JerMa88/BMC_Gastroenterology_Peer_Reviews huggingface dataset:
Review for 10.1186/1471-230X-10-138 (2010)

Reviewer's report
Title:The gene-reduction effect of chromosomal losses detected in gastric
cancers
Version: 1Date:19 August 2010
Reviewer: Jun Yu
Reviewer's report:
This manuscript reported the cell-adverse effect of gene reduction in relation to
gastric cancer differentiation types. They demonstrated that detection of loss of
heterozygosity using microsatellite analysis may have the potential as a method
of pretreatment genetic diagnosis marker. They concluded that the cell-adverse
effect of gene reduction is more tolerated in intestinal-type gastric cancers than in
diffuse-type cancers, and the loss of high-dose genes is associated with
hematogenous metastasis. The study is generally well designed. However, there
are several major comments should be addressed:
Major Compulsory Revisions
1) As shown in Table 3, in high-risk genotypes, age is positively correlated with
LOH level. When it comes to low-risk genotypes, age is negatively correlated
with LOH level. This phenomenon should be discussed accordingly?
2)The age and gender should be included in the models of multivariate analysis,
no matter they were significant or not.
Minor Revisions
1) Page8, Paragraph 1, Line 1: “One hundred forty-five” should be “One hundred
and forty-five”.
2) Page8, Paragraph 1, Line 4: “One hundred sixteen” should be “One hundred
and sixteen”.
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-10-138 (2010)

Reviewer's report
Title:The gene-reduction effect of chromosomal losses detected in gastric
cancers
Version: 2Date:8 November 2010
Reviewer: Yong Sung Kim
Reviewer's report:
Authors corrected one by one for all requirements I request.
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-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:22 July 2010
Reviewer: Hiromu Suzuki
Reviewer's report:
In this manuscript, Hong et al. demonstrated that methylation of transitional CpG
sites are influenced by (1) distance from retroelements, (2) lack or presence of
CpG island, (3) H. pylori infection in non-cancerous gastric mucosa and (4) LOH
status in cancer. These findings are quite interesting and important, although the
first and second points are already described in their previous reports. However,
there are several concerns as listed below, which requires revision of this
manuscript before acceptance.
Major Compulsory Revisions
1. Does methylation in the transitional CpG sites correlate with gene expression
in the specimens used in this study? Only the SAGE tag results in normal
stomach is shown, and this point is not mentioned.
2. Is there any correlation between the transitional CpG sites methylation and
neighboring CpG island methylation? It is of interest to see whether CpG islands
are methylated or not, when the neighboring transitional CpG sites are
methylated by H. pylori infection.
3. Page 18: Are there any functional evidence for the statement "In cancer tissue
that undergoes the LOH event that reduces a gene dose, the remaining gene
copies have the increased possibility of using the nuclear proteins and this would
lead to the demethylation of transitional-CpG segments"? If so, please include a
citation for this statement. If not, please show functional evidence that
hypomethylation is a consequence of LOH in cancer.
4. Page 21: "This study suggests that the concurrent methylation of multiple
CpGisland genes initiates and sustains the adaptive differentiation of newly fixed
stem cells in the gastric mucosa infected with H. pylori, and that the LOH-induced
DNA demethylation and discordant methylation of stomach-specific genes may
facilitate gastric carcinogenesis by reactivating a stem-cell intrinsic program."
This study does not provide enough functional evidences to draw this conclusion.
Minor Essential Revisions
5. "Overmethylation" and "Undermethylation" are not commonly used terms to
describe DNA methylation, and the authors have used "hypermethylation" and
"hypomethylation" in their previous manuscript (Kim YH et al. BMC Cancer,
2006). Is there any specific reason to use these uncommon terms in this
manuscript?
Level of interest: An article of outstanding merit and interest 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-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:25 July 2010
Reviewer: Rommel Burbano
Reviewer's report:
Major Compulsory Revisions:
-The authors should clarify the number of gastric cancer samples used on the
paper. In Methods section, they mention n=70 (48 males and 22 females).
However, in page 9 of the manuscript they cited “40 duplicated DNAs of the
same tissue, 48 pairs of 1-cm-adjacente tissues...”
-There is no information regarding the histological type of the gastric cancer
samples used in the manuscript. Is there any difference in the methylation status
according to the histopathological type?
-In pages 10 and 11, the authors classified on or no chromosome lost in
diffuse-type of gastric cancer as LOH-B (baseline level) and as LOH-L (low level)
in intestinal and mixed type. Why?
-The authors concluded that “concurrent methylation of multiple CpG-island
genes initiates and sustains the adaptive differentiation of newly fixed stem cell in
the gastric mucosa infected with H. pylori”. However, no comment about stem
cells is made in the methods or results sections. How the authors conclude such
information about stem cells? Is there any marker that was used to check if the
cells used in DNA extraction were newly fixed stem cells?
Minor Essentials Revisions:
-The authors checked for H. pylori status of non-cancerous tissue samples. How
is the H. pylori status of the gastric cancer tissue samples? Is there any
difference in the methylation status between gastric cancer tissue samples H.
pylori positive and H. pylori negative?
-The authors should explain the 5-level and 10-level classification (including the
intermediary status) of methylation status. In a previous paper (Hong et al.,
2009), they explain the 5-level. I believe that a better explanation should improve
the manuscript;
-The first paragraph of the Results section is about results of a previous paper.
Please, transfer it to the Discussion section. However, if they are results of the
current manuscript (although similar of the obtained previously), please cite the
methodology used in the Methods section;
-The last paragraph of page 13 should be transferred to Methods section;
-In page 13, 1st and 2nd lines, the authors can substitute 20 percent for 20%;
-In page 14, lines 14-17: The authors say that PGC and TFF1 are
stomach-specific genes weakly active when compared with the two master
stomach-specific genes. In which tissue? The authors also say that those genes
are densely methylated in bone marrow. And in the stomach?
-Is there any microsatellite in which the authors observed LOH more frequently?
And how about LOH and histologic type?
-In page 18, please change H202 for H2O2 (there is a zero instead of an “O”).
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-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:30 July 2010
Reviewer: Yong Sung Kim
Reviewer's report:
The overmethylated genes in Helicobacter pylori infected gastric mucosa are
demethylated in gastric cancers.
The manuscript by Hong et al., presents evidence that the hypermethylated
genes under the influence of retroelement methylation in the HP-positive gastric
mucosae are demethylated in the gastric cancers influenced by LOH. Initially, to
delineate the CpG methylation patterns of CpG-island-containing and -lacking
genes in view of the retroelements, the methylation status were examined in the
transitional-CpG sites of CpG-island-containing genes and CpG-island-lacking
genes in HP-negative and -negative gastric mucosae or additional gastric cancer
tissues using MSP. They observed the CpG-island-containing genes were
hypermethylated depending on the proximity to the nearest retroelement in the
HP-positive gastric mucosa and the CpG-island-lacking genes were similarly
methylated independent on HP infection. And they also found that both the
methylation level of CpG-island-containing and -lacking genes tended to be
decreased according to LOH-level-dependent manner in gastric cancers.
Overall this is an impressive body of work on the different epigenetic regulation of
genes between CpG-island-containing house-keeping and -lacking stomach
specific genes during gastric carcinogenesis connecting to LOH event. The result
may provide an insight to understand the mechanism of epigenetic regulation for
the dynamic changes of methylation on different class of gene during gastric
carcinogenesis.
Comments:
Authors said that hypermethylated genes in HP-positive gastric mucosa are
demethylated in gastric cancers. They examined the HP infection in gastric
mucosae samples but not in gastric cancer samples. If the HP infection is
examined in gastric cancer samples and the methylation status is compared
between HP positive and negative, their opinion may be clearer. How do you
think about it?
Introduction section: the concept of the transitional-CpG sites has to be defined
for reader, though it has been described in the previous publications.
Page 7: In subsection of Collection of tissue samples, HP-positive or –negative
cases tested were described as each 50 cases. But actually authors analyzed
with 100 HP-positive and 100 HP-negative cases to examine the methylation
status, respectively. Correction is needed.
Page 8: In lane, ‘1,040’ µl may be a misprint. Correction is needed.
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.
Review for 10.1186/1471-230X-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 2Date:5 November 2010
Reviewer: Hiromu Suzuki
Reviewer's report:
The authors have answered to my comments and revised the manuscript, and I
think now it is suitable for publication.
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-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 2Date:8 November 2010
Reviewer: Yong Sung Kim
Reviewer's report:
Authors corrected one by one for all requirements I request.
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-10-137 (2010)

Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 2Date:10 November 2010
Reviewer: Rommel Burbano
Reviewer's report:
The authors have performed the requested alterations and now this reviewer
agrees that this manuscript is ready to be published.
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.
Review for 10.1186/1471-230X-10-135 (2010)

Reviewer's report
Title:Giant flat adenomas of rectum successfully treated in two steps by
endoscopic submucosal dissection and endoscopic mucosal resection.
Version: 1Date:6 March 2010
Reviewer: Hiroyuki Imaeda
Reviewer's report:
The major revisions
1. Authors need to mention the endoscopic procedure time of each case.
2. Authors performed combined ESD/EMR. Wasn’t it difficult to examine
histopathologic assessment of the resected specimens because of piecemeal
resection?
3. Authors mentioned the difficulty in assessing the correct deeper submucosal
tissue plane in the center of the tumors. Was the cause the submucosal fibrosis
or bleeding?
4. Accurate histopathologic assessment of the resected specimens is essential
because the depth of the invasion and lymphovascular infiltration of the tumor is
associated with considerable risk for lymph node metastasis. However, large,
flat-elevated colorectal tumors tend to have a relatively benign course, and,
hence, endoscopic removal by using piecemeal EMR techniques has become
accepted. Authors should discuss this in Discussion.
5. Figure 1: Authors showed the figure of the resected site in D, but some part of
the lesion seemed to remain in the oral side. Authors need to show the figure of
the clearer resected site. Moreover, authors showed the figure of the scar after 3
months, but the ordinary scar after EMR/ESD looks as Figure 2e and Figure 3f.
Why was the scar reddish and granular?
The minor revisions
1. p2, line 18: Authors should change ‘‘gastrointestinal’’ to ‘‘rectal’’.
2. p5, line 7: Authors mentioned ‘‘hood knife’’. Was it hook knife?
3. p6, line 19: Authors mentioned other systems in Discussion, but authors
should mention it in Case reports.
4. p6, line 20: Authors should refer the manuscript of ESD methods using a thin
gastroscope reported by Uraoka et al (Gastrointest Endosc 2007;66:836).
5. p10, Figure 2 and 3: Authors mentioned ‘‘anterior’’. Was it anal side?
6. p7, line 18: Authors should omit ‘‘(Hooke-EMR)’’.
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-10-135 (2010)

Reviewer's report
Title:Giant flat adenomas of rectum successfully treated in two steps by
endoscopic submucosal dissection and endoscopic mucosal resection.
Version: 1Date:9 March 2010
Reviewer: Naoto Sakamoto
Reviewer's report:
“Comments for authors”
In this manuscript, authors have claiming the effectiveness of combined
ESD/EMR resection for gastrointestinal neoplasm.
However, there are some crucial problems.
Major
1) Although authors have planned to perform ESD in all 3 cases with many
devises, they reconciled to continue ESD because of the technical difficulty and
finally performed EPMR. However, same method have already recognized as a
usual method in this field 1).
2) Authors described that they obtained the complete dissection of the polyp and
the complete histological evaluation from the piecemealed samples. I cannot
believe that it is possible to obtain the complete histological evaluation from the
rugged ulcer after tumor resection (Fig. 1-3). The rugged ulcer suggested that
many piecemeal resections might be performed and it should cause unreliable
histological evaluation because of burning effect. I think they should describe
how many piecemeal resections were performed. Also, I strongly recommend
authors to indicate restructured histological view.
Minor
1) Authors described that combined ESD/EMR resection seems effective, safe
and reliable for resection of huge gastrointestinal neoplasm. If so, what is the
control, ESD or well-planned EPMR? Authors should describe about this point
and show the data with statistical analysis.
Ref. 1) Shinji Tanaka, Shiro Oka, Iwao Kaneko, et al. Endoscopic submucosal
dissection for colorectal neoplasia: possibility of standardization
Gastrointestinal Endoscopy2007, 66, 100-107
Review for 10.1186/1471-230X-10-135 (2010)

Reviewer's report
Title:Giant flat adenomas of rectum successfully treated in two steps by
endoscopic submucosal dissection and endoscopic mucosal resection.
Version: 2Date:6 April 2010
Reviewer: Yutaka Saito
Reviewer's report:
Major Compulsory Revisions
The author must respond to these before a decision on publication can be
reached.
Level of interest: An article of insufficient interest to warrant publication in a
scientific/medical journal
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-10-135 (2010)

Reviewer's report
Title:Giant flat adenomas of rectum successfully treated in two steps by
endoscopic submucosal dissection and endoscopic mucosal resection.
Version: 2Date:7 April 2010
Reviewer: Hiroyuki Imaeda
Reviewer's report:
Stroppa et al. revised the manuscript about usefulness of treatment by combined
ESD and EMR for giant flat adenomas of rectum. But major revisions are
necessary on the points described below.
I have the following comments and remarks.
The major problems
1. Authors mentioned that two-three large pieces not less than 3 cm in diameter
were obtained. However, authors showed excised lesion less than 2cm in
diameter in Figure 3e. Authors should show larger excised lesions.
2. Authors mentioned that Figure 1d and 1e showed removal of the lesion.
However, these figures were not taken on the same day (Figure 1d showed the
date of 10/ 2006 and Figure 1e showed that of 2/ 2007). Moreover, authors
showed Figure 1f 3 months after ESD/EMR, however, authors had showed this
figure as 12 months after ESD/ EMR before.
The minor problems
1. p6, line 5: Although authors described results of ESD for early gastric cancer
reported by Imagawa. Authors should omit this paragraph.
2. p8, line 23: Authors had better omit ‘‘nongranular laterally spreading
tumors···biopsy,’’ and change ‘‘rectal polyps’’ to ‘‘rectal laterally spreading
tumors.’’
Level of interest: An article of limited interest
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-10-135 (2010)

Reviewer's report
Title:Giant flat adenomas of rectum successfully treated in two steps by
endoscopic submucosal dissection and endoscopic mucosal resection.
Version: 2Date:8 April 2010
Reviewer: Naoto Sakamoto
Reviewer's report:
Although authors answered some of our comments, they did not respond
adequately to the demands of the most important questionable point.
Authors described that they obtained the complete dissection of the polyp and
the complete histological evaluation from the piecemeal samples. However, they
still not have understood the definition of “complete dissection”. We cannot
believe that it is possible to obtain the complete histological evaluation from the
rugged ulcer after tumor resection, and anxious about the risk of over looking of
sm invasion or lymph-vascular invasions.
If authors would like to convince us, they should obtain the complete histological
evaluation. In addition, they have to demonstrate restructured histological
specimens reflecting macroscopic specimens in additional Figure.
Review for 10.1186/1471-230X-10-135 (2010)

Reviewer's report
Title:Rectal laterally spreading tumors successfully treated in two steps by
endoscopic submucosal dissection and Endoscopic Mucosal Resection
Version: 5Date:21 June 2010
Reviewer: Hiroyuki Imaeda
Reviewer's report:
Stroppa et al. revised the manuscript about usefulness of treatment by combined
ESD and EMR for giant flat adenomas of rectum. But authors did not answer
some of my comments, especially major problem No. 1.
The major problems
1. Authors mentioned that two-three large pieces not less than 3 cm in diameter
were obtained. However, authors showed excised lesion less than 2cm in
diameter in Figure 3e. Authors should show larger excised lesions.
Level of interest: An article of limited interest
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-10-134 (2010)

Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 1Date:25 January 2010
Reviewer: S H Duncan
Reviewer's report:
Noor et al have examined differences in the composition of the microbiota of
stool samples from IBS and UC samples whilst in remission compared to that of
healthy controls using DGGE. The paper is well written and the authors
acknowledge that their results are surprising, in that Bacteroides species were
less prevalent in stool samples from the disease state compared to healthy
controls. The authors could perhaps speculate on this more than has been
covered in their discussion.
Minor essential revisions
1. Are the p values not actually “equal to” rather than “less than” in the abstract
2. In the background section, the authors should add additional references which
do attempt to assign particular bacterial species into those that may be beneficial
or detrimental to gut health. For example, see Sartor et al 2008 (PNAS) and
Sokol et al 2008 (PNAS).
3. The level of uncultured bacterial species in the human large intestine is
probably not as high as has been suggested in this article. Eg See paper by Tap
et al 2009 (Env Microbiol).
4. The power of DGGE should not be overstated as it is generally considered as
a low resolution method.
5. There would merit in comparing the profiles of faecal samples from patients
during active disease and in remission.
6. Freezing the samples prior to extracting DNA may have resulted in differential
loss of particular bacterial groups including the Gram negative Bacteroidetes.
The authors should comment on this.
7. Did any of the sequenced bands give multiple products?
8. Given the surprising results in this study, it would have been valuable to
employed an independent technique to analyse the samples too.
9. Figure 1a. Please add labels to the sample lanes to indicate which samples
were derived from control, IBS or UC subjects.
10. Table 1. Define what you mean by average similarity and state how many
bases were sequenced per sample.
11.Figure 2 is too small and therefore difficult to see.
12.How were the samples for these profiles selected?
Review for 10.1186/1471-230X-10-134 (2010)

Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 2Date:6 May 2010
Reviewer: Grietje Holtrop
Reviewer's report:
The statistical concerns raised in my previous report have been
clarified/addressed and I have no further comments. There is no need to present
error plots and/or normality tests in the manuscript.
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-10-134 (2010)

Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 2Date:17 May 2010
Reviewer: Gunnar Loh
Reviewer's report:
As stated in my firs report, the major findings reported in the manuscript
"Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the
gut microbiota" are of confirmative nature. Both changes in gut microbiota
composition in UC and IBS patients, including decreasing proportions of
Bacteroides spp. in IBD patients, have been reported previously. The
significance of the finding that UC and IBS patients differ in microbiota
composition is not clear to me. The conclusion that Bacteroides spp. are involved
in UC and IBD is based on non-significant differences in DGGE profiles between
the study subjects and the sequencing of very short 16S rRNA gene fragments
(~250bp) and therefore not necessarily valid.
Level of interest: An article of insufficient interest to warrant publication in a
scientific/medical journal
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-10-134 (2010)

Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 2Date:20 May 2010
Reviewer: S H Duncan
Reviewer's report:
The revised version of the manuscript by Noor et al is much improved and
therefore I would now recommend acceptance of this version following further
minor revisions.
Abstract: In the abstract it is stated that the number of subjects (n=46) differs
from that in the materials and methods section (n=50).
End of background section: The final sentence should be modified as a reduction
in microbial diversity in the disease state may be detrimental but loss of
Bacteroides compared to the control may not protective. The authors need to
consider whether or not their data illustrates changes in microbial composition
reflects the cause or consequence of disease.
Conclusion section: Again I would recommend that the authors should not over
claim the point that Bacteroides may be protective given that several other
studies have demonstrated that this is not the case but that instead their data
reveals a loss of diversity in the disease state. This loss of diversity may have a
number of significant consequences as, for example, dysbiosis may impact on
microbe-microbe interaction, microbe-host interactions and changes in microbial
metabolite profiles.
General: There are still a number of typographical errors in the manuscript that
needs to be corrected.
Review for 10.1186/1471-230X-10-134 (2010)

Reviewer's report
Title:Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of
the gut microbiota
Version: 3Date:5 October 2010
Reviewer: S H Duncan
Reviewer's report:
The authors have attended to most of the key points raised in previous reports
however there are still a few typographical errors in the current version of the
manuscript. I would recommend acceptance of this version
Level of interest:. The paper does make some interesting points on the microbial
diversity of faecal samples from healthy versus colonic disease subjects and
suggests that further work needs to be done in this research area. Given that
DGGE was the method of choice to study these samples however it will not give
the resolution of certain other molecular methods which is a weakness of the
study but this is acknowledged in the manuscript.
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-10-133 (2010)

Reviewer's report
Title:Intestinal Epithelial Serum Amyloid A Modulates Bacterial Growth and
Protects from Experimental Colitis
Version: 1Date:22 September 2010
Reviewer: Aldo AM Lima
Reviewer's report:
* Major Compulsory Revisions
This is an interesting paper showing the modulation of SAA on E. coli in vitro
growth and pro-inflammatory response of experimental colitis in a mouse model.
Major concern on this paper is how to fit the clinical results on the finding from
the in vitro and in vivo results. As showed in the clinical results, the cases
(Crohn's diseases) increased the SAA1/2 RNA expressions with the diseases
which are against the controling of inflammation compared to control health
volunteers. Since the in vivo model are not close comparable to clinical disease, I
would suggest to delete this part without prejudice to the whole nice work. I agree
that more work will be necessary to explain the modulation of SAA in Crohn's
diseases and the authors stated that in the discussion.
* Minor Essential Revisions
Some minor points:
1. Suggested for new title: Intestinal epithelial serum amyloid A modulates
bacterial growth in vitro and pro-inflammatory responses in mouse experimental
colitis;
2. At some how I felt hard to follow the abstract before read the whole paper.
Please revise saying the three isoforms of SAA/add if all forms types of
IECs/delete result clinical results since no conclusion could be make using these
results;
3. Add a few more keywords would help;
4. What is the nomeclature denomination for gene and protein for SAA?;
5. on methods 2nd paragraphic please spell the letters "OCT";
6. Results, subitem SAA protects against DSS colitits; please revise if lost weight
was statistical significant since it is not clear there or in the correspondent Fig. 5;
7.Do the authors have a chance to add IEC cells with internalized E. coli?;
8. Figure 1 was hard to follow as described without saying what we should look in
term of colors etc; specially Fig1 F and it maybe good to add arrows to show
better those points.
* Discretionary Revisions
Delete clinical results.
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-10-133 (2010)

Reviewer's report
Title:Intestinal Epithelial Serum Amyloid A Modulates Bacterial Growth and
Protects from Experimental Colitis
Version: 2Date:5 November 2010
Reviewer: Herbert Tilg
Reviewer's report:
After going through all aspects I believe this MS should be accepted and
published. The authors responded properly discussing potential weaknessess.
The finding per se is very interesting.
Review for 10.1186/1471-230X-10-132 (2010)

Reviewer's report
Title:Mycoplasma hyorhinis infection in gastric carcinoma and its effects on the
malignant phenotypes of gastric cancer cells
Version: 1Date:9 August 2010
Reviewer: zheng hua-chuan
Reviewer's report:
Minor essential revisions
In the manuscript entitled " Mycoplasma hyorhinis infection in gastric carcinoma
and its effects on the malignant phenotypes of gastric cancer cells“, Yang et al.
reported that the existence of Mycoplasma hyorhinis was positively correlated
with lymph node metastasis, Lauren’s classification, TNM staging and patient
age of gastric cancer. Mycoplasma hyorhinis promoted tumor cell migration,
invasion and metastasis, which was possibly associated with the enhanced
phosphorylation of EGFR and ERK1/2, while the antibody against p37 protein
could block these biological events, mentioned above. Overall, the design of the
manuscript is very nice and of greatly scientific significance although the current
manuscript suffers from no novel findings and numerous grammatical and syntax
errors.
Minor comments:
1. It is very rare to say “Lauren Typing” in stead of “Lauren’s classification”.
2. Please give the full name when abbreviation for the first time appears.
3. In Page 5 line 2, please tell how to process the gastric cancer tissues.
4. In nested PCR, what amount of DNA has been added in PCR mixture?
5. The description bout the second set of PCR primers is confusing for
Mycoplasma hyorhinis examination. What about the first set?
6. It is better to give a brief description about why to use the mouse B16f10 cell
for the metastatic experiments of C57B/6.
7. What about the Mycoplasma hyorhinis existence in non-neoplastic mucosa
adjacent to gastric carcinoma.
8. The positive rate of Mycoplasma hyorhinis existence was a little higher by
nested-PCR than immunohistochemistry(IHC). However, sensitivity of
nested-PCR is much higher using 10-fold dilution of the first PCR product.
Therefore, the data of IHC should be confirmed by Western blot if possible.
9. Please give the statistical description in the figures and their legends.
10. In page 13 line 7, have you analyzed the association between Mycoplasma
hyorhinis existence and prognosis of gastric carcinoma patients?
11. There were many mistakes in spelling, syntax and grammar throughout the
manuscript. For example, “we……” is frequently used in the paper. It is
necessary to revise the manuscript by a native English-speaker.
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.
Review for 10.1186/1471-230X-10-132 (2010)

Reviewer's report
Title:Mycoplasma hyorhinis infection in gastric carcinoma and its effects on the
malignant phenotypes of gastric cancer cells
Version: 1Date:20 August 2010
Reviewer: Yasuo Takano
Reviewer's report:
This article showed the possibility that Mycoplasma hyorhinis may be linked to
gastric carcinogenesis. It is generally well written and is focused on the
interesting oncologic field. However, some minor points should be revised.
1. Mistakes in spelling and grammar are often found. Authors should receive
English correction by native English speaker.
2. Authors should write the full name of abbreviations when they are written
firstly.
3. Authors should describe the details of nested PCR since mention of this
procedure is relatively poor.
4. Authors should explain the reason why mouse B16f10 cells was used for the
metastatic experiment of C57B/6.
Level of interest: An article of outstanding merit and interest in its field
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-10-130 (2010)

Reviewer's report
Title:The increasing role of endoscopy in the management of intestinal
obstruction: a 20-year retrospective study
Version: 1Date:18 May 2010
Reviewer: David I Watson
Reviewer's report:
This study claims to evaluate the role of endoscopy in the management of
intestinal obstruction, and concludes that it is becoming increasingly important.
The data presented does not support this conclusion.
The authors have really only evaluated colonoscopy in suspected large bowel
obstruction. The title and the use of words throughout the paper should be
changed to reflect this reality.
Colonoscopy should replace endoscopy throughout the paper. Endoscopy
implies gastroscopy in the English language literature – the paper did not
consider gastroscopy.
The authors have inflated the apparent importance of their data set by
emphasising how many surgical and colonoscopy records they evaluated. This is
a retrospective study of 655 patients indentified from colonoscopy and surgical
records. The 26,000 and 18,000 denominators used inflate the apparent value of
the data set.
A proper review of management of bowel obstruction would start with hospital
diagnosis at discharge. The authors’ case selection has excluded all the patients
who did not undergo surgery or colonoscopy. This means that their interpretaton
of the importance of their data is limited by an incomplete data set – ie it would
be expect that there would be another missing 20,000 to 30,000 patients who
presented with bowel obstruction, but did not require intervention over the same
time frame. By not including these patients, and by using a retrospective case
note review methodology, the authors cannot really show that they have helped
anyone by undertaking colonoscopy. What would have happened if they didn’t do
colonoscopy? What were the complications associated with undertaking
colonoscopy? Were there any downsides? Using colonoscopy, does not prove
that it is useful. For all we know it could have been harmful?
There is little detail provided about the surgical interventions.
I don’t think the paper has really looked at the question of small bowel
obstruction at all, and this should be acknowledged clearly.
The %values in tables 1 and 3 should be reversed – ie calculate denominators
across rows in table 1, not columns, and in tabled 3, calculate the % down the
rows.
Table 2 shows that only 20/203 patients undergoing colonoscopy have had a
therapeutic intervention, and the paper does not provide any information about
whether this was successful or not. More than 90% had a colonoscopy which
was not therapeutic. This is less than 3% of the overall study group, and might be
only 1-2% of all patients presenting with bowel obstruction to the hospital (if the
patients not having an intervention are included). This means that colonoscopy
has a more limited and less useful role than the paper claims.
Level of interest: An article of limited interest
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-10-130 (2010)

Reviewer's report
Title:The increasing role of endoscopy in the management of intestinal
obstruction: a 20-year retrospective study
Version: 1Date:23 May 2010
Reviewer: Andreas Shamiyeh
Reviewer's report:
Answer to question:
1: The topic is clear and the aim is well defined. The theme itself is upcoming at
the moment. Actually a multicenter trial supported by E.A.E.S is dealing with this
question.
2: The methods are well explained: The authors write that all patients gave
informed consent during surgery…. I guess written informed consent was given
prior to… this should be cor-rected.
Statistics are ok.
Management of good clinical practice: is it a routine in the clinic to do a oral
gastrografin pas-sage?
Results: Obstruction is not well defined. e.g. how many patients had rectal
cancer., how many patients had miserere? Are there any patients with immediate
postoperative ileus to be treated. Die they try to clean the bowel prior to
endoscopy?.....
Treatment options: In how many patients could the endoscopic intervention spare
a stoma?
Did they had any complications by the use of a stent (perforation? dislocation?)
How many patients had oglivie syndrome or morbus hirschsprung.
Discussion: The autors state, that first it is important to reach the terminal ileum
or cöcum. This is not in every case of obstrucition necessary (e.g. rectal cancer
and ileus)
What about on table coloscopy?
3: The data sound believable
4: ok
5: Discussion and conclusion are well balanced
6: yes, it is an retrospective study, however it represents a large number of
treated patients in an referral centre.
7-9: ok
Conclusion: The paper is important. In many countries endoscopy has gone far
away from the surgeons hand. This may lead surgeons in case of an intestinal
obstruction not even to think about an endoscopy.
To give this work more importance, the patients characteristics and the results
should be explained better (see questions above)
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-10-130 (2010)

Reviewer's report
Title:The role of colonoscopy in the management of intestinal obstruction: a
20-year retrospective study
Version: 2Date:30 July 2010
Reviewer: Andreas Shamiyeh
Reviewer's report:
no further comments
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-10-131 (2010)

Reviewer's report
Title:Lymphatic marker podoplanin/D2-40 in human advanced cirrhotic liver-
Reevaluations of microlymphatic abnormalities
Version: 1Date:29 August 2010
Reviewer: Armin Thelen
Reviewer's report:
The present manuscript describes a study about the specifity of the monoclonal
antibody D2-40 to stain lymphatic vessels in human liver tissue. Furthermore, it
analyzes the quantity of lymphatic vessels in normal and cirrhotic liver
specimens. In general, the subject of the manuscript is interesting and it is well
structured and well written. However, there are some issues which may be
addressed prior to publication.
Minor:
1. The most critisism of the study is the low number of analyzed tissue
specimens (only 5 in each group). That is not important for the analyzation of the
speciity of the antibody but it is a disadvantage for the analyzation and the
comparison of the vesel density between the different study groups. Therefore, it
may be helpful to adress this shortcoming of the study in the discussion section
2. First paragraph of the section “Materials and methods”: It is not clear to me
which groups of tissue speimens come from patients wh underwent resection
and who underwent liver transplantation as both are described as tissues from
cirrhoic livers. Authors may specify this.
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-10-131 (2010)

Reviewer's report
Title:Lymphatic marker podoplanin/D2-40 in human advanced cirrhotic liver-
Reevaluations of microlymphatic abnormalities
Version: 1Date:15 September 2010
Reviewer: sinan akay
Reviewer's report:
1. Is the question posed by the authors well defined? Yes.
2. Are the methods appropriate and well described? Yes.
3. Are the data sound? Yes.
4. Does the manuscript adhere to the relevant standards for reporting and data
deposition? Yes.
5. Are the discussion and conclusions well balanced and adequately supported
by the data? Yes.
6. Are limitations of the work clearly stated? Yes.
7. Do the authors clearly acknowledge any work upon which they are building,
both published and unpublished? Yes.
8. Do the title and abstract accurately convey what has been found? Yes.
9. Is the writing acceptable? Yes.
Although there was no proliferation marker investigated in the article, the word
“proliferation” is used for lymphatic endothelial cells.
Advice on publication: Although the article includes patients with cirrhosis, results
of the study are descriptive and may be it will be more convenient to publish this
article in a preclinical journal. The discussion of the article does not contain any
discussion about the formation or reabsorption of ascites.
Review for 10.1186/1471-230X-10-129 (2010)

Reviewer's report
Title:Laparoscopic versus conventional appendectomy - a meta-analysis of
randomized controlled trials
Version: 1Date:18 July 2010
Reviewer: Ray Garry
Reviewer's report:
This is a well written meta-analysis of an important topic. You have followed
standard Cochrane protocols and I think this paper would make a useful additio
to the literature
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-10-129 (2010)

Reviewer's report
Title:Laparoscopic versus conventional appendectomy - a meta-analysis of
randomized controlled trials
Version: 1Date:30 August 2010
Reviewer: Anette Sundfor Jacobsen
Reviewer's report:
In the Abstract, authors set out to compare therapeutic effects and safety.......via
a meta-analysis. This purpose must follow through in the discussion and
conclusion.
Effect size as included in the methods / abstract should be immediately
described and explained. the conclusion in the abstract does not refer to
Therapeutic effect and or safety.
In Background - I do not agree that Lap Appendectomy has not gained
widespread acceptance. In the majority of surgical units - this is what we do.
Background last sentence - suggest saying ....LA or OA gives better patient
outcome rather than saying - is superior.
Method - OK.
You have included SAGES and EAES, what about IPEG?? (International
Pediatric Endosurgery Group)
I think hospital cost shopuld be left out if all the studies included cannot be
compared. When the paper deals with several articles from countries where the
funding models are so disparate, this does not serve as any useful parameter.
While we study immediate or early postoperative complications, it is much more
interesting I think to look at incidences of late adhesive obstructions. It could be
postulated that a minimally invasive approach will in the long term lead to lower
incedences of adhesions and or adhesive obstructions. This would be a true
benefit of a minimally invasive approach.
Methodological quality assessment: second sentence can be excluded, as this is
in the table.
Operating time - many studies focus on operating time, and with a Minimally
Invasive approach - we all get better with time - I question the continued focus on
operating time, I do not see this as so important.
When we study Postoperative pain, The way this is studied, it will only tell us if
Pain was well managed in the hospital (studies) rerally it should be analgesia use
that was studied to see if there was any clinical difference.
Thirty studies reported post-op wound infection rates.
What proportion of cases were perforated or simple, and how does this relate to
the cases studied. When we do a meta-analysis of appendectomy studies - we
also know that all these cases are not the same, and studies will all have
selection bias.
relating to UTI - do the articles studied comment on patient cathetrisation and
relation to UTI??
The discussion has numerous grammatical and syntax errors.
I think Figure 1 - 12 should be combined and summarised as results only into
perhaps two tables.
Having 12 figures or tables is meaningless, and may be of interest to
statisticians, but not to a surgical or GE readership.
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, and I have assessed the statistics in my report.
Declaration of competing interests:
i declare that I have no competing interests