JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-025-03608-5 (2025)

Title: A Foundation Systematic Review of Natural Language Processing Applied to
Gastroenterology & Hepatology
Version: 2 Date: 18 Dec 2024
Reviewer's report:
Your manuscript presents a comprehensive and well-structured review of NLP applications
in gastroenterology and hepatology. The adherence to PRISMA guidelines, along with a
thorough evaluation of study quality and risk of bias, is commendable. This review significantly
contributes to the field and highlights NLP's potential to transform clinical practice and research.
However, a few areas need clarification and refinement.
Recommendations for Minor Revisions
Reproducibility: Explicit links to public datasets or repositories used in the studies are essential
for transparency.
Practical Relevance: To enhance the review's practical value, include specific examples of NLP
findings in clinical practice.
Study Heterogeneity: Clarify the diversity of NLP methods and datasets among the studies and
discuss how this heterogeneity was managed.
Limitations: Expand the discussion on limitations to address biases, generalizability, and gaps
in the reviewed studies.
Conclusion: Your manuscript is well-prepared and should make a significant impact.
Nevertheless, addressing these points will enhance its clarity and relevance.
Review for 10.1186/s12876-025-03646-z (2025)

Title: A Comprehensive Analysis of Percutaneous Liver Biopsy Characteristics and
Pathological Manifestations in a Large Patient Cohort (2009-2024)
Version: 3 Date: 09 Dec 2024
Reviewer's report:
This retrospective study done to analyze the characteristics of patients undergoing percutaneous
liver biopsies and investigate the pathological manifestations of four principal liver diseases
across different age groups: chronic hepatitis B, chronic hepatitis B complicated by metabolic
dysfunction-associated steatotic liver disease (MASLD), liver function abnormalities, and
standalone MASLD. its not clear from the study  whether the liver biopsies were done as a part
of the study protocol or  they were done only when  diagnosis was not clear , otherwise  fibroscan
of the liver / liver elastography  are non invasive procedures which are carried out for the above
mentioned diseases  to assess degree of fibrosis and monitor progression to fibrosis
Review for 10.1186/s12876-025-03646-z (2025)

Title: A Comprehensive Analysis of Percutaneous Liver Biopsy Characteristics and
Pathological Manifestations in a Large Patient Cohort (2009-2024)
Version: 3 Date: 09 Dec 2024
Reviewer:  Speranta Iacob
Reviewer's report:
Major Revision required: The manuscript will be revised for acceptance after addressing the
following points:
1. Discuss the implications of the low Pearson’s correlation coefficients.
2. Acknowledge the absence of FibroScan and CAP measurements as a limitation.
3. Provide a detailed discussion on the biological mechanisms linking EASIX to liver fibrosis
and mortality.
4. Clarify the generalizability of the findings to non-U.S. populations.
5. Expand the discussion on the clinical utility and integration of EASIX into practice.
Review for 10.1186/s12876-025-03646-z (2025)

Title: A Comprehensive Analysis of Percutaneous Liver Biopsy Characteristics and
Pathological Manifestations in a Large Patient Cohort (2009-2024)
Version: 3 Date: 17 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
changes are satisfactory, can be accepted for publication.
Review for 10.1186/s12876-025-03646-z (2025)

Title: A Comprehensive Analysis of Percutaneous Liver Biopsy Characteristics and
Pathological Manifestations in a Large Patient Cohort (2009-2024)
Version: 4 Date: 30 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
The authors response is satisfactory
Review for 10.1186/s12876-025-03646-z (2025)

Title: A Comprehensive Analysis of Percutaneous Liver Biopsy Characteristics and
Pathological Manifestations in a Large Patient Cohort (2009-2024)
Version: 6 Date: 10 Jan 2025
Reviewer:  Suzan Hamed
Reviewer's report:
The author's response is satisfactory.  They fulfilled all the requirements.
Review for 10.1186/s12876-025-03621-8 (2025)

Title: Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-
analysis and bioinformatics analysis
Version: 0 Date: 16 Nov 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Abbreviations should be presented on their first appearance in the text Language of
publications extracted should be reported Wouldn't it be better to calculate OR based on data
extracted  Which bio-informatic method has been used to add authors? Shouldn't a multivariated
analysis been performed including risk factors like tumor stage or lymph node metastasis?
Methods Had authors tried to approach original publication authors in order to get raw data for
their study? Results Was method of SNHG method to determine its expression homogeneous
across all studies?
Review for 10.1186/s12876-025-03621-8 (2025)

Title: Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-
analysis and bioinformatics analysis
Version: 0 Date: 27 Nov 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors ,please address the following points below
-This manuscript presents a significant and well-executed investigation into the prognostic role
of SNHG expression in esophageal cancer, employing a combination of meta-analysis and
bioinformatics tools.
-The question remains whether SNHG is specific to esophageal cancer or serves as a general
biomarker for various cancers. Furthermore, would its application in clinical settings necessitate
additional validation across diverse patient populations?
-The findings related to overall survival (HR: 1.392, 95% CI = 0.876–1.908) warrant further
clarification. Although the hazard ratio (HR) suggests a potential association with poorer
survival outcomes, the wide confidence interval (0.876–1.908) encompasses 1, indicating a lack
of statistically significant association. This point merits clearer articulation to prevent possible
misinterpretation by the readers.
-Similarly, the reported HRs for subgroup analyses (e.g., SNHG2, SNHG5, SNHG12) could
benefit from additional context, as the wide confidence intervals may create confusion regarding
the statistical significance of the findings. A more thorough explanation is necessary to
determine whether these results reflect true associations or variability in the data.
-Enhancing the flow of the results section would contribute to a clearer narrative that is easier
to follow.
-The characterization of "SNHG2, SNHG5, and SNHG12" as favorable markers could also be
articulated more precisely. It would be beneficial to specify whether this assessment is grounded
in expression levels or other molecular characteristics.
-The statement that "bioinformatics has been explored" is somewhat ambiguous. While the use
of bioinformatics is commendable, offering more detailed information regarding the methods
or databases utilized—such as gene expression databases and survival analysis tools—would
enhance the transparency and rigor of the study. Additionally, indicating how the bioinformatics
findings correspond with the statistical outcomes from the meta-analysis would provide further
clarity.
-Lastly, it is crucial to specify whether the studies included in the analysis were conducted in
the same geographical region, examined similar types of esophageal cancer (e.g., squamous cell
carcinoma or adenocarcinoma), or adhered to comparable study designs. This information is
essential for assessing the generalizability of the findings.
Review for 10.1186/s12876-025-03621-8 (2025)

Title: Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-
analysis and bioinformatics analysis
Version: 2 Date: 23 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
changes are satisfactory, can be accepted for publication.
Review for 10.1186/s12876-025-03621-8 (2025)

Title: Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-
analysis and bioinformatics analysis
Version: 3 Date: 07 Jan 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
The responses are satisfactory.
Review for 10.1186/s12876-025-03621-8 (2025)

Title: Aberrant SNHG expression predicts poor prognosis in esophageal cancer using meta-
analysis and bioinformatics analysis
Version: 3 Date: 07 Jan 2025
Reviewer:  Mohamed H. Zidan
Reviewer's report:
Dear Authors,
All my concerns have been replied to sufficiently, and the manuscript has improved remarkably
Thank you
Kind regards
Review for 10.1186/s12876-025-03645-0 (2025)

Title: Collagen turnover biomarkers to predict outcome of patients with biliary cancer
Version: 4 Date: 14 Jan 2025
Reviewer:  Shimaa Abdelsattar
Reviewer's report:
The performed study and results could have implication for research and clinical practice in the
future. Therefore, the present article could be accepted for publication
Review for 10.1186/s12876-025-03638-z (2025)

Title: Which scoring systems are useful for predicting the prognosis of lower gastrointestinal
bleeding? Old and New
Version: 2 Date: 07 Dec 2024
Reviewer:  Ali S. Taha
Reviewer's report:
Ku Bean Jeong et al. Which scoring systems are useful for predicting the prognosis of lower
gastrointestinal bleeding? Old and New.
The authors aimed to evaluate the predictive accuracy of various scoring systems for 30-day
mortality and prolonged hospital stay (#10 days) by analyzing the areas under the receiver-
operating characteristic curves, taking into account factors such as patient age, laboratory
findings, and comorbidities (ABC); AIMS 65; Glasgow-Blatchford; Oakland; Rockall(pre-
endoscopy); SHA2PE; and CHAMPS scores.
They found that “In terms of forecasting 30-day mortality, the AIMS 65, CHAMPS, and
ABC scoring systems demonstrated superior performance (p<0.001). For predicting prolonged
hospital stay, the SHA2PE score exhibited the highest accuracy among all evaluated systems
(p<0.001).
My comments are as follows:
The Blatchford score, Rockall score, and AIMS were specifically designed to assess UPPER GI
bleeding (UGIB). They are known world-wide purely for this condition. To apply them to LGIB
would cause confusion to non-Gastro specialists in Emergency Departments where patients with
bleeding present before being seen by the Gastroenterologists.
The other scoring systems focus on comorbid conditions (best assessed by the established
Charlson score) and the functional status of the patient. These can be very difficult and time
consuming to assess in a busy Emergency Department.
The exception to these is the SHA2PE score that assesses Systolic pressure, Hemoglobin value,
Antiplatelet therapy, Anticoagulant therapy, Pulse, and Emergency room bleeding. This has
been designed for and validated in LGIB.
I believe that these factors impact the practicality and the novelty of the current work by Dr
Jeong and colleagues
Review for 10.1186/s12876-025-03638-z (2025)

Title: Which scoring systems are useful for predicting the prognosis of lower gastrointestinal
bleeding? Old and New
Version: 2 Date: 08 Dec 2024
Reviewer's report:
Which Scoring Systems Are Useful for Predicting the Prognosis of Lower Gastrointestinal
Bleeding? Old and New
The authors conducted a large retrospective study evaluating the performance of scoring
systems in predicting outcomes for patients presenting to the emergency department with
lower gastrointestinal bleeding (LGIB). The inclusion of recently developed scoring systems
(e.g., CHAMPS, SHA2PE) adds value to the study and provides important insights into LGIB
risk stratification. However, there are several issues that should be addressed to improve the
manuscript.
Major concerns
Patient Selection
1. The exclusion of patients without colonoscopic confirmation of LGIB may introduce selection
bias, especially in cases where endoscopy was contraindicated due to poor general conditions.
2. The study includes patients with malignancies but does not provide staging data. Malignancy
stages can significantly impact the mortality rate, which is the primary outcome of the study.
Consider adding this data or discussing its potential impact as a limitation.
3. Please clarify if the exclusion criteria (e.g., upper gastrointestinal bleeding or variceal
bleeding) were consistently and rigorously applied across all cases in the dataset.
Comparison Between Scoring Systems
4. The choice of AUROC as the primary metric for comparison is appropriate. However, please
provide the AUROCs for each scoring system and the p-values comparing the scoring systems
for each outcome. For example, compare AIMS 65 with Oakland for predicting 30-day mortality
(e.g., see Chang A, et al., Clin Endosc. 2021). Consider providing these comparisons in an
additional table or as part of Figures 2 & 3") could be more helpful
Statistical Analysis
5. While the study uses multivariate logistic regression effectively, the Hosmer-Lemeshow test
results and their implications for model fit should be reported in greater detail.
6. Adjustments for potential confounding variables (e.g., anticoagulant use, comorbidities) are
acknowledged, but it would be beneficial to expand on interactions between these factors.
Discussion
7. It would be helpful to discuss why certain scores, such as SHA2PE for prolonged hospital
stays, performed better than others and how this aligns with clinical utility.
8. While the results favor AIMS 65, CHAMPS, and ABC for mortality prediction, the discussion
could benefit from an exploration of why these scores excel despite variations in included
variables. For example, the simplicity of AIMS 65 may enhance its clinical adoption compared
to the complexity of CHAMPS.
Review for 10.1186/s12876-025-03629-0 (2025)

Title: Mechanistic investigation and the optimal dose based on baicalin in the treatment of
ulcerative colitis--A preclinical systematic review and meta-analysis
Version: 3 Date: 28 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
The authors should stess they had not studied UC which a human disease but animal models
of UC Abstract Authors should point out that they mainly searched animal studies Thus they
studies mainly animal models not UC Methods Was there any restriction in the language of
publications? Criteria for data biases should be provided Why highest dose has been selected
in the analysis and not most effective dose?  was there any possibility to group  doses utilized?
Why authors have selected 100 mg/kg dose? Statistics Does funnel plot analysis was performed?
Review for 10.1186/s12876-025-03629-0 (2025)

Title: Mechanistic investigation and the optimal dose based on baicalin in the treatment of
ulcerative colitis--A preclinical systematic review and meta-analysis
Version: 4 Date: 08 Nov 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Only humans suffer from UC Thus authors should use UC animal models not UC in
animal models suggesting that animals suffer from UC Authors could extend results section
providing numerical values and percentages while they could reduce the size of background
and methods section  Methods Authors should explain how they managed to overcome barriers
posed by mixing different animal models Results The single study model not described should
be better described
Review for 10.1186/s12876-025-03629-0 (2025)

Title: Mechanistic investigation and the optimal dose based on baicalin in the treatment of
ulcerative colitis--A preclinical systematic review and meta-analysis
Version: 4 Date: 09 Nov 2024
Reviewer:  Amira A A Othman
Reviewer's report:
I want to extend my congratulations to all those involved in this work. All the required
amendments have already been made carefully and satisfactorily. I hope that the research will
be presented to science.
Review for 10.1186/s12876-025-03629-0 (2025)

Title: Mechanistic investigation and the optimal dose based on baicalin in the treatment of
ulcerative colitis--A preclinical systematic review and meta-analysis
Version: 5 Date: 12 Dec 2024
Reviewer:  Amira A A Othman
Reviewer's report:
I want to extend my congratulations to all those involved in this work. All the required
amendments have already been made carefully and satisfactorily. I hope that the research will
be presented to science.
Review for 10.1186/s12876-025-03629-0 (2025)

Title: Mechanistic investigation and the optimal dose based on baicalin in the treatment of
ulcerative colitis--A preclinical systematic review and meta-analysis
Version: 6 Date: 20 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
The responses are satisfactory and the changes are done , the manuscript can be accepted for
publication.
Review for 10.1186/s12876-025-03622-7 (2025)

Title: Dietary Phytochemical Index and the Risk of gallstone disease: A case-control study
Version: 2 Date: 25 Oct 2024
Reviewer:  Yara Mahfouz
Reviewer's report:
This research project is very interesting, given the important role that phytochemicals play in
preventing diseases, including gallstone disease. The introduction is well written and follows a
relevant flow from disease description, causes and factors, reaching the objectives of the study.
The type of the study is a solid choice since it compares cases and controls. The methodology
is well detailed and easily repeatable. The choice of McCarty’s Phytochemical Index relies on
previously published valid data, and the FFQ and IPAQ are validated questionnaires, which
adds to the strength of the study. Some minor comments were given to the methodology section.
Results are in line with the pre-defined objective. However, some suggestions were made to
improve the manuscript results section, such as including more confounding dietary factors, in
addition to other comments. Discussion is well-written, although a clarification should be made
regarding the discussed dietary components (vitamins and minerals) that are not phytochemicals.
Review for 10.1186/s12876-025-03647-y (2025)

Title: Quantitative proteomic studies of the intestinal mucosa provide new insights into the
molecular mechanism of ulcerative colitis
Version: 0 Date: 03 Apr 2024
Reviewer's report:
This an original study entitled “Quantitative proteomic studies of the intestinal mucosa provide
new insights into the molecular mechanism of ulcerative colitis”. The theme is of considerable
current interest for the important clinical implications in terms of therapeutic outcomes as well
as research direction, but there are several issues that the authors should address:
1. Even though this original paper is very interesting there is a huge problem with English
language. The authors should ask a native English speaker to look at the whole manuscript. It is
very hard to read and focus on the content of this study in that form..
2. Keywords should be presented in alphabetical order.
3. Page 5: Study design: healthy control persons?
4. Page 5: What does “another 15 pairs of patients” mean? What was n?
5. Statistical analysis is not described at all. There is no information on the tests used.
6. Table 1./Figures: All abbreviations used should be explained.
7. Some Figures (Figure 1, Figure 3, presented in the manuscript are low quality, simply
unreadable, please improve the quality of the images.
8. Figure 7A: There is no scale bar.
Review for 10.1186/s12876-025-03647-y (2025)

Title: Quantitative proteomic studies of the intestinal mucosa provide new insights into the
molecular mechanism of ulcerative colitis
Version: 0 Date: 21 Sep 2024
Reviewer's report:
This article presents a unique study that delves into the pathogenesis of ulcerative colitis (UC)
through the innovative quantitative proteome analysis of the intestinal mucosa.
The authors described collecting mucosa from non-inflamed and inflamed areas and using it for
proteome analysis, but was the presence of inflammation determined endoscopically? Was the
inflammation in the biopsied tissue assessed histologically? Please describe clearly.
It is important to note that drugs administered to patients can influence the expression of
molecules in the mucosa, including cytokines. Therefore, the authors should consider the drugs
used in the enrolled patient and interpret the results obtained. Please discuss in the Discussion.
The duration of the disease, not age, also causes differences in the molecules expressed in the
mucosa. The authors need to take this into account when interpreting the results.
Interestingly, the present study identified enhanced expression of TXNDC5 in the colonic
mucosa of UC. However, the mechanism by which TXNDC5 is upregulated in the mucosa of
UC has yet to be investigated in detail. A detailed study of this mechanism using suitable cell
lines is needed.
Review for 10.1186/s12876-025-03647-y (2025)

Title: Quantitative proteomic studies of the intestinal mucosa provide new insights into the
molecular mechanism of ulcerative colitis
Version: 1 Date: 16 Dec 2024
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?
No - there are major issues
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: My overall impression of the manuscript is mixed. The previous
reviewers comments were sufficiently addressed, but the work is not particularly novel or
original, yet presents itself as such. Their main finding around TXNDC5 was previously reported
by whole transcriptomics (https://pmc.ncbi.nlm.nih.gov/articles/PMC9498489/) but the authors
do not cite this paper nor state their work is orthogonally confirmatory, which it is. If they
presented it as such, I would have less objection. As it stands, they overstate the novelty of their
findings.
REQUESTED REVISIONS:
The study itself is solid. The issue is the interpretation and overstating of the novelty of their
finding, as described previously."
Review for 10.1186/s12876-025-03647-y (2025)

Title: Quantitative proteomic studies of the intestinal mucosa provide new insights into the
molecular mechanism of ulcerative colitis
Version: 2 Date: 12 Jan 2025
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: Yes, the authors have responded to my comments and revised the
manuscript appropriately. It is suitable for publication.
Review for 10.1186/s12876-025-03611-w (2025)

Title: Liver cancer risk  and changes in lifestyle habits after successful hepatitis C virus therapy
                                                                               Post-DAA HCV therapy: lifestyle
changes and liver cancer risk
Version: 3 Date: 12 Nov 2024
Reviewer's report:
This is a well-conducted study that clearly informs practicing physicians that patients with
chronic Hepatitis C who achieve a high sustained virologic response (SVR) still remain at risk for
metabolic dysfunction- associated with liver disease (MASLD) and alcohol-related liver disease
(MetALD). The overall incidence of hepatocellular carcinoma (HCC) was low in this cohort,
which limits further analysis for risk stratification in these patients.
Another limitation of the study is that the authors did not address other decompensating events
related to the development of portal hypertension, such as ascites, encephalopathy, or variceal
bleeding, in the study subjects during the 48-month follow-up period.
In addition to obesity, diabetes is a significant risk factor for the progression of MASLD;
however, the overall prevalence of diabetes in this cohort was low. It is well-known that
treatment for Hepatitis C can improve insulin resistance and diabetes control, yet no information
was provided regarding diabetes management during the follow-up period.
The main outcome of the study was the development of hepatic steatosis, but steatosis was
identified in only 6% of patients, which is inconsistent with findings from other epidemiological
studies. The diagnosis of hepatic steatosis was based on ultrasound, which may not accurately
reflect the presence of hepatic steatosis in this population
Review for 10.1186/s12876-025-03611-w (2025)

Title: Liver cancer risk  and changes in lifestyle habits after successful hepatitis C virus therapy
                                                                               Post-DAA HCV therapy: lifestyle
changes and liver cancer risk
Version: 3 Date: 23 Nov 2024
Reviewer's report:
The authors present the results of a prospective study in patients with advanced liver disease
having achieved SVR in HCV infection analysing a change in life style habits after cure.
They included 182 patients and followed them until development of liver cirrhosis, death or loss
to follow-up with ultrasound, laboratory work-up, anthropometric measurements, and lifestyle
habit questionnaires. At 48 months, where were statistically significant increases in BMI and
alcohol consumption.
The study addresses a relevant clinical question and is well designed. Statistical methods are
appropriate and applied correctly. Discussed literature is relevant and up-to-date. The authors
also correctly discuss limitations of the study.
Major remarks:
In the abstract the authors state to follow-up until development of LC, death or loss to follow-
up, in the methods part of the paper it is until 4th year of follow-up, HCC occurrence or death.
The ethics section even mentions data collection until completion of 10 years after SVR. Could
you please specify the length of follow-up and correct the abstract consistently?
The authors give data on development of hepatic steatosis. How was that assessed? Ultrasound
or CAP measurement? The method section reports ultrasound for HCC surveillance but does
not mention fat assessment.
The AUDIT-test is designed to assess risk of alcohol addiction as well. Could you also report
on the points achieved in that screening test?
In the methods section the authors point to additional file 1 after introducing the methods to
assess alcohol consumption, but file 1 gives information on definition of obesity and hip-waist-
ratio.
Additional File 2 (survey questions) is not related to in the main file. Which document contains
S3 table mentioned in figure legend 3?
In figure 3 below the x-axis is “enol consumption” – probably alcohol consumption?
The audit questionnaire categorizes alcohol consumption to never, once per month, 2-4 times
per month, 2-3 times per week and almost daily. How were these categories accumulated in the
analysis?
The audit questionnaire also asks for the amount of alcohol consumed. Can you give data on the
amount of alcohol that patients consume in g/week or month?
Review for 10.1186/s12876-025-03634-3 (2025)

Title: Prevalence of Common Diarrheagenic Enterobacteriaceae in Iran (2000-2023): A
Systematic Review and Meta-Analysis
Version: 2 Date: 24 Sep 2024
Reviewer:  Siamak Heidarzadeh
Reviewer's report:
Dear Editor-in-Chief
My report as a reviewer
Title: " Exploring the Incidence of Bacterial Gastroenteritis across Iran: A Comprehensive
Systematic and Meta-Analysis review " by  Mozhgan Derakhshan-sefidi, Somayyeh Nadi-
Ravandi, Maryam Mirfakhraei, Sareh Bagheri-Josheghani.
Manuscript ID: 0a5b66c5-fab7-429a-9866-916b422bc52a
Journal: BMC Gastroenterology
Overall; authors of this manuscript present a topic of interest which deserves to be published.
Review for 10.1186/s12876-025-03634-3 (2025)

Title: Prevalence of Common Diarrheagenic Enterobacteriaceae in Iran (2000-2023): A
Systematic Review and Meta-Analysis
Version: 2 Date: 26 Sep 2024
Reviewer's report:
It is a very good practical article. The importance of the topic should be explained more,
especially in children. In the discussion, negative cultures caused by antibiotic use and incorrect
sampling should be discussed.
Review for 10.1186/s12876-025-03634-3 (2025)

Title: Prevalence of Common Diarrheagenic Enterobacteriaceae in Iran (2000-2023): A
Systematic Review and Meta-Analysis
Version: 2 Date: 28 Sep 2024
Reviewer's report:
I have read Derakhshan-sefidi et al.'s study entitled "Exploring the Incidence of Bacterial
Gastroenteritis across Iran: A Comprehensive Systematic and Meta-Analysis review". An
interesting topic with a large number of studies at a local scale! Please find below my comments
for revision. These comments aim to improve the study's scientific rigor, transparency, and
comprehensive understanding of the findings:
1. Remove Begg's test from the Abstract. Also, please add heterogeneity (I-squared index)
throughout the manuscript.
2. In the Abstract, revise '10.6% (95% CI, 9.1-12.4%)' to '10.6% (95% CI, 9.1-12.4)'.
3. Why did you start your database search from 2000 instead of from the beginning?
4. It would be better to add Embase to your database.
5. Clarify which authors contributed to article screening and data collection.
6. It is important to explain your eligibility criteria in more detail, e.g., type of studies, their
purpose and outcomes assessed, etc.
7. Mention the version of the CMA software.
8. In the Results, please revise 'A total of 724 articles were initially identified' to n=3701 articles
primarily identified.
9. Elaborate on the strengths and limitations of your study in the Discussion.
Review for 10.1186/s12876-025-03636-1 (2025)

Title: Remimazolam for procedural sedation in gastrointestinal endoscopy: real-life, single
center observational study
Version: 3 Date: 17 Sep 2024
Reviewer's report:
The paper is very difficult to read, especially the methods section. I think that a complete review
of the paper, either from a linguistic or a "organisational" point of view is essential. I therefore
suggest deeply revising the paper before a new submission.
- It is not clear which was the target desired for procedural sedation (deep sedation?). 6/25
patients needed propofol "rescue" administration during EGDS; this proportion of failures seems
quite high for "standard" EGDS, especially considering that in most centers propofol is not used
by the endoscopists and that midazolam is usually used with success as a single agent for EGDS.
- Methods section is very confusing and difficult to read and requires a complete revision
- It is stated that the target study population was 100 patients. First of all, it is not well explained
how was the ideal study population calculated. Secondly, only 73 patients were finally enrolled,
why?
- A clear definition of inclusion criteria is missing. The period of study is not reported; it is
not completely clear if the enrolled patients were consecutive random patients referred to your
center in a certain time frame
- The reported long recovery time should be better clarified
Review for 10.1186/s12876-025-03636-1 (2025)

Title: Remimazolam for procedural sedation in gastrointestinal endoscopy: real-life, single
center observational study
Version: 3 Date: 04 Nov 2024
Reviewer:  Hisatomo Ikehara
Reviewer's report:
This study by Conigliaro et al. demonstrated the utility of remimazolam in sedation for EGD
and lower endoscopy. As a recent ultrashort-acting sedative in the field of gastrointestinal
endoscopy, remimazolam’s effects were examined in Italy. To enhance scientific robustness,
revisions are recommended based on the following comments:
Comment 1
Please clarify whether this study employed a prospective or retrospective design. Additionally,
specify the study period, recruitment process for the 73 participants, and if any participants
dropped out.
Comment 2
Although the target number of cases was set at 100, only 73 were enrolled. Please provide the
statistical rationale for the analysis with 73 cases.
Comment 3
The initial and total doses of remimazolam differed between EGD and lower endoscopy, with
three cases requiring propofol as a rescue sedative during EGD. Given the expectation of shorter
duration for upper endoscopy, the total dose of remimazolam was high. Add statistical analysis
and discussion on this point.
Comment 4
Confirm whether fentanyl was administered to study participants and, if so, indicate the dosage.
Review for 10.1186/s12876-025-03636-1 (2025)

Title: Remimazolam for procedural sedation in gastrointestinal endoscopy: real-life, single
center observational study
Version: 4 Date: 17 Dec 2024
Reviewer:  Hisatomo Ikehara
Reviewer's report:
The authors have thoroughly addressed all the reviewers’ concerns. The revised manuscript is
now clear, well-structured, and needs no further revisions.
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 3 Date: 24 Oct 2024
Reviewer's report:
In this study, the authors mainly explored the role of VDR in the pathogenesis of BA, and the
1,25(OH)2D3/VDR pathway reduces double-stranded RNA virus-induced biliary epithelial cell
damage by inhibiting autophagy. They demonstrated that VDR downregulation is a marker of
poor prognosis in BA patients. Overall, there are several issues the authors need to solve to
further improve the manuscript.
Major:
1. Base on the Fig2A and Fig3A, the transfection efficiency is low both in the overexpressed
plasmid and siRNA experiments. Please provide more detail information of transfection
experiments, or  provide long exposure and short exposure WB data.
2. Some slices are missing in the consecutive sections of liver tissue of Fig1A.
Minor:
1. “In the liver, VDR is mainly expressed in liver parenchymal cells and especially hepatic non-
parenchymal cells such as hepatic stellate cells, sinus endothelial cells, Kupffer cells, and bile
duct epithelial cells”, the logic is incorrect.
2. In the third sentence of “VDR activators may provide an effective approach for the treatment
of BA”, the two groups with different results were written with the same name.
3. The names of genes and protein should be uniformed. For examples, P62 and p62, p53 and
SCR and Scr”.
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 3 Date: 26 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract The study is an original work and not a review Thus abstract should explain
method and present findings!  Methods Number of tissue section collected belong in the
results The same is valid for patients characteristics (Table 1) Cafaperazone is antibiotic
and corticosterods are immunosuppressants Table 2 also belongs in the results Nevertheless
characteristics recorded should be described in methods section Eliza for cytokines measurement
should be described The same suggestion pertains Western Blotting Authors should avoid
entering phrase following manufacturer instructions They better provided a brief description
Results Qualitative comparisons based on certain scales should be followed by scale desciption
Qualitative comparisons and significant quantitative ones should be presented in the text
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 4 Date: 11 Nov 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Still results section remains limited and lacks any numerical values Authors should
expand its length on the expense of the background and methods section After-all there are data
for more than one papers   Statistics Sample size for various levels of the study design should
be calculated For instance were the initial groups 38 and 10 large enough? Why had the authors
not selected to examine equal number of controls? Were study samples not large enough to
evaluated co-founding factors effect?
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 4 Date: 13 Nov 2024
Reviewer's report:
In this study, Cheng et al. investigated the effects of Vitamin D3 and VDR on double-
stranded RNA (dsRNA)-induced biliary epithelial cell (BEC) damage, proposing that VDR
activation mitigates dsRNA-induced damage and apoptosis by inhibiting autophagy, both in
vitro and in vivo. They suggest that the 1,25-VD3/VDR/Src axis alleviated poly(I:C)-induced
HIBEC damage and apoptosis through the PLA2/PKC/ERK pathway. However, there appear
to be several substantial over-interpretations, and some conclusions lack supporting evidence.
Specific comments are provided below:
1. To facilitate readability, it is recommended to separate the main text from the figure legends.
Including figure numbers directly in the text will reduce the need for readers to frequently cross-
reference the results with figure legends.
2. Figure 6 is missing from the manuscript, making it challenging to fully understand the results.
Please ensure that all referenced figures are included in the final version to allow for a thorough
assessment of the data.
3. In the in vitro study, poly(I:C) induced HIBEC damage and apoptosis through autophagy
promotion, and both chloroquine and 1,25-VD3 were found to mitigate poly(I:C)-induced
HIBEC injury and apoptosis by autophagy inhibition. The authors also indicate that VDR
knockdown counteracts the protective effect of 1,25-VD3 against poly(I:C)-induced HIBEC
damage. A clearer explanation of the interaction between chloroquine and VDR in this context
is needed, specifically addressing their respective roles and potential overlap in mechanism.
4. The in vitro study employed poly(I:C) to induce HIBEC damage, while the in vivo model
involved RRV injection to induce hepatic jaundice in newborn mice. Given that poly(I:C) and
RRV both affect dsRNA signaling, but through pathways beyond TLR3, a detailed rationale for
using these different agents is needed to support experimental feasibility and relevance.
5. The manuscript contains inconsistencies in abbreviation usage, specifically between
"IBDECs" and "HIBEC." Please ensure that all abbreviations are consistent throughout the text
or provide clarification on any distinctions.
6. In Figures 2E, 3E, and 4B, axis labels need to be corrected for consistency and accuracy. This
will improve clarity and ease of interpretation for the readers.
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 5 Date: 07 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors , please address the following points below
-While the findings from the mouse model and retrospective clinical data are promising, there
is a notable lack of discussion regarding the challenges associated with translating these results
into clinical practice. For instance, the long-term effects of vitamin D receptor (VDR) activation
on other immune or metabolic pathways in patients with biliary atresia (BA) remain uncertain. A
comprehensive exploration of dosage, treatment duration, and safety profiles would significantly
enhance the clinical implications of these findings.
-The retrospective clinical analysis only offers a correlation between calcitriol treatment and
improved outcomes. To establish causality and accurately assess the efficacy of VDR activators
in BA, it is essential to conduct a prospective randomized controlled trial (RCT).
-Moreover, it would be advantageous to provide a detailed examination of how autophagy
inhibition specifically benefits bile duct epithelial cells (BECs) and whether long-term
suppression of autophagy could result in any adverse consequences.
-The study does not adequately address the potential off-target effects of chloroquine, nor does
it consider whether its inhibition of autophagy might lead to unintended consequences in other
cell types or organs. Furthermore, there is insufficient exploration of potential interactions with
other immune or inflammatory pathways that may influence clinical outcomes.
-A more thorough analysis of how the autophagic process in BA differs from that in conditions
such as alcoholic liver disease or cirrhosis would clarify the proposed therapeutic strategy.
Additionally, the relationship between SRC activation and the ERK1/2 pathway in the context
of BA warrants further investigation.
-Incorporating extended follow-up periods in animal models to evaluate the long-term benefits
of VDR activation would bolster the rationale for its therapeutic application in BA. ---Overall,
while this approach represents a novel strategy for addressing virus-induced BA—specifically
through the modulation of autophagy and inflammation in bile duct epithelial cells—further
validation in larger clinical cohorts and more diverse BA models is essential to establish the
clinical utility of VDR-based therapies.
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 8 Date: 16 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
-While the study focuses on autophagy as a primary mechanism of VDR action, it could further
explore other potential molecular pathways involved in BA progression. For example, the role
of VDR in modulating inflammation or immune responses (e.g., via cytokines) is mentioned but
could be explored in more detail.
-The study focuses on poly(I:C)-induced damage, which mimics viral infection, but it would be
interesting to examine whether VDR activation offers protection against other forms of stress,
such as bacterial infections or bile acid-induced damage, which are also relevant to BA.
-While the RRV-induced BA mouse model is an appropriate choice for studying viral-induced
liver injury, it may not fully capture the complexity of BA, which is believed to be influenced by
both environmental and genetic factors. The inclusion of additional models or a more nuanced
discussion of model limitations could provide a more comprehensive view of VDR’s role in BA.
-Although in vitro experiments examine various doses of 1,25-VD3, it would be useful to include
a more detailed analysis of dose-response effects in clinical settings. The optimal dose and
duration of treatment for BA patients remain uncertain and would be important to clarify for
future clinical trials.
-The study focuses primarily on poly(I:C)-induced damage in BECs, which may not fully
replicate the diverse etiologies of BA, such as those caused by cytomegalovirus or environmental
toxins like biliatresone. More work is needed to extend these findings to other forms of BA.
Review for 10.1186/s12876-025-03640-5 (2025)

Title: Vitamin D3/VDR alleviates double-stranded RNA virus -induced biliary epithelial cell
damage by inhibiting autophagy
Version: 9 Date: 23 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
The responses are satisfactory, the manuscript can be accepted for publication.
Review for 10.1186/s12876-025-03642-3 (2025)

Title: Cardiometabolic Index as a Predictor of Gallstone Incidence in U.S. Adults: Insights from
NHANES 2017-2020
Version: 0 Date: 17 Dec 2024
Reviewer's report:
In this manuscript entitled “Association Between the Cardiometabolic Index and Gallstone
Incidence in American Adults: Evidence from the NHANES 2017-2020 Dataset”, the authors
examined the association between cardiometabolic index and gallstones. It is impractical to
calculate the Cardiometabolic Index during routine health screenings, and its application in
daily clinical practice is limited. Moreover, the manuscript lacks clarity regarding diagnostic
capabilities, as it does not present the results of receiver operating characteristic analysis for
determining cut-off values. Consequently, this paper do not reach the level for publication.
Review for 10.1186/s12876-025-03642-3 (2025)

Title: Cardiometabolic Index as a Predictor of Gallstone Incidence in U.S. Adults: Insights from
NHANES 2017-2020
Version: 0 Date: 19 Dec 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
-While the introduction mentions complications like cholecystitis and pancreatitis, a brief
mention of how these complications directly relate to mortality or quality of life could strengthen
the urgency of addressing GSD as a public health concern.
-The rationale behind excluding individuals due to incomplete CMI information, missing
gallstone data, and insufficient covariate information is clear. However, it would be beneficial
to explain why specific variables (e.g., educational attainment or marital status) were considered
essential for inclusion in the final analysis. This would help justify the exclusion of participants
more transparently.
-The inclusion of dietary factors such as calorie and fat consumption is a strength, but it might
be beneficial to clarify how these variables were adjusted for. For example, how was energy
intake (calories) factored into the analysis of CMI? Were macronutrient intake patterns (e.g.,
carbohydrate vs. fat intake) considered? A brief explanation of how these dietary variables were
handled would provide more context for the readers.
-The CMI threshold of 0.996 is identified as significant, but it is not clear how this threshold was
determined and what it means in practical terms. More explanation about why this particular
value was chosen or how it might be clinically relevant would enhance understanding.
-The results from propensity score matching (PSM) and IPW are described as validating the
findings, but the discussion could go further in explaining the implications of the confidence
intervals (e.g., wide CIs in PSM) and how they relate to the precision of the estimates.
-The genetic component of GSD is mentioned in the context of existing GWAS findings that
identify genetic loci related to cholesterol and lipid metabolism. However, further exploration
of how genetic predispositions might interact with CMI to influence GSD risk would be
beneficial. For instance, how might genetic polymorphisms that affect cholesterol metabolism
(e.g., ABCG5, ABCG8) influence the impact of metabolic factors like CMI? Expanding on the
potential gene-environment interactions could help frame CMI within a more comprehensive
etiological model of GSD.
Review for 10.1186/s12876-025-03642-3 (2025)

Title: Cardiometabolic Index as a Predictor of Gallstone Incidence in U.S. Adults: Insights from
NHANES 2017-2020
Version: 1 Date: 06 Jan 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
The responses are satisfactory.