Reviewer ’s report  
 
Title: Histological, immunohistochemical and mRNA gene expression responses in coeliac  
disease patients challenged with gluten using PAXgene fixed paraffin -embedded duodenal  
biopsies  
 
Version: 0 Date: 26 Aug 2019  
 
Reviewer: Rizwan Ahamed  
 
Reviewer's report:  
 
I commend the authors for the detailed assessment of morphometric measurements of mucosal 
changes in coeliac patients. May I request clearing of a few queries?  
1. Was  assessment done for whether the patients developed any clinical symptoms following 
gluten challenge as it is well reported that they can occur as early as two weeks?  
2. I would like to know if serial measurements of antibodies like IgA antigliadin antibodies or 
IgA ttg antibodies were done subsequent to gluten challenge. If so, could there be any correlation 
between antibody titres and mo rphometric measures on biopsy.  
 
3. Was it possible to discern a cut off value for any morphometric parameter subs equent to 
gluten challenge that makes it significant?  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn  adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is rec ommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain  or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financially from the publication of this manuscript, either now or in the fut ure? 
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of  the manuscript?  
 
5. Do you have any other financial competing interests?   
 
6. Do you have any non -financial competing interests in relation to this paper?   
 
If you can answer no to all of the above, write 'I declare that I have  no competing interests' 
below. If your reply is yes to any, please give details below.  
 
i have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for public ation, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses. I agree for my report to be made available under an Open Access Creative Commons  
CC-BY license ( http://creativecommons.org/licenses/b y/4.0/ ). I understand that any comments  
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title: Histological, immunohistochemical and mRNA gene expression responses in coeliac  
disease patients challenged with gluten using PAXgene fixed paraffin -embedded duodenal  
biopsies  
 
Version: 0 Date: 26 Aug 2019  
 
Reviewer: Rizwan Ahamed  
 
Reviewer's report:  
 
I commend the authors for the detailed assessment of morphometric measurements of mucosal 
changes in coeliac patients. May I request clearing of a few queries?  
1. Was  assessment done for whether the patients developed any clinical symptoms following 
gluten challenge as it is well reported that they can occur as early as two weeks?  
2. I would like to know if serial measurements of antibodies like IgA antigliadin antibodies or 
IgA ttg antibodies were done subsequent to gluten challenge. If so, could there be any correlation 
between antibody titres and mo rphometric measures on biopsy.  
 
3. Was it possible to discern a cut off value for any morphometric parameter subs equent to 
gluten challenge that makes it significant?  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn  adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is rec ommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain  or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financially from the publication of this manuscript, either now or in the fut ure? 
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of  the manuscript?  
 
5. Do you have any other financial competing interests?   
 
6. Do you have any non -financial competing interests in relation to this paper?   
 
If you can answer no to all of the above, write 'I declare that I have  no competing interests' 
below. If your reply is yes to any, please give details below.  
 
i have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for public ation, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses. I agree for my report to be made available under an Open Access Creative Commons  
CC-BY license ( http://creativecommons.org/licenses/b y/4.0/ ). I understand that any comments  
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
Please review this paper.
user
Reviewer ’s report  
 
Title: Histological, immunohistochemical and mRNA gene expression responses in coeliac  
disease patients challenged with gluten using PAXgene fixed paraffin -embedded duodenal  
biopsies  
 
Version: 0 Date: 26 Aug 2019  
 
Reviewer: Rizwan Ahamed  
 
Reviewer's report:  
 
I commend the authors for the detailed assessment of morphometric measurements of mucosal 
changes in coeliac patients. May I request clearing of a few queries?  
1. Was  assessment done for whether the patients developed any clinical symptoms following 
gluten challenge as it is well reported that they can occur as early as two weeks?  
2. I would like to know if serial measurements of antibodies like IgA antigliadin antibodies or 
IgA ttg antibodies were done subsequent to gluten challenge. If so, could there be any correlation 
between antibody titres and mo rphometric measures on biopsy.  
 
3. Was it possible to discern a cut off value for any morphometric parameter subs equent to 
gluten challenge that makes it significant?  
 
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
Yes 
 
Does the work include the necessary controls?  
If not, please specify which controls are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn  adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Yes 
 
Are you able to assess any statistics in the manuscript or would you recommend an  
additional statistical review?  
If an additional statistical review is rec ommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain  or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financially from the publication of this manuscript, either now or in the fut ure? 
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organization that 
holds  or has applied for patents relating to the content of  the manuscript?  
 
5. Do you have any other financial competing interests?   
 
6. Do you have any non -financial competing interests in relation to this paper?   
 
If you can answer no to all of the above, write 'I declare that I have  no competing interests' 
below. If your reply is yes to any, please give details below.  
 
i have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for public ation, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses. I agree for my report to be made available under an Open Access Creative Commons  
CC-BY license ( http://creativecommons.org/licenses/b y/4.0/ ). I understand that any comments  
which I do not wish to be included in my named report can be included as confidential comments  
to the editors, which will not be published.  
 
I agree to the open peer review policy of the journal  
assistant