JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/1471-230X-12-124 (2012)

Reviewer's report
Title:Modified endoscopic submucosal dissection with enucleation for treatment
of gastric subepithelial tumors originating from the muscularis propria layer
Version: 1Date:23 May 2012
Reviewer: Seok-Reyol Choi
Reviewer's report:
This paper described the Modified endoscopic submucosal dissection used for
enucleation of gastric subepithelial tumors originating from the muscularis propria
layer. This kind of concept is not noble, but this procedure is not yet widely
accepted. Thus, this paper has values to contribute the advent of endoscopic
procedure for exploring subepithelial tumors.
I would like to point out three major revisions.
1. Page 7 and Figures. I do not understand the modified ESD exactly. What is
the transverse incision exactly? Longitudinal incision and transverse incision
makes cross shape incision? The Figure 1d does not show cross-shape incision.
I think not a picture but a simple illustration will explain this procedure more
properly. Please insert an illustration that explains the modified ESD, especially
two incision lines.
2. According to result, authors removed three tumors at fundus. As all
endoscopists know, it is not easy to remove EGC and SMT at fundus. Please
describe more how to remove those three lesions in method or discussion.
3. One of the important issues in this kind of procedures is that we could not
evaluate the resection margin. Practitioners can enucleate the SMT, but they are
not able to check whether the resection margin is clear or not pathologically. In
this matter, I would like to listen to authors’ opinion. So called endoscopic
complete enucleation can guarantee pathologic complete resection? Please
describe to this in method and discussion.
I raised a few questions to the authors. However, I think that the authors did very
good job. They handled subtle big SMTs which might need surgery. They
preserved the function of the stomach with successful enucleation of SMTs.
Furthermore, they exactly diagnosed the property of tumors.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-124 (2012)

Reviewer's report
Title:Modified endoscopic submucosal dissection with enucleation for treatment
of gastric subepithelial tumors originating from the muscularis propria layer
Version: 1Date:4 June 2012
Reviewer: Arjun Koch
Reviewer's report:
Major points
1. My major concern is to whether there was a correct indication for ESD in the
cases described to begin with. Our current guidelines state that lesions over 3 cm
should be resected. Only 3 lesions in this series were greater than 3 cm of which
one could not be resected endoscopically! Furthermore all lesions proved to be
of a low malignant potential so there was little need for resection. The authors
should explain why they felt that resection was indicated.
2. The authors demonstrate an ESD technique with enucleation for the treatment
of gastric subepithelial tumors originating from the proper muscle layer. Similar
reports have been published recently and should be referenced. (e.g. “Bing-Rong
Liu et al, Endoscopic muscularis dissection for upper gastrointestinal
subepithelial tumors originating from the muscularis propia.” Surg Endosc April
2012)
3. p5. ..."Expectant management with life-long endoscopic screening causes
tremendous economic and emotional burden for these patients"... Were is the
evidence for this statement? Even though this statement seems to be used to
justify resection, a periodic endoscopic follow-up of patients is advised on page
12...
4. There is no concrete description about the usefulness of the modified ESD
technique. The usefulness of modified ESD should be explained more.
5. Although the main theme is ESD for gastric subepithelial tumors originating
from the muscularis propia layer, there is no explanation of Leiomyoma except
GIST in discussion.
Minor points
1. There is no product name of an electrosurgical snare which used to shorten
the procedure time.
2. There is no description about the settings of the HF electric devices.
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-124 (2012)

Reviewer's report
Title:Modified endoscopic submucosal dissection with enucleation for treatment
of gastric subepithelial tumors originating from the muscularis propria layer
Version: 2Date:6 August 2012
Reviewer: Arjun Koch
Reviewer's report:
I congratulate the authors with their manuscript and I believe they have put real
effort in making all changes as requested by the reviewers.
The explanatory figures are a welcome addition to the manuscript.
My major concerns have been answered to satisfaction and I have no objection
against acception as it is after a few minor language improvements.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-124 (2012)

Reviewer's report
Title:Modified endoscopic submucosal dissection with enucleation for treatment
of gastric subepithelial tumors originating from the muscularis propria layer
Version: 2Date:12 August 2012
Reviewer: Seok-Reyol Choi
Reviewer's report:
Dear Author
I appreciate for your effort to incorporate many kinds of information in this paper.
I am satisfied with your amendment. Furthermore, I would like to say that this
kind of technique will improve patients' quality of life, especially lesions at cardia
or upper body. I hope you make another advance. I think that this current form is
available for publishing.
I will be waiting for another advance in the near future.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-12-122 (2012)

Reviewer's report
Title:Blastocystis spp. incidence in patients with gastrointestinal symptoms: a
case-control study
Version: 2Date:14 March 2012
Reviewer: Dilara Ogunc
Reviewer's report:
Dear Editor,
I think this manuscript was, overall, good but needs some corrections.
Minor essential revision:
In the first sentence of the abstract: Blastocystosis should be used instead of
Blastocystis spp.
Kind regards
Dilara Ogunc,MD
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-122 (2012)

Reviewer's report
Title:Blastocystosis in patients with gastrointestinal symptoms: a case-control
study
Version: 3Date:1 June 2012
Reviewer: Chad Porter
Reviewer's report:
Major compulsory revisions
1) The authors should conduct more sophisticated statistical analyses such as
multiple logistic regression to control for potential covariates or confounders.
2) The authors should explicity state the study design. Based on the methods
and results, it appears as though this was a cross-sectional study, but it is not
entirely clear based on author responses.
3) Tables 1&2 should be combined.
4) The authors need to significantly expand the discussion to include the
limitations of the reported study. Such discussion should include limitations of the
study design, sources of potential bias, the lack of assessment of potentially
important confounder, etc.
Minor Essential Revisions
1) Numerous grammatical and punctuation errors remain in the submitted
document and should be corrected.
2) Phrasing in parts of the discussion is confusing. For example, in sentence 2 of
paragraph 2 of the discussion, the authors state "...intestinal inflammation
induced by this parasite has a significant role in the discreminatory diagnosis
from other IBDs." It is unclear what is meant here. What are the other IBDs? How
does inflammation from this parasite assist in diagnosis?
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-122 (2012)

Reviewer's report
Title:Blastocystosis in patients with gastrointestinal symptoms: a case-control
study
Version: 4Date:26 July 2012
Reviewer: Chad Porter
Reviewer's report:
Major Compulsory Revisions
Given the case-control nature of the study and the inherent sources of bias
associated with that study design, detailed information should be included
regarding the control population (ie, were these patients diagnosed with IBS,
Crohn’s disease, ulcerative colitis, other diseases).
The authors should expand on the testing for pathogenic organisms. For
example, the authors list “Campylobacter, Salmonella, Shigella” as the
pathogenic bacterias for which they surveyed. However, there is no mention of
diarrheagenic E. coli or assessment of any potential viral causes of the
gastrointestinal complaints listed. Were these assessed? If not, that should be
mentioned in the limitations.
Discretionary revisions
Analyses for the association between age and Blastocystis spp. similar to those
presented in the last paragraph of the results would enhance the quality of the
paper and provide supporting data that the observed associations are not the
results of uncontrolled confounding.
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-121 (2012)

Reviewer's report
Title:Increased proton pump inhibitor and NSAID exposure in irritable bowel
syndrome: results from a case-control study
Version: 2Date:14 June 2012
Reviewer: Xianrui Wu
Reviewer's report:
The manuscript by Keszthelyi and colleagues aimed to evaluate the association
between exposures of several certain medications and the development of IBS
symptoms in a large-population-sized case-control study. Major finding was that
NSAIDs and PPIs were more frequently used in IBS patients when compared
with controls. A number of issues need to be discussed and clarified.
Major Compulsory Revisions
1. As noted, comorbidities (rheumatic disorders, GERD, ect) were not adjusted in
the study. This raised the question that the relationship between drug use and
development of IBS symptoms might be a reflection of the true association
between underlying comorbidities and IBS. This could be addressed in either of
the following two ways: 1) run the multivariate analysis with comorbidities
included in the model; 2) select the controls by matching for comorbidities with
the IBS patients.
Minor Essential Revisions
2. Several studies, including a recently published systemic review (Ruepert L, et
al. Cochrane Database Syst Rev. 2011;(8):CD003460.), showed that SSRIs use
could improve the IBS related symptoms. While results from this study indicated
that exposure of SSRIs was positively associated with IBS. Wondering whether
the authors can comment on the controversies.
3. Methods, paragraph 4. The authors mentioned that “The control group
consisted of 408 individuals randomly selected from the general population…”.
What method is applied to select the potential controls from the general
populations?
4. Table 1, which statistical analysis was applied to compare age and BMI
between IBS patients and controls? This was not consistent with what was
described in the methods (statistical analysis).
5. Table 3, OR [95% CI] was calculated for different types of drug use. Was this
the result from the univariate analysis or the result after adjusting for other
potential risk factors? This needed to be clarified.
6. Full name needed to be provided when the abbreviation was used for the first
time in the manuscript.
Discretionary Revisions
7. No significant association between drug use and IBS subtype was found in this
study. Do the authors have the data regarding the relationship between drug use
and severity of the IBS related symptoms?
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-121 (2012)

Reviewer's report
Title:Increased proton pump inhibitor and NSAID exposure in irritable bowel
syndrome: results from a case-control study
Version: 2Date:25 June 2012
Reviewer: saurabh mukewar
Reviewer's report:
The authors have conducted an interesting study to compare use of NSAIDs,
PPIs, SSRIs between IBS patients and controls. The authors have concluded
that given nature of the study a causal relationship between exposure of these
medication and development of IBS cannot be established. However, there was
a significant difference between IBS and controls with regards to exposure of
these medications.
I have one major concern regarding criteria used for exposure of medications:
All patients having had at least one prescription for a period of four weeks for a
PPI/NSAID in the 180 days prior to the time of the index visit were considered
exposed – Were the patients included had exposure to PPIs/NSAIDs 6 months
before onset of symptoms or 6 months before the time of visit ? Since diagnosis
of IBS requires, history of 6 months of symptoms and as mentioned by the
authors many patients who were seen were referred to gastroenterologist. These
patients may have been exposed to PPIs/NSAIDs after onset of symptoms.
Authors need to clarify this and clearly state that patients with exposure of these
medications prior to onset of symptoms were included and not prior to their first
visit. Being a tertiary center many patients may have had symptoms for many
months prior to being seen in the clinic.
If patients with use of PPIs/NSAIDs after onset of symptoms were included than
this study merely shows association between IBS, dyspepsia, chronic pain
conditions and medications used for treatment of the same. Based on effects of
NSAIDs and PPIs on gastrointestinal permeability and microflora: a better to
study would be to compare severity of IBS symptoms between IBS patients
taking PPIs/NSAIDs and IBS patients not taking PPIs/NSAIDs.
Other comments:
ABSTRACT
Results: Should add a statement that PPI use was not significantly correlated
after controlling for dyspepsia.
METHODS
“In other cases, diagnosis according to Rome III criteria (symptoms for at
least 6 months) was confirmed using questionnaires sent to patients to assess
symptom duration
following initial symptom onset.” – Unclear what this means. Were these cases
with <6 month history of IBS symptoms.
“The control group consisted of 408 individuals randomly selected from the
general population in
Maastricht, the Netherlands” – Were there 287 controls or 408 controls?
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Review for 10.1186/1471-230X-12-121 (2012)

Reviewer's report
Title:Increased proton pump inhibitor and NSAID exposure in irritable bowel
syndrome: results from a case-control study
Version: 3Date:16 July 2012
Reviewer: Xianrui Wu
Reviewer's report:
Major Compulsory Revisions
I still have some concerns regarding the major revisions. What method was
applied to calculate the corrected OR in the multivariate analysis? What variables
were included into the multivariate model? Why the authors only provide OR
values for the drug use (Table 3)? They also need to give detailed information of
OR values for other adjusted variables, and incorporate them into the “Results”
accordingly.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-121 (2012)

Reviewer's report
Title:Increased proton pump inhibitor and NSAID exposure in irritable bowel
syndrome: results from a case-control study
Version: 3Date:28 July 2012
Reviewer: saurabh mukewar
Reviewer's report:
Addressed issue of duration of exposure prior to onset of symptoms.
Other comments:
ABSTRACT
Results: Should add a statement that PPI use was not significantly correlated
after controlling for dyspepsia. - made necessary changes to abstract.
METHODS
“In other cases, diagnosis according to Rome III criteria (symptoms for at
least 6 months) was confirmed using questionnaires sent to patients to assess
symptom duration
following initial symptom onset.” – Unclear what this means. Were these cases
with <6 month history of IBS symptoms. - addressed
“The control group consisted of 408 individuals randomly selected from the
general population in
Maastricht, the Netherlands” – Were there 287 controls or 408 controls?
- addressed
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Review for 10.1186/1471-230X-12-119 (2012)

Reviewer's report
Title:Macro-AST: Misleading Finding in an Adolescent with MCAD-deficiency
Version: 1Date:26 May 2012
Reviewer: James Leonard
Reviewer's report:
This paper is a short case report.
MCAD deficiency is the most common disorder of fatty acid oxidation and its
management has proved to be straightforward. Complications without symptoms
appear to be rare.
In this paper an adolescent with MCAD was found to have a raised AST. There
are really two points. A raised AST activity may be of no importance and
investigation of asymptomatic patients with MCAD deficiency is rarely indicated.
Abstract - Background: The simple distinction between catabolism and anabolism
is somewhat misleading. There are continuous cycles of anabolism following
meals and catabolism during periods of fasting such as during the night. Patients
with MCAD only become unwell with more prolonged fasting or when is it
combined with another metabolic stress such as an infection.
Abstract - Case presentation: line 6 for ‘rather an unspecific finding’ read ‘rather a
non-specific …’
Abstract - Conclusion: The lesson is not so much that the patient needs to be
seen in a metabolic clinic but rather that the general practitioner needs more
information: best from a specialist.
Case presentation:
An important point is that the patient remained well so that attending a
specialised clinic did not seem necessary. It should be remembered that a
specialist appointment usually means time off school and time off work for the
parents as well as travel costs. What is needed is ready access to information.
Telephone clinics and readily available specialist advice save time and money.
This should be the future, not more clinics.
Conclusion paragraph 1 line 7: ‘during anabolism’ see earlier comment. This
phrase should read ‘when well’
Paragraph 3 line 3: If the acyl carnitines were responsible for macro-AST all
patients with MCAD would have raised AST but they do not.
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-119 (2012)

Reviewer's report
Title:Macro-AST: Misleading Finding in an Adolescent with MCAD-deficiency
Version: 2Date:18 July 2012
Reviewer: James Leonard
Reviewer's report:
The authors have replied to the reviewer's comments satisfactorily
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I have no competing interests
Review for 10.1186/1471-230X-12-119 (2012)

Reviewer's report
Title:Macro-AST: Misleading Finding in an Adolescent with MCAD-deficiency
Version: 2Date:21 July 2012
Reviewer: Terry Derks
Reviewer's report:
From a clinical point of view, this reviewer agrees with the statement of one of
the other reviewers ("An important point ...... not more clinics). Therefore, the
authors cannot conclude "This case illustrates ...... adolescence and adulthood"
(abstract). This statement in the abstract and conclusion should be removed.
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-119 (2012)

Reviewer's report
Title:Macro-AST: Misleading Finding in an Adolescent with MCAD-deficiency
Version: 2Date:27 July 2012
Reviewer: Devin Oglesbee
Reviewer's report:
Dear Authors,
Your manuscript is much improved. I have no additional revision requests.
Congratulations.
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-12-117 (2012)

Reviewer's report
Title:Study of the effects of antivirus therapy in patients with chronic liver
disease due to hepatitis C virus infection
Version: 1Date:25 May 2012
Reviewer: Sohail Muhammad Afzal
Reviewer's report:
Minor Revisions:
The study presented in the manuscript by mubeen et al. showed the importance
of homocysteine as a biomarker for HCV therapy efficacy through comparative
levels of plasma homocysteine before, during and after the therapy along with
other parameters. The manuscript is well written and may be considered for
publication subject to following revisions:
1. It seems that the study is based on multigenotype of HCV, while response to
antiviral therapy differs for each genotype. Therefore, it is suggested that the title
may be revised to highlight the significance of homocysteine as a biomarker for
antiviral therapy efficacy in chronic HCV patients, which is the major emphasis of
the study.
2. The article in based on HCV patients in Pakistan, so it should address HCV
prevalence in Pakistan in ‘introduction’.
3. It should be clear for relapse patients, whether Hcy decreased during therapy
and (increased again after therapy) or the therapy had no effect on Hcy levels?
4. The results showed that the antiviral therapy was effective only for 43%
patients. So the conclusion may be revised to mention the need of other more
efficient drugs with better efficiency. Like direct acting drugs which are under
investigation now a days.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-117 (2012)

Reviewer's report
Title:Study of the effects of antivirus therapy in patients with chronic liver
disease due to hepatitis C virus infection
Version: 1Date:14 June 2012
Reviewer: Irfan Ahmad
Reviewer's report:
In the manuscript of Mustafa et al. entitled Study of the effects of antivirus
therapy in patients with chronic liver disease due to hepatitis C virus infection, the
authors have put an interesting effort to monitor the effect of the gold standard
therapy for the treatment of hepatitis C patients. However I feel some
points/issues can be clarified before it is published.
Major Compulsory Revisions
From Table 2, It seems ALT level in Non res-ponders is low as compare to other
groups before treatment. Is it statistically significant? if yes then what is the
impact of this finding on the consideration to start gold standard therapy to
Hepatitis C patients.
Discretionary Revisions
Authors did not describe the Genotype of Hepatitits C in patients group. Is there
any correlation between Genotype of Hepatitis C virus and response of combined
gold therapy?
Authors did not mention the Hcy levels during the treatment. It could be
interesting to see patent response of hcy during the therapy.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Review for 10.1186/1471-230X-12-118 (2012)

Reviewer's report
Title:Autophagy and apoptosis-related genes in chronic liver disease and
hepatocellular carcinoma
Version: 2Date:7 May 2012
Reviewer: Ying-Hong Shi
Reviewer's report:
The manuscript presented by Kotsafti et al. describes the expression level of
autophagy and apoptosis related genes and proteins in liver tissues and HCC,
furthermore, the high Beclin 1, Bcl-xl and Bad levels in CH and CIRR tissue and
low expressions of those proteins in HCC indicted that an interaction between
autophagy and apoptosis.
Major Compulsory Revisions:
1, The results of expression level of autophagy and apoptosis related genes were
based on the relative small group of 85 patients including CH, CIRR and HCC.
The sample size should be expanded or another independent cohort of similar
patients were needed to validate the correlation.
2, The expression level of Beclin 1, Bcl-xl and Bad (mRNA and protein) in tissue
is not a true indictor of activity of autophagy and apoptosis. Alternative studies
(autophagy and apoptosis activity in cell lines or in vivo study) are mandatory to
demonstrate that conclusions that Beclin 1, Bcl-xl and Bad are down-regulated in
HCC, and higher expression in CH and CIRR.
3, In Figure 3, only two pairs of HCC and PHCC were not convincing to get the
definite results of the protein levels in HCC.
4, In previous published studies, The Bcl-XL is overexpressed in a great
percentage of HCCs (Takehara T, Hepatology 2001; Ding ZB, Cancer Res,
2008). The authors should interpret the reasons of this discrepancy or provide
other data to demonstrate their different result.
Level of interest: An article of limited interest
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-118 (2012)

Reviewer's report
Title:Autophagy and apoptosis-related genes in chronic liver disease and
hepatocellular carcinoma
Version: 3Date:2 July 2012
Reviewer: Muriel Priault
Reviewer's report:
Minor essential revisions:
The authors have convincingly addressed all the concerns raised after the first
review. There are still spelling errors in the material and methods section (1rst
group: 3 femaleS, 2nd group: 2 femaleS, 3rd group: 1 female).
Also, I would recommend that the western blots shown Fig 3 are not cut so close
to the band of interest, notably for Bcl-xL, which undergoes known
post-translational modifications: it seems that depending on the samples, a
slower migrating band appears above the main band. Even if the authors do not
comment on the upper band and do not take it into account in their interpretation,
this visual information is definitely be very valuable for some readers. Please
modify this accordingly.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Review for 10.1186/1471-230X-12-118 (2012)

Reviewer's report
Title:Autophagy and apoptosis-related genes in chronic liver disease and
hepatocellular carcinoma
Version: 3Date:9 July 2012
Reviewer: Ying-Hong Shi
Reviewer's report:
The authors have addressed major concerns in this manuscript and gave some
explaination for confusing data in the disscussion.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests
Review for 10.1186/1471-230X-12-116 (2012)

Reviewer's report
Title:Subgenotype reclassification of genotype B hepatitis B virus
Version: 1Date:24 July 2012
Reviewer: Mahmoudreza pourkarim
Reviewer's report:
Minor Essential Revisions
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Review for 10.1186/1471-230X-12-116 (2012)

Reviewer's report
Title:Subgenotype reclassification of genotype B hepatitis B virus
Version: 1Date:13 August 2012
Reviewer: Samad Amini-Bavil-Olyaee
Reviewer's report:
Shi and coworkers evolutionary reanalyzed all complete HBV genome sequence
genotype B to reconstruct and introduce a novel classification of HBV
subgenotypes B phylogenetically. Their finding is relevant since nine HBV
subgenotypes B had been reported worldwide without a conclusive analysis.
They showed that HBV subgenotypes B5, B6’, B3, B7, B9, B8 and Bx do not
meet subgenotypes definitions according to Pourkarim et al’s HBV
subgenotyping roles. They then classified those isolates as
quasi-subgenotype-B3. I have only some concerns that should be addressed to
improve their work:
1- Tables 1 and 2 should be mixed together (as Table 1) and also all mean
nucleotides distance should be presented as “percentage ± SD” that it makes all
variables constant within the manuscript. Therefore, SD from upper part of each
table should be removed and is brought up in front of each variable.
2- The authors should add a new table (Table 3) to present the comparison of
mean nucleotide divergence (percentage ± SD) of B1, B2, QSB3, B4 and B5
(previous B6).
3- Please edit “quasi-genotype B3” to “quasi-subgenotype B3” in the entire
manuscript.
4- Table 3 should be renamed to Table 2 and all data should be presented as
mean percentage ± SD, and all SD should be removed.
5- Please define a cut-off value for the bootstrap numbers in the trees. I would
recommend 45% as cut-off and vanish all values below 45% in trees.
6- If the authors really want to follow Pourkarim at al (Ref 25) roles, then they
should remove all recombinant strains from all analysis. I would suggest that. Of
course the authors mentioned that all B2 are recombinant, I am wondering that
all 655 isolates are recombinant or not. If few of them are recombinant, so they
can be excluded from analyses.
7- Please check that whether isolates EU660226 and GQ377595 and Bx isolates
are recombinant or not (using BootScan analysis); if so, please remove them
form trees and analysis.
8- Please add scale bar for trees.
9- Please add this references to the manuscript. Pourkarim et al. HBV
subgenotype misclassification expands quasi-subgenotype A3, CMI;17(6):947-9.
Note to AE: I would suggest “Minor Revision”.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-115 (2012)

Reviewer's report
Title:The effect of sulindac, a non-steroidal anti-inflammatory drug, attenuates
inflammation and fibrosis in a mouse model of chronic pancreatitis
Version: 5Date:7 July 2012
Reviewer: Jan D'Haese
Reviewer's report:
The authors have sufficiently changed the criticized issues. I therefore suggest to
accept the current manuscript without further revisions.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-115 (2012)

Reviewer's report
Title:The effect of sulindac, a non-steroidal anti-inflammatory drug, attenuates
inflammation and fibrosis in a mouse model of chronic pancreatitis
Version: 5Date:17 July 2012
Reviewer: Matthias Sendler
Reviewer's report:
The authors change the discussion in a way to explain their result more in the
context to chronic pancreatitis, this makes the paper more conclusive. They can
show a direct effect of sulindac on fibrosis development and the general immune
response. The paper is well written and sounds fine.
The question are mainly answered by the authors, they can show an effect of
sulindac on the activation of stellate cells by the activation marker alpha SMA
which is one of the key mechanisms in fibrogenesis. The influence of sulindac on
the immune regulation could be shown by real-time PCR as well as in western
blot analysis.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-114 (2012)

Reviewer's report
Title:Obesity and diabetes mellitus and/or hyperlipidaemia are independent risk
factors for pre-transplant portal venous thrombosis in liver recipients
Version: 3Date:29 April 2012
Reviewer: aurelie plessier
Reviewer's report:
The authors report the incidence and risk factors for portal vein thrombosis in
patients with cirrhosis prior to liver transplantation. Obesity and diabetes or
hyperlipidemia are significantly associated to PVT in multivariate analysis. This is
an interesting manuscript although minor essential revisions are needed.
1. Number of JAK 2 mutation screening is not clearly reported.
2. Thrombophilia screening seems to be missing (65 out of 89 in the thrombotic
group and 228 out of 376 in the non thrombotic group). Indeed study population
is said to be of 293 men and 144 women. But it seems that only 290 were
screened. This is not very clear and should be clarified in paragraph recipients p
4. Other form aspects should be corrected
3. What explanation can be given as to the "protective effect" of nephrotic
syndrome and smoking which are inversely associated to the absence of
thrombotic event
Level of interest: An article of outstanding merit and interest in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests below
Review for 10.1186/1471-230X-12-114 (2012)

Reviewer's report
Title:Obesity and diabetes mellitus and/or hyperlipidaemia are independent risk
factors for pre-transplant portal venous thrombosis in liver recipients
Version: 4Date:27 June 2012
Reviewer: massimo primignani
Reviewer's report:
In this revised manuscript I have just few questions/ suggestions. The main
refers to the title of the study: since at multivariate analysis the only variable
associated with pre-transplant PVT was obesity I suggest to modify the title,
quitting diabetes and/or high lipid., as follows : "Obesity is an independent risk
factor for pre-transplant PVT in liver recipients" .
This relevant point should be more emphasized in the discussion. Moreover,
since diabetes and/or high lipid values loose their signifcance at multivariate
analysis, I suggest to taper any other conclusion ragarding this point. tAs far as
genetic thrombophilia is concerned, the fact that the rate of FV Leiden and
Prothrombin gene mutation in the study population coincide with the rate
observed in the general population proves that genetic thrombophilia has no role
in pre-transplant PVT in cirrhosis. This is an important point and should be more
emphasized
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-12-113 (2012)

Reviewer's report
Title:Cholecystomucoclasis: Revaluation of Safety and Validity in the Aged
Population
Version: 2Date:24 March 2012
Reviewer: Theodoros Pavlidis
Reviewer's report:
Rejection
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-113 (2012)

Reviewer's report
Title:Cholecystomucoclasis: Revaluation of Safety and Validity in the Aged
Population
Version: 2Date:20 May 2012
Reviewer: luca antonio aldrighetti
Reviewer's report:
Major Compulsory Revisions
I believe that this is a retrospective study where patients were enrolled to
Cholecystomucoclasis or standard cholecystectomy on the basis of
intraoperative findings. There is therefore a selection bias but I think that this is
consistent with the aim of he study (to understand if Cholecystomucoclasis may
be offered in complex cases instead of cholecystectomy) so it doesn't damage
the value of the paper
Minor Essential Revision
I would suggest the authors to discuss the role of ERCP in treating biliary fistula
in patients treated both by standard cholecystectomy and Cholecystomucoclasis
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Review for 10.1186/1471-230X-12-112 (2012)

Reviewer's report
Title:The Effect of Hospital Volume on Patient Outcomes in Severe Acute
Pancreatitis
Version: 3Date:25 April 2012
Reviewer: Atsuhiko Murata
Reviewer's report:
Authors investigated the hospital volume-outcome relationship in patients with
severe acute pancreatitis based on the Taiwan National Health Insurance
Research Database. They found that increasing hospital volume was associated
with a reduced risk of hospital mortality after adjusting for patient and hospital
characteristics while the volume effect on hospital mortality disappeared after
adjusting for treatment covariates. They concluded that these findings support
volume-based selective referral for patients with severe acute pancreatitis and
suggest that differences in levels or processes of care across hospitals may have
contributed to the volume effect.
I think that this paper is well-designed and well-written. However, some revisions
are required. Please consider the following points.
Major compulsory revisions
1. Authors found that there was a significant association between hospital
volume and the mortality of patients with severe acute pancreatitis in Model 1
(taking account into the patient and hospital characteristics). However, the
volume effect disappeared in Model 2 (taking account into not only patient and
hospital characteristics but also selected treatments such as cholecystectomy or
life-support measures). This finding is very interesting and highly suggestive.
Authors should describe the reasons why the volume effect on hospital mortality
disappeared after adjusting for treatment covariates, as well as comparisons with
the previous papers. Please clarify the mechanism of these results.
2. There is very little description of the hospital length of stay (LOS) or hospital
charges in the Discussion. While there was a significant association between
hospital volume and LOS, the hospital volume was not independent factor for
hospital charge in both Model 1 and 2. Why hospital volume did not affect
hospital charge in this study?
3. How the results of this study influence the treatments for severe acute
pancreatitis in Taiwan? In order to explain the importance of this study for severe
acute pancreatitis, it is necessary for authors to describe the health policy and
future research for the treatments of severe acute pancreatitis in Taiwan.
Minor essential revisions
1. What is the meaning of excluding the patients in the 1990’s?
2. There are three kinds of hospital ownership in Table 1. What does the
hospitals without profiting mean?
Discretionary revisions
1. Authors had better use lower case letters in the title of reference 5. (Effect of
hospital volume on clinical outcomes########)
2. In Table 3, the column of hospital volume has been partly obscured.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-112 (2012)

Reviewer's report
Title:The Effect of Hospital Volume on Patient Outcomes in Severe Acute
Pancreatitis
Version: 6Date:20 June 2012
Reviewer: Atsuhiko Murata
Reviewer's report:
I think that this manuscript does not require further revision.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Review for 10.1186/1471-230X-12-112 (2012)

Reviewer's report
Title:The Effect of Hospital Volume on Patient Outcomes in Severe Acute
Pancreatitis
Version: 6Date:7 July 2012
Reviewer: Gilaad Kaplan
Reviewer's report:
The authors have adequately addressed the reviewer commments.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
No competing interests.
Review for 10.1186/1471-230X-12-109 (2012)

Reviewer's report
Title:Longitudinal fluctuations in PD1 and PD-L1 expression in association with
changes in anti-viral immune response in chronic hepatitis B
Version: 1Date:29 March 2012
Reviewer: Frank Tacke
Reviewer's report:
This is an interesting and concisely written article on fluctuating levels of PD1
and PDL1 in patients chronically infected by hepatitis B virus. My major concern
is that many studies have investigated on this topic before, thus limiting the
novelty of the article. Moreover, the findings in this paper are mainly
observational.
Specific concerns are (all major compulsory revisions):
1. Figures 1 and 2 need quantitative evaluations (data partially presented in
Figure 6), and it is important to also back-calculate to the total number of cells.
Statistical significant differences need to be indicated in the figure. The legend is
misleading - these are not 15 independent experiments, but 15 individual patient
samples.
2. It is important to comprehensively analyze PD1 and PDL1 expression from
livers in a quantitative manner. Numbers of positive cells and the expression
level (minimally extracted from qPCR data) need to be given.
3. The relevance and the specificity of the findings remain obscure. Thus, I
believe it is crucial to have two additional control populations, at least for
circulating cells: HCV-infected patients and NASH patients, both groups matched
for the fibrosis stage as assessed by histology.
4. Findings on PD1 and PDL1 should be correlated to disease stage not only
based on serum levels (ALT, HBV-DNA), but also based on histology (staging,
grading).
5. The authors need to point out more clearly what the key point of the paper is.
This would somewhat overcome the limited novelty of the study.
Minor essential revisions:
6. Presentation of FACS data is not optimal. Labeling of the axes is difficult to
read.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-109 (2012)

Reviewer's report
Title:Longitudinal fluctuations in PD1 and PD-L1 expression in association with
changes in anti-viral immune response in chronic hepatitis B
Version: 1Date:17 April 2012
Reviewer: Christoph Jochum
Reviewer's report:
The paper is reasonably well written and contributes to the field.
However there a few comments to make:
1. The recruiting of the patients is not clearly described. As I understood the
patients were recruited in the onset of an acute inflammatory phase . Were the
patients recruited retrospectively or prospectively? were there patients who were
recrited but did not develop a severe inflammation. Were patients known
chronically infected patients oe were there patients with an acute hepatitis B
included?
This should be clarified, how exactly the patients were recruited.
2. It is not clear from which material the RT-PCR was made. In paragraph 6 of
the method section it is stated that total RNA was isolated from tumor and liver
tissue. What tumor tissue? Did the patients have an HCC? Please clarify from
which cells the total mRNA was obtained.
3.The authors stated, that PD! level returned to normal in T4 the questions is
what is normal, is normal the level before the flare or is normal the values of a
normal healthy population. this should be clarified.
4. Minor Comment: the units of quantitative HBsAg and serum ALT should be
mentioned in the Table 1(?).
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-12-109 (2012)

Reviewer's report
Title:Longitudinal fluctuations in PD1 and PD-L1 expression in association with
changes in anti-viral immune response in chronic hepatitis B
Version: 3Date:29 May 2012
Reviewer: Frank Tacke
Reviewer's report:
The authors have addressed most of my comments. The manuscript should now
edited for language and grammar by a native speaker.
Level of interest: An article of importance in its field
Quality of written English: Not suitable for publication unless extensively edited
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-12-109 (2012)

Reviewer's report
Title:Longitudinal fluctuations in PD1 and PD-L1 expression in association with
changes in anti-viral immune response in chronic hepatitis B
Version: 3Date:10 June 2012
Reviewer: Christoph Neumann-Haefelin
Reviewer's report:
Major compulsory revisions:
The authors addressed my previous major comments 2+3 satisfactorily, however,
comment 1 was not addressed adequately. I still doubt that figure 1 shows any
pentamer-positive response. A true positive pentamer response is displayed in
Fig. 3B. A suggested in the previous comments, the authors really need to
display a) background staining without pentamer and b) pentamer control
stainings from healthy controls.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.