JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-024-03364-y (2024)

Title: The role of marital status in gallbladder cancer: a real-world competing risk analysis
Version: 0 Date: 31 May 2024
Reviewer's report:
This study investigated the impact of marital status on the survival rate of gallbladder cancer
(GBC) patients and established a predictive model graph to evaluate the probability of cancer
specific death (CSD) in individual patients. Multiple statistical analysis methods were used to
verify the reliability of the research results. There are also some limitations to the research,
such as selective bias in retrospective studies and the relatively small size of external validation
samples. In addition, the application scope of the model may be limited by the PSM method,
requiring more external validation and further research to verify its accuracy and reliability.
Specifically, the following issues need to be clarified:
The description of research background and purpose is not clear enough: although the study
mentioned that gallbladder cancer (GBC) is one of the main malignant tumors in the biliary
system, and its incidence rate is on the rise, when introducing the research purpose, it did
not clearly explain why to explore the relationship between marital status and GBC and the
significance of building a prediction model map.
The literature review is not sufficient: Although there has been some research on the impact of
marital status on other cancers mentioned in the introduction, there is a lack of comprehensive
overview of existing research, especially in the literature review of the impact of marital status
on GBC, which is relatively brief.
Insufficient explanation of variable selection and matching methods: Although the propensity
score matching (PSM) method was mentioned to reduce the impact of confounding factors, it
was not detailed which variables were selected for matching and the principles and methods
of matching. These pieces of information are crucial for understanding the interpretability of
research design and results.
The presentation of the results is not clear enough: In the results section, although a large amount
of data and statistical analysis results are provided, there is no clear summary and explanation
of the main results. Meanwhile, there are a large number of charts, but some of them may not
have clear content and explanations, making it difficult for readers to understand.
There is a logical jump in the discussion section: in the discussion section, the author shifted from
explaining the research results to discussing previous research, lacking coherence. In addition,
the discussion section failed to delve into the clinical significance of the research results and
the direction of future research.
Language expression needs further improvement: there are some issues with inaccurate
and fluent language expression in the article, which affects the overall readability and
professionalism of the article.
Review for 10.1186/s12876-024-03364-y (2024)

Title: The role of marital status in gallbladder cancer: a real-world competing risk analysis
Version: 0 Date: 03 Jun 2024
Reviewer's report:
Thank you for the opportunity to review the original research article entitled “The role of
marital status in gallbladder cancer: a real-world competing risk analysis” submitted to “BMC
Gastroenterology” for consideration for publication.
There are some issues with the entire article, and I have the following suggestion:
1.The author needs to add a flowchart of the validation cohort screening process.
2."From 2010 to 2015, relevant patient data was extracted from the SEER 18 Regs Custom Data
Set." Why not expand the selection of patient years in order to increase the sample size?
3.Patients with incomplete demographic, clinic-pathological, therapeutic, or follow-up data were
excluded in this study. The reason for the presence of the "unk" classification in tumor size in
Table 1 still remains unclear.
4.There are inconsistencies in the descriptions. ”An additional independent analysis was
undertaken, wherein patients were randomly assigned to two groups for the development of a
prognostic model: a training cohort (50%, n = 1597) and a validation cohort (50%, n = 1596).”
In fig 1, Training cohort = 1091, validation cohort = 1091.
5.How was the sample size of the external validation cohort determined?
Review for 10.1186/s12876-024-03306-8 (2024)

Title: Causal relationship between gut microbiota and constipation: a two-sample Mendelian
randomization study
Version: 2 Date: 04 Feb 2024
Reviewer's report:
In this study, MR was used to analyze the causal relationship between gut microbiota and
constipation for the first time. The authors identified specific types of microbes associated with
constipation, which affords a fresh constipation into the pathogenesis of this disease and the
possibility of developing treatment strategies. However, this analysis
was primarily based on GW AS data from European populations, presenting a limitation.
Future studies involving a broader range of racial and ethnic groups are imperative to
avoid biased estimates and enhance the universality of the findings.
Review for 10.1186/s12876-024-03306-8 (2024)

Title: Causal relationship between gut microbiota and constipation: a two-sample Mendelian
randomization study
Version: 2 Date: 29 Mar 2024
Reviewer:  Mohamed Hashim
Reviewer's report:
This is a novel study. I think, it will open the way to more research in this field.
Review for 10.1186/s12876-024-03306-8 (2024)

Title: Causal relationship between gut microbiota and constipation: a two-sample Mendelian
randomization study
Version: 6 Date: 16 May 2024
Reviewer:  Mohamed Hashim
Reviewer's report:
In spite of limitations of the study, this is a novel  study in the field.
I think the authors responded to comments.
Further studies are needed for further elaboration.
Review for 10.1186/s12876-024-03306-8 (2024)

Title: Causal relationship between gut microbiota and constipation: a two-sample Mendelian
randomization study
Version: 6 Date: 18 May 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (Brief or other article types: is there a clear objective?)
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: This is a repeat review of the revised manuscript
"The causal relationship between gut microbiota and constipation: a two-sample Mendelian
randomization study ", which was, indeed, much improved after  revision, with added material
in Discussion and the small changes done throughout. Please do further set of the small changes
outlined below (this will not require re-reviewing": 1) in the first paragraph of Abstract :"....with
recent observational studies implicating dysfunction of the gut microbiota IN constipation.
While observational studies indicate a relationship, causal  connection between microbial
composition and constipation remain unclear. " 2) in the following phrase, change the grammar
tense: "Liu et al [15] demonstrated that constipation significantly changes the diversity of
intestinal microbial communities and affects the fecal metabolites". 3) In ".... the two protective
bacteria, demonstrate a substantially stronger effect..." remove comma. 4)  "...the gut microbiota
of the Japanese population differs markedly from THAT OF other populations [48]".
ADDITIONAL REQUESTS/SUGGESTIONS:
This is manuscript of good quality. Please see small grammar/ flow changes requested above.
MS may be published without the need of further reviewing, after changes made
Review for 10.1186/s12876-024-03352-2 (2024)

Title: Appropriateness of Colonoscopies in a Tunisian Endoscopy Center: Factors and EPAGE-
I/II Criteria Comparison
Version: 4 Date: 30 May 2024
Reviewer:  Rui Sousa Magalhães
Reviewer's report:
Comments to authors:
I read with much interest the original article presented, focusing in a study analysing criteria for
appropriateness of colonoscopies and the comparison between EPAGE-I and EPAGE-II. The
study comprises a single-center cross-sectional analysis. The primary outcome was to assess the
rate of appropriateness of colonoscopies at the specific center.
Major points:
- If possible, the key words would benefit to be changed according to MESH terms.
- In an advisory note I would recommend to shorten the title
Methods:
- Despite providing a link to the EPAGE criteria, the manuscript would benefit from a brief
explanation on how the score works, for instance, regarding the values attributed to each
criterion. Can the authors provide one?
- Regarding the sentence, “The following endoscopic findings were categorized as relevant:…
microscopic colitis, infectious colitis and eosinophilic colitis.” Can the authors specify what
endoscopic findings they used to diagnose these three entities?
Results
- From 1972 colonoscopies 361 were deemed incomplete. This is a rather high number. Can the
authors provide any reasoning?
- The authors refer to 283 colonoscopies with bad preparation, this seems rather high. What is
the protocol implemented?
- The authors refer to 157 colonoscopies with bad tolerance, are all colonoscopies performed
under no sedation?
- Regarding the sentence, “Screening colonoscopies in asymptomatic patients or with known
IBD represented 4.5% of the overall indications” How is the screening protocol implemented
in your hospital?
- “The agreement between EPAGE I and EPAGE II criteria was slight using the weighted version
of k (k= 0.153)” EPAGE I and II have several criteria and criterion combination. Can the authors
comment on how this factor can difficult the k analysis? And how to overcome it?
- The diagnostic yeld of 8.5 for angiodysplasia and 9.8 for IBD is rather high, can the authors
comment on this?
Discussion
- The discussion is extensive and would benefit to be shortened.
- Post polypectomy surveillance has specific guidelines. Can the authors comment on the benefit
of applying EPAGE II criteria?
- Regarding the criterion uncomplicated diarrhoea, can the authors provide information on how
long the symptom needs to be affecting the patient for it to be considered positive?
- Haematochezia is a criterion for colonoscopy. Can the authors comment on this. And how the
EPAGE criteria interfer with this statement?
- The reference 28 is from 2009, there are recent guidelines regarding post polypectomy
surveillance, does the EPAGE II has this into account?
- Regarding the sentence from the introduction section: “Due to limited resources, we critically
reviewed our clinical practice in order to help propose efficient strategies to control the growing
demand in our endoscopy unit.” What measures do the authors propose?
Review for 10.1186/s12876-024-03352-2 (2024)

Title: Appropriateness of Colonoscopies in a Tunisian Endoscopy Center: Factors and EPAGE-
I/II Criteria Comparison
Version: 4 Date: 21 Jun 2024
Reviewer's report:
It is a single center cross-sectional study aimed to compare appropriateness of colonoscopy by
means of European Panel on the Appropriateness of Gastrointestinal Endoscopy (EPAGE) I
and II criteria. The authors observed appropriate colonoscopies in 43.2% and 76.4% when they
applied EPAGE I and II criteria respectively. Further, they noted a low agreement between the
EPAGE I and II (k=0.15). They concluded that EPAGE II criteria is a valid tool for reducing
inappropriate colonoscopies. However, the EPAGE II criteria were published in 2009 and are
not nowadays completely applicable because of the new recommendations on surveillance
after polypectomy (Rutter MD, et al. Gut 2020;69:201–223. doi:10.1136/gutjnl-2019-319858;
Hassan Cesare et al. Post-polypectomy colonoscopy surveillance: ESGE Guideline Update
2020). This concept should be mentioned in the discussion.
Maior revisions
1- In table 2, surveillance post polypectomy, there are different value in comparison to the text !
(1.7% vs 19.7% and 34% vs 27.4% (which are true ??)
2- In line 19 : “ On univariate analysis… “ the authors should insert values and statistics
demonstrating that  “…appropriate indication was associated with age (> 50 years) but not
with gender, with both sets of criteria. Appropriateness of indication was significantly higher
in hospitalized patients”
Minor revisions:
1- Please insert number page in your manuscript
2- The aim should be correct because of the appropriateness of colonoscopy is established by
EPAGE criteria (in your sentence it seems that you are applying another criterium).
3- In table 1, 7th  line is written in French language.
4- In table 1, specify the following abbreviations (head of table): AN, A, U, I, NA as well as in
table 3; specify that in the brackets is the value in percentage.
5- In table 2, line 3, there is a different value 23.3% in comparison to the text (23.3%).
6- In table 4 , insert 95%CI and specify the CCR abbreviation.
Review for 10.1186/s12876-024-03352-2 (2024)

Title: Appropriateness of Colonoscopies in a Tunisian Endoscopy Center: Factors and EPAGE-
I/II Criteria Comparison
Version: 6 Date: 12 Jul 2024
Reviewer's report:
The  work is interesting  and highlights a topic  which is  always important.
Review for 10.1186/s12876-024-03352-2 (2024)

Title: Appropriateness of Colonoscopies in a Tunisian Endoscopy Center: Factors and EPAGE-
I/II Criteria Comparison
Version: 6 Date: 01 Aug 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Changes are satisfactory, I recommend acceptance.
Review for 10.1186/s12876-024-03336-2 (2024)

Title: Safety and effectiveness of tofacitinib in Korean adult patients with ulcerative colitis:
post-marketing surveillance study
Version: 1 Date: 04 Apr 2024
Reviewer's report:
Thank you for submitting your paper.
I have questions regarding the following points, please answer them.
##JAK inhibitors are indicated and positioned for ulcerative colitis in intractable cases in which
at least one biological drug is ineffective or insufficiently effective.  In this cohort, bionaive
cases account for the majority, but are the indications and positioning of JAK inhibitors different
from international standards in South Korea? If so, please also mention the reason.
##Is there a difference in the incidence of adverse events between elderly and young people?
##Are the safety profiles and efficacy different for maintenance doses of 10 mg BID and 5 mg
BID? If the dose was changed and remission was maintained, would adverse events increase
with longer duration of 10 mg BID administration?
##Regarding herpes zoster risk management, how many patients received vaccinations? Did
the risk of developing HZ be reduced by whether or not vaccination was administered?
Review for 10.1186/s12876-024-03336-2 (2024)

Title: Safety and effectiveness of tofacitinib in Korean adult patients with ulcerative colitis:
post-marketing surveillance study
Version: 1 Date: 05 Apr 2024
Reviewer's report:
This article is very valuable because it examines the efficacy and safety of tofacitinib for
ulcerative colitis in a prospective one-year observation of patients treated with tofacitinib.
Please consider the following
1) Regarding the patient disposition of the study in Fig. 1
What is the reason for excluding three patients who were treated with Tofa for less than 8 W?
Are cases of discontinuation due to lack of therapeutic effect included?
Similarly, 41 cases were excluded for a duration of less than 52 W. What was the reason for this?
2) Do you know the overall treatment retention rate of the patients, and if so, How about the
Kaplan-Meier curve?
3) About the patient demographic and baseline characteristics in Table 1
In the previous UC treatment you mention biologics, do you know how many biologics patients
have used?
The treatment effect is divided into bio naïve and experienced, but the information on
experienced should be described in detail.
Immnosuppressants are used in 70 cases, but thiopurine is used in 39 cases. What other drugs
have been used?
4) Safety
What is set as the Hb level or lower for anemia?
5) I am very surprised to see 0% occurrence of HZ.
Authors mention vaccination, but do authors know what the incidence of varicella itself was?
6) AEs in Table 2
I think ulcerative colitis is better than Colitis ulcerative.
Review for 10.1186/s12876-024-03336-2 (2024)

Title: Safety and effectiveness of tofacitinib in Korean adult patients with ulcerative colitis:
post-marketing surveillance study
Version: 3 Date: 31 May 2024
Reviewer's report:
I think this is a valuable paper that sheds light on the actual clinical practice of tofacitinib.
However, the figures and tables have not been properly submitted and are not worthy of peer
review (Fig. 3 and Fig. 4).Please correct and resubmit promptly.
Please also mention the following points:
##The frequency of patients with a history of biologic therapy is low. I believe that the
international standard for the indication of JAK inhibitors is that patients have failed to respond
to at least one biologic agent. Please explain the reason for this and the specific background
of Korea.
##Please indicate whether there was a difference in the remission maintenance dose of
tofacutinib and the incidence of adverse events.
##The incidence of shingles seems to be low. Is there any reason for this, such as a high
vaccination rate?
Review for 10.1186/s12876-024-03375-9 (2024)

Title: Clinical characteristics and management of liver abscess in The Gambia, a resource
limited countries
Version: 3 Date: 23 May 2024
Reviewer's report:
Authors have described on findings and management of liver abscess.
The have mentioned about giant liver abscess, however the definition of giant liver abscess is
not described
As this study is from resource limited setting where many investigations can't be done. Authors
should mention learning points for them from study in resource limited setting
Review for 10.1186/s12876-024-03375-9 (2024)

Title: Clinical characteristics and management of liver abscess in The Gambia, a resource
limited countries
Version: 6 Date: 09 Jun 2024
Reviewer's report:
This paper has fundamental drawback in methodology - treatment section. It says  it is a
retrospective study. data collected retrospectively from records.
In the methodology  authors describe a strict  management startegy. To treat with antibiotics if
the abscess size is less then 5 cm and aspirate and give antibiotics if it is over 5 cm. this 5cm is
highly arbitrary and there is no such division in clinical practice. Aspiration /admission  is all
individualized. I do not think such a practice is acceptable and possible even in resource poor
setting.
Similarly in treatment it says large abscess after aspiration was observed for 4 hours and if vitals
were stable they were discharged. These patients having large abscesses usually need aggressive
IV antibiotics and such strict protocol cannot be practiced.
Review for 10.1186/s12876-024-03375-9 (2024)

Title: Clinical characteristics and management of liver abscess in The Gambia, a resource
limited countries
Version: 6 Date: 28 Jun 2024
Reviewer:  Dhruba Narayan Sah
Reviewer's report:
First I would like to congratulate you for researching this disease. Well, it has been done in
resource-limited settings, but there might still be a role of pigtail drainage in certain patients,
which might be necessary in managing liver abscesses. Again for comparison between the two
groups, it would be better if you had included more samples.
Overall it's well written with few minor grammatical errors. Thank you.
Review for 10.1186/s12876-024-03375-9 (2024)

Title: Clinical characteristics and management of liver abscess in The Gambia, a resource
limited countries
Version: 7 Date: 31 Jul 2024
Reviewer:  Bhishma Pokhrel
Reviewer's report:
Proofreading is needed to ensure the accuracy of the English language
Abstract is very short and  lack the information on the design of the study, findings etc.
Methodology is vague and needs to be properly written.
The  result section needs to be specific and doesn't need to be compared with the other
studies .Missing demographic variables . No figures and tables.
The discussion section is lacking and should be properly written comparing the finding of this
study with other similar studies elsewhere .
Review for 10.1186/s12876-024-03357-x (2024)

Title: Percutaneous endobiliary radiofrequency ablation and stent placement for unresectable
malignant biliary obstruction: a propensity score matching retrospective study
Version: 1 Date: 24 May 2024
Reviewer's report:
The list of the literature contains recent publications, but my suggestion is that the CVIR paper,
published in 2012, that reported the first in man percutaneous intraductal RFA using 8 French
bipolar RF catheter (Habib™ PERF; EMcision Ltd, London, UK) should be mentioned and used
for discussion
Images are adequate, but  quality is poor
Review for 10.1186/s12876-024-03357-x (2024)

Title: Percutaneous endobiliary radiofrequency ablation and stent placement for unresectable
malignant biliary obstruction: a propensity score matching retrospective study
Version: 1 Date: 19 Jun 2024
Reviewer's report:
This is an interesting paper that describes the usefulness of percutaneous RFA and stent
placement. Please add the method of percutaneous drainage (unilateral or bilateral), the diameter
and length of the metal stent used, and the treatment method in case of stent occlusion. Please
evaluate the treatment outcomes of each group, unilateral and bilateral.
Review for 10.1186/s12876-024-03357-x (2024)

Title: Percutaneous endobiliary radiofrequency ablation and stent placement for unresectable
malignant biliary obstruction: a propensity score matching retrospective study
Version: 4 Date: 05 Jul 2024
Reviewer's report:
This paper has been revised. Please include illustrations of RFA and stent treatment to make it
easier for readers to understand.
Review for 10.1186/s12876-024-03357-x (2024)

Title: Percutaneous endobiliary radiofrequency ablation and stent placement for unresectable
malignant biliary obstruction: a propensity score matching retrospective study
Version: 4 Date: 10 Jul 2024
Reviewer's report:
My congratulations with interesting paper. Only concern is  about image quality  - I suggest,
you can find better images done on the higher quality X-Ray   unit
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 0 Date: 24 Jun 2024
Reviewer's report:
He S, et al reported the manuscript entitled “The newly proposed plasma-glycosylated
hemoglobin A1c/high density lipoprotein cholesterol ratio serves as a simple and practical
indicator for assessing non-alcoholic fatty liver disease: an observational study based on a
physical examination population”. They concluded that the newly proposed HbA1c/HDL-C
ratio serves as a simple and practical indicator for assessing NAFLD. Many biomarkers have
been reported for the screening of NAFLD from many countries. For this purpose cost benefit,
high sensitivity, and high specificity are required. This paper is interesting and describes
important points, however, there are some questionable results.
Major points
1. In Table 1 baseline characteristics of the subjects are classified into 4 groups, in which
the percentage of women in Q4 is significantly lower than other 3 groups. Subjects in Q4
is the highest risk population for the development of NAFLD. It has been reported that the
development of NAFLD in females is significantly increased after menopause. However, the
present result is opposite compared to previous reports. How do you explain this point?
2. In Fig 3 AUROCs for the screening of NAFLD between HbA1c/HDL-C and HDL-C are very
close. Is there any clinically meaningful point to use HbA1c/HDL-C instead of HDL-C alone?
Did you compare the diagnostic ability of the HbA1c/HDL-C with previously reported NITs for
the screening of NAFLD?
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 0 Date: 25 Jun 2024
Reviewer's report:
In the article titled “The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density
Lipoprotein Cholesterol Ratio Serves as A Simple and Practical Indicator for Assessing Non-
alcoholic Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population”, the authors have studied the association between the HbA1c/HDL-C ratio and
NAFLD in 14,251 individuals. The authors found a significant positive association between the
HbA1c/HDL-C ratio. The manuscript is well constructed, and the statistical analyses support
the conclusion. Still, I have concerns regarding the clinical utility of the findings. As the field is
moving from a diagnosis of exclusion (NAFLD) to an inclusive diagnosis of MAFLD, using of
a single parameter for the diagnosis or screening is counterintuitive.
Major comments
1. Title: “Indicator for Assessing Non-alcoholic Fatty Liver Disease” is a vague term. Are the
authors proposing HbA1c/HDL-C ratio for the diagnosis of NAFLD or is it a screening marker.
This needs to be clarified in the title and the manuscript.
2. Lines 240-242: Recommendations for HbA1c/HDL-C ratio cut-offs for the prevention of
NAFLD in general population are beyond the scope of this study. Such recommendations
would require longitudinal studies. Authors should refrain from making such arbitrary cut-offs.
Optimum cut-off values obtained from ROC analyses are not cut-offs for prevention in general
population.
3. Figure 3: The authors have shown that HbA1c/HDL-C ratio performs better than HbA1c or
HDL-C alone in ROC analysis. What about other predictors of MAFLD like WC, BP, and TG?
Does adding HbA1c/HDL-C ratio to WC, BP, or TG improve the AUC of these parameters?
This analysis would help in understanding the incremental value of HbA1c/HDL-C ratio over
these parameters.
Minor comments
1. Table 2: Table 2 analyses are repetitive. HbA1C/HDL-C ratio is a continuous variable and
authors have shown that it is significantly associated with NAFLD using logistic regression.
Dividing HbA1C/HDL-C into quartiles and quantifying the OR does not provide any additional
information.
2. Table 3: Abbreviations are incorrectly shown as FPG/HDL-C ratio.
3. Discussion section has repetitions of results. E.g., lines 221, 223, 239-240. These can be
removed.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 2 Date: 10 Jul 2024
Reviewer's report:
I agree to accept  the revised  manuscript.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 2 Date: 15 Jul 2024
Reviewer:  Mustafa Cesur
Reviewer's report:
The authors tried to find a new  practical indicator for screening metabolic associated fatty
liver disease (MAFLD). But they haven't mentioned any cut off number. They showed only
relationship of HbA1c and HDL ratio with MAFLD. There is no cut off value, there is only
correlation. So the ratio can not be an indicator.
I suggest to make a correlation HbA1c and HDL ratio to FIB-4 scores of the subjects, and to
have  a value as an indicator. This will improve the study.
Moreover the result part is not clear. Especially the quartils neeed wide definition. To make a
quartil (Q) definiton is better.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 2 Date: 19 Jul 2024
Reviewer's report:
The authors have addressed all the comments satisfactorily. I have no further comments.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 2 Date: 21 Jul 2024
Reviewer's report:
In the article titled 'The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density
Lipoprotein Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening
Metabolic Associated Fatty Liver Disease: An Observational Study Based on A Physical
Examination Population,' the authors studied the association between the HbA1c/HDL-C ratio
and MAFLD. The manuscript is well-written and has been significantly revised based on the
reviewers' comments. However, the authors have shown that predictors of MAFLD such as WC,
BP, TG, FLI, and HSI are significantly better in screening for MAFLD. It is not clear what value
the HbA1c/HDL-C ratio will add in assessing MAFLD.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 3 Date: 28 Jul 2024
Reviewer's report:
The authors have thoroughly addressed the comments.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 3 Date: 30 Jul 2024
Reviewer's report:
This paper is acceptable.
Review for 10.1186/s12876-024-03362-0 (2024)

Title: The Newly Proposed Plasma-Glycosylated Hemoglobin A1c/High-Density Lipoprotein
Cholesterol Ratio Serves as A Simple and Practical Indicator for Screening Metabolic
Associated Fatty Liver Disease: An Observational Study Based on A Physical Examination
Population
Version: 3 Date: 06 Aug 2024
Reviewer:  Mustafa Cesur
Reviewer's report:
The authors made the suggested corrections succesfully. I want to point only one thing. In line
50 the first paragraph of the manuscript starts with MAFLD. It should be like that; Metabolic
associated fatty liver disease (MAFLD).
Review for 10.1186/s12876-024-03320-w (2024)

Title: Dietary Habits as Associated Factors with Irritable Bowel Syndrome among Medical
Students: Evidence from a Cross-Sectional Study
Version: 2 Date: 30 May 2024
Reviewer's report:
Thank you for inviting me to review this paper. Here are some comments that might be beneficial
to the authors.
-In the title, "risk factors" cannot be used. Cannot infer causation from a cross-sectional study.
-In the abstract:
The rationale mentioned is not valid. State other important reasons.
In the results, state multivariable analysis results only.
Conclusion should be tailored to the multivariable analysis only.
Introduction:
-More up to date references are missing.
-Why did the authors focus on medical students specifically? Why not all university students or
the general population? This needs to be elaborated in the paper.
-The authors state "Ibb University, located in Yemen's second-largest governorate by population
and hosting students from various regions, provides an ideal setting for investigating the
prevalence and associated risk factors of IBS in a diverse and representative student population."
You cannot say that. You are still prone to selection bias. I suggest removing this idea.
Methods:
-In the statistical analysis paragraph: On what basis did you include the independent variables
in the regression model? usually, you need to include factors that showed a p < 0.250 in the
bivariate analysis in the regression model.
Results:
-The figures and table 2 can be removed...just insert those results in the text.
-In the "average marginal effects" paragraph, the authors did an analysis on females only. Why
did you do a stratification analysis? This should be introduced in the introduction (if authors
want to keep it) and mention it in the statistical analysis paragraph.
Discussion:
-your study showed a prevalence of 26%, whereas a quick search of the literature showed a
prevalence of 48.6% in Lebanon (https://pubmed.ncbi.nlm.nih.gov/37605160/). Can the authors
compare their results to those of that study and explain why they have a smaller percentage
despite using the same scale (ROME IV)?
-The majority of the discussion is based on the bivariate analysis, which should not be discussed.
Please discuss multivariable results only; you have carbonated beverages and drinking coffee
(close to significance)
-Add clinical implications paragraph: how would other researchers benefit from your study?
CONCLUSION
-in the first sentence, the authors state "a higher prevalence"....higher than what?
-Modify the conclusion based on multivariable results only.
-Authors state "In contrast, for women, the consumption of carbonated soft drinks was found
to significantly increase the risk of developing IBS symptoms in females." This is based on the
stratification analysis....please see my previous comment to see if the authors would want to
keep this idea or remove it.
I hope those comments would help the authors. Good luck with the revision.
Review for 10.1186/s12876-024-03320-w (2024)

Title: Dietary Habits as Associated Factors with Irritable Bowel Syndrome among Medical
Students: Evidence from a Cross-Sectional Study
Version: 2 Date: 10 Jun 2024
Reviewer:  Yasir Khayyat
Reviewer's report:
Thanks for including me in the process of review of the Manuscript Titled: Dietary Habits as
Risk Factors for Irritable Bowel Syndrome among Medical Students: Evidence from a Cross-
Sectional Study.
Reviewer Comment:
The Manuscript Authors are from several countries which are China ,Yemen and Mauritania.
A. Study Participants and Methods and Abstract Section Comments: It referred to the study
participants from Yemen , However,I am not clear of the role of the authors participated from
other countries,please clarify this point ,so that it does not confuse or refer to the study been
from several countries.
B.Methods: It is mentioned that Female students with abdominal pain relates to Menstural cycles
are excluded from study enrollment,Please clarify if there is re-enrollment in time related to the
female patients outside of the menstural period in which the abdominal pain satisfy the criteria
of ROME 4 Criteria.
Statistical Analysis:Well presented and explained especially the part relate to sample size
calculation.
C. Discussion is comperhensive and elaborated the findings.
D.Tables and Figures: Clear and self explanatory.
E.Refrences are appropriate to the topic.
Review for 10.1186/s12876-024-03320-w (2024)

Title: Dietary Habits as Associated Factors with Irritable Bowel Syndrome among Medical
Students: Evidence from a Cross-Sectional Study
Version: 5 Date: 04 Jul 2024
Reviewer's report:
Thank you dear authors for the thorough revision.
I have one comment regarding the choice of variables with a p < 0.250. The answer is wrong. It
is not due to other studies or to the framework. Please add this reference to the statistical analysis
paragraph and remove your ideas.
Reference: Bursac Z, Gauss CH, Williams DK, Hosmer DW. Purposeful selection of variables
in logistic regression. Source Code Biol Med. 2008 Dec 16;3:17. doi: 10.1186/1751-0473-3-17.
Congratulations. Good luck for future endeavors.
Review for 10.1186/s12876-024-03320-w (2024)

Title: Dietary Habits as Associated Factors with Irritable Bowel Syndrome among Medical
Students: Evidence from a Cross-Sectional Study
Version: 5 Date: 04 Jul 2024
Reviewer:  Yasir Khayyat
Reviewer's report:
Thanks very much for taking the time to respond to our query
Review for 10.1186/s12876-024-03372-y (2024)

Title: Diagnostic Yield of Bidirectional Endoscopy for Iron Deficiency Anemia in Young
Patients
Version: 1 Date: 20 Jun 2024
Reviewer's report:
The authors aimed to investigate the diagnostic yield of bidirectional endoscopy in men younger
than age 45 and premenopausal women.
Main Comment:
- The study is retrospective in nature, and despite being done over a 14-year period, only a small
number of patients were included.
Other comments:
- For men with IDA, endoscopic evaluation is recommended by current guidelines and there is
no age threshold of 45 stated by authors.
-    Please describe how patients were selected for this study. Did you search in the procedure
indication?
-    The authors mentioned that they aimed to look at the diagnostic yield for pre-menopausal
women. However, women were included based on their age, not menopausal status.
- For classification of endoscopic findings in patients with pathology proven gastritis, please
mention whether gastric pathology was seen endoscopically or not.
- While the title indicates the yield of bi-directional endoscopy, authors included 20 patients
who did not have bidirectional endoscopy.
- Authors should mention how patients were selected for biopsy, and total number of patients
who had biopsies taken.
- The abstract needs to be more concise, and conclusion should include main study finding
according to main study aim and avoid speculation.
- Please provide some details about symptoms.
- Please include section about statistical analysis
Review for 10.1186/s12876-024-03355-z (2024)

Title: Decoding IBS: A Machine Learning Approach to Psychological Distress and Gut-Brain
Interaction
Version: 0 Date: 11 May 2024
Reviewer's report:
Dear authors, this is an interesting study with findings that could help us with making IBS groups
more homogenous and target for individualized treatment.
Some comments from the text:
The aim not clearly stated in the background
Method: Few participants were involved, Is there a power calculation done.
Results:  few patients, few controls compared to IBS patients.
Review for 10.1186/s12876-024-03355-z (2024)

Title: Decoding IBS: A Machine Learning Approach to Psychological Distress and Gut-Brain
Interaction
Version: 0 Date: 23 Jun 2024
Reviewer:  Hanna-Jairala Ignacio
Reviewer's report:
Congratulations to the authors. I believe that it should be accepted with minor changes.
It would be useful to include in the introduction, two articles referring to prevalence data directly
related to the objectives of the study:
Worldwide Prevalence and Burden of Functional Gastrointestinal Disorders, Results of Rome
Foundation Global Study Gastroenterology. 2021 Jan;160(1):99-114.e3.
Global prevalence of psychological distress and comorbidity with disorders of gut-brain
interactions. American Journal of Gastroenterology. 2024;119:165-175
The methodology in relation to the statistical analysis and the presentation of results seems to
me to be correct and very carefully presented.
In the section 4.1 Summary of the results, I would add statistical data as a summary of the results
previously presented in a broad way, as well as the statistical significance of these results.
The findings allow to make more categorical "conclusions", it seems to me that this section
(conclusions) should be rewritten by pointing out the association found in the study.
Review for 10.1186/s12876-024-03355-z (2024)

Title: Decoding IBS: A Machine Learning Approach to Psychological Distress and Gut-Brain
Interaction
Version: 0 Date: 26 Jun 2024
Reviewer:  Hiroshi Mihara
Reviewer's report:
Questions and Comments:
On the use of K-means clustering with k=3:
You have set the number of clusters to 3 for the K-means algorithm. Have you considered
including the results for k=2 and k=4 in your discussion to assess whether 3 is indeed the optimal
number of clusters?
On the specificity of the disease classification:
It is noted that your model accurately predicted the membership to the IBS group in 80% of the
cases in an unknown dataset. However, this accuracy was achieved in distinguishing between
only IBS and healthy controls. If the dataset were to include other disease groups, such as
patients with Functional Dyspepsia (FD), it is expected that the accuracy of discrimination would
decrease. Therefore, it is essential to clarify that the capability demonstrated is specific to the
binary distinction between these two groups.
Discussion of DGBI:
DGBI is mentioned in the abstract and introduction but not discussed. You indicate that the
sample is divided into three clusters, with only two and three being associated with DGBI. Is
it your understanding that cluster one includes a group not related to DGBI? Please elaborate
on your thoughts regarding this.
Clarification of abbreviations:
What does ME stand for?
IBS subtypes within the clusters:
Due to the small sample size, you have not factored IBS subtypes into the analysis. However,
what were the proportions of IBS-C, IBS-D, and IBS-M within the three identified clusters?
Recommendation for introduction:
It would be beneficial to summarize the overall findings and recent reports on IBS and the use
of machine learning and AI in the introduction. Discuss how AI has been applied to determine
treatment approaches and diagnose IBS with improved efficacy through colonic endoscopy
image analysis. Have there been any reports on clustering IBS patients using machine learning?
If so, how does your work differ?
Citation of relevant literature:
Given that there are publications on diagnosing and classifying IBS using machine learning, it
would be appropriate to reference how your findings differ from these existing studies.
Noman Haleem et al., Open Res Eur, 2023 Jan 27:3:19.
Elahe Mousavi et al., Sci Rep, 2023 Oct 28;13(1):18483.
Kazuhisa Tabata et al., Published: February 17, 2023, https://doi.org/10.1371/
journal.pdig.0000058.
Tarkan Karakan et al. Gut Microbes. 2022 Jan-Dec;14(1):2138672.
Review for 10.1186/s12876-024-03355-z (2024)

Title: Decoding IBS: A Machine Learning Approach to Psychological Distress and Gut-Brain
Interaction
Version: 1 Date: 04 Jul 2024
Reviewer:  Hanna-Jairala Ignacio
Reviewer's report:
Great job. I think that is going to be an important reference for this topic.
Review for 10.1186/s12876-024-03370-0 (2024)

Title: Lymphangiogenesis in the Liver of Biliary Atresia
Version: 0 Date: 28 Apr 2024
Reviewer's report:
The authors showed some positive data, together with more negative data. But as a paper more
related to clinic, it gives some guidance.
1. Please clarify the method to define the portal area.
2. The number of LVs per unit portal area (/mm2) and the number of Ly0 per unit portal area
(/mm2) in control liver disease group are much higher than that in BA group. It is interesting,
please discuss it more.
Review for 10.1186/s12876-024-03370-0 (2024)

Title: Lymphangiogenesis in the Liver of Biliary Atresia
Version: 0 Date: 14 May 2024
Reviewer's report:
1, In the background section, it would be beneficial to include more information about BA and
human age, as well as LVs in other diseases.
2, At the end of the background section, it appears that the relationship between LVs and PV
is an important aspect of this study, but the final data shows no correlation. The "Conclusions"
section does not mention PV. Therefore, consider either rewording the aim section or adding
more information about the potential reasons for the lack of correlation between LV and PV.
3, In Figures 2 and 3, it might be better to include the actual data value points over the box plots.
Review for 10.1186/s12876-024-03370-0 (2024)

Title: Lymphangiogenesis in the Liver of Biliary Atresia
Version: 2 Date: 27 Jul 2024
Reviewer's report:
After revision, the current manuscript contains more detailed background content, improved
logical clarity throughout, and a more comprehensive analysis of the results in the discussion
and conclusion sections. It is now an acceptable and publishable paper.
Review for 10.1186/s12876-024-03346-0 (2024)

Title: ncRNA-mediated SOX4 overexpression correlates with unfavorable outcomes and
immune infiltration in hepatocellular carcinoma
Version: 2 Date: 03 Oct 2023
Reviewer's report:
In their article, Li and colleagues analysed the correlation between SOX4 expression in HCC
and tumor immunity using data from The Cancer Genome Atlas and UALCAN databases.
Additionally, the authors correlate SOX4 expression, cancer immune characteristics, and
infiltrated immune cell gene marker sets in patients with HCC using data from the Tumor
Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-
Immune System Interactions databases, together with an evaluation of SOX4 expression in HCC
tissues and the correlation of SOX4 expression with survival rate. Then, the authors identified
the MCM3AP-AS1/hsa-miR-204-5p axis as the most likely upstream ncRNA-related pathway
for SOX4 in HCC.
Despite it would be a quite interesting work that could possibly point out that ncRNA-mediated
upregulation of SOX4  correlates with the immune infiltration level and poor prognosis in HCC,
there several crucial points that need to be addressed and some clarified before the manuscript
can be further considered for publication.
- A first general concern focuses on the fact that there is no experimental validation for the
findings emerging from the in-silico bioinformatics analyses reported along the manuscript.
- Starting from Fig. 1, in particular panel B-F, it is clear that there is a difference in SOX4 mRNA
expression level between normal and tumor specimens. But what about protein expression level
in the same experimental condition?
- In Fig. 2 the authors confirm at gene expression level the over expression of SOX4, however
any experimental validation using SOX4 over expression or silencing has been conducted in the
cellular models available in the manuscript to further validate the in-silico findings. This is a
crucial aspect that need to be addressed.
- The same applies for the upstream regulation analyses showed in Fig. 7, that identified
mir-204-5p as the most regulatory SOX4 miRNA. Mimics and Antagomir experiments are
needed here before the authors could sustain their hypothesis. A similar experimental approach
is needed for the MCM3AP-AS1.
-  There are some typos within the text that need to be corrected.
Review for 10.1186/s12876-024-03346-0 (2024)

Title: ncRNA-mediated SOX4 overexpression correlates with unfavorable outcomes and
immune infiltration in hepatocellular carcinoma
Version: 3 Date: 25 Jun 2024
Reviewer's report:
Despite the limitations due to experimental validation lack, the authors have addressed with
additional bioinformatic analyses and literature based confirmations most of my concerns , thus
the manuscript can be now considered suitable for publication