JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/1471-230X-9-9 (2009)

Reviewer's report
Title:Fatty acid composition of subcutaneous adipose tissue and gastric
mucosa: is there a relation with gastric ulceration?
Version: 3Date:15 December 2008
Reviewer: Caroline M Pond
Reviewer's report:
Variable style of citation of references (sometimes [1]. sometimtes .[1]) should be
standardized.
Everywhere use n-3, n-6 etc. and in italics
p 2 First sentence of abstract must mention 'dietary' and 'human'. Word order in
third sentence is very clumsy. Avoid the common mistake of implying that free
fatty acids are present - almost all were components extracted from larger lipids.
Last sentence of 'methods' should be clarified.
P 5. 'FAs that compose' change to 'FAs incorporated into' The many
one-sentence paragraphs should become one paragraph.
p 6 Use roman type for H. pylori in italicized headings.
P 8 'Adipose tissue FAs' change to 'FAs extracted from adipose tissue lipids'
P 10 gastric mucosal FAs' change to 'FAs extracted from the gastric mucosa
lipids'
p 20 fatty not tatty and rephrase the titles as above.
Embolden or add ** to data that are significantly different at p<0.05 in both
Tables to make them more easily identified.
Emphasise in the Conclusions and Abstract that all fatty acids that were
significantly different between groups of patients represent only a very small
fraction of the total extracted, perhaps by adding words like 'low-abundance' or
'minority'. Minor components are difficult to quantify accurately and may be
biologically insignificant as well.
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Three novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 1Date:27 July 2008
Reviewer: Songbin Fu
Reviewer's report:
In the manuscript of “Three novel mutations in the lactase gene (LCT) underlying
congenital lactase deficiency (CLD)”, the authors amplified and re-sequenced the
coding region of LCT in four CLD patients. By sequencing they identified three
novel mutations and predicted the function of these mutations by the
bioinformatics programs. It is an interesting paper and the main suggestions are
listed below:
Major compulsory revisions:
1. By sequencing, the authors found three novel mutations in four patients. In the
section of results, the authors pointed out that these mutations were not found in
the control subjects. However this was not listed in the methods, the authors
should introduce it in the methods.
2. Although the authors predicted the function of these mutations by
bioinformatics programs, it remained quite challenging to understand precisely
some statements in this paper. In addition, it is questionable if this functional
prediction was sufficiently compelling and novel. Importantly, I would strongly
suggest that the authors make a considerable effort to clean up the language,
such as the first paragraph in page 13. The authors should use shorter sentence
to express themselves effectively in the whole paper.
3. The mutations occurred in the upstream of LCT in the patients of the
adult-type hypolactasia mostly, I think the author should explain why they did not
sequence the upstream of LCT in the CLD patients.
Minor essential revisions
The table should be three-line formatted and the figure should be more attractive.
There are some errors in grammar usage throughout the manuscript. I urge the
authors to have it edited in detail by a native English speaker if at all possible.
Discretionary revisions
There should be more functional analysis about the three mutations in addition to
the prediction by the program.
The manuscript could be considered for publication after revision.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Not suitable for publication unless extensively edited
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Three novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 1Date:8 August 2008
Reviewer: Dallas M Swallow
Reviewer's report:
Major points
There are errors in the English. This is largely an issue of incorrect use of definite
and indefinite articles and pronouns.
It needs careful checking by an English speaking person. For example
throughout weight should be stated as ‘his weight’
Some sentences are unclear;
• Since the reports by Holzel et al, published data about CLD in continental
Europe and other parts of the world cannot be found.—please reword
• The Blosum62 score for substitution from serine to proline is -1 (range from -4
to +11; low to high probability of substitution).[17]
--this sentence makes no sense to me—(there is either a substitution or not).
• It is noteworthy, that in these two conditions the values of lactase activity are
partially overlapping despite of different underlying molecular mechanism.[2, 5-8,
10] Therefore, further studies are needed to explain the
phenotype-genotype-correlation in human lactase deficiencies.-
--this sentence seems not to make any sense. The difference from adult
hypolactasia is that these people had normal levels as small children
Minor (essential) points
Why is case 3 described as case 3 and 4?
Typographical error. Chance on page 12 line 4 should read change
The diagram of the gene with the active sites is inaccurately drawn—and not all
four are thought to be functional. The spacing between the two pairs should be
about 200 amino-acids. Please ammend
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Four novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 2Date:16 September 2008
Reviewer: Songbin Fu
Reviewer's report:
The authors had improved the manuscript in some aspects, while there are still
some questions.
Major Compulsory Revisions
1. There were five patients with CLD in their study, in which one was Italian; two
were Trukese while the authors did not introduce the origins of the other two
patients. There were two Trukese patients while there were no Trukese who
were involved in the control subjects.
2. In the section of results, the authors wrote the genotype of the parents of the
patient while they did not mention the parents in the methods section.
3. The results of case 2 were too obscure to understand.
4. Kuokkanen M had identified the mutations underlie CLD in Finnish families in
2006, why did the author say this study is the first report of CLD mutations in
patients living on continental Europe?
5. There are still so many long sentences, such as some in the section of
abstract and discussion, they are difficult for the reader to understand.
Minor Compulsory Revisions
There are some grammar errors in the manuscript, such as in the second line of
P4 “where” should be “which”.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Four novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 2Date:30 September 2008
Reviewer: Dallas M Swallow
Reviewer's report:
Minor essential revisions
1 Most of the errors in the English of the original text have been corrected,
though new ones have been introduced in the altered text (see below).
Abstract. ‘Found from one/another ’ should read ‘found in one/another’
Living on Continental Europe should read ‘in Continental Europe’—but would
‘outside Finland’ be more precise?
All four novel mutations were predicted—(page 14)—should read ‘All four novel
mutations were examined by—
Line 4 of that paragraph should read ‘of occurring’—not ‘to occur’
Later in that paragraph –were considered to be pathogenic
Page 6 ‘based on the disappeared symptoms’—should read ‘based on the
disappearance of symptoms’
2 Some sentences are still unclear and I suggest wordings below—if this is what
is meant;
• Since the original reports by Holzel et al (1,9), there has been a lack of
published data about CLD countries other than Finland.
• The Blosum62 score for substitution from serine to proline etc –showed that
there is a low probability of either substitution occurring in a functional protein.
3 I am still not happy with the following sentence which is potentially very
confusing to the reader
‘It is noteworthy, that in these two conditions the values of lactase activity are
partially overlapping in spite of their having different underlying molecular
mechanism.[2, 5-8, 10] Therefore, further studies are needed to explain the
phenotype-genotype-correlation in human lactase deficiencies.-‘
I suggest that you should say:
‘It is noteworthy that the values of lactase activity are partially overlapping with
those found in adults with hypolactasia, but the major difference is that as
children these people had high lactase activity like lactase persistent people
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Four novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 3Date:18 November 2008
Reviewer: Songbin Fu
Reviewer's report:
The manuscript had been improved according my comments, there is only a little
mistake in the manuscript, such as the gene name “LCT” should be italic.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-8 (2009)

Reviewer's report
Title:Four novel mutations in the lactase gene (LCT) underlying congenital
lactase deficiency (CLD)
Version: 3Date:25 November 2008
Reviewer: Dallas M Swallow
Reviewer's report:
Minor Essential Revisions
I am still not comfortable with the sentence about researching the difference
between the effect of deficiency in children and adults.
It seems plain to me that to be deficient in lactase as a baby will have much more
severe consequences than for an adult. Milk is so much more important in the
diet. There also will have been less time for the gut bacterial flora to adapt to
cope with lactose--as occurs in many adults. It would be preferable to turn this
sentence around into such a speculation.
The comment of reviewer 2 can be addressed as follows:
The English is still not perfect so suggest the following version:
""Deletion of five bases c.1692-1696delAGTGG in exon 6 leading to frameshift
mutation V565fsX567 (Table 1) was found in Finnish patient heterozygous for the
founder mutation Y1390X [10]. The deletion was located in a conserved region of
the LCT gene (Figure 1)and (see below). Unfortunately parental DNA was not
available for the analysis. The deletion was not found in 98 anonymous Finnish
blood donors.""
Also the authors do not make it clear that a truncated protein is predicted
--because I assume that this will be the consequence of the change of reading
frame. This should be stated.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Review for 10.1186/1471-230X-9-7 (2009)

Reviewer's report
Title:Susceptibility to intestinal infection and diarrhoea in Zambian adults in
relation to HIV status and CD4 count
Version: 1Date:3 July 2008
Reviewer: Gilbert R Kaufmann
Reviewer's report:
The study has been conducted in an interesting location, but the data need a lot
of clarification. The introduction is very interesting and informative. However, the
results section is very shortly described and incomplete. In particular, certain
comments from findings in the literature are mentioned in the introduction and in
the discussion, but no data are shown in the results section. What are the new
findings of this study? This needs to be worked out more clearly. Although
interesting, I believe that paper needs a major revision.
A table with the patient demographics is missing. How many patients were
children? Were children more susceptible to gastrointestinal infections?
It would be interesting to show CD4 T-cell count and the occurrence of
HIV-associated gastrointestinal infections.
What is the exact definition of diarrhoea? It would be important to mention the
definition in the Methods section.
Why is the prevalence of diarrhea not higher in HIV positive patients? I think that
this finding needs an explanation.
Why was serum retinol concentration measured?
What are the results of the questions asked by study nurses?
How many patients had co-infections?
58 patients were HIV seropositive at one time or another: what is meant by
‘another time’?
Certain non-pathogenic protozoa were less common in HIV-1 infected adults:
which ones and why?
What are the new results from this study? This needs to be explained in more
detail in the discussion section.
What is the percentage of co-infections in patients?
Overall 14 of 123 individuals had CD4 counts under 200 cells/mcL: why 123
individuals?
Are certain pathogens more common in this cohort than in European countries or
in the US?
In particular, it would be interesting to have an analysis of the age of the patient
and the occurrence of gastrointestinal infections (children vs adults).
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-7 (2009)

Reviewer's report
Title:Susceptibility to intestinal infection and diarrhoea in Zambian adults in
relation to HIV status and CD4 count
Version: 1Date:5 July 2008
Reviewer: Eric Houpt
Reviewer's report:
I reviewed the manuscript “Susceptibility to intestinal infection and diarrhoea in
Zambian adults in relation to HIV status and CD4 count.”
Overall the manuscript is important and should be published because its size is
excellent and it addresses important uncertainties in the etiology of
HIV-associated enteric disease in Africa. The weakness is the reliance on
microscopy (was this read by a single microscopist, or more than one?) without
antigen detection or PCR. The authors should also elaborate on details of enteric
culture (which media, etc) since this can skew results. It is also not mentioned
clearly how mixed infections were handled.
I would suggest softening the language, for instance “Certain parasites were less
frequently detected in more watery stools, confirming their lack of pathogenicity”
would be better stated “consistent with their lack of pathogenicity,” because it is
not possible to state with complete confidence that, for instance, I. butschlii can
never be a pathogen. Likewise, “Certain protozoa were less common in HIV
infected participants, probably due to self-treatment with antimicrobials” is
overstated and would be better termed “possibly,” since certainly the flora of an
HIV patient could be different for other reasons such as immunosuppression, and
use of antimicrobials was not described in this paper.
Finally, the high rate of recovery of Citrobacter rodentium should be discussed,
since this is not frequently reported.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-7 (2009)

Reviewer's report
Title:Susceptibility to intestinal infection and diarrhoea in Zambian adults in
relation to HIV status and CD4 count
Version: 2Date:1 September 2008
Reviewer: Gilbert R Kaufmann
Reviewer's report:
Thank you very much for your feedback regarding the revised manuscript. Most
of the comments were addressed appropriately and many points have been
clarified.
Review for 10.1186/1471-230X-9-7 (2009)

Reviewer's report
Title:Susceptibility to intestinal infection and diarrhoea in Zambian adults in
relation to HIV status and CD4 count
Version: 2Date:9 October 2008
Reviewer: Joanna Stewart
Reviewer's report:
The following is limited to a statistical review of the paper
Major
1. The data reported is clustered by individual as there are up to 36 data points
reported per person. The authors demonstrate that in fact there is a strong
cluster effect at least in occurence of disease but it appears many of the
statistical analyses quoted have not included a random person effect in the
model. Ignoring the person effect could possibly make the p values quoted quite
incorrect if in fact for example the relationship of infection and diarrhoea differs in
different people. All p values quoted should come from analyses including a
person effect.
2. What was the timing of the measure of infection compared to diarrhoea? Was
it the data from the end of the month with the diarrhoea being from during the
preceeding month? Is this timing issue going to cause a problem in that the
diarrhoea episode may have occured 4 weeks earlier? In fact an episode may
occur a couple of days after the stool collection but would be associated with the
infections a month later. At the very least the timing issue needs discussion
Minor
Table 3 in the third line of the paragraph 'Association between infection and
reported symptoms of diarrhoea' should be table 4
Discretionary
It is not clear why there are p values in table 1. Are these testing the difference of
each of the other factors by gender? If this is so they would seem unnecessary
are this would not seem relevant to the study. Simply displating the
demographics is all that is required.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-7 (2009)

Reviewer's report
Title:Susceptibility to intestinal infection and diarrhoea in Zambian adults in
relation to HIV status and CD4 count
Version: 3Date:3 December 2008
Reviewer: Joanna Stewart
Reviewer's report:
The authors have responded to my suggestions and I have no further comments
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-5 (2009)

Reviewer's report
Title:Studies on best positive predictors for sustained virologic response to
interferon alpha plus ribavirin therapy in Naive Chronic Hepatitis C Patients
Version: 2Date:10 June 2008
Reviewer: Claudio Tiribelli
Reviewer's report:
The author addressed my critiques in a acceptable way although the main
reservations I had still holds i.e. the nature of retrospective studies, the poor
selection of the patients and the largely confirmatory results. I understand that
the ethnicity is different from what previously reported in other larger and
prospective studies, but this is not enough to have this paper published as full
Ms. I suggest to shorten the text and submit as short report.
Level of interest: An article of limited interest
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I have no competing interests.
Review for 10.1186/1471-230X-9-5 (2009)

Reviewer's report
Title:Studies on best positive predictors for sustained virologic response to
interferon alpha plus ribavirin therapy in Naive Chronic Hepatitis C Patients
Version: 3Date:10 December 2008
Reviewer: Giuliano Ramadori
Reviewer's report:
Upon your request to comment on (i) whether the reviewer's concerns are
justified and thus whether they should preclude the publication of the paper and
(ii) the suitability of the paper for publication:
To my view, the comments of the reviewers are fully justified. However, both
minor and major issues were not seriously enough addressed by the authors.
For instance, there are still many spelling and grammar mistakes within the text.
The text might have been edited twice by a native speaker as stated by the
authors in their reply, but probably not by somebody with a sufficient scientific
background. Regarding that point, the authors should have made demand on a
more professional help.
Another point is the multitude of minor mistakes and inconsistencies which are
still not completely corrected. For instance, a mistake in Table 1 although stated
by the authors to be corrected (‘the percentage of genotype 3 females is not
18.78’) is still present.
Regarding major concerns, i.e. largely confirmatory results and the suggestion to
focus on the ethnic differences in responsiveness, have not been adequately
addressed.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Review for 10.1186/1471-230X-9-6 (2009)

Reviewer's report
Title:Tryptophan degradation in Irritable Bowel Syndrome: Evidence of
indoleamine 2,3-dioxygenase activation in a male cohort.
Version: 1Date:14 July 2008
Reviewer: Sylvie Bradesi
Reviewer's report:
Major Compulsory Revisions
In this study, the plasma levels of tryptophan and its metabolites were assessed
in a male IBS cohort (n=10) and healthy controls. Results indicate increased
levels of kynurenine and neopterin and decreased levels of kynurenic acid in IBS
patients compared with controls. These data are preliminary observations for the
study of the altered tryptophan metabolism in IBS. The limited data and
limitations of the study are clearly stated.
In the discussion, it is stated that plasma kynurenine levels and
kynurenine/trytophan ratio are higher in IBS patients "providing compelling
evidence of increased tryptophan breakdown". This statement in in contrast wih
the actual data showing that tryptophan levels are not altered in IBS patients.
Although, it is briefly discussed later in the discussion, conclusions should be
consistent throughout the mnuscript.
Minor Essential Revisions
the nature of the samples whould be indicated in the abstract
Discretionary Revisions
The authors indicate that interferon gama levels could not be reported because
they were below the limit of quantitation of the analysis method. Could a different
analysis method be used to assess the current samples for interferon gamma?
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-6 (2009)

Reviewer's report
Title:Tryptophan degradation in Irritable Bowel Syndrome: Evidence of
indoleamine 2,3-dioxygenase activation in a male cohort.
Version: 1Date:17 July 2008
Reviewer: Dietmar Fuchs
Reviewer's report:
This paper describes enhanced degradation of tryptophan in the peripheral blood
of patients with inflammatory bowel disease. Authors conclude that
inflammation-induced indoleamine 2,3-dioxygenase may represent the
biochemical background of this observation. The study is well performed and
sound. However, it suffers from the small number of patients (n = 10; kynurenic
acid was measured in only 6 of them!), and so the rather lengthy discussion of
the data is not really justified. The manuscript can go as a brief and preliminary
report instead of a full paper.
Interestingly the significance to distinguish patients and controls is much greater
than that for tryptophan or ratio. Authors should comment on that finding. Authors
should briefly comment on the rather huge overlap of tryptophan and kynurenine
between groups. Neopterin has been described as a potential marker of disease
activity in IBD patient, however not cited.
Authors measured tryptophan metabolic abnormalities + neopterin. To
substantiate the association between neopterin and tryptophan degradation the
correlation should be calculated and shown as a graph.
Discussion, line 8: ... decreased availability of tryptophan… has not been found
in patients. So to discuss potential consequences of subnormal tryptophan
seems rather obsolete.
Tables 1 and 2 are not really necessary, content can be easily included in the
text. All marker concentrations were independent of age, so the details for all
individual compounds are not necessary. Group comparisons are given anyhow
(text and figures).
Concentrations of tryptophan and catabolites should be given in µmol/L instead
of ng/mL.
Minor:
should read L-kynurenine instead of l-kynurenine throughout
References (instead of referances)
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-9-6 (2009)

Reviewer's report
Title:Tryptophan degradation in Irritable Bowel Syndrome: Evidence of
indoleamine 2,3-dioxygenase activation in a male cohort.
Version: 1Date:31 July 2008
Reviewer: John Potokar
Reviewer's report:
This is a fairly straightforward small study that compares levels of tryptophan
metabolites in 10 male IBS patients compared with 26 controls. It is an
“investigative” study rather than a clear hypothesis driven research study, but the
findings are nonetheless intriguing, and the discussion attempts to integrate and
synthesise the results with what is know re IBS together with stress induced 5-HT
metabolism.
The methods appear reasonable, but it is not clear why there were only 10 IBS
patients and 26 controls. Was the study powered for just 10 patients and what
was this sample size based on? The IBS group is much older [48 vs 32] and
neither groups are adequately described - this needs to be addressed before
publication. Were their any age associated confounders that might be relevant?
Were any of either group on serotonergic medication? Were their differences in
smoking between the 2 groups (IDO activity is reduced in smokers). Where were
the controls recruited from?
The manuscript is well written, with only the odd typo e.g. p9 last sentence
remove “there”. The discussion is reasonably clear although on p11 I am not
clear how this study clarifies that if the increased tryptophan degradation is IDO
dependent, the knock on consequences for serotonergic signalling are greater
than if it is TDO-mediated.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-6 (2009)

Reviewer's report
Title:Tryptophan degradation in Irritable Bowel Syndrome: Evidence of
indoleamine 2,3-dioxygenase activation in a male cohort.
Version: 2Date:28 November 2008
Reviewer: John Potokar
Reviewer's report:
Dear Hans
I have read manuscript and am happy with changes made and feel it should be
accepted for publication. Two minor typos noted: In line 8 of discussion should
read ....this pathway than absolute..etc not that; On p 11 line 4, should read This
may be due...not This my..
Hope this clear
Please confirm receipt
best wishes
John
Review for 10.1186/1471-230X-9-6 (2009)

Reviewer's report
Title:Tryptophan degradation in Irritable Bowel Syndrome: Evidence of
indoleamine 2,3-dioxygenase activation in a male cohort.
Version: 2Date:3 December 2008
Reviewer: Dietmar Fuchs
Reviewer's report:
Autors have properly addressed and clarified the amendments raised earlier.
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-9-4 (2009)

Reviewer's report
Title:An association between colonic adenoma and abdominal obesity : A cross
sectional study.
Version: 4Date:25 September 2008
Reviewer: Anette Hjartåker
Reviewer's report:
Major comments
1. In its present version this manuscript has several weaknesses. First, the new
information provided by the study could favorably be compressed to a short
communication. Second, the language needs to be thoroughly revised. The
message of several of the sentences is difficult to grasp due to poor language
(e.g. 3rd sentence of the Result section in the abstract).
2. If the authors do not want to write a short communication, I suggest adding
additional analysis. It could for instance be of interest to perform the analysis not
only according to waist circumference, but also to BMI throughout the paper.
Also, the data could be analyzed according to the size and the number of polyps.
3. The authors analyze the differences in basal characteristics between cases
and controls by paired t-tests. This is wrong. The observations are independent
and should be analyzed by means of two sample (unpaired) tests (if the variables
are satisfactory normally distributed). This error needs to be corrected in all parts
of the manuscript.
Minor comments
1. Method section, subjects: Did all 1187 subjects undergo colonoscopy? How
many of these had a polyp?
2. Result section, last paragraph: The last three sentences are not related to the
hypothesis under study. Rather the authors should focus on anthropometric
variables as suggested above.
3. Discussion: The paragraph starting with “previously, many…”, on the whole,
only repeat what is already said in the discussion and could be deleted (or
shortened).
4. References: Please correct the abbreviation for reference no 2.
5. Table 1: Two digits for the p-values are enough (if above 0.01). If the p-value
is below 0.001, please write p < 0.001 (not 0.000). (But all the values are subject
to change when unpaired tests are performed).
6. Table 3: Units for all the variables in the model need to be added. Are all
variables except sex and smoking added to the model as continuous variables?
Are the conditions for using continuous variables met? Further, for the nutritional
variables it could be better to provide the odds ratio for an increase in energy
intake of e.g. 100 kcal/d and for an increase of fat of e.g. 10 g/d. The column with
p-values can be deleted.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Not suitable for publication unless extensively edited
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-4 (2009)

Reviewer's report
Title:An association between colonic adenoma and abdominal obesity : A cross
sectional study.
Version: 4Date:26 September 2008
Reviewer: patricia thompson
Reviewer's report:
1.Is the question posed by the authors well defined? The question posed by the
authors is well defined. They report a positive association between abdominal
obesity, defined by set cutoffs of waist circumference, and colorectal adenoma
using a cross sectional study of 165 cases and 365 polyp free controls.
2. Are the methods appropriate and well described? The methods used are
appropriate and are well described. The population that was used and the
measurements are well described.
3. Are the data sound? The data are sound and replicate what is an already a
fairly well recognized association between abdominal obesity and colorectal
adenoma.
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition? Generally, the manuscript does adhere to the relevant standards for
reporting and data deposition.
5. Are the discussion and conclusions well balanced and adequately supported
by the data? The discussion and conclusions are supported by the data.
6. Are limitations of the work clearly stated? The author’s do not clearly state the
limitations other than to say that they have limitations. This needs to be
improved. Major Compulsory Revision
7. Do the authors clearly acknowledge any work upon which they are building,
both published and unpublished? The author’s do not do a good job summarizing
the wealth of information on obesity, including waist circumference, and risk of
colorectal adenoma. This is a major weakness in the manuscript that must be
addressed in a revision. The statement that these studies should be replicated in
other prospective populations should be removed and the authors should include
discussion of the Harvard studies from the nineties that reported the strong
positive association between central obesity measured as waist and risk of
adenoma. This is categorized as a Major Compulsory Revision.
8. Do the title and abstract accurately convey what has been found?
The title and the abstract do communicate the major message of the manuscript
9. Is the writing acceptable? The author needs an English editor to review the
manuscript as part of the revision. The language is quite broken and in places
suffers from incomplete thoughts and sentences. This will greatly improve the
readability of the manuscript by a wider audience. This is categorized as a Major
Compulsory Revision.
Additional comment: This manuscript would be greatly improved by a multivariate
analysis that included the biochemical parameters of metabolic syndrome. It
would also raise the novelty and impact. This is considered a Discretionary
Revisions.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-9-4 (2009)

Reviewer's report
Title:An association between colonic adenoma and abdominal obesity : A cross
sectional study.
Version: 5Date:19 November 2008
Reviewer: Anette Hjartåker
Reviewer's report:
The manuscript has improved a lot after the revision. Unfortunately the abstract
is missing in the version I have access to, so I cannot comment on that.
I have some minor comments:
Introduction:
1. Please include a statement regarding the association between BMI and
adenoma.
2. Also, I suggest referring to the latest report from WCRF/AICR, 2007.
3. The 1st paragraph is a mix of issues regarding colorectal cancer in particular
and cancer in general. I suggest restricting the presentation to colorectal issues.
4. First sentence in 2nd paragraph: exchange “… the opportunity.. ” to “an
opportunity..”
Methods:
5. Please give some more details about the dietary assessment method used. A
food frequency questionnaire is usually used to record habitually diet during the
last year, month etc, i.e. giving retrospective data.
6. The BMI category 23.0-25.0 and the BMI category # 25 are overlapping.
Please correct.
7. The 2nd sentence in the 3rd paragraph (starting with “We excluded…”) needs
to be rewritten.
Results:
8. As you did analyze abdominal obesity according to number of polyps, I think
you should mention this in the result section even if you did not find any
statistically significant association. It is of interest to know that you found an
association between having/not having polyps and abdominal obesity, but that
you did not find an association between number of polyps and abdominal
obesity. This should also be commented on in the discussion.
9. In the 3rd and 4th sentence in the 3rd paragraph: Omit the exact numbers and
present only the percentages. n are in any case given in table 2.
Table 1:
10. Please add that the figures are age- and gender adjusted.
Table 2:
11. The absolute numbers (n) should be given in brackets instead of the
percentages. Total n for the abdominal group and total n for the normal group
could be included in their respective column headings (analogous to table 1).
Tables 3 and 4:
12. The wording “OR and “Adjusting OR” are misleading as also the first OR is
adjusted according to the footnote. Please rewrite, e.g. Adjusted OR, model 1
and adjusted OR model 2, + inclusion of correct reference to the footnotes.
13. Please include n for each category in the tables.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: Yes, and I have assessed the statistics in my report.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-4 (2009)

Reviewer's report
Title:An association between colonic adenoma and abdominal obesity : A cross
sectional study.
Version: 5Date:27 November 2008
Reviewer: Suminori Kono
Reviewer's report:
The authors responded to the comment well, and the paper has been improved
much. Yet English editing is still required.
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Review for 10.1186/1471-230X-9-4 (2009)

Reviewer's report
Title:An association between colonic adenoma and abdominal obesity : A cross
sectional study.
Version: 5Date:5 December 2008
Reviewer: patricia thompson
Reviewer's report:
In the revised manuscript YoungJoo Kim et al., have been highly responsive to
the previous reviewer comments, attempting to address issues that were raised
by each of the three previous reviewers. The readability of the manuscript is
greatly improved.
Minor Essential Revisions
There remain minor but not insignificant issues with word choice, grammar and
sentence structure that could use further attention.
Examples:
Discussion, first sentence, second paragraph “Many studies have been
concluded on the association”… should be changed to Many studies have been
conducted on the association …
Discussion, second paragraph
However studies conducted on central obesity as a risk factor of colon adenoma,
‘has’ should be changed to have been limited and the association remains
controversial.
Other minor issues that need to be addressed:
Discussion sentence stating that “BMI was not significantly associated with
adenoma after adjusting for waist circumference, which concurs with the findings
of previous studies” - needs referencing.
Discretionary Revisions
Because waist is so strongly associated with risk in this study of an Asian study
population, it would be of high value for the discussion to include one concise
paragraph about differences in the relative importance of specific body
composition measures in different populations. In general, BMI and waist
circumference are highly correlated in Caucasian populations and thus,
adjustment of one for the other often attenuates the effect. Here, waist after
adjusting for BMI is presenting as a very strong risk factor for colorectal
adenoma. It would be of interest to discuss the relationship between metabolic
syndrome and waist circumference versus BMI measures in an Asian population.
In the absence of an opportunity to directly measure the relationship between
metabolic syndrome and risk, a thoughtful discussion of the relationship with
waist versus BMI in the Asian population would be useful to a reader and raise
the overall impact of the manuscript.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
'I declare that I have no competing interests'
Review for 10.1186/1471-230X-9-3 (2009)

Reviewer's report
Title:Paraoxonase-1 is related to inflammation, fibrosis and PPAR delta in
experimental liver disease
Version: 1Date:27 September 2008
Reviewer: Nathalie Janel
Reviewer's report:
Marsillach and colleagues showed the relationships between paraoxonase-1
(PON1) expression and MCP-1 production, in a experimental model of chronic
liver disease. This is an interesting study, but three points need to be clarified in
order to accept the figure 6.
Major Compulsory Revisions:
In figure 2, despite the increased hepatic PON1 protein expression, the serum
PON1 expression was decreased. Can you explain this important point?
In figure 4, there is an increased activity of cathepsin B at 6 weeks of CCL4
treatment compared to control, but an increased hepatic PON1 concentration.
Can you really assume that the decreased PON1 protein degradation explains
the increase hepatic levels of PON1 at 6 weeks of treatment?
In figure 5, despite the increased hepatic PON1 protein expression, the lactonase
activity was decreased. Can you explain this important point?
Minor Essential Revisions:
In figure 1, if you give histograms for control and treated rats, we should added
the micrographs of protein expression for the control group.
Level of interest: An article of outstanding merit and interest in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests below.
Review for 10.1186/1471-230X-9-3 (2009)

Reviewer's report
Title:Paraoxonase-1 is related to inflammation, fibrosis and PPAR delta in
experimental liver disease
Version: 1Date:29 September 2008
Reviewer: Mehmet Horoz
Reviewer's report:
The authors investigated the chronological sequence and quantitative
relationships between PON1 expression and activity, free radical production,
MCP-1 expression, and fibrosis in an experimental model. They sugegested a
hepato-protective role of PON1 against inflammation, fibrosis and liver disease
mediated by MCP-1.
Although the hepato-protective role of PON1 have been suggested in previous
report, the association of PON1 with MCP-1 is novel. the study is well designed
and the findings is well presented. In my opinion, reviewed paper doesn't need
major changes
There are only two minor points that should be addressed by the authors during
revision.
1-More detailed description of the statistical analysis.
2-There are a few grammatical errors that should be fixed.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-3 (2009)

Reviewer's report
Title:Paraoxonase-1 is related to inflammation, fibrosis and PPAR delta in
experimental liver disease
Version: 1Date:24 October 2008
Reviewer: Fabio Marra
Reviewer's report:
MAJOR COMPULSORY REVISIONS
1. No explanation is provided as to why mRNA levels drop and protein is
increased. After 12 weeks, protein levels should follow those of steady-state
mRNA levels, otherwise one of the two determinations may be not reliable. The
intrahepatic levels of PON1 must be reassessed using an alternative method, to
confirm the present results.
2. No direct proof of the interaction between MCP-1 and PON1 is provided. It is
said that the two proteins are directly related, but actually in the discussion it is
stated that when PON1 is high, MCP-1 is low (page 10). How should one
understand? Similarly, the possible regulation of PON1 by PPAR-delta or
cathepsin B is only hypothetical, and this should be clearly stated. It is said that
cathepsin B decreased during CCl4 administration, but I could not gather this
information from Figure 4.
MINOR ESSENTIAL REVISIONS
1. The role of PON1 has been previously shown in the liver, including data with
PON1 overexpression. It should be more clearly stated to what extent this study
provides novel information
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Review for 10.1186/1471-230X-9-3 (2009)

Reviewer's report
Title:Paraoxonase-1 is related to inflammation, fibrosis and PPAR delta in
experimental liver disease
Version: 2Date:1 November 2008
Reviewer: Nathalie Janel
Reviewer's report:
no revision
Level of interest: An article of outstanding merit and interest in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
no conflict of interest
Review for 10.1186/1471-230X-9-3 (2009)

Reviewer's report
Title:Paraoxonase-1 is related to inflammation, fibrosis and PPAR delta in
experimental liver disease
Version: 2Date:1 November 2008
Reviewer: Mehmet Horoz
Reviewer's report:
The manuscript is acceptable in its revised form.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.