JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-02792-6 (2023)

Title: Innovative angiography: a new approach to discover more hepatic vein collaterals in
patients with cirrhotic portal hypertension
Version: 0 Date: 14 Jan 2023
Reviewer's report:
Major points:
Looking at Figure 4 panel C, it is unclear to me why there was only a small discordance
between WHVP and PP, however, there was substantial discordance between HVPG and PPG.
Since FHVP/VCIP should basically be the same, what is the explanation for this discordance?
The same applies to Figure 6, panel A. Even in Figure 5, differences in WHVP and PP seem
substantially lower than those in HVPG/PPG. How was PPG calculated? If the RAP was used,
it should be exchanged for the VCIP (or FHVP, if VCIP was not measured) – see Baveno VII
recommendations.
Moreover, since sedation/analgesia impacts pressure measurements, the regimens should be
reported. Were the regimens the same when measuring WHVP and PP, or was sedation/analgesia
added/increased before the portal puncture for PP?
Comparing the data presented in Figure 5 (i.e., those without collaterals on conventional
angiography) to previous work (which also used conventional angiography: synthesized
in https://pubmed.ncbi.nlm.nih.gov/15908290/ or https://pubmed.ncbi.nlm.nih.gov/33068638/),
the observed poor correlation is surprising. What are the explanations by the authors? How was
alcoholic cirrhosis diagnosed? Are biopsies/liver stiffness measurements available to rule-out
INCPH/PSVD?
The latter is particularly important, as the reported prevalence of vein-vein communications in
conventional angiography seems very high for alcoholic cirrhosis – (erroneous) inclusion of
some INCPH/PSVD patients may explain this finding.
At my institution, we avoid injecting large amounts of contrast/with high pressure, assuming
that the unphysiologically high pressures/flow may affect the endothelium/sinusoids, and
thus, WHVP. Can the authors provide data on WHVP measured before and after ‘innovative
angiography?’
Minor points:
I (and most likely potential readers) cannot follow this paragraph: ‘The contrast medium was
retained in the liver parenchyma and could not enter the portal vein or the hepatic venous
collateral return. Therefore, the absence of collateral branches of the hepatic vein is an important
reason for the overestimation of WHVP and HVPG.‘ Please rephrase/explain.
Numbers should be added to the Figures.
Review for 10.1186/s12876-023-02792-6 (2023)

Title: Innovative angiography: a new approach to discover more hepatic vein collaterals in
patients with cirrhotic portal hypertension
Version: 0 Date: 07 Feb 2023
Reviewer's report:
The paper deals with an important topic, authors incorporated innovative method of visualization
of hepatic vessels in patients with portal hypertension, during TIPS. Rationale for the study is
clear, discussion is well written and highly informative.
Several improvements are highly recommended:
1. More details on innovative angiography procedure - to explain  parameters of contrast
injection, why specific values, e.g. pressure, have been chosen.
2. Results section could easily be presented in different form, e.g. table, which would make it
easier to read.
3. More images which would directly compare the findings in regular and innovative
angiography would be valuable.
Review for 10.1186/s12876-023-02786-4 (2023)

Title: Soluble CD163 is a predictor of fibrosis and hepatocellular carcinoma development in
nonalcoholic steatohepatitis
Version: 1 Date: 11 Oct 2022
Reviewer's report:
In this study, the authors firstly demonstrated the increased serum sCD163 levels were strongly
associated with the progression of fibrosis, inflammation grade, and hepatocyte ballooning. The
serum sCD163 levels alterations from the first-time to second-time liver biopsies have increased
in inflammation and fibrosis progressed patients compared to fibrosis and inflammation
improved patients. Lastly, the sCD163 levels indicated could serve as a serum marker for NASH
prognosis and liver carcinogenesis.
The novel prognostic markers for HCC patients with NAFLD backgrounds are of paramount
importance. The wide differences in sCD163 levels between the first-time and second-time liver
biopsies only detected in inflammation and fibrosis progressed patients are interesting, and it
has the potential of being a non-invasive marker to evaluate the liver tissue changes. However,
I still have some issues for the authors to improve:
1. Fig. 2: The diagnosability of sCD163 should be compared with the other existing serum
markers by the AUC, sensitivity, specificity, PPV, and NPV, and listed in a table. Besides,
whether the combination of sCD163 and the other existing serum markers could improve
diagnosability should be studied further.
2. Fig. 3: The information about the therapy methods of those 119 patients with NAFLD who
underwent repeated biopsies should be mentioned.
3. Fig. 4: The levels of sCD163 of HCC patients, who have no NAFLD background, should be
compared together in Fig. 4a.
4. The multivariate analysis should be performed to investigate whether the sCD163 levels
could serve as an independent marker for NAFLD diagnosis, NASH prognosis, and liver
carcinogenesis.
5. CD68 is a marker of macrophages, and CD163 could distinguish M2 macrophages from M1
macrophages, so the relationships between M2 macrophages and NASH/NAFLD progression
should be discussed further.
6. It is inconsistent that the description in Results, line 130: “119 patients with NAFLD who
underwent repeated biopsies” and the description in Discussion, line 180: “287 patients with
NAFLD who underwent repeated liver biopsies”.
7. The names of horizontal and vertical coordinates should be presented in Figures.
8. Figure S2, line 12: “b. sCD168” ?
Review for 10.1186/s12876-023-02786-4 (2023)

Title: Soluble CD163 is a predictor of fibrosis and hepatocellular carcinoma development in
nonalcoholic steatohepatitis
Version: 1 Date: 28 Oct 2022
Reviewer's report:
Dear authors
Thank you for your efforts.
Revising your manuscript ,it needs the following clarifications:
Could this sCD63 differentiate simple steatosis from NASH?
Please define clearly at which time point the levels of sCD163 are described through out your
manuscript  whether at base line or follow up and also in the title of table 1.
Lines 65-66:  What do you mean?
Lines 88 : Please add the details of liver core tissue obtained  ( length, number of portal tracts, .....)
Lines 124-127 : the sensitivity and specificity for fibrosis and steatosis are low to be
defined as "suitable".
Line 131-137: Please define "progression, stationary and improvement" of fibrosis and steatosis
in terms of  score changes .
Lines: 145-146 "13 had HCC and 15 died " is it all cause mortality ? cause of death ?
The discussion is long actually lines 159-171 is a new introduction.
Please add the p value for Figure 1c ,1d.
Review for 10.1186/s12876-023-02786-4 (2023)

Title: Soluble CD163 is a predictor of fibrosis and hepatocellular carcinoma development in
nonalcoholic steatohepatitis
Version: 1 Date: 02 Nov 2022
Reviewer's report:
The authors assessed soluble CD163 as a predictor of fibrosis and hepatocellular carcinoma
development in nonalcoholic steatohepatitis; the study is interesting and well written; However:
=Sample size analysis and power of the study is needed to validate the results of the study.
=Discussion: Comparison with other markers are needed to better demonstrate the validity of
this marker.
=References need to be updated with important references about some markers in HCC
development in hepatic patients; I suggest some revlevant references:
-El-Gebaly F, Abou-Saif S, Elkadeem M, et al. Study of Serum Soluble Programmed Death
Ligand 1 as a Prognostic Factor in Hepatocellular Carcinoma in Egyptian Patients. Curr Cancer
Drug Targets. 2019; 19(11):896-905.
-Watany M, Badawi R, Elkhalawany W, et al. Study of Dickkopf-1 (DKK-1) Gene Expression
in Hepatocellular Carcinoma Patients. J Clin Diagn Res. 2017 Feb; 11(2):OC32-OC34.
-Elhendawy M, Abdul-Baki EA, Abd-Elsalam S, et al. MicroRNA signature in
hepatocellular carcinoma patients: identification of potential markers. Mol Biol Rep. 2020
Jul;47(7):4945-4953.
Review for 10.1186/s12876-023-02786-4 (2023)

Title: Soluble CD163 is a predictor of fibrosis and hepatocellular carcinoma development in
nonalcoholic steatohepatitis
Version: 3 Date: 23 Apr 2023
Reviewer's report:
The author addressed the comments of the reviewers. So, l suggest acceptance of the article.
Review for 10.1186/s12876-023-02778-4 (2023)

Title: A systematic review and meta-analysis#The therapeutic and preventive effect of
Lactobacillus reuteri DSM 17938 addition in children with diarrhea
Version: 2 Date: 19 Feb 2023
Reviewer's report:
Dear Editor
Thanks for the opportunity to review the manuscript titled, " A systematic review and meta-
analysis# The therapeutic and preventive effect of Lactobacillus reuteri DSM 17938 addition
in children with diarrhea’’. The authors present a meta-analysis of 9 studies with a total of 963
patients that met the eligibility criteria to evaluate the ability of Lactobacillus reuteri DSM 17938
to treat and prevent various types of diarrheal diseases in children. Based on their analysis the
authors concluded that " Addition of Lactobacillus reuteri in the treatment plan has a significant
effect on reducing the number of diarrhea and reducing the symptoms of diarrhea, but has no
obvious effect on the prevention of diarrhea’’. the overall conclusion reached by the authors is
reasonable.  the manuscript is well written, the methods are rigorous and the results are well
presented in tables, the claims appropriately were discussed in the context of previous literature.
Best wishes,
Review for 10.1186/s12876-023-02778-4 (2023)

Title: A systematic review and meta-analysis#The therapeutic and preventive effect of
Lactobacillus reuteri DSM 17938 addition in children with diarrhea
Version: 2 Date: 24 Feb 2023
Reviewer's report:
"The authors have addressed the considerable issues related to the effect of adding Lactobacillus
reuteri to manage diarrheal diseases among "children" through a systematic review and meta-
analysis. However, it is recommended pay attention to the following comments, which are
expected to help authors improve the quality of the manuscript."
*The main text needs English spelling, punctuation, grammar check and editing.*
( some sentences are repeated twice in the maintext, for e.g. the second line in “Inclusion and
exclusion criterion” subsection.)
Abstract
• It is necessary to report more information regarding the design of the study and statistical
methods used for analysis in the material and methods sub-section.
Introduction
• Objective of the study well not organized and needs correction.
• What is the exact aim of this review? Efficacy on children, or adults, or both groups?
In the background section, the aim of the study is clearly reported on the children’s population,
but the studies on adult population are also considered in analysis, please clarify this.
Methods
• Please clearly state the research question using PICO format.
• Please specify the more details about methods used to assess risk of bias in the included studies,
such as how many reviewers assessed each study and whether they worked independently.
• As you know, bias is distinguished from quality. According to the design of included studies
in this review, which one have you assessed? Which Cochrane tool was used for assessment?
Please provide a relevant reference and an approporaite subsection's title.
• Please completely define the methods used to screening and data collection from records,
including how many reviewers screened and collected data from each record, whether they
worked independently, any processes for obtaining or confirming data from study investigators,
how agreements to be reached and disagreements dealt with, etc.
• The data extracted from the included studies for meta-analysis are not clear. It is better to report
appropriate information about data extracted for analysis.
Results
• Please present assessments of risk of bias results for each included study in the result section.
• Information about primary and secondary outcomes are not reported in Table1.
• Why did you pooled studies on children with studies on adults in analysis? It would
have been better to analyze these studies separately in subgroup analysis.
Review for 10.1186/s12876-023-02763-x (2023)

Title: Non-alcoholic fatty liver disease in hemochromatosis probands with iron overload and
HFE p.C282Y/p.C282Y
Version: 3 Date: 13 Feb 2023
Reviewer's report:
In this manuscript, Barton et al report their examination the effect on selected outcomes of
the diagnosis of non-alcoholic fatty liver disease (NAFLD) in a selected population of iron
overloaded (per serum ferritin) probands homozygous for the HFE C282Y mutation. They
excluded those with other known risk factors for NAFLD, including self-reported heavy alcohol
consumption. They observe an association between NAFLD and ferritin levels as well as type II
diabetes. They also noted higher prevalence of an elevated ALT/AST in the group with NAFLD.
These observations are of interest in further characterizing  liver disease in HFE-associated
hereditary hemochromatosis. The following suggestions and questions are raised:
1) For clarity, in the Abstract Results section, second sentence. Change the first word from
"These ..." to "The following ..."
2) Regarding alcohol consumption. The investigators define “heavy” alcohol consumption as
>14g per day (self reported). The CDC defines heavy alcohol consumption as 8 or more drinks
(14g/drink) per week for women and 15 or more drinks per week for men. Please either use these
definitions or provide basis for the cutoff used in this study.
3) The manuscript states “Thirty-five probands (53.0%) underwent liver biopsy. Of these, 11 had
NAFLD (68.6% (11/15)) and 24 did not have NAFLD (48.0% (24/50)) (p = 0.1653).” Should
this not be 24/35 that did not have NAFLD?
4) Please provide a breakdown of the tests used to diagnose NAFLD (biopsy, ultrasound, CT)
in the subjects.
5) Please add a footnote to the reported transferrin saturation levels in the table to flag that these
were obtained without regard to fasting state.
6) The manuscript states (p13) “Odds ratios were SF (1.0-1.0) and T2DM (1.1-22.3).” Please
clarify in the sentence the groups compared, and please correct the reported OR for SF.
7) The authors postulate that “combined effects of increased hepatic iron and hepatic steatosis
account in part for higher prevalences of elevated ALT and elevated AST in hemochromatosis
probands with p.C282Y/p.C282Y who also have NAFLD.” Do the authors mean elevations in
each? The ALT/AST?
8) What measurements, in addition to serum ferritin, were performed to assess hepatic iron
concentration in the subjects? Are these informative in assessing the combined effect of liver
iron and NAFLD on transaminase levels?
9) Have the authors considered utilizing the NAFLD index (ANI) score? It might be informative
to assess the ANI in this population, and to consider its potential as a continuous variable.
10) It would be informative in the discussion for the authors to compare, where possible, each of
the relevant outcomes (and correlations) across four groups: C282Y/C282Y subjects +/- NAFLD
in their study and the general (preferably comparable) population +/- NAFLD from the literature.
11) Please provide figures for the significant  logistic regression analyses.
Review for 10.1186/s12876-023-02763-x (2023)

Title: Non-alcoholic fatty liver disease in hemochromatosis probands with iron overload and
HFE p.C282Y/p.C282Y
Version: 4 Date: 07 Mar 2023
Reviewer's report:
The authors have addressed the concerns of this reviewer and have produced an informative
body of work.
Review for 10.1186/s12876-023-02763-x (2023)

Title: Non-alcoholic fatty liver disease in hemochromatosis probands with iron overload and
HFE p.C282Y/p.C282Y
Version: 4 Date: 27 Mar 2023
Reviewer's report:
I thank the authors for their close attention to all the reviewer's comments. I think this makes a
valuable contribution to an improved the understanding of the development of liver disease in
pC282Y/p.C282Y hemochromatosis
Review for 10.1186/s12876-023-02772-w (2023)

Title: Randomised clinical trial: 3-year interim analysis results of the VISION trial to
evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive
oesophagitis
Version: 1 Date: 24 Nov 2022
Reviewer's report:
The results of an interim analysis of the evaluation of the safety of vonoprazan are appropriately
reported. The association of vonoprazan with adverse effects, especially with the development
of epithelial and endocrine tumors, is of great interest.
1. The association of Hp infection with the development of epithelial tumors is important. In this
study, it seems that urea breath test was performed  depending on the presence of endoscopic
gastritis (n=2) (12p, line 244). However, endoscopic atrophy was observed in about 40% of
cases in the vestibular region at the beginning of treatment (Table 4), and it is possible that Hp
infection cases were included in this group. If possible, please describe the results of Hp-IgG
antibody and urea breath test in such cases.
2. If a urea breath test is performed after endoscopy (line 173 on page 9), a false negative result
may be possible. Please tell me if the test was performed on a different day.
3.  The number of cases excluded due to AEs in Fig 1 is high for vonoprazan (n=10), but
the details of the exclusion need to be described. If possible, the degree of AE should also be
described.
Review for 10.1186/s12876-023-02772-w (2023)

Title: Randomised clinical trial: 3-year interim analysis results of the VISION trial to
evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive
oesophagitis
Version: 1 Date: 14 Dec 2022
Reviewer's report:
Randomized clinical trial: 3-year interim analysis results of the VISION trial to evaluate the
long-term safety of vonoprazan as maintenance treatment in patients with erosive oesophagits.
The study design was straightforward and the writing was clear and professional, although a
few details are required to be added. I have several comments as follows. This study mainly
evaluated histopathological change of the gastric mucosal under 3-year maintenance therapy,
which showed no neoplastic/dysplastic alteration of epithelial cells.
1. The authors should mention the histological evaluation method, at least clarify the biopsy
position (e.g. antrum or fornix) and add “Gastrin” in line 180.
2. The definition of G-cell hyperplasia, atrophy ECM and hyperplastic ECM was unclear.  Some
of patients (VPZ:32.8%, LPZ: 25.4%) exhibited G-cell hyperplasia at the start of healing phase.
Was G-cell hyperplasia recognized in control as well?
3. The authors concluded that no neoplastic/dysplastic alteration of epithelial cells in
pathological examination, however, one patient presented foveolar-type adenoma at week 156.
The authors should mention about this patient.
4. 10 patients (7.4%) in the vonoprazan group discontinued treatment because of AE. This should
be mentioned in detail and discussed to evaluate the long-term safety of vonoprazan.
5. The authors showed that pepsinogen I and pepsinogen II were elevated (Figs. 5,6,8). If any
speculation, it would be better to discuss it.
Review for 10.1186/s12876-023-02772-w (2023)

Title: Randomised clinical trial: 3-year interim analysis results of the VISION trial to
evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive
oesophagitis
Version: 3 Date: 08 Mar 2023
Reviewer's report:
Thank you for your response for each question.  I could understand for several problems.
I expect that you make a presentation for even more long-term safety.
Review for 10.1186/s12876-023-02772-w (2023)

Title: Randomised clinical trial: 3-year interim analysis results of the VISION trial to
evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive
oesophagitis
Version: 3 Date: 14 Mar 2023
Reviewer:  Kenta Watanabe
Reviewer's report:
This is a well designed study that provides convincing evidence of the long-term safety arising
in the 3-year usage of vonoprazan using both histopathological assessment and endoscopic
findings.
The authors interpret their data very well and the findings are very convincing.
In particular, no neoplastic/dysplastic alteration of epithelial cells and no occurrence or increase
in intestinal metaplasia is very interesting and noteworthy.
Review for 10.1186/s12876-023-02772-w (2023)

Title: Randomised clinical trial: 3-year interim analysis results of the VISION trial to
evaluate the long-term safety of vonoprazan as maintenance treatment in patients with erosive
oesophagitis
Version: 4 Date: 17 Apr 2023
Reviewer:  Kenta Watanabe
Reviewer's report:
Thank you for adding the detailed description. Several questions have been resolved.
I look forward to your report on the long-term results.
Review for 10.1186/s12876-023-02784-6 (2023)

Title: Upper gastrointestinal endoscopic findings in functional constipation and irritable bowel
syndrome diagnosed using the Rome IV criteria: a cross-sectional survey during a medical
check-up in Japan
Version: 0 Date: 16 Mar 2023
Reviewer:  Konosuke Nakaji
Reviewer's report:
The article described the EGD findings associated with FC and IBS patients who underwent
screening purposes in the Japanese cohort. The authors found that corpus erosion and read
streaks are significantly associated with FC, and erosive gastritis and duodenitis are significantly
associated with IBS. There is a trend of red lines and IBS. IBS with erosive and duodenitis has
more phycological factors and abdominal pain in this morphology. This unique study presents
an issue that has not been investigated previously, has high scientific soundness and is worth
publishing. However, there are some minor concerns about this article. 1. In this study’s design,
the authors should explain the definition of continuous use (p.6, line 15) (e.g., how many months/
years). Please briefly explain why acid secretion inhibitors are excluded from this study in the
discussion. 2. In the methods, the authors use GIF-XP290N (probably mainly for screening /
patient accessibility) as an endoscope. The authors may present the modalities (e.g., WLI/NBI/
indigo carmine) and procedure (e.g., no sedation). 3. Table 1 needs the unit(U/mL) for the serum
Hp antibody. 5. Please add arrows in the endoscopic pictures to explain the findings. I am very
interested in reading the article.
Review for 10.1186/s12876-023-02784-6 (2023)

Title: Upper gastrointestinal endoscopic findings in functional constipation and irritable bowel
syndrome diagnosed using the Rome IV criteria: a cross-sectional survey during a medical
check-up in Japan
Version: 0 Date: 05 Apr 2023
Reviewer's report:
In this paper entitled “Upper gastrointestinal endoscopic findings in functional constipation
and irritable bowel syndrome diagnosed using the Rome IV criteria: a cross-sectional survey
during a medical check-up in Japan”, the authors examined the upper GI endoscopic findings
and symptoms of subjects with FC and IBS of individuals undergoing a medical check-up.
I would like to add a comment, which I believe would make this article better.
Major comment
1. In this study, the authors examined H. pylori antibodies and history of eradication, but these
cannot be used to evaluate current, existing, or uninfected H. pylori infection. Since H. pylori
status has a significant impact on upper gastrointestinal endoscopy, this item should be added
to the limitation.
Review for 10.1186/s12876-023-02784-6 (2023)

Title: Upper gastrointestinal endoscopic findings in functional constipation and irritable bowel
syndrome diagnosed using the Rome IV criteria: a cross-sectional survey during a medical
check-up in Japan
Version: 1 Date: 23 Apr 2023
Reviewer:  Konosuke Nakaji
Reviewer's report:
The article has been revised well and improved. No further comments are available.
Review for 10.1186/s12876-023-02779-3 (2023)

Title: Clinical features and images of malignant lymphoma localized in the pancreatic head to
differentiate from pancreatic ductal adenocarcinoma: A case series study.
Version: 2 Date: 21 Mar 2023
Reviewer's report:
Very interesting study. I have the following comments:
1) The study includes only 8 patients so i would specify in the title that this is a case series.
2) English grammar should be improved
3) The authors stated that they used FNA for tissue sampling. The authors should specify exactly
which needle was used, the caliper, the sampling technique. Comment also this aspect in the
discussion, citing the recent evidence on this regard (cite PMID: 29026598 , PMID: 35915956,
PMID: 33481633)
4) The authors should comment that there are now highly performing end-cutting needles for
FNB, that are much better for tissue sampling of MLs (see PMID: 36657607)
Review for 10.1186/s12876-023-02779-3 (2023)

Title: Clinical features and images of malignant lymphoma localized in the pancreatic head to
differentiate from pancreatic ductal adenocarcinoma: A case series study.
Version: 2 Date: 24 Mar 2023
Reviewer:  Thomas Togliani
Reviewer's report:
This is  an interesting report on the role of imaging techniques and biochemistry to differentiate
pancreatic lymphoma from PDAC. The topic is original and the clinical outcomes seem
attractive.
The only remark I have is that the additional diagnostic role of these information should not be
compared to EUS-guided FNA but to FNB. In fact, the histological and immunohistochemical
capabilities of FNB currently represent the diagnostic gold standard for pancreatic masses
(PDAC, lymphoma, NETs, autoimmune pancreatitis); moreover, EUS elastography and
contrast-enhanced EUS could give a further help in the differential dignosis of pancreatic
masses.
Thus, the relevance of the described clinical and imaging data could be slightly reduced when
compared to the currently available high-quality EUS procedures.
Review for 10.1186/s12876-023-02779-3 (2023)

Title: Clinical features and images of malignant lymphoma localized in the pancreatic head to
differentiate from pancreatic ductal adenocarcinoma: A case series study.
Version: 4 Date: 20 Apr 2023
Reviewer:  Thomas Togliani
Reviewer's report:
The revised version of the manuscript includes additional sentences that were needed.
Review for 10.1186/s12876-023-02769-5 (2023)

Title: Peripheral blood T-lymphocyte subsets are potential biomarkers of disease severity and
clinical outcomes in patients with ulcerative colitis: a retrospective study
Version: 1 Date: 23 Jan 2023
Reviewer's report:
The presented manuscript describes the subsets of T lymphocyte were associated with severity
and outcome of UC. This is an interesting report.
However, I would like to ask the authors to correct the following points.
#The categorization of activities from "mild" to "moderate" is too broad. I recommend adding
an analysis by categorizing them into three categories: mild, moderate, and severe.
#It is interesting to know why CD3+HLA-DR+T lymphocytes are more prevalent in more severe
cases of UC. I recommend a more detailed discussion of this point.
Review for 10.1186/s12876-023-02769-5 (2023)

Title: Peripheral blood T-lymphocyte subsets are potential biomarkers of disease severity and
clinical outcomes in patients with ulcerative colitis: a retrospective study
Version: 1 Date: 26 Jan 2023
Reviewer:  Dawesh P Yadav
Reviewer's report:
The study is well conducted and is informative. It may be useful for monitoring disease activity
in UC patients.
Though the difference in percentage of T cell subsets is not marked, still it is statistically
significant.
Author may have correlated the percentage of T cell subsets with fecal calprotectin level also
and response to conventional treatment in that subset of patients.
Review for 10.1186/s12876-023-02769-5 (2023)

Title: Peripheral blood T-lymphocyte subsets are potential biomarkers of disease severity and
clinical outcomes in patients with ulcerative colitis: a retrospective study
Version: 1 Date: 24 Feb 2023
Reviewer's report:
We read with interest of this study which aimed to explore the compositional changes of
T-lymphocyte subsets among UC patients and healthy controls and the correlation of T-
lymphocyte subsets and disease severity. But there are several issues need to be addressed.
1. The related topics has been published in Zhonghua Yi Xue Za Zhi. 2011 Jun 21;91(23):1605-8,
Gastroenterology 2005;128:1868-78, Clin Res Hepatol Gastroenterol 2017;41:693-702.,. Please
further clarify the  novelties in this work.
2. We hope to see whether there is predictive values of baseline T-lymphocyte subsets for
assessing treatment response of biologic agents of UC patients, such as Remicade, adalimumab,
or vedolizumab.
3. How healthy controls was defined was not clear? All received endoscopy assessments?
4. Is there any correlations between the T-lymphocyte subsets in blood and colon?
5. Instead of amounts of T-lymphocyte subsets, we focus on the function or activated status of
these cells, could you provide any data to further analysis?
6. Should consider other type of colitis as control.
Review for 10.1186/s12876-023-02769-5 (2023)

Title: Peripheral blood T-lymphocyte subsets are potential biomarkers of disease severity and
clinical outcomes in patients with ulcerative colitis: a retrospective study
Version: 3 Date: 08 Apr 2023
Reviewer:  Dawesh P Yadav
Reviewer's report:
Major points raised by editor and reviewers have been answered , so revised manuscript may
be accepted
Review for 10.1186/s12876-023-02769-5 (2023)

Title: Peripheral blood T-lymphocyte subsets are potential biomarkers of disease severity and
clinical outcomes in patients with ulcerative colitis: a retrospective study
Version: 3 Date: 16 Apr 2023
Reviewer's report:
I believe they are answering the reviewers' questions appropriately and revising the text.
Review for 10.1186/s12876-023-02715-5 (2023)

Title: Three-dimensional pelvic ultrasound is a practical tool for the assessment of anal fistula
Version: 3 Date: 11 Dec 2022
Reviewer's report:
The presented manuscript describes usefulness of the pelvic three-dimensional(3D) US for
assessing anal fistula. Pelvic ultrasonography is noninvasive, and if it can be proven to be
equivalent to MRI in positive results, it would be a great benefit to patients and to society.
However it requires some revisions as listed below.
1. The authors need to describe the indications for surgery in this study
2. How many experts performed the echo?  How many years has the expert been performing
echoes?  The authors are recommended to give detrails about the experts.
3. The authors are requested to define Accuracy rate.
Review for 10.1186/s12876-023-02715-5 (2023)

Title: Three-dimensional pelvic ultrasound is a practical tool for the assessment of anal fistula
Version: 3 Date: 11 Dec 2022
Reviewer's report:
The authors have  reflected the regional data on the subject .
The following suggestions are offered for enhancing the manuscript:
1. The language requires correction throughout the manuscript
2. The discussion seems to be  inadequate . It needs to be written with more discussion of relevant
work on the same subject. the following maybe added and discussed:
a.  Almeida IS, Jayarajah U, Wickramasinghe DP, Samarasekera DN. Value of three-
dimensional endoanal ultrasound scan (3D-EAUS) in preoperative assessment of fistula-in-ano.
BMC Res Notes. 2019;12(1):66. Published 2019 Jan 29. doi:10.1186/s13104-019-4098-2
b. Emile SH, Magdy A, Youssef M, Thabet W, Abdelnaby M, Omar W, Khafagy
W. Utility of Endoanal Ultrasonography in Assessment of Primary and Recurrent Anal
Fistulas and for Detection of Associated Anal Sphincter Defects. J Gastrointest Surg. 2017
Nov;21(11):1879-1887. doi: 10.1007/s11605-017-3574-z. Epub 2017 Sep 11. PMID: 28895031.
c. Mantoo S, Mandovra P, Goh S. Using preoperative three-dimensional endoanal ultrasound
to determine operative procedure in patients with perianal fistulas. Colorectal Dis. 2020
Aug;22(8):931-938. doi: 10.1111/codi.14993. Epub 2020 Feb 17. PMID: 31991037.
d. Sharma, A., Yadav, P., Sahu, M. et al. Current imaging techniques for evaluation of
fistula in ano: a review. Egypt J Radiol Nucl Med 51, 130 (2020). https://doi.org/10.1186/
s43055-020-00252-9
3. The figures should be labelled and adequately described too
Review for 10.1186/s12876-023-02760-0 (2023)

Title: The effect of melatonin on irritable bowel syndrome patients with and without sleep
disorders: a randomized double-blinded placebo-controlled trial study
Version: 2 Date: 20 Dec 2022
Reviewer:  Mohammadreza Davoudi
Reviewer's report:
The authors have largely done a nice job addressing the comments on the initial version of this
manuscript. A few additional items that would strengthen the paper include:
* The introduction is quite long and would benefit from being more focused.
* please provide more information about pervious studies limitations. ( in introduction)
* It would be helpful to have more details of the IBS characteristics of the sample from a clinical
perspective, rather than the self-report of the patient given information.
* Your discussion needs important revision ( where is your finding explanation placement?)
* Plese revise your paper regarding gramatical issues .
Review for 10.1186/s12876-023-02760-0 (2023)

Title: The effect of melatonin on irritable bowel syndrome patients with and without sleep
disorders: a randomized double-blinded placebo-controlled trial study
Version: 2 Date: 12 Jan 2023
Reviewer:  Jie Liu
Reviewer's report:
It is a very good RCT evaluating the therapeutic effect of melatonin on IBS. But I think some
issues should be addressed.
1.Sample size: the authors should report the detailed data about previous study by Lu et al.11,
such as (total effective rate: 86.0% vs 83.6%).
2.Inclusion and exclusion criteria: the authors must tell us if medications that could potentially
affect sleep quality were excluded
3.Patients: it is amazing for me that no patients were drop out for 8 weeks. In addition, a total
of 136 patients were enrolled, but there are 68 patients combined with sleep disorders. It means
that 50% of IBS patients were combined with sleep disorders? Please report this data in relavant
references.
4.Analysis: normal distribution of quantitative parameters can be presented by x±s, but the non-
distributed data should be presented by interquartile ranges.
5.Results: the data presented in Table 2. is insufficient. The authors can report the parameters
post treatment to avoid non-distributed data. In additon, it is intersting to explore the effect of
melatonin on IBS with and without sleep disorder: between Melatonin-receiving sub-group in
Group with sleep disorders and Melatonin-receiving sub-group in Group without sleep disorders.
6.Reference interpretation in Discussion is not enough. It is necessary to compare the parameters
in the current study with references.
Review for 10.1186/s12876-023-02761-z (2023)

Title: Ischemia prediction score (IsPS) in patients with strangulated small bowel obstruction:
a retrospective cohort study
Version: 2 Date: 26 Jan 2023
Reviewer:  Weiwei Ding
Reviewer's report:
Thanks for the invitation. I have several comments on this manuscript.
1. In the DC, one third required small bowel resection, and the other two thirds without bowel
resection. Would the authors provide more information about the etiology of SBO.
2. The definition of “Reduced wall enhancement”was not universally accepted. would the
authors provide some references?
3. In my opinion, the non-distended bowels need to be resected, instead of the dilated bowels.
The “transition zone” that indicates the passage between compressed and decompressed small
bowel may be our most concerns. Would the authors comment on this?
4. The CT findings of Ascites maybe quite different. Bloody or non-bloody ascites? This may
be contribute to the surgical outcome and pre-operative decisions.
Review for 10.1186/s12876-023-02761-z (2023)

Title: Ischemia prediction score (IsPS) in patients with strangulated small bowel obstruction:
a retrospective cohort study
Version: 2 Date: 13 Feb 2023
Reviewer's report:
I congratulate the authors with tis work.
Adhesive small bowel obstruction is an important cause for morbidity and mortality in
emergency abdominal surgery; Recognizing the need to perform emerency surger vs.
conservative trial is one of the most important clinical challenges in the management of small
bowel obstruction.
A few question:
A decrease in CT value of 30% was considered positive for potential ischemia. How was tis cut-
off derived? Could the cutt-off value be further optimized?
Although the results are promising, there is still some substantial risk of missing a case of
ischemia. Have the authors also considered to include other CT signs in their score?
Please furter elaborate on the future researc and development.
Finally, there are some grammar issues throughout the manuscript, it is adviced to involve a
native speaker.
Review for 10.1186/s12876-023-02688-5 (2023)

Title: Novel Chemokine-Related LncRNA Signature Correlates with the Prognosis, Immune
Landscape, and Therapeutic Sensitivity of Esophageal Squamous Cell Cancer
Version: 1 Date: 28 Jan 2023
Reviewer's report:
Advanced ESCC is a heterogeneous disease with a dismal prognosis. Chemokines have a
substantial impact on tumor formation and immune infiltration. However, only a few researchers
have focused on the utilization of chemokine-related lncRNAs in the prognostic prediction of
ESCC. The authors built a robust prognostic model based on chemokine-related lncRNAs and
explored the TME in high- and low-risk subgroups. Overall, this theory is engaging, robust, and
replicable. However, the following problems still need to be solved.
1. The language of the manuscript needs to be fully embellished.
2. The P values were incorrectly written. Please use "capital" and "italic" consistently.
3. Cites in the article need to be improved to make the contents more complete.
3.1 In the Method part, the cites need to be improved: CIBERSORT R scripts were used to
quantify the relative proportion of infiltrating immune cells (DOI: 10.3389/fgene.2022.984273);
“Lasso regression analysis” was used to filter genes associated with prognosis (DOI: 10.3389/
fgene.2022.983672); “ssGSEA” method was adopted to differentiate patients sorted by risk
score (DOI: 10.3389/fimmu.2022.1018685).
3.2 In the discussion part, the contents, as well as related cites, also need to be improved: the
immune system plays important role in the development of cancers, as well as immunotherapy
(DOI: 10.3389/fimmu.2022.1022808). The authors analyzed the TME, therefore these contents
are essential to be discussed. Notably, tumor cells can produce many exosomes that may contain
chemokines and lncRNAs, which can transmit signals between tumor cells and promote their
growth and metastasis (DOI: 10.3389/fimmu.2022.1089410). Hence, the authors need to discuss
possible application prospects based on the in vivo distribution of chemokines.
Review for 10.1186/s12876-023-02757-9 (2023)

Title: A New Prediction Model of Hepatocellular Carcinoma Based on N7-methylguanosine
Modification
Version: 4 Date: 12 Feb 2023
Reviewer's report:
It is very honored to be invited the reviewing the manuscript entitled “A New Prediction Model
of Hepatocellular Carcinoma Based on N7-methylguanosine Modification”. The manuscript in
novel. Besides, they used many interesting methods. I think the manuscript is within the scope.
Some of the problems should be solved before acceptance.
Firstly, Although the methods are very novel, the author should make a more proper discussion
about the analysis. Besides, the shortness of the informatics analysis also should be involved.
Second, In whole manuscript, there are many errors, which should be checked. The English
writing level should be improved.
Third, in discussion part, I think the authors should focused more on the results.
Fourth, Although all the conclusions are sound, it should be noted that these assays, as such, can
only be viewed as a prioritization method for further analysis. Thus, in the discussion section, it
is necessary to explain all pros and cons of the used assays. For example, limitations of the data
mining approach are thoroughly explained in the following papers:
1. Ye S, Liu Q, Huang K, Jiang X, Zhang X. The comprehensive analysis based study
of perfluorinated compounds-Environmental explanation of bladder cancer progression.
Ecotoxicol Environ Saf. 2022 Jan 1;229:113059. doi: 10.1016/j.ecoenv.2021.113059. Epub
2021 Dec 8. PMID: 34894427.
2. Zhang X, Zhang T, Ren X, Chen X, Wang S, Qin C. Pyrethroids Toxicity to Male
Reproductive System and Offspring as a Function of Oxidative Stress Induction: Rodent Studies.
Front Endocrinol (Lausanne). 2021 May 27;12:656106. doi: 10.3389/fendo.2021.656106.
PMID: 34122335; PMCID: PMC8190395.
3. Zhang T, Wu J, Zhang X, Zhou X, Wang S, Wang Z. Pharmacophore based in silico study with
laboratory verification-environmental explanation of prostate cancer recurrence. Environ Sci
Pollut Res Int. 2021 Nov;28(43):61581-61591. doi: 10.1007/s11356-021-14970-8. Epub 2021
Jun 28. PMID: 34184217.
4. Ren X, Zhang T, Chen X, Wei X, Tian Y, Li G, Zhang X, Zhang W, You Z, Wang S, Qin
C. Early-life exposure to bisphenol A and reproductive-related outcomes in rodent models: a
systematic review and meta-analysis. Aging (Albany NY). 2020 Sep 30;12(18):18099-18126.
doi: 10.18632/aging.103620. Epub 2020 Sep 30. PMID: 32996894; PMCID: PMC7585097.
Review for 10.1186/s12876-023-02757-9 (2023)

Title: A New Prediction Model of Hepatocellular Carcinoma Based on N7-methylguanosine
Modification
Version: 4 Date: 17 Feb 2023
Reviewer's report:
The paper named “A New Prediction Model of Hepatocellular Carcinoma Based on N7-
methylguanosine Modification” conducted by Yang et al. has been evaluated. I think this study
has certain innovation and clinical significance. In this study, the author identified a novel
lncRNAs signature associated with m7G predicts the prognosis of HCC. However, some obvious
limitations impair the overall quality. Before it is suitable for publication, I suggest the author
make substantive modifications.
1. However, I noticed that some of the figures have a low resolution which makes them hard
to read. I would suggest that the authors increase the resolution of these figures, which would
make them easier to read and understand. This would also make it easier for readers to fully
understand the results and make use of it. I believe that increasing the resolution of these figures
would greatly improve the manuscript.
2. Some previous studies have used similar methods. Although it will lose some innovation, I
think it will benefit the reader if the authors could include the following references, which would
provide readers with a more complete understanding of the whole study (PMID: 33850225,
PMID: 34099740, PMID: 33148208 ...). Meanwhile, the introduction part should be improved
by refering to the following studies (PMID: 32474508, PMID: 32474508).
3. Detailed description of all sections is required.
4. State the * and statistic value in the method section or otherwise mention in every figure
legend. e.g., *p>0.05.
5. Check the reference style and abbreviation of journals.
6. Some typos are there; rectify those (Minor).
7. The relationship between immune cell infiltration and specific pathways should be well
discussed in the relevant section.
Review for 10.1186/s12876-023-02759-7 (2023)

Title: Predicting Cholangiocarcinoma in Primary Sclerosing Cholangitis: Using Artificial
Intelligence, Clinical and Laboratory Data
Version: 2 Date: 05 Dec 2022
Reviewer's report:
From line 112 to line 117, the defined diagnosis of cholangiocarcinoma includes cases without
histopathology or cytopathology. The authors included patients who would not be treated as
cholangiocarcinoma in clinical practice.
In the manuscript, the CA19-9 was used to diagnose and predict cholangiocarcinoma; the
reviewer thinks the process is not logically appropriate.
The study aimed at the prediction of cholangiocarcinoma among PSC patients. In line 126, the
author included medical records of healthy controls; the reviewer cannot find them in the flow
chart of the supplementation material. Have the health controls been analyzed?
Table_4 demonstrates the predictive model of the baseline cohort; the reviewer cannot find
the author described their process of validation. The readers would like to know the process
of training and validation comprehensively. Did the author divide their data from training and
validating? The author mentioned Monte Carlo methods in table_4 and the reviewer cannot find
the description of how the author performed the simulation.
The author included 300 cases of BA cohort in their cohort. In table_5, the reviewer finds
the colinearity of the data (CDCA=LDCA+HDCA+UDCA). If the author put all the CDCA,
LDCA, HDCA, and UDCA in the data matrix, the statistical inference would be misleading in
a regression model.
The author utilized r,  python, and their related packages for treating missing values, modeling,
and validating. The packages and their versions should be stated.  It would be better when the
author demonstrated their processes step by step in a Jupyter Notebook.
Review for 10.1186/s12876-023-02759-7 (2023)

Title: Predicting Cholangiocarcinoma in Primary Sclerosing Cholangitis: Using Artificial
Intelligence, Clinical and Laboratory Data
Version: 4 Date: 08 Feb 2023
Reviewer:  Kuan-chih Chen
Reviewer's report:
In this study, the authors demonstrated better performance for predicting cholangiocarcinoma
(CCA) in primary sclerosing cholangitis patients through artificial intelligence combined with
clinical and laboratory data. Although the manuscript was well-constructed and informative.
There are still several questions.
1. In your data set, can you describe more about different types of CCA (such as the location of
CCA) if available? Do you think that will affect your result?
2. Do you think that image data may be helpful for the prediction of CCA in PSC patients? Can
you have some discussion in the discussion part to explore its possible role?
Review for 10.1186/s12876-023-02759-7 (2023)

Title: Predicting Cholangiocarcinoma in Primary Sclerosing Cholangitis: Using Artificial
Intelligence, Clinical and Laboratory Data
Version: 6 Date: 23 Mar 2023
Reviewer's report:
Line_43, AI-based model better than statistical models? The reviewer regards statistical methods
(CoxPH) that the authors used as a broadly defined AI.
Line_382, the adjective 'large' is not necessary.
Line_101~103, the sentence is complicated and not friendly to readers.
In Line_191 and line_219, the sentences 'patients without IBD diagnosis were set IBD duration
as 0 years.' are repetitive.  The author should clarify when a PSC patient without IBD entered this
cohort, the IBD duration was zero. Was the IBD duration increasing when the study proceeded?
For example, the  IBD duration is 3 in the third year when a patient without IBD entered the
study.
Review for 10.1186/s12876-023-02759-7 (2023)

Title: Predicting Cholangiocarcinoma in Primary Sclerosing Cholangitis: Using Artificial
Intelligence, Clinical and Laboratory Data
Version: 6 Date: 03 Apr 2023
Reviewer:  Kuan-chih Chen
Reviewer's report:
No further comments since the authors have already responded to the questions point-by-point
very well.