My View Points on SCI papers and Review Process

1. My View Points on SCI papers and Review Process HuiCai, M.D. Renal Division Emory University School of Medicine Atlanta, Georgia October 23, 2012

2. Outlines • SCI background • SCI in china • Detail in SCI manuscript review process • How to address the problems that you encountered during SCI submission

3. What is SCI ISI: Institute for Scientific Information SCI: Science Citation Index (科学引文索引) or (Stupid Chinese Index) Impact Factor (影响因子) Journal Citation Report (期刊排行榜)

4. The Impact Factor • One of the quantitative tools for ranking, evaluating, categorizing, and comparing journals • A measure of the frequency with which the "average article" in a journal has been cited in a particular year or period • To provide a gross approximation of the prestige of journals in which individuals have been published

5. SCI Publications • Quality is more important than quantity • Papers published in a good journal are usually better than those published in a less known journal

6. Significance of IF • Use IF to judge the quality of journals/magazines • Guide our submission of manuscripts to journals/magazines • Help decide subscriptions to journals/magazines

7. The Journal Citation Reports • The Science Edition contains data from roughly 6,620 journals in the areas of science and technology. China has 81 journals included

8. Using the SCI Wisely • ISI does not recommend that SCI users depend solely on citation data in their journal evaluations • Citation data are not meant to replace informed peer review • The best way for academic evaluation: Combined peer review and SCI citation

10. Unique Features of SCI • 即通过以前发表的论文被其它论文的引用情况，来说明论文的影响力 • 不仅作为一部文献检索工具使用，而且成为评价科研成就、学术水平的一种权威依据 • 大学、科研机构、个人被SCI收录的论文总量及被引用的次数，基本可以反映大学、科研机构、个人科学研究，尤其是基础研究的能力与学术水平 • “勿轻视SCI，忽滥用SCI.”

11. ISI Database-Web of Science • Science Citation Index Expanded (SCI- Expanded ) 1945—present • Social Sciences Citation Index (SSCI)--1956-present • Arts & Humanities Citation Index (A&HCI)--1975-present

12. Top SCI Journals (2004)

13. Top SCI Journals (2008)

14. Top SCI Journals Usually publish the results from the research projects that make breakthrough in theories, methods or techniques which have broad and significant implications

15. Majority of SCI Journals Will publish the results from research projects that utilise available theory, methods or techniques to solve problems or filling gaps of knowledge in the chosen discipline

16. Top 10 SCI Journals from China (2003)

17. Top 10 SCI Journals from China (2008)

18. Your Research Projects

19. Your reseach interests • Your grant application • You are completing your work as proposed. • Surprising findings • Basic frame of your manuscript (MS) • Personal habits • Collaboration work • Collegial discussion

20. Where do you submit your MS • This is very important!! • Research area • Pure basic sciences vs clinical research vs translational research • Familiar with mission of each Journal • Specialty vs General • Productivity vs Quality

21. High profile journals

22. High Profile clinic papers

23. How to write SCI paper • Firstly decide which journal you want to submit your paper • Follow required format • It is very helpful to use Reference Manager or Endnote for citation of your reference • Cover letter and suggesting potential reviewers or excluding reviewers • Finding out turn-around time and WAIT!

24. Introduction • Long vs short introduction • At least covering rationale why you want to perform your study. • You need to introduce relevant background • In the end, you usually briefly summarize what your key findings are in your manuscript

25. Methods and Materials • This is the least difficult part of your papers. • But you should quote what you have used if you have published the methods before. • Actually you can write down even you have not completed your research project. • Detail vs brief • In clinical research paper, it is very important to include population data, including criteria, excluding criteria, drop-out rate, follow-up, etc.

26. Results • It is better to use subtitle to present your results. • Arrange your figures or tables accordingly. • Simply layout the results, but you need to tell what you were looking for and used what method in the beginning of each section. • In the end of each section, explain the meaning of your results, i.e. indicating or suggesting that …

27. Discussion • First paragraph: Reiterate what your important findings are. • Last paragraph: Summarize your key or novel finding and its significant in the field. • Middle few paragraphs: Difficult parts. • Usually expanding your findings, meaning, mechanism, speculation. • Discussing the difference of your study from published data and explain why • You can quote other investigators’ similar findings to support your conclusion.

28. Last part of your manuscript • Acknowledgement • Disclosure • Reference

29. Basic Review Process • After submission according to Journal’s requirments. • Editorial review processing: Can turn down your paper within 7-10 days without even sending out you paper. • Assign the reviewers: Usually assign two reviewer and but most 3 reviewers. In latter case, associate editor or chief editor will be serves the third reviewer. • Review usually takes 2-3 weeks to completion. • Editorial decision • Then lthey will send a letter to you.

30. Editor Decision • Editorial level rejection • Reviewer assignment • How to choose the reviewer? • Final decision

31. Review Criteria • Overall Manuscript Rating (Required): TOP 10%, 25%, 50%, 75%Significance of Research Findings (Required): TOP 10%, 25%, 50%, 75%Novelty of Findings (Required): TOP 10%, 25%, 50%. 75%Experimental Design and Quality of Data (Required): TOP 10%, 25%, 50%, 75%Recommendation (Required): Reject, Major revision, Minor revision, Accept

32. Review Criteria cont • Has the author stated that they have IACUC, IRB, or equivalent approval, if the study involves animals or humans? (Required): Yes, or NoIs there any question of violation of APS's Guiding Principles in the Care and Use of Animals? (Required): Yes, or NoIs the manuscript the right length? (Required): Yes, or NoAre all of the figures and tables necessary? (Required): Yes, or NoIs the use of figure color scientifically necessary? (Required): Yes, or No

33. Cover Letter • Very important. • It should include the following components: • Your title of MS • Brief introduction of paper: new or novel. • Suggesting reviewers for reviewing your MS including reviewers’ name, title, contact information. • Suggesting reviewers that you don’t want them to revise your MS.

34. Sample of Cover letter for 1st submission

35. Sample of Cover letter for 1st submission Cont

36. Sample of Cover letter for 1st submission Cont

37. Cover lettre format • Dear Editor： • Thank you for your prompt review of our work. We wish to thank the reviewers for their constructive comments. We appreciate the opportunity to improve our manuscript and found the comments and suggestions very helpful in revising our manuscript. In response to your E-mail from February 10, 2008 concerning the manuscript—MS #2008-12-1275, entitled “***************”, we have made a great efforts to address all the concerns raised by reviewers. •  The following are the changes made in the revised manuscript: •  To address the physiological relevance of our study, we have performed additional experiments including immunohistochemistry, western blot and RT-PCR to show endogenous sortilin expression in the kidney, •   We have performed additional experiments to determine the effect of 。。。. These new data are incorporated into the revisedFigure 2A and 2B. • We have provided a complete negative control for Co-IP showing that EGFP-tag itself does not immunoprecipitate NCC. The new data will be added to the revised Figure 3B. The original Figure 3B is replaced by new Figure 3C. • In addition, we have revised parts of the introduction, results, discussion and methods highlighted in red font according to the new data and reviewers’ suggestions in this revised manuscript. •  Our point by point responses to the comments of the reviewers follow. The reviewer’s comments are shown in italics and are followed by our responses. •  We believe that the above mentioned efforts have significantly improved this revised manuscript and hope that it is acceptable for publication in your journal. Thank you in advance for your efforts on this revised manuscript. •  Sincerely, •  Name

38. Sample of Cover letter for revision • Dear Dr. Siegel: • Thank you for your prompt review of our work. We wish to thank the reviewers for their constructive comments. Although editor and reviewers found our work interesting, the manuscript was not acceptable for publication without major revision. We greatly appreciate the opportunity to improve our manuscript and found the comments and suggestions very helpful in revising our manuscript. In response to your E-mail from February 10, 2009 concerning the manuscript—MS JASN-2008-12-1275, entitled “WNK4 enhances the degradation of sodium chloride cotransporter (NCC) through the lysosomal pathway via sortilin, a novel lysosomal targeting receptor”, we have made a great efforts to address all the concerns raised by reviewers. Given the need for new experiments to response to reviewer concerns, I called Ms. Bonnie O'Brien in JASN editorial office and requested the extension of times for revision. The due day for the revision was extended to the end of June 2009.

39. Sample of Cover letter for revision Cont • The following are the changes made in the revised manuscript: • To address the physiological relevance of our study, we have performed additional experiments including immunohistochemistry, western blot and RT-PCR to show endogenous sortilin expression in the kidney, especially in distal convoluted cells. These new results are added as new Figure 6 in the revised manuscript. • We have performed additional experiments to determine the effect of sortilin WT and sortilin TRU on NCC protein expression in the absence of WNK4 to serve as additional control groups. These new data are incorporated into the revisedFigure 2A and 2B. • To more carefully examine the effect of sortilin on NCC protein expression and avoid the concerns of type 2 error, we have performed more experiments and re-done the statistical analysis by ANOVA as suggested by reviewers. The new data are shown in the revised Figure 2D in the revised manuscript.

40. Sample of Cover letter for revision Cont • We have provided a complete negative control for Co-IP showing that EGFP-tag itself does not immunoprecipitate NCC. The new data will be added to the revised Figure 3B. The original Figure 3B is replaced by new Figure 3C. • Based upon the suggestion by reviewer #2 we have re-done immunostaining experiments with quantitative analysis to compare the control group with the WNK4 group and shown that WNK4 does increase NCC colocalization with the lysosomal marker in the presence of lysosomal inhibitors, Leupeptin and E64, indicating that WNK4 promotes NCC targeting to lysosome for degradation. The original Figure 6 has been replaced by new Figure 7 in the revised manuscript. • As suggested by reviewer #2, original Figure 7A has been omitted and the statement concerning interaction between WNK4 and sortilin has been modified in the text. The Figure 7B is re-labeled as new Figure 8 in the revised manuscript.

41. Sample of Cover letter • In addition, we have revised parts of the introduction, results, discussion and methods highlighted in red font according to the new data and reviewers’ suggestions in this revised manuscript. • Our point by point responses to the comments of the reviewers follow. The reviewer’s comments are shown in italics and are followed by our responses. • We believe that the above mentioned efforts have significantly improved this revised manuscript and hope that it is acceptable for publication in JASN. Thank you in advance for your efforts on this revised manuscript. • Sincerely, •  M.D. • Assistant Professor of Medicine and Physiology

42. Accepted Letter • Dear Dr. On behalf of Editor-in-Chief Eric Neilson and Associate Editor, Dr. Alfred George, I am pleased to inform you that your manuscript is now suitable for publication without further revision and will appear in the nextavailable issue of the Journal of the American Society of Nephrology (JASN) following receipt of the final manuscript files.We aim for the papers we publish to be accessible to a wide readership and have been paying particular attention to the titles and abstracts. Titles should be 10-12 words long without colons, and abstracts devoid of unnecessary jargon and detail. Please check through these parts of your paper once more before uploading the final files. The editors reserve the right to modify the title and abstract further as needed to improve readability.  Please make sure to check the revised versions on your proofs for any errors.

43. Accepted Letter cont • The final version of your manuscript will need to be uploaded into Manuscript Central as a revised manuscript. Please submit the text and tables in one Word file.  Your figures will need to be uploaded as a TIFF or EPS file.   We do not in general allow any modifications to the figures unless those modifications have been requested by the editors or reviewers. Any other changes must be requested and granted before the paper is accepted for publication.It is a pleasure to receive and publish manuscripts of this quality in JASN.  I deeply appreciate your support of the journal, and we look forward to the opportunity to consider further manuscripts from your group.Sincerely yours,Vivian Siegel, PhDExecutive Editor, JASN

44. Minor revision letter • Dear Dr. • The review of your manuscript that was submitted to the JASN is complete and the Associate Editors and referees have provided us with an assessment of the paper. • The Editors and Reviewers find the work interesting and potentially appropriate for publication in JASN. However, a number of concerns have been raised by the reviewers, which preclude us from publishing the manuscript in its current form. We would like to be able to reconsider the manuscript and hope you can successfully address the concerns outlined below by the reviewers. • Among these, the issues of most importance to address in a revised manuscript are the reviewers’ comments regarding the need to test a second structurally unrelated Epac agonist, and better explanation for certain disproportionate effects (e.g., lack of proportional correlation between degree of transporter phosphorylation and urea permeability).

45. Minor revision letter cont • We hope you will be able to address these issues and submit a revised manuscript to us. Please let me know how you choose to proceed. If you choose to resubmit, we request that the revised manuscript be submitted electronically according to the "Instructions for Authors" available on our web site (www.jasn.org). The revised manuscript must be submitted within three months of receipt of this letter. If we do not receive the revision by that time, you will need to submit the paper as a new submission. • The Editorial Team of the Journal of the American Society of Nephrology thanks you very much for the opportunity to review this interesting work. Please contact me if you have any questions, or wish to discuss timing of the resubmission. •  Sincerely, •  Vivian Siegel, PhD • Executive Editor, JASN

46. Major revision letter • Dear Dr. : Experts in the field have carefully reviewed your manuscript titled, "RAS-GRP1 STIMULATION ENHANCES UBIQUITINATION AND ENDOCYTOSIS OF THE SODIUM CHLORIDE COTRANSPORTER," and, although they found merit in your study, they have raised a number of serious concerns that preclude its acceptance in the present form. Concerns were raised regarding data interpretation and presentation. However, I invite you to respond to the reviewers' comments and revise your paper accordingly. The revised version will be reevaluated by the original reviewers. Please be aware that this invitation does not guarantee eventual acceptance of your manuscript.The revision is due by 5th Mar 2010, six (6) months from today. If you do not request an extension to this deadline or submit a revised manuscript within 6 months, we will consider the manuscript withdrawn from submission to American Journal of Physiology - Renal Physiology. However, if you wish to submit the manuscript to another journal within the 6-month time frame, you must officially withdraw your manuscript from the journal American Journal of Physiology - Renal Physiology. Please contact at dpisconte@the-aps.org if you wish to withdraw your manuscript.To successfully submit a revision, follow the instructions below.Regards,MDEditor-in-ChiefAmerican Journal of Physiology: Renal Physiology

47. Reject letter • Dear Dr. Your manuscript has been reviewed by referees who specialize in the subject matter addressed by the submitted material. The general and specific comments of the referees are below. Although the referees felt the study was very interesting, I regret to inform you that the reviewers raised serious questions about several aspects of the study and submitted low priority ratings. In particular, both referees had the folowing concerns: 1) that the data quality was not always adequate, 2) that some of the conclusions drawn were not supported fully by the data given, 3) that additional controls are needed, 4) that some of the data appears internally inconsistent and 5) that the study lacks focus. Accordingly, I must reject your manuscript for publication in the American Journal of Physiology - Renal Physiology. I hope that the reviewers' comments will be of assistance to you if you decide to submit your work elsewhere. If you choose to rewrite your manuscript and resubmit it to AJP: Renal Physiology, you must resubmit it online as a de novo manuscript where it may be assigned to a new Associate Editor and new reviewers. It will not be treated as a revision. You must complete all required submission forms and pay the $50 submission fee. No exceptions will be made. I thank you for submitting your work to the American Journal of Physiology - Renal Physiology, and hope that the outcome of this particular review will not discourage you from sending future manuscripts to us.Regards,Associate EditorAmerican Journal of Physiology - Renal Physiology

48. How to respond to reviewer’s critiques • Rule of thumb: • Answer all the questions. • Carry out 4/5 suggested additional experiments for Major revisions • For minor revisions, answer all the questions and usually perform the suggested experiments rather easily. • Again, cover letter is very important and needs to lay out what you have done in the revised MS. • Use the itemized bullet to tell reviewer what you have done to address their concerns.

49. Questions

50. Thank You • GOOD LUCK WITH YOUR PAPER SUBMISSIONS !!!