JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-03047-0 (2023)

Title: Risks and Benefits of TIPS in HCC and Other Liver Malignancies: a literature review
Version: 1 Date: 23 Oct 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?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The Authors made substantial changes to manuscript based on the
previous reviews. I have the following queries:
1. Page 12: ""Qiu et al., and Yan et al. describe that after TIPS placement, predominantly
HE grades 1-2 occurred (in 37.5%, 9.5%, and 9.8% of all patients after TIPS placement,
respectively), and HE grades 3-4 were rare (in 2.5%, 2.4%, and 0.8% of all patients after
TIPS placement)""... What do figures 37.5%, 9.5%, 9.8% and 2.5%, 2.4%, 0.8% mean? This is
confusing. I am not sure when reading this what are the actual proportions.
2. Page 13: ""In a systematic review of 21.461 patients ..."" I am assuming this is 21,461 patients.
Please correct it."
Review for 10.1186/s12876-023-03051-4 (2023)

Title: Long-term outcomes after enterostomy for very early-onset inflammatory bowel disease
with interleukin-10 signaling deficiency
Version: 2 Date: 03 Aug 2023
Reviewer's report:
This report importance of timely enterostomy. Fundamental treatment for IL-10 signaling
deficiency is hematopoietic stem cell transplantation (HSCT). However, enterostomy is also
important for better prognosis. This report will be helpful for management of peri-HSCT period.
There are some comments:
The authors adapted the significant P is <0.10, not <0.05. I think that this is not widely accepted.
As for Risk factor analysis of stoma closure, the authors wrote there is difference in multiple
intestinal lesions for the time of stoma closure. However, 95% CI is 0.37-27.77. There is no
tendency.
There are some minor points:
In Introduction, “shed light on higher quantity management for VEOIBD patient” will be higher
quality management.
In Results, the age at diagnosis was not consistent between the text and table.
As for Table 2, it is better to describe not only numbers but also %.
As for Table 3, “Number of “ in each line is busy. Simply “patients with HSCT+ stoma closure
(n) is enough.
As for Table 4, the order of groups is different between the text and table. It is better to be
consistent.
Figure 1B shows annual number of patients. However, there are no discussion about these data.
If so, this figure is not necessary.
Review for 10.1186/s12876-023-03051-4 (2023)

Title: Long-term outcomes after enterostomy for very early-onset inflammatory bowel disease
with interleukin-10 signaling deficiency
Version: 2 Date: 29 Sep 2023
Reviewer's report:
This study seems to include the same patient population that has been published previously
Aliment Phaemacol Ther 20223;55:1411-122).  form the same hospital. Even with some
completely similar results as e.g., time from stem cell transplantation to stoma closure (19,6
months). This should have been specified in the Methos section. It is impossible to see what the
indication for stoma-closure was. This would have been an interesting result.
There are several other issues of concern. Why is there no information on stoma closure in
patients without stem cell transplantation? Why were 4 patients without a stoma closure in the
stem cell transplantation group excluded. What is meant by “normal stoma closure group” in
fig. 1.
What were the reasons for choosing 18 months to distinguish between early versus late stoma
closure?
The conclusion is unclear and not based on the results.
Review for 10.1186/s12876-023-03050-5 (2023)

Title: A meta-analysis of the prognostic impact of tissue Golgi protein 73(tGP73) in
hepatocellular carcinoma
Version: 1 Date: 13 Sep 2023
Reviewer's report:
In this meta-analysis, Wei-Ming Yu et al. aimed to investigate the prognostic role of
tissue Golgi protein 73 (tGP73) in hepatocellular carcinoma (HCC) and its relationship with
clinicopathological features. The study focused on the expression of tGP73 in HCC tissue
and its potential impact on patient outcomes. The authors highlighted the limited existing
research on this topic and the absence of a consensus. Their objective was to provide insights
into the prognostic significance of tGP73 in HCC and its clinical implications. The research
methodology employed in this study appears reasonable and exhibits a degree of innovation.
However, there are several potential issues that require attention. I have a major comment which
is described below. I recommend that this article major revised.
Basic reporting:
1. In the abstract, the author mentions, "Relevant publications were searched for in PubMed,
EMBASE, OVID, the Cochrane Library, and the Web of Science database up to March 2023."
However, in the "Material and Methods" section, the author states, "The search was updated to
November 30, 2021." This discrepancy in dates appears to be an oversight on the part of the
author.
2. In the "Material and Methods" section, in the "Inclusion and Exclusion Criteria" part, the
author has already indicated the inclusion of HCC as the inclusion criterion. Therefore, there
is no need to reiterate the exclusion of non-HCC cases in the exclusion criteria. The exclusion
criteria should encompass supplementary items not covered by the inclusion criteria, rather than
redundantly restating the inclusion criteria.
3. In Figure 4, the author states, "The shapes of the funnel plot are symmetric visually." However,
from the visual assessment of the plot, symmetry does not appear to be well-established. Could
the author please clarify the criteria used to judge symmetry in this context?
4. The headers in Table 1 seem to be duplicated, possibly due to formatting issues in the word
processing or table editing software. Table 2 could also be formatted using a three-line table
format to maintain consistency with Tables 1 and 3.
5. In the discussion section, it would be beneficial for the author to provide a more explicit
explanation of why tGP73 is considered an independent risk factor for OS (Overall Survival)
and DFS (Disease-Free Survival) in HCC (Hepatocellular Carcinoma) patients undergoing
hepatectomy. For instance, the author may want to elaborate on the statistical methods used
to establish tGP73's independence from other variables and discuss the biological or clinical
rationale supporting its role as an independent prognostic factor. This would enhance the
scientific clarity of the statement.
Generally, this paper holds some significance, however, some sections require revision. I
recommend the draft be majorly revised.
Review for 10.1186/s12876-023-03050-5 (2023)

Title: A meta-analysis of the prognostic impact of tissue Golgi protein 73(tGP73) in
hepatocellular carcinoma
Version: 3 Date: 31 Oct 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 have adequately responded to my initial critique
addressing all points I raised, and have amended the manuscript to my satisfaction. My overall
impression has not changed from my previous comment regarding this point.
ADDITIONAL REQUESTS/SUGGESTIONS:
The manuscript looks fine now, including the language quality and no further changes are
necessary.
Review for 10.1186/s12876-023-03003-y (2023)

Title: Evaluation of vital genes correlated with CD8+ T cell infiltration as prognostic biomarkers
in stomach adenocarcinoma
Version: 2 Date: 04 Jul 2023
Reviewer:  Anjali Dhall
Reviewer's report:
Comment 1: Introduction need revision. Add latest cancer statistics information in the
introduction section of manuscript.
Comment 2: Please revise the sentences of line number 48; for instance “advanced patients”.
Comment 3: In the literature various deconvolution methods are available such as : xCell,
TIMER, EPIC, quantiseq etc. Please explain the other methods also in introduction or discussion
section and provide the reason of implementing CIBERSORT in the manuscript.
Comment 4: Please specify the “Common gene expression data” Line number 82.
Comment 5: Please explain “paracancerous” tissue samples.
Comment 6: ADD spaces after in line 241.
Comment 7: Please explain T,M,N, and G stages in the manuscript.
Comment 8: References are missing for TIMER, XCELL and EPIC algorithm.
Comment 9: Incorporate the other STAD associated gene signatures reported in the previous
studies.
Comment 10: Discrepancy in the Figure 1 legend and text mentioned in the result section of
manuscript, please clarify it.
Comment 11: The authors should improve the overall language of the manuscript as per the
journal standards.
Review for 10.1186/s12876-023-03003-y (2023)

Title: Evaluation of vital genes correlated with CD8+ T cell infiltration as prognostic biomarkers
in stomach adenocarcinoma
Version: 2 Date: 28 Jul 2023
Reviewer's report:
Reviewer comments to author:
This paper discusses the evaluation of vital genes correlated with CD8+ T cell infiltration
as prognostic biomarkers in stomach adenocarcinoma (STAD). While the risk score model
consisting of four gene expressions seems promising for STAD prognosis, most of the results
are based on analysis of public databases. Only RT-PCR has been conducted as in-vitro analysis,
and the sample size is small. Thus, it remains uncertain whether these genes can truly serve as
prognostic biomarkers in STAD related to CD8+ T cell infiltration.
Major revisions needed:
1. Please consider performing IHC analysis of CD8+ TILs using STAD samples with a larger
sample size to evaluate the correlation between gene expression and the number of CD8 TILs.
2. The correlation coefficient (0.11) between the risk score and CD8+ T-cell infiltration seems
quite low. Please determine if there is a statistically significant correlation.
3. Please conduct mechanistic analysis to prove the correlation between these four genes and the
infiltration of CD8+ T cells into the tumor. Alternatively, discuss possibilities based on existing
reports in the discussion section.
4. Additionally, perform mechanistic analysis to demonstrate the correlation between these four
genes and drug sensitivity or discuss possibilities from existing reports in the discussion section.
I hope these comments will be helpful.
Review for 10.1186/s12876-023-03003-y (2023)

Title: Evaluation of vital genes correlated with CD8+ T cell infiltration as prognostic biomarkers
in stomach adenocarcinoma
Version: 4 Date: 16 Sep 2023
Reviewer's report:
Additional experiments have further clarified the impact of this risk score model using vital 4
genes on STAD prognosis, and thus I read this part with great interest. However, this paper
includes a major problem especially for the evaluation of  CD8+ TILs that cannot be ignored,
and as a result, the clinical part holds only limited meaning.
1. Please perform immunohistochemical (IHC) analysis about CD8+ TILs using STAD resected
samples in your institution to evaluate the association between risk score and the extent of CD8+
TILs. I  think it's not time-consuming  process.
To describe that "the risk score was positively correlated with CD8+ T cell infiltration" in
abstract, this is essential experiment.
2.Please discuss the supposed mechanisms about the correlation between these four genes and
the infiltration of CD8+ T cells into the tumor, rather than just stating that a previous report
exists.
3. The chemotherapies usually used in gastric cancer are fluorouracila , oxaliplatin and cisplatin.
Please evaluate the relationship between risk score and IC50 of  these three drugs.
I hope these comments will be helpful.
Review for 10.1186/s12876-023-03003-y (2023)

Title: Evaluation of vital genes correlated with CD8+ T cell infiltration as prognostic biomarkers
in stomach adenocarcinoma
Version: 5 Date: 10 Oct 2023
Reviewer's report:
Thank you for addressing my comments. Additionally, please answer these comments below.
## It is very unfortunate that immunostaining cannot be performed. The results in the paper are
based only on gene expression level analysis and public database analysis, and it still remains
unclear whether this risk score truly correlates with CD8+TIL. Therefore, if you cannot perform
protein expression analysis such as immunostaining, please mention it in the limitation in the
discussion.
## Although these genes, EPS8L3, MUC13 and PLEKHS1, have been shown to be involved
with cancer cells, it remains unclear how they interact immunologically. Please add another
immunological discussion. If not, please state in the discussion that these mechanisms have not
been shown in the previous report.
I hope these comment will be helpful.
Review for 10.1186/s12876-023-03046-1 (2023)

Title: Laparoscopic Ladd’s procedure for intestinal malrotation in small infants with midterm
follow-up
Version: 1 Date: 05 Jul 2023
Reviewer's report:
The authors present a retrospective review of 55 cases of Ladd’s procedure, comparing
demographics and outcomes between laparoscopic and open techniques, finding that
laparoscopic Ladd’s is a safe and feasible option in most patients >6 months old.
Although this is an interesting and important topic, there are currently over 120 reports on this
in PubMed, many of which come to a similar conclusion as this article. As a result, it is unclear
what novel or added findings the authors are contributing to the literature on this subject.
Please comment on why the procedure was not significantly different, as this has been a major
factor against LL in the past
Please comment on the conversion to open procedures further regarding bleeding and
straightening the duodenum
Is it necessary to include a complete description of the surgery is needed given the audience
of the article?
Review for 10.1186/s12876-023-03046-1 (2023)

Title: Laparoscopic Ladd’s procedure for intestinal malrotation in small infants with midterm
follow-up
Version: 1 Date: 07 Jul 2023
Reviewer's report:
This is a report comparing the outcomes of laparoscopic surgery and open surgery for infants
with malrotation of the intestines. The report specifically focuses on the laparoscopic Ladd
procedure, which is generally considered challenging in young children. The study found that
the hospitalization period was significantly shorter in the laparoscopic group compared to the
open surgery group, etc.…, indicating the advantages of laparoscopy.
The paper is logically structured and presents information clearly. As the authors suggest,
proficiency in laparoscopic techniques is necessary. However, if that proficiency can be
achieved, I understand the authors' viewpoint that this procedure could become a feasible option.
Please answer some my questions.
Major points
1. How was the selection made between laparoscopic and open surgery? There is a possibility of
bias, such as selecting cases with lower risk for laparoscopy or a concentration of laparoscopic
surgeries in the later period of the observation period. As this is a retrospective study, some
degree of bias is inevitable, but additional information regarding the selection criteria for each
group would be necessary.
2. Despite approximately 70% of cases involving midgut volvulus, the study excluded cases that
underwent emergency Ladd procedure. Is it possible that not all cases with midgut volvulus at
the authors' institution underwent emergency Ladd procedure? It would be helpful to provide
clarification on the differences between included and excluded cases in the study.
3. It seems that the reasons for performing surgery other than midgut volvulus were associated
anomalies. It would be beneficial to provide specific details in the Results regarding these
associated anomalies (ex. Duodenum atresia).
4. Although it is mentioned that two cases in the laparoscopic Ladd (LL) group were converted
to open surgery due to intraoperative bleeding and intestinal swelling, it would be helpful to
have additional information about the age of the cases and the presence of midgut volvulus. It
would be valuable to discuss the factors that make laparoscopic surgery difficult or unsuitable
in certain cases and explore the considerations surrounding this aspect.
Minor point
1. It appears that bowel fixation was not performed. It might be worth adding a section on surgical
techniques to mention that bowel fixation was not performed.
Review for 10.1186/s12876-023-03046-1 (2023)

Title: Laparoscopic Ladd’s procedure for intestinal malrotation in small infants with midterm
follow-up
Version: 2 Date: 04 Oct 2023
Reviewer's report:
Thank you very much for your thoughtful response. Most of the corrections I accept. However,
I am sorry about the volvulus, but I am confused. I understand midgut, as you answered, I
understand that small bowel volvulus is different from large bowel volvulus, and I understand
that only small bowel volvulus was done as an emergency surgery. So, what does the volvulus
in the cases we have discussed ultimately refer to? Please clarify the volvulus listed in the result.
Review for 10.1186/s12876-023-03031-8 (2023)

Title: High neutrophil-lymphocyte ratio indicates a worse response to ursodeoxycholic acid in
primary biliary cholangitis: a retrospective cohort study
Version: 2 Date: 06 Oct 2023
Reviewer's report:
In the present manuscript, the authors analyzed how the neutrophil-to lymphocyte ratio might
change depending on the UDCA treatment in PBC patients. The great value of this research is
the large number of patients.
The research described and the conclusions drawn are a good starting point for further analyses
(especially cell culture). Some sections, like the introduction, discussion, and conclusion, are
hard to read and need improvement. Please rearrange this section for better understanding
and make it easier to follow the researcher's thoughts. The discussion must be written more
consistently. Also, the discussion section needs to include the part with the limitations of this
study.
The literature concerning the analyzed factors is nicely cited in the article.
Review for 10.1186/s12876-023-03019-4 (2023)

Title: Role of Colectomy in the Management of Appendiceal Tumors: A Retrospective Cohort
Study
Version: 2 Date: 02 Sep 2023
Reviewer:  Konosuke Nakaji
Reviewer's report:
Thank you for allowing me to review this attractive article. This retrospective study presented
evidence of surgical procedures for appendiceal tumors in the US cohort. The study found that
the incidence and rate of RHC for NEN decreased. In the National Cancer Database, RHC
was significantly associated with increased survival versus appendectomy for stage 2 disease
of all tumor types and stage 1 non-mucinous adenocarcinoma. It is an interesting real-world-
based study and worth publishing. However, there are some concerns about this article. 1. In
this cohort, are there cases of RHC following appendectomy according to the histopathological
results? In our experiences, we found the incidence of Stage 4 is more common in appendiceal
tumors than Stage 2, as seen in conventional colon cancer. For this reason, this evidence may
not be helpful in other countries’ comfort. I humbly request to discuss these issues. 2. The
authors recommended presenting the flow diagram of patient inclusion. 3. It seems unbelievable
to decrease the incidence of NEN in this cohort. The authors should discuss how to decrease the
incidence of NEN in their cohort. 4. The authors are recommended to present this geographical
disparity as an atlas of maps of the US. The authors could discuss the differences in their
evidence between Oriental and Oceania countries. 5. They did not discuss how to diagnose
appendiceal tumors (e.g., coloscopy, CT, or after surgery).6. The authors present the outcomes
in the statistical analysis. They should present primary and secondary outcomes in the method
section.
Review for 10.1186/s12876-023-03019-4 (2023)

Title: Role of Colectomy in the Management of Appendiceal Tumors: A Retrospective Cohort
Study
Version: 2 Date: 04 Sep 2023
Reviewer's report:
I really was amazed by experimental design and the meticulesity the authors show in addressing
each point. But I hope the author re-uploads higher quality Figures.
Review for 10.1186/s12876-023-03019-4 (2023)

Title: Role of Colectomy in the Management of Appendiceal Tumors: A Retrospective Cohort
Study
Version: 2 Date: 05 Oct 2023
Reviewer's report:
Editor-in-Chief
BMC Gastroenterology
I am writing to express my opinion regarding the revised manuscript titled "Role of
Colectomy in the Management of Appendiceal Tumors", which was recently submitted to BMC
Gastroenterology.
Having thoroughly reviewed the revised manuscript and the authors' responses to rewievers'
inquiries and comments, I would like to share my thoughts on its acceptability for publication.
In my opinion, authors should mentione the type of study desigen at the end of Title or in method
section or both of them.
Sincerely,
Review for 10.1186/s12876-023-03019-4 (2023)

Title: Role of Colectomy in the Management of Appendiceal Tumors: A Retrospective Cohort
Study
Version: 4 Date: 26 Oct 2023
Reviewer:  Konosuke Nakaji
Reviewer's report:
The authors have responded to the reviews' comments well and revised them appropriately. No
further comments are available.
Review for 10.1186/s12876-023-03045-2 (2023)

Title: COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma
Version: 1 Date: 01 Feb 2023
Reviewer:  Zhen-zhai Cai
Reviewer's report:
1.There have been relevant reports on the bioinformatics analysis and biological function of
COL10A1 in pancreatic cancer. What do you think is the innovation of your article? For example
(PMID: 36530986, PMID: 36105715)
2.The author believes that COL10A1 can promote the tumorigenesis by regulating CD276
in pancreatic cancer. The evidence is insufficient, and relevant recovery tests need to be
supplemented.
3.It needs to be proved that COL10A1 can affect the phenotype related to pancreatic cancer by
regulating the expression of CD276 in pancreatic cancer. For example, Transwell cell invasion
assay, CCK-8 assay, Wound-Healing Assay, etc.
Review for 10.1186/s12876-023-03045-2 (2023)

Title: COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma
Version: 1 Date: 09 Feb 2023
Reviewer's report:
In this study, the authors described the role of COL10A1 in PDAC tumor
Progression, and identified CD276 as a potential target of COL10A1 to promote PDAC
tumorigenesis. There are several limitations to the study which are outlined below.
1. Importantly, COL10A1 viewed as an oncogene in PDAC of this study is contradicted its
low levels among the bioinformatics analysis of GSE62165. Furthermore, COL10A1 as one of
down-regulated DEGs from GSE62165 data is noncoincident to its high expression from the
GEPIA database, a public database. So based on those data, it is not concluded that COL10A1
promoted PDAC development.
2. In the bioinformatics analysis procedure, it was not defined the fold change range of DEGs,
only claimed that the up-limited value is # 2.0 fold change. Followed by the PPI network of
DEGs, it obtained 10 hub genes including COL10A1, however, authors had no certain proof to
target gene as its consequent exploration in PDAC.
3. In wound healing assays, data is controversial, figure 3D where at a 24-hour point, wound
healing lines of both si-NC cells and si-COL10A1 cells showed no significant difference, but the
chat below has revealed significance. Figure 4C where according to the Spearman-Correlation
of both COL10A1 and CD276 valued, it was not supported the association of them. Based on
the only evidence of knockdown experiment, it is not convinced that COL10A1 and CD27 had
related regulation directly or indirectly, need the more molecular mechanism to provide strong
evidence for the conclusion
4. The manuscript should be edited overall for English grammar and language use. Furthermore,
it existed that figures noted are not very clear and some spellings are mistakes.
Review for 10.1186/s12876-023-03033-6 (2023)

Title: Histopathological features of glandular atrophy of the lamina propria of the gastric mucosa
during its occurrence and development
Version: 0 Date: 24 Sep 2023
Reviewer's report:
-It is known that gastric carcinomas develop on the background of atrophic gastritis. The process
of morphological changes in the gastric epithelium, glandular epithelium, and stroma during the
transformation from atrophy to carcinoma has not been fully elucidated. Therefore, the article
has the potential to contribute to science. However, the methods section in the abstract is not
sufficiently clear. It is not specified which immunohistochemical studies were conducted and
how the findings were obtained. There are minor errors in the use of English. It is recommended
to review the writing style.
-The image in Figure 2a does not fully depict the described morphological features and should
be replaced with a more demonstrative image.
-Figure 6a is oriented upside down.
-The histological features and immunophenotype in Table 2 are quite long and read more like
text than a table. The features should be presented in a shorter, bulleted format.
Review for 10.1186/s12876-023-03033-6 (2023)

Title: Histopathological features of glandular atrophy of the lamina propria of the gastric mucosa
during its occurrence and development
Version: 1 Date: 04 Nov 2023
Reviewer's report:
The requested edits have been made in the manuscript. In the first column (Type) of Table 2,
words should not be divided (proliferation, transformation, intraepithelial, intramucosal). In the
last line, in the nucleus properties section, instead of "large and irregularity", use "large and
irregular".
Review for 10.1186/s12876-023-03034-5 (2023)

Title: The value of endoscopically-placed metal clips for transcatheter arterial embolization in
the treatment of recurrent acute non-variceal upper gastrointestinal bleeding
Version: 3 Date: 05 Nov 2023
Reviewer:  David L. Carr-Locke
Reviewer's report:
The revised manuscript is satisfactory and has included  all of the Reviewers' suggestions
Review for 10.1186/s12876-023-03030-9 (2023)

Title: Texture and color enhancement imaging improves the visibility of gastric neoplasms:
Clinical trial with image catalogue assessment using conventional and newly developed
endoscopes
Version: 2 Date: 27 Jul 2023
Reviewer's report:
The authors showed that TXI, a new Image enhanced endoscopy, improves the visibility scale
of gastric neoplasms compared to WLI. Although several reports similar to those of the authors
have already been published, it is worthwhile to calculate the sample size and to study it in
consecutive cases. However, I have several concerns.
My comments are as follows:
#. It is worthwhile to enroll consecutive cases. It is noted in the discussion section, but should
be noted in the methods section.
#. The possibility that a new method bias may exist based solely on the endoscopist's judgment
of visibility cannot be ruled out. This should be mentioned in the limitation.
#. Table 2: The authors use analysis of variance in their statistics, but the data they examined do
not seem to be normally distributed. The authors should confirm whether the statistical method
is appropriate or not.
#. The following papers have conducted similar studies and should be referenced.
Kawasaki A, et al. DEN Open. 2022 Nov 24;3(1):e186.
Review for 10.1186/s12876-023-03030-9 (2023)

Title: Texture and color enhancement imaging improves the visibility of gastric neoplasms:
Clinical trial with image catalogue assessment using conventional and newly developed
endoscopes
Version: 2 Date: 03 Oct 2023
Reviewer:  Jun-Hyung Cho
Reviewer's report:
The major concerns about this manuscript are as below;
First, the characteristics of enrolled lesions should be deleted in the result section of abstract. H.
pylori infection status, tumor morphology and so on are needed only in the manuscript body.
Second, the authors mentioned only LCI among the IEE in the background section of manuscript.
However, many studies using BLI and NBI were published in this field.
Third, the authors used two kinds of endoscopes including CE (GIF-H290Z) and NE (GIF-
XZ1200). Please explain about the difference between them, for example, resolution power and
image quality. Why did not authors use the magnification? The lesion characteristic can be
diagnosed by magnifying mode than non-magnification.
Fourth, I cannot understand the difference between the TXI-1 and TXI-2 in Figure 1. Were the
endoscopic images in Figue 1 captured by CE (GIF-H290Z) or NE (GIF-XZ1200)?
Fifth, the visibility scales between the expert and novice endoscopists were not described in the
result section.
Sixth, reference No 24 is not proper due to old publication. Lauren`s histological classification
is better than that.
Seventh, I think the number of total images was not 1,872 but 312 from 52 lesions.
Eighth, Table 2 is hard to be interpreted and more description is required for the readers.
Ninth, the degree of atrophy should be classified into close type and open type in Table 2.
Lastly, the degree of intestinal metaplasia may be associated with the endoscopic visibility.
Therefore, the authors should investigate the degree of intestinal metaplasia in baseline
characteristics.
Review for 10.1186/s12876-023-03030-9 (2023)

Title: Texture and color enhancement imaging improves the visibility of gastric neoplasms:
Clinical trial with image catalogue assessment using conventional and newly developed
endoscopes
Version: 4 Date: 04 Nov 2023
Reviewer:  Jun-Hyung Cho
Reviewer's report:
The manuscript was well revised according to reviewers` comments.
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 2 Date: 19 Mar 2023
Reviewer's report:
The authors' findings suggest a strong connection between fatty acid metabolism (FAM) and
HBV-associated HCC. Through LASSO-penalized Cox regression, the authors constructed a
prognostic model using data from the TCGA database. The model was then validated by their
in-house cohort of HBV-associated HCC patients. Further studies indicated that targeting FAM
could be a strategy to block the accumulation of Tregs in the tumor microenvironment of HBV-
associated HCC. However, there are several concerns regarding their investigation.
Point 1: None of the subtitles in the RESULTS section are conclusive.
Point 2: In lines 193-195 of the manuscript, it is stated that “As a result, FAM pathway was
clearly enriched in adjacent normal tissue both in GSE94660 (Fig. 2A) and GSE121248 (Fig.
2C), indicating that most FAM genes are down-regulated in tumor tissue.”. It seems like the
results of the Fig. 2B, Fig. 2D, but not the Fig. 2A and Fig. 2C.
Point 3: Is there any relationship between the 12 genes in the Survival analysis section and the
5 genes in the Construction of the prognostic signature section? Besides, the descriptions about
these two parts are unclear.
Point 4: The author should provide a detailed description of the performance of the prognostic
signature in the GEO datasets (GSE94660 and GSE121248).
Point 5: What are the advantages of the prognostic signature in this study compared to other
previously reported predictive signatures? Better performance?
Point 6: Line 256, “To identify HBV-associated genes, mRNA expression level of the five-gene
signature was assessed between 30 HBV-positive and 15 HBV-negative HCC tumor tissue, and
in parental HepG2 cells compared with the daughter HepG2.2.15 cells containing two head-to-
tail dimers of HBV genomic DNA.”. The assessment of the mRNA expression levels of the five-
gene signature seems irrelevant to the identification of the HBV-associated genes.
Point 7: The author should give a reasonable explanation for the contradiction between the
Fig.8A and Fig.8B.
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 2 Date: 30 Apr 2023
Reviewer's report:
The article has abundant data and clear conditioning, which basically solves the questions raised
by the original reviewers. I hope the author can improve several suggestions:
1. The discussion section may try to suggest a causal relationship rather than just a correlation,
even if the conclusion is only exploratory
2. The format needs to be further optimized, such as inconsistent line spacing
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 2 Date: 13 Jun 2023
Reviewer's report:
1. Power Analysis of the sample size should be done. Power analysis descriptions and the power
value of the study should be given in the Data Collection section.
2. In the statistical analysis section; It should be added that Kaplan-Meier survival analysis,
LASSO-penalized Cox regression analysis, time-dependent receiver operating characteristic
(ROC) curve analysis, nomogram analysis and correlation analysis are used. It should also be
written that R software is used.
3. Test Set is the set where validation is done. The training and test set sample rates should be
specified (such as 60%-40% or 70%-30%).
4. Statistical results are given with figures, not tables. However, the readability level of numerical
values on the figures is low. Figures should be given more clearly and statistical significance
(p-values) should be added.
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 4 Date: 12 Oct 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: * A link between FAM and HBV-associated HCC has been
described by authors, pointing to a possible treatment approach that targets FAM to prevent
the buildup of Tregs in the tumour microenvironment of HBV-associated HCC. Five
genes (ACADVL, ACAT1, ACSL3, ADH4, and ECI1) were found to demonstrate efficient
discrimination and prediction for the prognosis of HBV-associated HCC in both the TCGA
cohort and the validation cohort.
* After review the manuscript is more elaborated and easy to understand.
* The authors have provided suitable justifications/updates over the reviewer comments.
* This manuscripts meets the best practice after modifications.
* This will help the scientific community to take a step further in HBV associated HCC research.
ADDITIONAL REQUESTS/SUGGESTIONS:
The authors have elaborated the review comments and modified the manuscript where required."
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 4 Date: 18 Oct 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?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors have responded to the best of their ability to the concerns
raised in the prior evaluation of the manuscript. The authors have formulated an interesting
hypothesis and have undertaken the appropriate analyses. Ways in which the work falls short
of best practice include the limited sample size and the inability to create training and test sets.
However, these concerns were already raised and addressed by the authors.
ADDITIONAL REQUESTS/SUGGESTIONS:
Reviewer 1 brought up an important question that was not adequately addressed in the response
to reviewers section, nor in the revised manuscript. The question pertained to  the advantages
of the prognostic signature in this study compared to other previously reported predictive
signatures. It would be imperative to know how the prognostic signature in this work compares to
known predictors of HBV-associated HCC including serum levels of alpha-fetoprotein (AFP) or
its variants (i.e., AFP-L3), circulating levels of HBV DNA, and/or the presence of liver fibrosis
or cirrhosis. All of these are associated with the development of HCC and poor outcomes in
individuals with HBV."
Review for 10.1186/s12876-023-03026-5 (2023)

Title: Establishment of a prognostic signature based on fatty acid metabolism genes in HCC
associated with hepatitis B
Version: 6 Date: 31 Oct 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 have responded to the concern raised in my comments
by providing a paragraph in the discussion section about prognostic indicators."
Review for 10.1186/s12876-023-03043-4 (2023)

Title: Platelet/Albumin ratio and plateletcrit levels are potential new biomarkers for assessing
endoscopic inflammatory bowel disease severity
Version: 3 Date: 27 Aug 2023
Reviewer:  Cher Shiong Chuah
Reviewer's report:
Can the authors comment on whether they are aware or use faecal calprotectin testing in their
clinical practice (AUC of calprotectin is superior to platelet/albumin ratio in the established
literature - has been in use for over 20 years and it is much more accurate)?
What are the implications of these findings?  I don't think these findings are particularly novel.
We already know that patients with IBD have high platelet counts and low albumin is a general
marker of chronicity. The performance of this ratio is barely better than CRP.
Limitations of this ratio should be clearly discussed - On the basis of an AUC of 0.705 I would
not base any clinical decision-making on it as it is too inaccurate.
Review for 10.1186/s12876-023-03043-4 (2023)

Title: Platelet/Albumin ratio and plateletcrit levels are potential new biomarkers for assessing
endoscopic inflammatory bowel disease severity
Version: 3 Date: 30 Sep 2023
Reviewer's report:
The authors focused on the PLT/ALB ratio to search for new biomarkers in inflammatory
bowel disease and confirmed that the PLT/ALB ratio and PCT biomarker are useful among
inflammatory biomarkers for assessing endoscopic IBD activity in patients with UC and CD.
Although there are currently several studies on biomarkers to evaluate disease activity in
inflammatory bowel disease, the authors' report is very interesting because it is a simple method
that can be confirmed using ordinary blood test data.
Although the number of cases is large and the study is well done, a few points need to be
confirmed before publication.
1) How long before and after blood tests and endoscopy were clinical symptoms identified in
ulcerative colitis and Crohn's disease?
2) In the Conclusion section, the authors state that the PLT/ALB ratio is the most useful test
for assessing endoscopic activity compared to other tests, especially in CD, which seems to be
comparable to others. The authors should elaborate on the reasons for this conclusion.
Review for 10.1186/s12876-023-03043-4 (2023)

Title: Platelet/Albumin ratio and plateletcrit levels are potential new biomarkers for assessing
endoscopic inflammatory bowel disease severity
Version: 4 Date: 25 Oct 2023
Reviewer:  Cher Shiong Chuah
Reviewer's report:
Thank you for clarifying on the lack of faecal calprotectin data.  The data would suggest a
limited role for platelet albumin ratio in the setting of the unavailability of calprotectin however
the strength of performance of this biomarker is limited. I hope the authors will consider the
introduction of calprotectin testing into their service which although more expensive remains
generally cheaper than colonoscopy.
Review for 10.1186/s12876-023-03043-4 (2023)

Title: Platelet/Albumin ratio and plateletcrit levels are potential new biomarkers for assessing
endoscopic inflammatory bowel disease severity
Version: 4 Date: 08 Nov 2023
Reviewer's report:
Thank you for your reviced manuscript. The author has corrected the problems pointed out, and
this manuscript is in a condition worthy of acceptance.
Review for 10.1186/s12876-023-03027-4 (2023)

Title: Renal and bone side effects of long-term use of entecavir, tenofovir disoproxil fumarate,
and tenofovir alafenamide fumarate in patients with hepatitis B: A network meta-analysis
Version: 1 Date: 19 May 2023
Reviewer's report:
There are some comments:
Results
There is no forest plot in the Results section. Could you please explain the reason?
The duration of the studies is different. And there is no subgroup analysis about it.
Conclusion
The conclusion of this study has been suggested by the most updated guidelines. According
to AASLD 2018 Hepatitis B Guidance, TAF is associated with lower rates of bone and renal
abnormalities than TDF; In cases of suspected TDF-associated renal dysfunction and/or bone
disease, TDF should be discontinued and substituted with TAF or entecavir. And according
to EASL 2017 Clinical Practice Guidelines on the management of hepatitis B virus infection,
patients on TDF at risk of development and/or with underlying renal or bone disease should be
considered for a switch to ETV or TAF.
Check the data in the tables and the full text.
In the duration part of Table 1, there are some studies with years. However, there are some
studies with numbers only.
In Synthesis of results section, you said “ETV reduced eGFR less than TDF, SMD=3.60
(95%Cl:1.94~5.26), which was statistically significant. TAF reduced eGFR less than TDF,
SMD=4.27 (95%Cl:2.62~5.93)”. SMD should be -3.60 and -4.27. The same questions are also
observed in Bone events section.
Check the grammar and language carefully.
In Introduction section, you said “Introductiong”, the spelling of introduction is not right.
In the first paragraph of Introduction section, you said “More than 257 million people worldwide
are chronically infected with hepatitis B and more than 887,000 people die from HBV infection
each year.” Could you make sure that the number is the same each year?
In the first paragraph of Discussion section, you said “At present, nucleoside analogues have
become the international consensus for the first-line treatment of chronic hepatitis B.” The
nucleoside analogues for HBV treatment include lamivudine, adefovir dipivoxil, entecavir,
telbivudine, TDF and TAF. However, the first-line treatment of chronic hepatitis B is entecavir,
TDF and TAF.
In the third paragraph of Discussion section, you said “Previous studies have shown that TAF
has higher plasma stability than TDF, because both TDF and TAF are precursors of Tenofovir”.
The first letter of tenofovir should be lower-case.
Review for 10.1186/s12876-023-03027-4 (2023)

Title: Renal and bone side effects of long-term use of entecavir, tenofovir disoproxil fumarate,
and tenofovir alafenamide fumarate in patients with hepatitis B: A network meta-analysis
Version: 1 Date: 10 Jun 2023
Reviewer's report:
The article by Z. Liu et al is a meta-analysis of studies comapring TDF, TAF and ENT regarding
the side effects.
The authors concluded that TDF has the weaker side effects profile on kindeys and bones
compared to ENT or TAF.
The article did not add anything in the existing literature. The conclusion and suggestions by
authors in the last paragraph of discussion is included in EASL guidelines several years before.
In order to have the article improve the authors should add information regarding time of follow
up and use only studies with longer FU or make a comparison between studies with short or
long FU. In addition safety in pts with advanced liver disease may add something new.
Age is also an important issue.