JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-02782-8 (2023)

Title: Severe Combined Immunodeficiency: Improved survival leading to detection of
underlying liver disease
Version: 3 Date: 30 Dec 2022
Reviewer's report:
I find merit in the present study.
Non immunological effects of ADA SCID represent important aspects in the clinical evaluation
and management of the patients and also in assessing post-therapy life expectancy. Even if the
study presents a small cohort evaluation due to the rarity of pathology, the authors conclusions
are well detailed and convincing.
In my opinion it could be accepted for publication on BMC Gastroenterology with just minor
correction
Correct the sentence pag 15 line 11 “inactivated S-adenosylhomocysteine hydrolase (SAH)
enzyme causing…”
Review for 10.1186/s12876-023-02782-8 (2023)

Title: Severe Combined Immunodeficiency: Improved survival leading to detection of
underlying liver disease
Version: 9 Date: 10 Apr 2023
Reviewer's report:
The study evaluates a small patient cohort but this is essentially due to the rarity of the pathology
and to the wide spectrum of the ADA deficiency phenotype. In my experience the authors’
conclusions are well detailed and convincing. The quality of this paper has been improved within
the second revision and it represents an interesting evaluation of the non-immunological aspects
of the pathology from which the scientific community could benefit. I my opinion it is suitable
for publication on BMC Gastroenterology
Review for 10.1186/s12876-023-02807-2 (2023)

Title: Trend analysis of Hepatitis B and C among patients visiting health facility of Tigrai,
Ethiopia, 2014-2019
Version: 1 Date: 31 Mar 2023
Reviewer's report:
General comments
The paper is technically and statistical analysis of the data sounds good and the claims are fully
supported by the experimental data. The availability of data adheres to the expected standards of
our research community. Also, the claims are appropriately discussed in the context of previous
literature. However, the author must address the following comments to make the manuscript
potentially suitable for publication.
1. The laboratory test method for screening HBV and HCV infection and the performance
(sensitivity and specificity) of the test method are not presented method section. The authors
should say something about it.
2. If the rapid diagnostic kits for screening HBV and HCV are used, the strength and limitations
of the kits must be stated.
3. In the conclusion section, the author recommended “dental extraction should be practiced in
health institutions” is it your objective? Did you assess dental extraction as a factor for infection?
Your conclusions and recommendations are not in line. So it needs some revision.
Review for 10.1186/s12876-023-02803-6 (2023)

Title: Changes in the salivary metabolome in patients with chronic erosive gastritis
Version: 2 Date: 21 Oct 2022
Reviewer's report:
The manuscript by Liu et al. entitled: ”Changes of salivary metabolomics in patients with
chronic erosive gastritis” describes the application of RP and HILIC-LC-MS based untargeted
metabolomics to study metabolic signature of CEG disease. In my opinion, besides the effort
made by Authors, the manuscript should not be accepted for publication in the current version.
The major issues that should be considered before manuscript resubmission have been listed
below:
1. The main drawback of this study is a lack of proper metabolite identification. The metabolite
identification is based only on searching through HMDB database. This is only putative
identification only based on monoisotopic masses. At least MS/MS fragmentation spectra should
be provided according to Metabolomics Standards Initiative (MSI) criteria. Without at least
such confirmation of metabolite identities is not possible to make any proper biochemical
interpretation and conclusions of the study.
2. In the manuscript the term metabonomics has appeared mainly in the discussion section.
Please clarify it, because based on the tittle and methodology described in the manuscript, the
metabolomics approach was applied. These definitions are not the same.
3. Please describe more details about procedure used for saliva samples preparation, especially
the volume of reagents and sample used. There is an information: “take an appropriate amount
of sample, add precooled methanol / acetonitrile / aqueous solution (2:2:1, V / V)…”. It is not
useful to repeat the procedure in other studies.
4. Have any other normalization strategy been tested for the raw data?
5. For calculation of p-value the multiple testing for p-value correction should be applied, such
as FDR procedure.
6. For PCA plots there is a lack of explanation of CT-CEG and CT-N groups
7. In the Table with metabolite annotation data please provide which were detected by RP and
HILIC mode, respectively. It will be worthy to include also measured mass, RT, fragmentation
spectra, ionization mode for each potential metabolite.
8. There are many language errors in the manuscript. The text of the manuscript should be
inspected, corrected  and revised before resubmission.
Review for 10.1186/s12876-023-02803-6 (2023)

Title: Changes in the salivary metabolome in patients with chronic erosive gastritis
Version: 2 Date: 01 Dec 2022
Reviewer's report:
Several places English is very poor and difficult to understand. Too much variables are coming
as outcome and these variables are having no any sense. Instead of revealing several useless
variables, the study should come out with 2 or 3 major contributory variables. There is some
problem in KEGG pathways analysis. It is not correct.
Review for 10.1186/s12876-023-02803-6 (2023)

Title: Changes in the salivary metabolome in patients with chronic erosive gastritis
Version: 2 Date: 05 Jan 2023
Reviewer's report:
The authors have applied various statistical tests to screen potential biomarkers that can identify
diseases from saliva samples of CEG patients using metabolomics.
I do not have any major concerns except one.
My only concern is that the method part does not address the issue of imbalanced class design.
Please refer to Section 3 (Results).
“Among 64 patients in this study, there were 31 females and 33 males with an average age of
49.64 ± 6.80 years old. Among the 30 participants in the healthy control group, there were 14
males and 16 females”...where the study has 31 females and 33 males out of n=64. In the next
step among the healthy control participants, 14 were males and 16 females.
This is a balanced class design which might create bias towards a particular set of findings,
for example, important/potential predictors in saliva of CEG patients.  Since, the authors are
using  Receiver operating characteristic (ROC) to determine potential predictors in saliva of
CEG patients, I would like to check if there are significant differences (or no difference) in
identifying the potential predictors when there is an imbalanced class.
Imbalance class example: out of n=64 patients, 10 are males and 54 are females. Subsequently,
out of 30 healthy control participants- 5 females and 25 males.
Review for 10.1186/s12876-023-02803-6 (2023)

Title: Changes in the salivary metabolome in patients with chronic erosive gastritis
Version: 4 Date: 06 Mar 2023
Reviewer's report:
I would like to thank for time and effort spent by Authors to improve quality of the manuscript.
I have still some issues that should be addressed in the revised manuscript.
1. Which internal standard was used for saliva samples preparation procedure?
2. Why this internal standard was not considered for data normalization instead of total ion
signal approach?
3. Please provide fragmentation spectra which were used for metabolite identification displayed
in Supplementary Table 1
Review for 10.1186/s12876-023-02815-2 (2023)

Reviewer’s report
Title:  Glucose metabolic upregulation via phosphorylation of S6 ribosomal protein affects tumor
progression in distal cholangiocarcinoma
Version: 2 Date: 26 Apr 2023
Reviewer's report:
No further comments.
Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of this
manuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If
your reply is yes to any, please give details below.
'I declare that I have no competing interests'
Reviewer Publication Consent . I agree for my report to be made available under an Open Access
Creative Commons CC-BY License ( http://creativecommons.org/licenses/by/4.0 ) if this manuscript is
accepted for publication. Any comments that I do not wish to be included in the published report have
been included as confidential comments to the editor, which will not be published. If you are not happy
for us to publish this report, please contact the editorial office before completing the review. If you
wish, you can include your name in your published report. Please note you must decide whether to
include your name at the start of the process and confirm this decision whenever prompted. If you
change your decision later, we will not be able to publish your name.
I agree to the terms of the CC-BY 4.0 license; please do not publish my name with my report. (default)
Is the study design appropriate to answer the research question (including the use of appropriate
controls), and are the conclusions supported by the evidence presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are  the  images  in  this  manuscript  (including  electrophoretic  gels  and  blots)  free  from  apparent
manipulation?
Yes
Review for 10.1186/s12876-023-02800-9 (2023)

Title: Postoperative serum interleukin-6 levels correlate with survival in stage I-III colorectal
cancer
Version: 2 Date: 04 Apr 2023
Reviewer's report:
Very interesting study. My comments:
1) The authors should comment also on other inflammatory-based potential biomarkers in CRC
patients, such as lymphocyte-monocyte ratio
2) English grammar should be improved
3) Regression figures (scatter plots) are low quality....please upload better images
4) Please add number at risk to KM survival curves
5) The authors should comment on the potential implications of their findings also on colorectal
adenomas, citing the recent paper PMID: 27005802
Review for 10.1186/s12876-023-02800-9 (2023)

Title: Postoperative serum interleukin-6 levels correlate with survival in stage I-III colorectal
cancer
Version: 2 Date: 05 Apr 2023
Reviewer's report:
1. This is a good study, but it includes few indicators.
2. There are many factors related to the survival time of patients with colorectal cancer
after surgery. This includes preoperative nutritional status, underlying diseases, and whether
accelerated recovery was taken after surgery. The author simply takes part of inflammatory
mediators as the evaluation of postoperative survival of patients, which is not scientific and
innovative enough.
3. As a survival study, it is recommended to include more subjects.
4. I hope the author can be more rigorous in statistical treatment and choose more accurate
statistical methods.
Review for 10.1186/s12876-023-02800-9 (2023)

Title: Postoperative serum interleukin-6 levels correlate with survival in stage I-III colorectal
cancer
Version: 2 Date: 08 Apr 2023
Reviewer's report:
This is a novel and  important study to identify relationship between postoperative IL-6 and
CRC patients outcome. Some comments and questions about the study:
1. As an potential way to verify the effect  of high IL-6 levels to poor prognosis, the  measurement
and calculation formula of absolute lymphocyte counts should be revealed in Materials and
methods.
2. As mentioned in  discussion, PCT and CRP would be more useful in predicting infective
complications rather than tumor recurrance and survival. Meanwhile, as a promosing and  rising
prognosis  factor in several cancers, neutrophil to lymphocyte ratio (NLR) might be  crucial to
analyze and compare  with IL-6 levels in your research.
3.  In your article, what is the median day  post-operative for measuring value of CRP, PCT and
IL-6 levels?  (3d, 7d, 2w, or 3m)
4. The strength of this article was revealing  the  impact of  post-operative serum IL-6 rather
than PCT and CRP level to poor  prognosis  in CRC patients; However, it may be interesting to
compare  the preoperative level of  CRP and PCT level in  low or high IL-6 subgroups (Table1.)
and the prognosis significance in Kaplan#Meier analysis.
5.  Page 3,  Method, Enrollment of patients,  Please check the list number 4. and 5.  in exclusion
criteria .(4#3, 5#4).
6. Figure 2. Correlation of postoperative IL-6 level etc.... Please check the postoperative within
1 week (A).
Review for 10.1186/s12876-023-02800-9 (2023)

Title: Postoperative serum interleukin-6 levels correlate with survival in stage I-III colorectal
cancer
Version: 3 Date: 27 Apr 2023
Reviewer's report:
This is an excellent paper. We evaluated the prognosis of patients with colorectal cancer using
simple, readily available indicators. The overall design of the study is reasonable and the results
are credible. The conclusion of this study has a good guiding significance for simplifying
prognostic evaluation indicators or models of cancer patients. It is suggested that the authors
continue to extend the follow-up time to further optimize the prediction threshold of IL-6.
Review for 10.1186/s12876-023-02702-w (2023)

Title: Effectiveness of betadine-coating gastrostomy tube to reduce peristomal infection after
percutaneous endoscopic gastrostomy: a randomized controlled trial
Version: 3 Date: 07 Jan 2023
Reviewer:  Anna Cominardi
Reviewer's report:
The work is about a relatively new topic and it's well-written.
Although betadine coating gastrostomy tube method doesn't reduce peristomal infection after
PEG, the study underlines the importance of 24-h delta CRP as predictor of peristomal wound
infection and all-cause infection within 14 days after PEG. We could easily use it in daily practice
since it is low-cost and routinely performed.
The study design is exhaustively described.
I have only some concerns:
- line 47: best cut-off point instead of points
- line 249-250: "Delta WBC, CRP, and hospitalization days were associated with higher all-
cause infection rates in univariable analysis..". I don't understand why you cite also delta WBC
since in the univariate analysis reported in table 3 the P value for delta WBC isn't statistically
significant (0.061).
SInce oral microbes represent most of the peristomal infection after PEG you can add some
suggestions in your text to overcome this (e.g. use of different antibiotics,...).
Review for 10.1186/s12876-023-02702-w (2023)

Title: Effectiveness of betadine-coating gastrostomy tube to reduce peristomal infection after
percutaneous endoscopic gastrostomy: a randomized controlled trial
Version: 3 Date: 14 Jan 2023
Reviewer:  Michael Wilsey
Reviewer's report:
This is a randomized controlled trial to test the effectiveness of a povidone-iodine-coating
gastrostomy tube to reduce peristomal infection after percutaneous endoscopic gastrostomy.
This is the first study to assess the efficacy of Betadine coating for preventing PEG peristomal
infection. The paper’s premise is interesting and novel in the field of GI.  The methods and study
design are clear. The title properly reflects the subject of the paper, the paper seems appropriate,
and the key messages are short, accurate, and clear.
A few comments:
1.  Was a power analysis performed to detect differences in infection rates based on other
peristomal infection studies?
2.  Some centers use topical Betadine ointment application after PEG tube placement.  Based on
the current findings, would the authors consider commenting on evidence in the literature and
the potential utility of this intervention?
3. I wonder if the authors would consider their RCT a pilot study, as it is limited by a small sample
size, as a prelude to an appropriately powered study focusing on the efficacy of a povidone-
iodine coating gastrostomy tube to reduce peristomal infection rates.
Review for 10.1186/s12876-023-02789-1 (2023)

Title: Branched-chain Amino Acids Supplementation Improves Liver Frailty Index in Frail
Compensated Cirrhotic Patients: A Randomized Controlled Trial
Version: 2 Date: 03 Mar 2023
Reviewer's report:
This is a 16-week, single center randomized trial of BCAA supplementation (twice daily) - 26
g of protein among patients with frailty and cirrhosis. LFI decreased by 0.36 points vs. 0.14
in intervention vs. control. There was a 4-week run  in period with counseling and exercise
recommendations for both groups.
The patients were largely child A and some were child C. The proportion of frailty reversion
was about 1/3 in intervention and none in the control group.
Quality of life (physical and mental) improved in the BCAA group and not in the  control group.
Frailty reversion is important and protein supplementation has potential to combat frailty and
reverse sarcopenia. The methods are clear and the manuscript is well-written.
My main questions are :
1. It is difficult to believe that there would be some many patients who are currently frail and
without recent decompensations. When was frailty measured? How many patients ruled out
the study  for not meeting frailty criteria? This should be included in the CONSORT diagram.
It seems that most of the patient met frailty criteria due to concomitant cirrhosis and older
age, but non on the  basis of decompensation. I am willing to accept this, but please provide
more information on how many were not candidates due to decompensations and due to lack
of meeting frailty criteria.
2. How was body composition measured? BIA is only mentioned in the discussion. This should
also be in the methods.
3. Beyond 2-week monitoring and BCAA, did the intervention group receive any other
counseling?
4. Figure 2 is a bit confusing to interpret. The Figure legends should clearly specify what is
shown in  each panel.
5. Discussion should specify that the findings do not apply to patients with decompensated
cirrhosis (if i am reading the exclusion criteria correctly). Future studies should evaluate
BCAA for decompensated cirrhosis and also compared BCAA to standard dietary protein
supplementation (nighttime snack).
Review for 10.1186/s12876-023-02789-1 (2023)

Title: Branched-chain Amino Acids Supplementation Improves Liver Frailty Index in Frail
Compensated Cirrhotic Patients: A Randomized Controlled Trial
Version: 2 Date: 26 Mar 2023
Reviewer's report:
This open-labeled randomized controlled trial was conducted to evaluate the efficacy of 16
weeks of branched-chain amino acids (BCAA) supplementation for cirrhotic patients with
frailty, defined by liver frailty index (LFI) #4.5. A total of 54 patients (Child-Pugh, class
A 68.5% and class B, 31.5%) were randomly assigned in a 1:1 ratio to receive twice daily
BCAAs supplementation (210 kcal, protein 13.5 g, BCAA 2.03 g) versus no nutritional
supplementation for 16 weeks. The authors found that the proportion of frailty reversion at week
16 was significantly higher in the BCAA group compared to the control group (36% vs. 0%).
They concluded that a 16-week BCAA supplementation improved frailty in frail compensated
cirrhotic patients. This manuscript is well-written and provides insights into the management of
cirrhotic patients. I had some suggestions that would help clarify this study.
1. What specific treatments are available for certain liver diseases, such as alcoholism and
chronic viral hepatitis infection? These management practices may have an impact on the
outcome of this study.
2. To compare changes over the 16 weeks of intervention, repeated-measures ANOVA should
be used, with the outcomes assessed in the study as the dependent variable and time, study group,
and time-by-group interaction as the independent variables.
3. For a small sample size, the absolute changes (delta) in clinical and laboratory parameters at
baseline and week 16 are clinically insignificant. To compare the differences between the two
groups, a non-parametric test should be used.
4. The compliance data for each arm should be provided in the results section.
5. Given that there was an improvement in BMI and serum albumin with BBCA supplementation
compared to control, it is unclear why no improvement in SMI was observed between the BCAA
and control groups.
6. Since the nutritional formula used in the interventional arm of the study contains calories
from carbohydrates, fat, and BBCA as a protein source, it is difficult to determine whether the
positive effects of the study intervention are attributable to BBCA supplementation or nutritional
improvement. This should be emphasized in the study's limitations.
Review for 10.1186/s12876-023-02789-1 (2023)

Title: Branched-chain Amino Acids Supplementation Improves Liver Frailty Index in Frail
Compensated Cirrhotic Patients: A Randomized Controlled Trial
Version: 3 Date: 09 Apr 2023
Reviewer's report:
All of my comments were appropriately addressed by the authors.
Review for 10.1186/s12876-023-02789-1 (2023)

Title: Branched-chain Amino Acids Supplementation Improves Liver Frailty Index in Frail
Compensated Cirrhotic Patients: A Randomized Controlled Trial
Version: 3 Date: 25 Apr 2023
Reviewer's report:
My comments were addressed.
There is a small typo in  Table 3 title, "BCCA" instead of BCAA
Review for 10.1186/s12876-023-02765-9 (2023)

Title: The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric
cancer with MSS
Version: 0 Date: 30 Jun 2022
Reviewer:  Xiaojing Chang
Reviewer's report:
The authors analyzed and evaluated the role of TFB and its correlation with tumor immunity,
gene mutation characteristics, immunological and clinical characteristics of patients in MSS
and non-EBV (+) gastric cancer using data from TCGA-stomach adenocarcinoma (STAD)
cohort. The data and figures showed here are interesting and meaningful. But, there are many
orthographic errors through the manuscript.
1. In Fig 2, authors should add the caption of “***”.
2. How about the PFS and or DFS and the profiles combined with chemotherapy between TFB-
low group and TFB-high group.
Review for 10.1186/s12876-023-02765-9 (2023)

Title: The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric
cancer with MSS
Version: 0 Date: 05 Jul 2022
Reviewer's report:
In this study, Zhu et al. made use of the TCGA gastric cancer dataset to investigate the clinical
significance of tumor fusion burdens. There are some major concerns regarding the methods
and data presented.
The word ‘excellent’ in the title sounds weird. Results from this study did not support the
conclusion. The better ‘immunogenicity’ of low-TFB patients as compared with those with high-
TFB was just a prediction based on gene expression profiles of immune markers. Regarding
prognosis, the data actually showed no significant difference.
The methods section just mentioned ‘methods as in previous reports’ or ‘data collected from
published studies’ with references. This is not acceptable. Methods should be described in detail
and data should be provided in a supplemental dataset.
It seems this study focused on gastric cancer patients who were non-EBV(+) and MSS, fulfilling
both. However, in the analyses, data were on either non-EBV(+) or MSS patients, which was
quite confusing. Why did Fig 1D focus on non-EBV(+) only?
Fig 6B&D, the comparisons of 2-year or 3-year survival rates were not rigorous.
What does it mean by ‘The patients were categorized as TFB-high or TFB-low group according
to the upper quartile of TFB values in the entire cohort.’? 25% are TFB-high and the remaining
are TFB-low#then why were there 61 vs 172 patients (totaling 233)?
Any specific gene fusion events are of clinical significance in this cohort?
There are more than 319 gastric cancer cases in TCGA. More cases should be included in the
analysis.
Review for 10.1186/s12876-023-02765-9 (2023)

Title: The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric
cancer with MSS
Version: 0 Date: 28 Jul 2022
Reviewer:  Zhixue Zheng
Reviewer's report:
Thank you for letting me review your manuscript. The manuscript makes a good effort to
analysis the relationship between tumor fusion burden and non-EBV(+) gastric cancer with MSS
by using the online database TCGA, but I do have some comments: 1) There are numerous
typos in the article which needs re-reading and improving spelling and grammar for easier to
understand; 2) Why you choose the non-EBV(+) GC patients for analysis? You should give some
reasons; 3) The vertical coordinate of Fig.2 D is inconsistent with the notes; 4) The Discussion
section needs to be carefully revised to make it more closely related to the theme.
Review for 10.1186/s12876-023-02765-9 (2023)

Title: The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric
cancer with MSS
Version: 1 Date: 15 Jan 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
No - there are major issues
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
No - there are major issues
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
No - there are major issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are major issues
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
No - manuscript has some fundamental flaw(s)
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors performed meta-analysis of publicly available NGS
data top assess relation of tumor fusion burden to tumor immunogenicity and molecular
characteristics of gastric cancer. The manuscript still needs extensive modifications before
further consideration. The structure of the paper is confusing and should be better structured,
in particular Materials and Methods section. It is also not clear what specific outcome and
significance in the field this report brings. As this is a purely computational analysis, some kind
of experimental validation of in silico results should be implemented. Further, the text is difficult
to read and should be improved by English editing service.
REQUESTED REVISIONS:
The structure of the paper is confusing and should be better structured, in particular Materials
and Methods section. It is also not clear what specific outcome and significance in the field this
report brings. As this is a purely computational analysis, some kind of experimental validation
of in silico results should be implemented. Further, the text is difficult to read and should be
improved by English editing service.
ADDITIONAL REQUESTS/SUGGESTIONS:
The Materials and Methods section needs to be revised and it is not clear what specific outcome
and significance in the field this report brings. "
Review for 10.1186/s12876-023-02765-9 (2023)

Title: The characteristics and clinical relevance of tumor fusion burden in non-EBV (+) gastric
cancer with MSS
Version: 2 Date: 30 Mar 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors adequately addressed my comments and revised their
manuscript accordingly."
Review for 10.1186/s12876-023-02781-9 (2023)

Title: Angiotensin Receptor Blockers Might be Protective against Hepatic Steatosis after Liver
Transplantation
Version: 2 Date: 27 Nov 2022
Reviewer's report:
This work provided novel clinical data regarding the effect of ARBs in the development of
NAFLD in liver transplant recipients. The study type chosen (case-control) as well as the
assessment of steatosis via ultrasounds were plausible methods to answer the research question.
The team had a reasonable sample size (N = >30) of liver transplant recipients from a single
center and had access to blood profiles for the patients who were followed in the outpatient clinic.
A major limitation of this study was the lack of health parameter information (BMI, past medical
history, pre transplant biopsy, lipid panel) of the liver donors, as well as the year in which the
team started following up the transplant patients (only end date was noted). The study would
also be bolstered if there were data regarding the level of compliance (consistency, doses missed,
etc.) in ARB therapy in the outpatient clinic.
It would be interesting to test the effect of each ARB and not the entire class. In this study
valsartan was group together with losartan despite these two having different half-lives in the
body.
The investigators should also explore the effect of ACE inhibitors and the incidence rate of
NAFLD since these types of drugs act on the same cascade as ARBs.
Figures 1 and 2 were missing a y-axis label, these should be added for further clarity.
Table 2 suggests that exposure to ARBs renders patients almost three times more likely to
develop NAFLD, flipping the odds-ratio values is suggested for more clarity and consistency
with the rest of the paper.
Review for 10.1186/s12876-023-02776-6 (2023)

Title: The m6A/m5C/m1A regulator genes Signature Reveals The Prognosis and Related with
Immune Microenvironment for Hepatocellular Carcinoma
Version: 3 Date: 10 Feb 2023
Reviewer's report:
The paper named “Construction of a prognostic model for N6-Methyladenosine(m6A), 5-
Methylcytosine(m5C), N1-methyladenosine(m1A)-Related genes and its relationship with
immune microenvironment in Hepatocellular Carcinoma” conducted by Liu et al. has been
evaluated. I think this study has certain innovation and clinical significance. In this study,
the author developed a novel m6A, m5C and m1A-related genes' prognostic model which
could be applied as a potential prognostic tool for HCC and might guide the choice of
immunotherapies. However, some obvious limitations impair the overall quality. Before it is
suitable for publication, I suggest the author make substantive modifications.
1. I noticed that some of the figures have a low resolution which makes them hard to read. In
particular, texts in Figure 7 are hard to read due to the small font size and low resolution. I would
suggest that the authors increase the resolution of these figures, which would make them easier
to read and understand. Also, why the legends of Figure 1, Figure 2, Figure 4, Figure 5 and
Figure 7 are embedded in figures, while others not? This looks very confusing. Meanwhile, what
if Figure 7-1 and Figure 7-2 ??? This would also make it easier for readers to fully understand
the results and make use of it. I believe that increasing the resolution of these figures would
greatly improve the manuscript.
2. Some previous studies have used similar methods. Although it will lose some innovation, I
think it will benefit the reader if the authors could include the following references, which would
provide readers with a more complete understanding of the whole study (PMID: 33850225,
PMID: 34099740, PMID: 36283420, PMID: 34306023...).
3. Detailed description of all method sections is required.
4. State the * and statistic value in the method section or otherwise mention in every figure
legend. e.g., *p>0.05.
5. Check the reference style and abbreviation of journals.
6. Some typos are there; rectify those (Major).
7. The author performed GSEA analysis based on KEGG set, why not added other set like
Hallmark and GO?
8. The relationship between immune cell infiltration and specific biological pathways should be
well discussed in the relevant section.
Review for 10.1186/s12876-023-02776-6 (2023)

Title: The m6A/m5C/m1A regulator genes Signature Reveals The Prognosis and Related with
Immune Microenvironment for Hepatocellular Carcinoma
Version: 3 Date: 08 Mar 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are minor issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are minor issues
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The manuscript was a bioinformatics study focused on the role of
RNA modification proteins in the pathogenesis of HCC.  Evidence is presented that shows a
correlation between the differential expression of YTHDF1, YBX1, TRMT10C and TRMT61A
and HCC survival.  However, very little is said about the putative mechanisms whereby these
differentially expressed genes contribute to hepatocarcinogenesis, nor any mention of them as
potential biomarkers in blood because they have all been documented to be secreted.  It is not
clear that these proteins would be better than existing immune based markers associated with
HCC. Further, these differentially expressed proteins have been shown earlier to contribute to
the pathogenesis of HCC, so it is not clear how much new conceptual ground is provided by
this work.
REQUESTED REVISIONS:
How do the results of this study improve our ability to develop biomarkers since nothing is said
about generating ELISAs for clinical samples?  What new conceptual ideas are presented here?
What about the mechanisms whereby these up-regulated proteins contribute to HCC and their
rationale for further development as biomarkers?
ADDITIONAL REQUESTS/SUGGESTIONS:
Provide rationale to suggest that correlations presented in the paper have a biological basis for
cause and effect.  Are these correlations only present in tumor bearing patients, or do they occur
in patients with chronic liver disease and no HCC?"
Review for 10.1186/s12876-023-02776-6 (2023)

Title: The m6A/m5C/m1A regulator genes Signature Reveals The Prognosis and Related with
Immune Microenvironment for Hepatocellular Carcinoma
Version: 5 Date: 14 Apr 2023
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The concerns have largely been met.  Please proceed with
publication.
ADDITIONAL REQUESTS/SUGGESTIONS:
No"
Review for 10.1186/s12876-023-02663-0 (2023)

Title: High-Dose Polyethylene Glycol-3350 and Gatorade Solutions for Patients with Previous
Inadequate Bowel Preparations for Colonoscopy are Safe and Effective
Version: 2 Date: 06 Nov 2022
Reviewer:  Keng Hoong Chiam
Reviewer's report:
This study looks at the role of using high-dose PEG with Gatorade solutions in patients whose
previous colonoscopic assessments were substandard due to inadequate bowel preparation. It is
the first of its kind to venture into using higher-than-usual bowel preparation formulation and
compare it against historical controls from a previous study by similar authors. I commend their
effort in looking for novel alternatives to tackle such common issues faced by endoscopists daily.
Per the limitations mentioned, this is not a randomised study, and the patients selected to undergo
the colonoscopy have had some experience with taking bowel preparation. They would thus be
more careful in overseeing their diet and be more adherent to the prescribed bowel preparation
regime for fear of missed lesions. The use of historical controls would also hinder the impact of
the study as the population chosen was different (younger). Nevertheless, I understand the need
for such a comparison owing to the unique population studied. My concern for this study is the
low patient numbers, risk of confounding factors and the lack of blinding for the subjects. These
issues may give rise to a risk of bias. Despite these concerns, the study methodology is clear and
sets a good foundation for future researchers to look into how investigators can take this further.
Review for 10.1186/s12876-023-02663-0 (2023)

Title: High-Dose Polyethylene Glycol-3350 and Gatorade Solutions for Patients with Previous
Inadequate Bowel Preparations for Colonoscopy are Safe and Effective
Version: 2 Date: 05 Jan 2023
Reviewer's report:
Dear the Editor,
I have reviewed the manuscript  ID 30c5977c-6923-4679-85c3-92d60b14a940 entitled “High-
Dose Polyethylene Glycol-3350 and Gatorade Solutions for Patients with Previous Inadequate
Bowel Preparations for Colonoscopy are Safe Effective”. However, there are some major
concerns as the following;
Major concerns
1. This manuscript was redundant and difficult to follow. For example, the authors should
explain the definition of step 1 and step 2 again in the manuscript and give more detail when
they initiated step 2 in the manuscript, not only put them in the abstract, etc. The manuscript
should be rewritten.
2. It was unclear that why the authors had to use the historical controls in this study as the
quality of bowel preparation has its cut-point number to categorize to poor, good or excellent
preparation.
3. The result part should contain the content of result in the text as well, not only refer the
information to the tables.
4. As there were a lot of digits in this manuscript, especially in the discussion part. The author
should provide the most simplify data to the reader.
Review for 10.1186/s12876-023-02780-w (2023)

Title: AST/ALT ratio, APRI, and FIB-4 compared to FibroScan for the assessment of liver
fibrosis in patients with chronic hepatitis B in Bandar Abbas, Hormozgan, Iran
Version: 0 Date: 10 Feb 2023
Reviewer's report:
The study "AST/ALT ratio, APRI, and FIB-4 compared to FibroScan for the assessment of
liver fibrosis in patients with chronic hepatitis B in Bandar Abbas, Hormozgan, Iran" aimed to
compare aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio, AST to platelet
ratio index (APRI), and fibrosis-4 (FIB-4) with FibroScan results for the evaluation of hepatic
fibrosis in CHB patients. There are no elements of originality, and the study is not rigorous
enough.
The study has some important limits.
- The major limit of the study is the lack of gold standard (liver biopsy), all results being analyzed
compared to Fibroscan. Fibroscan is a method that estimates the stage of fibrosis and can be
subject to errors of interpretation. This aspect should be emphasized more in the discussion
chapter
- For the prediction of fibrosis using Fibroscan, certain cutoff values of liver stiffness were
chosen. Why were these values chosen and not others? There is no bibliographical quota inserted
in this respect.
- Between the Fibroscan examination and the moment of blood tests collection there is a time
interval of maximum one month, which is not correct. Fibroscan examination and laboratory
tests should have been performed on the same day or at a difference of one day in order to be
comparable
- How were the FIB4, APRI and AST/ALT/ratio cutoff values chosen for the assemenst of Se,
Sp, VPP and VPN?
- Is there a statistically significant difference between the values of FIB4, APRI and AST/ALT/
ratio depending on the stage of fibrosis estimated by Fibroscan?
- The statistical significance of the AUROC difference between Fibroscan, FIB 4, APRI and
AST/ALT ratio is not analyzed
- The article requires Corrections of English
Review for 10.1186/s12876-023-02780-w (2023)

Title: AST/ALT ratio, APRI, and FIB-4 compared to FibroScan for the assessment of liver
fibrosis in patients with chronic hepatitis B in Bandar Abbas, Hormozgan, Iran
Version: 0 Date: 28 Feb 2023
Reviewer's report:
This manuscript describe that the assessment of liver fibrosis by APRI and FIB-4 correlates with
that by Fibroscan. Unfortunately, however, it is not possible to conclude as the author states
because liver fibrosis assessment by Fibroscan does not always accurately reflect liver fibrosis.
Therefore, we can only conclude that APRI and FIB-4 can achieve similar results without the
use of the Fibroscan, an expensive measuring instrument.
In particular, the assessment of liver fibrosis  by Fibroscan tends to be higher in cases with high
liver inflammation, i.e., high ALT. Therefore, it is an idea to reexamine the results separately
for cases with low ALT and high ALT levels.
Review for 10.1186/s12876-023-02780-w (2023)

Title: AST/ALT ratio, APRI, and FIB-4 compared to FibroScan for the assessment of liver
fibrosis in patients with chronic hepatitis B in Bandar Abbas, Hormozgan, Iran
Version: 0 Date: 02 Mar 2023
Reviewer:  Pathik Parikh
Reviewer's report:
Fibroscan has limitations with Obesity.
1. It would be worthwhile looking at the correlation of fibroscan with these variables with and
without obesity
2. Fibroscan inter-observer variations
3. If histopathology is available for any of these patients, adding data on these would be
worthwhile
4. FIB Plus if feasible being a recent score should also be considered
5. Corelating hepatitis B activity - infection or disease; eAg positive and negative for the amount
of fibrosis if available can be included
Review for 10.1186/s12876-023-02780-w (2023)

Title: AST/ALT ratio, APRI, and FIB-4 compared to FibroScan for the assessment of liver
fibrosis in patients with chronic hepatitis B in Bandar Abbas, Hormozgan, Iran
Version: 1 Date: 15 Apr 2023
Reviewer's report:
In the revised version, the authors answered my questions. The article is improved compared to
the initial version, but, obviously, the same major limits remain (lack of biopsy).
However, through the changes made, it is clearer that the study aimed to compare AST/ALT
ratio, APRI, and FIB-4 with FibroScan results. Also, the limits of the study are emphasized more
clearly in the discussion chapter.
Review for 10.1186/s12876-023-02773-9 (2023)

Title: Emphasis on the Clinical relationship between Alpha-Fetoprotein and Hepatoid
adenocarcinoma of the stomach: a retrospective study
Version: 2 Date: 27 Dec 2022
Reviewer's report:
Thank you very much.
There are few points to revisite:
1. In my opinion the paper is not including  pathology perspective of these rare entity. With this
title,  I have expected to see at least the pathologic criteria  for diagnosis (which is an conflicting
issue),  diagnostic approach / diagnostic pitfalls for pathologic diagnosis. The tittle should be
revisited to turely  indicate that the article addresses clinical course and prognostic data.
2. Table 1:'pTNM (IV)' is written.IV should be omitted.
Surgical resection ( the last line) should be aligned.
3. line 112.... , 'invaded the plasma membrane, or invaded adjacent tissue or organs. ' Did you
mean peritoneal membrane? It would be better to say serosa. (also in the lines 133-134 and some
others in the  discussion part )
4. Table 2: size (cm)
Thank you
Review for 10.1186/s12876-023-02773-9 (2023)

Title: Emphasis on the Clinical relationship between Alpha-Fetoprotein and Hepatoid
adenocarcinoma of the stomach: a retrospective study
Version: 2 Date: 31 Jan 2023
Reviewer's report:
It was great honor to have opportunity of reviewing your valuable study.
Your study handled hepatoid adenocarcinoma of stomach that is rare.
However, there was conflicting result compared to previous study. You decribed surgery is
independent risk factor of prognosis of the malignancy; HR = 2.663 in univariate analysis and
HR = 2.289 in multivariate analysis.  According to reference study that this study cited, surgery
was associated with good prognosis. However, result of this study was not consistent with
previous study and authors did not mention this point.