A mega-analysis of genome-wide association studies for major depressive disorder. Mol. Psychiatry 18, 497–511 (2013).

• 6.Kendler, K. S. ‘A gene for...’: the nature of gene action in psychiatric disorders. Am. J. Psychiatry 162, 1243–52 (2005).

• 7.Cramer, A. O. J., Kendler, K. S. & Borsboom, D. Where are the Genes? The Implications of a Network Perspective on Gene Hunting in Psychopathology. Eur. J. Pers. 286, 270–271 (2011).

• 8.Fried, E. I. & Nesse, R. M. Depression sum-scores don’t add up: why analyzing specific depression symptoms is essential. BMC Med. 13, 1–11 (2015).

• 9.Lee, S. H. & Wray, N. R. Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. PLoS One 8, e71494 (2013).

• 10.Van der Sluis, S., Posthuma, D., Nivard, M. G., Verhage, M. & Dolan, C. V. Power in GWAS: lifting the curse of the clinical cut-off. Mol. Psychiatry 18, 2–3 (2012).

Authors

• EI Fried, University of Leuven, Belgium

• S van der Sluis, VU Medical Center, Amsterdam, The Netherlands

• AOJ Cramer, University of Amsterdam, The Netherlands

PDF of this commentary (DOI: 10.13140/RG.2.1.3480.4963) available at: http://eiko-fried.com/wp-content/uploads/Nat_Correspondence_blog.pdf

On date unavailable, commented:

None

On 2015 Sep 23, Angelo Gaitas commented:

The entire response appears in the PLOS1 comment section under response: http://www.plosone.org/article/comments/info:doi/10.1371/journal.pone.0127219

In two recent articles [1, 2] two techniques for removing or inactivating blood borne pathogens were introduced. The initial experiments were performed in vitro under simplified conditions. First, the primary achievement of the PDT work deserves clarification [1]. PDT is a powerful therapeutic modality, but its clinical application has been hampered by the inability of light to penetrate deep layers of the tissue, which is mainly due to hemoglobins in the blood readily absorbing photons. Utilizing a millimeter- diameter transparent tube for extracorporeal blood circulation allows PDT to function well despite the presence of hemoglobins in blood. Another point that deserves clarification is that the tube capturing device is not a microfluidic device [2]. This technique can be adapted using existing medical tubing without the need for complicated microfluidics and micro-fabrication. The device is a medical tube that has been chemically modified using simple steps to adapt the internal surface for cell capturing. 

We would like to take this opportunity to respond to concerns brought up in [3]. We start off by addressing concern (1), which speculates about the possibility of overheating during the use of near IR light. Our control data (Fig.3 and Fig.4 of [3]), confirmed that controls illuminated without photosensitizer-antibody conjugates did not undergo cell death, whereas those with photosensitizer-antibody conjugates underwent significant cell death under identical conditions. Thus it is clear from our data that temperature did not affect the outcome. It has been shown that 660 nm irradiation is safe and effective [4-6]. 

Moving on to concern (2) part (a) that brings up the problem of using the CD-44 antigen as a target. Limitations of antibody specificity are common knowledge and not unique to CD-44, but to all antibodies. To our knowledge, a targeting method that exclusively binds only to cancer cells does not yet exist, making the use of such a compound an unreasonable standard for publication. We used CD-44 antibody to demonstrate feasibility. As targeting methodologies advance and better selectivity to target cells becomes available, this technique will have improved selectivity. Our experiments were designed to avoid non-specific damage to other cells by pre-staining pure cancer cells with the photosensitizer-antibody conjugates and subsequently removing extra free conjugates before spiking into blood (described in detail in [1]). This elimination of the possibility of side effects due to undesired binding to other blood cells and excess free photosensitizer-antibody conjugates precluded the need for a toxicity study, particularly because we were at the proof-of-principle stage.

Part (b) of concern (2) suggests that we may have caused non-specific damage to non-cancerous cells by ROS' convection in the blood stream. We believe that this is highly unlikely. One of the authors has been conducting research focusing on ROS and PDT for years, in collaboration with other researchers [7-15]. This research demonstrated that PDT is extremely selective to targeted cells [13]. 

 Part (c) of concern (2) states that we should have used additional cytotoxicity assays, such as Annexin V, TUNEL, and MTT. However, because none of these techniques are cell-type specific, they would be useless for the particular objective they were suggested. Once our line of investigation reaches a more mature stage, we plan to undertake more useful studies, such as applying separate fluorescent tags, or radio labels, in addition to a cell viability assay and analyzing cell death with a cell sorting technology, such as FACS, MACS, density gradient centrifugation, etc.  

Concern (3) is that the capturing work [2] lacked purity confirmation concerning non-specific capturing of blood cells. Though purity confirmation is critical in diagnostic testing, our work was strictly limited to in vitro conditions, using spiked pure PC-3 cells as a model. To visualize and quantify PC-3 cells in the presence of whole blood, PC-3 cells were pre-labeled using a fluorescence tag (Calcein AM) and the extra free dye was subsequently removed before spiking PC-3 cells into blood. Because only PC-3 cells can have fluorescence in the blood mixture, and because quantification was based on fluorescing cells, false-positive results from other blood cells can be reasonably excluded. Furthermore, if other blood cells were captured but not identified by our detection method our data would then indicate that the simple tube captured cancer cells despite being blocked by other blood cells. If our technique were applied to CTC diagnosis, independent isolation procedures could be used to ensure the purity of captured cells. In contrast, if used for therapy, the purity of captured cells would not be as critical, provided that CTCs are effectively removed. If, by chance, capturing is hampered by accumulation of non-specific binding in filtering the entire blood volume, this issue can be addressed with strategies such as scaling up the tube and carefully determining the tube dimensions, flow rate, frequency of tube replacements, etc. 

Finally, concern (4), points out that the experimental conditions were not translatable to clinical applications. Part (a) regards scaling up the system to show high throughput. The concept of extracorporeal cleansing of the entire blood volume has been used for years in cases such as hemodialysis. We already are working on optimizing the technique for larger blood volume processing. Part (b) of concern (4) discusses the static no-flow condition as being unrealistic. This issue was brought up during the review process, and we provided with our results showing data under constant flow conditions by peristaltic pump (to be published in future publication). The reviewers agreed that the use of a no-flow condition as a conservative approach during a proof-of-concept stage was appropriate.

Despite its preliminary nature, we believe that our work communicates novel ideas, an important objective of research and publication. Given the number of research articles dealing with diagnostics and microfluidics, perhaps a further point of confusion came about by thinking of our work in those terms. We want to clarify that diagnostics were not the primary objective in our work. Furthermore, as it becomes evident by this response our experimental design was carefully devised to minimized unnecessary interferences. We hope that this response mitigates any confusion and addresses the concerns raised. 

1. Kim G, Gaitas A. PloS One. 2014;10(5):e0127219-e.
2. Gaitas A, Kim G. PLoS One. 2015;10(7):e0133194. doi: 10.1371/journal.pone.0133194.
3. Marshall JR, King MR. DOI: 101007/s12195-015-0418-3. 2015;First online.
4. Ferraresi C, et al. Photonics and Lasers in Medicine. 2012;1(4):267-86.
5. Avci P, et al. Seminars in cutaneous medicine and surgery; 2013.
6. Jalian HR, Sakamoto FH. Lasers and Light Source Treatment for the Skin. 2014:43.
7. Ross B, et al. Biomedical Optics, 2004
8. Kim G, et al. Journal of biomedical optics. 2007;12(4):044020--8.
9. Kim G, et al Analytical chemistry. 2010;82(6):2165-9.
10. Hah HJ, et al. Macromolecular bioscience. 2011;11(1):90-9.
11. Qin M, et al. Photochemical & Photobiological Sciences. 2011;10(5):832-41.
12. Wang S, et al. et al. Lasers in surgery and medicine. 2011;43(7):686-95.
13. Avula UMR, et al.Heart Rhythm. 2012;9(9):1504-9.
14. Kim G, et al. R. Oxidative Stress and Nanotechnology, 2013. p. 101-14.
15. Lou X, et al. E. Lab on a Chip. 2014;14(5):892-901.
16. https://www.roswellpark.org/patients/treatment-services/innovative-treatments/photodynamic-therapy.
17. Yin H, et al. Artificial organs. 2014;38(6):510-5.
18. Yin H, et al. Journal of Photochemistry and Photobiology B: Biology. 2015.

On 2015 Aug 29, Michael King commented:

Our recent commentary discusses this paper:

http://link.springer.com/article/10.1007/s12195-015-0418-3

In cancer research, the discovery and study of circulating tumor cells (CTCs) have seemed to open a world of possibilities. We now have the potential to gain cellular and molecular understanding of individual cases of metastatic cancer without invasive procedures. This area of research is, however, not without some basic pitfalls. In this commentary, we address some of these pitfalls by considering two recent examples in the published literature and discuss ways to overcome their limitations with the hope of informing those who may be entering the growing field of CTC research. Careful research design should always be followed to prevent incomplete or misleading studies from entering the literature, and thereby avoid setting back this burgeoning field.

On 2015 Sep 27, Ivan Oransky commented:

The first author of this paper is appealing the retraction: http://retractionwatch.com/2015/09/22/author-appeals-retraction-after-co-authors-dispute-nature-comm-paper/

On 2016 Nov 02, Eiko Fried commented:

What the study actually found is this: none of the 171 serum proteins differed between MDD cases and controls, seeing that none of the 171 markers differed after controlling for multiple testing.

The authors do not report this most important core finding of their study in the abstract, and instead claim that 28 of the 171 markers differed between the two groups. I struggle to understand why the authors chose to report the uncorrected findings instead of the proper statistical results — the corrected findings – in the abstract.

On 2017 Jan 19, Jameson Voss commented:

This paper identifies an interesting association between calories in the national food supply per capita and average population body weight. It was recently recognized by an independent review as an important work in the field. The recognition is appropriate as the analysis was based on worldwide comprehensive data, stratification of countries by income, assessment of longitudinal changes, incorporation of a mathematical model of weight gain and other strengths. The association is plausible and builds on other work connecting the food supply and body weight.

Despite these strengths, readers should be cautious about how they interpret the title and discussion. First, the title uses a causal phrase “major driver” which was also echoed in the recent review (linked above). Readers should be aware this title refers to an ecologic association and avoid making causal inferences about outcomes at a population or individual level based on this type of observational study design. Secondly, readers might misinterpret the term “major” as though the authors found the association to be stronger than other obesity correlates, but the paper did not provide an empiric comparison with any other obesity correlate. Finally, the discussion about opportunities for future research could also be misunderstood. The authors argue against testing the association with a study that moves people to different food systems by claiming it would be impractical. That might discourage readers from pursuing probative designs like “packet randomized experiments” which can utilize quasi-random assignment of migration (e.g., international adoptions, foreign exchange students, military household moves, etc.). If done properly, these studies can eliminate confounding among individuals, but confounding at the location persists. When participants are assigned to locations with higher energy in the food supply, they would simultaneously face other local, regional, or national exposures. That is, all exposures found at a location are assigned together as a single “packet,” so national food supply could be confounded by other differences between places (e.g., infrastructure, hygiene, ambient light, pollution, temperature, etc.).

There are empiric methods of handling packet level confounding, but it can be eliminated with a design called cluster randomization. Within the United States, an industry affiliated organization has worked to lower national per capita food energy supply and this has coincided with worsening average waist circumference, but it cannot be known if these trends are caused by the lower energy available in the food supply (as discussed here). Instead, system interventions could be randomized to different systems or subsystems or implemented at randomized start times or randomized locations.

While ecologic studies have confounding at both the location and subject level, there is still possible utility for prediction if the confounding remains stable across periods. Interventions, on the other hand, work based on causation and can have unintended consequences. Thus, readers should continue to feel encouraged to investigate net harms and benefits of altering the food supply.

The views expressed in this comment are those of the author and do not necessarily reflect the official policy or position of the Air Force, the DoD, or the U.S. Government.

On 2016 Apr 26, Ivan Oransky commented:

A researcher tried to publish a letter on this study, but the journal said prior publication on PubPeer meant he couldn't: http://retractionwatch.com/2016/04/26/does-posting-on-pubpeer-count-as-prior-publication-journal-says-yes-rejects-letter-rebutting-campus-sexual-assault-study/

On 2017 Aug 02, Gregory Francis commented:

The journal Perspectives on Psychological Science used to have an on-line commenting system. They seem to have discontinued it and removed all past comments. In April 2013, I published a comment on this article. I reproduce it below.

Simonsohn's arguments are without merit

Simonsohn presents two arguments to discredit the publication bias analyses I have published over the past year. Neither of these arguments are convincing to me, but some people seem to be taking them seriously. I treat them in more depth in a recent paper (Francis, 2013), but it might be helpful to have a comment with the article itself.

Whether to ignore data that appears to be biased

I have argued that sets of experiments that appear to be biased should be treated as "non-scientific" and be replaced by new experiments. Such a recommendation is admittedly a cautious approach, but I feel that such caution is warranted for scientific investigations; especially when it is fairly easy to gather new data. For example, in my POPS article, to which Simonsohn's directs his reply, the publication bias analysis suggests that the aversiveness memory effects reported by Galak & Meyvis (2010) appear to be biased. My recommendation to ignore their data is not so very harsh, since it is quite easy for interested researchers to gather new (unbiased) data and determine the magnitude of the effect. There may be situations where gathering new data is more difficult and such situations might justify efforts to try to mitigate effects of bias. However, existing statistical methods are not very good at compensating for bias, and they do not attempt to compensate for other types of questionable research practices that can also trigger the bias analysis.

Simonsohn raises an interesting issue about the relation between statistical significance and practical significance. His example of a literature of 100 studies, all with p<.05 and power of 97%, highlights a particularly bad property of bias. As Simonsohn describes it, bias appears to be present (the bias test gives .97¹⁰⁰ = 0.0476) but small because, given the power values, one would expect just three non- significant findings out of 100 experiments. Thus, Simonsohn concludes the bias is small because it appears to be small relative to what is published. Such a view would be fine if there was no reason to suspect bias, but it is difficult to maintain this view given that the analysis suggests there is bias. The bias could be small, but there may have been another 100 non-significant findings that were suppressed, in which case the bias is quite large. There is no way for a reader to know the extent of the bias.

One of the fundamental goals of science is to reduce uncertainty in measurements, but the appearance of bias introduces uncertainty about the experimental results and conclusions. The responsibility for making a strong scientific argument rests with the authors; and if their results appear to be biased, then it is difficult to make such an argument.

Cherry picking

Simonsohn charges that my analyses are ironically biased with the very practice that is used to produce the biased experiment sets that I criticize. To this charge, I reply "guilty", but I have an explanation. There are different types of biases; and some biases misrepresent empirical data, while other biases are simple byproducts of scientific exploration. Understanding the differences between these types of bias is very important.

Biases that misrepresent the data

If a researcher runs 10 direct replication experiments and gets six experiments to reject the null hypothesis and four experiments to not reject the null, then bias is going to be introduced if only the six significant experiments are reported. (Whether such bias will be detected by the bias analysis depends on the estimated power of those experiments.) A meta-analysis across those six published experiments will almost surely overestimate the true effect size, because the experiments with samples having small effect sizes tend to not reject the null. When the experiments are connected by a theoretical link (in this case by the idea that the experiments are measuring the same effect size), this kind of bias misrepresents the true state of nature, which is clearly a problem for a scientific field.

Biases that do not misrepresent the data

If a researcher runs 10 experiments on unconnected topics (separate studies on afterimages, reading rates, Stroop reaction times, aversiveness ratings of memories, etc.) and gets six experiments to reject the null and four experiments to not reject the null, then a bias is introduced by publishing only the six significant experiments. However, this kind of bias is mostly benign because it does not misrepresent the published data. Suppose the study on afterimages finds a significant effect with a standardized effect size of 0.6. None of the other experiments tell us anything about the effect size of afterimages, so whether those experiments are published or not does not influence the scientific conclusions that are drawn about afterimages from this published study.

The publication bias analyses I have reported over the past year have the latter type of bias. Whether other papers have bias or not is irrelevant to the conclusion about bias for Galak & Meyvis (or any other paper). This is not to say that the bias analysis cannot make a Type I error and conclude bias when it does not exist. If we cannot tolerate making a Type I error, then we should not make decisions.

An important caveat is that the selective reporting of my analyses prohibits us from estimating the proportion of biased papers in the field. Trying to make such an estimate from the reported analyses changes the bias from being benign to one that misrepresents the data. Importantly, just because this particular interpretation is inappropriate does not mean that the individual analyses are inappropriate.

In conclusion, Simonsohn's arguments are without merit. His claim that ignoring the data is unwise leads to scientifically vacuous arguments; and his claim of cherry picking is true but its meaning is misunderstood.

Francis, G. (2013). Replication, statistical consistency, and publication bias. Journal of Mathematical Psychology. http://dx.doi.org/10.1016/j.jmp.2013.02.003

Conflict of Interest: None declared

On 2015 Jul 15, Peter Hajek commented:

The key question is what effect this has on cigarette sales. If it is reducing cigarette sales, it is a positive development.

On 2015 Jul 15, Holly Brothers commented:

This is really interesting - I'll be happy to get access to the article. It reminds me of the RadioLab episode highlighting Jasper Lawrence who used hookworms to battle his hyperimmune responses (allergies and asthma) http://www.radiolab.org/story/91691-sculptors-of-monumental-narrative/.

On 2015 Dec 17, Peng Chen commented:

I realize that you have work very hard to publish all these excellent papers! Good job! Well done! And, I love U :)

On 2015 Jul 22, BSH Cancer Screening, Help-Seeking and Prevention Journal Club commented:

The HBRC journal club read with interest this paper that uses an innovative qualitative method to examine the barriers to colorectal cancer (CRC) screening experienced by people from medically under-served areas in the US. The paper offers an account of how macro level factors, such as the socio-political context, combine with individual level factors to determine uptake of CRC screening.

The authors used a participatory research method and PhotoVoice technique to engage participants in the research project, which took place over several months and included training sessions, group meetings, and individual meetings. We felt that one of the strengths of this approach was that it allowed rapport to be built over time, and that participants could express themselves in ways other than by just verbalising their thoughts and feelings. The photos taken by participants served as the “jumping off point” for the group discussions, which we felt helped obtain a richer picture of what people have to go through in order to obtain screening. Using each participant’s photos as a catalyst for the discussions may have encouraged a more evenly distributed participation across participants, because each participant was expected to contribute to the meetings. Although many of the barriers mentioned in this paper focused on the costs of colonoscopy screening and may therefore not necessarily generalise to healthcare contexts that use different screening methods or are free at the point of delivery, such as in the UK, some of the opportunity costs mentioned by participants did resonate with the journal club and may be more widely applicable. For example, those undergoing flexible sigmoidoscopy screening in the UK may also be faced with the opportunity cost of having to take (potentially unpaid) time off work.

We felt the authors could have commented more on the possible limitations of their study. The chosen study method required a great deal of commitment and active participation from participants. Although the researchers note that the Photovoice method may address shortcomings of other qualitative work in this field, which “may simply generate ‘impression management discourses’”, we felt that the method does not necessarily circumvent these discourses, but may just elicit more “crafted” image discourses. In addition, the high level of commitment expected from participants in the current study may mean that only those who were most highly motivated and health conscious self-selected to participate, which may limit the generalisability of the study findings. The authors chose to focus on the obstacles experienced by those who had been screened, but those may not necessarily be the same as the obstacles faced by people who have not screened. The HBRC journal club would encourage further study in samples of participants who are not engaged with screening. We also felt that the results were presented in a way that suggested a broad consensus among participants and wondered whether there were any dissenting voices? Some of us felt that a greater emphasis could have been placed on the experience of facilitators to screening uptake, although some felt that this was adequately addressed by discussing the importance of social support around the time of screening. Finally, we felt that the paper formed a good illustration of some of the barriers and facilitators to CRC screening that we already know about, but some of us felt that it did not offer many new insights, and wondered whether the wealth of data collected in the study could have generated any novel insights? We recognise that journal requirements may only allow for a limited discussion of all findings in a study, and we would argue that online supplements could make a valuable contribution to convey the results of this type of study, for example, as a photo gallery with accompanying quotations.

In sum, the HBRC journal club really enjoyed reading this paper and feel that the Photovoice method is a great method for doing explorative research in certain groups, because of the high level of active involvement of participants in the research project, and the meaning and value added by their pictures which may complement verbal explanations of behaviour. This study shows that decisions about screening are not just up to the individual, but are made in a socio-political context that can help or hinder individuals to obtain screening, and has important implications for policy making in preventive healthcare.

Conflicts of interest. We report no conflict of interests and note that the comments produced by the group are collective and not the opinion of any one individual.

On 2015 Jul 27, Chuan-Wei Jang commented:

In the paper, we failed to specify the sources of some antibodies used in the additional experiments a reviewer requested after our initial submission. These antibodies are:

H3K4me2: Active Motif, 39141

CenpA: Abcam, ab33565

TRF1: Alpha Diagnostic International, TRF12-A

TRF2: Novus, NB110

Beta-Actin: Abcam, ab8826

On 2015 Jul 16, Chuan-Wei Jang commented:

The figures in the paper have been reduced in size and resolution in the print publication process, and thus some details are compromised in their final form. The original high resolution figures can be viewed or downloaded from here.

On 2017 Apr 12, Siegfried Hekimi commented:

We obtained very different results that suggest that CLK-1 functions exclusively in ubiquinone biosynthesis and not in the nucleus to affect the mtUPR. In a paper entitled: A single biochemical activity underlies the pleiotropy of the aging-related protein CLK-1. By Liu et al. http://www.nature.com/articles/s41598-017-00754-z?WT.feed_name=subjects_energy-metabolism

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 NCT0210086. We believe the correct ID, which we have found by hand searching, is NCT02100865.

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 2016 Feb 29, Jim Johnson commented:

Thanks Dave. Actually there are 2 related bioRxiv pre-prints. One is from the SFP facility and reports on the male littermates from this study. The other is from a conventional facility (same facility as the 2012 Mehran et al paper reports on).

Hyper-variability in Circulating Insulin Levels and Physiological Outcomes to High Fat Feeding in Male Ins1-/-:Ins2+/- Mice in a Specific Pathogen-free Facility Nicole M Templeman, Arya Mehran, James Johnson bioRxiv doi: http://dx.doi.org/10.1101/031799

Hyper-variability in Circulating Insulin and Physiological Outcomes in Male High Fat-fed Ins1-/-:Ins2+/- Mice in a Conventional Facility Arya Mehran, Nicole M Templeman, Xiaoke Hu, James Johnson

On 2016 Feb 28, Dave Bridges commented:

A preprint was posted by this group describing similar experiments in male mice: http://dx.doi.org/http://dx.doi.org/10.1101/031799

On 2017 Jul 13, Randi Pechacek commented:

Elisabeth Bik wrote a blog describing this paper on microBEnet in a discussion about human microbiomes at sea.

On 2016 May 25, André Morandini commented:

I disagree with some points presented. A reply was submitted and not accepted. But published in Bulletin of Marine Science (http://dx.doi.org/10.5343/bms.2016.1018)

Succession of generations is still the general paradigm for scyphozoan life cycles

Abstract: A recent study proposed an unorthodox view of the long-known metagenetic life cycle of scyphozoan jellyfish. We argue that misinterpretations and imprecise information generated a misleading view of such life cycle patterns. In favor of our reasoning, we present the historical understanding of metagenesis, and contend that it can still be used as a shared general life cycle pattern for Scyphozoa, as well as for other medusozoans.

On 2015 Aug 24, Bill Cayley commented:

A good example of when "Less" is "More": https://lessismoreebm.wordpress.com/2015/08/24/in-california-primary-care-continuity-was-associated-with-reduced-emergency-department-use-and-fewer-hospitalizations/

On 2015 Jul 15, thomas samaras commented:

A number of findings indicate that lower birth weight and smaller body size are strongly related to low CHD.

During the 20th C, Papua New Guinea was characterized by slow growth, low BMI and short height. Based on a 70-year tracking period no evidence of CHD or stroke was found among the natives. Many other indigenous populations show a similar relation between small size and the absence of CHD and stroke.

A study by M. Eriksson (50-80 year old men) found a progressive increase in risk of heart attacks with increasing birth weight. The lowest birth weight quartile had the lowest risk (15% vs 25% for highest birth weight).

Another study reported by Yajnik found that higher birth weight and better nourished urban Indians had 4 to 5 times the risk of CHD and diabetes as rural children that had lower birth weight and reduced nutrition. A WWII study of US twins found that lower birth weight identical twins had the highest life expectancy of 82 years. Higher birth weight fraternal twins had a life expectancy of 80.5 years. WWII singletons (highest birth weight) had a life expectancy of 78 years. The longer life expectancy indirectly points to lower CHD. Birth weight is strongly correlated with height, weight and BMI.

Increasing BMI cannot be a driver for lower CHD because virtually all CHD risk factors get worse with increasing BMI starting from a BMI of less than 21. For example, HDL, APO A and sex hormone binding globulin decrease with increasing BMI. Blood pressure, cholesterol, TG, APO B, LDL also increase. Left ventricular mass and pulse wave velocity also increase with BMI, both independent CVD risk factors.

On 2015 Oct 04, Mohit Sharma commented:

Intialmost and the most cancer specific Hallmark present universally in all malignant tumors

On 2016 Aug 18, David C. Norris commented:

This JAMA Viewpoint hinges on a categorical claim: “probability is not meaningful in an individual context.” In a subsequent exchange with Van Calster, Steyerberg and Harrell¹ , the authors have backed away slightly from this precipice, stating that it was rather the verifiability (and not meaningfulness) of ‘individual probability’ that was at issue—and indeed that only a frequentist probability notion was targeted by this statement.² The authors also explain that their original citation of Cohen³ in the context of this statement was meant “to direct the reader to the excellent discussion by Cohen of the limitations of the frequentist notion of probability”² . Cohen’s discussion is indeed excellent, and the reader who follows up this citation cannot fail to find a forceful rebuke of this Viewpoint's entire treatment of ‘probability’, delivered no less with particular reference to the very context under consideration—medical decision making:

Nor is it open to a frequency theorist to claim that all important probabilities are indeed general, not singular. It often seems very important to be able to calculate the probability of success for your own child’s appendectomy... ^3(p49)

Cohen proceeds from this observation to advance a Bayesian perspective; why Sniderman, D’Agostino and Pencina don’t do likewise would be a mystery if they did not reveal some peculiar methodological preoccupations in the ensuing development of their argument.

Eschewing a (meaningful|verifiable) notion of ‘individual probability’, the authors substitute the petitio principii of ‘individual risk’—the continuous, probabilistic character of which they conceal through the conceit of “clinically meaningful risk categories” [emphasis mine]. Tellingly, they label these categories “clinically meaningful” because they have forfeited the philosophic basis for making them so. Ultimately, what makes any concept clinically meaningful is its openness to connection with the values and circumstances of individual patients. Classification schemes that prematurely close patients’ decision problems have precisely the opposite character. Without such artificial categories, however, the characteristically incoherent⁴ frequentist approach to decision-making under uncertainty would lack even a semblance of that singular uncertainty which confronts the patient-physician dyad.

The authors conclude by calling on physicians to mop up this shambles. They utter the shibboleth, “models cannot replace the physician,” then incant some vague magic by which physicians should restore the individual patient to a scheme that has excluded the individual from its very epistemology. Mathematically, the requisite magic translates to conditioning on individuals after frequentist methods have already averaged individuals out.^4(pp61,509)

The ‘art of medicine’ has long enough been defined by quixotic attacks upon mathematical impossibilities. Physicians of the future will gladly relinquish the merely computational tasks of medicine to predictive models and other forms of automation. They will rather find a purposive role in the creative, irreplaceably human endeavor of helping patients to formulate their medical decision problems in alignment with their values and circumstances,⁵ and to decide these problems in accordance with appropriate evidence drawn from ever-improving⁶ predictive models.

1] Van Calster B, 2015

2] Sniderman AD, 2015

3] Cohen, L. Jonathan. An Introduction to the Philosophy of Induction and Probability. Oxford : New York: Clarendon Press; Oxford University Press, 1989.

4] Robert, Christian P. The Bayesian Choice: From Decision-Theoretic Foundations to Computational Implementation. 2nd ed. Springer Texts in Statistics. New York: Springer, 2007.

5] Moroff SV, 1983

6] Mazzola E, 2015

On 2015 Jul 30, Marco Weiergräber commented:

In their response Dibue-Adjei and Schneider state that they have decided to sample and analyze beyond the nominal sampling rate of the transmitter and state that this is done by other groups as well. To prove this two references (Raver SM et al., 2013 and Black SW et al., 2014) are mentioned. First, sampling beyond the nominal sampling rate is virtuell and does not generate real data points. According to the Nyquist-Shannon sampling theorem, frequency reconstruction beyond half of the nominal sampling rate of the transmitter, i.e. 125 Hz in this case, is not possible. The Nyquist-Shannon limit has been violated in Dibue et al. (2013) Second, the references given (Raver SM et al., Black SW et al., 2014) do not support the statement of Dibue-Adjei and Scheider in their response. Gamma is analyzed up to 60 and 80 Hz respectively in both references. With a transmitter bandwidth of 1-50Hz this could be tolerable. However, unlike in Dibue et al. (2013), the Nyquist-Shannon limit of 125 Hz has not been violated in both references. Indeed, a literature screen does not reveal any violation of the Nyquist-Shannon limit despite those published in Dibue et al. (2013, 2014) and Kamp et al. (2014).

On 2016 Apr 29, Leigh Jackson commented:

The long and short of this review is that no good evidence could be found to show that acupuncture is effective for asthma in children.

Two studies showing possible evidence of slight benefit were found.

In one of these studies - Scheewe et al. - patients with bronchial asthma received drug therapy as well as traditional acupuncture. There was no sham control.

In the other trial - Stockert et al. - patients with intermittent or mild asthma received probiotic drops as well as laser acupuncture. Each treatment had a placebo control.

The evidence of benefit found in this review, such as it is, could conceivably be due to traditional or laser acupuncture or both; or to the other treatments or combinations of treatments; or in the case of Scheewe et al. simply to the placebo effect.

On the basis of the evidence examined in this review, what is now needed is not large-scale RCTs, but successful independently replicated RCTs of the different forms of acupuncture versus sham controls alone.

On 2017 Dec 26, Evgeniy Gorbunov commented:

Subetta is not homeopathic drug. We have already answered to E.V. Dueva to the similar comment regarding another drug produced using the same biotechnological platform (please see here: https://www.ncbi.nlm.nih.gov/pubmed/28036118).

There are two references in Materials and Methods sections regarding Subetta manufacturing: to United States patent US8535664 (ref. 8), which E.V. Dueva mentioned in her comment; to the previously published work, where the drug preparation is briefly described (ref. 6).

The study was performed blindly by independent laboratory using validated experimental approach. The article is fully transparent for the readers so they have an opportunity to familiarize themselves with these results and make their own opinion.

The article passed peer-review process in accordance with the journal requirements. During the peer-review process, all necessary information had been provided including the images of blots.

On 2017 Dec 09, Evgenia V Dueva commented:

Subetta is made from antibodies diluted beyond Avogadro’s limit (12 consecutive dilutions of 1:100, see Google patents US8535664) and thus contains no active molecules. The authors do not mention homeopathy in their article, but this clearly is a homeopathic drug.

The results obtained by the authors are likely false positives considering the very low prior probability of a drug with no active molecules having any specific effect on insulin or any other receptors.

The authors did not provide any images of their blots, or information on the protein concentrations that they used. Without this critical information, it is unclear how the article passed peer-review.

On 2015 Jul 08, David Keller commented:

The CREST-2 investigators recognize that asymptomatic carotid stenosis should be screened for & get intensive medical treatment

The CREST-2 clinical trial will study subjects having asymptomatic carotid stenosis, and will randomize them to receive invasive treatment (such as endarterectomy or stenting), or to receive no invasive treatment. All patients will receive the same background "intensive medical therapy" (1).

The USPSTF recommends against screening for asymptomatic carotid stenosis for the purpose of treating it with intensive medical therapy, stating: "There is no evidence that identification of asymptomatic carotid artery stenosis leads to any benefit from adding or increasing medication doses (beyond current standard medical therapy for cardiovascular disease prevention)." (2) Yet, CREST-2 subjects will all be given intensive medical therapy, instead of the standard medical therapy which the USPSTF advises for them.

Dr. Chaturvedi, CREST-2 corresponding author, stated their position very clearly in an email to me dated 7/8/2015: "You are correct that intensive medical therapy has never been tested against standard medical therapy. However, we felt that for clinical trial purposes, the "best" form of medical therapy should be tested."

So, the CREST-2 subjects will be identified by screening, and will be treated with "intensive" medical therapy, despite the fact that USPSTF still recommends against screening for asymptomatic carotid stenosis, or treating it with anything stronger than "standard preventative" medical therapy. The CREST-2 investigators are ignoring these recommendations, as should all physicians.

"Significant but asymptomatic atherosclerotic stenosis in any artery is an indication for intensive medical therapy", is a statement which has not been proved directly, but which has accumulated enough circumstantial evidence from the statin trials to have achieved the status of a clinical axiom. For example, the CREST-2 investigators were not willing to expose any of their patients with asymptomatic carotid stenosis to the risk of standard preventative medical therapy, despite the current dictum of the USPSTF (which is a mandate in many health systems). To deny screening for asymptomatic carotid stenosis, and to fail to treat it with intensive therapy when it is discovered, are not sensible or even ethical, given only minor extrapolation on the evidence we do have.

It is time for the USPSTF to bring their recommendations into alignment with current best practices, as exemplified by the CREST-2 protocol.

References:

1: Chaturvedi S, Howard G, Meschia J. Carotid Endarterectomy for Asymptomatic Stenosis.JAMA Intern Med. 2015;175(7):1241-1242. doi:10.1001/jamainternmed.2015.1118.

2: United States Preventative Services Task Force web site, accessed 7/7/2015. http://www.uspreventiveservicestaskforce.org/Page/Document/RecommendationStatementFinal/carotid-artery-stenosis-screening

On 2016 Aug 22, Vincent J Lynch commented:

We have recently become aware of potential contamination in the Wooly Mammoth samples reported in this paper, M25 in particular (for details please see the preprint by Rogers and Slatkin available at https://arxiv.org/abs/1606.06336). While potential contamination of the M25 and M4 genomes with other Wooly Mammoth DNA may render these samples unusable for some analyses, we do not believe that the results or conclusions reported in Lynch et al. are adversely affected. Specifically our analyses focused on fixed, derived substitutions that occurred in the mammoth stem-lineage. The identification of mammoth-specific fixed, derived amino acid substitutions is unlikely to be affected by contamination of the M25 and M4 genomes with aDNA from other mammoths because these changes are by definition fixed in the genome of all mammoths.

We have reanalyzed our data including the additional mammoth samples reported by Palkopoulou et al. (PMC4439331) and replicated all but 105 (91.3%) of the amino acid changes reported in Lynch et al., including the mammoth-specific TRPV3 substitution. Downstream enrichment analyses were also replicated. We are preparing a manuscript describing these reanalyses and will post a link to the preprint when it is available.

On 2016 Mar 16, Vincent J Lynch commented:

Hi Mick,

We may have been able to use the existing data if they were at high enough coverage and available prior to our sequencing of the Asian elephant genomes. But we were likely sequencing the genomes at the same time as Wilkie et al. (2013), thus they just would not have been available to use. We also sequenced each Asian elephant to ~30x whereas Wilkie et al. (2013) and Dastjerdi et al. (2014) sequenced to 5x and 2.5x (as you obviously know). The lower coverage may have made using the existing data less informative.

Vinny

On 2016 Mar 10, Mick Watson commented:

Hi Vinny

Thanks for the reply. I guess my question would be whether you needed to generate new data on Asian elephant genomes, or could have just used existing data

Cheers Mick

On 2015 Aug 05, Vincent J Lynch commented:

Hi Mick,

Although I was aware of this work, we didn't think it was appropriate to cite Dastjerdi et al. (2014) or Wilkie et al. (2013) because we did not use the data reported in these papers or even characterize the Asian elephant genomes we generated. Rather we just used the Asian elephant data we generated to polarize nucleotide changes in order to identify those that were mammoth-specific.

Vinny

On 2015 Jul 09, Mick Watson commented:

Quite surprised this paper didn't recognise previous efforts to sequence Asian elephant genomes:

http://www.gigasciencejournal.com/content/3/1/12

On 2015 Jul 09, Bill Cayley commented:

A good example of when "Less" may be "more" - https://lessismoreebm.wordpress.com/2015/07/09/performance-of-alternative-strategies-for-primary-cervical-cancer-screening-in-sub-saharan-africa-systematic-review-and-meta-analysis-of-diagnostic-test-accuracy-studies/

On 2015 Nov 02, David Mage commented:

This is an interesting article about SIDS and possible CNS involvement but the author seems to ignore two mandatory requirements for any such explanation: The first requirement is to account for SIDS unique left-censored 4-parameter lognormal age distribution that shows there is no ʺcritical age of vulnerability in SIDS" because the same equation fits all the SIDS age data from birth to well beyond one year. Schwartz (PMID: 3549041) correctly stated ʺAny viable hypothesis must account for its characteristic age distribution;" The second requirement is to account for the 50% excess male fraction of SIDS. It is not clear why the author now in 2015 fails to even mention male gender as a risk factor for SIDS as he correctly wrote in his 2008 EMBO Report (PMID: 18246101) that ʺ61% of SIDS cases occur in males," and he should have cited PMID: 5129415 that concluded ʺthe general disadvantage of males has long been recognized. The biologic differences must originate in the genetic differences between the sexes and those genetic differences are the consequence of disparity in the number of X-chromosomes." In addition U.S. linked birth and death certificate data (wonder.cdc.gov) show that the rate of ICD-10 R95 SIDS increases with live birth order, but infant deaths from CNS causes (ICD-10 P91.6 Hypoxic ischemic encephalopathy of newborn) do not, and furthermore, the ages of these CNS deaths are not lognormally distributed and they do not have the same 50% male excess as SIDS.

On 2015 Oct 06, Christopher Southan commented:

A list of molecularly resolved clinical inhibitors is available from the Guide to PHARMACOLOGY http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=2330

On 2015 Nov 05, David Attwell commented:

Contractile pericytes should not be confused with smooth muscle cells. David Attwell, University College London, E-mail D.Attwell@ucl.ac.uk

The original definition of pericytes by Zimmermann (1923) (translated into English here) included in this cell class the contractile cells on capillaries which Hill et al. (2015) (reviewed here) re-name in their paper to be smooth muscle cells (despite their clear morphological difference from classical arteriolar smooth muscle cells). Unfortunately, because Hill et al. re-named pericytes in this way, the title and text of their paper are misleading. Zimmermann (1923), and most workers since in the field of vascular biology, would define as pericytes the spatially-isolated contractile cells on capillaries that Hill et al. (2015) observe to control capillary blood flow in health and disease, confirming previous papers showing that pericytes have this role (Hall et al., 2014; Yemisci et al., 2009). Further discussion can be found in: Attwell, Mishra, Hall, O’Farrell & Dalkara (2015) What is a pericyte? J Cereb Blood Flow & Metab. advance online publication.

On 2015 Jul 27, Arnaud Chiolero MD PhD commented:

This is a very insightful comment regarding the difficulties of pre-registration of protocols of analyses using observational study data

On 2017 Feb 18, Egon Willighagen commented:

InChI 1.05 was release on 27 January 2017: http://www.inchi-trust.org/downloads/

On 2016 Aug 24, M Mangan commented:

After more than a year, with extensive back-and-forth with the journal and the authors, we were refused access to the data from this research.

This is disappointing, of course. Although the journal did later make a statement to clarify some of the erroneous methods desciption (as a comment on the paper's site), they did not require fixes to the publication. "The reference to triplicates in the Methods section of the article refers to the sampling and not to the measurements."

Further, in the correspondance, the authors admitted that they did not test for glufosinate--despite noting that they tested for the presence of crops with the resistance to this herbicide. So they cannot claim that their testing for herbicides was complete and claims of their detection of herbicides is flawed. If you ignore one of them, your claims of what is at the highest levels is of little value. Again, the journal did not require the authors to address this error.

Statistical issues and flawed design should make the reader wary of the work within and the subsequent claims and conclusions.

On 2015 Oct 08, M Mangan commented:

In apparent violation of PLOS policy, the authors of this paper refuse to provide the data underlying the claims for this work.

This work has also been used in an attempt to influence regulatory policy from government agencies. However, citing many flaws of the work, including incomplete reporting of the data, regulators have dismissed the claims made.

See: http://www.efsa.europa.eu/en/efsajournal/pub/4258

On 2015 Aug 07, Ivan Oransky commented:

Here's a second look at this study by F. Perry Wilson of Yale: http://www.medpagetoday.com/Endocrinology/Obesity/52492

On 2015 Aug 01, DAVID ALLISON commented:

Video Exaggerates Effects.

In 1954, Huff [1] showed that representing data with 2D graphics of 3D objects could mislead if geometric principles were neglected. In the video accompanying this article [2] describing liraglutide weight loss results, at 1 minute, 26 seconds, a cartoon patient injects liragultide and shrinks in size. We measured an 11.4% reduction in depicted ‘waist diameter’. If waist perimeters approximate circles, this implies an approximately equivalent percent reduction in waist circumference (WC). Yet, the investigators report only a 7.3% reduction (not placebo corrected) in mean WC with liragultide. This alone indicates that the video exaggerates average change among treated patients. Further, a simplifying approximation of the human body as a cylinder of uniform mass [3] and empirical observations [4] suggest that weight scales to WC to the power of lambda, with lambda > 1. This implies that the 11.4% waist reduction shown portrays a figure with an implied weight reduction >11.4%. Yet, mean intervention body weight dropped only 7.9%.

Concerns exist about misleading before and after photographs in weight loss advertisements [5]. Standards for weight loss drawings similarly need to avoid inadvertently misleading clinicians and patients.

David B. Allison, University of Alabama at Birmingham

Diana M. Thomas, Montclair State University

Steven B. Heymsfield, Pennington Biomedical Research Center

References

1) Huff D. How to lie with statistics. New York: Norton; 1993.

2) Pi-Sunyer X, Astrup A, Fujioka K, et al. A Randomized, Controlled Trial of 3.0 mg of Liraglutide in Weight Management. N Engl J Med 2015;373:11-22.

3) Heymsfield SB, Martin-Nguyen A, Fong TM, Gallagher D, Pietrobelli A. Body circumferences: clinical implications emerging from a new geometric model. Nutr Metab (Lond) 2008;5:24.

4) Heymsfield SB, Heo M, Pietrobelli A. Are adult body circumferences associated with height? Relevance to normative ranges and circumferential indexes. Am J Clin Nutr 2011;93:302-7.

5) Weight Loss Advertising: An Analysis of Current Trends: A Federal Trade Commission staff report. Federal Trade Commission: https://www.ftc.gov/reports/weight-loss-advertisingan-analysis-current-trends [accessed 8/1/15].

On 2015 Sep 08, Atanas G. Atanasov commented:

The authors personal PDF copy of the manuscript can be downloaded free of charge at: http://homepage.univie.ac.at/atanas.atanasov/PiperineCongeners.html

On 2015 Jul 06, Alexis Verger commented:

If anyone is interested, our structural model of the ERM transactivation domain (TAD) in complex with MED25 is available in figshare as a Pymol session

http://figshare.com/articles/MED25_interaction_site_with_the_TAD_of_ERM/1468391

On 2017 Jun 09, GERALD SMITH commented:

In Ma et al. (1), we isolated Schizosaccharomyces pombe ctp1 point mutations, which we interpreted to separate genetically two known meiotic activities that depend on Ctp1 for meiotic DNA break repair. A later paper by Jensen and Russell (2) claimed these activities are not genetically separable. We believe the disparity in interpretation stems largely from the use of meiotic cells in our studies but mitotic cells by Jensen and Russell. We maintain that in meiotic cells the activities are genetically separable.

During S. pombe meiosis, Rec12 (Spo11 homolog) makes DNA double-strand breaks (DSBs) and remains covalently linked to each 5’ end. The Mre11-Rad50-Nbs1 (MRN)-Ctp1 complex endonucleolytically removes Rec12 covalently linked to a short oligonucleotide (Rec12-oligo), an activity called “clipping.” The recessed 5’ end is then further digested, an activity called “resection,” to form a long 3’ single-stranded DNA tail that forms with intact DNA a joint DNA molecule to continue DSB repair. We concluded that most of the dozen ctp1 point mutants we studied retained nearly wild-type levels of resection but little clipping activity during meiosis. These conclusions were based on concordant genetic and physical analyses. Although we isolated these mutants based on a mitotic screen, we drew all of our conclusions from meiotic data.

In our physical assays for clipping, we found in wild-type cell extracts abundant Rec12-oligos, which were absent or barely detectable in ctp1 mutant extracts, either point mutant or complete deletion (ctp1Δ). Failure to clip off Rec12 leaves irreparable DSBs and consequently inviable spores; the ctp1 point mutants had 10- to 30,000-fold, and ctp1Δ 100,000-fold, reductions of viable spore yields compared to wild type. These results indicate that the ctp1 mutants have strongly reduced clipping activity.

To assay resection, we induced in meiotic cells a DSB at a well-defined site, using either the I-SceI or the I-PpoI homing endonuclease. Physical assays using Southern blots showed that resection of the DSB end proceeded as rapidly and extensively in the ctp1 point mutants as in wild type but slowly and to a much lesser extent in the ctp1Δ mutant. The homing endonucleases form DSBs without a covalently bound protein; I-SceI-dependent recombination thus requires resection but not clipping. In the ctp1 point mutants, the frequency of this recombination was equal to, or even twice as high as, that in ctp1+ cells, which was ~5 times higher than that in the ctp1Δ mutant. Thus, both physical and genetic assays indicate that resection is robust in the ctp1 point mutants.

In interpreting these results, it is important to consider the role of Exonuclease I (ExoI), which could potentially resect DSB ends and produce recombinants. The MRN complex blocks ExoI access to DSBs in meiotic cells, but the Ku complex blocks ExoI in mitotic cells. Thus, ExoI plays no apparent role in DSB repair in meiotic cells with an intact MRN complex; instead, MRN promotes access of Ctp1 to DSB ends. For example, in meiotic cells exoIΔ has no significant effect on I-SceI-dependent recombination, but ctp1Δ reduces it by a factor of ~5 (3). Conversely, in rad50Δ mutants ctp1Δ has no significant effect, but exoIΔ reduces recombination by a factor of ~4. As expected, the ctp1Δ exoIΔ double mutant is like ctp1Δ in rad50+ cells but like exoIΔ in rad50Δ mutants.

Jensen and Russell (2) assessed the mitotic activity of two of our ctp1 point mutants, along with ctp1+ and ctp1Δ, by analyzing the number and sizes of colonies formed on agar plates containing DNA damaging agents and spotted with 5-fold serial dilutions of cell cultures. Their results, like ours, showed that ctp1-6 and ctp1-25 are more DNA damage-resistant than the ctp1Δ mutant, indicating that the point mutants retain some activity. Removal of the Ku complex, by pku80Δ, suppressed these sensitivities but only if ExoI was present. Removal of ExoI enhanced the sensitivity to some agents (e.g., methyl methanesulfonate) but not, or only slightly, to others (e.g., ionizing radiation). In each of these various combinations, the point mutants were more resistant than the ctp1Δ mutant, confirming our results that the point mutants retain some activity. In nine out of ten cases, the ctp1-6 exoIΔ and ctp1-25 exoIΔ mutants were more resistant than ctp1Δ exoIΔ, which was completely sensitive to the agents tested. This result shows that the ctp1 point mutants retain an activity that can be supplied by ExoI, which we take to be resection.

Jensen and Russell proposed that the ctp1 point mutations reduce, but do not abolish, a single activity. They further proposed that this residual activity is sufficient to repair a single DSB per cell (as in the I-SceI and I-PpoI experiments we reported) but not multiple DSBs per cell [as in the experiments with wild-type Rec12, which makes about 60 DSBs per meiotic cell (4)]. This proposal is hard to reconcile with our physical assays of clipping and resection noted above. It is not clear to us how a single Ctp1 activity could be altered, in either KM or kcat, to resect one DSB in a cell with wild-type kinetics but not clip Rec12 off 60 DSBs in a cell if resection and clipping result from the same activity, since both processes take about the same amount of time. Rather, we think the mutant proteins have greater reductions of clipping activity than of resection activity. Reduction of the number of Ctp1 molecules per cell, from 60 or more to about 1, could account for our results, but we consider this an unlikely explanation for the many mutants we studied. Instead, we think our mutants have retained nearly wild-type levels of resection but have strongly reduced levels of clipping, in meiotic cells. Whether the active sites for these two activities are in Ctp1, the MRN complex, or both is not addressed by our experiments. Without tests of a very large number of Ctp1 mutants under many conditions, we think the conclusion that the two activities are not genetically separable is unwarranted.

Lijuan Ma, Neta Milman, Mridula Nambiar, and Gerald R. Smith

References:

1. Ma, L., Milman, N., Nambiar, M. and Smith, G.R. (2015) Two separable functions of Ctp1 in the early steps of meiotic DNA double-strand break repair. Nucleic Acids Res., 43, 7349-7359.

2. Jensen, K.L. and Russell, P. (2016) Ctp1-dependent clipping and resection of DNA double-strand breaks by Mre11 endonuclease complex are not genetically separable. Nucleic Acids Res., 44, 8241-8249.

3. Farah, J.A., Cromie, G.A. and Smith, G.R. (2009) Ctp1 and Exonuclease 1, alternative nucleases regulated by the MRN complex, are required for efficient meiotic DNA repair and recombination. Proc. Natl. Acad. Sci. USA, 106, 9356-9361.

4. Fowler, K.R., Sasaki, M., Milman, N., Keeney, S. and Smith, G.R. (2014) Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome. Genome Res., 24, 1650-1664.

On 2016 Mar 03, Liam McKeever commented:

Ms. Allard,

Thank you for your thoughtful comments. Using [tiab] would certainly increase the specificity of the search without much loss to sensitivity. The technique of this tutorial assumes that the article indexed for MEDLINE has been properly indexed, which will not always be a correct assumption. While I consider this assumption an acceptable and explainable loss in sensitivity in exchange for what is usually a considerable increase in specificity, the technique you are describing may actually be a perfect compromise.

Sincerely,

Liam McKeever,MS,RDN

On 2016 Feb 29, Rhonda J Allard commented:

While I see the point you make about being sure your search strategies take into account both Medline and non-Medline articles, I don't believe you need to create two searches to accomplish this goal. The following search strategy (in my opinion), is as effective:

fasting AND (alternate day* OR alternating day*) -- it retrieves 120 articles

Notes: 1) The term fasting will map to Fasting [Mesh] and also search "fasting" in all fields. This will retrieve both Medline and non-Medline articles. 2) Anytime you use double quotes for phrase searching or the asterisk for truncation you are turning off the "Automatic Term Mapping" and searching all of PubMed.

If the searcher is concerned with the amount of irrelevant articles they might retrieve when using keywords, another trick is to limit keywords to the title or abstract using [tiab], see below:

military retrieves 127,746 results (it maps to Military Personnel[Mesh] and searches for "military" in All Fields) whereas (Military Personnel[MH] OR military[tiab]) retrieves 56,624 results. This second search limits the search results to where the topic is the military. The term military can appear in the Author Affiliation field or as part of another MeSH term.

On 2016 Feb 25, Liam McKeever commented:

Mr. Bramer,

 Your point here is well taken but really represents a calculated shortcoming of that particular search, not the technique. The search in our paper was only designed to demonstrate the different aspects of the techniques in the paper. We kept it short on purpose for the publication. Obviously, in performing a review, a thorough analysis of any and all possible relevant MeSH terms must be considered. Generally, in practice, this technique becomes a somewhat iterative process where search results are checked against articles of known relevance. Early in the process, an article is often found missing from the list. Any article that does not show up in the list is analysed and the search strategy is revised. I then use a Boolean 'NOT' to subtract the search that has already been scanned by the reviewers from the new search. In this way, no one has to duplicate their efforts and the search parameters remain as tight as possible. Generally, the search process is continued right up to publication and adapts as necessary along the way. This is just a different way to go about the process. 
 As for your techniques having a 2-3% specificity. Do you realize that means only 2-3% of the citations irrelevant to your search are properly classified as such? Did you maybe mean to indicate a 97-98% specificity? If so, I do not see how you would manage a specificity that high without sacrificing sensitivity.If you have a citation that demonstrates the validity of a such a technique, I would be very interested to see it.

Liam McKeever, MS, RDN

On 2016 Feb 25, Wichor Bramer commented:

Dear Mr McKeever,

Thank you for your detailed response to my remarks. Let me respond in return to some of your answers.

2

I was indeed referring that a thorough systematic review search ORs tiab terms with MeSH terms, not ANDs it as you do in your final search strategy. It depends on the goal of your research whether you focus on sensitivity of specificity. If you state you want to perform an exhaustive search strategy (such as is needed for systematic reviews), you should aim for sensitivity (without loosing too much specificity of course, but in the literature for SR searches a specificity of 2-3% is very normal). In your search strategy you will find relevant Medline articles on alternate day fasting only if they are also indexed with the MeSH terms you added. However you will miss important articles that have other relevant MeSH terms such as Varady KA, 2011, which has the MeSH terms Diet, Reducing, Weight Loss and Obesity/therapy. Hence you use MeSH terms to restrict your free text searches, which is not an improvement.

4

I was not objecting complicated searches in general, believe me, my SR searches are far more complicated than the one you show here (see for example: Malfliet A, 2015). However, I object unnecessary complicatedness that does not improve the search results. If I can get better results, only adding a few articles but not missing the above mentioned relevant article, by simply searching for:

("Alternate Day Fasting" OR "fasting on alternating days" OR "alternate-day fasting") NOT (animals[mh] NOT humans[mh])

I don't understand why making it much more complicated with all these steps is a payoff in thoroughness, transparence and manipulability.

Adding to that a new point of critique: are you aware that your search relies on automatic term mapping as well? If a search results page in PubMed says: Quoted phrase not found that means PubMed will try to do automatic term mapping. If you checked search details you would see that the phrase "fasting on alternating days" is reportedly not found, and replaced by

(("fasting"[MeSH Terms] OR "fasting"[All Fields]) AND alternating[All Fields] AND days[All Fields])

meaning that the user is not in control and the formula is neither robust nor reproducible nor transparent.

Sincerely, Wichor Bramer

Information specialist Erasmus MC (involved as search coordinator in hundreds of review per year)

On 2015 Nov 11, Liam McKeever commented:

Mr. Bramer,

Thank you for your critique of our work. We will respond to your comments in order in which they were written.

1. Regarding the likelihood that someone would rely heavily on a "related citations" feature to perform a review, the initial impetus for writing the paper came from such comments from seasoned researchers indicating they rely heavily on this technique. After reading the paper, this is often the first point people argue. Obviously, I would not expect a librarian to rely on such inadequate techniques, but it is happening in the field and so we addressed it. Remember that there are many forms of review where the methods of review are not made explicit, such as in grant writing. Here, researchers are more likely to fall back on the methods with which they are most familiar. For that audience, these comments were appropriate.

2. You state that there are robust search strategies which utilize both MeSH Terms and free text terms and that this has the added benefit of culling articles which may have been improperly categorized by the MEDLINE indexers. If you are referring to restricting (with Boolean AND) a MeSH search to only those folders which include certain text words in the [all fields], our strategy incorporates this. If you are instead describing duplicating your MEDLINE search by using free text words connected to the MeSH search with a Boolean OR, that is something entirely different.<br> It is true that re-searching the MEDLINE index with free text words opens the door to locating a possibly misplaced citation, but it comes with a steep cost. Let us define some terms. The sensitivity of search is the ability of that search to identify a truly relevant article. The specificity of a search is its ability to reject truly irrelevant articles. There is always a tradeoff between sensitivity and specificity. We would argue that a good search maximizes both sensitivity and specificity. The MEDLINE MeSH-term indexing method is both sensitive and highly specific. The reason for this that MEDLINE indexers read every article and catalog it according to the meaning of the article as opposed to a simple word count. To combine a MeSH-based search with a text-based version of the same search negates the entire purpose of having MEDLINE indexers. This would create a search that is highly sensitive but not very specific. Search strategies low in specificity may bypass the human error of the MEDLINE indexers, but possibly increase the human error of the scientists performing the review due to the unnecessary increase in volume of irrelevant citations.

3. It is for this reason that we must separate the search between the MEDLINE and nonMEDLINE database. We use the robust MeSH search techniques to search the MEDLINE database and restrict the less robust “free text” based techniques to search only the ~10% of PubMed that has not been indexed for MEDLINE. This creates a search that is both sensitive and specific. Failing to separate the searches decreases the specificity of your search by increasing the percentage of irrelevant citations.

4. You ask why this search needs to be so complicated. All searches are complicated. They only appear uncomplicated when you type in something simple and allow PubMed to do the thinking for you. The search on Alternate Day Fasting was chosen because it was simple enough to allow the reader to see the steps involved. Those steps are designed to put the control back in the hands of the user and refrain from relying too heavily on algorithms and automated term mapping. This requires some work up front, but the payoff is a thorough, reproducible formula that is transparent and easily manipulated as project needs change.

Sincerely, Liam McKeever, MS, RDN

On 2015 Nov 10, Wichor Bramer commented:

This article does not really give a good example of how to create search strategies. The title of the article states that it describes a method for exhaustive searches for literature reviews. I will discuss the contents of the article likewise.

The solutions described here as common are not common practice in a sense that they are performed as described by researchers writing a systematic review. Hardly any researcher will think that related citations is the proper way to do an exhaustive search. Robust search strategies can be built in both medline and non-medline part of PubMed with one search strategy using both mesh terms and free text terms, which is very common practice among both researchers and information specialists. That way not only the most recent articles are retrieved by the free text terms, but also articles where MeSH terms are incorrectly assigned will be found.

There is no need to limit the MEDLINE component to MeSH only searches, as text search might find extra relevant articles, nor is there a need to limit non-Medline part to text only searches, as this will not retrieve any articles, so no irrelevant articles as well.

The ultimate search strategy presented here is very complicated:

((("Fasting"[MeSH] OR "Obesity/diet therapy"[MeSH] OR "Weight Loss/physiology"[Mesh]) AND "Humans"[MeSH]) AND ("alternate day fasting" OR "fasting on alternating days" OR "alternate-day fasting")) OR (("Alternate Day Fasting" OR "fasting on alternating days" OR "alternate-day fasting") NOT medline[sb])

Why shoud it be so complicated? With this search articles on alternate day fasting are only retrieved if they also have one of the MeSH terms shown. Is that necessary? Each article found with this method has one of the phrases ("alternate day fasting" OR "fasting on alternating days" OR "alternate-day fasting") in the text. In that case one can just search for those phrases, and not much more. You don’t need 32 steps for that.

That search is not systematic either, but the described method does not provide a step by step approach to create a systematic search. The authors should have consulted with an information specialist before writing an article on a topic like this.

On 2015 Aug 12, Liam McKeever commented:

Dear Ms. Gluck,

Thank you for your comments. Training in the use of multiple databases was not the point of this paper. This paper was written in response to a recognition that many of the methods researchers use to perform their systematic reviews are not in fact systematic. A systematic review is meant to bring scientific methods into the process of writing a review. This means the methods of the review must be reproducible. Currently, many reviews that attempt to be truly systematic employ only the MEDLINE database because of its organized system of medical subject headings. If they do this correctly, they can perform an exhaustive search of the MEDLINE database. Our paper provided a technique for taking this systematic approach into an exhaustive search of both the MEDLINE and the PubMed databases, leading to a master formula, which could then be picked apart and improved upon by the scientific community. The techniques translate well to other databases and have recently been translated to EMBASE.

The argument that a complete systematic review should include an attempt to collect all relevant articles from multiple databases is well taken and commonly accepted. Preventing publication bias however is a much bigger picture than including multiple databases in a search strategy and was beyond the scope of this paper. To get all the null findings necessary to overcome publication bias would also mean including studies that either never entered or did not survive the peer review process. While such attempts should be made, a more achievable goal would be the thorough analysis of the publication bias present in a review where the search methodology is both explicit and reproducible.

The selection of appropriate databases for a systematic review, as you implied, varies greatly by profession. It was therefore also not in the scope of this paper. I do think there is some value in considering what it actually means than not all databases contain all journals. I find it highly unlikely that a bio-medically relevant journal would not be indexed in MEDLINE simply because they neglected to apply. It is much more likely that they applied and were rejected. Just as a systematic review has inclusion criteria at the level of the articles selected, databases have inclusion criteria at the level of the journals selected for cataloging. The degree of research quality and scope of topic areas are considered and determined to either meet or not meet the standards of the database. When we select a database for a systematic review, we are defining our inclusion criteria at the level of the journal. With this in mind, assuming adequate search methods were used and provided a thorough analysis of publication bias has been performed, one could make the argument that a properly selected major database pairing, like MEDLINE and PubMed may be acceptable for a systematic review. From a scientific methods perspective, we feel what is most important is that the inclusion criteria at all levels are explicit and that is what this paper attempts to facilitate.

Sincerely, Liam McKeever, MS, RDN

On 2015 Aug 06, Jeannine Gluck commented:

The authors give the impression that an exhaustive and comprehensive search can be carried out in a single database. Not so. While PubMed/MEDLINE clearly covers a very large number of publications, no database is comprehensive. EMBASE, for one example, has better coverage of the European and pharmaceutical literature. There are many subject-specific databases, any one of which may be relevant for a search in a particular aspect of the health sciences. Researchers looking at educational or sociological aspects of their field would do well to consult resources in those disciplines.

Workshops on systematic reviews emphasize, first and foremost, the requirement that multiple sources be consulted in order to minimize bias. This article was not about systematic reviews, per se. Still, any researchers calling their search "exhaustive" would do well to heed this advice. Had the authors included a librarian on their team, this serious oversight would not likely have happened.

On 2015 Dec 22, John Tucker commented:

While addressing the important issue of commercial influence in the practice of medicine, the article's treatment of the issues surrounding "lifestyle drugs" relies too heavily on the values and stereotypes of the authors. Arguably, the most defining feature of "maladies" such as obesity, impotence, hair loss, and diminished libido is the wide range of importance attached to them by different people. The authors' failure to recognize that the values of others may differ from their own results in a paper that mostly misses the key issues in this controversial area.

The shortcomings of this approach become apparent in a striking way in the article's introduction, in which three female authors, two of which are apparently under 40 years of age, pronounce impotence "a normal part of male aging". This view conflates "commonplace" with "unworthy of medical intervention", and if applied consistently would suggest that we should not develop drugs for the treatment of other diseases of aging such as arthritis and macular degeneration. It dismisses the desire of many older couples to maintain an active sex life, and appears rooted in stereotypes of what is appropriate behavior for older people.

Likewise, the development of drugs that treat low sexual desire in women is criticized based on the argument that "there is no reliable evidence that hypoactive sexual desire disorder is a real medical condition". Unfortunately, the authors provide no definition for what constitutes "a real medical condition", and thereby dodge the central issue of what is an appropriate subject for pharmacological therapy. They simply appear to have decided that the concerns of women who are troubled by their lack of libido are invalid, and they "shouldn't worry about it". This is a remarkable value judgment to make on behalf of others.

There are complex issues here, and they are worthy of address in greater depth than the intellectual shortcuts taken in this paper.

On 2015 Jul 20, David Keller commented:

Why have these benefits not been reported by Parkinson disease patients taking these anti-malarials?

I am skeptical about this report for the following reason: chloroquine is an old anti-malarial drug which must have been taken by many Parkinson's disease patients over the decades. If the benefits in humans are similar to those reported in the rat model, then surely it would have been observed and reported before. How do the authors explain this apparent contradiction?

On 2015 Sep 08, Alexandra Alexiev commented:

This paper was featured in a microBEnet post here: http://microbe.net/2015/09/08/another-important-paper-microbiome-studies-strongly-influenced-by-sample-processing-and-pcr-primer/

MicroBEnet is a blog that writes about microbiology of the built environment and is funded by the Sloan Foundation to do outreach and science communication.

On 2016 Jan 02, Mihaela Zavolan commented:

Regulation of BAF170 seems to be a general property of miRNAs from the seed family of miR-302 and is also conserved between mouse and human:

Gruber AJ, Grandy WA, Balwierz PJ, Dimitrova YA, Pachkov M, Ciaudo C, Nimwegen Ev, Zavolan M. Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Res. 2014 Aug;42(14):9313-26. doi: 10.1093/nar/gku544. Epub 2014 Jul 16. PubMed PMID: 25030899; PubMed Central PMCID: PMC4132708.

The same family of miRNAs also regulates DNA methylation:

Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel CG, Zavolan M, Svoboda P, Filipowicz W. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol. 2008 Mar;15(3):259-67. doi: 10.1038/nsmb.1391. Epub 2008 Mar 2. PubMed PMID: 18311153.

Benetti R, Gonzalo S, Jaco I, Muñoz P, Gonzalez S, Schoeftner S, Murchison E, Andl T, Chen T, Klatt P, Li E, Serrano M, Millar S, Hannon G, Blasco MA. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat Struct Mol Biol. 2008 Mar;15(3):268-79. doi: 10.1038/nsmb.1399. Epub 2008 Mar 2. Erratum in: Nat Struct Mol Biol. 2008 Sep;15(9):998. PubMed PMID: 18311151; PubMed Central PMCID: PMC2990406.

On 2016 Jun 03, Robert Dettman commented:

This article was fully retracted by the authors. http://www.cell.com/cell-reports/fulltext/S2211-1247(16)30443-0

On 2015 Nov 05, David Attwell commented:

Contractile pericytes should not be confused with smooth muscle cells. David Attwell, University College London, E-mail D.Attwell@ucl.ac.uk

The original definition of pericytes by Zimmermann (1923) (translated into English here) included in this cell class the contractile cells on capillaries which Hill et al. (2015) re-name in their paper to be smooth muscle cells (despite their clear morphological difference from classical arteriolar smooth muscle cells). Unfortunately, because Hill et al. re-named pericytes in this way, the title and text of their paper are misleading. Zimmermann (1923), and most workers since in the field of vascular biology, would define as pericytes the spatially-isolated contractile cells on capillaries that Hill et al. (2015) observe to control capillary blood flow in health and disease, confirming previous papers showing that pericytes have this role (Hall et al., 2014; Yemisci et al., 2009). Further discussion can be found in: Attwell, Mishra, Hall, O’Farrell & Dalkara (2015) What is a pericyte? J Cereb Blood Flow & Metab. advance online publication.

On 2015 Oct 05, S Sundar commented:

ARV-7 dynamics and re-induction of hormone sensitivity by chemotherapy in Prostate cancer.

This report by Antonarakis’s group regarding reversal of ARV-7 positivity by Taxane chemotherapy is likely to have a significant impact on the sequencing of various hormonal and chemotherapeutic agents .

The two previous independent reports of re- induction of hormone sensitivity by chemotherapy could probably be explained by this mechanism whereby chemotherapy induces favourable changes for hormone therapy to be effective again after prior hormonal resistance[1][2].

The previous reports of re-induction of hormone sensitivity by chemotherapy utilised Docetaxel monotherapy as well as Chlorambucil and Lomustine combination therapy. Hence it could be hypothesised that the reversal of ARV-7 dynamics and consequent re-induction of hormone sensitivity is a class effect of chemotherapy induced selection pressure. Exploitation of this phenomenon would significantly optimise the use of existing hormonal and chemotherapeutic agents in prostate cancer.

References:

1. Cox RA, Sundar S. Re-induction of hormone sensitivity to diethylstilboestrol in androgen refractory prostate cancer patients following chemotherapy. Br. J. Cancer 2008; 98(1):238–239.

2. Shamash J, Davies A, Ansell W et al. A phase II study investigating the re-induction of endocrine sensitivity following chemotherapy in androgen-independent prostate cancer. Br. J. Cancer 2008; 98(1):22–24.

On 2015 Jun 29, Torsten Seemann commented:

The software can be found here: https://sourceforge.net/projects/isquest/

On 2016 Jan 25, Jacob H. Hanna commented:

Thank you for the valuable information.

We highlight that the gene expression data in Chd4 null embryos presented in this paper, and the immuno-staining for Oct4/Nanog on Mbd3 null embryos in Kaji et al. Development 2007 <PMID 17287250>, both show formation of hallmarks of pluripotency in vivo at the pre-implantation epiblast ( http://imgur.com/lsM6kbV ). This is in contrast to Nanog null embryos for example, that cannot sustain Oct4+ cells at E3.5-E4.5 ICMs ( http://imgur.com/lsM6kbV ).

As Mbd3 KO ESCs derivation in vitro is not compromised under optimized growth conditions (e.g. 2i/LIF (Rais et al. Nature 2013), KSR/LIF or high quality FBS/LIF conditions), we will be also testing Chd4 KO ESC derivation from null mice to finalize the discussion and provide a more complete and solid answer.

On 2016 Jan 25, Brian Hendrich commented:

This paper is about the function of Chd4 in cells of preimplantation stage embryos. It is not about ES cells. Anyone wishing to attempt derivation of Chd4-null ES cells can obtain our Chd4 floxed mouse line which has been deposited with MRC Harwell (http://www.har.mrc.ac.uk/) for distribution.

On 2016 Jan 23, Jacob H. Hanna commented:

I would first like to congratulate the authors on this elegant and important paper. The Hendrich group has previously purported in Kaji et al. Development 2007 paper that it is absolutely impossible to derive Mbd3-/- ESCs from Mbd3 null E3.5 embryos. This result was surprising considering that the authors show in the same paper presence of Oct4+/Nanog+ cells in Mbd3-/- ICMs. Further, Mbd3-/- ESCs are "hyper-naive" and resist differentiation even in the absence of LIF (Kaji et al. Nature Cell Biology 2006, Reynolds et al. Cell Stem Cell 2012). Our group has revisited this result in Rais et al. Nature 2013, and was able to efficiently derive Mbd3-/- ESCs in serum free enriched 2i/LIF conditions. This suggests that the main conclusion of Kaji et al. 2007 Development paper Kaji K, 2007 titled "Mbd3 is required for development of pluripotent cells", is invalid and constitutes an artifact possibly due to using a low quality fetal bovine serum (FBS) batch.

In O'Shaughnessy-Kirwan et al. Development 2015 have generated Chd4 null mouse embryos and show that Oct4+/Nanog+ ICM is formed in vivo, just like in Mbd3-/- embryos Kaji K, 2007. This indicates again that Mbd3/Chd4/NuRD is dispensable for the formation of pluripotent cells in vivo. It is disappointing that the authors did not describe attempts to derive Chd4 knockout ESCs in this work and explain their ambiguous and controversial results on NuRD complex null ESC derivations Kaji K, 2007.

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 Jul 25, David Keller commented:

Yet another treatment is proved futile for slowing neuro-degeneration

Pioglitazone, meet minocycline, co-enzyme Q-10, creatine, and vitamin E. They are all losers in the search for a neuro-protective agent to slow the progression of diseases like Alzheimer's and Parkinson's.

This result is particularly disappointing given the recent observational study which found the use of thiazolidinediones ("glitazones") to be associated with reduced incidence of Parkinson's disease [1].

Note: pioglitazone is the only widely-used glitazone since the FDA restricted the use of rosiglitazone (Avandia) due to safety concerns.

Reference:

1: Brauer R, Bhaskaran K, Chaturvedi N, Dexter DT, Smeeth L, Douglas I. Glitazone Treatment and Incidence of Parkinson's Disease among People with Diabetes: A Retrospective Cohort Study. PLoS Med. 2015 Jul 21;12(7):e1001854. doi: 10.1371/journal.pmed.1001854. eCollection 2015 Jul. PubMed PMID: 26196151.

On 2015 Aug 06, Andrea Messori commented:

Equivalence of sofosbuvir-ledipasvir (12 weeks) and ABT-450/ ritonavir/ ombitasvir/dasabuvir (12 weeks) in previously untreated patients with genotype 1 HCV infection

By Andrea Messori, PharmD, Sabrina Trippoli, PharmD

HTA Unit, Tuscany Region, ESTAR, Regional Health Service, 50100 Firenze, Italy

Some debate is ongoing on which procurement methods can contribute to reduce the high prices of direct-acting antiviral agents (DAAs) indicated for the treatment of hepatitis C (1-4). Two techniques are particularly suitable for this purpose: a) price-volume agreements (3,4); and b) competitive tenders (1,2). In this brief report, we re-examine the results published by Trippoli et al. (5) to evaluate how these findings can be a suitable clinical basis for undertaking competitive tenders according to the current Italian regulation.

At the end of 2012, a national regulation was issued in Italy (“decreto Balduzzi” [6,7]) concerning the acquisition tenders run by our NHS. According to this regulation, when these tenders are aimed at drugs that belong to the same pharmacological class, a preventive authorization must be obtained from our National Medicines Agency (Agenzia del Farmaco, AIFA) to certify that the agents under examination are therapeutically equivalent. Otherwise, these tenders can no longer be performed. Hence, defining equivalence is, in Italy, not only a matter of scientific interest but also a prerequisite for making procurement decisions within our NHS.

In the field of DAAs, the main practical need for conducting tenders is to promote a competition between the two main combination treatments presently available: a) the combination of sofosbuvir and ledipasvir (manufactured by Gilead), abbreviation: SOF/LED; and: b) the four –drug combination manufactured by Abbvie (that includes ABT-450/ ritonavir/ ombitasvir/dasabuvir); abbreviation, ARIOD. To avoid an excessive heterogeneity in the clinical material included in this assessment, we restricted our analysis to the treatments based on a duration of 12 weeks and to the indication of previously untreated patients infected by genotype 1. The end-point was the achievement of sustained virologic response at 12 weeks after the end of therapy (SVR12). It can be seen that these criteria are similar to those employed by Trippoli et al. (5). As regards the margin of equivalence, we adopted the value of ±10% around the overall meta-analytical rate calculated for both treatments.

By running a PubMed query, we searched for more recent studies not included in the meta-analysis of Trippoli et al., but we found none. Furthermore, since the present analysis was essentially based on a proportion meta-analysis design, we replaced the all-in-one Bayesian model adopted by Trippoli et al. with the more traditional random-effect frequentist model of proportion meta-analysis (software: Open Meta-Analyst, version 4.16.12, Tufts University).

Overall, our proportion meta-analysis included 3 studies for SOF-LED and 3 studies for ARIOD (see Appendix 1 for details). Figure 1 shows the Forest plot with the trial-specific rates of SVR12 achievement and the meta-analytic rates estimated separately for SOF-LED and for ARIOD. The overall meta-analytic rate estimated for SOF-LED and ARIOD (6 studies) was 95.5%; hence, the equivalence margin was from 85.5% to 100%. Both SOF/LED (rate of SVR12 achievement, 97.1%; 95% CI of SVR12: 94.4% to 99.8%) and ARIOD (rate of SVR12 achievement, 93.1% ; 95% CI: 85.6% to 100%) satisfied our pre-specified criterion of equivalence. It should be noted that, while most equivalence analyses generally adopt 90%CIs, our analysis employed a more selective confidence interval of 95%.

In conclusion, these results indicate that SOF-LED and ARIOD, given for 12 weeks, are therapeutically equivalent in treatment-naïve patients with genotype 1 infection; this conclusion, formally based on a meta-analysis, confirms the message of equivalence that several experts have reported in narrative terms (1). As regards safety, several recent reviews have examined this point (8-11) and none of them have suggested that there is any difference between these two combination treatments. Hence, this overall picture of the literature indicates that SOF-LED and ARIOD can be included in competitive tenders aimed at the procurement of treatments for patients with the characteristics mentioned above.

References

1. Wilensky G. A New Focus on Prescription Drug Spending. JAMA 2015;314(5):440-441.

2. Brunetto MR, De Luca A, Messori A, Zignego AL. Reducing the price of new hepatitis C drugs in the Tuscany region of Italy. BMJ 2015;350:h3363 doi: 10.1136/bmj.h3363 (Published 24 June 2015), available at http://bmj.com/cgi/content/full/bmj.h3363?ijkey=xYS3zhzXoox8A8t&keytype=ref

3. Messori A. Newest treatments for hepatitis C: how can we manage sustainability? Clin Infect Dis. 2015 Aug pii: civ667. [Epub ahead of print], prepint available at http://www.osservatorioinnovazione.net/papers/cid2015pricing.pdf

4. Messori A. Managing the high cost of innovative drugs: anti-cancer agents vs direct-acting antivirals for hepatitis C (Comment posted 2 April 2015), Ann Intern Med 2015, available at http://annals.org/article.aspx?articleid=2212249#tab

5. Trippoli S, Fadda V, Maratea D, Messori A. Bayesian network meta-analysis to evaluate interferon-free treatments in naïve patients with genotype 1 HCV infection. Eur J Gastroenterol Hepatol 2015 Aug;27(8):983-984

6. Messori A, Fadda V, Maratea D, Gatto R, Trippoli S, De Rosa M, Marinai C. Intravenous proton pump inhibitors for stress ulcer prophylaxis in critically ill patients: determining statistical equivalence according to evidence-based methods. Int J Clin Pharmacol Ther. 2014 Oct;52(10):825-9.

7. Messori A, Fadda V, Gatto R, Maratea D, Trippoli S. Differentiating between “no proof of difference” and “proof of no difference” for new oral anticoagulants. BMJ. 2014; 348: g1955.

8. Kohli A, Shaffer A, Sherman A, Kottilil S. Treatment of hepatitis C: a systematic review. JAMA. 2014 Aug 13;312(6):631-40.

9. Feeney ER, Chung RT. Antiviral treatment of hepatitis C. BMJ. 2014 Jul 348:g3308.

10. Pawlotsky JM. New hepatitis C therapies: the toolbox, strategies, and challenges. Gastroenterology. 2014 May;146(5):1176-92.

11. Ferenci P, Kozbial K, Mandorfer M, Hofer H. HCV targeting of patients with cirrhosis. J Hepatol. 2015 Jun 19. pii: S0168-8278(15)00393-1. doi:10.1016/j.jhep.2015.06.003. [Epub ahead of print]

APPENDIX 1. INFORMATION ON THE TRIALS INCLUDED IN THE PROPORTION META-ANALYSIS.§

AUTHOR SVR12 (n/N) RATE (95% CI) TREATMENT

Kowdley, 206/216, rate=0.954 (0.926 to 0.982), SOF-LED

LONESTAR, 18/19, rate=0.947 (0.847 to 1.048), SOF-LED

Afdal, 211/214, rate=0.986 (0.970 to 1.002), SOF-LED

Kowdley, 70/79, rate=0.886 (0.816 to 0.956), ARIOD

Pearl-IV, 185/205, rate=0.902 (0.862 to 0.943), ARIOD

Pearl-III, 207/209, rate=0.990 (0.977 to 1.004), ARIOD

§The complete bibliographic details of the studies are available from the paper by Trippoli et al. (5). Abbreviations: SOF/LED, sofosbuvir+ledipasvir; ARIOD, ABT-450/ ritonavir/ ombitasvir/dasabuvir; CI, confidence interval.

FIGURE 1. PROPORTION META-ANALYSIS BASED ON A RANDOM-EFFECT MODEL

Rates of SVR12 achievement with sofosbuvir+ledipasvir (12 weeks; 3 studies) and with ABT-450/ ritonavir/ ombitasvir/dasabuvir (12 weeks; 3 studies). The parameter I² is an index of heterogeneity. The Forest plot of this figure is available at http://www.osservatorioinnovazione.net/papers/trippoli-reanalysis.jpg . Abbreviations: SOF/LED, sofosbuvir+ledipasvir; ARIOD, ABT-450/ ritonavir/ ombitasvir/dasabuvir; C.I., confidence interval.

On 2016 Oct 24, Sean Ekins commented:

A slide presentation on this topic from an ACS in 2015 http://www.slideshare.net/ekinssean/applying-cheminformatics-and-bioinformatics-approaches-to-neglected-tropical-disease-big-data

On 2015 Nov 18, Chris Del Mar commented:

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

On 2016 Apr 13, Manoochehr Karami commented:

Title: Death Suicide: Stop Saying "Completed Suicide"

Authors: Manoochehr Karami(PhD)Social Determinants of Health Research Center and Department of Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran.

Ali Ghaleiha(MD) Behavioral Disorders and Substance Abuse Research Center &Department of Psychiatry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran

The World Health Organization has considered suicide as a serious public health problem with more than 800000 deaths annually worldwide (1). Researchers use different terms including "Died by Suicide", "Committed Suicide" and "Completed Suicide" for attempted suicide leading to death (2-5). Among these, completed suicide is the most popular term, especially during the recent years. Although "Completed Suicide" is more accurate to indicate outcome of attempted suicide, "Death Suicide" is an alternative term without second thought to replace "Completed Suicide". In conclusion, authors, journal editors and readers are advised to consider "Death Suicide" to avoid ambiguity and misclassification of suicide cases.

References:

1. World Health Organization. Suicide Fact sheet N°398 2015 [cited 2015 August]. Available from: http://who.int/mediacentre/factsheets/fs398/en/.

2. Khazaei S, Karami M, Sohailzade M, Sohrabnegad A. Determinants of complete suicide: A cross sectional study. Journal of Ilam University of Medical Sciences. 2013;21(6):240-7.

3. Pallaskorpi SK, Isometsa ET, Henriksson MM, Suominen KH, Lonnqvist JK. Completed suicide among subjects receiving psychotherapy. Psychotherapy and Psychosomatics. 2005;74(6):388-91.

4. Suominen K, Isometsa E, Suokas J, Haukka J, Achte K, Lonnqvist J. Completed suicide after a suicide attempt: A 37-year follow-up study. American Journal of Psychiatry. 2004;161(3):562-3.

5. Wu A, Wang JY, Jia CX. Religion and Completed Suicide: a Meta-Analysis. Plos One. 2015;10(6).

On 2016 May 23, Stanton A Glantz commented:

In June 2015 we published our paper “The smoking population in the USA and EU is softening not hardening” in the journal Tobacco Control. We showed that as smoking prevalence has declined over time, quit attempts increased in the USA and remained stable in Europe, US quit ratios increased (no data for EU), and consumption dropped in the USA and Europe. These results contradict the hardening hypothesis which is often used as part of the tobacco industry’s strategy to avoid meaningful regulation and protect its political agenda and markets, claiming that there is a need for harm reduction among those smokers who “cannot or will not quit.” Indeed, rather than “hardening” the remaining smoking population is “softening.”

In February 2016 we received an email from Robert West, editor of the journal Addiction, informing us that Addiction was about to publish an article by Plurphanswat and Rodu entitled “A Critique of Kulik and Glantz: Is the smoking population in the US really softening?” whose sole purpose was to critique our Tobacco Control paper, and offered to let us respond to the criticism.

The fact that Plurphanswat and Rodu sent their paper to Addiction was unusual because normal scientific procedure would have had them sending a letter to the editor of the journal that originally published the work (Tobacco Control).

As detailed below, we did respond, noting that Plurphanswat and Rodu’s paper followed the well-established pattern of tobacco industry-funded researchers trying to create controversy about research inconsistent with industry interests, the fact that Rodu had understated his financial ties to the industry, and, of course, showing how their criticism was based on statistical error that they made.

Addiction rejected our response because we would not delete the first two points and limit our response only to the statistical issue.

This blog post includes the response that Addiction rejected so that readers of Plurphanswat and Rodu’s critique do not think we did not have a response. We also include a summary of our interactions with the journal and the related email correspondence.

THE REJECTED RESPONSE

Consider the Source

“Harm reduction” is a key part of the tobacco industry’s strategy to avoid meaningful regulation and protect its political agenda and markets.[1] This agenda is premised on the existence of “hard core” smokers who “cannot or will not” quit.[2-4] Our paper, “The smoking population in the USA and EU is softening not hardening”,[5] undermined this agenda because it showed that, contrary to the hardening hypothesis, as smoking prevalence has declined over time, quit attempts increased in the USA and remained stable in Europe, US quit ratios increased (no data for EU), and consumption dropped in the USA and Europe.

There is a longstanding pattern of tobacco industry-funded experts writing letters criticizing work that threatens the industry’s position, first described in 1993 by then-JAMA Deputy Editor Drummond Rennie.[6] Rodu and various co-authors have written several such letters.[7-10] Another similarity to past efforts is industry-linked experts submitting critiques of a paper published in one journal to another,[11-15] which is also the case here, with this critique of our paper published in Tobacco Control being published in Addiction. One would have expected any criticism to have been published as a letter in Tobacco Control.

Addiction requires “full disclosure of potential conflicts of interest, including any fees, expenses, funding or other benefits received from any interested party or organisation connected with that party, whether or not connected with the letter or the article that is the subject of discussion.” As with another investigator supported by the tobacco industry,[16] the conflict of interest statement Plurphanswat and Rodu provide may not truly reflect the extent of Rodu’s involvement with the tobacco industry. For example:

• Rodu’s Endowed Chair in Tobacco Harm Reduction Research at the University of Louisville is funded by the U.S. Smokeless Tobacco Company (US Tobacco) and Swedish Match North America, Inc.[17]

• Rodu is a Senior Fellow at the Heartland Institute, which has received tobacco industry funding.[18-20]

• Rodu is a Member and Contributor to the R Street Institute, which has received tobacco industry funding.[19,21]

• Before moving to Louisville, Dr. Rodu was supported in part by an unrestricted gift from the United States Smokeless Tobacco Company to the Tobacco Research Fund of the University of Alabama at Birmingham.[8]

• Rodu was a keynote speaker at the 2013 Tobacco Plus Expo International, a tobacco industry trade fair to discuss “How has the tobacco retail business evolved; where was it fifteen years ago, where is it today and where is it going”.[22]

• Rodu has worked with RJ Reynolds executives between at least 2000 and 2009 to help promote industry positions on harm reduction, including specific products.[23-26]

The substance of Plurphanswat and Rodu’s criticism is that the statistically significant negative association between smoking prevalence and quit attempts and the positive association between prevalence and cigarettes smoked per day both become non-significant when more tobacco control variables are included in the model (state fixed effects, cigarette excise taxes, workplace smoking bans and home smoking bans). The problem with including all these variables is that it results in a seriously overspecified model, which splits any actual effects between so many variables that all the results become nonsignificant. The regression diagnostic for this multicollinearity is the Variance Inflation Factor (VIF); values of the VIF above 4 indicate serious multicollinearity. For the United States, adding all the other variables increases the VIF for the effect of changes in smoking prevalence from 1.8 in our model for quit attempts to 16.7, and from 1.8 in our model to 17.9 for cigarettes per day, respectively. Plurphanswat and Rodu’s model is a textbook case of why one has to be careful not to put too many variables in a multiple regression.

The Plurphanswat and Rodu criticism misrepresents our conclusions. We did not argue that drops in prevalence caused increased quit attempts and reduced consumption; we simply present the observation that, as prevalence falls, quit attempts increase and consumption fall or remain constant, which is the exact opposite of what the hardening hypothesis predicts.

The references and the full email correspondence with Addiction is available at http://tobacco.ucsf.edu/addiction-refuses-allow-discussion-industry-ties-criticism-our-“softening-paper”

On 2016 May 19, Brad Rodu commented:

We conducted an additional analysis of the American data used in this study, which has been published in Addiction: Plurphanswat N, 2016

The original authors ran a linear regression of state-level measures of quit attempts, quit ratios and cigarette consumption on smoking prevalence using data sets from the Tobacco Use Supplements to the Current Population Surveys from 1992–2011. However, they did not include relevant tobacco control variables such as cigarette excise taxes, workplace and home smoking bans, and other unobserved, time-invariant, state-specific factors that could have accounted for the observed associations.

We extended the original model by including these readily available variables, and we found that the original results were not robust; there was a large drop in the coefficients and they became statistically non-significant. These findings do not support the original authors' claim that the smoking population is "softening."

Since 2005 Dr Rodu has been supported by the Kentucky Research Challenge Trust Fund and by unrestricted grants to the University of Louisville from tobacco manufacturers (Swedish Match AB, U.S. Smokeless Tobacco Company, Reynolds American Inc. Services, Altria Client Services, and British American Tobacco). Dr Plurphanswat has been supported by these grants since 2013.

On 2016 Nov 25, Leonid Schneider commented:

Dr. Ana Pedro has published a critical post-publication peer review of this paper on my website. She highlights several technical inconsistencies of Melo et al 2015. https://forbetterscience.wordpress.com/2016/11/24/post-publication-peer-review-of-a-multimillion-dollar-heavy-nature-paper-by-ana-pedro

On 2015 Jul 17, Bill Cayley commented:

An example of when "less medical" might be "better": https://lessismoreebm.wordpress.com/2015/07/17/physical-fitness-exercise-versus-cognitive-behavior-therapy-on-reducing-the-depressive-symptoms-among-community-dwelling-elderly-adults-a-randomized-controlled-trial/

On 2016 Aug 23, Ben Goldacre commented:

This trial has the wrong trial registry ID associated with it on PubMed: both in the XML on PubMed, and in the originating journal article. The ID given is NCT0082231. We believe the correct ID, which we have found by hand searching, is NCT00822315.

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 2017 Aug 11, Alex Vasquez commented:

The concern being addressed (after the documentation of human DNA, at least in fragmented form) is whether or not such “vaccine DNA” could be incorporated into the living “human DNA” of the host recipient; however, that is only one rather minor concern with the injection of human DNA from one person’s cells into the body of another living human being. From an immunology and inflammology standpoint, the concern is the likelihood that exogenous human DNA would trigger inflammatory responses after being perceived by the immune system and received by receptors for DAMPs (damage associated molecular patterns). Whether this amount of inflammation triggered from human DNA in vaccines is great or small, frequent or uncommon is unknown due to the lack of adequate vaccine testing; however, one would expect it to be of greater consequence in “genetically susceptible” persons and also when co-administered in various mixtures with other vaccines and with their pro-inflammatory ingredients such as aluminum (which exacerbates the release of human DNA[1]), mercury (known to promote immune sensitization) and allergenic antibiotics common in vaccines, including streptomycin[2], polymyxin B[3], neomycin[4], gentamicin and kanamycin[5].

[1] "Although DNA DAMPs are closely associated with the development of autoimmune disease, DNA DAMPs also contribute to the activation of acquired immune responses following vaccination with alum adjuvant. Previous studies have shown that genomic DNA from dying cells induces the maturation of antigen-presenting cells as well as antigen-specific antibody and cytotoxic T cell responses. This suggests that self-DNA DAMPs can activate innate immune responses that induce acquired immunoresponses. Recently, Marichal et al. demonstrated that the adjuvanticity of alum was dependent on self-DNA released from cells at the alum inoculation site (Marichal et al., 2011). NLRP3 appears to be a key sensor in the induction of alum-mediated innate immunity, although its function is only partially dependent upon alum adjuvanticity. " Jounai et al. Recognition of damage-associated molecular patterns related to nucleic acids during inflammation and vaccination. Front Cell Infect Microbiol. 2013 Jan 8;2:168 [2] Romano et al. Anaphylaxis to streptomycin. Allergy. 2002 Nov;57(11):1087-8 [3] Henao MP, Ghaffari G. Anaphylaxis to polymyxin B-trimethoprim eye drops. Ann Allergy Asthma Immunol. 2016 Apr;116(4):372 [4] Goh CL. Anaphylaxis from topical neomycin and bacitracin. Australas J Dermatol. 1986 Dec;27(3):125-6 [5] Sánchez-Pérez et al. Allergic contact dermatitis from gentamicin in eyedrops, with cross-reactivity to kanamycin but not neomycin. Contact Dermatitis. 2001 Jan;44(1):54