JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-024-03311-x (2024)

Title: A Meta-Analysis of Randomized Controlled Trials Evaluating the Effectiveness of Fecal
Microbiota Transplantation for Patients with Irritable Bowel Syndrome
Version: 4 Date: 28 Mar 2024
Reviewer:  Tahne Vongsavath
Reviewer's report:
line 15: recommend changing wording. of "we conducted a meta-analysis for the first time" to
something like "we conducted a first of its kind" or something similar.
line 16: warrants small description on what "emotions" were investigated. Seems like a emphasis
on depression?
line 36: "mixed stool" is this referring to stool from multiple donors?
Line 37: Needs more information on depression  Discussion of depressive symptoms and IBS
in the introduction would also be warranted.
Line 52: consistenc -> consistency
Lines 61-63: Would consider rewording, for smoother word flow. "Previous studies indicate the
pathogeneis includes various factors such as ..."
Line 65: again emotions is a very general term
Line 68: "These factors result" recommend rewording, not sure which factors are being described
in this statement
Line 70-72: "on the gut microbiome" for IBS treaments, and explored diverse approaches in its
manipulation such as ....
Line 73: what treatments do these patients remain symptomatic on?
Line 161: please insert numeric for citation
Table 1: science mispelled, what were the differences between rounds 1 and 2 of exclusion for
not meeting inclusion criteria
Line 192: RCTs that reported
Line 199: Would remove either "there were only 9" OR "which is fewer than 10"
Line 201: the three studies that reported long term outcomes
Lines 229-236: please decrease spacing
Line 291: please include p value
Table 2: different spelling of diarrhea used here
Line 305: "in prior meta-analysis" is redundent in this sentance
Line 308: brief wording on what the secondary outcome was
Line 313-315: via colonoscopy; is this overall or also time dependant?
Line 323: has shown vs proven
line 325-326: wordy, may neec sentace combination or revision
line 363: may want to stray from using words like verify
line 394: please include limitations header
supplemental table 1: add additional table for overview of included studies (second included
table) and reference in the text
Review for 10.1186/s12876-024-03311-x (2024)

Title: A Meta-Analysis of Randomized Controlled Trials Evaluating the Effectiveness of Fecal
Microbiota Transplantation for Patients with Irritable Bowel Syndrome
Version: 4 Date: 04 Apr 2024
Reviewer's report:
The authors submit their original work to explore the relationship between FMT in treating IBS
based on global improvement of IBS symptoms between FMT and placebo. The authors found
inconsistent results which will need further investigation. I would like to thank the authors for
their hard work on submitting this manuscript to BMC Gastroenterology and I enjoyed reading
their outcomes. Their hard work is admirable. While I do think the current work may be worthy
of publication as this type of comparison has rarely been done before based on my literature
search, I would recommend the authors address the major issues listed below before further
consideration.
Overall:
There are major grammatical errors throughout the entire manuscript. Please revise and check
the entire manuscript be written in past tense.
Methods:
The authors did not use PRISMA guidelines which is essential for the literature review and meta
analysis. Can the authors please go back and make sure they follow PRISMA guidelines when
screening for included studies?
The authors should include a quality assessment tool for each included study. Please
use NIS study quality assessment tool: https://www.nhlbi.nih.gov/health-topics/study-quality-
assessment-tools for quality of studies rating. The risk of bias is not adequately sufficient in
this context.
Again, I applaud the authors for their hard work. I look forward to reading the revised
manuscript.
Review for 10.1186/s12876-024-03312-w (2024)

Title: Association and Temporal Sequence of Pneumonia and Gastrointestinal Bleeding after
Acute Ischemic Stroke
Version: 1 Date: 24 Mar 2024
Reviewer:  Zhu Shi
Reviewer's report:
This study used a prospective, large-size AIS cohort to compare two common complications on
the occurrence time, and the results were interesting. However, I have a few concerns about it.
1. It may be inaccurate to define the timing of SAP and GIB only in terms of diagnosis
establishment. This is due to the fact that the clinical symptoms of GIB may be more insidious
than ARP.
2. The occurrence of GIB is not only directly related to the use of antithrombotic and
anticoagulant drugs, but also closely related to risk factros including age, female gender,
previous history of gastric ulcer, and positivity of H. pylori. In the present study yet there was
no difference between GIB and non-GIB patients, which was different from previous studies
and the reasons need to be analysed in discussion.
3. In fact, both SRP and GIB often occur in patients with posterior circulation infarcts and those
with more severe stroke (higher NIHSS score). The relationship is most likely to be correlative
rather than causal-effect. A stratified analysis of the distribution and extent of infarction would
be more convincing.
Review for 10.1186/s12876-024-03312-w (2024)

Title: Association and Temporal Sequence of Pneumonia and Gastrointestinal Bleeding after
Acute Ischemic Stroke
Version: 1 Date: 06 Jun 2024
Reviewer:  Vikramjeet Singh
Reviewer's report:
The study presented by Zhang et al. is very interesting and highlights the association of co-
morbidities such as pneumonia and gastrointestinal bleeding with ischemic stroke conditions in
patients. I have a few suggestions to add further information to the manuscript to increase its
impact and readership.
1)  In the discussion section, it will be important to discuss the major causes of post-stroke
pneumonia namely immunosuppression, and how this might be treated in the future (https://
www.nature.com/articles/s44161-024-00462-8).
2) Please provide an example of anti-platelet and anti-coagulant therapies in the patients in the
manuscript text (In addition to the tables).
3) Please explain what were the prophylactic interventions to prevent GIB.
4) Elaborate PNE in the legend of Figure 2.
5) I will suggest language proofreading.
Review for 10.1186/s12876-024-03312-w (2024)

Title: Association and Temporal Sequence of Pneumonia and Gastrointestinal Bleeding after
Acute Ischemic Stroke
Version: 3 Date: 28 Jun 2024
Reviewer:  Vikramjeet Singh
Reviewer's report:
The authors have adequately discussed my concerns and improved the manuscript accordingly.
I have no further questions.
Review for 10.1186/s12876-024-03305-9 (2024)

Title: Abnormal Platelet Parameters in Inflammatory Bowel Disease: A Systematic Review and
Meta-Analysis
Version: 1 Date: 03 Apr 2024
Reviewer:  Tahne Vongsavath
Reviewer's report:
Data synthesis and data analysis
-and/or interquartile range, we employed the methodologies proposed by Wan et al. (17)and
Luo et al. (18) to estimate the sample mean and SD. A positive WMD indicated higher platelet
parameter values in IBD patients. Please edit this text to be the same size and font
Meta-analyses
-please include citations when references which articles reported *** ie "encompasssing eight
articles"
-hrombopoietin, a key factor in platelet formation, were significantly higher in patients with IBD
than in the general population (29) why is this? any current theories?
Review for 10.1186/s12876-024-03305-9 (2024)

Title: Abnormal Platelet Parameters in Inflammatory Bowel Disease: A Systematic Review and
Meta-Analysis
Version: 1 Date: 05 Apr 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
No - there are major issues
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are major issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are major issues
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Maybe - with major revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: - The topic is interesting, mainly if possible clinical applications for
patients' monitoring are taken into account
- The authors have done an extensive search in the literature, associated with a deep statistical
analysis
- However I have a few concerns about methodology: - they included papers published from
1975! In those years diagnosis and knowledge of IBD were completely different from recent
years, and this could potentially have an impact on PLT analyses. Maybe it could be interesting
to divide and analyze two groups of patients based on the date of publications.
- the authors excluded from the analysis patients who had taken immunosuppressants; but
nowadays a great number of IBD subjects undergo these treatments. And excluding them "a
priori" could be a major bias for the analysis
REQUESTED REVISIONS:
as suggested above
ADDITIONAL REQUESTS/SUGGESTIONS:
methods as already said
Review for 10.1186/s12876-024-03305-9 (2024)

Title: Abnormal Platelet Parameters in Inflammatory Bowel Disease: A Systematic Review and
Meta-Analysis
Version: 1 Date: 05 Apr 2024
Reviewer's report:
The authors shared their work entitled "Abnormal Platelet Parameters in Inflammatory Bowel
Disease: A Systematic Review and Meta-Analysis".
The study is robust. There are however some issues I would like the authors to clarify:
1.  in your inclusion criteria, what was the definition of adults, did all studies have patients ages
18 and more? or was it different cut offs of adults?
2. The authors assessed for heterogeneity and yet used random-effects model irrespective of
heterogeneity.  Can they explain why?
3. the authors had no restrictions on the languages, was any translation services/help used during
the screening process? Should they be included or mentioned in the acknowledgements?
4. The authors included subgroups for region ie asia europe etc, but failed to explain why they
did so in the methods and  the results obtained in the discussions. The results cannot be linked
with racial or ethnic differences as those areas cover a vast range.
Review for 10.1186/s12876-024-03302-y (2024)

Title: Prevalence, characteristics, and risk factors of non-alcoholic fatty liver disease in North
East of Iran: a population-based study
Version: 0 Date: 21 May 2023
Reviewer's report:
The study investigated the prevalence, characteristics, and risk factors of NAFLD in POCM.
Overall, the paper is well-written, but there are a few issues in the Methods section that should
be clarified and corrected.
Methods:
- In line 5 of section 2.2, "y" should be changed to "gr."
- While it is stated that viral hepatitis is one of the exclusion criteria for the study, but section
2.2, line 14 does mention this as a potential underlying disease alongside diabetes mellitus,
hypertension, etc.  It would be advisable to update this section to ensure that viral hepatitis is
correctly accounted for as an exclusion criterion.
- The Methods section should include a clear explanation of how WC, BMI, and BFT were
determined in the subjects, as well as the preparation for the biochemical tests performed on the
subjects. If the findings are published in a previous study, please reference it.
References:
Please ensure that the journal format is observed when referencing sources. Kindly abbreviate
the name of the journal.
Review for 10.1186/s12876-024-03302-y (2024)

Title: Prevalence, characteristics, and risk factors of non-alcoholic fatty liver disease in North
East of Iran: a population-based study
Version: 2 Date: 10 Jun 2024
Reviewer:  Habibollah Rahimi
Reviewer's report:
Thank you for making requested revisions, here you can find the reviewer' comments on them.
1- In the results section_ table 5; please make it clear to the readers what is dependent variable in
model before. Moreover, it seems the authors have used the grades of  NAFLD as the dependent
variable; in this case since you should apply ordinal regression model, not Logistic model. In
both tables, please check multicollinearity.
Reviewer's response; Accepted
Further comments
1. In the results section_ Association of clinically important; Please clarify to the readers that
what are grades of dependent variable in the model, is that included healthy not-NAFLD cases
or not. Please write it.
Reviewer's response; Accepted
2. In the results section_ table 3; please explain the reason of using 3 different model concurrently
whilst according to the statistical standpoint, you should recruit backward or forward model
building approach and adopt just a model with the best goodness-of-fit. Moreover, the BMI
variable has been used in model with two scales; you should only use one of them. Finally,
present the measure of association in Odds Ratio.
Reviewer's response; Accepted
3. In the discussion section; the authors have pointed to Tables and presented some findings
again, it is not usual in discussion section, please remove them and onlu summarize main
findings in the first paragraph.
Reviewer's response; Accepted
Sincerely,
Review for 10.1186/s12876-024-03289-6 (2024)

Title: Step-up approach for the treatment of infected necrotising pancreatitis: real life data from
a single-centre experience with long-term follow-up
Version: 1 Date: 19 Oct 2023
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are minor issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: Dear authors
I read with great interest your study and I want to congratulate you for the effort made. This is
a very interesting topic and your study adds some data about "real life".
I have some comments to improve the quality of the manuscript:
- The abstract is too long; please reduce it to essential results- result section: please begin with
"the study included 41 patients...." Then you can cite tables. In its present form the results section
does not give the study results but it enumerates the tables...
- The results section is too long. please try to reorganize it.
- 75% of patients were referred from other centres. please describe it and also describe pre
drainage treatment.
- Did patients receive antibiotics before the diagnosis of infected necrosis? it would be a very
interesting data to add.
- Time to resolution of infection. Please specify criteria to define infection resolution.
- It would be very interesting to show characteristics of patients who need the second step
compared with those of patients in which the first step was effective. Is there any risk factor?
REQUESTED REVISIONS:
Please see my comments above.
Review for 10.1186/s12876-024-03289-6 (2024)

Title: Step-up approach for the treatment of infected necrotising pancreatitis: real life data from
a single-centre experience with long-term follow-up
Version: 2 Date: 20 May 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: dear authors
thanks you for your improvements
ADDITIONAL REQUESTS/SUGGESTIONS:
it's now ok
Review for 10.1186/s12876-024-03289-6 (2024)

Title: Step-up approach for the treatment of infected necrotising pancreatitis: real life data from
a single-centre experience with long-term follow-up
Version: 2 Date: 27 May 2024
Reviewer:  Arnaldo Amato
Reviewer's report:
Dear Authors,
I read your revised version of the manuscript and found you implemented it according to received
suggestions.
Even if some limitations cannot be corrected due to the methodology itself of the study, I think
now it can be considered for publication.
Review for 10.1186/s12876-024-03301-z (2024)

Title: Risk factors for endoscopic postoperative recurrence in patients with Crohn's Disease:A
protocol for systematic review and meta-analysis
Version: 1 Date: 01 Apr 2024
Reviewer:  Amirreza Keyvanfar
Reviewer's report:
Dear authors,
I appreciate your time and effort involved in this systematic review and meta-analysis regarding
risk factors for endoscopic postoperative recurrence in patients with Crohn's disease. The study
topic is novel, interesting, and within the journal's scope. Your manuscript can assist clinicians to
better manage the patients. You followed a transparent and rigorous method to investigate factors
affecting ePOR in Crohn's disease patients. In my opinion, it can be considered for publication
after some revisions. Please address my concerns to improve the quality of your manuscript.
1-Abstract, result, please mention P-values in addition to OR and CI.
2-Why did you not perform subgroup analysis based on study design (case-control vs. cohort
study)?
3-The manuscript is well written in English. However, it has a few grammatical errors. Please
consult an English editor to improve the grammar, punctuation, fluency, and style.
4-limitations, Please mention that your manuscript suffers from language bias.
5-Table 1, two studies (Shen and Yamada) had no reports for endoscopic recurrence. Is it correct?
Please check them.
Review for 10.1186/s12876-024-03301-z (2024)

Title: Risk factors for endoscopic postoperative recurrence in patients with Crohn's Disease:A
protocol for systematic review and meta-analysis
Version: 1 Date: 02 Apr 2024
Reviewer's report:
The authors submit their original work in the form of a systematic review and meta analysis
investigating the risk factors for postoperative recurrence of endoscopy after initial surgical
intervention for patients with Crohn’s disease. The authors conclude that multiple risk factors
and postoperative prophylactic medication as a protective factor. However, there are still limited
published work at this time.
I would like to thank the authors for their hard work on submitting this manuscript to BMC
Gastroenterology and I enjoyed reading their outcomes. Their hard work is admirable. While I
do think the current work may be worthy of publication as this type of comparison has never
been done before based on my literature search, I would recommend the authors address the
minor issues listed below before further consideration.
Methods:
In the inclusion criteria, the authors write “…(2) the exposure group was CD patients with
ePOR.” How did they define ePOR? Please clarify if it was at anytime an endoscopy procedure
was done after initial surgical intervention.
I would highly recommend the authors use NIS study quality assessment tool: https://
www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools instead of NOS for quality of
studies rating.
Discussion:
I agree with the limitations mentioned. Please also mention lack of controlling confounders in
your meta-analysis that is subject to control from the original studies.
Other minor edits
Can the authors check that the entire manuscript be written in the past tense?
Again, I applaud the authors for their hard work. I look forward to reading the revised
manuscript.
Review for 10.1186/s12876-024-03299-4 (2024)

Title: Deciphering the Role of KLRB1: A Novel Prognostic Indicator in Hepatocellular
Carcinoma
Version: 0 Date: 13 May 2024
Reviewer's report:
In this manuscript the authors investigate in silico the role of KLRB1-CD161 in published HCC
datasets (TCGA and scRNASeq datasets). They then perform an analysis of CD161 expression
via FACS on HCC patients undergoing resection and during follow up.
They observe a correlation of KLRB1 expression activating immune cell signatures in the TCGA
dataset fitting to  single-cell datawith KLRB1 expression in NK and T cells within HCC TME.
Their clinical analysis  showed reduced KLRB1 expression on NK and T cells in HCC patients
compared to health individuals, with lower expression levels linked to higher recurrence rates
and  reduced survival.
Overall the study is largely descriptive and finds associations of relapse or survival with CD161.
However, conclusions remain limited and the cellular correlates of CD161 expression remain
unexplored.
Major criticism
There is no further phenotypic and functional analysis in the study with respect to the two
major T cell populations expressing CD161,  Tc17 cells and MAIT cells.  It remains unclear if
confounders that could explain the difference in CD161 expression are connected to risk factors
of HCC per se. In the FACS data which was newly generated in this work, differences in CD161
expression between groups appear small but significant. An optimized cutoff effect of CD161
expression is calculated for CD8 and NK cells using X-tile 3.6.1 software.  This categorizes
the expression of KLRB1 on CD8+ T cells and NK cells into high and low expression groups.
Subsequently, KLRB1 expression levels below 17.2% on CD8+ T cells and 32.4% on NK cells
were classified as low expression, while levels above these thresholds were designated as high
expression. This is essentially generating optimized cutoffs for stratification but there is no
biologic interpretation why these cutoffs would be used and why different cutoffs for CD8 T
cells and NK cells would be used. At the very least, this needs to be reproduced in a validation
cohort.
Review for 10.1186/s12876-024-03299-4 (2024)

Title: Deciphering the Role of KLRB1: A Novel Prognostic Indicator in Hepatocellular
Carcinoma
Version: 0 Date: 07 Jun 2024
Reviewer's report:
In this study, the authors focused on the prognostic role of  KLRB1 as a novel prognostic
indicator in hepatocellular carcinoma.  The research content of this paper meets the needs of
clinical practice and has certain reference values for clinical guidance. Besides, the paper is
clear, well-structured, and well-written. I suggest a minor English polishing.
Review for 10.1186/s12876-024-03274-z (2024)

Title: Comparison of conventional MRI analysis versus MRI-based radiomics to predict the
circumferential margin resection involvement of rectal cancer
Version: 1 Date: 21 Jan 2024
Reviewer:  Pablo Palma
Reviewer's report:
The abstract is well-structured and provides understanding of the research objective, methods,
and results.
The cohort of patients included raises a number of important questions: How can there be
such a high number of patients with circumferential margin involvement where no neoadjuvant
treatment has been applied?
The statistical metrics (AUC) are appropriately used to quantify the predictive performance of
each model.
Consider providing more context on the clinical implications and potential applications of the
study findings.
In this context, the implications of an affected circumferential margin, both before and after
surgery, are not well defined and explained, especially in the introduction and discussion of the
manuscript, and should be thoroughly reviewed.
It would be very interesting if the authors could comment on the value of this research in patients
after neoadjuvant treatment, as a re-staging of their rectal cancer.
Review for 10.1186/s12876-024-03274-z (2024)

Title: Comparison of conventional MRI analysis versus MRI-based radiomics to predict the
circumferential margin resection involvement of rectal cancer
Version: 1 Date: 29 Jan 2024
Reviewer:  Svetlana Balyasnikova
Reviewer's report:
Dear Authors,
Thank you for your analysis,
It is critical to correctly stratify patient according to their imaging risk factors into group who
would require and benefit from neoadjuvant CRT and those who are unlikely to get any benefit.
It has been proven that MRI is efficient and robust methos or assessing the primary rectal tumour
including the CRM status pre and post CRT. In order to get accurate diagnosis on MRI high-
resolution images are required. Only high resolution T2-sequences enable accurate identification
of fine details and therefore findings appropriate patient for surgical treatment along of combined
with preoperative therapy.
Unfortunately looking at your data, I can see that you used not high-resolution MRI protocols,
meaning that accuracy of you T2-images is suboptimal. Therefore, it can not be considered as
standard, and analysis seems to be done incorrectly. Please consider repeating the analysis on
the high-resolution MRI to compared results of conventional assessment vs radiomics.
Review for 10.1186/s12876-024-03274-z (2024)

Title: Comparison of conventional MRI analysis versus MRI-based radiomics to predict the
circumferential margin resection involvement of rectal cancer
Version: 3 Date: 06 Mar 2024
Reviewer:  Pablo Palma
Reviewer's report:
The article has undoubtedly improved, especially as far as my revisions regarding clinical
involvement are concerned.
However, I miss the clarifications regarding other issues already indicated: The cohort of patients
included raises a number of important questions:
1. How can there be such a high number of patients with circumferential margin involvement
where no neoadjuvant treatment has been applied?
2. It would be very interesting if the authors could comment on the value of this
research in patients after neoadjuvant treatment, as a re-staging of their rectal
cancer.
Review for 10.1186/s12876-024-03274-z (2024)

Title: Comparison of conventional MRI analysis versus MRI-based radiomics to predict the
circumferential margin resection involvement of rectal cancer
Version: 4 Date: 11 Apr 2024
Reviewer:  Pablo Palma
Reviewer's report:
Dear authors, I attach a PDF file of my first review of your interesting manuscript. Unfortunately,
reading your latest version, I note that my review/questions/comments have not been, unless I
made a mistake, taken into account. I believe that the included series of patients needs these
clarifications in order to validate its publication.
Best
Review for 10.1186/s12876-024-03274-z (2024)

Title: Comparison of conventional MRI analysis versus MRI-based radiomics to predict the
circumferential margin resection involvement of rectal cancer
Version: 5 Date: 07 May 2024
Reviewer:  Pablo Palma
Reviewer's report:
Thank you for your improvements which make the publication now, after the revisions, better
expressed from the point of view of the clinical and prognostic importance of MRI staging.
Review for 10.1186/s12876-024-03290-z (2024)

Title: Comparative Safety Assessment of Nasogastric versus Nasojejunal Feeding Initiated
Within 48 Hours Post-Admission versus Unrestricted Timing in Moderate or Severe Acute
Pancreatitis: a Systematic Review and Meta-Analysis
Version: 1 Date: 01 May 2024
Reviewer:  Felipe David Mendonça Chaim
Reviewer's report:
The points raised were duly answered and corrected throughout the text, and I consider the article
suitable for publication.
Review for 10.1186/s12876-024-03297-6 (2024)

Title: Evaluating Vonoprazan and Tegoprazan for Gastroesophageal Reflux Disease Treatment
in Chinese Healthcare: An EVIDEM Framework Analysis
Version: 3 Date: 13 Mar 2024
Reviewer's report:
This study evaluated two new acid blockers in China, VPZ and TPZ, using the EVIDEM
framework. It involved two expert panels: one assigned weights and scored evidence, while the
other conducted literature reviews and evaluated value. VPZ's value slightly surpassed TPZ's,
with potential for EVIDEM in Chinese healthcare. Overall, the study is novel and worthy
of publication after revisions. My main suggestion is to have statisticians or pharmacologists
carefully review the statistical methods of the study to evaluate their rigor.
Review for 10.1186/s12876-024-03297-6 (2024)

Title: Evaluating Vonoprazan and Tegoprazan for Gastroesophageal Reflux Disease Treatment
in Chinese Healthcare: An EVIDEM Framework Analysis
Version: 4 Date: 11 May 2024
Reviewer's report:
Thanks to the author for revising this manuscript according to my comments, and all my concerns
have been appropriately addressed. It’s a novel study to evaluate Vonoprazan and Tegoprazan
for Gastroesophageal Reflux Disease Treatment in Chinese Healthcare by using EVIDEM
Framework Analysis, which was the first time used in Chinese Healthcare. However, it is worth
noting that there is a lack of literature on the direct comparison of the efficacy of Vonoprazan and
Tegoprazan. As a result, the effects of the two drugs can only be reflected through the comparison
with PPI, which may affect the quality of the "Comparative outcomes of the intervention matrix".
In addition, The authors included fewer Chinese studies in the "Comparative outcomes of the
intervention matrix", in which the primary objective of this study was to evaluate the efficacy
of VPZ and TPZ in the treatment of GERD in Chinese healthcare facilities, this further reduced
the persuasiveness of the results. To address the above shortcomings, The author expanded the
literature search range to ensure that all relevant literature was included in the development of
the evidence matrix, and all experts were carefully screened to ensure that they had sufficient
insight into the relevant fields. The double-blind approach was also used to control the subjective
factors and minimize bias in the evaluation process. At the same time, the authors provided
a comprehensive overview of the research methodology, including a search formula for each
database to ensure the study's reproducibility. Overall, after this time revision, the authors have
elaborated the research process and methodology, as well as provided insightful discussion
of the results, which I believe meets the criteria for publication. It is important to highlight
that the EVIDEM Framework Analysis has the potential capability to assess the utilization of
pertinent pharmaceuticals within Chinese healthcare facilities. I am eagerly awaiting the author's
forthcoming study, which will incorporate the latest studies and utilize novel methodologies to
minimize the potential bias.
Review for 10.1186/s12876-024-03297-6 (2024)

Title: Evaluating Vonoprazan and Tegoprazan for Gastroesophageal Reflux Disease Treatment
in Chinese Healthcare: An EVIDEM Framework Analysis
Version: 4 Date: 12 Jun 2024
Reviewer's report:
Thank you for inviting me to review this manuscript. The authors have utilized the EVIDEM
framework to assess the value contributions of vonoprazan (VPZ) and tegoprazan (TPZ),
revealing that VPZ offers a slightly superior value proposition compared to TPZ. These findings
could provide more information for healthcare decision-making.
The methodology employed in this study is its cornerstone, which has been the primary focus of
my evaluation. Nonetheless, upon reviewing the author’s responses to the previous reviewer’s
comments, it is evident that the methodological concerns have been adequately addressed.
Consequently, I have no additional comments.
Review for 10.1186/s12876-024-03291-y (2024)

Title: Dilated Common Bile Duct is Commonly Associated with Main Duct Intraductal
Papillary Mucinous Neoplasm of the Pancreas
Version: 0 Date: 31 Mar 2024
Reviewer's report:
In this paper, the association between CBD dilatation and pancreatic cystic disease was shown.
34 patients showed dilatation of CBD in IPMN cases. Please show the number of patients in
each type of IPMN.
The distribution of CBD diameter in each type of IPMN was not shown. Please add the figure
of this.
The term "MCN" and "MCA" are mixed. If it is not intentional, please unify all terms to MCN.
It is better to use the term from the WHO classifications. Please change "intraductal papillary
neoplasm of the bile duct" to "intraductal papillary neoplasm".
Some cases of blanch duct type IPMN show MPD dilatation. How do you differentiate mixed
type IPMN in these cases? Is it included in the mixed type?
Have you evaluated the main pancreatic duct? Is there any correlation between MPD and CBD
diameter? Please discuss whether the condition of the MPD is relevant to the cause of CBD
dilatation.
Review for 10.1186/s12876-024-03291-y (2024)

Title: Dilated Common Bile Duct is Commonly Associated with Main Duct Intraductal
Papillary Mucinous Neoplasm of the Pancreas
Version: 1 Date: 23 Apr 2024
Reviewer's report:
The study is primarily observational, and the extension of its findings to speculate on the etiology
of Intraductal Papillary Mucinous Neoplasm of the Bile Duct (IPMB) seems to significantly
overreach the scope of the presented data. Such conjectures require a more robust experimental
framework to substantiate the conclusions drawn.
Additionally, the manuscript lacks sufficient detail in the statistical analysis, particularly in the
description of logistic regression methods utilized in Tables 4 and 5. This deficiency hampers
the ability of the readership to fully grasp the methodology and undermines the reproducibility
of the study.
To move forward, it would be imperative to refine the scope of your conclusions to more closely
align with the data and enhance the clarity and depth of your statistical analysis.
Review for 10.1186/s12876-024-03291-y (2024)

Title: Dilated Common Bile Duct is Commonly Associated with Main Duct Intraductal
Papillary Mucinous Neoplasm of the Pancreas
Version: 1 Date: 01 May 2024
Reviewer's report:
In this paper, the words "dilation" and "dilatation" have been used. Are there differences in the
definitions of the two words? Are both words used on purpose?
The unit of measure should be "slash", but in some places it is a backslash. Please correct.
The mean cyst level of amylase in MCN is not listed in the column "The mean cyst level of
amylase". Please add the result and change "the mean cyst level of amylase" to "the mean cyst
level of amylase and CEA".
The mixed type should have characteristics of the main pancreatic duct type, but was not found
to be associated with CBD dilatation. Please discuss why this difference was made. Is there a
difference in pancreatic duct diameter between the two groups? Please list the diameter of the
main pancreatic duct in each group.
Review for 10.1186/s12876-024-03291-y (2024)

Title: Dilated Common Bile Duct is Commonly Associated with Main Duct Intraductal
Papillary Mucinous Neoplasm of the Pancreas
Version: 3 Date: 01 Jun 2024
Reviewer's report:
On page 6, the explanation of multiple comparisons uses Tukey-Cramer, but isn't the correct
term Turkey-Kramer?
Review for 10.1186/s12876-024-03291-y (2024)

Title: Dilated Common Bile Duct is Commonly Associated with Main Duct Intraductal
Papillary Mucinous Neoplasm of the Pancreas
Version: 4 Date: 10 Jun 2024
Reviewer's report:
Thank you for your cooperation. Your revisions are much appreciated and have greatly improved
the manuscript.
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 1 Date: 09 Jan 2024
Reviewer:  Shrikant Pawar
Reviewer's report:
reject
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 1 Date: 14 Mar 2024
Reviewer's report:
I have completed my review of the manuscript by Yingai Zhang et al., which presents a
comprehensive data analysis on the identification of biomarkers in Hepatocellular Carcinoma
(HCC) progression. While the study is extensive in data handling and presents valuable insights,
there are several concerns that I believe need to be addressed:
1 There is an inconsistency in the "Screening of differentially expressed genes (DEGs)" section
where the authors mention "CAH-B 1293 differential genes between HC and LC with 565 up-
regulated and 728 down-regulated." This description does not align with the methodology part.
It is unclear what the "CAH-B 1293 differential genes between HC and LC" actually represents.
2 The authors state twice that "with adjusted (adj.) p < 0.05 and |logFC| = 1 were regarded as
significant DEGs." However, it should be |logFC| > 1 for a gene to be considered significantly
differentially expressed.
3 In the same DEGs section, the manuscript refers to "33 datasets" obtained from gene expression
matrix GSE114783. This terminology is misleading, as what is described appears to be "33
samples," which is fundamentally different from "datasets."
4 The choice of 20 as the soft threshold in WGCNA, despite an R2 of 0.98, may not necessarily
enhance the biological relevance of the network and could potentially lead to an overly sparse
network. A threshold of 19 might be a more cautious approach.
5 The exclusion of the normal group in WGCNA could limit the ability to distinguish between
disease-specific gene modules and those broadly expressed under different conditions. Including
data from a normal control group could significantly enhance the interpretability of the analysis.
6 The rationale behind intersecting the three modules obtained from WGCNA with TCGA
differential genes is not entirely clear. Additionally, the brown module contains as many as 2779
genes, which may require further subdivision and analysis to determine specific gene relevance.
7 The PPI analysis utilizes the MCODE plugin, selecting the first cluster without discussing the
contents of the second or subsequent clusters. This selection process appears somewhat arbitrary
and may benefit from a more systematic approach.
8 The discussion section of the paper is quite limited and does not adequately address the
findings of this research. Moreover, the implications and significance of the identified common
biomarkers need further elaboration to clarify their role in the context of HCC progression.
I believe that addressing these issues would greatly improve the manuscript and provide clarity
and robustness to the findings. I look forward to the authors' response and an updated version
of the manuscript.
Sincerely,
Li Yin
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 1 Date: 24 Mar 2024
Reviewer:  Kazunori Kawaguchi
Reviewer's report:
Authors analyzed gene expression using various state of HBV infected patients including
HCC from database. Though they found 9 genes were associated with chronic liver injury
development such as CAH, LC, HCC regarding HBV infection there is no novelty since these
molecules were already reported and there is no further analysis for these 9 molecules.
Major points:
1. Though they listed 9 genes for HBV related chronic liver injury development and poor
prognosis, these genes have already been reported in HCC. The reason of lack of originality
arises they and other researchers used same databases, that leads to pick up same candidate
genes listed. By analyzing identical databases without using original clinical samples, it leads
to obtain similar results.
2. It is very unclear about the status of background of the liver in HCC cases by reading
manuscript. There is little information of clinical samples data. There is no information about
HBV infection status such as HBe, HBV-DNA, HBV genotype, fibrosis or chronic liver
injury state, and another fundamental clinical information including HCC staging, pathological
information, and background of patients. This information should be listed clearly in the table.
3. In the discussion they did not explain how 9 genes were important for HBV infected chronic
liver injury.
Minor points:
1. This manuscript looks like unclear since there is no explanation of what kind of genes
candidate. They just expressed ‘key genes’ in the title and abstract, no explanation what kind of
function for HBV related chronic liver injury.
2. In the result for the explanation Figure 4F, 9 genes were identified, in the manuscript. In this
portion authors should explain what kind of genes found.
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 1 Date: 25 Mar 2024
Reviewer:  Maryam Ranjpour
Reviewer's report:
The study entitled "Finding key genes co-expressed in hepatitis, cirrhosis and hepatocellular
carcinoma based on multiple bioinformatics techniques " written by  Yingai Zhang et al, is an
informative study.
The authors have used bioinformatics to report 9 genes that have potential to be introduced as
common biomarkers for CAH-B and HCC or LC and HCC. However, there is no validation.
It would be interesting to validate some of the genes at least.
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 2 Date: 30 Apr 2024
Reviewer:  Shrikant Pawar
Reviewer's report:
reject
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 2 Date: 02 May 2024
Reviewer:  Maryam Ranjpour
Reviewer's report:
The manuscript entitled "Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-
expressed in hepatitis, cirrhosis and hepatocellular carcinoma based on multiple bioinformatics
techniques" written bhang et al. Semms to be in a good shape for publication.
The authors have made the correction and I believe it is in a good shape for publication at the
moment.
Review for 10.1186/s12876-024-03288-7 (2024)

Title: Finding key genes (UBE2T, KIF4A, CDCA3, and CDCA5) co-expressed in hepatitis,
cirrhosis and hepatocellular carcinoma based on multiple bioinformatics techniques
Version: 2 Date: 24 May 2024
Reviewer:  Kazunori Kawaguchi
Reviewer's report:
Looking the author’s response and revised manuscript, I think it is acceptable as satisfied
publication. Thank you very much for giving the opportunity to review and I was impressed
by authors’ effort.
Review for 10.1186/s12876-024-03279-8 (2024)

Title: IRIS U kit usefulness in transanal total mesorectal excision for lower rectal cancer to
avoid urethral injury
Version: 3 Date: 01 May 2024
Reviewer's report:
This paper demonstrated the utility of using the IRIS-U kit during the execution of taTME
for rectal cancer resection in the deep pelvis, highlighting its ability to visualize safe
demarcation lines. Although the effectiveness of taTME has been previously validated, the risk
of intraoperative injury to the urogenital organs has been a significant concern. This paper
proposes a novel method that reduces the risk of ureteral injury through a relatively simple and
reproducible approach, and it is deemed worthy of publication. However, here are some points
to be revised. I pointed four things to be revised.
##In the discussion, the author indicated the utility and safety of taTME for deep pelvic. rectal
cancer at their institution, as well as the oncological adequacy of the resection. They mention that
adequate lymph node dissection was performed, but it may be beneficial to include the number
of lymph nodes harvested in the oncological evaluation section of Table 1.
##The author stated in the discussion that this technique is particularly suitable for males with
obesity and a narrow pelvis. If possible, it would be good to show that there any correlation
between high BMI in patients and subsequent complications or margin length as presented in
Table 1.
Review for 10.1186/s12876-024-03279-8 (2024)

Title: IRIS U kit usefulness in transanal total mesorectal excision for lower rectal cancer to
avoid urethral injury
Version: 3 Date: 06 May 2024
Reviewer's report:
Ishii M et al. have made a retrospective study regarding the application of IRIS U kit to perform
the transanal total mesorectal excision for lower rectal cancer. The authors advocated that the
IRIS U kit can effectively avoid urethral injury.
The manuscript was well written and the surgical procedure regarding the use of IRIS U kit
was well described I have no major criticisms. However, the present study was too preliminary
because the ISIR U kit was applied in only 10 patients undergoing ta-TME. In order to enhance
the readability of this article, I would like to suggest the authors cite and made some discussions
based on the similar studies from the Asian fellow researchers:
1. Asian Journal of Surgery. Volume 42, Issue 6, June 2019, Pages 674-680
2. Asian Journal of Surgery. Volume 45, Issue 11, November 2022, Pages 2197-2202
3. Asian Journal of Surgery. Volume 43, Issue 1, January 2020, Pages 330-338