JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-02832-1 (2023)

Title: Dietary protein intake and mortality among survivors of liver cirrhosis: a prospective
cohort study
Version: 1 Date: 24 Mar 2023
Reviewer's report:
The authors investigated the association of dietary protein intake with the cirrhosis-related
mortality. This study is clinically valuable. But there are some comments.
Major comments:
1.The current study aimed to evaluate the potential association of dietary protein intake with the
cirrhosis-related mortality. What are the causes of patients death?The authors have described
the exclusion criteria. Were there any patients accepted liver transplantation?
2.Whether complications such as gastrointestinal bleeding and infection affected the results?
How about the impact of treatment ? For example, patients with advanced liver cirrhosis usually
have hypoalbuminemia and albumin transfusion, which should also be considered as a potential
confounder when investigating the association of dietary protein intake and cirrhosis-related
mortality. So more important  potential confounders should be considered.
3.As the authors mentioned, the present study has limitations that should be considered,
including relatively small study population, inevitable recall bias using food frequency
questionnaire (FFQ) and missing of about 15% of enrolled patients. So further details of the
study quality control protocol should be provided, such as how the FFQ data was obtained from
the patients.
Minor comments:
1.In page 7 line 150-151, the author described that “the prevalence of malnutrition was
significantly higher in nondynapenic obese patients than in non-dynapneic obese patients”. Two
groups are same?Please check again.
2.Please check the data for more clarification statement such as Table 2,etc.
Review for 10.1186/s12876-023-02832-1 (2023)

Title: Dietary protein intake and mortality among survivors of liver cirrhosis: a prospective
cohort study
Version: 1 Date: 27 Mar 2023
Reviewer's report:
In line 149-150, i can't figure out what the author wants to convey.
In line 164-167, the conclusion made by the author is inconsistent with the data in the figure,
please check the consistency.
I also have a question about the research design. In the statistical analysis process, why the
author used the total mass of protein intake instead of the standardized mass of protein intake
(g/kg estimated dry weight)?
Review for 10.1186/s12876-023-02832-1 (2023)

Title: Dietary protein intake and mortality among survivors of liver cirrhosis: a prospective
cohort study
Version: 1 Date: 29 Mar 2023
Reviewer's report:
General comments:
The manuscript reports on the effect of dietary protein intake on mortality rates in patients
with liver cirrhosis. The study employed multivariate adjustment and Cox regression models to
calculate the risk ratio (HR) and 95% confidence interval. The results suggest that a higher intake
of total and dairy protein and lower intake of animal protein are associated with a reduced risk
of mortality in cirrhotic patients. The manuscript has some innovative aspects and is significant
in guiding the diet of patients with liver cirrhosis. However, there are several areas where the
manuscript needs improvement.
Specific comments:
1. Survival curve: This article studied the impact of different dietary protein on mortality rate in
patients with liver cirrhosis, with a follow-up time of up to 4 years and 43 deaths during follow-
up. Why was there no survival curve?
2. Models: The authors defined three models to control for potential confounders. However,
most of the significant results were found in Model 3, while Model 1 and Model 2 were not
further mentioned. It would be helpful to analyze and discuss the reasons for this result.
3. Grouping: Participants were grouped into three categories based on tertiles of dietary protein
intake, with T1 as the reference group. However, the basis for this grouping into tertiles was
not explained. Why not compare participants based on the median by dividing them into two
groups? It would be beneficial to explain the rationale behind this grouping
4. Results section: The manuscript needs more detailed explanations of the findings. The study
results are only partially described with statistical differences, and additional information is
needed. Including corresponding chart numbers after the textual description of the research
results would enhance readability.
5. English quality: The English quality of the manuscript needs improvement, with grammar
mistakes requiring correction.For example, on lines 160-161. Please carefully correct the
grammar mistakes.
Review for 10.1186/s12876-023-02832-1 (2023)

Title: Dietary protein intake and mortality among survivors of liver cirrhosis: a prospective
cohort study
Version: 4 Date: 19 May 2023
Reviewer's report:
I have carefully reviewed the revised version of the manuscript and am pleased to see that the
author has made appropriate changes based on my feedback. The quality of the manuscript has
significantly improved, and I  recommend that it be accepted for publication in this journal.
Review for 10.1186/s12876-023-02861-w (2023)

Title: Associations and gastrointestinal symptoms in women with endometriosis in comparison
to women with irritable bowel syndrome: A  study based on a population cohort
Version: 1 Date: 04 May 2023
Reviewer's report:
Overall, the article was informative  of key overlaps between endometriosis and IBS. Starting
from the beginning, it would be helpful to make it clearer that there are two separate research
aims - one being exploring associations and the other relating to gastrointestinal symptoms.
Making this clearer within the background and abstract will avoid confusion - initially I was
interpreting the main aim of the article is exploring misdiagnosis of either disease/differential
diagnosis. However, it seems that the misdiagnosis between the two diseases is a subsequential
finding due to an overlap of gastrointestinal symptoms and associations rather than differential
diagnosis.
Also, mentioning why these associations were chosen in the background with peer reviewed
articles referenced would also help to justify the associations. Giving the reader a reason as
to why BMI, alcohol and smoking was chosen to explore associations with and between both
diseases would be useful to know, and how they interact with both diseases could be more clearly
and explicitly explained - for example, alcohol impacts endometriosis by etc and IBS by, etc,
leading to gastrointestinal symptoms including etc.
Also - was there also any ethics approvals/processes necessary to obtain this data?
The analysis did account for some confounding factors, however it would have been useful to
account for additional including stress/anxiety and other conditions such as Crohns, allergies
and intolerances. These play a significant role in not only the physical manifestation of
gastrointestinal symptoms, but the patients perception of the existence and severity of symptoms.
I agree that exploring  associations between definitively diagnosed endometriosis and IBS be
difficult as laparoscopy of the gold standard of diagnosis and side effects from this invasive
surgery can cause/have symptoms that mimic IBS/gastrointestinal symptoms. This was great to
mention as you did in the end of the article as a limitation. It would be useful to investigate
further the stages of endometriosis and adjust for severity in correlation with gastrointestinal
symptoms. It was touched in in terms of lesion position, which is a determining factor of stage,
however, this would be another analysis that could be explored in the future.
Overall, the article is very informative in discussing the association between these two diseases
in relation to gastrointestinal symptoms. With limitations mentioned, there has been thorough
exploration of these associations and provides the reader with an insight into the common overlap
of two very different diseases, which can lead to mis diagnosis and impact on quality of life.
In the future, it would be useful to explore deeper confounding factors including adjusting for
stage, other diseases over a long period of time. Great work.
Review for 10.1186/s12876-023-02861-w (2023)

Title: Associations and gastrointestinal symptoms in women with endometriosis in comparison
to women with irritable bowel syndrome: A  study based on a population cohort
Version: 5 Date: 20 Jun 2023
Reviewer's report:
I appreciate the positive replies of the authors and agree with the changes made. I think the
manuscript can be accepted for publication.
Review for 10.1186/s12876-023-02852-x (2023)

Title: Lower end of treatment HBsAg and HBcrAg were associated with HBsAg loss after
nucleos(t)ide analog cessation
Version: 1 Date: 06 Mar 2023
Reviewer's report:
title: do not include cut off values of hbsag etc in your title.
Introduction:  too long, try to be more concrete.
Methods:
- describe which tests were used for HBV DNA, HBV RNA and HBcrAg quantification,
including lower limit of detection. Not solely refer to your previous published paper.
- summarize the Chinese NA stop criteria
- include re-treatment criteria
- can you include an ethical statement, did every patient give written consent?
- include your endpoints
Results:
- give patient characteristics. Do not refer to your previous published paper.
- it suggests that many HBV RNA data is missing during follow-up. Please state of how many
patients data was available regarding HBV RNA. Plus include this in your limitation section
- table  1:  HBV RNA is 0 log. But this is an impossible  value. Please re-check.
-  regarding group B: 19 patients is a very small group to draw conclusions from. Include this
in your discussion.
discussion: discuss not only results from other studies, but also try to explain the rationale behind
the differences and/or similarities with your results.
English: check grammar and be consistent for the use of British vs America English.
Review for 10.1186/s12876-023-02852-x (2023)

Title: Lower end of treatment HBsAg and HBcrAg were associated with HBsAg loss after
nucleos(t)ide analog cessation
Version: 1 Date: 30 Mar 2023
Reviewer's report:
1. Follow-up of 24 months was short, but the overall quality of this paper is good.
2. Please confirm whether there is a description of liver stiffness value in the admission criteria
of patients.
3. in the last paragraph of discussion, “HBeAg-positive patients with HBsAg # 135 IU/mL
or HBcrAg # 3.6 logU/mL stopping NA treatment may have more chance to be off-treatment
HBsAg loss" is not an appropriate description, because a small number of e antigen positive
patients may have low levels of HBsAg, less than 135 IU/mL, but obviously cannot be
discontinued of NAs.
4. It is worth discussing whether the relevant description of "patient signing informed consent"
is required.
Review for 10.1186/s12876-023-02852-x (2023)

Title: Lower end of treatment HBsAg and HBcrAg were associated with HBsAg loss after
nucleos(t)ide analog cessation
Version: 2 Date: 01 May 2023
Reviewer's report:
Reviewer 1
Query 6: please do include an ethical statement in your method section. It should be stated there.
Query 8. Please include your patient characteristics in a table. Besides the characteristics
summed in your result section, also include:
- mean/median HBsAg levels at EOT
- mean/median HBV RNA levels at EOT
- mean/median HBcrAg level at EOT
- mean/median ALT levels at EOT
- ethnicity
- HBeAg status at the start of nucleotide analogs
- liver stiffness measurement at EOT (i.e. number of patients with fibrosis/cirrhosis)
Query 9. Still, at the beginning of your study, you start with 99+44=143 patients at risk, and at
24 months follow-up 28+68=96. What happened with the other 47 patients?
Query 11: I understand your statement that results might still be representative, please include a
statement (in well-written English) in your discussion section, including an explanation of what
impact the small cohort could have had.
Query 12: The explanation regarding the number of HBsAg loss is very weak (page 14, line
15-17). It must be possible to say more about the similarities/differences between the studies
and how these could be explained.
In response to your statement about HBsAg level cut-offs (page 16, line 2-5): you state that
HBsAg cut-offs could not solely be used as a criterium. Please also include a statement about
which other criteria should be used.
Page 16, line 19-21: why is it unclear if HBcrAg is a good marker to select patients for
NUC cessation? You only summarized differences in results between studies, not how these
differences could be explained. Which limitations of HBcrAg are there and why?
Query 13: Please consider consulting someone for academic proofreading. The quality of
English is still poor.
Review for 10.1186/s12876-023-02860-x (2023)

Title: An adjusted Asia-Pacific colorectal screening score system to predict advanced colorectal
neoplasia in asymptomatic Chinese patients
Version: 4 Date: 10 Jan 2023
Reviewer's report:
Despite the interesting argument and the well-conducted study, this paper cannot be considered
for publication if an English certified translation of the Ethical approval is not provided.
Review for 10.1186/s12876-023-02860-x (2023)

Title: An adjusted Asia-Pacific colorectal screening score system to predict advanced colorectal
neoplasia in asymptomatic Chinese patients
Version: 4 Date: 06 Apr 2023
Reviewer's report:
In the manuscript, “An adjusted Asia-Pacific colorectal screening score system to predict
advanced colorectal neoplasia in asymptomatic Chinese patients”, Chenchen et al. describe that
adjusted Asia-Pacific Colorectal Screening (A-APCS) score, a cost-effective screening approach
for colonoscopy, may be useful in clinical application for predicting advanced colorectal
neoplasia (CAN) than previous APCS score. However, the A-APCS score could be overfitted
to the Second hospital, Cheeloo College of Medicine, Shandong University in this study. The
c-statistic of validation data from the same hospital was marginally not significant.
Major)
The authors need to add Cohen's kappa value between A-APCS and APCS scores in each dataset.
To visualize the distribution of the stratification group by each score, the authors should draw
Venn diagrams between A-APCS and APCS in the patients with ACN.
As the authors wrote in the discussion, this study is conducted in a single center and validation
is not satisfying statistical significance.  If another validation in a different center is satisfying
the statistical test, it would be more convincing results.
Minor)
The flags of Figure 1 are a, b, c, and d but the flags of Figure 3 are A and B, even though the
description is pointing them as a and b. Unification of format is needed.
Review for 10.1186/s12876-023-02860-x (2023)

Title: An adjusted Asia-Pacific colorectal screening score system to predict advanced colorectal
neoplasia in asymptomatic Chinese patients
Version: 7 Date: 06 Jun 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 satisfactorily responded to the comments made by
both reviewers and made relevant changes. The manuscript can be accepted for publication. I
have no further comments.
Review for 10.1186/s12876-023-02860-x (2023)

Title: An adjusted Asia-Pacific colorectal screening score system to predict advanced colorectal
neoplasia in asymptomatic Chinese patients
Version: 7 Date: 17 Jun 2023
Reviewer's report:
The authors responded appropriately to the reviewer's comments and presented a well-studied
work. I appreciate your thoughtful response and the additional information requested
Review for 10.1186/s12876-023-02857-6 (2023)

Title: Efficacy of Crohn's Disease Exclusion Diet in Treatment -naïve Children and Children
Progressed on Biological Therapy: A Retrospective Chart Review
Version: 1 Date: 02 May 2023
Reviewer:  Harishankar Gopakumar
Reviewer's report:
Dear Authors,
It was a pleasure to read your work titled “Efficacy of Crohn's Disease Exclusion Diet in
Treatment -naïve Children and Children Progressed on Biological Therapy: A Retrospective
Chart Review”. The findings of this study are very interesting and encouraging.
As the authors have mentioned, the main limitation of this study is the limited number of patients
evaluated, lack of endoscopic correlation and the retrospective nature of the study. However,
the results are very encouraging and should prompt future well designed prospective studies. I
only have a few minor comments to add.
Minor.
- Hyphen instead of period. Line 117, page 5.
- I recommend p-value in decimals instead of %. Line 180, page 7.
- Please correct typo/spelling. Start instead of star. Line 185, page 8
Review for 10.1186/s12876-023-02857-6 (2023)

Title: Efficacy of Crohn's Disease Exclusion Diet in Treatment -naïve Children and Children
Progressed on Biological Therapy: A Retrospective Chart Review
Version: 1 Date: 08 May 2023
Reviewer's report:
In this case series, María Clara Jijón Andrade, et al. reported their experience with the outcomes
of Crohn’s disease exclusion diet (CDED) plus partial enteral nutrition (PEN) in the paediatric-
onset CD at disease onset and after the loss of response to biologics. They conclude that treatment
with CDED plus PEN was well tolerated and achieved an excellent clinical remission rate in
treatment-naive patients. The benefit was less in patients who initiated the strategy after losing
the response to biologics. The study question is valid and very relevant in clinical practice.
However, the study is limited by small sample size and absence of endoscopic information as
mentioned by the authors.
The manuscript can be improved by addressing the following concerns.
- Consider revising the introduction section to include more details on CDED. It currently
focuses more on CD than CDED.
- Include baseline values for calprotectin, ESR, CRP, Albumin, Hb and iron level for both groups
in Table 1.
- Authors found that CRP and Wt Z-score did not show significant improvement despite
significant improvement in other parameters. Authors may want explain why no improvement
was noticed in these parameters in the discussion section.
- Consider performing univariate/multivariate analysis to find out which variables are associated
with remission in both groups (variables like age, sex, medications, location of CD, behavior of
CD, duration of disease and other relevant variables can be studies).
Review for 10.1186/s12876-023-02831-2 (2023)

Title: Identification and immunological characterization of cuproptosis-related molecular
clusters in Ulcerative Colitis
Version: 2 Date: 11 Feb 2023
Reviewer:  Mehmet Ali Kosekli
Reviewer's report:
The paper titled 'Identification and immunological characterization of cuproptosis-related
molecular clusters in Ulcerative Colitis' is reviewed. Authors studied  immunological
characterization of cuproptosis-related molecular clusters in subjects with Ulcerative Colitis.
Comments:
a- Background data should be improved in introduction. Cuproptosis is associated with
inflammation (Front Immunol. 2022 Aug 4;13:930278. doi: 10.3389/fimmu.2022.930278).
On the other hand, gastrointestinal conditions (Iran J Colorectal Res 2022;10(3):2-13. DOI:
10.30476/ACRR.2022.97244.1160), and even functional bowel disorders (Fam Med Prim Care
Rev 2020; 22(2): 107–110. DOI: 10.5114/fmpcr.2020.95311) are characterized with some
degree of inflammatory burden.   Indeed, high degree of inflammatory molecules have been
reported in patients with UC (Wiener klinische Wochenschrift (2015)127:262-265.  DOI
10.1007/s00508-014-0683-5). Thus, studying immunological characterization of cuproptosis-
related molecular clusters in Ulcerative Colitis makes sense. Improve introduction accordingly
please.
b- Methods and results were presented well enough to conduct similar work and to understand
the study outcomes in an easy way.  Figure are informative.
c- Discussion needs to be improved. First, please state main outcomes at the beginning of
the discussion.   Second, please comment on clinical usage of the study results, and third,
conclusions should be a separate paragraph.
Overall, I recommend revision of the issues as mentioned above before reconsideration.
Review for 10.1186/s12876-023-02831-2 (2023)

Title: Identification and immunological characterization of cuproptosis-related molecular
clusters in Ulcerative Colitis
Version: 2 Date: 20 Feb 2023
Reviewer's report:
In this study, the authors performed systematic bioinformatics and machine learning manner
among ulcerative colitis samples, exploring some diagnostic effects of ulcerative colitis
disease, coppercytosis, and the immune phenotype analysis, proving some new insights to treat
inflammatory bowel disease. There are several limitations to the study which are outlined below.
1. The part of the discussion is needed to extend deeply, not just exhibit your results of research
work equally. For instance, the synergistic and antagonistic effect of CRGs and correlation
analysis of immune cells infiltration in your cohorts is not declared biological significance.
2. It has not explained why you chose 14 genes including DLST etc. as your representative
CRGs in your research.
3. You performed both a consensus cluster and PCA analysis to obtain two relatively
independent groups in 55 UC samples, however, the resultant analysis of coppercytosis and
immune cells infiltration only occurred in PCA analysis, so your purpose of conducting a
consensus cluster is not clear and needed to be more specification.
4. In the WGCNA of 55UC samples, based on the number of your samples, the Soft Threshold
power was up to 16 or 17, you should illustrate whether power value is appropriate or not. In
the WGCNA both in figure 5 and 6, Module Eigengene colors were not annotated further by
biological significance, such as the associated phenotypes and pathways
5. In the part of machine learning, the panel of 5 genes in RF model is not consistent with your
figure 9 A
6. Importantly, since your validation based on the machine model is not more perfected when
the ratio of UC and control approaching closely (2:1 in GSE107597 cohort) than the ratio being
largely (7:1 in GSE92415 cohort), you should analyze or make a specification
Review for 10.1186/s12876-023-02831-2 (2023)

Title: Identification and immunological characterization of cuproptosis-related molecular
clusters in Ulcerative Colitis
Version: 2 Date: 20 Feb 2023
Reviewer's report:
Pu et al. explored the prognostic significance of cupropotosis gene signatures in ulcerative
colitis in this manuscript. They identified distinct clusters in a single dataset model. This is an
interesting manuscript with the potential to be improved.
1. The authors need to expand the methodology in order to gain a better understanding of the
raw data used in the study and the normalization methods employed.
2. Deconvolution algorithms for identifying immune cell distributions from whole RNA-Seq
data are complex. Several algorithms have emerged, and a consensus needs to be established
by comparing results from different methods, such as XCELL, EPIC, MCPCounter, and
ESTIMATE. The authors need to quantify the immune signatures using these parameters.
3. The authors need to expand on the cut-offs and statistical parameters used in CIBERSORT.
4. The authors need to validate their findings in an independent dataset in order to strengthen
their results.
5. The authors should also validate their findings using internal experimental samples, such as
through gene expression analysis techniques like real-time PCR or quantifying relevant proteins.
6. Recently, several gene signatures have been identified. The authors need to compare their
strength with other gene signatures and mention the strength and limitations of their model.
7. The authors can explore several publications for comparison, some of them are: Zhang, L.,
Mao, R., Lau, C.T., Chung, W.C., Chan, J.C., Liang, F., Zhao, C., Zhang, X. and Bian, Z.,
2022. Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis
based on machine learning methods. *Scientific Reports*, *12* (1), pp.1-13. and Ning, Yumei,
Kun Lin, Jun Fang, Xiaojia Chen, Xinyi Hu, Lan Liu, Qiu Zhao, Haizhou Wang, and Fan
Wang. "Pyroptosis-Related Signature Predicts the Progression of Ulcerative Colitis and Colitis-
Associated Colorectal Cancer as well as the Anti-TNF Therapeutic Response." *Journal of
Immunology Research*
 2023 (2023).
8. In the above references and similar others, these types of gene signatures have been identified.
It is important to compare these gene signatures and assess their strengths in order to give better
insights to the readers. This will significantly improve the manuscript.
Review for 10.1186/s12876-023-02831-2 (2023)

Title: Identification and immunological characterization of cuproptosis-related molecular
clusters in Ulcerative Colitis
Version: 2 Date: 21 Feb 2023
Reviewer's report:
The paper named “Identification and immunological characterization of cuproptosis-related
molecular clusters in Ulcerative Colitis” conducted by Pu et al. has been evaluated. I think this
study has certain innovation and clinical significance. In this study, the author comprehensively
explored the cuproptosis-related genes in ulcerative colitis. However, some obvious limitations
impair the overall quality. Before it is suitable for publication, I suggest the author make
substantive modifications.
1. However, I noticed that some of the figures have a low resolution which makes them hard
to read. I would suggest that the authors increase the resolution of these figures, which would
make them easier to read and understand. 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 or statistical 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: 35277527, PMID: 33223511, PMID:
34358932 ...).
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 (Minor).
7. the relationship between immune cell infiltration and specifc pathways should be well
discussed in the relevant section.
8. The result of figure 9D seems to be over-fitting. Can the author take measures or explain how
he avoids the risk of over-fitting?
Review for 10.1186/s12876-023-02831-2 (2023)

Title: Identification and immunological characterization of cuproptosis-related molecular
clusters in Ulcerative Colitis
Version: 4 Date: 22 Apr 2023
Reviewer's report:
The authors checked and made some changes in the later version of their manuscript, but there
still are some limitations.
1. I had only found pathway annotated in the module selected in two clusters of UC 55 samples,
it still was the absence of pathway or molecular function annotated in the module selected in UC
and control groups in a total of 88 samples. However, through the WGCNA analyses, when you
obtained the module-trait relationships, those significant modules should have been analyzed to
associate some biological, such as pathway, biological progress, molecular function, and so on.
2. Importantly, authors have designed to overlap the WGCNA analyses within both clusters of
UC 55 samples and other groups in a total of 88 samples, where included the same samples of UC
55 ones again and other ones of 31 normal tissue, and obtained DEGs, which are subsequently
step to the machine learning program, however, the kind of the crosstalk interaction seems not
to be meaningful to achieve DEGs for prediction of US occurrence.
3. Manuscript should improve the written quality and adjust the disposition of result data,
allowing readers to readily accept the authors’ hypothesis.
4. In the WGCNA analyses of clusters among 55 UC tissues, however, ME grey, which otherwise
represented less weighted genes, meant no significant ones, showed the distinction of module-
trait relationships within them. It should be confirmed data again.
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 0 Date: 21 Feb 2023
Reviewer's report:
In the “Statistical Analysis” part of the “Methods” section, the authors said that “Categorial
variables were expressed as total numbers and percentages”, where the “Categorial” should be
revised as “Categorical”.
In the “Clinical characteristics of NAFLD-HCC patients” part of the “Results” section, the
authors said that “Compared with non-NAFLD-HCC patients, NAFLD-HCC patients were more
likely to be female, had lower #-GTP and higher LDH, ChE, and HOMA-IR level”, where the
“level” should be revised as “levels”.
In the “Comparison between MAFLD-HCC and NAFLD-HCC patients” part of the “Results”
section, the authors said that “In a comparison between MAFLD-HCC and NAFLD-HCC
group...”, where the “group” should be revised as “groups”.
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 0 Date: 01 Apr 2023
Reviewer's report:
Although the topic is of interest, there are fatal methodological drawbacks that hamper the study
conclusions:
1. MAFLD diagnosis is not mutually exclusive with other liver diseases, including chronic
hepatitis C a B (especially during the last year in the era of HCV viral eradication by DAAs
and HBV replication control)
2.  absence of evidence of hepatic steatosis does not rule out MAFLD diagnosis in patients with
cirrhosis (likely the majority of patients with HCC), if there's a previous evidence of excess
hepatic fat
3. the reason why i the study design the other ethological factors for liver disease was excluded
is unclear
4. as there was no systematic assessment of HCC incidence in the area, Authors cannot draw
reliable epidemiological conclusions
5. the main outcome should have been the prevalence and trends of MAFLD-only/MAFLD-
NAFLD and NAFLD-only as compared to other causes of liver disease in the general cohort,
and the comparisons between these different groups
6. the study is mono centric, retrospective, and the sample size is limited; results may not be
generalisable to other settings
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 0 Date: 11 Apr 2023
Reviewer:  Ludovico Abenavoli
Reviewer's report:
The aim of the article is to evaluate the clinical characteristics of patients with MAFLD and
HCC)in comparison with those with NAFLD and considered the validity and challenges of the
new criteria. The article is interesting and updated. I found the following suggestions for the
Author:
- Introduction section: HCC is a typical example of a virus-related cancer, it is also well known
to be strongly related to life style. Chronic alcoholism is a classic risk factor. However, more
recently, obesity has been recognized to strongly affect HCC development in males, versus
various other tumors. There is also growing evidences suggesting that type 2 diabetes increases
the incidence of HCC. Due to the globally increasing proportion of the obese people, obesity-
related HCC will likely continue to increased (PMID: 32582865)
- Methods section: is important to underline in thi section the alcohol consumption definition
degree of the included patients.  Alcohol intake play a pitola role in the onset and development
of HCC
- Discussion section: i suggests to report the pivotal role played by metabolic features in
development of HCC in MAFLD patients
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 1 Date: 24 Apr 2023
Reviewer:  Ludovico Abenavoli
Reviewer's report:
Dear Author,
the manuscript has been revised in line with the comments. No other changes are required
Regards
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 1 Date: 05 May 2023
Reviewer's report:
I have reviewed your revised manuscript. Fortunately, I have no more suggestions for the
manuscript, and I agree to accept  this paper.
Review for 10.1186/s12876-023-02851-y (2023)

Title: Impact and usefulness of the transition to the new MAFLD classification for non-B, non-
C HCC: A retrospective cohort study
Version: 1 Date: 23 May 2023
Reviewer:  Honglu Yu
Reviewer's report:
In Figure 1, the sentence “222 patients met MAFLD criteria other than the presence of hepatic
steatosis” should be deleted, because the sentence is irrelevant with the figure legend “Patient
selection and study design”. Besides, the sentence “222 patients met MAFLD criteria” is
inconsistent with what the authors said in Discussion section “found that a total of 222 (89%)
and 91 (36%) cases met the alternative criteria”.
Review for 10.1186/s12876-023-02766-8 (2023)

Title: Timing of endoscopy in patients with cirrhosis and acute variceal bleeding: A single-
center retrospective study
Version: 2 Date: 25 Oct 2022
Reviewer's report:
In this manuscript Peng and collegues perform a retrospective analysis aiming to determine the
best time point in performing upper endoscopy for patients with variceal bleeding.
Although the manuscript is in general well written, i highly doubt the general value of performing
another retrospective analysis given that we cannot answer the question under investigation with
this given study design.
In fact, numerous retrospective anlyses of the same kind already exist in the literature and two
larger recent meta-analysis of those studies ( Eur J Gastroenterol Hepatol 2021  and Scientific
Report 2020) analyze the same question with higher patient numbers. They all conclude with a
high remaining degree of uncertainty without being able to show superiority of early endoscopy.
I  thus strongly believe, that we do not need another after another retrospective series, but rather
a well powered prospective multi-center trial in order to  proceed in the field.
Review for 10.1186/s12876-023-02766-8 (2023)

Title: Timing of endoscopy in patients with cirrhosis and acute variceal bleeding: A single-
center retrospective study
Version: 2 Date: 10 Dec 2022
Reviewer's report:
The article is very interesting and tries to resolve an important issue such as the time to perform
urgent endoscopy  in variceal bleeding. It is well written and offers interesting data.
1.- The authors should make an effort to collect mortality at 6 weeks. This data would offer very
relevant information.
2.- I think that follow up the results is arduous and they are difficult to understand, the analysis
that the authors carry out on subgroups increases the difficulty in understanding them and does
not add much relevant information, so it seems to me that it could be eliminated or mentioned
that it has been done and leave it all in supplementary material.
3.- As mentioned in methods, the authors collected the patients with hepatocellular carcinoma.
Did they meet all the Milan criteria? Was the presence of hepatocellular carcinoma the same
between groups?
Review for 10.1186/s12876-023-02766-8 (2023)

Title: Timing of endoscopy in patients with cirrhosis and acute variceal bleeding: A single-
center retrospective study
Version: 4 Date: 08 Mar 2023
Reviewer's report:
Although I still doubt the value of another retrospective analysis of non-randomized data,
I would leave the descision about publication to the editor and the orther reviewers. The
limitations of this study should be clearly mentioned though.
Review for 10.1186/s12876-023-02859-4 (2023)

Title: Laboratory risk factors for coexistent primary biliary cholangitis in patients with Sjögren’s
syndrome: a retrospective study
Version: 1 Date: 10 Apr 2023
Reviewer's report:
In this study, the authors aimed to investigate the laboratory risk factors for the coexistence of
primary biliary cholangitis (PBC) in patients with Sjögren's syndrome (SS).
Overall, eighty-two patients with coexistent SS and PBC were studied . The clinical and
laboratory characteristics of the two groups were compared.
Among the compared features, they found that cytoplasmic, centromeric, and nuclear
membranous patterns of ANA and positive anti-centromere antibody (ACA) were observed
more frequently in the SS+PBC group (P < 0.05). Logistic regression analysis showed that
elevated IgM levels, high ANA titer, cytoplasmic pattern, and ACA were independent risk
factors for PBC coexistence in SS.
They concluded that elevated IgM levels, positive ACA, and high ANA titer with cytoplasmic
pattern also provide clues to clinicians for the early screening and diagnosis of PBC in patients
with SS.
The study is of interest with potential clinical relevance. However, some issues deserve further
data and should be addressed.
-Autoantibody detection: this is an important issue since the right interpretation of
immunofluorescence ANA patterns requires experienced laboratory in autoimmune diagnostic.
Could the Authors confirm that autoantibody test were performed in a referral laboratory for
autoimmunity?
-Clinical significance of ACA: according to literature data, ACA may be considered as a
clue for diagnosis and prognosis of PBC as previously demonstrated (Antibodies to SS-A/
Ro-52kD and centromere in autoimmune liver disease: a clue to diagnosis and prognosis of
primary biliary cirrhosis. Aliment Pharmacol Ther. 2007 Sep 15;26(6):831-8. doi: 10.1111/
j.1365-2036.2007.03433.x.) while other ANA IIF patterns are exclusively confined to PBC,
as previously demonstrated in a very large serological study (Antinuclear antibodies giving
the 'multiple nuclear dots' or the 'rim-like/membranous' patterns: diagnostic accuracy for
primary biliary cirrhosis. Aliment Pharmacol Ther. 2006 Dec;24(11-12):1575-83. doi: 10.1111/
j.1365-2036.2006.03172.x.). Please recall and discuss the study findings according to literature
data.
Review for 10.1186/s12876-023-02859-4 (2023)

Title: Laboratory risk factors for coexistent primary biliary cholangitis in patients with Sjögren’s
syndrome: a retrospective study
Version: 1 Date: 17 May 2023
Reviewer's report:
The coexistence of primary biliary cholangitis (PBC) in patients with Sjögren's syndrome (SS)
is well recognized in previous studies. Here, the authors in this retrospective study aimed to
analyze the clinical and laboratory characteristics of the two patient groups to investigate other
related risk factors for PBC in the SS group, in addition to established factors such as ALP
and AMA. Eighty-two patients with coexistent SS and PBC were studied and a comparison of
clinical and laboratory characteristics of the two groups was performed.
From the immunological point of view,  they found that cytoplasmic, centromeric, and nuclear
membranous ANA patterns were observed more frequently in the SS+PBC group.
Of interest, elevated IgM levels, high ANA titer, cytoplasmic pattern, and ACA were
independent risk factors for PBC coexistence in SS.
The study provides clinical results. To improve the clinical impact some points should be
addressed.
-In the setting of autoimmune diseases, the autoantibody test is a crucial point since
Immunofluorescence ANA pattern identification requires expertise and a referral laboratory.
The authors should add more information about autoantibody detection.
-an important point is the time of autoantibody detection. Was autoantibody detected at diagnosis
or during the follow-up? According to Table 1,  21 (25.6) of SS+PBC  patients had cirrhosis.
This is quite not usual at diagnosis. Please add details.
-Study population: the authors stated that patients with autoimmune hepatitis were excluded.
However, it is well known that PBC patients may have overlap features of AIH. It would
be therefore important to specify that in all patients, particularly in those with cirrhosis,
an overlap PBC/AIH  syndrome was excluded as previously described (Review article:
autoimmune hepatitis -- current management and challenges. Aliment Pharmacol Ther. 2013
Oct;38(8):887-913. doi: 10.1111/apt.12470.)
-Prognostic role of ACA:  the authors should discuss the different clinical/diagnostic/prognostic
significance of ANA in autoimmune liver disease, in particular the difference with other
antinuclear autoantibodies such as antibodies to speckled protein as recently summarized
(Autoantibodies to speckled protein family in primary biliary cholangitis. Allergy Asthma Clin
Immunol. 2021 Mar 31;17(1):35. doi: 10.1186/s13223-021-00539-0.).
Review for 10.1186/s12876-023-02805-4 (2023)

Title: Incidence, risk factors, and predictive modeling of stoma site incisional hernia after
enterostomy closure: A multicenter retrospective cohort study
Version: 2 Date: 19 Mar 2023
Reviewer:  Katsuhito Suwa
Reviewer's report:
The authors described the incidence of and the risk factors for incisional hernia following stoma-
closure procedure. The manuscript was well written and interesting. However, there are several
issues to be solved.
#1. In the title page, authors contributions should be declared for all authors.
#2. In the abstract, conclusion about prophylactic mesh placement is very abruptly and not
mentioned in the results.
#3. In your study, no case was performed prophylactic mesh placement. Therefore, in the
Introduction section, line 75-81 should be omitted.
#4.  What is your novelty compared with reference #3-5?
Review for 10.1186/s12876-023-02805-4 (2023)

Title: Incidence, risk factors, and predictive modeling of stoma site incisional hernia after
enterostomy closure: A multicenter retrospective cohort study
Version: 2 Date: 04 Apr 2023
Reviewer's report:
In the present manuscript tilted“Incidence, risk factors, and predictive modeling of stoma
site incisional hernia after enterostomy closure: A multicenter retrospective cohort study”#the
authors have explored the incidence and risk factors of SSIH and build a predictive model. The
results showed that age # 68 years, colostomy, BMI #25kg/m2, malignant tumor and emergency
surgery are the independent risk factors for SSIH. Based on the results, a predictive model for
the occurrence of SSIH was constructed to screen high-risk groups of SSIH. For patients at high
risk for SSIH, preventive intervention, such as prophylactic bio-mesh placement combined with
enterostomy closure, can be a feasible option to prevent SSIH occurrence. These findings are
interesting and novel, the results are enlightening to peers. In surmmary, it is recommended to
give priority to publication.
Review for 10.1186/s12876-023-02805-4 (2023)

Title: Incidence, risk factors, and predictive modeling of stoma site incisional hernia after
enterostomy closure: A multicenter retrospective cohort study
Version: 3 Date: 24 Apr 2023
Reviewer's report:
In the present manuscript tilted“Incidence, risk factors, and predictive modeling of stoma
site incisional hernia after enterostomy closure: A multicenter retrospective cohort study”#the
authors have explored the incidence and risk factors of SSIH and build a predictive model. The
results showed that age # 68 years, colostomy, BMI #25kg/m2, malignant tumor and emergency
surgery are the independent risk factors for SSIH. Based on the results, a predictive model for
the occurrence of SSIH was constructed to screen high-risk groups of SSIH. For patients at high
risk for SSIH, preventive intervention, such as prophylactic bio-mesh placement combined with
enterostomy closure, can be a feasible option to prevent SSIH occurrence. These findings are
interesting and novel, the results are enlightening to peers. In summary, it is recommended to
give priority to publication.
Review for 10.1186/s12876-023-02805-4 (2023)

Title: Incidence, risk factors, and predictive modeling of stoma site incisional hernia after
enterostomy closure: A multicenter retrospective cohort study
Version: 3 Date: 08 May 2023
Reviewer:  Katsuhito Suwa
Reviewer's report:
The authors well replied to all inquiries and the current study is worth for publications.
Review for 10.1186/s12876-023-02844-x (2023)

Title: METTL3 regulates N6-methyladenosine modification of ANGPTL3 mRNA and
potentiates malignant progression of stomach adenocarcinoma
Version: 1 Date: 19 Mar 2023
Reviewer's report:
The manuscript by Zhang et al. describes METTL3 regulates N6-methyladenosin modification
of ANGPTL3 mRNA and potentiates malignant progression of STAD. Although the aim
is interesting, this study is too premature to be published. Several issues below should be
considered to improve the quality of this article.
1. Out of six genes (METTL3, WTAP, YTHDF1, YTHDF2, YTHDF3, and HNRNPA2B1).
the authors selected only METTL3 based on reference. Some reports have well known other
candidates (WTAP, YTHDF family ..) can also mediate m6A modification. The authors need to
clearly demonstrate the reason why you selected METTL3 genes.
2. All membranes of western blots have a poor quality. I recommend to supplement whole
membrane as raw data.
3. Unlike your study, high expression of ANGPTL3 has observed in various cancer tissue,
including OSCC, HCC, and ovarian cancer, and it can promote cancer growth, motility, and
invasion. I understand that lower expression and stability of ANGPTL3 can maintain under the
METTL3-silenced condition. If so, did you check the effects of ANGPTL3 (migration, invasion,
and proliferation..), regardless of METTL3-silencing?
To further exactly address the your finding that METTL3 represses ANGPTL3 and its silencing
rescued METTL3 silencing-impeded proliferation, migration, and invasion of STAD, you need
to check the effects of ANGPTL3 in STAD under the control condition (without METTL3
sliencing).
Review for 10.1186/s12876-023-02858-5 (2023)

Title: Treatment and outcome of hepatorenal syndrome in Japan: A retrospective cohort study
using a national inpatient database
Version: 2 Date: 28 Mar 2023
Reviewer's report:
To authors
In this study, author investigated the real world data of HRS in Japan. They found that albumin
and dopamine was more frequently used for patients with HRS. This paper is interesting but
there are a few problems with the manuscript.
1. Male, length of hospital stay, CP score, and HCC are associated with death or liver
transplantation. These factors except for male are reasonable. Please explain or discuss the
reason for male.
2. Tolvaptan is used for liver disease only in Japan. Please discussed this issue.