JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 3 Date: 20 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
The aim and the main idea of the study should get clear from the aim section Nevertheless you
should get through the whole test to get the general idea Abstract Numerical values should be
given in the results section to justify the selection of the refered genes and the relevant nomogram
could be also described Introduction could be deminished to provide space for this change
Introduction data on HCC cause are irrelevant and could be omitted Methods demographic and
disease related parameters used in the evaluation model balancing the effect of the selected genes
with OS  should be presented Results Numerical values from the analysis performed for the
selected genes should be presented Nomogram formula should be provided Statistical significant
values should be provided in the test for the laboratory application of the selected genes
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 4 Date: 26 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Function of the final formula and data from in vitro and in vivo experiments with
SLC22A1 should be given by reducing the size of the introduction Genes selected for FA
metabolism analysis should be presented in the methods section Otherwise changes are adequate
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 4 Date: 27 Sep 2024
Reviewer's report:
This study indicated a considerable value of specific fatty acid metabolism-related genes in
the diagnostic and prognostic evaluation of hepatocellular carcinoma, which provide novel
insights into the disease's management, as well as has potential implications for personalized
treatment strategies. This study is methodologically sound and logically clear, with appropriate
modifications recommended.
1. Keywords should be further standardised and streamlined.
2. I recommend that the authors include more recent literature in their references. For example,
the authors cite ‘Global cancer statistics 2018/2020’. However, currently ‘Global cancer
statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in
185 countries’ has been published.
3. The authors state "The selection criteria for FAs-DEGs were log (fold-change) values # 0.5
and p-values < 0.05. " . However, p < 0.05 implies that the authors have used only nominal p-
values without multiple hypothesis correction. This is simply wrong. The authors should use
FDR or similar to control false-positive rate.
4. The authors only validated the genes in the model. The validity of the prognostic model should
be further validated in an independent HCC cohort.
5. Previous studies have used similar bioinformatics to develop potential biomarkers (doi:
10.7150/jca.91842; doi: 10.1016/j.tranon.2024.102001). I think it will benefit the reader if the
authors could include some references, which would provide readers with a more complete
understanding of the whole study.
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 5 Date: 16 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Numerical values of significant models should be provided Methods Diagnostic Model
construction Statistical method used should be provided ( which logistic analysis model was
used) They should also point out why 5 rats were enough as animal models
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 6 Date: 23 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Late diagnosis is not the only reason for treatment failure, which might be true if
liver transplantation is available Methods Statistics Power of the study calculation should be
provided Multivariate analysis and complex statistical instruments utilized should be described
Data in results section referring to statistics should be moved  in the statistics section Results The
numerical values for the top five genes should be presented Moreover p values should always
be followed by relevant numerical value
Review for 10.1186/s12876-024-03495-2 (2024)

Title: Investigating the Diagnostic and Prognostic Significance of Genes Related to Fatty Acid
Metabolism in Hepatocellular Carcinoma
Version: 7 Date: 04 Nov 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract OR is not a percentage Otherwise I think changes applied are adequate and the paper
could be accepted
Review for 10.1186/s12876-024-03481-8 (2024)

Title: Global and Regional Burden of Pancreatitis: Epidemiological Trends, Risk Factors, and
Projections to 2050 from the Global Burden of Disease Study 2021
Version: 1 Date: 08 Oct 2024
Reviewer:  Anand Krishnan
Reviewer's report:
Overall, the paper addresses an important issue and is well written. Some suggestions to improve
it further.
1. As the authors accept, pancreatitis could be acute , recurrent or chronic. It is not clear
what is being studied here. For acute conditions we use incidence and for chronic we measure
prevalence. In this study it is not clear how these have been combined into an incidence estimate.
2. The paper needs to describe the sources of its data (which are core to the establish credibility
of the estimate along with statistical treatment). Are these cohorts, surveys, registries, hospital
based studies, insurance data etc.
3. Statistical treatment is also opaque as is true for most GBD papers and needs to be described
better as to how did they move from studies to regional and global estimates.
Review for 10.1186/s12876-024-03481-8 (2024)

Title: Global and Regional Burden of Pancreatitis: Epidemiological Trends, Risk Factors, and
Projections to 2050 from the Global Burden of Disease Study 2021
Version: 1 Date: 08 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
The study is actually a sequence of a similar one performed before 2021 Abstract Risk factors
finally exctracted could be mentioned in the methods section  Percentages should be fused
with crude numbers Methods Risk factors could be mentioned and described in the text
variables measured should be described and mathematical formula for their calculation should
be given Multivariated analysis of various risk factors effect of the main parameters presented is
preferable to subgroup evaluation The later could be maintained but the formed would be more
informative Results ASIR percentages should not presented for every region in the text Higher
and lower values should be given as well as regions not following general trend The same is
valid for every other parameter evaluated Data should also be evaluated for alcohol consumption
and smoking habits if possible
Review for 10.1186/s12876-024-03481-8 (2024)

Title: Global and Regional Burden of Pancreatitis: Epidemiological Trends, Risk Factors, and
Projections to 2050 from the Global Burden of Disease Study 2021
Version: 2 Date: 15 Oct 2024
Reviewer:  Anand Krishnan
Reviewer's report:
Authors have addressed the comments of the reviewers adequately
Review for 10.1186/s12876-024-03481-8 (2024)

Title: Global and Regional Burden of Pancreatitis: Epidemiological Trends, Risk Factors, and
Projections to 2050 from the Global Burden of Disease Study 2021
Version: 2 Date: 16 Oct 2024
Reviewer:  Amira A A Othman
Reviewer's report:
I would like 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/s12876-024-03481-8 (2024)

Title: Global and Regional Burden of Pancreatitis: Epidemiological Trends, Risk Factors, and
Projections to 2050 from the Global Burden of Disease Study 2021
Version: 2 Date: 16 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Changes are satisfactory Thus I suggest document could be accepted for publication
Review for 10.1186/s12876-024-03467-6 (2024)

Title: Birth Characteristics and Risk of Colorectal Cancer
Version: 0 Date: 18 Jul 2024
Reviewer's report:
Dear editorial team,
Thank you for inviting me to review this manuscript. The study aimed to investigate the
relationship between birth characteristics and future risk of colorectal cancer. In overall, the
manuscript was well-structured and suitable for international journals. With all due respect,
some observations and considerations are noted as follows:
Introduction:
Linguistic and grammatical checks are necessary.
The authors may need to provide a clearer explanation relationship between low or high
birth weight and colorectal cancer (CRC). Specifically, they could hypothesize major possible
mechanisms to explain the potential relationship between birth weight and later development
of CRC.
Methods Section:
The "Cochrane Handbook" should be cited when describing the systematic review/meta-analysis
(SR/MA) methodology.
It should be stated which major guideline (e.g. MOOSE or PRISMA) was followed to conduct
this SR/MA.
The search strategy should be reproducible; I recommend the authors add the exact search terms/
keywords used, in a supplementary table (appendix).
The inclusion criteria specify only case-control and "prospective cohort" studies; however,
retrospective studies (e.g. Sandhu et al.) appear to also be included. This discrepancy should
be clarified.
The study quality assessment refers to "original authors" at the end, but this  was not properly
defined earlier.
The authors should check journal instructions to determine whether registration in databases
such as PROSPERO is required.
Results:
Figure 1 could be better organized to more clearly display the number of studies excluded
with reasons for exclusion (e.g. insufficiency in exposure/outcome assessment, study design,
statistical).
Table 1 should include study design and references for each study. Additionally, a new column
listing major adjusted factors would aid interpretation.
Discussion:
This section is well-written with suitable comparative examples.
The authors could add a paragraph discussing potential mechanisms linking birth weight to later
CRC risk, such as influences of hormone levels or microbiome composition and/or inflammatory
processes.
Given the low heterogeneity among studies, the authors should attempt to explain
inconsistencies in results regarding the association between birth weight and CRC across
different studies.
In summary, the comments aim to strengthen clarity, completeness and rigor of reporting to
improve the overall quality and impact of the manuscript.
I hope these comments will be helpful
Review for 10.1186/s12876-024-03467-6 (2024)

Title: Birth Characteristics and Risk of Colorectal Cancer
Version: 0 Date: 19 Jul 2024
Reviewer:  Maria Pais
Reviewer's report:
Abstract: Methods please add the initial literature year article. So that you will get the real facts.
Included studies screening flow disgram (Spelling correction) Which flow diagram you have
used like example Prisma, etc.
Literature whose data cannot be extracted (n=30)
Search strategy:
Mention all four databases how many article exterted examples 1065 How many from Pubmed,
like that.
Characteristics of included studies in meta-analysis mentioned in the figure form or graph
attraction will be more.
Special Note: Grammar mistakes as well as spelling please edit with standard person ok.
Review for 10.1186/s12876-024-03467-6 (2024)

Title: Birth Characteristics and Risk of Colorectal Cancer
Version: 1 Date: 07 Aug 2024
Reviewer's report:
Dear authors,
Thanks for considering comments.
Your final manuscript is revised according to the most of the reviews. However, there are "still"
some grammatical and spelling errors; Table 1 is not revised yet (adjusted factors and references
are needed).
According to Figure 1 (revised), authors have excluded studies  by "restriction on race/
age/ gender", and also "specific recruitment". These are not among your "exclusion criteria"
according to the method section. The other criteria mentioned in figure 1 (revised), is "short
follow-up", when authors did not specify the length of follow-up for inclusion.
Due to these points and vagueness in text, I think you need a fundamental reconsideration about
your research approach.
Review for 10.1186/s12876-024-03467-6 (2024)

Title: Birth Characteristics and Risk of Colorectal Cancer
Version: 3 Date: 14 Sep 2024
Reviewer's report:
This study explored the relationship between newborn birth characteristics and the incidence
of colorectal cancer (CRC) in adulthood. It found that factors like shorter birth length, lower
placental weight, and fetal growth restriction may increase CRC risk, while birth weight had
no significant effect.
Please see the following comments:
MEDLINE is essentially a subset of PubMed. MEDLINE refers to the bibliographic database of
life sciences and biomedical information that is accessible through PubMed. Therefore, listing
both PubMed and MEDLINE might be redundant. EBSCO is a database provider that hosts
multiple databases. Listing "EBSCO" without specifying which individual databases is less
informative.
I noticed that at least one potentially relevant study may have been omitted, which could
contribute to the meta-analysis. I recommend that the authors revisit the literature search to
ensure all pertinent studies are included. Additionally, incorporating EMBASE in the literature
review could address any gaps present in other databases and provide a more comprehensive
approach. Integrating EMBASE alongside other key databases would enhance the thoroughness
of the review.
Birth weight is positively correlated with both adult height and weight, and large adult body size
is a well-established risk factor for CRC. This raises the possibility that the association between
birth weight and CRC risk could be mediated by adult body size. Please consider discussing this
potential mediation effect in the discussion section.
The authors correctly identify the inconsistency in the classification of birth weight into "high"
and "low" categories across the included studies. Please discuss whether this misclassification is
non-differential or differential, and how it might affect the direction of the association observed.
Additionally, the phrase "the result is negative" is somewhat vague and could lead to confusion.
It would be helpful to clarify this statement for better understanding.
MINOR COMMENTS:
ABSTRACT:
It should be 95% CI; there are several "%" symbols missing before "CI."
The reference numbers are not in order.
Review for 10.1186/s12876-024-03475-6 (2024)

Title: The association between plant-based diet indices and risk of mortality in patients with
cirrhosis: a cohort Study
Version: 1 Date: 10 Sep 2024
Reviewer's report:
I thank the editor for inviting me to review this manuscript. I have several comments.
1. Please give the references for the classification of extremely low or high energy intake and
implausible BMI.
2. The authors should provide the diagnostic criteria for cirrhosis. Were the participants recruited
based on consistent diagnostic criteria for cirrhosis?
3. How was the outcome (i.e., mortality) measured? Was it solely through the telephone? If the
inquiry was made over the phone, did the researchers verify the outcome regarding whether
the participant had died? What methods were used for verification? Additionally, based on
my understanding, if a participant has passed away, would their family members have enough
patience to inform you of the exact time and causes of death? How did the authors control for
loss to follow-up? This is a crucial part of the article, and the authors should provide a detailed
explanation.
4. Are there any important confounding factors that the authors considered? For example,
physical activity.
5. I recommend that the authors include a flowchart showing the enrollment and exclusion
process, indicating how many participants were excluded at each step.
6. The study recruited participants with cirrhosis within the past six months. When the authors
used the FFQ to inquire about their diet, did they ask about the past year or the past six months?
These are all crucial pieces of information, but they are not described in the article.
7. In the statistical analysis section, there is a covariate called etiology. The authors should
provide a brief introduction and definition of it.
8. In Table 1, for categorical variables, in addition to providing percentages, the authors should
also include the actual counts.
9. The sample size of this study is relatively small, resulting in some hazard ratios (HR) being
very small and the 95% confidence intervals (CI) having a wide range. I recommend that the
authors calculate the statistical power.
Review for 10.1186/s12876-024-03475-6 (2024)

Title: The association between plant-based diet indices and risk of mortality in patients with
cirrhosis: a cohort Study
Version: 1 Date: 14 Sep 2024
Reviewer:  Yi-Chuan Yu
Reviewer's report:
The authors seek to investigate the relationship between plant-based diet indices and the risk
of mortality in an Iranian population. Overall, the methods section should be revised heavily to
improve its clarity and comprehensiveness. My specific comments are listed below.
1. Is 3955 the total person-month follow-up or the average follow-up time? Also, it will be more
intuitive to use person-year instead of person-month.
2. In the following statement: “ranked it as the 15th leading contributor to DALYs worldwide”,
what is the full name for “DAILY”?
3. The following statement: “The fact that some plant foods such as refined grains and drinks
sweetened with sugar have adverse effects on health”. Could the authors please clarify does
this means that the vegetarian diet score only includes refined grains and sugar drinks as
“vegetarian”?
4. How are the positive values and negative assigned to each of the food items? Please elaborate
on this in the introduction. For example, is -2 unhealthier than -1? What are the determinants
for -2 scored foods and -1 scored foods?
5. How can cirrhosis cases be identified?
6. What are the sample sizes for the excluded individuals? A detailed layout of why these
exclusion criteria should be included. In addition, please be specific on each of the exclusion
criteria. For example, what are considered to be various malignancies?
7. Are the questionnaires collected every year?
8. This is to echo the previous point, how scores are determined when assigning values to each
of the food items? Is the score developed in Iran? If not, the effect of these foods on human
health could be different across different populations.
9. Is there any information related to liver infection included or not (HBV, HCV)?
10. Have the authors tested the assumption of the Cox model?
Review for 10.1186/s12876-024-03475-6 (2024)

Title: The association between plant-based diet indices and risk of mortality in patients with
cirrhosis: a cohort Study
Version: 3 Date: 21 Oct 2024
Reviewer's report:
The authors provided explanations for the reviewers' comments in their response letter and
made corresponding revisions. However, several important issues were only addressed in
explanations and not reflected in the revised manuscript. For example, in comment 3, regarding
the determination of death outcomes, the authors stated in their response letter, "The cause
of death of the patients was determined based on their death certificate. In addition to the
death certificate, the cause and date of death were also recorded by searching the name of the
deceased in the registry system." However, the manuscript still states, "Follow-up questionnaires
regarding deaths or medical events were completed by telephone."
Review for 10.1186/s12876-024-03484-5 (2024)

Title: Comparative diagnostic efficacy of two-dimensional shear wave and transient
elastography in predicting the risk of esophagogastric varices and histological staging in patients
with primary biliary cholangitis
Version: 0 Date: 12 Aug 2024
Reviewer:  Giuseppe Losurdo
Reviewer's report:
In the present prospective study on patients with primary biliary cholangitis (PBC), Meng et
al found that TE and SWE had similar diagnostic accuracy regarding liver fibrosis staging, but
SWE showed a slightly better accuracy for predicting varices. Main comments:
1) Page 2 last two lines, I assume that a value is missing (only 95% CI was reported).
2) By looking at fig 1, I assume that this is a 2D-SWE and not a point SWE. Please be more
precise in Methods section.
3) The main problem is that histological diagnosis was based on Ludwig system, which is
specific for PBC, but it does not focus on entity of fibrosis. Indeed, TE and SWE were validated
according to Metavir.
4) Page 7: details of patients enrolment according to exclusion criteria should be reported in a
figure/flow diagram.
5) A correlation analysis between TE and SWE should be added.
6) In Methods, please report the used thresholds for F in TE ans SWE.
7) Some authors found a non optimal correlation between TE and SWE in PBC (see Losurdo G
et al, Diagnostics 2024), a result in disagreement with this study. Please comment on.
Review for 10.1186/s12876-024-03484-5 (2024)

Title: Comparative diagnostic efficacy of two-dimensional shear wave and transient
elastography in predicting the risk of esophagogastric varices and histological staging in patients
with primary biliary cholangitis
Version: 0 Date: 20 Aug 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Although methods section is an exact copy paste to similar studies abdominal wall thickening
should be further  defined  Instead of range standard deviation could be used in the results
Review for 10.1186/s12876-024-03484-5 (2024)

Title: Comparative diagnostic efficacy of two-dimensional shear wave and transient
elastography in predicting the risk of esophagogastric varices and histological staging in patients
with primary biliary cholangitis
Version: 1 Date: 02 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Remove number of patients from methods Methods laboratory tests evaluated should
be described in methods session
Review for 10.1186/s12876-024-03484-5 (2024)

Title: Comparative diagnostic efficacy of two-dimensional shear wave and transient
elastography in predicting the risk of esophagogastric varices and histological staging in patients
with primary biliary cholangitis
Version: 1 Date: 02 Sep 2024
Reviewer:  Giuseppe Losurdo
Reviewer's report:
Answers were fine
Review for 10.1186/s12876-024-03484-5 (2024)

Title: Comparative diagnostic efficacy of two-dimensional shear wave and transient
elastography in predicting the risk of esophagogastric varices and histological staging in patients
with primary biliary cholangitis
Version: 2 Date: 04 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Changes requested have been performed Patients characteristics  that affect tests are included
More demographic data would be grateful to be included but as the study  was based on  a
predifined protocol  they cannot be introduced at the moment
Review for 10.1186/s12876-024-03486-3 (2024)

Title: The Impact of Relaxing the Requirements for Dyspeptic Symptom Onset Frequency or
Duration in Rome IV Criteria on the Symptom Pattern and Diagnosis of Functional Dyspepsia
Version: 3 Date: 06 Sep 2024
Reviewer's report:
It is with great interest that I read the manuscript from Wang et al. Indeed, meeting Rome IV
criteria for functional GI disorders tends to be rather difficult.
Furthermore, it is indeed useful to include questions on the relationship of food intake to
symptom generation.
However, I think this manuscript needs improvement before it can be published. In attachment,
my comments.
Review for 10.1186/s12876-024-03486-3 (2024)

Title: The Impact of Relaxing the Requirements for Dyspeptic Symptom Onset Frequency or
Duration in Rome IV Criteria on the Symptom Pattern and Diagnosis of Functional Dyspepsia
Version: 3 Date: 14 Sep 2024
Reviewer's report:
The study “The Impact of relaxing the requirements for dyspeptic symptom onset frequency or
duration in Rome IV Criteria on the symptom Pattern and Diagnosis of functional dyspepsia”
aims to describe the symptom characteristics of Rome IV criteria defined FD in China and
explore the impact of relaxing the requirements for symptoms onset frequency, severity and
duration of the Rome IV criteria on diagnosing FD.
Authors have analysed a topic very interesting and actual, especially in clinical practice.
The Rome Foundation itself has already proposed a modification of the Rome IV diagnostic
criteria for clinical practice, stating that a diagnosis of DGBI can still be done even if diagnostic
criteria of frequency and duration are not satisfied, providing that nature and bothersomeness of
symptoms (e.g. interfering with daily activities or quality of life) are present. (Rome Foundation
Clinical Diagnostic Criteria for Disorders of Gut-Brain Interaction. Drossman, Douglas A.Tack,
Jan et al. Gastroenterology, Volume 162, Issue 3, 675 – 679)
The study design (retrospective cross-sectional) is, however, a methodological limitation of
this study, since the diagnosis of FD is mostly based on clinical judgement, presence of recall
bias does not allow to consider data consistent. Moreover, authors used a self-administered
questionnaire survey (not standardized) to assess GI symptoms and characteristics. Furthermore,
not all participants might exactly know the meaning of dyspepsia, thus over- or underestimating
the real burden of symptoms.
Introduction, line 15, authors report “characterized by meal-related symptoms such as meal
unrelated symptoms such as epigastric…” not clear, please correct
Discussion, line 8 “then” instead of “than”, please correct
Review for 10.1186/s12876-024-03486-3 (2024)

Title: The Impact of Relaxing the Requirements for Dyspeptic Symptom Onset Frequency or
Duration in Rome IV Criteria on the Symptom Pattern and Diagnosis of Functional Dyspepsia
Version: 3 Date: 15 Sep 2024
Reviewer's report:
Thank you for the invitation to review this work. I appreciate the effort and dedication that went
into conducting such a large-scale study with nearly 3,000 participants.
One area I would like to inquire about is whether a power analysis has been conducted.
Additionally, the limitations section is thoughtfully crafted and clearly outlines the challenges
and potential constraints faced during the research.
A well-executed study.
Review for 10.1186/s12876-024-03486-3 (2024)

Title: The Impact of Relaxing the Requirements for Dyspeptic Symptom Onset Frequency or
Duration in Rome IV Criteria on the Symptom Pattern and Diagnosis of Functional Dyspepsia
Version: 4 Date: 04 Oct 2024
Reviewer's report:
Congratulations on the work provided. Compared to last review, it is a step forward.
However, first of all, my biggest concern remains the "own questionnaire". Apart from the
early satiety definition as mentioned earlier, I see that in the questionnaire Q2 you asked about
"retrosternal burning sensation" (= heartburn) and then about "heartburn". It is the same. In the
discussion and table 3, it is "acid reflux" and "heartburn". I think the authors should use one
translation. And just make a statement about the fact that the Rome questionnaire has not been
used (in the limitations).
Furthermore, the manuscript still needs language polishing.
67: "cure" needs to be "explanation"
70: FD is considered a heterogeneous condition… (remove "as")
71: which may negatively impact the efficacy of … (remove "on")
81: duration criteria for at least (instead of "of at least")
88: maybe refer to "Rome Foundation Clinical Diagnostic Criteria for Disorders of Gut-Brain
Interaction. Drossman, Douglas A.Tack, Jan et al. Gastroenterology, Volume 162, Issue 3, 675
– 679)"
115: (ii) patients who were pregnant or lactating
117-119: (vi) current use of steroids or nonsteroidal anti-inflammatory drugs; (vii) patients who
declined to participate in this study.
191: meet the Rome IV criteria (not "meets")
196: age (Supplementary Table 2), gender (Supplementary Table 1)
239: "proposed to subdivide"
Table 3: maybe explain shortly what p# is
No further comments
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 1 Date: 06 Sep 2024
Reviewer:  Kuntesh K. Jani
Reviewer's report:
you may discuss failure cases of the proposed system
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 1 Date: 10 Sep 2024
Reviewer's report:
The manuscript is valid, adds to the body of evidence and attempts to provide a solution that will
fit all systems. This is not the first time an attempt like this has been made, as a similar approach
is described in the following that has not been included in the reference list:
https://pubmed.ncbi.nlm.nih.gov/35931065/
The introduction lacks several seminal references to show that the authors know the field; I have
highlighted the sentences (and provided extensive editorial work) in the attached folder.
The missing references are as follows from the first highlighted sentence to the rest:
1.https://pubmed.ncbi.nlm.nih.gov/34016545/
2.https://pubmed.ncbi.nlm.nih.gov/33005262/
3.https://pubmed.ncbi.nlm.nih.gov/33448511/
4.https://pubmed.ncbi.nlm.nih.gov/36338789/
5.https://pubmed.ncbi.nlm.nih.gov/35834249/
Including images as an integral part of the manuscript can be problematic and confusing, as they
interfere with the reviewing process (usually placed at the end of the manuscript to allow for
speedy review).
Spacing 1.5 is not necessary; it can also be upsetting.
The figure that demonstrates the study path needs to be redrawn.
Thanks
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 1 Date: 19 Sep 2024
Reviewer's report:
The work on automated capsule endoscopy recognition is highly impressive and demonstrates a
significant advancement in the field of small bowel lesion diagnostics. However, there are still
some issues in the article.
1. There is no numbering provided to the section and sub-sections, so that it will be more easy
to refer and understand.
2. A statistical graph or figure can be included in the introduction section to give a pictorial idea
about the present scenario of gastrointestinal diseases throughout the world.
3. A paragraph needs to be added in introduction, stating the objective and major contribution
(in bullet points).
4. A section needs to be added for elaborating some prior state of work on this area of research.
5. The dataset section needs to be more elaborated, giving a detailed about the dataset that is
considered in this work.
6. Could you elaborate on why you chose these CNN models - DenseNet121, EfficientNetB2,
HRNet-W18, ResNet50, and MobileNetv3-large?
7. Do add detailed explanations of each performance metric, particularly the specific meaning
and application scenarios of accuracy, precision, recall, specificity, AUC and F1 score.
8. Figure 3 should be referred at the beginning of the methods section so that the reader can get
a pictorial idea about the whole work from initial phase.
9. The section heading of “Application Development” is repeated.
10. To enhance the quality of the paper, a critical discussion can be added mentioning the pros
and cons of the proposed work.
11. Go through the article thoroughly for grammatical and typological errors.
12. Re-write the conclusion so as to incorporate an overall outcome of the study, limitations
and future scope.
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 2 Date: 01 Oct 2024
Reviewer's report:
Thank you for addressing the feedback and revising the  article. The updated version now
provides a more comprehensive overview, highlighting both the clinical significance of your
work and the broader implications for future research. The inclusion of potential applications
and acknowledgment of limitations gives the conclusion a well-rounded perspective, reinforcing
the impact of your study.
The revisions have significantly enhanced the clarity and depth of your conclusion, making it
a strong, forward-looking end to an impressive body of work. Congratulations on successfully
completing the revision!
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 2 Date: 08 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
During capsule endoscopy reading a flowing video rather than single pictures were evaluated
and specific gravity of every picture is examined within the context of neighburing ones Authors
should stress this difference even from the abstract Methods Quality of bowel preparation should
be taken into consideration Authors have selected rather homogenious populations for every
capsule brand ; 3 different hospitals each one of them using a different capsule Why were
neoplasias and submucosal lesions excluded? Was there any access to verification of lesions after
enteroscopy or MR enterography avaible? Otherwise the goldstandard should be stressed Why
the pictures selected were representative to everyday practice should be explained Statistical
method to access the parameters measured should be presented Results Significant results should
be presented in the text and not only in tables Pictures from different capsule endoscopy types
should be presented since the vast majority of pictures come from PillCam
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 3 Date: 10 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Authors have applied marginal changes Because it seems that three different capsules have been
used from three different sets It should be clarified if it is true In such a case the best model
should be evaluated if it works the same for each one of them There is much diffrences between
quality of pictures provided Sample size should be calculated for each one of them and the
assumptions should be provided  Authors should explain why they put show much effort in
identifing lemphangiecyasias and foreign bodies
Review for 10.1186/s12876-024-03482-7 (2024)

Title: Establishing an AI Model and Application for Automated Capsule Endoscopy
Recognition Based on Convolutional Neural Networks (with Video)
Version: 4 Date: 15 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
I think that authors do not intendto make more changes Thus the documents is ready for approval
Review for 10.1186/s12876-024-03479-2 (2024)

Title: Blood Lipid Profiles Associated with Metastatic Sites in Advanced Gastric Cancer
Version: 5 Date: 05 Jul 2024
Reviewer's report:
Dear Author,
Your data is good but your article is too long. You need to shorten your article. Some tables
containing meaningless data may be extracted. The study needs a more concise writing.
Best Regards
Review for 10.1186/s12876-024-03479-2 (2024)

Title: Blood Lipid Profiles Associated with Metastatic Sites in Advanced Gastric Cancer
Version: 6 Date: 22 Aug 2024
Reviewer's report:
I would like to commend you on your research idea, which addresses an important and
timely topic in oncology. Exploring the correlation between peripheral blood lipid levels and
clinicopathological parameters in patients with advanced gastric cancer is insightful. The focus
on changes in lipid levels during disease progression may provide valuable contributions to
the field. However, I have identified several statistical issues that require revision. Given the
importance of your research and its potential impact, I recommend a major revision to ensure
the robustness and accuracy of your findings.
Comment 1: Create a new version of Table 3 where, for each lipid parameter, a multiple
regression analysis is performed to assess the adjusted effect of each metastasis type as an
independent variable on that lipid parameter as the dependent variable, while controlling for the
presence of other metastasis types.
Comment 2: Revise Table 4 by conducting a two-way ANOVA to determine if there are
differences among the four groups (Peritoneum Metastasis + in males, Peritoneum Metastasis +
in females, Peritoneum Metastasis - in males, Peritoneum Metastasis - in females). If the results
are significant, follow up with a post hoc pairwise comparison using Bonferroni correction.
Comment 3: The lipid parameters showed low specificity, making ROC curve analysis
unnecessary for determining cutoff values. You can include the lipid parameters as continuous
variables in both simple and multiple logistic regression models without categorizing them
beforehand
Review for 10.1186/s12876-024-03479-2 (2024)

Title: Blood Lipid Profiles Associated with Metastatic Sites in Advanced Gastric Cancer
Version: 7 Date: 11 Sep 2024
Reviewer's report:
Dear Authors
Thank you for effectively responding to the comments. I have no additional comments about
the results but I have two comments to further improve the presentation of the results:
1- In the new Table 3: This table in its shape is best to be moved to the supplementary information
for those who need to look at the specific distribution of the + and -, meanwhile make the Table
3 in the manuscript with the attached format: the rows only indicate the metastasis type  and
make the value in the intersect between each row and column to be the adjusted mean difference
between + and - with its associated 95% CI.
2- The quality of Figure 1 needs to be improved, very hard to read. The Figure shows many of
the significant associations as diamonds on the no significance line corresponding to the OR =1.
Turn Figure 1 into a Table, this will help the reader to easily capture the significant associations
in the simple and multiple logistic regression analyses.
Review for 10.1186/s12876-024-03479-2 (2024)

Title: Blood Lipid Profiles Associated with Metastatic Sites in Advanced Gastric Cancer
Version: 9 Date: 06 Oct 2024
Reviewer's report:
Dear Authors,
Thank you for effectively addressing the comments. However, the narrative text under the title
"Correlation between Serum Lipids and Metastatic Sites in Gastric Cancer" should describe the
findings of the new Table 3. The text still describes the old Table 3, which was transferred to the
supplementary material. The narrative for the new Table 3 should include the mean differences,
along with their 95% CI and p-values, for the significant associations using a pattern like this:
"Patients with peritoneal metastasis had significantly lower levels of total cholesterol (MD = ...,
95% CI: ... to ..., p = 0.001), compared to those without peritoneal metastasis, while controlling
for other metastasis sites.
Review for 10.1186/s12876-024-03476-5 (2024)

Title: Endoscopic Morphology of Gastric MALT Lymphoma Correlate with API2/MALT1
Fusion and Predict Treatment Response After Helicobacter pylori Eradication
Version: 3 Date: 15 Oct 2024
Reviewer's report:
The logic leading to the Conclusion within the Abstract appears incomplete. To ensure a more
cohesive flow toward the Conclusion, the authors may consider making several adjustments to
clarify the progression from the research background, through methods and findings, to a well-
supported conclusion. Below is an example of a revised version with improved connections
between sections and some grammatical corrections. Note: This example is provided as a
reference; the authors should carefully examine and revise the content to align with the actual
analysis results.
Abstract
Background: The presence of API2/MALT1 fusion in gastric mucosa-associated lymphoid
tissue (MALT) lymphoma predicts poor response to Helicobacter pylori (Hp) eradication
therapy. This study aimed to assess the correlation between the endoscopic morphology of
MALT lymphoma and API2/MALT1 fusion and evaluate treatment responses to Hp eradication
based on morphological subtypes.
Methods: A retrospective review was conducted on patients diagnosed with gastric MALT
lymphoma between January 2011 and December 2022. Endoscopic morphology was categorized
as superficial, non-superficial, or mixed type. The superficial type was further classified into
gastritis superficial lesion and localized superficial lesion based on border clarity. Logistic
regression models evaluated the impact of clinical and endoscopic characteristics on anti-Hp
therapy effectiveness.
Results: Among the 114 patients included, 93 (81.6%) were Hp-positive, and API2/MALT1
fusion was detected in 58 (50.9%) cases. The regular arrangement of collecting venules (RAC)
sign was noted in 21 (18.4%) cases. API2/MALT1 fusion was more common in localized
superficial lesions than in gastritis superficial lesions (66.7% vs. 32.1%, p=0.01). Following
Hp eradication, the remission rate for localized lesions was 34.3%, significantly lower than for
gastritis lesions (66.7%, p=0.01). Both endoscopic morphology (OR=0.26, 95% CI 0.09–0.75)
and API2/MALT1 fusion (OR=14.29, 95% CI 4.19–48.67) impacted the efficacy of anti-Hp
therapy. However, multivariate analysis identified API2/MALT1 fusion as the only independent
predictor of treatment outcome (OR=12.18, 95% CI 3.49–42.55, p<0.001).
Conclusion: Gastric MALT lymphomas with superficial-type morphology, particularly those
with defined borders resembling early gastric cancer, were associated with API2/MALT1
fusion and a lower remission rate after Hp eradication therapy. This suggests that endoscopic
morphology, along with API2/MALT1 fusion status, could help predict the therapeutic response,
with API2/MALT1 fusion serving as a critical indicator of treatment resistance.
Review for 10.1186/s12876-024-03476-5 (2024)

Title: Endoscopic Morphology of Gastric MALT Lymphoma Correlate with API2/MALT1
Fusion and Predict Treatment Response After Helicobacter pylori Eradication
Version: 3 Date: 15 Oct 2024
Reviewer's report:
The authors have well-handled comments from previous reviewers.
Review for 10.1186/s12876-024-03476-5 (2024)

Title: Endoscopic Morphology of Gastric MALT Lymphoma Correlate with API2/MALT1
Fusion and Predict Treatment Response After Helicobacter pylori Eradication
Version: 4 Date: 21 Oct 2024
Reviewer's report:
The abstract has been appropriately revised.
Review for 10.1186/s12876-024-03469-4 (2024)

Title: Title#Construction of a Combined Prognostic Model for Pancreatic Ductal
Adenocarcinoma Based on Deep Learning and Digital Pathology Images
Version: 1 Date: 29 Jul 2024
Reviewer's report:
This article explores the construction of a prognostic model for pancreatic ductal
adenocarcinoma (PDAC) based on deep learning and digital pathology images, and improves
the accuracy of survival prognosis prediction by combining pathological risk models and
clinical risk models. The article still has some shortcomings and needs further modification
and improvement. Specific doubts: Data volume and sample representativeness: The data set
of the article comes from a single center, and the sample size is relatively small (142 cases).
The lack of multi-center and larger sample size verification may affect the universality and
credibility of the results. Lack of external validation: No external data set was verified in the
study, which makes it impossible to fully verify the generalization ability and stability of the
model. It is recommended that the author add an external validation set for evaluation in further
research. Model interpretability issues: The article mentions that the specific meaning of the
features extracted by the deep learning model is unclear, which may become an obstacle in
clinical application. It is recommended that the author increase the explanation and visualization
of important features in the model to improve the transparency and clinical acceptability of
the model. Image processing and feature extraction methods: Whether the selection of image
preprocessing and feature extraction methods is optimal is worth discussing. Although the
three pre-trained models (MobileNet_v3_small, ResNet18, and DenseNet121) used in the article
performed well, no comparative study was conducted on other potentially better models. It
is recommended to further explore and compare different deep learning models and feature
extraction methods. Unclear details of statistical methods: The description of the parameter
selection and validation process of the LASSO regression and Cox regression models in the
article is relatively simple. It is recommended to add detailed statistical method descriptions,
including specific criteria for parameter selection and details of cross-validation methods.
Selection and validation of biomarkers: In the selection process of clinical risk features, are
there any potentially important biomarkers that have not been considered? It is recommended to
screen and validate more biomarkers to improve the predictive ability of the model. Discussion:
The discussion of existing research is relatively brief and fails to fully reflect the innovation and
contribution of this study. It is recommended to increase the review and comparison of the latest
research in related fields to highlight the innovation and advantages of this article.
Review for 10.1186/s12876-024-03469-4 (2024)

Title: Title#Construction of a Combined Prognostic Model for Pancreatic Ductal
Adenocarcinoma Based on Deep Learning and Digital Pathology Images
Version: 1 Date: 30 Jul 2024
Reviewer:  Zongren Ding
Reviewer's report:
The author utilizes clinical data from PDAC patients and whole slide images (WSI), employing
logistic regression and machine learning algorithms to construct a model for stratifying PDAC
patients, which holds certain clinical guidance significance.The article is innovative and easy
to read and understand. However, I would like the authors to address my queries noted below
to strengthen the work.
1.This is a single-center study conducted in China. Please provide an introduction that discusses
the epidemiological status of PDAC in China or Asia, rather than focusing on the situation in
the United States.
2.Please provide information on all variables prior to the Lasso regression. For PDAC, I am
particularly interested in indicators such as CA19-9, CEA, bilirubin, GGT, ALP, and tumor size.
3.The combined model significantly outperformed both the single PRS model and the single
CRS model in fitting survival data, with a likelihood ratio test result of P < 0.001. Please include
graphical representations, such as ROC curve comparisons, to illustrate this finding.
4.The clinical model constructed by the authors has a C-index of 0.75 in the validation group,
while the best deep learning model only achieved 0.73. Please explain or discuss the rationale for
using a deep learning model, as implementing deep learning is known to be a challenging task.
Overall, I suggest making the necessary modifications to address the points mentioned above.