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andyfu125

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[资源] 一篇SCI paper的分娩全纪录经验之谈【转贴】

近来偶然看到一篇文章：
BMC Cancer. 2006 Jul 19;6:191. Links
Peroxisome proliferator-activated receptor gamma and spermidine/spermine N1-acetyltransferase gene expressions are significantly correlated in human colorectal cancer.
Linsalata M, Giannini R, Notarnicola M, Cavallini A.
文章本身没有特别的地方，杂志IF也只是在2-3之间。引人注意的是，在文章末尾杂志提供了Pre-publication history（http://www.biomedcentral.com/1471-2407/6/191/prepub）。由于文章大都老板亲自操刀，我很难体完全验一篇文章从投到发的全过程。人家杂志社目的可能在于强调fairplay，但像我这样的菜鸟却可以学到一些东西。现将这些资料整理如下，与感兴趣的战友们一起学习学习。

这是该文章的大致内容：
ODC（鸟苷酸脱羧酶）和SSAT（精胺/亚精胺N1-乙酰移酶）在polyamine（多胺）代谢过程中发挥重要调节作用；转录因子PPARγ参与调节脂肪细胞分化和葡萄糖代谢。作者在40个结肠癌病例中发现三种基因协调表达，并提出这可能和肿瘤发生相关。另外，由于k-ras突变在结肠癌发生过程中与细胞增殖和分化相关，作者还相应检测了这些基因在k-ras突变中的表达。

文章从一投到published一共历时两个半月：
Version1 （Original manuscript）Date: 4 May 2006
Version2 Date: 26 June 2006
Version3 Date: 5 July 2006
Published Date:19 July 2006

以下是一投后（Version1）三位reviewer的意见：
Reviewer 1（Debora L Kramer，不可思议，原文件中居然还附上reviewer的姓名！！！）：
一，评价
General（整体评价）
The authors present a reasonable interpretation of the data without overstating their findings. However, the differences between K-ras positive and negative data was marginal and thus, added little to the story.

Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached)
无

Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author can be trusted to correct)
无

二，建议
What next?: Accept after minor essential 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（原稿是意大利人写的）
Statistical review: No
Declaration of competing interests:
No.

整体来说这位Viewer还是很认真的，看名字好像是日尔曼人？！

附该reviewer在相关领域代表性文章：
Cancer Res. 2005 Jun 15;65(12):5390-8.
Tucker JM, Murphy JT, Kisiel N, Diegelman P, Barbour KW, Davis C, Medda M, Alhonen L, Janne J, Kramer DL！！！, Porter CW, Berger FG.
Potent modulation of intestinal tumorigenesis in Apcmin/+ mice by the polyamine catabolic enzyme spermidine/spermine N1-acetyltransferase.

Reviewer 2（Natalia A Ignatenko）：
一，评价：
General（整体评价）
无

Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached)
无

Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author can be trusted to correct)
The main significance of this paper is the analysis of the correlation between PPAR gamma mRNA levels and the presence of K-ras mutations in tumor samples. The polyamine metabolism in human colon adenocarcinomas has been extensively studied before.（这段评论似乎应该出现在General部分）
I would suggest the authors to discuss their results in greater details. Authors also should explain why did they focus on the evaluation of the mutational status of codon 12 and did not analyse codon 13 or 61 mutations.

二，建议
What next?: Accept after minor essential revisions
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being published
Statistical review: No
俄罗斯人有点儿漫不经心。

附该reviewer在相关领域代表性文章：
Mol Carcinog 2004, 39:91-102.
Ignatenko NA！！！, Babbar N, Mehta D, Casero RA, Gerner EW: Suppression of polyamine catabolism by activated Ki-ras in human colon cancer cells.

Reviewer 3（Francis RAUL，呵呵，劳尔！！！）：
一，评价：
General（整体评价）
This original study is well conducted and methods are clearly described. The data are concisely reported but the following aspects need clarification.

Major Compulsory Revisions (that the author must respond to before a decision on publication can be reached)
无

Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author can be trusted to correct)
1. Background, two last lines of page 4:
There is an apparent contradiction between the sentence: ”Induction of SSAT” typically gives rise to “growth inhibition”, and the following sentence “Moreover , increased SSAT activity has been observed in breast cancer”. This assumption has to be better explained or rephrased since it does not confirm that activation of SSAT is associated with an anti-proliferative effect.
附加所提及的原文
“Moreover, increased SSAT activity has been observed in breast cancer in comparison to normal tissue [10] and it has been suggested that high levels of the SSAT expression can exert tumour-suppressive effects [11-12].”

2. In the text of Results, Discussion and in Table 3:
The terms mutated K-ras or K-ras negative; K-ras wild-type or K ras positive are used alternatively and renders the text confusing. The same term should be used throughout the manuscript to distinguish mutated from non-mutated K-ras.
How are you excluding that tumor samples may present a mutated K-ras at another location than codon 12?

3. Discussion, end of page 10:
Do the authors mean that an increase of SSAT without a concomitant downregulation of the polyamine biosynthetic pathway (ODC inhibition) is unsufficient for counteracting tumor development? This point which is also evoked in the conclusions should be discussed by the authors (with some references). 考虑到这篇文章只做了表达检测，没有做调节，作者的这个论点确实有些玄，这位Raul够毒。
附加原文：
“Therefore, we can suppose that the increase in polyamine catabolic activity, as a result of PPARγ induction, could be not sufficient to counterbalance the abnormal increase in polyamine biosynthetic activity observed in tumour tissue.”

4. Table 3:
In order to standardize presentation with Tables 2, values for PPAR mRNA should be presented at the bottom of Table 3.表格就不传了，总之这个小建议作者后来采纳了。

二，建议
What next?: Accept after minor essential revisions
Level of interest: An article whose findings are important to those with closely related research interests
Quality of written English: Acceptable
Statistical review: No
Declaration of competing interests:
I declare that I have no competing interests below.
虽然接受了，但西班牙人不失犀利。

附该reviewer在相关领域代表性文章：
Int J Oncol. 2006 Aug;29(2):423-8.Links
Potentiation of apple procyanidin-triggered apoptosis by the polyamine oxidase inactivator MDL 72527 in human colon cancer-derived metastatic cells.Gossé F, Roussi S, Guyot S, Schoenfelder A, Mann A, Bergerat JP, Seiler N, Raul F！！！.

以下是作者对上述评审意见的反应：
Author's response to reviews（针对Version1的）
首先，作者向编辑表示文章格式已经按要求作出相应改动，并强调在一位a native English speaking colleague的帮助下“English has been improved”。接下来是作者对几位reviewer的回复：

Reviewer 1 (Debora L. Kramer)
“We agree with comment of the reviewer.”这个没什么说的，基本上就是顺风话。

Reviewer 2 (Natalia A. Ignatenko)
Comment - Authors should explain why did they focus on the evaluation of the mutational status of codon 12 and did not analyse codon 13 or 61 mutations ?
Answer - We have focused our attention on the evaluation of the mutated codon 12 of the K-ras since this mutation is mostly frequent (27% - 30%) in colorectal tissue as compared to mutated codon 13 (5% - 6%). Moreover, the mutated codon 61 occurs more frequently in other cancer tissues (1-3). Therefore, the percentages of mutated codon 13 and 61 would be very low in the 40 patients considered in our study.
这位reviewer刚好是做k-ras mutant的，作者可是撞到枪口上了！！！不过回答也算有理有据。

Reviewer 3 (Francis Raul)
1. Comment - Background, two last lines of page 4: there is an apparent contradiction between the sentence: "Induction of SSAT .... typically gives rise to growth inibition......" and the following sentence "Moreover, increase SSAT activity has been observed in breast cancer......" .
Answer - We have rephrased and better explained these sentences (Background section, pag. 4, three last lines)
附加改动后原文：
“Induction of SSAT plays an important role in lowering the polyamine pool and typically gives rise to growth inhibition as well as exerting tumour-suppressive effects [10-11]. Particularly, Wallace et al. have hypothesized that the increase in SSAT activity may be an attempt to reduce the polyamine pool in tumour cells. [12]”
避开了原来的矛盾之处。

2. Question- In the text of results, discussion and in table 3. The terms mutated K-ras or K-ras negative; K-ras wild-type or K-ras positive are used alternatively and renders the text confusing.
Answer - Through out the manuscript we have used the terms mutated and non mutated K-ras to indicate the colorectal tissues with and without K-ras mutation, respectively.
Question- How are you excluding that tumor samples may present a mutated K-ras at another location than codon 12?
Answer - Regarding the presence of a mutated K-ras at another location than codon 12, please see answer to reviewer 2.
这个回答太COOL了！！！

3. Question- Discussion of pag 10: do the authors mean that an increase of SSAT without a concomitant downregulation of the polyamine biosynthetic pathway (ODC inhibition) is unsufficient for counteracting tumor development?.
Answer - This issue has been discussed in greater details and supported by some references in the text (Discussion section, pag. 10, lines 19-23, and pag. 11, lines 1-15). 由于实验结果有限，此番大修作者也是煞费苦心，但好在能自圆其说。由于背景知识所限加上内容过冗，这里就不将原文列出了。

4. Question- In order to standardize presentation with table 2, values for PPAR mRNA should be presented
at the bottom of table 3.
Answer - Values for PPARg mRNA have been presented at the bottom of Table 3.

最后，作者根据这些改动给出了Version 2 manuscript。

在Version 2 manuscript投出后，编辑就格式方面给出了一点建议，以下是作者对的反馈：
Author's response to reviews（针对Version2的）
“To BioMed Central Editorial Production Team. We send to you the revised manuscript with the following changes in the format:
1. the titles from the list of the authors have been removed;
2. the figure (Figure 1) and the tables (Tables 1 and 2) have been referred to in the text.“
Yours sincerely
Michele Linsalata, B.D.（这只是硕士论文哦）
大功终于告成！！！

我个人的一点看法：
搜了一下几位reviewer的文章，方向都和本文十分贴近，而且级别要高一些。看来要想发文章只能接受来自于国外同行们的“审判“。值得注意的是，这些资料中提供了reviewer的姓名，却是咄咄怪事。当然也可能是我看的文章有限，少见多怪。
虽然本文只局限于表达，但在修改过程中作者提到还准备深入进行调节方面的工作，估计他们下一篇文章能好许多吧。但也有人更愿意一口气把表达、调节甚至功能都做了，憋个大paper。何去何从，仁者见仁智者见智吧。
另外，Version1 manuscript我大致看过，感觉意大利人的英语已经不错了，可人家还是认真地找了native speaker帮助修改。一方面说明态度问题，同时更表明英文在文章发表过程中真的很重要。

看完的同时，给兄弟俺评价一下吧！！
你们的回复是我发帖的动力