JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-03049-y (2023)

Title: Epidemiology, risk factors, diagnosis, and treatment of intra-abdominal traumatic
neuromas - a narrative review
Version: 2 Date: 21 Sep 2023
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: The authors have sufficiently responded to the queries raised. I am
satisfied with the revisions. The manuscript maybe accepted in its current form.
ADDITIONAL REQUESTS/SUGGESTIONS:
Accept in current form
Review for 10.1186/s12876-023-03042-5 (2023)

Title: The use of fully covered self-expandable metal stents in the endoscopic treatment of portal
cavernoma cholangiopathy An Original Article
Version: 1 Date: 13 Aug 2023
Reviewer:  Toshio Tsuyuguchi
Reviewer's report:
#1. What is the reason for the very high incidence of cholecystitis after stenting compared to
malignant lower biliary stricture? Could it be due to compression of the gallbladder cystic duct
or bifurcation of the cystic duct by the portal vein?
#2. Why is the male-to-female ratio significantly skewed toward males? Are there differences
in the causes of PCC (portal cavernoma cholangiopathy)  in the region concerned?
#3. According to the flow chart in figure 1, 10 cases treated with plastic stenting were excluded.
However, 3 cases with a history of plastic stent implantation were also included in the 12 cases
analyzed.
#4. PCC  requires imaging of bile duct compression by the portal vein. Are contrast-enhanced
CT and ultrasound Doppler studies performed in all cases?
#5. It is easier to understand if authors summarize in a table the reports of previous studies in
which CMS was performed for PCC. It would be good to add to that table the studies in which
plastic stents were placed or FCSEMS was placed for hemorrhage.
#6. Why are there fewer relapses and better prognosis after 12 weeks of FCSEMS implantation?
It is unclear why bile duct stenosis does not recur in the long term, since the portal vein should
continue to drain.
Review for 10.1186/s12876-023-03042-5 (2023)

Title: The use of fully covered self-expandable metal stents in the endoscopic treatment of portal
cavernoma cholangiopathy An Original Article
Version: 1 Date: 21 Aug 2023
Reviewer's report:
Although this is an interesting paper reporting the efficacy of Fully covered self-expandable
metal stents for portal cavernoma cholangiopathy-related biliary strictures, it has some critical
issues.
1. The authors describe the design of this study as a single-center prospective observational
study, but is it a single-center retrospective observational study?
2. The authors state that they evaluated the outcomes of FCSEMS as initial treatment for PCC-
related biliary strictures, which is highly contradictory since 5 of the 12 patients were previously
and not initially treated.
3. The high incidence of cholecystitis due to FCSEMS placement in 7 of 12 patients (58.3%) is
unacceptable, even though five patients improved with conservative treatment.
Review for 10.1186/s12876-023-03055-0 (2023)

Title: Novel beagle model of gastric local fibrotic target lesions for the evaluation and training
of endoscopic techniques
Version: 1 Date: 14 Jul 2023
Reviewer's report:
The paper entitled "Novel beagle model of gastric local fibrotic target lesions for the evaluation
and training of endoscopic techniques" shows a new technique for endoscopy training. Indeed,
the paper shows relevance and is very well delimited. However, the English needs to be improved
in the whole text. Moreover, better clarification is needed in ethics, since it has no committee
acceptance number and talks about consent form.
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 3 Date: 26 Jul 2023
Reviewer's report:
This is a very interesting article. Through a retrospective study of 285 cases, it was found
that there is a correlation between the diameter of esophageal varices and bleeding after EVL.
Through CT examination, the diameter of varicose veins can be easily obtained. This result is
consistent with the principle of Laplace's law in liquid mechanics, so the results of the paper
have good credibility.
I would like to raise a question about this article, which layer is the standard for CT examination
of blood vessel diameter and is it the thickest diameter? Additionally, if CT shows a peripheral
blood vessel in the esophagus, how to detect its diameter.
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 3 Date: 11 Aug 2023
Reviewer's report:
Q1: Running title is not informative as your research point is prediction of CT in early variceal
rebleeding, not risk factors
2: How CT used as screening tool for HCC?
Q3: where is your reference for this information?  "Patients with cirrhosis sometimes
undergo CT scans to screen for hepatocellular carcinoma. " page 9
Q4: what about the safty due to using contrast?
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 3 Date: 30 Aug 2023
Reviewer:  Yan He
Reviewer's report:
The language of this article should be improved. Some of these mistakes are listed as follows.
In page 3, the authors said “Gastroesophageal varices are one of the most common complications
of…”, where the word “are” should be revised as “is”.
In page 7, the authors said “Eighty-three (29.1) patients had…”, where the number “29.1” should
be revised as “29.1%”.
The use of abbreviations and full names should be standardized. Some of these mistakes are
listed as follows.
In page 3, the authors said “…high AST to platelet ratio index (APRI) score…”, where the full
name of “AST” should be given.
In page 7, the authors said “…had a concomitant GV…”, where the full name of “GV” should
be given. And in page 7, the authors said “and PT time…”, where the full name of “PT” should
be given.
In page 4, the authors said “The present study aimed to evaluate CT performance in predicting
the risk of early rebleeding following EVL, in patients with cirrhosis”, however, not all patients
included had a history of variceal bleeding, so the description of “rebleeding” appears to be in
accurate. In addition, the authors said “…and 122 (42.8%) patients had hepatocellular carcinoma
(HCC)…”, the population heterogeneity in this study seems to be a bit large.
In page 4, the authors said “Proton pump inhibitors (PPIs) were not administered after EVL”, a
relevant article should be cited (PMID: 36741070).
In page 6, the authors said “All variables selected in univariate analysis (p < 0.20) were included
in the multivariate model”, why adopt a standard with p < 0.20?
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 6 Date: 17 Sep 2023
Reviewer's report:
On page 5# in the last line. "each patients were recorded", and on page 6 in the sentence "the
EV grades was F1, F2, and F3, respectively" the grammar seems to be incorrect.
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 6 Date: 13 Oct 2023
Reviewer:  Yan He
Reviewer's report:
The language of this article should be improved. Some of these mistakes are listed as follows.
In page 8, the authors said “Multivariate analysis of risk factors for early rebleeding after EVL”,
where the word “rebleeding” should be revised as “bleeding”.
In page 7, the authors said “...and total bilirubin (P = 0.050)...”, where the letter “P” should be
revised as “p”.
In page 9, the authors said “Patients with cirrhosis sometimes undergo CT scans to screen
for hepatocellular carcinoma...”, where the abbreviation “HCC” should be used to replace the
“hepatocellular carcinoma”.
In page 4, the authors said “Consecutive patients who had undergone EVL in Pusan National
University Yangsan Hospital from January 2009 to December 2018 were retrospectively
analyzed”, the time span of inclusion of the population is somewhat large, and the risk of
bleeding after EVL is also changing. So why don’t the authors use recent data?
In page 8, the authors discussed the risk factors for early bleeding after EVL, however, the
language is not generalizing.
Review for 10.1186/s12876-023-03038-1 (2023)

Title: Predicting the risk of early bleeding following endoscopic variceal ligation in cirrhotic
patients with computed tomography
Version: 10 Date: 07 Nov 2023
Reviewer:  Yan He
Reviewer's report:
In page 2, the authors said “EVL was performed for prophylaxis or acute variceal bleeding”,
does the “prophylaxis” here mean primary prophylaxis or secondary prophylaxis?
In page 3, the authors said “...undergo multiphase computed tomography (CT) scans to screen
for hepatocellular carcinoma”, where the abbreviation “HCC” should be given.
Review for 10.1186/s12876-023-03012-x (2023)

Title: Association between high expression of intratumoral fibroblast activation protein and
survival in patients with intrahepatic cholangiocarcinoma
Version: 1 Date: 09 Jul 2023
Reviewer's report:
Authors focused on the impact of CAFs on the prognosis of iCCA. The study demonstrates that
High intratumoral FAP expression was associated with worse survival. The study lacks novelty
and requires substantial revisions due to multiple areas that need improvement. Additionally,
the clinical implications remain unclear, indicating the need for a major revision.
Major comments:
1) The description of novelty and differentiation from previous reports is insufficient. It is
crucial to clearly articulate how this study differs from prior literature and highlight its novel
contributions.
2) The rationale behind the division of FAP expression into a smaller 25% tile and the use
of median for #-SMA remains unexplained. The current approach appears arbitrary and lacks
justification. Please provide a detailed explanation for the selection of these thresholds for
classification.
3) In cases with high FAP expression, larger tumor sizes and advanced stages were observed,
along with significantly shorter OS and RFS. The speculation regarding FAP's role in creating
a tumor-favorable environment and promoting tumor progression seems plausible. However,
it is crucial to explore the potential reasons why such functionality was not observed in the
peripheral regions where FAP was expressed. Please discuss the possible differences between
FAP-positive cells in the central tumor region and those in the peripheral region.
4) Based on the relationship between immunostaining and prognosis, does the study suggest
functional differences between fibroblasts expressing #-SMA and those expressing FAP? Please
elaborate on the potential roles of fibroblasts that express #-SMA but not FAP, as well as
fibroblasts that express FAP but not #-SMA.
5) The speculation regarding FAP-expressing fibroblasts maintaining cancer stem cells (CSCs)
is intriguing. In the context of anticancer treatment for iCCA, the presence of CSCs in the
central tumor region might be associated with chemotherapy resistance. However, in resected
cases, even if CSCs are present in the central tumor region, their relevance to recurrence seems
less likely because the central region would be completely resected. Instead, the presence of
CSCs in the tumor periphery might be associated with local recurrence. It is important to
provide additional explanations regarding why the abundance of CSCs in the center of resected
specimens is related to recurrence and overall survival.
Minor comments
1) The description regarding the exclusion of patients is confusing, particularly regarding the
reduction in the number of participants from 37 to exclude certain cases. Please revise the
wording to provide clarity.
Review for 10.1186/s12876-023-03012-x (2023)

Title: Association between high expression of intratumoral fibroblast activation protein and
survival in patients with intrahepatic cholangiocarcinoma
Version: 1 Date: 08 Sep 2023
Reviewer's report:
In this study, the authors investigated the expression pattern and prognostic significance of FAP
in the patients with intrahepatic cholangiocarcinoma. The manuscript is well written.
Review for 10.1186/s12876-023-03012-x (2023)

Title: Association between high expression of intratumoral fibroblast activation protein and
survival in patients with intrahepatic cholangiocarcinoma
Version: 1 Date: 05 Oct 2023
Reviewer:  Rui Liao
Reviewer's report:
This is an interesting study. However, the small sample size limited the credibility of the
conclusions, and further sample size expansion and validation is needed.
Review for 10.1186/s12876-023-03012-x (2023)

Title: Association between high expression of intratumoral fibroblast activation protein and
survival in patients with intrahepatic cholangiocarcinoma
Version: 2 Date: 17 Oct 2023
Reviewer's report:
Authors have effectively addressed the major concerns raised during the review process. The
paper has now reached an acceptable level for publication.
Review for 10.1186/s12876-023-03012-x (2023)

Title: Association between high expression of intratumoral fibroblast activation protein and
survival in patients with intrahepatic cholangiocarcinoma
Version: 2 Date: 23 Oct 2023
Reviewer's report:
In this revision, the manuscript has improved a lot. I recommend the accepatance of this
manuscript.
Review for 10.1186/s12876-023-03017-6 (2023)

Title: Prognostic model for oversurvival and tumor-specific survival prediction in patients with
advanced extrahepatic cholangiocarcinoma: a population-based analysis
Version: 1 Date: 10 Sep 2023
Reviewer's report:
In this study, authors developed a prognostic model using SEER database in extrahepatic
cholangiocarcinoma. The subject of the study was somewhat interesting and the results were
clearly described. However, there are some concerns that arise from our analysis, and I hope to
make more constructive suggestions about the clinical use of this prognostic model.
1. Is the AJCC stage included in the seer data? Distal bile duct cancer and perihilar bile duct
cancer have different TNM stage criteria, how the AJCC TNM stages were identified? T1 and
T2 T1 and T2 stages are unlikely to be distinguishable on CT/MR imaging.
2. Why was the AJCC analysed as 7th edition and not 8th edition?
3. Authors described inclusion and exclusion criteria in materials and methods, and a total of
403 patients were analyzed in this study. Please present the patient flow chart as Figure 1 (how
many ECCA patients were identified and excluded for this study).
4. Please check some errors.
e.g. Cancer-special mortality in Table 1. Same values of AUC were presented in Figure 5A and
5B.
5. In multivariate analyses, did lymph node metastasis was included? Authors mentioned that N
stage was linked with OS and CSS, but it was not shown in the Figure 3.
6. Authors included the T, N, M stage, and AJCC stage (III or IV) in the prognostic model.
However, AJCC stage derived from the combination of T, N, and M stages, shouldn't they be
included together in the model?
7. Authors divided the patients into groups with high and low risk using the nomogram. What
was the value on which the classification is based?
8. The clinical significance of the derived model could have been presented more specifically.
Authors said that nomogram would offers more precise prognostic predictions, then how should
physicians use this model specifically? For example, in patients who have undergone surgery, if
the model is able to divide the prognosis into two groups, it can provide a basis for recommending
adjuvant treatment.
Review for 10.1186/s12876-023-03017-6 (2023)

Title: Prognostic model for oversurvival and tumor-specific survival prediction in patients with
advanced extrahepatic cholangiocarcinoma: a population-based analysis
Version: 1 Date: 11 Sep 2023
Reviewer's report:
This study had as aim to study risk factor for prognosis  for patients with extrahepatic
cholangiocarcinoma (ECCA).
The authors explain that TNM system has limitations, such as its failure to consider age, adjuvant
therapy, and gender, prompted the development of new prognostic tools. In this research,
the authors identified survival risk factors for advanced ECCA patients and created novel
nomograms for predicting both overall survival (OS) and cancer-specific survival (CSS).
This study introduced novel nomograms for predicting both overall survival (OS) and cancer-
specific survival (CSS) in advanced ECCA patients.
While it is a well-conducted study with a large number of patients, I hvae some comments to
adress to the authors.
It remains unclear what type of surgery these patients underwent. Often, the extent of
lymphadenectomy associated with the primary surgery is crucial. The authors should thoroughly
discuss this aspect in the discussions.
Furthermore, I suggest mentioning other nomograms found in the literature, such as this one
(https://pubmed.ncbi.nlm.nih.gov/32474628/)." I suggest to cite this study please.
As future prospects, they should highlight the potential impact of artificial intelligence in
assisting us in selecting patients for the appropriate treatment path.
Review for 10.1186/s12876-023-03017-6 (2023)

Title: Prognostic model for oversurvival and tumor-specific survival prediction in patients with
advanced extrahepatic cholangiocarcinoma: a population-based analysis
Version: 5 Date: 05 Oct 2023
Reviewer's report:
I read this work with great interest prognosis of patients with extrahepatic cholangiocarcinoma.
Recently  it is common practice to forecast the prognosis of a wide range of diseases utilizing
clinically based nomograms, incorporating all risk variables into a thorough analysis.
The introduction is well done and explains well what the problem of the study is.
In the methods, although the OS is well specified and defined. CSS, however, is not. I think
that CSS is a very important aspect to treat in oncology, but the authors must clearly specify the
difference with OS, perhaps arguing a little more in the discussions.
In other words, how is it considered if the patient is lost to follow up or dies from other causes.
Then, how do the authors consider these other causes be linked to factors other than those of
the tumor disease?
Basically the OS curve must be lower than the CSS curve in general, but this is not the case
from the figures.
The authors need to discuss better in the discussions and provide an adequate explanation in the
response to my comment.
In conclusion it is a beautiful work and has a well-structured statistical analysis
Review for 10.1186/s12876-023-03017-6 (2023)

Title: Prognostic model for oversurvival and tumor-specific survival prediction in patients with
advanced extrahepatic cholangiocarcinoma: a population-based analysis
Version: 5 Date: 09 Oct 2023
Reviewer's report:
The authors' feedback was mostly valid, but we still have questions about some of the items,
and would like clarification.
Comment to response 6.
Authors mentioned that T/N/M stage and AJCC stage were not put together in the model. But,
in the figure 4, nomograms contain T, N, M and AJCC stage (III/IV) together. Please explain if
it is correct to include the confounding factors together in the model.
Comment to response 7.
I would recommend that the authors present the detailed cutoff level of score that led to the
division between high-risk and low-risk in this study.
Review for 10.1186/s12876-023-03017-6 (2023)

Title: Prognostic model for oversurvival and tumor-specific survival prediction in patients with
advanced extrahepatic cholangiocarcinoma: a population-based analysis
Version: 6 Date: 21 Oct 2023
Reviewer's report:
The authors' feedback was mostly valid.
Some typos are observed.
Example,
(1) "modle"  in the legend of Figure 6. ==> model
(2) "chemtherpy treatment"  in main text.  ==> chemotherapy
(3) "oversurvival " in the title and keyword ==> overall survival
Review for 10.1186/s12876-023-03052-3 (2023)

Title: Endoscopic and histopathological hints on infections in patients of common variable
immunodeficiency disorder with gastrointestinal symptoms
Version: 3 Date: 01 Sep 2023
Reviewer:  Timi Martelius
Reviewer's report:
The article deals  with an important subject of GI disease in CVID. There is scarcity of data in
the area and the pathogenesis and therapy is not well understood.   So this patient series is a
welcome addition to the existing data.
There are several typographical errors and some odd sentences.  I recommend checking the
English of the text and the spelling of words.
The data is well presented, but there are some concerns in the discussion and conclusions and
the limitations of the study.
Page 3 Row 15: Where does this 60% come from? Sounds overestimated, especially for such
severe findings as malabsorbtion.  E.g. Chapel gives 9% for enteropathy
Page 4 Row 14 I would leave "Whereas" out.
Page 4 Row 19  Why are these references after this quite obvious sentence?  Aren't they rather
referring to the previous sentence?
Page 6 row 4.  "A total of 87 CVID patients were hospitalized"  How many were followed in
the outpatient clinic?
Page 8 row 15.  These patients were quite severely affected with 89% with malabsorbtion.
This should be discussed in the discussion and compared with previous studies about CVID
enteropathy.  And also in the limitations section concerning the patient selection and biases.
Page 8 Row 21. I suppose this IgG level was at diagnosis, without immunoglobulin therapy?
This should be stated clearly.
Page 9 Row 8.  Were these GI infections present at the time of endoscopy or had they been
treated previously?
Page 10 Row 17.  This is a known feature of CVID, and that could be mentioned here.
Page 11 Row 13.  The almost total absence of colitis is surprising. Again compare with other
studies in the discussion.
Page 14 Row 5.  This sentence lacks a verb. Reformulate.
Page 14 Row 12-13.  The sentence starting with "However, it is hard.." is difficult to follow.
What do you mean?  Reformulate or remove.
Page 14 Row 19-20.  That NLH is caused by infection is still a theory although a
good one.  This should be emphasized in discussion.  Also the authors should mention
the lymphoproliferation present elsewhere in the body in CVID patients, such as GLILD,
splenomegaly and lymphadenopathy, where B-cell maturation defects are thought to play some
role.
Page 15 Row 4.   Chronic norovirus could be mentioned here.
Page 15 Row 15.  The percentage of your center's CVID patients that have had endoscopy is quite
low and consequently the clinical findings are quite severe (villus atrophy and malabsorbtion was
common).  This should be commented in  limitations and discussed in the discussion, comparing
findings with other endoscopy studies in CVID patients.
Page 16 Row 13.  This is controversial, since nodular lymphatic hyperplasia is very common
finding in CVID
Page 21 Table 1.  Are the infections in patients 4 and 5 really GI infections?
Review for 10.1186/s12876-023-03052-3 (2023)

Title: Endoscopic and histopathological hints on infections in patients of common variable
immunodeficiency disorder with gastrointestinal symptoms
Version: 3 Date: 16 Sep 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?
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 - 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: I read with interest the manuscript by Chen et al. The authors
performed a descriptive study on infections in patients with CVID with GI symptoms. I have
the following comments.
1. The introduction seems long and can be cut down. Be more precise to deliver the message.
2. Was there a particular protocol used for obtaining endoscopic samples from respective GI
site? Please clarify in methods.
3. Based on this study, can the authors propose an algorithm regarding what assessments and
workup needs to be undertaken if patient has GI symptoms and CVID? This will be helpful for
readers.
Review for 10.1186/s12876-023-03052-3 (2023)

Title: Endoscopic and histopathological hints on infections in patients of common variable
immunodeficiency disorder with gastrointestinal symptoms
Version: 4 Date: 16 Oct 2023
Reviewer:  Timi Martelius
Reviewer's report:
Thank you for your revision.  I am satisfied with your responses and the alterations.
You could still have a look at the English of the text with a native speaker and  contemplate if
you could  possibly simplify/clarify some sentences.
Review for 10.1186/s12876-023-03052-3 (2023)

Title: Endoscopic and histopathological hints on infections in patients of common variable
immunodeficiency disorder with gastrointestinal symptoms
Version: 4 Date: 16 Oct 2023
Reviewer's report:
The manuscript has improved greatly. I have no remaining major comments. However, as minor,
I suggest
1.  you in STable 1 use again italics as appropriate fir Scientific names of pathogens,
2. in STable 1 do not capitalize  Vitiligo, Psoriasis
3. in p.4/line 6 do not italicize species (x2)
4. on line 16 inflammation--> inflammatory
5. on line 17 add "the" before ileum
6. p.11, l. 5 use "appearance of colon"
7. p.12, l.9:enteropathy "lacks universal definition"
8. l.17: use "other conditions displaying villous atrophy"
9. p. 13, l. 9: rephrase pseudo-polyphonic (term used only/mostly  in music) into a more proper
adjective
10. use "...selective IgA deficiency, giardiasis..."
11. p. 14, line 3: Omit "The"
12. p.15, line 4 onwards: rephrase into ".. will be no definite CVID diagnoses, until the genetic
or other etiopathogenetic causes will defined  for all patients"
13. line 6: rephrase into: Gene analyses (WES/WGS/panel...)
Review for 10.1186/s12876-023-03052-3 (2023)

Title: Endoscopic and histopathological hints on infections in patients of common variable
immunodeficiency disorder with gastrointestinal symptoms
Version: 4 Date: 26 Oct 2023
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: Page 13, line 14 "....selective Aga deficiency syndrome" .. Please
correct this to IgA deficiency
Review for 10.1186/s12876-023-03036-3 (2023)

Title: Gastrointestinal Functioning and Menstrual Cycle Phase in Emerging Young Adult
Women: A Cross-Sectional Study
Version: 3 Date: 16 Sep 2023
Reviewer's report:
I appreciate the authors' efforts to improve this manuscript.  While most previous comments
have been addressed, some comments have yet to be addressed adequately. Here are my further
suggestions.
1. Please specify how you adapted the pain pictogram. How is it different from any existing
tool?  Did you pilot test this tool for its validity, reliability, and readability?  If not, you may
add it as a limitation.
2. In introduction,  citation(s) need to be added for average length of the follicular phase. Can
you also add the range of the length for follicular phase? Citation #9 does not address  vaginal
inflammation. Please correct.
3. It is still unclear to me how you classify people based on their menstrual cycle and what you
did with participants with shorter cycle (e.g., 22-25 days).   It may be helpful to use a figure to
show how you classify people into different menstrual cycle stages.
4. While the authors stated in their responses that they did not study women with visceral
pain related to the uterus. Most participants likely had dysmenorrhea given high prevalence of
dysmenorrhea in this age group (prevalence ~50%-90%).  Dysmenorrhea is a type of visceral
pain. For some people, such pain can be poorly localized.  Please discuss why the menses group
only reported more pain in hypogastric region, but not other regions.  Also, many people with
dysmenorrhea experience GI symptoms.  See citations a previous reviewer mentioned. Please
discuss why you did not find more GI symptoms among those in menses group compared to
other groups.
4. The authors stated that they originally included items concerning DGBI treatment, but the sole
purpose was to establish the sensitivity of the PROMIS-GI scales.  I am not clear on whether
the authors excluded people with DGBI who were not receiving medical treatments.
5. The within- and between- person differences have not been addressed in discussion.  It's
possible that the differences (or lack of differences) you found between menstrual cycle stage
were actually due to differences/lack of differences between individuals.
6. Given PROMIS-GI scales have a 7-day recall, what you measured at a given stage may not
capture symptoms at that stage.  Please discuss this as a limitation. This may contribute to a lack
of differences in PROMIS-GI scores between groups.
Review for 10.1186/s12876-023-03036-3 (2023)

Title: Gastrointestinal Functioning and Menstrual Cycle Phase in Emerging Young Adult
Women: A Cross-Sectional Study
Version: 4 Date: 30 Oct 2023
Reviewer's report:
Thank you for your time and efforts addressing reviewers' comments.  The manuscript has been
improved significantly. However, one previous comment has not been fully addressed in the
Discussion section.
While the authors stated in their responses that they did not study women with visceral pain
related to the uterus. Most participants likely had dysmenorrhea given high prevalence of
dysmenorrhea in this age group (prevalence ~50%-90%). Dysmenorrhea is a type of visceral
pain. For some people, such pain can be poorly localized. Please discuss why the menses group
only reported more pain in hypogastric region, but not other regions. Also, many people with
dysmenorrhea experience GI symptoms. See citations a previous reviewer mentioned. Please
discuss why you did not find more GI symptoms among those in menses group compared to
other groups.
Review for 10.1186/s12876-023-03041-6 (2023)

Title: Resection of the Primary Tumor Improves the Prognosis of Gastrointestinal
Neuroendocrine Neoplasms with liver metastases: Mutual Validation based on SEER Database
and Institutional Data
Version: 1 Date: 22 Sep 2023
Reviewer's report:
The paper analyzes an interesting topic, however some issues need to be addressed.
- The introduction as well as the discussion should be improved by adding more data that
highlight the need and the benefit of primary tumor resection also in the metatastic site.  This
is particularly true for GI NETs as  limiting the disease to the liver allows several potentially
curative treatment options, including liver resection or liver transplant. Of note, the resection of
the primary tumor reduces the risk of local complication, particularly in the case of small-bowel
NENs, such as occlusion, perforation and/or bleeding. Please refer to "Citterio, D.; Pusceddu,
S.; Facciorusso, A.; Coppa, J.; Milione, M.; Buzzoni, R.; Bongini, M.; Debraud, F.; Mazzaferro,
V. Primary
tumour resection may improve survival in functional well-differentiated neuroendocrine
tumours metastatic to the liver. Eur. J. Surg. Oncol. 2017, 43, 380–387".  On the other hand,
it is important to highlight that the benefit of primary tumor resection in metastastic pancreatic
nets is less clear.
Furthermore, in uknown primary origin NEN, the search for the primary tumor is warranted
as the resection of the primary tumor improves survival: please refer to "Rossi RE et al.
Multidisciplinary Approach to the Diagnosis of Occult Primary
Neuroendocrine Neoplasm: A Clinical Challenge. JCM 2023"
- Results: "Subgroup analysis demonstrated that PTR was associated with better prognosis
in patients aged 55 or older, those with colorectal primaries, T1 stage, and those without
extrahepatic metastasis". Please comment these results? Why do the authors think that the better
prognosis was observed in colo-rectal primaries rather than in small bowel primaries, which are
generally the majority?
- English language need to be properly checked by a mother tongue
- There are several ypo and grammar mistakes to be edited. Some examples:
- line 39 gastrointestinal please use GI
- line 162, our please do not use the capital letter
- line 193 our please use the capital letter
Review for 10.1186/s12876-023-03041-6 (2023)

Title: Resection of the Primary Tumor Improves the Prognosis of Gastrointestinal
Neuroendocrine Neoplasms with liver metastases: Mutual Validation based on SEER Database
and Institutional Data
Version: 1 Date: 10 Oct 2023
Reviewer's report:
Yifang, et al. compared clinical outcomes between PTR and non-PTR groups using propensity
score-matching. They concluded that PTR plays a positive role in the treatment of GINET and
expands the potential applicability of PRT.
This manuscript is generally easy to follow, and the data shown could be potentially interesting.
However, the study suffers from major study design flaws. For acceptance, the authors should
improve the following points:
Major comments:
# It is common to set the standardized difference at #0.1 in PSM. However, the authors set the
standard at #0.3. I think the authors' setting is too optimistic, and the authors should not state
that balance is achieved in PSM. I believe that the authors should reanalyze with a standardized
difference of #0.1.
# The study periods of both cohorts should be matched. The authors retrieved patient data from
SEER between 2000 and 2019, while they retrieved patient data from their institution between
2011 and 2022. Evidence such as everolimus, lanreotide, PRRT, and surufatinib have led to
significant advances in the treatment of metastatic NETs since 2011, and they have improved
the outcomes of GINET patients. Kaplan-Meier curves of FAH cohort (Figure 2) showed better
prognosis compared with SEER cohort. These facts suggested that treatment outcomes after
resection of primary tumor were different between FAH and SEER cohort.
# The authors emphasized that this study focused on Asian population. However, the clinical
behavior of NET does not depend on ethnic difference, it depends on tumor origin, especially
for colorectal NET. Authors should mention this point
Minor comments:
# In the columns of Table 1, the description of N is out of place.
# I wonder why the authors defined the cutoff of age as 55 years, which is generally a young age
for metastatic NETs, and the SEER cohort shows it. Also, the authors state that the prognosis is
better in older patients, but 55 years is not old to begin with.
# Yoshida, Tsukasa => Yoshida (Page 23)
# Duplicate periods. (Page 3)
Review for 10.1186/s12876-023-03041-6 (2023)

Title: Resection of the Primary Tumor Improves the Prognosis of Gastrointestinal
Neuroendocrine Neoplasms with liver metastases: Mutual Validation based on SEER Database
and Institutional Data
Version: 5 Date: 30 Oct 2023
Reviewer's report:
The paper has been properly edited as suggested. I do think that no further revisions are necessary
Review for 10.1186/s12876-023-03041-6 (2023)

Title: Resection of the Primary Tumor Improves the Prognosis of Gastrointestinal
Neuroendocrine Neoplasms with liver metastases: Mutual Validation based on SEER Database
and Institutional Data
Version: 5 Date: 05 Nov 2023
Reviewer's report:
The authors have carefully revised it.
I think the content is worthy of acceptance.
Review for 10.1186/s12876-023-03044-3 (2023)

Title: Coexistence of early gastric cancer and benign submucosal lesions mimic invasive cancer:
a retrospective multicenter experience
Version: 2 Date: 17 Jul 2023
Reviewer's report:
Early gastric cancer coexisting with submucosal lesions with morphology similar to advanced
cancer is often treated with excessive surgical resection. This study reports that gastritis cystica
profunda is the most common submucosal lesions and provides a useful algorithm for accurately
diagnosing cases amenable to endoscopic treatment.
However, we believe that the following points should also be mentioned.
1) The authors need to further clarify the rationale for their proposed predictive factors.
It should be mentioned whether the proposed predictors are based on the results of the present
study or on previous reports.
2) How many of these 18 cases fit the predictors? For example, it would be better to say how
many of the 18 cases met 4 or more of the predictors.
3) How to accurately diagnose the of submucosal tumor in cases where EUS cannot diagnose
submucosal tumor (4 cases) is an important point. It should be mentioned how such cases were
diagnosed in this report. If cystic lesions could not be accurately diagnosed, what were they
diagnosed as?
4) The second part of the algorithm (Figure 7) should consider the classification of cases in
which submucosal tumors could or could not be evaluated correctly by EUS.
Also, does this algorithm mean that endoscopic resection should be considered when a
submucosal cystic lesion including gastritis cystica profunda is suspected? I would like to know
the opinion of the author.
5) It seems to me that there is little need to make a diagnosis based on endoscopic findings alone,
and I would like you to mention whether there have been any cases in which the presence of a
submucosal tumor has been accurately diagnosed by CT or MRI, which are imaging modalities
other than EUS. Specifically, are there any cases in which the diagnosis was made using T2-
weighted MRI images?
Review for 10.1186/s12876-023-03044-3 (2023)

Title: Coexistence of early gastric cancer and benign submucosal lesions mimic invasive cancer:
a retrospective multicenter experience
Version: 2 Date: 20 Oct 2023
Reviewer's report:
I read the article with interest. I think the concept here is familiar for most of endoscopists in
their clinical practice. As described here, EGC with SMT is not frequent as only 3.5% of all their
cases and 67% of them was gastritis cystica profunda. I raise some comments including major.
Major
1. Diagnostic accuracy was compared between EGC with SMT and “simple EGC”. There is no
concrete description of the latter group. I don’t understand what simple EGC is. How many cases
were compared? What kind of lesions? This is fairly critical issue if you compare diagnostic
accuracies.
2. EUS was performed in only 10 cases and only 6 revealed the submucosal entity. Given the
data in table 3, only 30.77% (4/13) has been made definitive diagnosis by EUS, why authors
could conclude “early cardiac-differentiated cancer with gastritis cystica profunda is the most
common condition, and EUS is a useful modality” in their abstract and in the conclusion.
3. There are no detail results on over- or under- diagnosis in the analysis with different levels
of endoscopists.
4. In discussion, findings in EUS are discussed. However, it is narrative and not oriented with
the present result. Five characteristics were discussed but they are not appeared in the result.
Please discuss what you found in the study.
5. I’m not convinced with figure 2, case15. It seems to be not sufficiently inflated in observation
with white light imaging. Please consider other imaging or other cases.
Minor
No information is provided what the number in side means in figure 6.
Review for 10.1186/s12876-023-03044-3 (2023)

Title: Coexistence of early gastric cancer and benign submucosal lesions mimic invasive cancer:
a retrospective multicenter experience
Version: 3 Date: 08 Nov 2023
Reviewer's report:
Thank you for your revision. Except for "EGC" and "EGC-SML" should be explained in the
abstract, there is nothing to point our.
Review for 10.1186/s12876-023-03008-7 (2023)

Title: Clinical importance of weight gain and associated factors in patients with moderate to
severe ulcerative colitis: Results from the MOSAIK cohort in Korea
Version: 1 Date: 17 Apr 2023
Reviewer's report:
It was interesting to see a prospective study on the course of treatment and weight gain in
ulcerative colitis.
I think your paper is worthy of publication, but I would like a brief consideration.
The reason why the weight gain was remarkable in the pancolitis type is probably due to the
more active ulcerative colitis.Therefore, isn't it possible that comparisons with healthy body
weights before onset, rather than comparisons with body weights immediately before treatment,
may also be involved in the risk of adverse events?
I would appreciate it if you could consider.
Review for 10.1186/s12876-023-03008-7 (2023)

Title: Clinical importance of weight gain and associated factors in patients with moderate to
severe ulcerative colitis: Results from the MOSAIK cohort in Korea
Version: 1 Date: 10 May 2023
Reviewer:  Sen Yagi
Reviewer's report:
I think the results are very well summarized. Regarding the statement that "patients with
moderate to severe UC showed a significant increase in weight after treatment", is there any
possibility that the weight gain was due to the side effects of steroids?
Review for 10.1186/s12876-023-03008-7 (2023)

Title: Clinical importance of weight gain and associated factors in patients with moderate to
severe ulcerative colitis: Results from the MOSAIK cohort in Korea
Version: 4 Date: 18 Oct 2023
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: The authors have done a good job addressing all reviewer comments
and making the required (modest) revisions necessary for publication. The manuscript clearly
establishes weight gain as a positive marker of clinical improvement in UC patients.
ADDITIONAL REQUESTS/SUGGESTIONS:
N/A"
Review for 10.1186/s12876-023-03047-0 (2023)

Title: Risks and Benefits of TIPS in HCC and Other Liver Malignancies: a literature review
Version: 0 Date: 24 Jul 2023
Reviewer's report:
This is a clinically useful review on the efficacy and safety of TIPS in (mostly) HCC patients.
It is well structured and at the end of separate paragraphe there is a main message, which helps
the reader.
Of course despite the title "...and other liver malignancies" it is mostly focused -as expected-
in HCC. There are very few data for cholangio carcinoma, is this correct? For extrahepatic
malignancies there is an informative paragraph at the end of the analysis.
As  regards HCC, in the past a centrally located HCC was considered a (relative)
contraindication. What is the authors' impression on this?
Studies that were analyzed had at the exclusion criteria tumor >70% of the liver. This is really
too advanced. However, could we accept patients with tumors with 50 or 60% can easily go to
TIPS procedure (for any indication)? Should be an upper limit? What about the multifocality?
Was there any impact for TIPS placement?
In respect to the liver dysfunction deterioration, in which group of HCC patients that underwent
TIPS procedure, could the authors identify a high risk cut off (in Child's or MELD) that might
do the approach questionable?
Moreover, it is stressed that TIPS placement offered survival benefit, providing the opportunity
for HCC patients to receive TKI treatments. Presumably, this might apply -in a greater extent-
probably in immunotherapy approaches.
It would be also useful to identify, albeit difficult due to the nature of the study, to see what
percentage of HCC patients underoing to TIPS, did manage to receive a radical treatment for
their tumors.
There is no clear report of stenosis or TIPS dysfunction in the paper. This is something expected
as the paper has included studied from years ago, when the expertise and the quality of the stents
were not the same as they are now.
Review for 10.1186/s12876-023-03047-0 (2023)

Title: Risks and Benefits of TIPS in HCC and Other Liver Malignancies: a literature review
Version: 1 Date: 01 Oct 2023
Reviewer's report:
The paper is significantly improved and the authors have sorted out most issues raised in my
review. I believe it is a useful paper in the field and worth reading.