JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/s12876-024-03469-4 (2024)

Title: Title#Construction of a Combined Prognostic Model for Pancreatic Ductal
Adenocarcinoma Based on Deep Learning and Digital Pathology Images
Version: 4 Date: 12 Sep 2024
Reviewer's report:
It is a interesting study where authors use a multimodality deep learning model to predict the
prognosis of PDAC. But here are some questions.
1. When extracting the features of pathological images, how did the author deal with parts
that did not contain lesions? When a lesion divided into several patches, how to deal with this
situation?
2. The details of transfer learning should be included. For example, whether forzen the output
layers.
3. Compare to cox model, a machine learning can improve the performance of  multimodality
model.  Maybe you can refer to this research: The Development of a Prediction Model Based on
Random Survival Forest for the Postoperative Prognosis of Pancreatic Cancer: A SEER-Based
Study.
Review for 10.1186/s12876-024-03407-4 (2024)

Title: ICG-r15 Predicts Esophageal Varices in Compensated Liver Cirrhosis: A Noninvasive
Approach
Version: 0 Date: 11 Mar 2024
Reviewer's report:
This is a nice retrospective work by Xu Han and colleagues, which evaluates non-invasive
methods to detect high-risk esophageal varices in patients with compensated cirrhosis. Among
the methods evaluated, ICG-r15 appears to determine with good accuracy the presence of high-
risk esophageal varices in patients with compensated liver cirrhosis.
The results of the study show that measuring ICG-r15 can be a simple and quick tool for
evaluating portal hypertension in patients with liver cirrhosis.
However, I have some considerations:
I would like to know if the ICG measurement is performed routinely in all patients who undergo
upper digestive endoscopy, if so, this information should be written in the manuscript;
The ICG-r15 measurement was performed on the same day as the upper digestive endoscopy;
It is described that the sensitivity is 0.849 and the specificity is 0.662, but, in table 3, it is written
that the sensitivity is 0.662 and the specificity is 0.849 for ICG-r15. Please review the correct
information;
Still in table 3, the specificity and sensitivity are not in percentages as reported;
Over the 3-year period, how many patients were evaluated for the study and how many were
excluded.
Review for 10.1186/s12876-024-03407-4 (2024)

Title: ICG-r15 Predicts Esophageal Varices in Compensated Liver Cirrhosis: A Noninvasive
Approach
Version: 1 Date: 13 May 2024
Reviewer's report:
I suggest authors to answer the reveiwers' comments point by point. It is not  acceptable to
essentially present the same manuscript without answering the requests/comments.
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 2 Date: 26 Sep 2024
Reviewer:  Arthur de Sá Ferreira
Reviewer's report:
Comments
This manuscript reports an observational study investigating the effects of body posture (supine,
seated, upright) on liver stiffness in people with chronic liver disease and healthy subjects.
The study's rationale is well-posed, suggesting body posture may be a confounding factor
in estimating liver stiffness. Procedures seem sufficiently described to allow replication and
adequately used randomization of positions and blinding of examiners where possible. Statistical
analysis is adequate to the study’s aim and procedures. As recommended, results are reported
using point data, group summary, and distributions. Discussion section covers the clinical
implications and limitations/strengths of this study. I have only a few minor comments for the
authors to consider.
Minor comments
1. Study population. Please report what software was used for sample size determination, it is
important to give the authors credit. Based on the reporting I assume it was G*Power.
2. Figure 5. Consider presenting these results as in Figure 3.
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 2 Date: 30 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Abstract Numerical values belong to the results Were examinations performed in a random
way in diferent posturesor in a standard sequence ? Because liver stiffness is influence by
blood congestion and fat accumulation was any correction performed or since every patient
was a self-control correction was not needed? Numerical values apart from p values should
be provided in the results section Methods Were they any inclusion or exclusion criteria Like
age or presence of commorbidities Clinical and demographic parameters evaluated should be
reported and defined more data should be given about swear wave and transient elastography
performance Because liver stiffness is influence by blood congestion and fat accumulation was
any correction performed or since every patient was a self-control correction was not needed?
A correction is neccessary based in CAP value and echocardiogram Statistics A univariated
and multivariated analysis of LSM depending on demographic and clinical data might be useful
Representative pictures could be provided
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 3 Date: 15 Oct 2024
Reviewer:  Arthur de Sá Ferreira
Reviewer's report:
Thank you for the opportunity to discuss the findings of your research. All my comments were
well addressed. I have no new comments.
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 3 Date: 15 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
Methods Underlined comorbidities should be defined (eg DM) Otherwise the document seems
OK
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 4 Date: 18 Oct 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
I think authors have applied all requested changes Thus the document is ready for publication
Review for 10.1186/s12876-024-03473-8 (2024)

Title: Body Posture Can Modulate Liver Stiffness Measured by Transient Elastography: A
Prospective Observational Study
Version: 4 Date: 18 Oct 2024
Reviewer:  Arthur de Sá Ferreira
Reviewer's report:
All my comments were addressed in the previous review. I have no new comments.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 2 Date: 17 Aug 2024
Reviewer's report:
Thank you for the opportunity to review this manuscript. Overall, this is a well-conducted
retrospective cohort study examining the association between triglyceride-to-HDL cholesterol
ratio (TG/HDL-C) and risk of developing non-alcoholic fatty liver disease (NAFLD) in a large
Chinese population. The study has several strengths, including the large sample size, long
follow-up period, and thorough statistical analyses. However, there are a few areas that could
be improved to strengthen the manuscript:
Title and Abstract:
1. The conclusion in the abstract slightly overstates the findings. Instead of stating that TG/HDL-
C "could be used as a noninvasive indicator," it should be rephrased to reflect that it "may have
potential as a noninvasive indicator," pending further validation.
Introduction:
1. The rationale for conducting this specific study could be strengthened by more clearly stating
how it addresses gaps in previous research.
2. would be helpful to explain why TG/HDL-C ratio was hypothesized as a marker of NAFLD.
3. A more explicit identification of the aim of the study would be ideal.
Materials and Methods:
1. It is interesting that 2018 guidelines were used to diagnose NAFLD via ultrasound. Prior to
these updates were there no reported cases of NAFLD?
2. The justification for the specific TG/HDL-C ratio cutoffs used for quartiles could be explained.
Discussion:
1. Thorough discussion of the subgroup analysis results.
2. Consideration of potential mechanisms linking TG/HDL-C to NAFLD risk.
3. The generalizability of the findings to other populations should be discussed.
4. The potential clinical implications of the findings could be elaborated upon.
Conclusion:
The conclusion summarizes the main findings appropriately. However:
1. As in the abstract, the language regarding the potential use of TG/HDL-C as a clinical indicator
should be slightly tempered. Ex. The results suggest ……..
2. A brief statement on future research directions would be valuable.
Overall, this is a well-conducted study with important findings. Addressing these minor points
would further strengthen an already solid manuscript.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 2 Date: 22 Aug 2024
Reviewer:  George Sfikas
Reviewer's report:
An excellent and thorough analysis of all the data concerning a large sample of subjects with
Metabolic-associated fatty liver disease ( MAFLD). The idea to use a very common and easily
measurable predictive factor is simple and brilianr  at the same time. The anthropometric,
biochemical, epidemiological and imaging data verified the significance and the applicability
of this extremely  useful tool for diagnostic and predictive purposes. An excellent work. I only
recommend the use of the term MAFLD instead of NAFLD as more appropriate.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 4 Date: 28 Sep 2024
Reviewer's report:
Thank you for your revised manuscript. You have adequately addressed the reviewer's concerns.
I believe this revised version is acceptable for publication.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 4 Date: 02 Oct 2024
Reviewer:  George Sfikas
Reviewer's report:
An excellent and thorough analysis of all the data concerning a large sample of subjects with
Metabolic-associated fatty liver disease ( MAFLD). The idea to use a very common and easily
measurable predictive factor is simple and brilianr  at the same time. The anthropometric,
biochemical, epidemiological and imaging data verified the significance and the applicability
of this extremely  useful tool for diagnostic and predictive purposes. An excellent work. I only
recommend the use of the term MAFLD instead of NAFLD as more appropriate.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 5 Date: 18 Oct 2024
Reviewer's report:
I had already endorsed publication based on my prior review. I believe the authors have
adequately responded to all concerns  and addressed them in the revised manuscript
appropriately.
Review for 10.1186/s12876-024-03471-w (2024)

Title: Association between the triglyceride-to-high-density lipoprotein cholesterol ratio and the
incidence of metabolic dysfunction-associated fatty liver disease: A retrospective cohort study
Version: 5 Date: 20 Oct 2024
Reviewer's report:
THIS STUDY IS OF SIMPLE innovative APPROACH TO DEFINE THE RISK OF MAFLD
with great clinical impact ,I congratulate the authors for their effort and I think it will deserve
publication .
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 2 Date: 27 Jul 2024
Reviewer's report:
This is a very well written research. the objectives were clear and the data analysis was objective.
The results of the study reflect the burden of inflammatory bowel disease on the lives of patients
with it.
Retrospective data collected from medical records are a weak point of the study, as they may
contain inaccuracies or be incomplete; in addition to the reference center bias that tends to
produce better results when compared to other real-life studies.
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 2 Date: 02 Aug 2024
Reviewer:  Lucian Negreanu
Reviewer's report:
This is a single center experience with adherence to Ifx therapy in IMID.
Article is well written, comprehensive discussion and good motivation of the results.(patient
less adherent most frequently due to difficulty to arrive at the perfusion point).
We have the results at one year with very good adherence especially for rheumatology and
dermatology.
It can be an interesting experience for physicians in their decision to choose the therapy.
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 2 Date: 15 Aug 2024
Reviewer's report:
I think the study is well designed with interesting conclusions. The problem of compliance
with intravenous therapy is certainly linked to good education and involvement of patients in
treatment. Obviously the distance from medical centers has an impact, but this is certainly related
to the various local economic and political situations. Therefore the data emerging from this
study are data not applicable to other situations
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 2 Date: 15 Aug 2024
Reviewer:  Abel Quaresma
Reviewer's report:
Q1: In the abstract, it is stated: "Individuals with inflammatory bowel diseases had a 39.1%
higher risk of non-adherence to treatment compared with other patients." I suggest adding "in
our sample" because this result was found in the study sample and does not represent a general
data from the literature. Additionally, mentioning that this finding was significant (p < 0.025)
would enhance the abstract’s clarity.
Q2: The methods section notes that patients who did not respond to treatment were excluded
from the sample. This information should be included in the abstract, as it is well known
that a positive treatment response influences adherence. When only patients who responded to
treatment are evaluated, higher adherence rates are expected compared to if these patients were
included in the total sample. This is an important detail that should be included in the abstract.
Q3: In the conclusion, it is written: "As the study site is a reference unit with multidisciplinary
care and continuous monitoring of effectiveness, safety, and treatment adherence, the welcoming
and good degree of communication between professionals and patients may have contributed
to the high adherence rates." These details seem more relevant to the discussion than to the
conclusion. It would be clearer to conclude that: "Reception and a good level of communication
between professionals and patients can contribute to higher adherence rates."
Q4: In the references, two different fonts (Times New Roman and Arial) and two different
citation styles were found, which should be standardized (citations 2 and 3).
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 3 Date: 31 Aug 2024
Reviewer's report:
Trabalho bem escrito, claro, com resultados interessantes , apenas o viés de centro de referência,
que não pode ser sanado, porém não comprometendo a solidez dos resultados
Review for 10.1186/s12876-024-03455-w (2024)

Title: Adherence to infliximab treatment in patients with immune-mediated inflammatory
diseases from a Referral Center in Brazil: A cohort study
Version: 4 Date: 30 Sep 2024
Reviewer's report:
Well-designed study, with clear objectives and interesting results. The reference center bias
persists, but it is a factor that cannot be changed in the present context. Congratulations on the
excellent work.
Review for 10.1186/s12876-024-03461-y (2024)

Title: Causal relationship between Hypothyroidism and Ulcerative Colitis: a Bidirectional
Mendelian Randomization study
Version: 3 Date: 15 Aug 2024
Reviewer's report:
1---Your use of bidirectional Mendelian randomization is commendable. However, there may be
opportunities to strengthen the approach, perhaps by considering additional sensitivity analyses
or methods to validate your genetic instruments.
2---While your statistical approach is sound, providing more detail on your methods, particularly
for addressing potential pleiotropy, could enhance the reproducibility of your work.
3---it's exciting to consider the potential clinical implications of your work, it might be helpful
to temper these discussions with acknowledgment of the need for further research to confirm
and extend your findings.
4---Consider elaborating on how hypothyroidism and ulcerative colitis were defined in your
study. Clearer definitions could enhance the reliability of your outcome measures.
Review for 10.1186/s12876-024-03461-y (2024)

Title: Causal relationship between Hypothyroidism and Ulcerative Colitis: a Bidirectional
Mendelian Randomization study
Version: 3 Date: 22 Aug 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
Dear Authors, please address the following points below:
- Addressing potential pleiotropy, could significantly enhance the reproducibility and robustness
of your work. This could involve detailing the specific statistical techniques used, the rationale
behind their selection, and how potential sources of bias were accounted for.
-To further fortify the robustness of your method, it is advisable to consider conducting
additional sensitivity analyses and employing methods to validate the genetic instruments,
thereby ensuring the reliability and accuracy of your findings.
-Enhanced clarity and granularity on how hypothyroidism and ulcerative colitis were precisely
defined could significantly bolster the reliability and accuracy of your outcome measures, thus
fortifying the robustness of your study.
Review for 10.1186/s12876-024-03461-y (2024)

Title: Causal relationship between Hypothyroidism and Ulcerative Colitis: a Bidirectional
Mendelian Randomization study
Version: 4 Date: 10 Sep 2024
Reviewer:  Anwar Ashraf Abouelnasr
Reviewer's report:
changes are done , accepted for publication
Review for 10.1186/s12876-024-03461-y (2024)

Title: Causal relationship between Hypothyroidism and Ulcerative Colitis: a Bidirectional
Mendelian Randomization study
Version: 4 Date: 16 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
The text seem very interesting It would be great if authors could separate cases of thyroiditis
from the whole population of patients with hypothyroidism in order to minimize eterogenicity
They also should provide numerical values for the every significant autoimmunity marker in
results text not only in the table
Review for 10.1186/s12876-024-03461-y (2024)

Title: Causal relationship between Hypothyroidism and Ulcerative Colitis: a Bidirectional
Mendelian Randomization study
Version: 5 Date: 28 Sep 2024
Reviewer:  Panagiotis Tsibouris
Reviewer's report:
I think changes are adequate Thus I congratulate the authors and suggest that the document is
ready for publication
Review for 10.1186/s12876-024-03470-x (2024)

Title: Sleep disturbance in patients with cirrhosis and transjugular intrahepatic portosystemic
shunt
Version: 3 Date: 25 Aug 2024
Reviewer:  Narayan Dharel
Reviewer's report:
Zhao et al reports on SD among patients with  cirrhosis post TIPS in a small nonrandomized
single center study among 119 patients who underwent TIPS between August 2018 and
November 2019 in West China Hospital.
They used the standardized PSQI to assess sleep quality, and West Haven Criteria to define HE.
They assessed these patients 1 month prior to TIPS and then at undefined time points ? post TIPS
up to 12 months after TIPS. Some patients were followed for up to 24 months per their report.
They excluded 46 patients who reported SD symptoms prior to TIPS. Among 73 post TIPS
patients who did not have SD symptoms 1 month prior to TIPS, 19 developed SD symptoms
post TIPS with median onset at day 67. Of those 73 patients, 20 also developed symptoms of
OHE and 28 showed symptoms of MHE.  They reported no patients were lost to median follow
up of 18mo (12-24 m range).
They do not clearly state how often did they check for SD post TIPS, e.g.? every month or one
time? or they just followed the charts to see if patients were diagnosed w SD.
It does not seem they tried to correlate as to what could have triggered SD post TIPS. Ammonia
was in the past reported to correlate with SD. Did they check ammonia level ? If show, was there
any correlation? It would have been nice to see if a biochemical marker would correlate with
SD, particularly because many patients who had SD spontaneously improved. Wonder if they
improved because their MHE or ammonia improved with lactulose?
How often they assessed SD post TIPS? At what interval? Needs further clarification.
Did they check ammonia levels and was there any correlation with SD?
What is their explanation of those 9 of 13 patients whose SD improved without any intervention?
Minor comments:
TIPS needs to  be spelled out the first time it was mentioned at the first para of abstract,
background section.
Method does not specify at what points of time SD was assessed after TIPS
Not clear on what basis decisions were made to treat vs observe SD
Not mentioned if they tested Ammonia post TIPS and if it correlated
Table title will look better  on the top than at the bottoms.
Review for 10.1186/s12876-024-03470-x (2024)

Title: Sleep disturbance in patients with cirrhosis and transjugular intrahepatic portosystemic
shunt
Version: 4 Date: 21 Sep 2024
Reviewer:  Narayan Dharel
Reviewer's report:
I appreciate the authors taking time to respond and rewrite the report incorporating the comments
that were asked. I am comfortable with the explanation about ammonia and about how they
elected to intervene versus monitor SD post  TIPS. I am happy to see that authors have
incorporated that not having tested  the pre-and post intervention ammonia levels in the
limitation section. At this point, I have no further comments. Thank you
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 2 Date: 04 Jun 2024
Reviewer:  Ahmad M. Sultan
Reviewer's report:
the topic is not widely available for researchers, the idea is promising, however there are some
comments;
Major comments:
1 - The abstract is not clear, needed to read it multiple times
2- as regards the METHODS section:
-1  surgery approaches sub title is confusing - better changed to procedure approaches
-2  the timing of the procedure is not specified clearly to be after 6-8 weeks of the index surgery
-3 was these patients discharged and come back on a scheduled date ?
-4 was the t-tube closed prior to discharge ? and on follow up how many cases showed symptoms
or laboratory abnormalities because of the retained stones? or those patients were excluded?
( you mentioned incarcerated stones )
-5 what was the interval between T tube and subsequent choledochoscopy?
-7 were all cases successful for choledochoscopic extraction? was there any incomplete
procedures
3- the RESULTS section:
-1 table 1 shows previous LC, what does it refer to?
-2 the false negative rate for TTC was found to be 11 cases out of 249 case , as I understand
from table 2 ,  this is not 27.5% . please revise.
-3 the paragraph describing the choledochscopy is not clear and needs rewriting.
-4 there is no description of the management following failed cholechocoscopic extraction (CE)
-5 with the results of no significant difference between the 2 methods, I would like your comment
on the cost, the quality of life of these patients.
4-the Discussion section:
-1 too long
-2 did not discuss your causes of false positive TTC aside from 3 cases with bubbles
-3 the paragraph on 242 is irrelevant to the study design. however, the bile turbidity reported in
this series may point to the prolonged placement of the T tube and its possible complications.
-4 with the results of no significant difference between the 2 methods, I would like you to
comment on the quality of life of these patients. as usually, T tube cholangiogram can be
performed after 2 weeks, if negative it is removed  and if positive we arrange for ERCP
extraction. this ends the patients' problems earlier than the proposed and recommended tech.
5-the CONCLUSION
I think the conclusion is far from the results. adding choledoscopy did not prove statistically
significant difference. It provides advantages as mentioned.
please revise the false negative rate of TTC.
minor comments:
- using angiography instead of cholangiography, needs attention
- line 204 comment on b, needs revision
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 2 Date: 01 Jul 2024
Reviewer's report:
Review
In this manuscript, the authors perform investigated the role of T-tube cholangiography
and choledochoscopy in residual calculi after biliary surgery. They found that T-tube
cholangiography and choledochoscopy after biliary surgery had a good performance to enhance
the diagnostic accuracy of residual stones.
I have a concern about the novelty of this study.
1. The procedure of simultaneous choledochotomy and subsequent T-tube drainage is not a
standard procedure for cholelithiasis these days. Considering that the endoscopic procedure is a
minimally invasive treatment, this study does not have a reasonable rationale.
2. Although the results showed no significant difference between the two methods, the authors
concluded that simultaneous performance of T-tube cholangiography and choledochoscopy after
biliary surgery is recommended to enhance the diagnostic accuracy of residual stones and reduce
the incidence of bile duct stone remnants. This is not logical.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 2 Date: 01 Jul 2024
Reviewer's report:
Good idea, but some points should be corrected
- The timing of both techniques regarding the surgical intervention is not clearly described. Did
you mean that both methods were performed in the same surgical intervention setting? If so,
how could you perform the choledochoscopy through a sinus tract that is not yet established?
- Furthermore, I cannot imagine how you could introduce the choledochoscope after T-tube
removal. Why could the reverse not be performed if the techniques are used in the surgical
setting?
- Where are your follow-up data and variables of interest to measure, as well as their description
in the method section?
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 3 Date: 21 Jul 2024
Reviewer:  Ahmad M. Sultan
Reviewer's report:
Dear authors,
thank you for the effort in editing the manuscript.
Now it is much more easier to follow and implement.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 3 Date: 23 Jul 2024
Reviewer's report:
I am disappointed that the authors did not change their manuscript to address all my comments.
1. They should mention their rationale in the Introduction including the drawback of EST and
the indication of T-tube drainage in their institution.
2. No tests are 100% correct. It is not scientific to say “Although choledochoscopy did
not demonstrate a statistically significant difference, T-tube cholangiography can yield false-
negative results. Consequently, it is not advisable to use a negative T-tube cholangiography
result as the sole basis for removing the T-tube. Without performing choledochoscopy in the
presence of false-negative results, there is a risk that residual bile duct stones may cause acute
pancreatitis, posing a serious threat to patient safety and health.”. They need to describe the pros
and cons of adding an invasive procedure such as choledochoscopy.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 3 Date: 23 Jul 2024
Reviewer's report:
This study compares the T-tube cholangiography and postoperative choledochoscopy in
detecting residual stones after common bile duct stone removal. Adding to the comments of the
reviewers 1 and 2,   I would like to  make some suggestions.
In this paper the authors claim that  choledochoscopy is  the reference  standard in detecting
residual stones compared to T-tube cholangiography. In this case I would like that authors would
present the sensitivity and specificity of choledochoscopy.
In the discussion the limitations of postoperative  choledochoscopy should be presented more
precisely; the long  time for the maturation of the sinus tract .
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 4 Date: 30 Aug 2024
Reviewer:  Mohamad Raafat
Reviewer's report:
Thank you for allowing me to review the manuscript entitled “Diagnostic value of T-tube
cholangiography and choledochoscopy in residual calculi after biliary surgery”
A great effort was made by the authors to follow and answers the reviewers’ comments.
However, I am not satisfied with repose to major comments especially points: 1, 2, 3, 4, 6, 9.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 5 Date: 17 Sep 2024
Reviewer's report:
Thanks for the authors for the great job improving the article. Despite of that, there are still some
concerns that I think should be addressed.
With kind regards.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 5 Date: 30 Sep 2024
Reviewer:  Ahmad M. Sultan
Reviewer's report:
I would like to express my appreciation to the authors and their efforts in revising the manuscript.
Many revisions and good responses that improved the manuscript and its conclusion. However,
the corresponding author should have revised  the final version to be sent for revision.
I think it is worth publishing.
Review for 10.1186/s12876-024-03474-7 (2024)

Title: Diagnostic value of T-tube cholangiography and choledochoscopy in residual calculi after
biliary surgery
Version: 6 Date: 16 Oct 2024
Reviewer's report:
Thanks to the authors for they efforts, the manuscript has been improved and I think it is ready
to publish.
Regarding this topic:
Authors Response: The authors explain that they focused on diagnostic concordance and that
the evaluation of sensitivity and specificity was intentionally not included. They will clarify this
in the Methods section.
My thoughts and suggestion: The response is valid in the context of the study's objective.
However, adding information about sensitivity and specificity could have provided more context
regarding the effectiveness of each method. The clarification in the Methods will help readers
understand the approach.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 2 Date: 31 Jul 2024
Reviewer:  Athanasia Papazafiropoulou
Reviewer's report:
It is an interesting manuscript. Authors succeed to present their data in a clear way adding
information to the existing literature. Therefore, I have no corrections to do and the manuscript
can be published unaltered.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 2 Date: 01 Aug 2024
Reviewer:  Patroklos Katafygiotis
Reviewer's report:
#There are several words that should be capitalized.
#There are different versions of the number of cases used.
#Paragraph 3.1 is confusing since we know that the control group has been selected because
they do not have a disease. Therefore it does not have DM2.
#There is no grade of dysplasia in cancer. I think you are referring to the grading of the tumour.
#The conclusion is not entirely correct unless the adjusted OR is also mentioned.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 2 Date: 01 Aug 2024
Reviewer's report:
• The authors have studied a very important aspect.
• The research work is really good.
• There are some suggestions for the authors.
• Use a uniform writing style, at some places authors have used Calibri, while at the other Times
writing style is used.
• The authors have grouped the age data into different categories e.g. 45-50, 50-55,
• Did the authors count the 50 years of age two times? shouldn’t it be like 45-50, 51-55?
• Mention the corresponding author separately at the end of all authors’ affiliations.
• Divide the abstract into sections.
• Add keywords.
• In results (3), check the mean (± SD) age of the participants again, as it is mentioned as 63.27
(± 9.80) months.
• Follow the Journal format.
• There are a few grammatical mistakes, recheck the paper.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 3 Date: 20 Aug 2024
Reviewer:  Patroklos Katafygiotis
Reviewer's report:
#The paper presents a very interesting topic that has not been studied enough and the conclusions
to date are chaotic.
#I think there are still issues with the style of writing.
#The phrase "chance of contracting" does not fit the text in all the places it appears.
#Also the phrases "Patients from the same time" , "Inconclusive proof of CRC" needs to be
changed.
#The phrase "Genetic predisposition, IBD, and history of cancer that has metastasized to the
colon or rectum are considered confounding factors as exclusion criteria."  is partly a repetition.
#In paragraph 3.1 what is meant by "had more cases". In the same paragraph the phrase "insulin
consumption" is wrong.
#I think that the Discussion has a lot of room for improvement.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 3 Date: 22 Aug 2024
Reviewer:  Athanasia Papazafiropoulou
Reviewer's report:
It is an interesting manuscript. Authors succeed to present their data in a clear way adding
information to the existing literature. Therefore, I have no corrections to do and the manuscript
can be published unaltered.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 3 Date: 26 Aug 2024
Reviewer's report:
Thank you for addressing all of my previous comments in the revised version. I am pleased with
the revisions and believe the manuscript is now suitable for publication.
However, I have one minor suggestion: the phrase "the chance of contracting" used in reference
to cancer risk is not typically found in published literature. I recommend revising this to "CRC
risk" or a similar term that more accurately reflects the context.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 3 Date: 28 Aug 2024
Reviewer:  Panagiotis Halvatsiotis
Reviewer's report:
Congratulations for your work and your efforts to support with your data advanced knowledge
regarding possible burden of the antidiabetic treatment on colon cancer development. We
should always encourage investigators who orchestrate efforts and ideas to provide the
scientific community with new and significant information. I personally acknowledge that you
have contributed laboriously to define your objectives, but I have serious worries about the
methodology followed and the interpretation of your results. Noteworthy, the extensive analysis
of your data provided valuable information but there are some points that I would like to
comment on, and your response will be appreciated.
Comment 1
There is concrete knowledge that obesity is strongly related with both type 2 diabetes mellitus
and colon cancer occurrence. I am wondering if there are available data (BMI or WHR) of your
participants in order your results to be normalized for this parameter. Otherwise, you have to
commend about in the discussion section and to study limitations
Comment 2
You are referring several times in your manuscript the hypothesis that hyperinsulinemia may
contributes the tumor growth and I am also wondering if you can extract from the patient files
their fasting insulin levels or to calculate their HOMA Test indices in order to statistically
normalize your results to these  parameters.
Comment 3
Your study population seems to be older that the controls, therefore it would be advisable to
statistically evaluate and the median age of the participants, while there is an aging effect on
carcinogenesis.
Comment 4
According to Table 1 the cancer patients on sulfonylurea are  only 41 and 21 in the control group
respectively. Due to the very low participation of the studied criterion please inform us about
the power of the study.
Comment 5
In the conclusion section of your manuscript, you state that "Enhance screening for CRC may
be advisable, especially in sulfonylurea - treated patients....". I believe this statement should not
appear in your conclusion while you did not observe such a clear statistical  determination. This
statement should be incorporated in the discussion section where you should discuss possible
reasons for the different results between the adjusted and unadjusted model.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 4 Date: 14 Sep 2024
Reviewer:  Athanasia Papazafiropoulou
Reviewer's report:
It is an interesting manuscript. Authors succeed to present their data in a clear way adding
information to the existing literature. Therefore, I have no corrections to do and the manuscript
can be published unaltered.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 4 Date: 16 Sep 2024
Reviewer:  Patroklos Katafygiotis
Reviewer's report:
I hope you will continue the research by collecting more data on treatment, dosage of drugs used
in T2D and the probability of developing CRC.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 5 Date: 03 Oct 2024
Reviewer's report:
I appreciate the authors for their revisions to the paper. However, I feel that there are still some
areas that could be further refined.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 6 Date: 11 Oct 2024
Reviewer's report:
I would like to thank the authors once again for responding to the relevant comments.
However, in the previous two reviews, the comments regarding the sample size have not been
adequately addressed. I recommend that the authors consult with an analyst and provide a logical
justification for the sample size used. Since it is not possible to go back, I suggest they at least
calculate and report the power for their analyses. Simply presenting an 80% power is insufficient;
a thorough statistical analysis is required.
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 6 Date: 16 Oct 2024
Reviewer:  Ehab Elmongui
Reviewer's report:
Dear Author,
The sample size calculation should be clearly outstated in the methods section including all the
parameters used in the formula for case-control studies:
1- Odds Ratio (OR): The estimated effect size you aim to detect between the cases and controls
regarding the exposure (e.g., T2D or sulfonylurea use). This value could be based on previous
studies, pilot data, or a a defined value assuming a medium effect size.
2- Prevalence of Exposure in Controls (p0): The proportion of control subjects who are exposed
to the risk factor (e.g., having T2D or using sulfonylureas)
3- Desired Power (1 – #)
4- Significance Level (#)
5- Ratio of Controls to Cases (m)
6- Adjustment for Multiple Covariates: If multivariate analysis is planned, adjustments might
be needed to maintain adequate power considering potential confounders. For instance you may
use the Rule of Thumb commonly used in regression analyses to have at least 10 events per
variable (EPV). This means you should aim for at least 10 cases for each confounder you plan
to include in the model.
Best Regards
Ehab Elmongui, BPharmSC, PharmD, MSc, PhD(c) (Medical Statistics)
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 7 Date: 17 Oct 2024
Reviewer:  Ehab Elmongui
Reviewer's report:
Dear author,
You still need to formulate a paragraph with the following heading: 2.3. Sample size calculation
(before the Statistical analysis). In this paragraph you need to mention the software you used in
calculation and describe the parameters and their values that you used to reach the sample size
to enhance the reproducibility of the study
Review for 10.1186/s12876-024-03477-4 (2024)

Title: Effect of Diabetes Mellitus Type 2 and Sulfonylurea on Colorectal Cancer Development:
A Case-Control Study
Version: 8 Date: 21 Oct 2024
Reviewer:  Ehab Elmongui
Reviewer's report:
The author has addressed my concerns. I  have no further comments
Review for 10.1186/s12876-024-03453-y (2024)

Title: METABOLOMIC ANALYSIS TO PREDICT THE ONSET AND SEVERITY OF
NECROTIZING ENTEROCOLITIS
Version: 1 Date: 26 Aug 2024
Reviewer's report:
Thanks for inviting me to review this manuscript. A prospective study was conducted and urine
from preterm infants was longitudinally collected at birth (<48 hours), 14 and 28 days. Neonates
were followed for their development of NEC, SIP, or other GI conditions and compared to those
of matched healthy controls. Urine samples were then investigated by untargeted metabolomic
analysis based on mass-spectrometry afterwards. The conclusions demonstrated the urinary
metabolome is closely associated with underlying gastrointestinal disease beginning very early
in life. Furthermore, urinary metabolic features characterize NEC patients vs healthy controls
from birth until 28 days of life. Finally, untargeted metabolomics can identify patients who
will develop surgical NEC as early as birth, with a potential role for impaired fatty acid and
acylcarnitine metabolism.
This manuscript is interesting. However it remains some major concerns#
1. The inclusion criteria of the study were “All infants who were admitted to the NICU and who
were born at <34+0 gestational weeks (GW) or who had congenital heart disease (CHD)”. So
just wondering why infants with CDH should be involved? Because CDH may be an isolated
factor associated with abnormal metabolism and result in bias of data analysis. In terms of
NEC diagnosis, infants with Bell stage I should be excluded, which is suspected NEC but not
confirmed NEC.
2. Is any previous studies or literatures support the current timing of urine collection? In addition,
it is not clear the relationship between the timing of urine collection and NEC onset since the
characteristic of metabolism is time dependent.
3. Did authors compare the metabolic analysis results among plasma, urine and fecal samples
from each patient to find out which is the best resource to predict NEC onset and severity?
4. Multiple factors contribute to NEC onset and progression. Did authors try to combine the
metabolic analysis results with other NEC related clinical parameters for improving the accuracy
of NEC predictions?
Review for 10.1186/s12876-024-03465-8 (2024)

Title: Low geriatric nutritional risk index is associated with osteoporosis and fracture risk in
patients with chronic liver disease: a cross-sectional study
Version: 0 Date: 24 Sep 2024
Reviewer's report:
This study investigates the relationship between the geriatric nutritional risk index (GNRI),
osteoporosis, and FRAX in patients with chronic liver disease, and is considered to be a useful
study. However, there are clearly insufficient explanations and some concerns.
Major
1.      Background p4#Line87-88
The aim of this study was to investigate the relationship between GNRI, osteoporosis, and
FRAX-derived fracture risk in patients with CLD. However, the current background does not
fully explain why it is necessary to investigate the relationship between GNRI, osteoporosis,
and FRAX.
2.      Methods p4, Line92-94
The subjects of this study were 209 patients with CLD recruited from two hospitals. Subject
characteristics should be described in detail, such as whether they were inpatients or outpatients.
The goal of osteoporosis treatment is to reduce fractures. Also, FRAX is a risk predictor of
fracture. Therefore, the presence or absence of fractures and history of fractures is extremely
important in this study. It should be detailed in the patient background. Furthermore, it is
advisable to investigate not only history of fracture but also morphological fracture with respect
to the spine.
3.      Methods p4, Line96-99
The present study, the exclusion criteria were as follows: (1) alcoholic liver disease resulting
from heavy alcohol intake (>3 units/day), which causes severe The exclusion criteria were
as follows: (1) alcoholic liver disease resulting from heavy alcohol intake (>3 units/day),
which causes severe malnutrition and (2) patients with ascites, which causes weight gain
and overestimation of GNRI scores. The exclusion of 1 and 2 from the present study is
understandable. On the other hand, the relationship between 1 and 2 above and FRAX is also
interesting. It would be useful to know how much each increases the risk of fracture.
4.      P8, Line197-201
The authors' statistical analysis explained that the cutoff value of the GNRI for predicting
osteoporosis was 104.9. As described in the Methods, Bouillanne O et al.[15] classified the
GNRI risk categories into four: no risk (> 98), low risk (92 to # 98), intermediate risk (82 to <
92), and severe risk (< 82). Considering previous research, it is expected that there will be a very
large number of people with a GNRI below 104.9. What percentage of the subjects in this study
had a GNRI below 104.9 ? In addition, there was no discussion of the cutoff value calculated
from the ROC curve, and the authors should provide a detailed explanation of these results.
#. p8, Line210-222
Does a high FRAX mean a high history of fractures? Factors contributing to high FRAX should
be investigated. We believe that each of the survey items should be investigated and discussed.
In particular, a history of bone fractures should be investigated.
Minor
1.      Please indicate the units of the horizontal axis in Figure 3.