JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-025-04096-3 (2025)

Title: Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated
Blautia species and bile acid metabolic pathways
Version: 2 Date: 26 May 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below
1. Small Sample Size and Power
The study includes only 23 CCA patients and 29 controls, which may limit statistical power
and generalizability. PJustifythe sample size (e.g., power analysis). Acknowledge this limitation
more explicitly in the discussion, particularly regarding its impact on model performance and
biomarker discovery.
2. Lack of Validation Cohort
Findings are based on a single cohort without independent validation.
Include an external validation dataset, even if from a public database (e.g., GMrepo or HMP), or
clearly state this limitation and suggest that future studies will validate findings in independent
populations.
3. Causal Interpretation
While the study is observational, some interpretations suggest causal relationships between
dysbiosis and CCA. Rephrase these sections to avoid overinterpretation. Emphasize correlation
rather than causation unless supported by functional assays or longitudinal data.
4. Dietary and Environmental Confounders
While the authors state participants had similar diets, no detailed dietary or lifestyle data is
reported.Include more information about dietary intake, BMI, alcohol consumption, and other
potential confounders, or at least acknowledge this limitation in the discussion.
5. Lack of In-depth Functional Validation
Functional predictions are based on metagenomic annotation (e.g., KO pathways) without
metabolomic or transcriptomic validation. Discuss this as a limitation and, if available,
incorporate fecal bile acid profiling or qPCR validation of key taxa.
6. Insufficient Clinical Characterization of CCA Subtypes
CCA includes diverse subtypes (intrahepatic vs extrahepatic); these are not stratified in the
analysis. Clarify whether subtypes were included and explore whether microbial signatures
differ by subtype. If not feasible, at least report the subtype distribution.
7. Language and Clarity
While largely well-written, some sentences are overly complex or passive. Minor language
polishing for clarity and conciseness, particularly in the Discussion.
8. Data Availability Statement
The manuscript states data are available upon request but does not provide accession numbers
or repository information. Deposit raw sequencing data in a public repository (e.g., NCBI SRA)
and include accession numbers in the manuscript.
Review for 10.1186/s12876-025-04096-3 (2025)

Title: Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated
Blautia species and bile acid metabolic pathways
Version: 3 Date: 11 Jun 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
the responses are satisfactory
Review for 10.1186/s12876-025-04081-w (2025)

Title: Efficacy and Safety of Ultrasound-Guided Percutaneous Microwave Ablation for
Hepatocellular Carcinoma at Specific Anatomic Sites of the Liver: A Systematic Review and
Meta-Analysis
Version: 0 Date: 30 Mar 2025
Reviewer's report:
This is an interesting meta-analysis of nine studies reporting outcomes of US-guided microwave
ablation (MWA) for hepatocellular carcinoma (HCC). The authors aim to compare outcomes
between tumors located at specific anatomic sites of the liver and those in non-specific sites.
Below are a few points:
1. It is current practice to avoid treating tumors in challenging locations solely with US guidance
to minimize complications and optimize clinical outcomes. Given this, the clinical significance
of the study remains unclear.
2. The authors report that complication rates were comparable between specific and non-specific
tumor sites. However, there is no description of the nature or severity of these complications,
which limits clinical interpretation.
3. The most critical technical factor in tumor ablation is the minimal ablation margin, as
suboptimal margins are strongly associated with tumor recurrence. If an adequate margin cannot
be achieved, alternative curative treatments should be considered. However, ablation margins
were neither evaluated nor discussed in this meta-analysis.
4. In the inclusion criteria, tumors within 5 mm of the intestine or kidney are classified as specific
anatomic site tumors. How many such tumors were included in the study? Given that these
tumors can be safely ablated using hydrodissection, what was the rationale for including them
in the specific anatomic site category?
5. The exclusion criteria state that studies without a control group were excluded. However, this
is unclear, as most included studies are cohort studies rather than case-control studies.
6. Given that the same search criteria were applied across all databases, how do the authors
explain the presence of only 498 duplicate records? Additionally, how often did the authors
encounter missing data that required contacting the original study authors?
7. Several references, such as Reference 25 (Journal of Oncology), could not be retrieved. The
authors should carefully verify all references to ensure accuracy and completeness.
Review for 10.1186/s12876-025-04081-w (2025)

Title: Efficacy and Safety of Ultrasound-Guided Percutaneous Microwave Ablation for
Hepatocellular Carcinoma at Specific Anatomic Sites of the Liver: A Systematic Review and
Meta-Analysis
Version: 0 Date: 11 Apr 2025
Reviewer's report:
This systematic review and meta-analysis evaluates the efficacy and safety of ultrasound-guided
percutaneous microwave ablation (MWA) for hepatocellular carcinoma (HCC) at specific
anatomical sites compared to non-specific sites. The authors included nine studies (2,381
patients) and found no significant differences in 1-, 3-, or 5-year survival rates, complete ablation
rates, or major complications between groups. The study concludes that MWA is equally
effective and safe for HCC at challenging anatomical locations, supported by low heterogeneity
and robust sensitivity analyses.
Major Comments
1. Handling of Missing Data
- The manuscript reports "NA" entries in baseline characteristics (e.g., Liu A, 2018: missing
control group demographics). Clarify how missing data were addressed (e.g., exclusion,
imputation) to ensure validity.
2. Subgroup Analysis
- While heterogeneity was low, subgroup analyses based on *specific tumor locations* (e.g.,
subcapsular vs. near vessels/gallbladder) are absent. Such analyses could reveal nuanced
differences in outcomes and should be acknowledged as a limitation.
3. Study Design Heterogeneity
- The inclusion of both prospective and retrospective cohort studies introduces potential bias. A
sensitivity analysis excluding retrospective studies (if feasible) would strengthen conclusions.
4. Generalizability of Findings
- The definition of "specific sites" includes diverse locations (e.g., diaphragm, vessels,
gallbladder). The aggregated results may mask site-specific risks. Discuss whether outcomes
might vary for tumors adjacent to critical structures (e.g., gallbladder vs. diaphragm).
5. Clinical Relevance of Non-Significant Results
- While statistical non-significance is emphasized, the confidence intervals for major
complications (OR=1.44, 95% CI: 0.59–3.51) suggest a possible trend toward higher risk in
specific sites. This should be addressed in the discussion.
Minor Comments
1. Abbreviations and Definitions
- Define "PSM" (Propensity Score Matching) in Table 1 or the methods section. Ensure all
abbreviations (e.g., NOS) are consistently explained.
2. Standardization of Terminology
- Standardize terminology in Table 1 under "Location of Liver Cancer" (e.g., "Adjacent to large
vessels" vs. "Near diaphragm").
3. Figure/Table Referencing
- The manuscript references Figure 1 (PRISMA flow diagram) and Figures 2–3 (forest plots),
but these were not included in the provided content. Verify numbering and ensure all figures
are accessible.
4. Grammar and Syntax
- Minor revisions needed for readability:
- *Original:* "patients who are not candidates for surgery or who refuse surgery"
- *Revised:* "patients ineligible for or declining surgery"
5. Conflict of Interest Statement
- The declaration states "no conflict of interest," but authors from the same institution (928
Hospital) may warrant explicit confirmation of independence.
Review for 10.1186/s12876-025-04081-w (2025)

Title: Efficacy and Safety of Ultrasound-Guided Percutaneous Microwave Ablation for
Hepatocellular Carcinoma at Specific Anatomic Sites of the Liver: A Systematic Review and
Meta-Analysis
Version: 1 Date: 22 May 2025
Reviewer's report:
No comments.
Review for 10.1186/s12876-025-04110-8 (2025)

Title: Clinicopathological characteristics of 30 cases of pyloric gland adenoma: a single center
case series
Version: 3 Date: 09 Aug 2024
Reviewer's report:
This paper examines the clinical characteristics and endoscopic findings of PGA based on case
examples. The following points require careful consideration:
While there are commonalities in histological features and immunohistochemical staining
between PGA of the stomach and duodenum and that of the gallbladder, reports suggest that
they differ in genetic abnormalities and directions of cellular differentiation. These two entities
should be clearly distinguished, and analyzing them together seems challenging.
Since one of the aims of this paper, as indicated by its title, is to explore endoscopic
characteristics, the analysis should be limited to the stomach and duodenum, where endoscopic
findings can be observed.
Regarding gallbladder PGA, the discussion does not address it. To analyze it within a single
paper, it is necessary to include a discussion on gallbladder PGA as well. The conclusion omits
mention of the gallbladder.
Your consideration on these matters would be greatly appreciated.
Review for 10.1186/s12876-025-04110-8 (2025)

Title: Clinicopathological characteristics of 30 cases of pyloric gland adenoma: a single center
case series
Version: 4 Date: 20 Jun 2025
Reviewer's report:
Thank you for your thorough revision. The change in the title and the expanded discussion
on gallbladder PGA, including histological origin and molecular data, adequately address the
concerns raised in the initial review. The revised conclusion also reflects the study’s scope more
accurately. I have no further major concerns.
Review for 10.1186/s12876-025-04095-4 (2025)

Title: Long-term Quality of Life After Acute Pancreatitis: A Systematic Review and Meta-
Analysis
Version: 0 Date: 24 Feb 2025
Reviewer:  Erfan Arabpour
Reviewer's report:
Thanks for giving me the opportunity to review this manuscript. In this study, Xu et al.
systematically investigated the quality of life after AP. The manuscript is well-designed, and the
presentation of work is appropriate. In contrast to similar previously published meta-analysis
(PMID= 37619216), this study has more focus of quality of life domains. I have just several
minor points that kindly request to be addressed by the authors:
- Please cite the reference for this sentence (line 122-125): "If the SD value was not provided in
the complete text, it was calculated using the 95% confidence interval (CI) based on the sample
size, as suggested by the Cochrane Handbook."
- As recommended in PRISMA checklist, please provide the complete search strategy used for
each database in supplementary. Please also mention the citations that were excluded in full-
text screening as a supplementary table.
- In figure 1, please employ a consistent format to indicate the number of articles in that category.
For instance, as shown at the top of the figure, place the numbers (I mean "n= X") within
parentheses.
- Finally, kindly request performing a cumulative analysis if applicable. This would be
interesting by advancements in patients care, whether quality of life is less affected by AP.
Review for 10.1186/s12876-025-04095-4 (2025)

Title: Long-term Quality of Life After Acute Pancreatitis: A Systematic Review and Meta-
Analysis
Version: 1 Date: 26 Apr 2025
Reviewer:  Erfan Arabpour
Reviewer's report:
I want to thank the authors for addressing reviewers' concerns satisfactorily.  The manuscript
quality is enhanced significantly. I only have a minor comment. In figure 1 (PRISMA flowchart),
for better consistency, kindly request to revise the format of number of studies that were found
in each database (e.g. "PubMed (n=198)" or "Embase (n=226)")
Review for 10.1186/s12876-025-04095-4 (2025)

Title: Long-term Quality of Life After Acute Pancreatitis: A Systematic Review and Meta-
Analysis
Version: 1 Date: 28 Apr 2025
Reviewer's report:
Unfortunately, despite the authors' efforts, the main flaws have not been resolved and the authors
have only provided justifications. I was again unable to continue. This article has serious flaws,
especially in the results, method, and heterogeneity.
Review for 10.1186/s12876-025-04095-4 (2025)

Title: Long-term Quality of Life After Acute Pancreatitis: A Systematic Review and Meta-
Analysis
Version: 1 Date: 28 Apr 2025
Reviewer:  Sheza Malik
Reviewer's report:
Thank you for submitting the revised version of your manuscript titled "Quality of
Life After Acute Pancreatitis: A Systematic Review and Meta-Analysis" (Manuscript ID:
ac9822db-220b-4a59-a1e9-223ac79f2cf7).
We appreciate the considerable effort you and your co-authors invested in addressing
the reviewers’ and editorial comments. The revised manuscript demonstrates substantial
improvements, including:
Conducting an expanded and updated systematic search across multiple major databases.
Providing a detailed supplementary appendix containing search strategies, exclusion lists, and
justifications.
Strengthening the methodological transparency by elaborating on eligibility criteria, data
extraction methods, and risk of bias assessments.
Clarifying statistical methodologies, including heterogeneity assessment, model selection, and
sensitivity analysis.
Expanding the discussion section to meaningfully contextualize your findings against previous
systematic reviews, observational studies, and meta-analyses.
Refining the conclusions to accurately reflect the heterogeneity of findings while avoiding
overstatements.
Including important structural improvements, such as addition of PICO framework, ethical
declarations, appropriate citations, and better figure/table formatting.
The manuscript now meets the high standards required for publication, and the revisions have
significantly strengthened its clarity, scientific rigor, and relevance to the field.
I am pleased to inform you that your manuscript has been accepted for publication.
Review for 10.1186/s12876-025-04100-w (2025)

Title: Endoscopic characteristics and treatment modalities of gastrointestinal glomus tumors: a
multicenter retrospective study
Version: 1 Date: 19 Feb 2025
Reviewer's report:
The authors investigated the treatment outcomes of gastrointestinal glomus tumors.
Furthermore, this study seems to summarize the clinicopathologic features and endoscopic
findings. We think some descriptions were questionable. Below are my specific critics.
1. The small sample size is a concern. The authors describe endoscopic findings of submucosal
elevation and a certain frequency of ulceration, but this has already been described in previous
reports and is not novel.
2. Compared to previous reports, we believe the novelty is that a larger proportion of endoscopic
resections than surgical procedures were investigations of treatment outcomes. However,
regarding long-term prognosis, only 5 cases of endoscopic resection were investigated and
the duration was not so long (39.2 months). Furthermore, the surveillance method was only
a telephone interview and endoscopy, without CT or medical examination, which should be
mentioned in the “limitations” section.
Review for 10.1186/s12876-025-04100-w (2025)

Title: Endoscopic characteristics and treatment modalities of gastrointestinal glomus tumors: a
multicenter retrospective study
Version: 1 Date: 24 Feb 2025
Reviewer:  Hisatomo Ikehara
Reviewer's report:
Overall, this manuscript offers an interesting retrospective analysis on gastrointestinal glomus
tumors, highlighting the diagnostic and therapeutic role of endoscopic procedures. However,
critical revisions are required to address methodological clarity, detailed patient selection,
endpoint definitions, and statistical reporting. Revision is recommended to enhance transparency
and improve scientific rigor.
Comments
Comment 1: Please clarify and expand the patient selection criteria, including explicit inclusion/
exclusion details and the rationale behind the small sample size.
Comment 2: Clearly define primary and secondary endpoints, and improve the statistical
analysis by including confidence intervals and effect sizes.
Comment 3: Expand the discussion on study limitations, particularly regarding the retrospective
design, sample size constraints, and variability in follow-up duration.
Comment 4: Provide clearer indications for choosing endoscopic versus surgical treatment and
elaborate on the clinical applicability of your findings.
Review for 10.1186/s12876-025-04004-9 (2025)

Title: Lipid Metabolism Disturbance and Immune Dysfunction in HBV-Related Acute-on-
Chronic Liver Failure: A Retrospective Cohort Study
Version: 5 Date: 25 Apr 2025
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/s12876-025-04004-9 (2025)

Title: Lipid Metabolism Disturbance and Immune Dysfunction in HBV-Related Acute-on-
Chronic Liver Failure: A Retrospective Cohort Study
Version: 5 Date: 27 Apr 2025
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
the responses are satisfactory
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 0 Date: 20 Mar 2025
Reviewer's report:
This paper analyzed the common risk factors of PVT and EVB and the correlation between these
two major complications in patients with cirrhosis.
However, this article has many shortcomings.
1.Overall, the language of this article needs to be refined. The preface is too long to explain the
intention clearly, and it is written like a discussion and needs to be rewritten.
2.Please explain “no history of gastrointestinal bleeding prior to their first hospitalization”#is
this reasonable#
3.Feeling that the meaning is the same, not expressed clearly, “(1) All patients were divided into
EVB and non-EVB groups to analyze the influencing factors of EVB occurrence in patients with
cirrhosis; (2) All patients were divided into PVT and non-PVT groups to analyze the influencing
factors of PVT occurrence in patients with cirrhosis”.
4.The section of “Grouping and Observation Indicators”,not reasonable and no scientific
grouping.
5.The grouping is unscientific, and there are unscientific aspects to the results section, which
requires restatistics and rewriting of the results based on the grouping.
6.In the discussion section, the views of this article and the links to the relevant literature are
not fully explained clearly.
7.Throughout the full text, the writing is not standardized. For scientific papers, one paragraph
should not be too long, just 4-6 lines to illustrate the situation.The preface of this article is
too long, there is too little of the section of discussion, and the arrangement of paragraphs is
unreasonable.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 0 Date: 25 Mar 2025
Reviewer's report:
In this article, the researchers explored the common risk factors and causal links between portal
vein thrombosis (PVT) and esophagogastric variceal bleeding (EVB) among liver cirrhosis
patients. After looking back at data from 1,223 liver cirrhosis patients, they ultimately included
247 patients for a 10-year follow-up study.The purpose of this study is well-defined, with a
sufficient number of cases included and adequate follow-up duration. However, patient mortality
is a competing risk for the occurrence of PVT and EVB in liver cirrhosis, which should be taken
into account in the statistics. There are several factors that weren't included in the article, such
as the baseline degree of esophageal varices and treatment after esophageal variceal bleeding.
Therefore, it's suggested to add more data.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 2 Date: 18 Apr 2025
Reviewer's report:
The author clarified some issues, but there are still some parts that need to be further clarified
1. The author acknowledges that excluding patients who underwent surgical treatment during
the follow-up period would have an impact on the final outcome, but insisting on it,
which is questionable. It is incorrect to directly exclude these patients, because there are no
exclusion indications for these patients before treatment. Postoperative treatments such as liver
transplantation or splenectomy should be regarded as competing events for outcomes. Such
handling can minimize the confounding factors introduced by surgical treatment and increase
the number of patients at the same time. The impact of excessive exclusion of patients on the
outcome is very direct. The author did not specify how much the exclusion of this group of
patients affected the outcome, which casts doubt on the research results.
2. The author needs to cite literature on the reasons for age grouping to enhance persuasiveness.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 2 Date: 21 Apr 2025
Reviewer's report:
The authors gave point-to-point answers according to the requirements of the review and
made modifications to the full text according to the requirements, which meets the publication
requirements of this journal.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 3 Date: 29 Apr 2025
Reviewer's report:
The author revised the full text as required, which meets the publication requirements of this
journal.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 3 Date: 28 May 2025
Reviewer's report:
The manuscript presents interesting and potentially valuable research on PVT and EVB in
cirrhosis. However, several important clarifications and additions are necessary to strengthen
the methodological rigor, contextual relevance, and accuracy of the findings before it can be
considered suitable for publication.
1.  In the natural history of cirrhosis, the presence of pre-existing esophageal/gastric varices
(particularly their size and red wale signs) is a paramount risk factor for first bleeding. Crucially,
whether a patient is on established primary prophylaxis (e.g., non-selective beta-blockers or
endoscopic variceal ligation) significantly modifies this risk. The current analysis appears to lack
data on previous endoscopic findings (varices: yes/no, grade, features) and primary prophylaxis
status (yes/no, type). This omission is a significant limitation. We strongly recommend the
authors supplement their dataset and analysis to include these essential variables.
Specifically:
Report the proportion of patients with known pre-existing varices prior to the index event/study
period.
Report the proportion of patients receiving primary prophylaxis and the type used (NSBB, EVL,
combination, none).
Include these factors (previous varices, primary prophylaxis status) as covariates in multivariate
analyses of EGVB risk factors. Discuss how their inclusion (or absence in the current analysis)
impacts the interpretation of the identified risk factors. Failure to account for these well-
established modifiers substantially weakens the conclusions regarding novel or other risk
factors.
2. The manuscript utilizes a classification for Portal Vein Thrombosis (PVT) (e.g., partial/
complete, acute/chronic, extent). However, it does not explicitly state which specific
classification criteria or definitions were applied at the study center. To ensure clarity and
reproducibility, please explicitly reference the specific PVT classification standard used in your
center (e.g., Yerdel classification, European Association for the Study of the Liver (EASL)
guidelines definitions, American Association for the Study of Liver Diseases (AASLD) practice
guidance definitions, or an internally validated protocol).
3. On Page 5, Lines 96-97, the text states: " This study implemented three distinct patient
groupings to evaluate the relationships between clinical variables and outcomes" However, the
subsequent description (Lines 97-100) details only two distinct grouping methods.
Provide the missing description for the third grouping method  and ensure the results analysis
consistently reflects all three groupings mentioned.
Review for 10.1186/s12876-025-04094-5 (2025)

Title: Portal Vein Thrombosis and Esophageal-Gastric Variceal Bleeding in Cirrhosis: Shared
Risk Factors and Causal Relationship
Version: 4 Date: 04 Jun 2025
Reviewer's report:
The study retrospectively enrolled patients with no history of esophageal variceal bleeding or
portal vein thrombosis and analyzed their risk factors. Without any intervention, the article
observed the occurrence of these two clinical events alongside their associated risk factors.
Statistical methods were sound, and definitions were clearly established.
Review for 10.1186/s12876-025-04102-8 (2025)

Title: Sexual Function, Depression, and Quality of Life in Patients with Irritable Bowel
Syndrome
Version: 1 Date: 07 Aug 2024
Reviewer's report:
While the study "Sexual Function, Depression, and Quality of Life among IBS Patients" offers
significant insights and makes a meaningful contribution to understanding the multifaceted
impact of IBS, there are important areas that require improvement before it can be considered
for publication.  Below is the assessment considering the strengths and flaws identified.
A. Strengths:
1. clear aim and findings: this study presents its objectives and key findings in a clear and
structured manner.
2. comprehensive literature review: It provides a thorough background, referencing an extensive
array of studies that contextualize the fidings within the broader body of research. 3. focus on
QoL and sexual function: the emphasis on these often-overlooked aspects of IBS patient care
is laudable
4. gender-specific analysis: Including gender-specific findings provides a nuanced
understanding of the differential impacts on men and women.
5. use of control groups: The inclusion of two distinct control groups adds depth to the
comparative analysis.
B. Flaws
1. lack of power analysis: the absence of a power analysis is a significant methodological flaw
that undermines the reliability of the findings.
2. overemphasis on non-significant trends: the discussion sometimes overemphasizes trends that
are not statistically significant.
3. inconsistent focus: the narrative occasionally shifts abruptly between different aspects, leading
to a somewhat disjointed discussion.
4. repetition: redundancies in discussing sexual satisfaction and mood impact detract from the
clarity.
5. insufficient exploration of limitations: The study does not adequately address its limitations,
such as sampling method and potential biases.
6. potential confounding factors: a detailed presenttaion of confounding factors is lacking.
7. detailed control group comparisons: this study would benefit from a more detailed comparison
between the control groups.
Recommendations for improvement
- please include a power analysi to ensure the sample size is adequate.
- streamlines the discussion by eliminating repetition and maintaining a consistent focus.
- explicitly address non-significant findings: clearly state the non-significance of certain trends
or differences.
- acknowledge limitations: provide a discussion of the study's limitations.
- discuss confounding factors: include a comprehensive discussion of potential confounding
factors.
- enhance control group analysis: please provide a more detailed comparison of the control
groups.
The revisions should address the methodological flaws, enhance the clarity and coherence of the
discussion, and provide a more comprehensive analysis of the control groups. Thank you
Review for 10.1186/s12876-025-04102-8 (2025)

Title: Sexual Function, Depression, and Quality of Life in Patients with Irritable Bowel
Syndrome
Version: 1 Date: 08 Apr 2025
Reviewer's report:
Comorbidities are common in brain-gut axis disorders. (10.1111/apt.16589) The overlap
of diseases in irritable bowel syndrome (IBS) alters health-seeking behavior (10.1016/
j.cgh.2019.09.020). For example, it is known that these patients report comorbidities
more commonly during gynecological consultations. (10.1016/j.cgh.2019.09.020) Depression
(10.3390/nu13093061) and sexual dysfunction (10.1186/s12905-023-02272-9) have been
shown to be related to IBS, yet their impact on quality of life is a developing area.
The cross-sectional study under review addresses this topic. The authors conducted a survey
of 145 subjects: 47 patients with IBS, 49 patients with depression without IBS, and 49 normal
subjects. They assessed depression with the Beck Inventory II (BDI-II), sexual dysfunction with
the Female Sexual Function Index (FSFI) and the Male Sexual Function Index (MSFI), and
quality of life with the World Health Organization Quality of Life Brief Version (WHOQOL-
BREEF). They found no differences in the various variables investigated, such as age,
occupation, education, place of residence, and economic status, between the three study groups,
with the exception of smoking and medication use among depressed individuals. IBS patients
who were more depressed had a lower quality of life, while sexual function was associated with
better values among females in controls compared to IBS patients.
Although it contains relevant data, this study has shortcomings that must be addressed before
it can be considered for publication. The most important is the lack of a recent search for
information on the topics covered. For example, there is one study on sexual dysfunction that
was not considered for comparison purposes (10.1186/s12905-023-02272-9), as well as other
more recent studies on depression (10.3390/nu13093061). The second observation concerns the
conclusion; it cannot be stated as an answer that was not evaluated, for example: "Establishing
satisfactory sexual relationships, particularly in chronic conditions like IBS, holds significant
importance for alleviating disease symptoms and enhancing overall well-being." They did not
evaluate "the importance of alleviating symptoms." It should be rewritten to mention correlation
rather than causality, as suggested by statistical inferences. They do not mention the beta power
of the differences between groups, which, being small, can easily fall into a type II error.
There are minor spelling errors; for example, they do not define the WHOQOL BREF or the
questionnaires in their first mention. The first paragraph of the results is the statistical section
of methods, and there's no mention of the sample size calculation. Minor grammatical errors
need to be corrected.
Review for 10.1186/s12876-025-04105-5 (2025)

Title: Explainable Machine Learning Model for Predicting the Transarterial
Chemoembolization Response and Subtypes of Hepatocellular Carcinoma Patients
Version: 0 Date: 07 Sep 2024
Reviewer's report:
Comment on the manuscript by Zhang, et al.
This paper compared several machine learning algorithm for predicting TACE responder, and
found that CatBoost model is the most excellent for dividing patients undergoing TACE into
responders and nonresponders. SHAP method is applied for explication of the overall model
framework. Machine learning algorithm is one of the trend for developing clinical prediction
model, however, there are several concerns to be addressed.
1) Abstract should be rewritten.
Background; It is too long, and should be composed of 1 or 2 sentences.
Methods; This study is a retrospective, so it should be written based on STROBE statement. In
the criteria, patient number does not appear in Methods, but in Results.
Results; Data should be shown concretely and entirely. The current Results are very
nonobjective.
Conclusions; It should be reached from Results.
2) Introduction is redundant. Especially, description of TACE should be much simpler, or could
be removed.
3) The indication of TACE is nor described.
4) The number of TACE should be included in Table 1, which affects the survivals of patients
with HCC.
5) Machine learning algorithm can retrospectively cluster the patients undergoing TACE,
however, it can’t predict the prognosis of patients with HCC before TACE. This is my major
concern in this study. What is the clinical importance the hepatologists can obtain from this
study?
6) Despite of the complicated methods, the variables selected by machine learning algorithm is
quite commonplace (Fig. 6) and have been reported so many times. What is the novel finding
by this data?
Review for 10.1186/s12876-025-04105-5 (2025)

Title: Explainable Machine Learning Model for Predicting the Transarterial
Chemoembolization Response and Subtypes of Hepatocellular Carcinoma Patients
Version: 0 Date: 06 May 2025
Reviewer's report:
This study presents an interesting approach to predicting TACE response and identifying
subtypes in HCC patients through machine learning; however, there are some issues that need
to be addressed before the conclusions can be fully supported.
#In this study, while existing predictive scores such as HAP, ALBI, and up-to-seven are
incorporated as features, there is insufficient direct comparison of predictive performance
between the developed machine learning models and these existing scores. Please add this
comparison to the main text.
#Regarding the limitations of this retrospective study, there is inadequate discussion of selection
bias and data collection bias, and how these might affect the generalizability of the results. Please
elaborate on these points in the limitations section.
Review for 10.1186/s12876-025-04105-5 (2025)

Title: Explainable Machine Learning Model for Predicting the Transarterial
Chemoembolization Response and Subtypes of Hepatocellular Carcinoma Patients
Version: 1 Date: 31 May 2025
Reviewer:  Tomoyuki Nagai
Reviewer's report:
We have responded to the reviewers’ comments in a sincere and constructive manner, resulting
in a marked improvement in the quality of the manuscript. In particular, the study presents
high publication value owing to its clinical applicability, the development of an explainable AI
model, and its clear differentiation from prior studies. Notably, the authors emphasize the use
of routinely available clinical parameters, which clearly distinguishes this study from previous
studies relying on radiomics or other complex data modalities. The advantages of interpretability
and feasibility in real-world clinical implementation have been well discussed. In addition, the
visual clarity of the figures was enhanced.
However, there remain a few areas in which further refinement could strengthen the manuscript.
Specifically, the clinical relevance of the selected 10 variables and the novelty of the SHAP-
based interpretation could be articulated more explicitly. The authors should elaborate on
how the machine learning model integrates and weights these variables, many of which
are consistent with existing clinical knowledge, to enhance the predictive performance.
Furthermore, consideration of nonlinear effects and potential interactions among variables in the
SHAP analysis would further highlight the interpretability of the model, which is a key strength
of this study.
Addressing these points would further enhance the scientific rigour and overall quality of the
manuscript.
Review for 10.1186/s12876-025-04105-5 (2025)

Title: Explainable Machine Learning Model for Predicting the Transarterial
Chemoembolization Response and Subtypes of Hepatocellular Carcinoma Patients
Version: 1 Date: 02 Jun 2025
Reviewer's report:
After reviewing the revised manuscript and the authors' responses, all previously raised concerns
have been adequately addressed. The authors have systematically resolved every issues. No
further revisions are required.
Review for 10.1186/s12876-025-04105-5 (2025)

Title: Explainable Machine Learning Model for Predicting the Transarterial
Chemoembolization Response and Subtypes of Hepatocellular Carcinoma Patients
Version: 3 Date: 18 Jun 2025
Reviewer:  Tomoyuki Nagai
Reviewer's report:
We are pleased that the authors have provided comprehensive and systematic responses to all
reviewers’ comments, including those previously raised.
The revisions have been thoughtfully implemented, and the manuscript has been further
improved in both clarity and scientific rigor.
We appreciate the authors’ efforts to address the issues raised during the peer review process.
Review for 10.1186/s12876-025-04104-6 (2025)

Title: Endobiliary radiofrequency ablation in recurrence and unresectable perihilar
cholangiocarcinoma
Version: 0 Date: 22 Mar 2025
Reviewer's report:
Title: Endobiliary Radiofrequency Ablation in Recurrence and Unresectable Perihilar
Cholangiocarcinoma
This is a well-structured, prospective randomized controlled trial evaluating the safety and
efficacy of endobiliary radiofrequency ablation (EBRFA) combined with self-expandable
metallic stents (SEMS) versus SEMS alone in patients with unresectable perihilar
cholangiocarcinoma (pCCA). The authors demonstrate that EBRFA is a feasible and safe
procedure, although it did not show statistically significant improvement in stent patency or
overall survival compared to SEMS alone. The study adds value by addressing a critical gap in
palliative care for patients with unresectable pCCA.
However, several limitations should be addressed or more clearly discussed to strengthen the
manuscript.
1. A large proportion of patients (77%) had distant metastases at baseline, potentially
confounding survival outcomes. Subgroup analysis or exclusion criteria related to metastatic
status could be considered in future research.
2. One of the most critical limitations of this randomized controlled trial is that key prognostic
factors—such as tumor morphology (ID, PI, MF, combined), Bismuth classification, and the
presence of distant metastasis—were not fully considered during randomization. Although the
distribution of these variables between the SEMS and EBRFA groups was not statistically
different, the small sample size limits the power to detect imbalances, and the clinical
heterogeneity could have significantly influenced the outcomes. These factors are well known
to impact prognosis in pCCA and therefore should be discussed more thoroughly as potential
confounders in the Discussion section.
3. The authors conclude that EBRFA is a feasible and safe procedure. However, this conclusion
may be premature based on the current results. In the comparison between SEMS and EBRFA,
the rates of complications such as pancreatitis (11.8% vs. 22.7%) and mild cholangitis (29.4%
vs. 59.1%) were higher in the EBRFA group, although not statistically significant (p=0.376
and p=0.200, respectively). The stent patency time was also slightly shorter in the EBRFA
group (median 71 vs. 78 days). These trends raise concerns about the true safety profile of
EBRFA. Given the small sample size, it is possible that with a larger cohort, these differences
might become statistically significant, revealing higher morbidity with EBRFA. I recommend
the authors discuss this important limitation more clearly in the Discussion section.
Review for 10.1186/s12876-025-04104-6 (2025)

Title: Endobiliary radiofrequency ablation in recurrence and unresectable perihilar
cholangiocarcinoma
Version: 0 Date: 25 Mar 2025
Reviewer's report:
Thank you for the opportunity to review this manuscript. I commend the authors for addressing
an important clinical issue. However, several points need clarification and improvement. Please
find my comments below.
Major Comments
1. The study includes a relatively small sample size, which may lead to insufficient statistical
power. It is generally advisable to perform a sample size calculation prior to conducting an RCT,
particularly when stent patency and overall survival are the primary outcomes. Please provide a
detailed explanation in the manuscript regarding how the sample size was determined, or justify
why a formal calculation was not performed.
2. The manuscript specifies stent patency and overall survival (OS) as primary outcomes, yet
their definitions are not clearly stated. In particular, the criteria for defining stent occlusion
should be explicitly described, as this is essential for reproducibility. Additionally, please present
Kaplan-Meier curves for both stent patency and OS.
3. Five patients received percutaneous stent placement, but the specific criteria or rationale
for choosing this approach over endoscopic stenting are not clearly described. Furthermore, it
is unclear whether radiofrequency ablation (RFA) for these five cases was performed via the
percutaneous route or endoscopically. There is limited information in the Methods section, so
please provide additional details in both the Methods and Results sections, clarifying how and
why the percutaneous approach was chosen and how ablation was performed in these cases.
4. In the Results section, the manuscript states: “CCA patients who received EBRFA had a trend
in survival time to be better than patients who received SEMS (OS = 94 vs. 79 days, HR = 1.31,
p = 0.735).” However, with a p-value of 0.735, one cannot conclude that there is a meaningful
trend favoring EBRFA.
5.
Minor Comment
1. Abbreviations used in the tables are not fully explained. Please provide a clear list of all
abbreviations below each table so readers can interpret them easily.
Review for 10.1186/s12876-025-04104-6 (2025)

Title: Endobiliary radiofrequency ablation in recurrence and unresectable perihilar
cholangiocarcinoma
Version: 4 Date: 16 May 2025
Reviewer's report:
Major revise:
1. Table 2 shows that the overall incidence of cholangitis (mild + severe) is extremely high—
72.7% in the EBRFA group and 52.9% in the SEMS group. No definition or diagnostic criteria
for cholangitis are provided, making it difficult to assess the clinical relevance or compare
with existing literature. Given the high incidence, the conclusion that EBRFA is “safe” seems
overstated.
2. Several statements in the discussion overstate the findings. For example, phrases such as
“clinical efficacy... has been consistently improved” and “success rates of more than 90%” are
not directly supported by this study’s data. Moreover, claims of practicality and safety should be
qualified, as adverse event rates were numerically higher in the EBRFA group and no procedural
efficiency data were reported. I recommend moderating these conclusions to better align with
the results presented.
Minor revise:
3. In the results section, the proportion of double stent use is described as "1/39 (97.4%)", which
appears to be a typographical error. Given the fraction, the correct percentage should be 2.6%,
not 97.4%. Please revise this to avoid confusion.
Review for 10.1186/s12876-025-04104-6 (2025)

Title: Endobiliary radiofrequency ablation in recurrence and unresectable perihilar
cholangiocarcinoma
Version: 5 Date: 14 Jun 2025
Reviewer's report:
Thank you for your revisions. I have carefully reviewed the updated manuscript. At this point,
no additional revisions are requested.
Review for 10.1186/s12876-025-04056-x (2025)

Title: Correlation between neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio with
prognosis in gastric cancer patients undergoing neoadjuvant chemotherapy: a meta-analysis
Version: 0 Date: 11 Apr 2025
Reviewer:  Ali Ogul
Reviewer's report:
Evaluation
This study titled “Relationship between neutrophil/lymphocyte and platelet/lymphocyte ratios
and prognosis in patients with gastric cancer who received neoadjuvant chemotherapy: a meta-
analysis” is a meta-analysis evaluating the role of systemic inflammation markers in prognosis.
The fact that MOOSE and PRISMA criteria were followed and the data were understandable
constitutes the strengths of the study. Exclusion and inclusion criteria were clearly stated in
the study. It was seen that 16 studies were included with a comprehensive literature review. In
addition, the fact that tests were conducted in terms of publication bias and sensitivity tests were
performed are other strengths of the study.
On the other hand, the study has a limitation due to its retrospective nature. Another limitation
is that DFS and RFS data are missing in most of the publications included in the study.
In addition, the fact that NAC regimens are applied differently in different countries makes the
study heterogeneous.
Another shortcoming of the study is that the included studies have different cut-off values.
For these reasons, I believe that the study will make a scientific contribution to the literature.
However, the above-mentioned limitations should be discussed in more detail in the study. As
a result, it is recommended that it be accepted with major revision.
Review for 10.1186/s12876-025-04056-x (2025)

Title: Correlation between neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio with
prognosis in gastric cancer patients undergoing neoadjuvant chemotherapy: a meta-analysis
Version: 2 Date: 20 May 2025
Reviewer:  Ali Ogul
Reviewer's report:
The responses given by the authors to the editor and referees are quite satisfactory. The article
was scanned using 4 major databases and PRISMA and MOOSE criteria were followed. The
revised article will be publishable with a minor revision. It would be beneficial for the authors
to write the conflicting literature results regarding PLR in more detail (small sample group,
applied treatment regimens, possible metastatic sites...). It is appropriate to publish with this
arrangement.
Review for 10.1186/s12876-025-04056-x (2025)

Title: Correlation between neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio with
prognosis in gastric cancer patients undergoing neoadjuvant chemotherapy: a meta-analysis
Version: 2 Date: 27 May 2025
Reviewer's report:
The manuscript has been significantly improved based on all reviewers' and the editor's
comments. Suggestion: accept.
Review for 10.1186/s12876-025-04065-w (2025)

Title: Infliximab for Patients with Moderate to Severely Active Ulcerative Colitis: An Updated
Meta-Analysis of Randomized Controlled Trials
Version: 1 Date: 15 May 2025
Reviewer's report:
The authors applied comprehensive meta-analysis. They proposed infliximab with better
short/long-term clinical response, short/long-term clinical remission, short/long-term mucosal
healing on active ulcerative colitis than placebos, aminosalicylic acid preparations, steroids, or
immunosuppressive drugs, but shows no superiority in terms of adverse responses.
They comprehensive do researches and evidence quality grading. Besides, they had been point
the limitation of this meta-analusis.