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Quantification of urinary TIMP-2 and IGFBP-7 in cardiac surgery – Applying standards for reporting prognostic accuracy (Azra Bihorac, 23 January 2015)

We read with interest the results of the study by Wetz at el. examining the predictive performance of a novel urinary biomarker test (tissue-inhibitor of metalloproteinase 2 multiplied with urine insulin like growth factor binding protein 7, NephroCheckR) for the diagnosis of acute kidney injury (AKI) after cardiac surgery [1]. This test is the first FDA approved biomarker for risk stratification for AKI in critically ill patients, validated in two large multicenter trials [2-4]. In this study the definition and timing of outcomes, sample size and the reporting of statistical uncertainty all fall below standards in reporting and extrapolating the results of prognostic tests for clinical use [5, 6]. Measuring the occurrence of any stage of AKI up to sixty hours after surgery, as opposed to... read full comment

Comment on: Wetz et al. Critical Care, 19:3

Correcting a co-author's name (Hongying Yang, 22 January 2015)

The correct name of the sixth author is Peigen Huang, not Peigeng Huang. We are sorry for the mistake. read full comment

Comment on: Zhang et al. Radiation Oncology, 9:281

Good article (abby lee, 22 January 2015)

Thanks for this good article. It's so refreshing to learn so many about DNA. I know that bar code used for management of plant species at low cost, and I find a tutorial about creating barcode from ssrs, hope it's helpfu. read full comment

Comment on: Nybom et al. Investigative Genetics, 5:1

Primary Particle Properties (Joel Cohen, 22 January 2015)

The indicative primary particle diameter of TiO2 nanoparticles listed in Table 1 is 24 nm as detailed in Xia et al. 2013.... read full comment

Comment on: Cohen et al. Particle and Fibre Toxicology, 11:20

Addendum to the paper (Ron Nudel, 21 January 2015)

In our paper we presented relative risks (risk ratios) for HLA alleles that had low p-values in the case-control association analysis. However, our samples were selected on the basis of disorder status, and, therefore, a more appropriate way for assessing the strength of association would have been provided by odds ratios. We would therefore like to report the odds ratios for those five HLA alleles, as estimated using the same data used in the estimation of the relative risks: DR10 8.085; DQA1*0301 0.674; B57 0.449; DR4 0.599; DR12 0.255. Please note that this does not affect the conclusions of the study, as the observed odds and risk ratios are in the same direction. read full comment

Comment on: Nudel et al. Journal of Neurodevelopmental Disorders, 6:1

Changes in the posterior interosseous nerve - are they related to carpal tunnel syndrome rather than vibration? (Tim Davis, 21 January 2015)

I read this review article with interest but am concerned that the authors’ conclusion that use of hand-held vibrating tools causes damage to the posterior interosseous nerve is correct.  ... read full comment

Comment on: Dahlin et al. Journal of Occupational Medicine and Toxicology, 9:7

Methodological aspects should be respected. (Renato Monteiro Junior, 21 January 2015)

Commentary about paper: Dynamic stability requirements during gait and standing exergames on the Wii Fit(R) system in the... read full comment

Comment on: Duclos et al. Journal of NeuroEngineering and Rehabilitation, 9:28

Commentary on Conor M Minogue, Brian M Caulfield and Madeleine M Lowery: ¿Whole Body Oxygen Uptake and Evoked Knee Torque in Response to Low Frequency Electrical Stimulation of the Quadriceps Muscles¿. (Joseph Mizrahi, 21 January 2015)

This paper suggests a method for invoking whole-body exercise resulting from isometric activation of the knee extensor muscles by means of low-frequency electrical stimulation. The interest in eliciting cardio-pulmonary function, as is required in subjects with exercise limitations, is rather contrary to conventional approach in functional electrical stimulation of muscles whereby more effective performance is associated with lower energy consumption (1). Thus, `optimal¿ stimulation (expressed by means of stimulation frequency) is associated here with high oxygen uptake of the... read full comment

Comment on: Minogue et al. Journal of NeuroEngineering and Rehabilitation, 10:63

An editting error (Mingming Zhang, 21 January 2015)

Really sorry for any confusion caused by this editting error. The first citation appears twice in the first sentence of this manuscript. Further, we realized that it should be replaced by another reference that is "Sammarco GJ. Rehabilitation of the Foot and Ankle. Missouri, USA: Mosby-Year Book; 1995". read full comment

Comment on: Zhang et al. Journal of NeuroEngineering and Rehabilitation, 10:30

Addition (Kiriakos Daniilidis, 20 January 2015)

We have recently identified an error in our text with regard to the Lequesne score. We describe that "It is a 24-scale questionary in which low scores indicate low functional activity". The correct sentence is as follows: "It is a 24-scale questionary in which low scores indicate high functional activity". We apologise to the readers for the inconvenience. read full comment

Comment on: Daniilidis et al. Journal of Orthopaedic Surgery and Research, 10:1

How the PCR amplification performed? (Ren-Gang Zhang, 20 January 2015)

I am a reader. The first paragraph at Page 10 of 13 showed that the non-phosphorylated adapters were used. Thus, after ligation of digested DNA and adaptors, there should be two nicks on one DNA ligation product (Figure below). Between the steps of ligation and PCR amplification, there was no step to repair the nicks (see the 2b-RAD protocol of the paper). So comes the question, how the primers that annealed to the bottom adaptor extended (Figure below), as the PCR condition was: 98℃ for 30 s followed by 12 cycles of 98℃ for 30 s, 65℃ for 30 s, 72℃ for 30 s with a final Taq extension step at 72℃ for 5... read full comment

Comment on: Guo et al. BMC Genomics, 15:956

Clinical utilization of TIMP-2 and IGFBP7 for detection of AKI following cardiac surgery (Eric Hoste, 16 January 2015)

We read with great interest the study by Wetz et al on the use of the biomarkers tissue inhibitor metalloproteinase-2 (TIMP-2) and insulin growth factor-binding protein-7 (IGFBP7) for prediction of AKI after cardiac surgery [1]. The authors found that measurement of these biomarkers during the first day after surgery could identify patients at risk for AKI, while measurement 4 h after cardiopulmonary bypass (CPB) surgery or at the end of the procedure could not identify patients at risk for... read full comment

Comment on: Wetz et al. Critical Care, 19:3

Letter to the editor: Critics and Comments to the article (Sandeep Kumar Panigrahi, 15 January 2015)

I congratulate the authors for coming up with an interesting paper from the analysis of WHO SAGE secondary data. I would like to give few comments and would like to request the authors to address some queries. This would clarify similar doubts of other readers. Some studies and survey in USA and UK show that prevalence of obesity is more common in women of lower Socio-economic strata, while in men it is same for all income levels. Since NCD has relation with obesity how does it fit in this case, where epidemiological trends have come out to be something different in India. What can be the reasons have not been discussed in the discussion section. Second is that how can number of non-communicable diseases be said as continuous variable and analysis done accordingly? To my belief, it is... read full comment

Comment on: Pati et al. BMC Health Services Research, 14:451

Continuing Support for Grantham’s Genome Hypothesis (Donald Forsdyke, 15 January 2015)

Richard Grantham (1980), after examination of a mere 160 short sequences, proposed his ‘genome hypothesis.’ For nucleic acids he envisaged ‘manifold constraints and adaptations, of both structural and functional natures.’ These ‘could exist, independently of protein coding.’ Thus, there was ‘protein-independent molecular evolution of a non-neutral character.’ The distinctive ‘coding strategy of an organism’ was ‘at the heart of the problem of molecular evolution,’ and was likely to prove of fundamental importance for ‘speciation and systematics in general’ (Grantham et al.... read full comment

Comment on: Goncearenco et al. Biology Direct, 9:29

A correction for the manuscript of The progress of targeted therapy in advanced gastric cancer (Miao-zhen Qiu, 15 January 2015)

It is wrong to say that: 'According to the 2012 Chinese cancer registry annual report, gastric cancer is the third most common cancer and the second leading cause of cancer related death in China'. It should be 'According to the 2012 Chinese cancer registry annual report, gastric cancer is the second most common cancer and the third leading cause of cancer related death in China'. read full comment

Comment on: Qiu et al. Biomarker Research, 1:32

Reply to David Sexton (Manuel Corpas, 15 January 2015)

Thanks a lot David for your comment, I totally agree with your concern of the fact that there are many PIs who have no idea of what it takes for bioinformaticians to do their work. Nevertheless, even if more bioinformaticians are hired, will unsavvy PIs ever understand what it takes for a bioinformatics pipeline or anaysis ever to be carried out? read full comment

Comment on: Corpas et al. Source Code for Biology and Medicine, 7:3

The Command Line Is More Effective for Reproducibility and Re-Use (Jan T Kim, 15 January 2015)

An awkward command line interface (CLI) can surely be a pain, but fixing or mitigating that is very easy, compared to dealing with a program that can only be used interactively via a GUI. Many CLI based programs have had a more "user friendly" interface wrapped around them, e.g. the PHYLIP [1] programs have been wrapped for EMBOSS [2] in EMBASSY, and in turn there are various GUIs for EMBOSS; and Galaxy [3] provides a framework for wrapping a web interface around any tool that can be driven non-interactively. From this perspective, any CLI is much more conducive to re-use than a GUI that is the only way to use a... read full comment

Comment on: Corpas et al. Source Code for Biology and Medicine, 7:3

Baseline incidence of aspiration is way too high (Philip Jones, 14 January 2015)

There are several issues here:
1) The baseline incidence of aspiration you quote (11%) is far too high. Warner's retrospective review of 172,000 patients (Anesthesiology 78:1, 56-62) showed an incidence of 0.03%. Although these were in mostly fasted patients, even if your incidence were 100-fold higher, the baseline incidence would be only by 3%. To show a change from 3% to 0% with 90% power would require 680 patients. Therefore, your study is very likely to be underpowered.
2) What is the clinical significance of the pepsin test? It will be perhaps easy to show pepsin presence, but linking this in some meaningful way to clinical aspiration with bad effects will be difficult. read full comment

Comment on: Trethewy et al. Trials, 13:17

Professional medical writers (Yvonne Yarker, 14 January 2015)

The International Society for Medical Publication Professionals (ISMPP;, a global, non-profit organization that advocates for and educates on best practices, professional ethics, and transparency in medical publishing, would like to challenge a statement made by the authors in the Discussion of this article in regard to professional medical writers: ¿if they do not do a job that satisfies the sponsors¿ marketing department, they might go out of business¿. Firstly, publication budgets are rarely held by the marketing departments of drug and device companies these days. Secondly, professional medical writers who are members of ISMPP and other relevant professional associations agree to abide by a code of ethics which, among other things, includes an obligation to ensure... read full comment

Comment on: Lundh et al. Trials, 13:146

Efficiency and effectiveness of the use of an acenocoumarol pharmacogenetic dosing algorithm versus usual care in patients with venous thromboembolic disease initiating oral anticoagulation: study protocol for a randomized controlled trial (Rianne van Schie, 14 January 2015)

R.M.F. van Schie1, T.I. Verhoef1, F.J.M van der Meer2, A. de Boer1, A.H. Maitland-van der Zee1, for the EU-PACT study... read full comment

Comment on: Carcas et al. Trials, 13:239

The coronary sinus reducer in patients with refractory angina pectoris (Yoav Paz, 14 January 2015)

Jolic Ur EM et al. erroneously compare the Neovasc coronary sinus reducer (CSR) to the Beck procedure, which has almost nothing in common with the Neovasc CSR. Actually this statement can be concluded by reading references 6-10 in Jolic Ur EM et al. study protocol.[1] In the 1940s, Dr Claude Beck described two types of coronary sinus (CS) interventions.[2-4] The Beck I procedure consisted of 4 components: 1) external surgical narrowing of the CS; 2) abrading both the epicardium and inner pericardium (some kind of neurectomy procedure that was used for the treatment of refractory angina pectoris in those days); 3) spilling of powdered asbestos and 5% aqueous trichloracetic acid on the epicardium; 4) placing mediastinal fat over the treated epicardium. The Beck II procedure consisted of 2... read full comment

Comment on: Jolicœur et al. Trials, 14:46

Erratum in citations (Silvana TRIDICO, 14 January 2015)

Page 4. column 1, Murray et al (21) should read Murray et al (23) in which the correct citation is listed... read full comment

Comment on: Tridico et al. Investigative Genetics, 5:16

searches and filters (Kath Wright, 13 January 2015)

Mann and Gilbody compare the performance of three search strategies in identifying a reference set of diagnostic test accuracy studies of psychometric instruments.... read full comment

Comment on: Mann et al. Systematic Reviews, 1:9

related study idea (Erick Turner, 13 January 2015)

Thank you for undertaking this important work. This is not a comment on this protocol. Rather, I would like to suggest, as a possible future study, an alternate method that could be used to study publication bias in animal research: One could use FDA pharmacology reviews, which largely cover animal studies, then ascertain which studies covered in the review have been published. For each study that is published, one could examine outcome reporting bias by comparing the results in the review with those in the corresponding journal publication. This approach may offer some advantages over using published articles as the starting point. read full comment

Comment on: Briel et al. Systematic Reviews, 2:23

Plasticity of ER expression of Mammary Stem Cells which may harbor Anti-redox Machinery (Go Yoshida, 12 January 2015)

This research has elucidated the hierarchy model of mammary tissue and breast cancer from the novel perspective of the interaction between ER and ALDH. I would like to write the comment on the “stemness,” (including self-renewal potential, multi-lineaged differentiation and plasticity) in EpCAM-negative/lin-negative/CD49f-positive mammary cells.... read full comment

Comment on: Honeth et al. Breast Cancer Research, 16:R52