JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-023-02655-0 (2023)

Title: Prognostic significance of serum CA125 in the overall management for patients with
gastrointestinal stromal tumors
Version: 2 Date: 09 Dec 2022
Reviewer's report:
The authors of the paper "Prognostic significance of serum CA125 in the overall management
for patients with gastrointestinal stromal tumors", based on suggestions from the review,
followed the points mentioned and made changes to the manuscript. The authors completed the
information on the reference range for CA 125 and included the missing locations of GIST  in
the legend of Figures 1 and 2.
In my opinion, the manuscript can be published in this journal.
Review for 10.1186/s12876-023-02658-x (2023)

Title: Inflammation and nutritional status indicators as prognostic indicators for patients with
locally advanced gastrointestinal stromal tumors treated with neoadjuvant imatinib
Version: 0 Date: 14 Oct 2022
Reviewer's report:
Your study examined the significant relationship between pre-treatment SII, PNI, and prognosis
in patients with GIST who underwent neoadjuvant imatinib therapy.
Major comments
1. I am unable to confirm the duration and dosage of imatinib use following surgery. It would
be beneficial to describe how imatinib was given in this study following surgery in order to aid
in interpreting PFS or OS.
2. It might be good to double-check the SII and PNI values in the Optimal cut-off values section
of the result. Please check to see if there is a typo because it is displayed differently from the
value indicated in Figure 2.
3. It is unclear from Table 3 why the HR was more significantly higher in the cases of better
tumor response and post-treatment imatinib. Please verify that the analysis has not been reversed.
Minor comments
1. The spacing and periods are incorrect in a number of places. Please confirm.
2. Why was the presence of lumbar spine metal implant included in the exclusion criteria?
3.  In the Assessment section of the method, in the part explaining the criteria for response
group, moderate effect and medium effect seem to be the same, so it would be better to write
it in one word.
Review for 10.1186/s12876-023-02658-x (2023)

Title: Inflammation and nutritional status indicators as prognostic indicators for patients with
locally advanced gastrointestinal stromal tumors treated with neoadjuvant imatinib
Version: 2 Date: 17 Jan 2023
Reviewer:  Hira Fatima Waseem
Reviewer's report:
Reviewer Name: Dr. Hira Fatima Waseem
Designation: Lecturer of Biostatistics
Institute: School of Public Health
Affiliation: Dow University of Health Sciences, Karachi, Pakistan
Review for Submission ID a8dde500-1150-44e2-a915-ee64dc7e119d
Comments:
# In the abstract, page no. 12 and line no. 16, please correct the p-value of SII-PNI score
(p=0.022, 0.046).
# In the results, suggestion is to use symbol * in the significant p-value of Table 2 and 3 and
then describe in the table end the *p-value<0.05 was considered as significant.
# In the results, replace the capital ‘P’’ by small ‘’p’’ for p-value (e.g  page no. 15 and line no.
11 and 12)
# Please check the spelling of tumor. In some places, the author writes ‘’tumour ‘’ (e.g.  Page
no. 15 and line no. 11 and 12) while in Table 3, the author writes ‘’tumor’’.
# In the discussion, please only change the ‘’et al’’ in the italic form not the author name.
Review for 10.1186/s12876-023-02657-y (2023)

Title: Expression patterns and prognostic value of key regulators associated with m7G RNA
modification based on all gene expression in colon adenocarcinoma
Version: 3 Date: 06 Oct 2022
Reviewer:  Weinan Xue
Reviewer's report:
Summary: The authors explored the expression patterns and established a prognostic model
based on regulators related to m7G RNA modification.
Strength: The predictive effect was validated in an independent cohort.
Limitations:
The analysis results of the authors are all from the public database and limited to the RNA level,
there is a lack of validation in their own colon cancer samples.
There is a lack of experiments in vivo or vitro to explore the molecular function of four-genes
in the model.
Other issues
Abbreviated names only need to be marked when they first appear, such as “LASSO, m7G,
etc.”, other similar errors are no longer listed, this is not a reviewer's work, I suggest that the
entire article needs careful revision.
Abstract section
The authors should check the case of all letters and the consistency of punctuation. Some
punctuation marks are missing, this should not be a mistake that a rigorous scientific researcher
should make.
Introduction section
The Previous Results part is too complicated and has weak connection with the article. It is just
a list of researches results. This part should be written in the discussion part.
Method section
The method part looks very confusing. It should be written in several parts, each part
corresponding to the results.
Although the authors use public R packages, the relevant references should be quoted, so that it
can protect developers' intellectual property rights, this is very important.
The authors should resize the font in Figure 1, some of the text is covered by lines.
Results section:
Line 255, the author's explanation for choosing k=2 as the optimal number of clusters is not
clear enough, and a detailed explanation is suggested.
In Figure 3D, how the “high risk” and “low risk” are obtained through PCA, the author needs
to give a reasonable explanation.
In Figure 4A, 5A and 5B, the text in the figures is too small to see clearly.
It is suggested to unify the statement of grouping in clustering analysis, group or cluster?
Line 354, the author's description of the results is not rigorous. The results can only show that
the risk score is an independent risk factor, not the four-gene risk markers.
Line 374, as immunosuppressive cells, Treg cells are highly infiltrated in the low-risk group,
and the author did not give a reasonable explanation.
In Figure 10, what do the red lines and numbers represent?
The author should make a table containing the risk scores of all patients and put it in the
supplementary files. The supplementary documents only contain the original code but lack the
visual data.
Need to have someone who is an expert on scientific writing in English to proof reading this
manuscript. Some statements were not correctly presented.
Review for 10.1186/s12876-023-02657-y (2023)

Title: Expression patterns and prognostic value of key regulators associated with m7G RNA
modification based on all gene expression in colon adenocarcinoma
Version: 3 Date: 19 Oct 2022
Reviewer's report:
I was very pleased to read the paper entitled "Expression patterns and prognostic value of
key regulators associated with m7G RNA modification based on all gene expression in colon
adenocarcinoma". Nevertheless, I have some serious doubts as to whether it is suitable for
publication in this form. Firstly, I am sceptical of bioinformatics papers, i.e. papers that are based
solely on available databases. I believe that in addition to using databases, the results should
be supported by one's own research using tissue material or in vitro cells.  This would greatly
enhance the quality of the work.
Review for 10.1186/s12876-023-02641-6 (2023)

Title: Protective role of circRNA CCND1 in ulcerative colitis via miR-142-5p/NCOA3 axis
Version: 1 Date: 10 Nov 2022
Reviewer's report:
line 49: do not abbreviate a term that is not discussed
line 53: change overexpression to overexpressed
line 53: capitalize circ
line 56: change to circRNA CCND1
line 67, 72: remove the comma
line 73-76: rephrase the sentence. it has a structural error
line 97: change to build
line 128: restructure the expression
line 132: add country for the Aladdin
line 132: grammatical error "was got"
line 168: change lowly
line 170: elaborate more in detail for the conclusion of the first result
line 184-186: grammatical error
line 192: change to upregulated
Figure 4A, 5A, 5B: rearrange the labels because it's hard to read them
line 266: change to researcher
line 267: change to stimulation
line 271: find a better way to express "kind of cirRNAs"
line 273: change to upregulated
Overall: there are too many grammatical errors and some paragraphs need to be restructured. I
highly suggest reviewing the manuscript by a person who is English proficient. Also, I would
recommend developing the discussion part with more creative ideas, not just adding other
researchers' results. It would become a better manuscript with an explanation of why this study
is important and what limitations exist.
Review for 10.1186/s12876-023-02641-6 (2023)

Title: Protective role of circRNA CCND1 in ulcerative colitis via miR-142-5p/NCOA3 axis
Version: 1 Date: 11 Nov 2022
Reviewer:  Endre Anderssen
Reviewer's report:
This is an interesting study of the possible role of cricular RNAs in the inflammatory process
involved in UC. The authors show downregulation of a selected circular RNA in active UC, and
follow this up with an in vitro study using LPS stimulation of CaCo cells as a model for the
inflammatory process.
The model results are consisten with the circular RNA having a possible anti inflammatory
regulatory effect, mediated by interactions with a microRNA. However the conclusion that the
circular RNA CCND1 represses UC processes seems a bridge to far based on only observatio
of differential expression and stimulation studies in a cancer cell line. The results are intriguing
but an effect on UC as opposed to a cell line model has not been shown.
Tho the sience appears sound the paper is very poorly written with many grammar problems and
poor choices of words and should be edited by an english speaker.
Review for 10.1186/s12876-023-02651-4 (2023)

Title: Clinical characteristics and risk factors of organ failure and death in necrotizing
pancreatitis
Version: 1 Date: 20 Nov 2022
Reviewer's report:
Interesting  study.
The authors should provide in the statistical paragraph more information on the regression model
they used.
The authors should cite some potential non-surgical treatment for pancreatic necrosis (cite the
papers PMID: 34932991 and PMID: 35193984)
Review for 10.1186/s12876-023-02651-4 (2023)

Title: Clinical characteristics and risk factors of organ failure and death in necrotizing
pancreatitis
Version: 1 Date: 08 Dec 2022
Reviewer:  Serena Stigliano
Reviewer's report:
In the present study the authors have focused their attention on an important aspect of a less
common group of acute pancreatitis, the necrotizing pancreatitis. Indeed, there a few studies
investigating which are the factors associated with the worsening of clinical course in necrotizing
pancreatitis.
Despite English language should be revised, the argument is interesting and should be taken in
consideration for publication.
However I have some comments:
- The study is a retrospective study  and thus it can only describe an association between specific
features and the OF and death in NP. Therefore is better to modify this part: Thus, in our research,
we would not only addressed the risk factors of OF and death in NP patients, but further identified
simple parameters that can discriminate high-risk patients.
- At page 8: Patterns of necrosis in NP may involve a combination of pancreatic and
peripancreatic parenchyma, isolated peripancreatic necrosis, or, less commonly, isolated
pancreatic necrosis is written twice. Please check.
- In the methods section the authors say: Fluid requirements should be reassessed at frequent
intervals within 6 h of admission and for the next 24 – 48 h. The goal of aggressive hydration
should be to decrease the blood urea nitrogen.
Is it done? It is a retrospective study so it had to be collected. I suggest to remove this part.
In the results part:
- The mean age of onset in the no OF group was lower than that in the OF group, and the
difference was significant (P < 0.05) is the same concept of “Compared to patients without OF,
the OF patients were older (49.3±14.4 vs 45.5±13.5, p < 0.05)”. Please choose one of the two
sentences.
-Is not clear what authors means with this sentence: The main local complications among the
NP patients was ANC (78.2%), a similar incidence of ANC in the OF group (72.2%), and the
ratio in no OF group was 92.3%. Please rephrase.
- Authors should better specify what they mean with the term “shock”.
Review for 10.1186/s12876-023-02651-4 (2023)

Title: Clinical characteristics and risk factors of organ failure and death in necrotizing
pancreatitis
Version: 3 Date: 11 Jan 2023
Reviewer:  Serena Stigliano
Reviewer's report:
The authors have reply to my comment in exhaustive way.
I think the paper is now ready to be published.
Review for 10.1186/s12876-023-02644-3 (2023)

Title: Expression and function of myelin expression factor 2 in hepatocellular carcinoma
Version: 3 Date: 27 Jul 2022
Reviewer's report:
In this manuscript, Peng Zhang et al. argue that MYEF2 may be a new biomarker of HCC with
potential value in the diagnosis and prognosis of HCC and is a potential therapeutic target. The
authors suggest that MYEF2 may be a potential biomarker for HCC using various bioinformatics
tools and basic in vitro analysis. This paper is written simply and clearly, and the study of
MYEF2 in HCC is novel. However, the following issues should be considered for revision.
1. In Figure 1A, the author found that MYEF2 expression was upregulated in colorectal cancer,
leukemia, liver cancer, melanoma, and ovarian cancer in ONCOMINE database. Is MYEF2
also upregulated in these cancer types in the TCGA database? TCGA database has datasets for
33 types of cancer. The author might as well confirm the expression of MYEF2 in the TCGA
database.
2. In Figure 1B, the author mentioned that they obtained the expression of MYEF2 in HCC
tissues and normal liver tissues from THE HUMAN PROTEIN ATLAS, and MYEF2 was
mainly expressed in the nucleus and was expressed at high levels in HCC tissues but expressed
at low levels in adjacent tissues. How many samples have a positive expression of MYEF2 in
HCC tissue? The author also may as well provide a positive or negative ratio of MYEF2 in HCC.
3. The authors said that ethnic and geographical factors were the limitations of previous studies
and that they were studied as a combination of bioinformatics methods and experimental studies
to compensate for their shortcomings. Shouldn't the authors check on more diverse cell lines to
overcome their shortcomings? (Figure 3D)
4. Figures 4 and 5 show that silencing or overexpressing of MYEF2 inhibits or promotes cell
migration and invasion in HCC cells. Including the effect of MYEF2 overexpression in normal
human hepatocytes will support the author’s hypothesis that MYEF2 is a key oncogene.
Minor comment
1. In Table 1, the authors should accurately describe “tumor grade” and “pathologic T”.
2. The figure number does not match the figure.
3. In Figure 2C and Figure 3E, it is better to mark "number at risk" at the bottom of the ROC
graph.
4. SiRNA1, which has better knockdown efficiency, has worse wound healing results than
siRNA2. How will the authors explain that?
5. The language of the article needs a thorough and careful revision.
Review for 10.1186/s12876-023-02644-3 (2023)

Title: Expression and function of myelin expression factor 2 in hepatocellular carcinoma
Version: 3 Date: 24 Aug 2022
Reviewer's report:
In this study, Zhang et al. aimed to find a biomarker for the diagnosis and prognosis of
HCC. They found that MYEF2 may be a potential target. Although finding biomarkers for the
diagnosis and prognosis of HCC is an urgent and crucial matter, and MYEF2 has indeed never
been reported in HCC, there are, however, several suggestions I’d like to give that may improve
the article.
1. Please provide a higher resolution of image 1C. The quality doesn’t meet the standard for
publication, in my opinion;
2. Is it necessary to present all OS, DSS, PFS, and RFS results in fig 1D-1G? I think it is a bit
redundant;
3. SK-Hep1 cells is endothelial origin, it is therefore not a typical HCC cell line. Please modify
the article accordingly or present results of a different cell line;
4. The details of the 142 pairs of tissue are unclear;
5. Please provide a higher resolution of fig 3B. I would also suggest the authors to provide one
consecutive image with both HCC tissue and adjacent tissue to increase the reliability of this
result;
6. In the methods, the authors wrote, “Cell migration time: SK-HEP-1 cells, 20 h; PLC/PRF/5
cells, 14 d. Cell invasion time: SK-HEP-1 cells, 24 h; PLC/PRF/5 cells, 15 d.”. Why does it
take two weeks for PLC/PRF/5 cells to migrate or invade? And id indeed this cell line takes
such a long time to migrate and invade, then how can it be distinguished from cell proliferation?
Besides, cell contours in fig 6D are unrecognizable.
Review for 10.1186/s12876-023-02640-7 (2023)

Title: Characteristics, clinical outcomes and patient-reported outcomes of patients with
ulcerative colitis receiving tofacitinib: a real-world survey in the United States and five European
countries
Version: 1 Date: 10 Nov 2022
Reviewer's report:
There are still few reports on tofacitinib for UC, and this large-scale data is a very interesting
paper. I have a few questions.
# Table 2 shows patient backgrounds by history of biologics treatment, but it would be easier to
understand the content of the article if there was a background table for all patients.
# As for the method, I think it would be better if you specifically described the primary and
secondary endpoints.
# Did you analyze in table2 for each?
# You mentioned extra-intestinal complications on page 9. What kind of extra-intestinal
complications?
# In the item of disease activity during tofacitinib treatment on page 10, it is said that many of
the target patients are moderate to severe patients. What is the proportion of each?
Review for 10.1186/s12876-023-02640-7 (2023)

Title: Characteristics, clinical outcomes and patient-reported outcomes of patients with
ulcerative colitis receiving tofacitinib: a real-world survey in the United States and five European
countries
Version: 1 Date: 13 Nov 2022
Reviewer's report:
This article examines the therapeutic effect of tofacitinib for each administration period. This
is very useful to know the real-world therapeutic effect of tofacitinib. It is also interesting to
note that both physicians and patients were asked about the effectiveness of tofacitinib and their
satisfaction with the treatment. When such surveys are conducted, they often target a small
number of medical institutions or only one country. However, this survey was conducted on a
large number of physicians and patients in multiple countries, and the results indicate a high
level of treatment efficacy and satisfaction with tofacitinib, which is considered more credible. I
believe that this is very useful for physicians and patients who are considering using tofacitinib
in the future.
The following points should be reconsidered.
1. While tofacitinib is expected to have a high therapeutic effect, various side effects have been
reported. Does this article investigate the appearance of side effects? Also, does the appearance
of side effects affect the satisfaction of physicians and patients with the treatment?
2. I believe that satisfaction with treatment is also influenced by medical costs. Has the level of
satisfaction with medical costs been surveyed?
Review for 10.1186/s12876-023-02640-7 (2023)

Title: Characteristics, clinical outcomes and patient-reported outcomes of patients with
ulcerative colitis receiving tofacitinib: a real-world survey in the United States and five European
countries
Version: 3 Date: 31 Dec 2022
Reviewer's report:
I confirm that the authors have re-examined the points I raised in the previous peer review and
have added to and reflected them in the manuscript.
Review for 10.1186/s12876-023-02648-z (2023)

Title: The cost of illness analysis of inflammatory bowel disease
Version: 1 Date: 25 Sep 2022
Reviewer's report:
Dear Authors,
It was a pleasure to read your manuscript entitled "the cost of illness analysis of inflammatory
bowel disease". I comment the authors on their effort to analyze the challenging subject of cost
of IBD in the new era of biologics that has altered the natural course of these disease entities.
General
This is a well intended and timely study given the rapid evolution of biologics and other new
treatment modalities in IBD.There is a much needed information on economic burden of IBD in
the developing world.  However I am afraid this study suffers from severe heterogeneity given
the methods. The narration also needs significant revision to address the errors of language
struture.
Major
#1 As the  cost analysis involved self reported expenses,  this study could suffer from significant
heterogeneity.  This could further be affected as the study found that about 60% of the costs
were attributable to indirect expenses which could vary widely based on available resources and
purchasing power of the individuals in the study population.
#2 Cost diary method is known to have inconsistencies when compared to insurance reported
cost data. It is understood that the healthcare infrastructure in Iran, where this study was
conducted is different from Europe or the United states were payor systems are more well defined
and data easily available  for analysis. Hence I am not sure if there could be a better method.
#3 The authors mention that some of the data was extrapolated to a year from 3 month data. For
example the costs related to medications and physician visits. As these could vary over time this
could lead to significant  errors in the final estimate.
#4 Significant revision of narration is required before this manuscript can be considered ready
for publication. If I may so suggest, review by a native English speaker familiar with scientific
writing would greatly aid in this process.
Minor
#1 Some of the statements need more fact-checking and correlation with data in the relevant
demographics. For example, in the  abstract, the authors state that IBD is a condition involving
young adults. However it is a condition known to have  a bimodal incidence pattern and affects
individuals across all age groups.
# 2 Authors need to verify the accuracy of data. For example in Table 1 showing demographics,
the numbers based on age group do not add up to the total (167 Vs 168)
Review for 10.1186/s12876-023-02648-z (2023)

Title: The cost of illness analysis of inflammatory bowel disease
Version: 1 Date: 02 Nov 2022
Reviewer's report:
Thank you for this study assessing costs associated with inflammatory bowel disease in Iran.
Please clarify how this can be a cross-sectional analysis if you are assessing cost over time.
What was diagnostic criteria for confirming a diagnosis of IBD? Did this include only Crohn’s
disease and ulcerative colitis? What about other entities such as microscopic colitis? Was scope
or pathology required for confirmation of diagnosis?
Please define disease progression.
Please provide further detail regarding the calculation of sample volume. How did you calculate
estimates of cost? Where does margin error of 6% come from?
Why is physiotherapy relevant to cost associated with IBD in this situation?
Please justify scaling up by a factor of 4 to extrapolate cost over a 1-year period – ie, does this
mean a patient who underwent colonoscopy or surgery is then calculated to have 4 colonoscopies
or surgeries over the course of 1 year? This does not seem reasonable.
Was there a study protocol that defined the number of phone calls or point of contact required
for the data collection?
Are hours of paid household help considered and IBD-specific cost? What about household help
for people without illness or with alternate illnesses?
Did you obtain wage information for each patient based on occupation? Is absenteeism of
caregiver a cost borne by the patient or does that reflect an alternate caregiver reason for
absenteeism?
Is work productivity loss/absenteeism only related to hospitalization? Why is each
hospitalization assumed to be 14 days? How do you assess cost of hospitalization itself?
How did you define early retirement and assess if early retirement was a consequence of IBD?
Please comment on why aminosalicylates share the highest cost of medication type in
comparison to biologics.
Please include costs of each drug, procedure, surgery etc in a supplementary table.
The analysis conflates cost attributed to patients and estimated costs due to premature death
or cost of illness for country on a population level. It is difficult to understand some of the
conclusions when the cost information is rather opaque. There are significant methodological
questions regarding issues such as data acquisition and cost calculation. This is an important
question to understand with potential impacts at a population level. In the current form, this
study requires substantial revision and re-calculation for a more robust cost analysis.
Review for 10.1186/s12876-023-02652-3 (2023)

Title: The impact of intrahepatic cholestasis on pregnancy outcomes: a retrospective cohort
study
Version: 3 Date: 26 Aug 2022
Reviewer's report:
This was a retrospective cohort study of women with and without ICP in Hangzhou, China.
One of this study's strengths is the volume of patients included in the analysis with over 650
subjects analyzed.  With this large cohort a number of interesting observations were made
including a difference in mode of delivery between the cohorts as well as increase incidence of
hyperlipidemia between groups.
One of the issues with the study is the framing of the conclusion of HepB being an adverse
pregnancy outcome for subjects with ICP.  This is not really the correct conclusion in my mind.
It should be that subjects with ICP were more likely to have chronic or carrier status for HepB.
I dont think this should be described as an adverse pregnancy outcome, as it is part of the patient
demographics, not something that occurred because of, or isolated to during the pregnancy.
In review of Table 1, patient demographics, please double check some of the calculations
indicating statistical significance.  Some of the mean values are every close to each other, but
the p values are extremely low.  For example height and BMI are almost exactly the same with
extremely similar ranges, so I find it surprising that these were  as significant as reported.
The pregnancy complications and pregnancy outcomes section is very hard to read, so perhaps
consider re-wording.  The last few sentences of this section dont really make sense to me and
probably require more narrative.
Please double check the manuscript for grammatic and spelling errors.  There are several
throughout.
Review for 10.1186/s12876-023-02652-3 (2023)

Title: The impact of intrahepatic cholestasis on pregnancy outcomes: a retrospective cohort
study
Version: 3 Date: 29 Aug 2022
Reviewer's report:
Thank you for giving me evaluation opportunity this interesting work. The authors investigated
the impact of intrahepatic cholestasis of pregnancy on pregnancy outcomes. This is an interesting
and important point. Introduction section is substantial.
However, we have some questions in the material and methods section:
1 – Were levels of BA examined in all the women included in the study? Or only women with
ICP were tested for BA levels?
2 – page 6, by “score” do you mean Apgar score? If yes, is it Apgar score at the first minute?
3 – page 6, by “huge infants” do you mean fetal macrosomia?
In the results section:
4 - page 8, by “score” do you mean Apgar score?
Multivariate Binary Logistic Regression Analysis Results
5 – How can you explain the fact, that IUGR, mode of delivery, and fetal length appeared to
be risk factors for ICP?
6 – How can you explain the fact, that premature rupture of membranes, low birth weight infant,
number of deliveries, and gestational age (Pregnant day) appeared to be protective factors for
ICP?
In discussion section should be avoided repeating of the results of the current study.
7 - page 12, abbreviation “PE” with no explanation.
Table 3
8 – Abbreviation “PE” with no explanation
9 – When the Systolic and diastolic arterial pressure were assessed? On admission, in labor?
Also, in conclusion section, the exact conclusion of the study, at which aspect the study
contributed to the literature could be mentioned.
After this revision the study can be evaluated again. Thank you.
Review for 10.1186/s12876-023-02639-0 (2023)

Title: Health-related quality of life and anxiety levels among patients under surveillance for
intraductal papillary mucinous neoplasm
Version: 3 Date: 28 Dec 2022
Reviewer's report:
Dear Authors,
Thanks for the reply provided. The efforts made to answer the comments raised are appreciated.
I commend them and endorse the publication of the manuscript in its revised form.
Review for 10.1186/s12876-023-02649-y (2023)

Title: Evaluation of gut microbiota of Iranian patients with celiac disease, non-celiac wheat
sensitivity, and irritable bowel syndrome: are there any similarities?
Version: 1 Date: 04 Dec 2022
Reviewer:  Basilio Malamisura
Reviewer's report:
The studio is well designed. However, there is no reference to how the diagnosis of NCGS
was made. By now it is increasingly evident that the correct definition must be Non Celiac
Wheat Sensitivity probably linked to ATI's proteins. Clear presentation of results. Perhaps only
the number of patients studied should be higher. The conclusions it reaches are interesting,
especially due to the fact that the microbiological pattern found in IBS patients is very similar
to that of NCGS patients and healthy controls.
Review for 10.1186/s12876-023-02647-0 (2023)

Title: Colonic TRPV4 overexpression is related to constipation severity
Version: 2 Date: 24 Aug 2022
Reviewer's report:
Dr. Mihara and colleagues have examined regulatory mechanisms of TRPV4 expression by
co-culturing colon epithelial cell lines with intestinal bacteria and their derivatives. The topic
is interesting especially with regard to the relationship between chronic constipation and TRP
channels. This is an interesting area of research however I have a number of concerns as
described below.
1, The authors investigated the effects of intestinal bacteria at various time points. However,
the time pints is unclear in Fig.1A, C, Fig.2B, C, D, and Fig.4. Add each time points in results
and figure legends.
2, “In this study, we evaluated 12 representative clinical isolates of enterobacteria, followed by
10 standard isolates of enterobacteria that are known to alter TRPV4 expression (Table S1).
We did not intentionally select enteric bacteria that have been suggested to be associated with
constipation.”
The authors  should show the reason "not intentionally select enteric bacteria" because this study
focuse on the choronic constipation.
3, In supplementary Fig.1, the authors investigated only three bacteria in methylation. I think it
is better to investigate other bacteria such as E.coli. Furthermore, data of TRPV4 methylation
is important. This data should be shown as Fig.3.
4, Although, the authors discussed the effects of bacterial metabolites (Fig.2A and 4) and the
effects of TNF-alpha (Fig2C and 4), these results are complicated. Therefore, the authors should
add more information to discuss these points.
Review for 10.1186/s12876-023-02647-0 (2023)

Title: Colonic TRPV4 overexpression is related to constipation severity
Version: 4 Date: 09 Jan 2023
Reviewer:  Suhasini Rajan
Reviewer's report:
I would like to thank the authors for addressing all of my comments. I appreciate that the authors
have restructured the manuscript making it more understandable. The changes in the figures
now give a lot more strength to the manuscript.
My only minor concern is the inconsistent ways in which TNF#, TNF#R1 and TNF#R2 are
written throughout the manuscript.
Review for 10.1186/s12876-023-02645-2 (2023)

Title: Understanding illness experiences of patients with primary sclerosing cholangitis - a
qualitative analysis within the SOMA.LIV study
Version: 0 Date: 05 Nov 2022
Reviewer's report:
Review; Understanding illness experiences of patients with primary sclerosing cholangitis - a
qualitative analysis
Thank you for the opportunity to read this paper.
Just some comments
• Is the paper technically sound?
The abstract is accurate and complete.
Yes, the paper is technically sound, the research questions are clear—focusing on the experience
of living with PSC. The context is specialist centres for autoimmune liver disease in Germany.
The study design is appropriate to answer the research question.
In total 49 references- they are mostly actual. Sixteen references are more than 10 years old.
These references are mostly methodological or theoretical.
Please correct, ref 30. The Declaration of Helsinki  is the World Medical Association’s (WMA)
best-known policy statement. The current (2013) version is the only official one; all previous
versions have been replaced and should not be used or cited except for historical purposes.
The six steps in the analysis are not clearly presented, qualitative researchers do recognize them,
but I am not sure that all readers understand and can follow the procedure
• Are the claims fully supported by the experimental data? If not, what further evidence is
needed?
Yes, the findings/results are supported by the data.
A suggestion, present the result in the same order in the abstract as in the text- starting with the
overall theme, built by the three generated themes.
Figure 1.- is illustrative. But are the themes placed in that order due to a reason? When I read
the text, it seems as there is a process, or a transition, if so, there should be arrows showing that?
Or are the themes free, not associated or influencing each other in any way?
The findings/result are easy to follow and there are quotations, giving” evidence” and
representativeness.
• Is the statistical analysis of the data sound?
NA, this is a qualitative study
• Does the availability of data adhere to the expected standards of your research community?
Yes, it adheres to the expected standards
• Are the claims appropriately discussed in the context of previous literature?
As stated above, present the result preamble in the discussion in the same order as in the text-
starting with the overall theme, built by the three generated themes. The discussion then starts
in that order…
The discussion is interesting, and the findings are deepened by theoretically reasoning.
• Could the manuscript be revised to address any potential limitations?
Strengths and limitations are reflected upon. But there is no reflection about talking to people
about a sensitive topic without having the ability to see body language and reactions. Are
telephone interviews similar no matter if it is about marketing or life threating diseases?
How handle if the participants needed psychological support?
Thank you for an interesting and readable manuscript.
Review for 10.1186/s12876-023-02645-2 (2023)

Title: Understanding illness experiences of patients with primary sclerosing cholangitis - a
qualitative analysis within the SOMA.LIV study
Version: 0 Date: 08 Nov 2022
Reviewer's report:
This is an impressive and comprehensive paper highlighting the experience of people with a
rare liver condition. The qualitative approach is appropriate and provides meaningful findings in
line with the study objectives. I recommend this paper is published and I only have some minor
comments for suggested changes, outlined below.
Introduction – Clearly sets out the need for research to understand the psychosocial needs of
this patient group and the value of a qualitative approach. The sentence beginning line 49 is a
bit long and unclear. I suggest re-wording it or splitting it in two.
Lines 53-57: Could you provide more lay terminology or give definitions for the non-clinicians
please e.g. strictures, pruritis.
Methods –
P6-7 A little more explanation of the exclusion criteria listed in table 1 would be helpful here.
The authors seem to exclude people unnecessarily where there might be scope to illuminate
further important issues in ‘real world’ scenarios (e.g. some of the comorbidities) that could be
captured with a qualitative approach. I suspect this is related to the quantitative study component
(as noted), in which case it would be good to explore the possible limitations of the exclusion
criteria for the qualitative component.
Recruitment: It would be helpful for the reader to know more about the process. Who contacted
patients via email? How were potential participants provided with a patient information sheet
and were they given time to think about it? At what point was informed consent agreed and
by whom?
Findings –
The authors have developed logical themes that are well supported by the data.
P15 Embracing the threat: The authors mention, ‘after a period of adjustment’ (line 322). Can
they elaborate on how they deduced that adjustment had taken place (especially given the shifting
nature of it)? Was there a different depending on time since diagnosis?
Discussion –
The authors do well to embed their findings in the theoretical literature on health and illness.
In terms of clinical implications, the manuscript would be improved if the authors could
suggest more tangible ways in which HCPs can better support people with PSC. Can they give
more specific types of intervention to promote acknowledgement of the patient experience,
awareness raising, ‘educating’ patients and supporting self-management. This section could be
expanded with supporting literature of e.g. supported self-management interventions that might
be applicable before summarising with the bullet points.
Review for 10.1186/s12876-023-02645-2 (2023)

Title: Understanding illness experiences of patients with primary sclerosing cholangitis - a
qualitative analysis within the SOMA.LIV study
Version: 1 Date: 10 Dec 2022
Reviewer's report:
Thank you for all efforts made to amend this manuscript. Most of the comments of the reviewers
are taken into consideration.
Looking forward to see this paper published, it is an important research.
Review for 10.1186/s12876-023-02646-1 (2023)

Title: Transradial versus Transfemoral Approach for TACE: A Retrospective Study
Version: 1 Date: 17 Oct 2022
Reviewer:  Yangxun Pan
Reviewer's report:
Dr. Guo and colleagues presented an impressive comparison between the transradial and
transfemoral methods when conducting transarterial chemoembolization from retrospective
perspectives. The results indicated that transradial access was an effective and feasible
alternative to transfemoral access for TACE. However, I have several concerns and if the author
could address them, I would be glad to endorse this study for publishment.
Since the current study is likely technical research that discusses the methods of catheterizations,
the observative outcomes seem to be not appropriate if the author used the tumor response.
Additionally, in the inclusions of the methods section, hepatic malignancies were included in
this study, and it is generally known that different pathological types of tumors respond to the
treatment dramatically differently, which also indicated that the tumor response was unable to
be used as an evaluation in this study. I would highly recommend the author use other evaluative
criteria to measure the technical outcomes.
To further discuss the technical feasibilities between transradial and transfemoral methods, the
author needs to provide representative pictures under DSA, in order to answer the question of
whether both methods are able to catheter to similar levels of hepatic arterials, like second-level
right/left hepatic arterials. Accordingly, information on tumor locations in both groups should
also be provided in the baseline to guarantee comparability.
Finally, someone who is a native speaker needs to assist with the grammar throughout the
manuscript.
Review for 10.1186/s12876-023-02646-1 (2023)

Title: Transradial versus Transfemoral Approach for TACE: A Retrospective Study
Version: 2 Date: 27 Dec 2022
Reviewer's report:
Thank you for the corrections and revisions made. A lot of my questions have been answered
and the manuscript is clearer in its methods, results and discussion. A few notes:
- I would consider omitting the TACE data that were performed in conjunction with ablation.
The data is likely skewed when there is the addition of a complete separate procedure for the
same lesion, and this may not be valid (and overall may make your conclusions weaker).  There
should be a compelling reason why this data was included. Since there were so few of these
cases, it should not affect the conclusions too dramatically.
-In the results section under "efficacy," would recommend explicitly writing out the statistics
and data even though it is represented in the figures. This will make it clearer for the conclusion
(and also this seems to be the crux of the paper)
- Thank you for clarifying the arterial spasm definition. This makes it a lot clearer in the
discussion as well.  I also noted your manuscript did a good job with limitations and noting that
although you hypothesized arterial spasm could be the reason for tumor progression, the study
was not powered for that.
Overall, very interesting observations and I look forward to the next step in these study cohorts!
Review for 10.1186/s12876-023-02646-1 (2023)

Title: Transradial versus Transfemoral Approach for TACE: A Retrospective Study
Version: 2 Date: 31 Dec 2022
Reviewer:  Yangxun Pan
Reviewer's report:
Dear authors,
Thank you for the comprehensive review. The Manuscript has been further improved now.
I have one more minor comment before full acceptance.
Based on the Discussion section, the conclusion should specify the efficacy of the RA
route and recommend changing the Conclusion section to, Transradial access is a feasible
alternative to transfemoral access which has less hepatic arterial spam with the help of advanced
catheterization and has shorter hospitalization stays while reducing postoperative complications.
Finally, thank you again for your and your colleagues' work.
Review for 10.1186/s12876-023-02643-4 (2023)

Title: Short and Long-Term Follow-Up and Clinical Outcomes in Patients with Celiac Disease
in a Large Private Practice Setting
Version: 3 Date: 04 Oct 2022
Reviewer:  Kamran Rostami
Reviewer's report:
Interesting study that emphasise the importance of follow up components for coeliac disease. It
is a well written manuscript. The discussion can be shorter. I have no major comments
Review for 10.1186/s12876-023-02643-4 (2023)

Title: Short and Long-Term Follow-Up and Clinical Outcomes in Patients with Celiac Disease
in a Large Private Practice Setting
Version: 3 Date: 23 Nov 2022
Reviewer:  Mohammad Rostami-nejad
Reviewer's report:
I have read the paper with interest.
Despite the topic is interesting and has value in the research practice, it seems that it has two
major concerns:
1- the number of study group is not good enough therefore the power of study is low
2- the data collection is too old and therefore the reference list is belonged to the last decade.
In my opinion if the authors can improve the patients collection and add the recent referred
patients it could be reviewable otherwise it is rejected in the current format.
Review for 10.1186/s12876-023-02643-4 (2023)

Title: Short and Long-Term Follow-Up and Clinical Outcomes in Patients with Celiac Disease
in a Large Private Practice Setting
Version: 5 Date: 02 Jan 2023
Reviewer:  Anil K Verma
Reviewer's report:
I agree with the author's responses. I do not have further comments.
Review for 10.1186/s12876-023-02643-4 (2023)

Title: Short and Long-Term Follow-Up and Clinical Outcomes in Patients with Celiac Disease
in a Large Private Practice Setting
Version: 5 Date: 03 Jan 2023
Reviewer:  Kamran Rostami
Reviewer's report:
As mentioned before, this is an interesting and well written study with a reasonable sample size
that reflect the real life presentation of coeliac disease that include seropositive, seronegative and
atypical forms. The follow up of coeliac disease is indeed different in different clinical settings.
The recommendations are  clear and useful for implementing future systematic care for patients
diagnosed with coeliac disease.
Review for 10.1186/s12876-022-02545-x (2023)

Title: Causes of endoscopic misdiagnosis of gastrointestinal cyst as solid lesion
Version: 2 Date: 02 Jul 2022
Reviewer's report:
Comments to Author:
The author examined the causes of endoscopic misdiagnosis of gastrointestinal cyst and reported
the importance of EUS diagnosis. While this is a novel retrospective study focused on cyst, there
are several serious concerns to be resolved.
Major concerns:
1. This study focused on SMT in which the final diagnosis is the cyst, and examined the
differences in diagnostic performance of each factor, such as EUS and texture. I think this
method can calculate only sensitivity; however, the author calculated the sensitivity, specificity,
PPV, NPV, and accuracy. How did the author calculate these values?
2. This method may provide information on factors that improve the sensitivity to diagnose cysts
but does not reveal any useful factors for differential diagnosis. To solve this issue, it is necessary
to examine the diagnostic performance of each modality for all SMT, including non-cysts.
3. As the author mentioned, cysts do not need to be resected. There are 12 cases that were
correctly diagnosed as cysts preoperatively. What is the reason these lesions were resected?
4. There are many cases in which EUS and forceps palpation are not performed; the evaluation
method is not standardized. Considering that this is a study of a small number of cases, this is
a significant bias.
5. The final diagnosis was made by two definitions: 1. fluid outflow in endoscopic incision of
tumor or postoperative specimen; 2. pathological diagnosis of postoperative specimen was cyst.
Does this mean that there are cases where cysts are diagnosed only by fluid outflow?
6. As preoperative diagnosis, boring biopsy and EUS-FNA are important modality to improve
the diagnostic performance. What is the reason these modalities have not been examined?
7. How many endoscopists were evaluated for these cases? How many cases were excluded?
Please describe Methods in more detail.
8. Since this study does not examine EUS-FNA, this should not be mentioned in Conclusion.  If
you want to describe the usefulness of EUS-FNA from previous studies, you should do in the
Discussion paragraph.
Minor concerns:
1. Please show the flow chart of this study participants for better understanding.
Review for 10.1186/s12876-022-02545-x (2023)

Title: Causes of endoscopic misdiagnosis of gastrointestinal cyst as solid lesion
Version: 2 Date: 25 Aug 2022
Reviewer's report:
Dear,
With pleasure we read and reviewed your submission "Causes of endoscopic misdiagnosis of
gastrointestinal cyst as solid lesion".
Unfortunately the decision was made to decline your submission.  This mainly because the
observed findings and conclusions of the review are expected and do not contribute to new
insights.
In current clinical practice, EUS is the accepted method of choice to evaluate submucosal or
subepithelial lesions as referred to in current ESGE guidelines
Review for 10.1186/s12876-022-02545-x (2023)

Title: Causes of endoscopic misdiagnosis of gastrointestinal cyst as solid lesion
Version: 3 Date: 29 Sep 2022
Reviewer's report:
Thanks for the great effort of the authors. However, many points to be discussed:
1. The discussion is expected and no new knowledge added to the literature.
2. The number of operating endoscopists is high (18) in relation to small sample size which
could raise question of examination quality as it is operator dependent examination.
3. Why cysts with benign criteria are resected instead of follow up or FNA if uncertain?