Comments to Authors

Dear Mr Liu,I write you in regards to manuscript # JPR-2013-276 entitled "Effect of Light and N:P Supply Ratio on Nutrient Drawdown Patterns and Elemental Ratios in Batch-Cultured Chlorella sp." which you submitted to the Journal of Plankton Research.I am very sorry to have to say that in view of the criticisms of the reviewers found at the bottom of this letter and in the attached file, your manuscript cannot be accepted for publication in the Journal of Plankton Research.Summarizing, the Associate editor advises that all three reviewers recommend the manuscript be rejected and have significant concerns regarding the definition/description of major concepts and the experimental design and presentation of results. The AE hopes the authors find the reviews useful for a revision for another venue.I realise that this will be a disappointing outcome for you, but you will see that the specialist reviewers raise some fundamental concerns about your study. It may well be that by doing further work and presenting it in accordance with the reviewer's comments you might consider publishing the work at some point in the future.Thank you for considering the Journal of Plankton Research for the publication of your research. I wish you every success in finding an alternative forum for publication for this manuscript. JPR will not consider a revised version or any similar submission in future.I hope the outcome of this specific submission will not discourage you or your colleagues from the submission of future manuscripts.Yours sincerely,Dr Roger HarrisEditor-in-Chief, Journal of Plankton Researchjpr.editorialoffice@JPR Impact Factor has risen again to 2.435 in 2012; average interval from submission to first decision - 4 weeksReviewer(s)' Comments to Author:Reviewer: 1Comments to the AuthorManuscript: JPR-2013-276Title: Effect of light and N:P supply ratio on nutrient drawdown patterns and elemental ratios in batch-cultured Chlorella sp.Authors: Liu, J., Li, Z., Guo, J., Fang, F. & Yang, M.General comments:The authors investigated the impact of changes in N:P supply ratios and light on the N and P drawdown and C:N:P stoichiometry in Chlorella sp. Understanding the coupling between N and P limitation and elemental stoichiometry, including modulation by light availability, is interesting, though not new. The manuscript lacks an explanation on the novelty of the findings, and it is not clear what this study exactly adds to our understanding. More importantly, I have serious doubts on the applied experimental set-up, the results are very poorly presented and discussed, and the text needs thorough editing. Furthermore, there are many errors in the wording, references, and the use of terms. Below I listed a few points for the authors to improve the manuscript.1. The experiments were performed in batch cultures, where growth conditions change during the course of the experiment. For instance, nutrients are consumed, light availability is reduced and growth rate decreases. These dynamics are different compared to chemostats, where net population growth and the extent of nutrient limitation are fixed once in steady state (i.e. growth equals dilution rate). Working in batch cultures instead of chemostats has implications for applying theory, and in defining the limiting resource. It is not clear to me whether the authors are aware of this. E.g. how can the stoichiometry of cells keep pace with the nutrient supply ratio in batch cultures (Page 9, lines 57-59).2. The authors should more clearly describe the terms they use. For instance, what is exactly meant with their critical and optimal ratios? How did the authors calculated these ratios and which assumptions are needed? Also, it is not clear to me how nutrient drawdown was exactly assessed.3. Why are the critical and optimal ratios not based on the elemental ratios, but on the drawdown ratios? There is often not a direct correlation between drawdown and particulate elemental ratios, for instance due to excretion of organic nutrients.4. The authors should show the temporal changes in biomass and elemental ratios (and possibly nutrient concentrations). This will help to understand the observations, for instance, it will better illustrate when nitrogen, phosphorus and light become limiting. Did the authors also measure pH? In dense cultures, pH may increase to high levels and have consequences for phytoplankton growth.观测生物量与元素比例的变化，是否测量酸碱度，在高浓度的藻液中，酸碱度也可能成为限制的因素5. Exponential growth was set at growth rates >0.1. This seems very low to me, especially for Chlorella sp. What were the maximum growth rates at the different light intensities? I would define growth limitation when growth deviates from maximum growth rates.对数生长期的生长界限设置为0.1，可能偏低，特别是对于小球藻，在不同的光照条件下，最大生长速率是多少，当生长速率低于某一值时，就可以理解为生长收到了限制6. Did the authors test the ‘scraping’ of the organic matter from GF/F filters? How sure are the authors that all, or at least a known amount, was measured with the elemental analyzer? For the C:N ratios, this is obviously not a problem as these are measured at the same time, but it can be a problem for calculating C:P and N:P ratios.如何确保所有的有机物都被挂下来了，碳氮可以使用元素分析仪测量，磷呢7. The experimental set up should be explained in more detail. How long did the experiments run? How many replications were used? Were the cultures axenic? Were the cells acclimated to the respective light conditions and culture medium? In the discussion it is stated that cells were grown shortly in N and P depleted medium, which should be mentioned in the methods. How may these initial limitations have affected the observed dynamics? Do the authors also have NH4+ data? Why do the authors not show the cell count data? If available, this could then also be used for cellular C, N, and P quota, which will greatly help understanding the results.实验运行的时间，有没有重复，有没有外来生物污染，细胞是否适应了该光照强度与培养基，是否测量了氨氮，是否有细胞计数，如果有了，将可以用来说明细胞营养物含量8. The authors should better explain how they obtained the homeostasis coefficient H, and what the underlying assumptions are. It is also not clear to me how one can link the initial nutrient concentrations with the cellular stoichiometry obtained in stationary phase?内稳态指数如何计算，基本假设是什么9. Many aspects of the discussion are not clear or contain errors. For instance, how can phytoplankton cells reduce nutrient concentrations to levels lower than their R* (Page 11, lines 6)? Ribosomal RNA does not contain more P than N (Page 11, lines 36-37). How can the optimal nutrient supply ratio be critical for judging excessive nutrient consumption (Page 11, lines 52-57)? Phytoplankton do not require equal amount of nitrogen and phosphorus (Page 11, lines 58-60). It is not clear why nutrient assimilation capacity, rather than phosphate concentration, affected the total amount of nitrate taken up by the cells, as phosphate was the experimental variable.讨论不详细，包含错误，例如：细胞如何将将营养物质降低到低于R*,RNA包括更多的氮而不是磷，为什么最优氮磷比可以用来判断营养物的过量消费10. Although Chlorella sp. presumably can store excess N under P limitation, the discussion on this part is very hypothetical and would be stronger if the authors could back this up with cellular elemental data (Page 12, lines 10-25).在磷限制下，细胞可以存储更多的氮，是否可以使用细胞内部元素含量说明11. The meaning of paragraph 4.2 is not clear to me (Page 12, lines 27-56).12. Comparing the presented data with literature requires a more detailed explanation. For instance, how were the enlisted studies selected, based on which criteria? Are these all studies available on the topic? Were these studies also performed in batch cultures or in chemostats?与文献对比需要更多详细的解释，选择文献的标准是什么，是否都是研究的同一主题，是否使用的是相同的培养方式13. Do the authors have any idea about the light climate in the flasks? Denser cultures have more self-shading and thereby reduce the average light availability. In other words, are the authors sure about light limitation/inhibition? Is there information available on photosynthesis vs.irradiance relationships in Chlorella? When does limitation/inhibition occur? This is important for the discussion of light effects (Page 14, lines 12-60).对光环境的看法，随着细胞浓度的增加，细胞的自我遮蔽，是否有数据支持光照限制，这对讨论光照的影响很重要References1. Many references contain errors, or are incomplete.参考文献标注不全，包涵错误Figures and tables1.It is not clear to me what the difference exactly is between Figure 1 and 2, except for theswapped axes.图一与图二有什么明显的区别2.Although Figure 3 is potentially interesting, the currently described data is not supporting itentirely. A model parameterized with the data would be better for making such a scheme. 图三使用模型描述效果会更好3. For Figure 4 it would help if the authors write the specific ratios on the y-axes, instead of using arrows.4. Table 1: Is there not a standard BG-11 protocol the authors can refer to? What is A5?BG 11是否有标准配方，A5指的什么5. Table 5: Very unclear table. For comparison, it would help if the units for light intensities would be similar. 光照单位是否相同Reviewer: 2Comments to the AuthorGeneral:This MS is based on very interesting ideas, and could certainly further the field. Unfortunately, despite very good English there are too many unclarities in the MS that made it very difficult to follow what the authors had done. I think it is essential that we continue this kind of research. This MS, however, needs a thorough clean up and rewrite before it can be acceptable for publication.有很多地方没有叙述清楚以至于难以理解作者的意思，需要一个清晰的思路重新写作Specific:3:4 this is a very strange first sentence in an abstract. I would start with a general sentence on the background, or with a clear sentence why this was done.摘要先说明背景3:19 What is the critical ratio? This needs to be explained before it can be used.临界氮磷比是什么4:4 Have I missed something? Why use this tense. Better is Phytoplankton plays4:6 Very general, and why mention only N and P. Without having computed it, I would think that Si and Fe are more relevant on a world scale.，Si Fe 比氮磷更加重要4:10 Introduce abbreviations N and P4:12 Why call something a Redfield ratio, and then not cite Redfield?4:21 I do not understand this sentence. So non-balanced growth refers to light and carbon uptake here, or not? It cannot refer to the nutrients as such as these are used for the computation of the critical ratio.4:32 What are water blooms? An interesting citation here is: (Hillebrand et al. 2013) 为什么提到水华4:44 Introduce drawdown properly. What does this mean, how do you define and use it?适当的介绍drawdown,有什么意义，如何定义与使用4:50 I am not sure whether I agree. Even a fixed consumption ratio can involve luxury consumption 固定消费速率与过量消费的关系4:59 Is this not more or less the same under equilibrium assuming that algae are not homeostatic at all?5:3 I would argue that light is the only energy source in photoautotrophs. FULL STOP. Carbon availability can of course affect stoichiometry as well.是否考虑了碳的有效性5:15 So what is nutrient draw-down in the stationary phase? Is this relevant at all?在稳定期的营养物消费速率5:35 This sentence does not make sense5:48 What is nutrient co-limitation? Are the authors suggesting that only at the critical ratio the draw down is constant. That is not what they said earlier.6:8 Effects of light only on stationary cells?6:17 The institute of hydrobiology, which one?6:29 Why introduce a day-night rhythm? What was the volume of the vessels. Where was the light measured. This is relevant since the light extinction in dense vessels of algae is extremely strong. Why did the authors not bubble the cultures to make sure that the algae stayed In suspension?为什么不曝气6:39 Replication?6:47 I am completely confused on the experimental protocol. When were the cultures harvested? Was there one end-point measurements of everything, or a time course. Looking at the graphs I assume the former, but I cannot find it. Again what was the level of replication?实验重复7:8 I know that there was something suspicious in this paper, now I know. The authors used DEMONIZED water7:10 phosphorus not phosphorous7:28 I am confused. What does this mean particulate material was scraped from the filter?为什么是刮下来的7:50 I am very confused. An intercept of zero implicitly means that the draw down is exactly the same ratio as the availability. What would happen if the N:P ratio of the medium was 1000, I am sure there would be some N left at the end of the experiment, and no way are both nutrients zero.So I do not understand this.为什么截距是07:52 Her this needs to be defined very clearly, one is related to the draw down the other to the cellular content or not?8:10 There is no such publication as Sterner 2002没有这个参考文献8:38 Throughout batch cultivation? I do not see a time line.8:57 I see no difference between figs1 and 2. As far as I can see it exactly the same data are displayed. Except perhaps the ends of the curves where one of the nutrients was close to zero.图一与图二是一批数据9:2 first? Again some hidden timeline which is not presented.9:14 statistically different? How? 统计学的不同，为什么10:28 If I am honest, I have given up roughly here. There are so many points that I do not understand in this MS, that I find it impossible to continue reviewing this work in the detail I did until now. I believe the ideas are very valid, and the work is very interesting, but there are simply too many instances of unclarity, which makes it impossible to judge the merit of this work.11:51 two days? Triangular flask?11:59 Equal amounts of N and P. What kind of substances are made there?15:15 This is a very strange ending. No final sentence, no general conclusion没有结论Figs 1 & 2: the colour coding is inconsistent24:21 What is A5?A5是什么？Hillebrand, H., G. Steinert, M. Boersma, A. M. Malzahn, C. L. Meunier, C. Plum, and R. Ptacnik. 2013. Goldman revisited: faster growing phytoplankton has lower N:P and lower stoichiometric flexibility. Limnology & Oceanography 56:2076-2088.Reviewer: 3Comments to the AuthorThank you for inviting me to review this manuscript. Whilst the topic is of interest, and I normally both favour and support research in ecological stoichiometry and phytoplankton ecophysiology, I conclude that the large number of conceptual problems and methodological questions in the current manuscript unfortunately create major problems.大量的概念问题与方法问题I have made extensive editorial comments throughout the manuscript using Adobe Acrobat, and I very much hope that these suggestions will be of value to the authors when crafting a revised version for later submission to an alternative journal.。

HOW TO REVIEW A PAPERDale J.Benos,1Kevin L.Kirk,1and John E.Hall21Department of Physiology and Biophysics,University of Alabama at Birmingham, Birmingham,Alabama35294;and2Department of Physiology and Biophysics, University of Mississippi Medical Center,Jackson,Mississippi39216 M ost scientists acquire their training in manuscript review not through instruction but by actually doing it.Formal training in manuscript analysisis rarely,if ever,provided.Editors usually choose reviewers because of expertise in a given subject area and availability.If an individual repeatedly submitsbad reviews,it is likely that that person will not be asked to review a manuscriptagain.Being invited to review a manuscript is an honor,not only because you arebeing recognized for your eminence in a particular area of research but also becauseof the responsibility and service you provide to the journal and scientific community.The purpose of this article is to define how best to peer review an article.We willstipulate several principles of peer review and discuss some of the main elements ofa good manuscript review,the basic responsibilities of a reviewer,and the rewardsand responsibilities that accompany this process.Proper reviewer conduct is essen-tial for making the peer review process valuable and the journal trustworthy.ADV PHYSIOL EDUC27:47–52,2003;10.1152/advan.00057.2002.Key words:publications;ethics;peer review;reviewer responsibilitiesLike any skill,the art of reviewing manuscripts is one that improves with practice.Although a person is not born with the knowledge or ability of how to be a good reviewer,the characteristics(e.g.,fairness,thor-oughness,integrity)of that person certainly contrib-ute to the activity.Unfortunately,it is rare tofind a scientist whose formal training has incorporated in-struction in the art of reviewing.Nonetheless,the techniques of peer reviewing a manuscript can be nurtured and developed.Yet,peer review is a recog-nized and critical component of the overall publica-tion process that confers“added value”to a submitted paper.Moreover,editors are dependent on the iden-tification of a cadre of“good”reviewers that they can rely on for quality control and process efficiency. Reviewers,for the most part,act in this capacity from a sense of duty,selflessness,and a desire to contribute in an important way to the maintenance of high stan-dards and veracity in their specific areas of research. Usually,no monetary compensation is,or should be, provided.This article will serve as an introduction to peer re-view.Our intent is to identify issues and ethics of the review process,not to provide a comprehensive set of guidelines for all aspects of the review process. We will focus on the peer review of research manu-scripts submitted to scientific journals,but many of the elements of peer review can be applied to other areas,such as grants and books.Several questions will be addressed.What constitutes a good review and reviewer?How should the review of a manuscript be approached?What elements of a review are most useful to the authors and editors?Should a manuscript be reviewed differently depending on the nature of the journal?It is our contention,based on experience,1043-4046/03–$5.00–COPYRIGHT©2003THE AMERICAN PHYSIOLOGICAL SOCIETY on March 7, 2006 Downloaded fromthat if a reviewer acts as an“author advocate,”then many potential problems that may arise during the peer review process will be avoided.For example,a reviewer should treat a manuscript being reviewed as he/she would want his/her own paper treated,i.e., provide a critique that is positive,critical yet objec-tive,and balanced,contains no personally offensive comments,and is returned promptly.When specific criticisms are made,the reviewer should indicate pre-cisely what the problems are and how they may be overcome.A confusing or uninformative critique is not helpful either to the authors or to the editor.If the reviewer disputes a point made by the authors,he/ she should provide explicit justification for his/her argument(e.g.,literature citations).Unjustified biases on the part of the reviewer have no place in peer review.A reviewer also has a responsibility to famil-iarize him/herself with all aspects of the manuscript unless directed by the editor to focus on a specific area.This may entail reading previous,related articles from the authors or other papers in thefield.It is fair to assume that the authors of the submitted manu-script are passionate about their work and that they have made a legitimate effort to perform and interpret their experiments carefully.However,the other hat that a reviewer must wear is that of the“journal advocate.”As a journal advocate,the reviewer’s job is to make sure that the best possible science appears in print.The purpose of peer review is to ensure1) quality,checking that no mistakes in procedure or logic have been made;2)that the results presented support the conclusion drawn;3)that no errors in citations to previous work have been made;4)that all human and animal protocols conducted follow proper review and approval by appropriate institu-tional review committees;and,very importantly,5) that the work is original and significant. ELEMENTS OF MANUSCRIPT REVIEW Manuscript review can be divided into two main cat-egories:the technical and the ethical.Both aspects are primarily concerned with making the manuscript better and ensuring that it is reporting trustworthy data.An example of reviewer instructions is presented as Table1.Note that points1,2,4,5,and6are con-cerned with more technical issues.Is the writing clear, concise,and intelligible?Is the manuscript logical?Does it make a significant and novel contribution to thefield?Are there any fatal methodologicalflaws?Are all thefigures clear and necessary?Point3deals primarily withethical issues.Are there any concerns with regard to theproper use and care of animals?If human studies weredone,were they conducted with the prior approval ofthe subjects and institutions?Did the human protocolsconform to prevailing ethical and legal standards?Point7likewise falls under an ethical realm,only not for theauthors but for the reviewer.The manuscript must betreated in a confidential manner.Thus a reviewer mustnot only provide an unbiased evaluative analysis of the structural components of a manuscript but must do soin an acceptable,ethical context.REVIEWER’S ETIQUETTE ANDRESPONSIBILITIESIt is important to remember that a reviewer is asked toprovide an informed opinion about a manuscript.Thedecision whether the manuscript will be published ismade solely by the editor.Thus the editor must beable to discern very precisely the reviewer’s thoughtsand weigh that opinion with or against those of theother reviewers and his/her own.An editor will ap-preciate a substantive evaluation of a manuscript.If areviewer disagrees with the conclusion of an author,it is incumbent upon the reviewer to provide defini-tive reasons or appropriate citations,not simply makeremarks such as,“I just don’t believe your data,”or“Itcan’t possibly be so.”If a reviewer has a bias againstthe author,he/she should recuse him/herself from reviewing the paper.A reviewer must be knowledge-able about the topic and have a clear understanding ofthe historical context in which the work was done.Because many manuscripts nowadays are collabora-tive efforts between different laboratories using amyriad of different techniques,it is unlikely that anysingle reviewer will be expert in all of the protocols encountered in a given paper.The reviewer should comment only on those aspects of the work withwhich he/she has familiarity;making the editor awareof this is helpful.Again,let us reiterate,the most important rule is to follow the golden rule:treat all manuscripts in the same manner that you would wantyour own treated.The responsibilities of a reviewer can be summarizedas follows.on March 7, 2006Downloaded from1.The reviewer should provide an honest,critical assessment of the research.The reviewer ’s job is to analyze the strengths and weaknesses of the research,provide suggestions for improvement,and clearly state what must be done to raise the level of enthusiasm for the work.The reviewer should not manipulate the process to force the authors to address issues interesting or important to the reviewer but peripheral to the objective(s)of the study.2.The reviewer should maintain con fidentiality about the existence and substance of the manuscript.It is not appropriate to share the manuscript or to dis-cuss it in detail with others or even to reveal the existence of the submission before publication.There are some exceptions,if approved by the editor.One exception is that the reviewer may want a junior colleague to have the experience of reviewing and therefore may ask him/her to collab-orate on a review.However,if this is done,your collaborator on the review should also agree to maintain con fidentiality,and the editor should be informed of the participation of this additional per-son.Some journals require editor approval before a colleague or student is asked to view a submitted paper;others do not.3.The reviewer must not participate in plagiarism.It is obviously a very serious transgression to take data or novel concepts from a paper to advance your own work before the manuscript is pub-lished.4.The reviewer should always avoid,or disclose,any con flicts of interest.For example,the re-TABLE 1Criteria for manuscript review1.Scienti fic quality of the workⅢAre the methods appropriate and presented in suf ficient detail to allow the results to be repeated?ⅢAre the data adequate to support the conclusions?2.PresentationsⅢWriting:Is it clear,concise,and in good English?ⅢTitle:Is it speci fic and does it re flect the content of the manuscript?ⅢAbstract:Is it brief and does it indicate the purpose of the work,what was done,what was found,and the signi ficance?ⅢFigures:Are they justi fied?Are they sharp,with lettering proportionate to the size of the figure?Are there legends to explain the figures?ⅢTables:Can they be simpli fied or condensed?Should any be omitted?ⅢTrade names,abbreviations,symbols:Are these misused?3.Research violationsⅢAre there violations of the Guiding Principles in the Care and Use of Laboratory Animals?ⅢIf the research involved human subjects,were the studies performed in accordance with the Declaration of Helsinki?If you have concerns about the welfare of animal or human subjects used by the authors,include written comments to the editor.4.RatingⅢAssign a rating on the reviewer form;rank the manuscript relative to other work in the same field.5.Con fidential commentsⅢProvide comments regarding the novelty and signi ficance of the manuscript.ⅢProvide a recommendation about the manuscript ’s suitability for publication in the journal;these comments will not be returned to the author(s).ments for authorsⅢOn the reviewer form,provide speci fic comments,preferably numbered,on the design,presentation of data,results,and discussion.DO NOT include recommendations for publication on the second page.ⅢPlease be certain that your comments to the author(s)are consistent with your rating recommendation.7.Privileged documentⅢThis manuscript is a privileged communication;the data and findings are the exclusive property of the author(s)and should not be disclosed to others who might use this information in their research.ⅢThe manuscript,illustrations,and tables should be destroyed upon completing the review or,if anticipating a revision,kept con fidential until the review process is complete.ⅢIf you have shared responsibility for the review of this manuscript with a colleague,please provide that person ’s name and institutional af filiation.on March 7, 2006 Downloaded fromviewer should decline to review a manuscript ona subject in which he/she is involved in a conten-tious dispute and does not feel that a fair review can be provided.The reviewer should also avoid biases that influence the scientific basis for a review.One example of this is a bias that favors studies with positive rather than negative results.Another example is if the reviewer has a close personal or professional relationship with one or more of the authors such that his/her objectivity would be compromised.Scientific merit should be the basis for all reviews.5.The reviewer should accept manuscripts for re-view only in his/her areas of expertise.Although editors try very hard to match manuscripts with the most expert reviewers,sometimes mistakes are made.It is unfair to the authors and to the overall review process if the referee does not have the expertise to review the manuscript ad-equately.The exception to this general rule is when an editor specifically asks for your view as a“nonexpert”or seeks your opinion on a special aspect of the manuscript(e.g.,statistics).6.The reviewer should agree to review only thosemanuscripts that can be completed on time.Sometimes,unforeseen circumstances arise that preclude a reviewer from meeting a deadline,but in these instances the reviewer should immedi-ately contact the editor.It is unfair to the authors of the manuscript for reviews to be inordinately delayed by tardy referees.Delaying a review can sometimes lead to charges by the authors that the reviewers(who undoubtedly work in the same area)are“stonewallng”in order to publish their related workfirst,thus establishing priority.7.The reviewer also has the unpleasant responsibil-ity of reporting suspected duplicate publication, fraud,plagiarism,or ethical concerns about the use of animals or humans in the research being reported.8.The reviewer should write reviews in a collegial,constructive manner.This is especially helpful to new investigators.There is nothing more discour-aging to a new investigator(or even to a more seasoned one)than to receive a sarcastic,destruc-tive review.Editors are not trying to determinethe scientific prowess or wittiness of the re-viewer.The reviewer should not shy away fromdiscussing the weaknesses(or strengths)of astudy,however.No one likes to have a paperrejected,but a carefully worded review with ap-propriate suggestions for revision can be veryhelpful.In fact,an author should prefer to havehis/her paper rejected if the review process un-covered errors in the study.SUMMARYReviewing is both a privilege and responsibility.Ittakes time to prepare a useful,critical review.More-over,it clearly is a service to the journal,to the authors,to science at large,and to the reviewer be-cause the reviewer becomes privy to the latest incutting-edge research.Most journals do not pay refer-ees,although most do provide acknowledgement inprint to the editorial board and external referees ineach issue of the journal and/or,like the American Physiological Society,by holding a yearly PublicationsBanquet at the Experimental Biology meeting.Peerreview is the heart and soul of scientific publishing.Editors rely on reviewers to assess quality and to determine which of the many manuscripts competingfor space will be published.Therefore,the most im-portant reward for you as a reviewer is your contri-bution to the quality of published science.We submit that,regardless of the perceived preemi-nence of any particular journal,you should approachthe review of each research paper the same way.Table2provides a checklist for the essential elementsthat should be addressed in any review.Table3sum-marizes what a handling editor is concerned withwhen evaluating the quality of a review and reviewer.TABLE2Checklist for reviews:issues for comment1.Importance of research question2.Originality of work3.Delineation of strengths and weaknesses ofmethodology/experimental/statistical approach/interpretationof results4.Writing style andfigure/table presentation5.Ethical concerns(animal/human)on March 7, 2006Downloaded fromFrom a practical point of view,publishing your own manuscripts depends on the quality and altruism of other peer reviewers,and you undoubtedly desireyour own work to be evaluated carefully and fairly.There are many aspects of providing good construc-tive reviews.Some of these are best learned through your mentors and your own experience.However,the most important traits are courtesy,fairness,and punctuality.Thus,when peer reviewing,follow the golden rule:treat other manuscripts as you wouldwant your own to be treated.The entire peer review process,which in essence determines the public record of science,is based on trust —trust between authors and editors and trust between editors and reviewers.The quality and integrity of the entire sci-enti fic publishing enterprise depends in large mea-sure on the quality and integrity of the reviewers.RESOURCES Very little de finitive research into the practice and effectiveness of peer review has been done,although groups such as the Council of Science Editors,the American Medical Association,the American Chemi-cal Society,the American College of Emergency Phy-sicians,and the Committee on Publication Ethics rec-ognize the importance of such information.Forexample,the Journal of the American Medical Asso-ciation has sponsored four International Congresses on Peer Review in Biomedical Publications (10).The September 2001issue of Academic Medicine was dedicated to a discussion of review criteria and re-viewer behavior for research manuscripts (5).A book summarizing the latest research on different aspects of peer review has been published by the British Medical Journal (4).A number of general articles on peer review and the role of a reviewer have been published (2,6,7,9).Several articles concerning reviewer selection criteria and evaluation also exist (1,3,8).AUTHOR AFFILIATIONSDale J.Benos,PhD,is a former Editor-in-Chief of theAmerican Journal of Physiology -Cell Physiology ,serves on five editorial boards of biomedical journals and has served on nine others in the past.He iscurrently Chair of the Publications Committee of theAmerican Physiological Society and Chair of the De-partment of Physiology and Biophysics at the Univer-sity of Alabama at Birmingham.Kevin L.Kirk,PhD,is Professor of Physiology and Biophysics at the University of Alabama at Birming-ham.He is a member of two editorial boards and is Director of the Integrated Biomedical Sciences Grad-uate Program at the University of Alabama at Birming-ham.John E.Hall,PhD,served as Editor-in-Chief of the American Journal of Physiology -Regulatory,Inte-grative,and Comparative Physiology ,is currently Editor-In-Chief of Hypertension ,and is a member of the editorial boards of eight other journals.He is Past President of the American Physiological Society and Chair of the Department of Physiology and Biophysicsat the University of Mississippi Medical Center.We thank Margaret Reich for helpful discussions and comments on the manuscript.Address for reprint requests and other correspondence:D.J.Benos,Dept.of Physiology and Biophysics,The Univ.of Alabama at Bir-mingham,1918Univ.Blvd.,MCLM 704,Birmingham,AL 35294–0005(E-mail:benos@).Received 11December 2002;accepted in final form 20March 2003References1.Baxt WG,Waeckerle JF,Berlin JA,and Callaham ML.Who reviews the reviewers?Feasibility of using a fictitious manu-script to evaluate peer reviewer performance.Ann Emerg Med32:310–317,1998.2.Black N,van Rooyen S,Godlee F,Smith R,and Evans S.What makes a good reviewer and a good review for a general medical journal?JAMA 280:231–233,1998.3.Caelleigh AS,Shea JA,and Penn G.Selection and qualities of reviewers.Acad Med 76:914–916,2001.4.Godlee F and Jefferson T.Peer Review in Health Sciences .London:BMJ Publishing Group,1999.TABLE 3Editor ’s evaluation of review and reviewer 1.Thoroughness and comprehensiveness2.Timeliness3.Citing appropriate evidence to support comments made to author4.Providing constructive criticism5.Objectivity6.Clear statement to editor as to the appropriateness and priority of research for publication on March 7, 2006 Downloaded from5.Joint Task Force of Academic Medicine and the GEA-RIME Committee.Task force report—review criteria for re-search manuscripts.Acad Med76(9),2001.6.Polak JF.The role of the manuscript reviewer in the peer reviewprocess.Am J Roentgenol Radium Ther165:685–688,1995.7.Siegelman SS.Assassins and zealots:variations in peer review.Radiology178:637–642,1991.8.Van Rooyen S,Black N,and Godlee F.Development of thereview quality instrument(RQI)for assessing peer reviews ofmanuscripts.J Clin Epidemiol52:625–629,1999.9.Weller AC.Editorial.Peer review in US medical journals.JAMA263:1344–1347,1990.10.Weller AC.Peer review:do studies prove its effectiveness?TheScientist October29,2001,p.39.on March 7, 2006Downloaded from。

How to peer review?General ideas1.Don’t share the manuscript or to discuss it in detail with others. The reviewer shouldmaintain confidentiality.（对所评阅的文章必须保密）2.To provide an honest, critical assessment of the work.To analyze the strengths and weaknesses, provide suggestions for improvement, and clearly state what must be done to raise the level of enthusiasm for the work.（对文章的优缺点做出评论，并明确指出应该怎么修改才能提升现有的文章质量）3.The reviewer should write reviews in a collegial, constructive manner. A carefully wordedreview with appropriate suggestions for revision can be very helpful.（以建设性的、学术性的口吻对文章进行评价，并给出建设性的修改再投递的意见）4.Support your criticisms or praise with concrete reasons that are well laid out and logical.（给出的评价应该附加有支撑观点的具体原因）5.评阅步骤：(1)Read the manuscript carefully from beginning to end before considering the review.Get a complete sense of the scope and novelty.(2)Move to analyzing the paper in detail, providing a summary statement of yourfindings and detailed comments.(3)Use clear reasoning to justify each criticism and highlight good points and weakerpoints.(4)If there are positive aspects of a poor paper, try to find some way of encouraging theauthor while still being clear on the reasons for rejection.（如果被拒绝的文章中有部分闪光点，可以鼓励作者。

1、目标和结果不清晰。

It is noted that your manuscript needs careful editing by someone with expertise in technical English editing paying particular attention to English grammar, spelling, and sentence structure so that the goals and results of the study are clear to the reader.2、未解释研究方法或解释不充分。

In general, there is a lack of explanation of replicates and statistical methods used in the study.Furthermore, an explanation of why the authors did these various experiments should be provided.3、对于研究设计的rationale:Also, there are few explanations of the rationale for the study design.4、夸张地陈述结论/夸大成果/不严谨：The conclusions are overstated. For example, the study did not showif the side effects from initial copper burst can be avoid with the polymer formulation.5、对hypothesis的清晰界定：A hypothesis needs to be presented。

6、对某个概念或工具使用的rationale/定义概念：What was the rationale for the film/SBF volume ratio?7、对研究问题的定义：Try to set the problem discussed in this paper in more clear,write one section to define the problem8、如何凸现原创性以及如何充分地写literature review:The topic is novel but the application proposed is not so novel.9、对claim,如A＞B的证明，verification:There is no experimental comparison of the algorithm with previously known work, so it is impossible to judge whether the algorithm is an improvement on previous work.10、严谨度问题：MNQ is easier than the primitive PNQS, how to prove that.11、格式（重视程度）：In addition, the list of references is not in our style. It is close but not completely correct. I have attached a pdf file with "Instructions for Authors" which shows examples.Before submitting a revision be sure that your material is properly prepared and formatted. If you are unsure, please consult the formatting nstructions to authors that are given under the "Instructions and Forms" button in he upper right-hand corner of the screen.12、语言问题（出现最多的问题）：有关语言的审稿人意见：It is noted that your manuscript needs careful editing by someone with expertise in technical English editing paying particular attention to English grammar, spelling, and sentence structure so that the goals and results of the study are clear to the reader.The authors must have their work reviewed by a proper translation/reviewing service before submission; only then can a proper review be performed. Most sentences contain grammatical and/or spelling mistakes or are not complete sentences.As presented, the writing is not acceptable for the journal. There are problems with sentence structure, verb tense, and clause construction.The English of your manuscript must be improved before resubmission. We strongly suggest that you obtain assistance from a colleague who is well-versed in English or whose native language is English.Please have someone competent in the English language and the subject matter of your paper go over the paper and correct it ?the quality of English needs improving.Reviewer 4Reviewer Recommendation Term: RejectOverall Reviewer Manuscript Rating: 25Comments to Editor: Reviewers are required to enter their name, affiliation and e-mail address below. Please note this is for administrative purposes and will not be seen by the author.Title (Prof./Dr./Mr./Mrs.): Prof.Name: XXXAffiliation: XXXXXXXXXXXXXXXXXXXXXXXXXXxManuscript entitled "Synthesis XXX。

Dear Editor,Please, find below the itemized list of the corrections brought to our ms (N°NPP-07-0364RR) on the basis of the last reviewers comments.Reviewer #11.There is only one major concern about the question.... "that recent studies... of cha nges in 5-HT RNAm and protein expression induced by memory formation and drugs..., eventually lead to arborization? The authors in the rebuttal letter stated that: "It is likely they might contribute. The point is that we do not know how these 5-HT protein and RNAm receptors are expressed in the mouse brain so that we cannot speculate on their role in promoting dendritic spine growth in mice treated with the 5-HT4Rs agonist". However, in the new introduction authors mentioned that "there is not yet evidence that such compounds enhance learning-induced structural plasticity" (last lines of the first paragraph). This last statement seems speculative and/or not justified by the available evidence.This statement has been deleted along with the following reference:Izquierdo I, Medina JH (1995) Correlation between the pharmacolog y of long-term potentiation and the pharmacology of memory. Neurobiol Learn Mem 63:19-32Associate editor1. I was surprised that the authors did the control experiment reviewer #3 requested (i.e. to check spine densities in cortical regions unassociated with olfactory memory) but make no mention of these results in the Discussion.A sentence in the discussion section (1st paragraph) states now that, in mice trained or pseudo trained in the OTM, “the compound was not found modify spine density on pyramidal neurons laying in the primary visual cortex area, a region unrelated to the memory pathways”2. I am still concerned about the small number of experimental subjects that make up each group. A concern is that the effect sizes reported are not huge and this statistic is only reported in the legends to Figures 1 and 3 yet they refer to significant effects in figures 2 and 4 as well but give no values in the figure legends.In the revised version of the manuscript the sample size issue was addressed replicating experiments. The main effect (SL65.0155 enhancing learning-induced spine growth) was observed (i) across different batches thus increasing its internal validity and (ii) on several related measurements (behaviour and morphology of apical, oblique and basal dendrites). Keeping in mind that the C57Bl/6 strain is an inbred strain (showing minimal inter-individual variability in behaviour and brain characteristics) it is rather customary using 6-8 per group. Moreover, unbiased sampling procedures applied throughout the experiment (blind counting of spines, random selection of the brains t o be processed for spine analysis) made us comfortable with the validity of the statistical results.The statistical values are now reported also in figures 2 and 4. In addition, new symbols indicating t he correct p-level for post-hoc tests have been added to figure 2.Minor changes1. Text (Typographical errors corrected)Page 8, paragraph title: correct concentration for SL65.0155 is 0.01mg/KgPage 8, line 8 and last line: correct name is RS39604Page 8, line 9: correct name is SL65.01552. FiguresSymbols indicating p level have been changed on figure 2 according to post–hoc results described in the results section.3. Acknowledgment section has been addedWe thank the reviewers for their suggestions along with their positive comments and hope that our manuscript can be now considered for publication in Neuropsychopharmacology.Martine A mmassari-TeuleCorresponding author。

编辑反馈的内容编辑反馈的内容Anatomical entity recognition with a hierarchical framework augmented by external resources PLOS ONEThank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit, but is not suitable for publication as it currently stands. Therefore, my decision is "Major Revision."We invite you to submit a revised version of the manuscript that addresses all of the concerns raised by the two reviewers. It is critical that you specifically address the following issues: 1) Provide more details on your methodology and data sources (possibly with examples), so that the reviewers can better evaluate the summary results provided in the tables; 2) Describe precisely what will be publicly available; 3) Thoroughly edit your revised manuscript before submission. Please note that PLoS ONE does not provide copy editing.We encourage you to submit your revision within forty-five days of the date of this decision.When your files are ready, please submit your revision by logging on to and following the Submissions Needing Revision link. Do not submit a revised manuscript as a new submission. Before uploading, you should proofread your manuscript very closely for mistakes and grammatical errors. Should your manuscript be accepted for publication, you may not have another chance to make corrections as we do not offer pre-publication proofs.If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.In addition, when submitting your revision please include the following items:A rebuttal letter that responds to each point brought up by the academic editor and reviewer(s). This letter should be uploaded as a 'Response to Reviewers' file.∙ A clean revised manuscript as your 'Manuscript' file.∙ A marked-up copy of the changes made from the previous article fileas a 'Revised Manuscript with Track Changes' file. This can be done using 'track changes' in programs such as MS Word and/orhighlighting any changes in the new document. ∙For more information on how to upload your revised submission, see our video:/everyone/2021/05/10/how-to-submit-your-revised-manuscript/If you choose not to submit a revision, please notify us.Yours sincerely,Ramin Homayouni, Ph.D.Academic EditorPLOS ONEJournal requirements:When submitting your revision, we need you to address these additional requirements:1. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold your manuscript until you get in touch with us with the accession numbers or DOIs necessary to access your data. If you wish to make changes to your data availability statement, please describe these changes in your cover letter and we will make them on your behalf.Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have beenconducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.Reviewer #1: PartlyReviewer #2: Yes2. Has the statistical analysis been performed appropriately and rigorously?Reviewer #1: NoReviewer #2: Yes3. Does the manuscript adhere to the PLOS Data Policy?Authors must follow the , which requires authors to make all dataunderlying the findings described in their manuscript fully available without restriction. Please refer to the author’s Data Availability Statement in the manuscript. All data and related metadata must be deposited in an appropriate public repository, unless already provided as part of the submitted article or supporting information. If there are restrictions on the ability of authors to publicly share data —e.g. privacy or use of data from a third party— these reasons must be specified.Reviewer #1: YesReviewer #2: No4. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographicalor grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: NoReviewer #2: Yes5. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, includingconcerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)Reviewer #1: This paper presents an interesting hierarchical framework to recognize anatomical entities, which is important in healthcare domain. Authors also bring the importance and the challenges of this task. To the best of my knowledge, I summarize my comments and suggestions as follows:1) Features for the sequence labeling problems under CRF are comprehensive and acceptable. Authors include baseline natural language features, semantic features from external knowledge about Wikipedia and WordNet, co-reference, and dictionary matching.2) Authors conducted relatively comprehensive experiments to show the contribution of each individual features and combination of features to the overall precision and recall.3) Problem introduction and annotation are good too.However, some major points need to be fixed:1) The writing of this paper is really poor. All table references are not correct, grammar errors can be seen almost every paragraph. It is very very difficult to read. It took me hundreds of hours to understand what authors try to deliver. Let me just show examples based on the abstract: a) The first sentence is not a complete sentence. "To develop....in medical records."b) "They infer relevant anatomical...in the record but also by other diverse..." ==> "They infer relevant anatomical entities based on bothexplicit anatomical expressions in the record and other diverse... "c) "The hierarchical framework was demonstrated..." ==> "The hierarchical framework was demonstrated...in F1 comparing to ???"many others in the paper!!!!!2) For the annotation, authors used A3 to check (A1, A2), then obtain the coefficient. Why not A3->(A1, A2), A1->(A2, A3), and A2->(A1, A3), then obtain the average coefficient? What if there is a annotation conflict, meaning that all 3 annotators do not agree? In addition, authors claim that their golden standard is not perfect, then why you still use them to do evaluations?3) From the experimental results, CF seems to be the smallest contribution to the precision in table 5 and table 8, then why adding CF gets a lotincrease in table 6 and 9? I don't believe this result. Can you give some explanations.In addition, some suggestions,It would be great if the paper gives some formal definition of eachconcept and shows some real or toy examples in figure. They can help readersto catch the point.Reviewer #2: The manuscript by Yan Xu et al. describes the construction of an anatomical entity recognition framework based on a machine learning algorithm. This framework can recognize not only explicit expressions of anatomical entities, but also implicit expressions such as diseases, clinical treatments, and clinical tests. The authors insisted that the recognition ofthe implicit expressions was important because the implicit expressions are abundant in clinical records and it is from these implicit expressions that medical experts can infer the anatomical entities described in the documents.The framework consists of three layers of entity recognizers, all of which are based on conditional random field (CRF) models. The first layer is themulti-class CRF recognizer developed for the 2021 and 2021 I2B2 challenge;this layer recognizes entities of three semantic classes: diseases, clinical treatments, and clinical tests. The other two recognizer layers are developedin this study. One (the second layer) is for explicit anatomical expressionand the other (the third layer) is for implicit expression.For use in the training and testing of the CRF models, the authorscarefully made an annotated corpus of 300 clinical records (i.e., thedischarge summaries in this study). The resulting annotations include 16690 explicit anatomical entity tokens and 5564 implicit anatomical entity tokens.The authors used the following features for the construction of the CRF models and considered the relative impact on the recognition performance using precision, recall, and F-score: baseline features (a standard set of useful features for general named entity recognition tasks), ontological features DF1 and DF2 (based on some of the representative anatomical ontologies: UMLS, MeSH, RadLex, and BodyParts3D), coreference features, and world knowledge features WF1, WF2, WF3, and HF, which is based on the dictionary constructed from the terms in Wikipedia and WordNet,whose definition sentences contain explicit anatomical entities, for the purpose of extracting implicit anatomical entities; HF is referred to as a hierarchical feature.This study is original and addresses an important task in processing medical documents in general. Their analytical approach seems to be sound in the sense of ordinal research on natural language processing. Therefore, this manuscript seems to warrant publication in PLOS ONE.The main criticism I have is the lack of consideration of concrete instances of anatomical dictionaries, clinical record corpuses, annotations, and experiment results. The authors only provided several numerical tables of the precision, recall, and F-score. All the main conclusions were drawn from observation of these numerical tables. Although I know that this style is common in NLP research papers, I believe that without an investigation of concrete instances, readers cannot evaluate the relative impact of the many factors that will affect the final performance.With only a little thought, one can list up many factors that affect the final results: data sources selection for the construction of the anatomical dictionaries, relative contribution of the (four) data sources on the performance, whether there exists some particular anatomical term in the four dictionaries that has a significant effect on the performance, the total size of anatomical dictionaries, semantic type of terms included in the anatomical dictionaries, type of clinical records, total number of clinical records and sentences which are annotated by the experts, target semantic types, the choices of machine learning algorithms, and the selection of the features for the CRF models, as well as many other factors. However, observation of the series of numerical tables yields only limited information about the impact of the factors and what entities can/cannot be recognized under the proposed framework.Therefore, at very least, the authors should provide a part of the list of 16690 ―explicit anatomical entity tokens‖ and 5564 ―implicit an atomical entity tokens‖ with their numbers of occurrences in the corpus, because these define the problem that this manuscript is addressing.In addition, the authors should discuss what terms in the anatomical dictionary match the annotated tokens and/or the results of theBegin/Inside/Outside (BIO) calling by the CRF model. Then some explanation ofthe relative impact of the framework components should be provided based onthe concrete instances of matching results.A second criticism concerns the reproducibility of this study. Althoughthe authors wrote at the end of the abstract section, ―The resources constructed for this research will be made publicly available.‖ since the resources needed for the reproduction of this study are not provided at this time, I could not evaluate whether the results can be reproduced using the resources that the authors say will be eventually provided. I know that the authors have made a great contribution to the NLP research field, not only by introducing novel concepts, but also by providing many useful resources, including software and annotated corpuses, and so I believe that the resources that will be available to the public will be quite useful for NLP researchers, but I believe that it is quite important to meet the reproducibility criteria stated in the publication criteria of PLOS ONE(―described in sufficient detail for another researcher to reproduce the experiments described‖), and in order to meet these criteria, I expect thatthe authors will need to write additional paragraphs describing in sufficient detail how to reproduce the result tables. I believe that the results havebeen largely affected by the content of the dictionaries and annotatedcorpuses constructed by the authors, and therefore, without these resources,it will be quite difficult for other researchers to reproduce exactly the results described in the tables.Minor pointsPage 8, lines 7–10I do not understand the meaning of the numbers described in Table 4.What is the denominator of ―Coverage of explicit named entity‖? Total number of annotated tokens in the corpus? Or number of unique tokens annotated? In typical cases, rather simple anatomical terms such as ―brain‖, ―liver‖, and ―blood‖ frequently appear in the corpus, and of course these are matched readily to the anatomical dictionaries.Page 12, lines 7–13.The table numbering in the main text is not consistent with the actualtable numbers. (Table 4, ..., Table 9 in the main text should be Table 5, …, Table 10.)Page 14, lines 3–5Near the top of the DISCUSSION section, the author wrote: ―While the features based on the dictionary of anatomical entity expressions greatly improved the performance on explicit anatomical entities, they do not enhance th e performance on explicit anatomical entities.‖ But the second occurrence of the word ―explicit‖ should be ―implicit‖.6. If you would like your identity to be revealed to the authors, please include your name here (optional).Your name and review will not be published with the manuscript.Reviewer #1: (No Response)Reviewer #2: (No Response)[NOTE: If reviewer comments were submitted as an attachment file, theywill be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.]。