Writing and presenting in English

1. Writing and presenting in English Dr. Hai-Feng CHEN 10/15/2013

2. Writing Abstracts,Proposals, and Letters • good abstracts • clear proposals • appropriate letters

3. ABSTRACTS • An abstract is an extract of the essence of your work. • Abstracts are not summaries; they are more concise and clearer than summaries. • Abstracts give what was discovered, how it was done, how it fits with other research, and what it suggests for future research.

4. ABSTRACTS • The difficulty in writing an abstract is that the abstract must be short. • Most journals tell authors to send in abstracts of as few as 150 words or less. • Conference abstracts sometimes require as few as 50 words. • Writing a good abstract requires extreme discipline.

5. ABSTRACTS • Writing an abstract requires unusual cognitive and linguistic discipline. • Excess words must be carefully eliminated. • The clarity of the words will determine. • If others will read your work. • If readers will accurately report its information to others.

6. ABSTRACTS • Stay within or under the required number of words. • Edit carefully. • Have a colleague who knows your work well edit. • Edit again. • Check your word choices and structures against other recent abstracts in the journal to which you plan to send your paper.

7. PROPOSALS • Proposals for presenting at conferences are relatively easy to write. • However writing proposals for grants is considerably more difficult.

8. Proposals to Conferences • Writing proposals for presenting at conferences is similar to writing abstracts. • Brevity is important. • Each conference will have its proposal requirements and deadlines posted on its website. • Usually the conference prefers a one-page proposal.

9. Proposals to Conferences • The proceedings are usually published so that this gives you a publication. • However, give careful consideration before having your work published this way. • Because a science journal will not consider publishing work that has been published elsewhere.

10. Proposals for Grants • lengthy matters • requiring information about your research • the background • its purpose • its value to the grant-giving organization

11. Proposals for Grants • First-time applications for a grant are often unsuccessful, but do not be discouraged. • If yours is rejected, detailed information about why it has been rejected will accompany the rejection. • Next you should carefully rewrite the grant addressing the reasons it was rejected, and resubmit.

12. Cover Letters • Submissions to journals today are done electronically, and including a brief electronic cover letter is appropriate. • Such letters are easy to write and have no need to be original, witty, or eloquent.

13. Cover Letter

15. Cover Letter • Dear Prof. P. J. Stang, • Please find the enclosed our manuscript “Mechanism of KIX Binding Induced pKID Folding”, submitted to JACSfor publication. • Sincerely yours, • Prof. Chen

16. Cover Letter • Manuscript ID 09-PONE-RA-09147 • Dear Prof. Langowski, • Please find the enclosed modified version of our manuscript “***”, and the detailed answers to the points raised by referees. • In this modified manuscript, we invite Prof. O. Wiest to improve the language. We also took into account all the observations of the referees, and we add some comments in the manuscript. • We would like to thank them for the very thorough reading of our manuscript and useful remarks. • Sincerely yours, • Prof. Chen

17. Comment of referee 1 • This work is a simulation analysis of the folding kinetics of pKID. Interestingly, an analysis of the induced fit verus conformational selection mechanism is presented. • The manuscript appears to be technically sound apart from the following points: • Minor points: • (a) Multiple trajectories have been performed and the author needs to compare the results obtained from the individual simulations and use them to assess error bars for all quantities evaluated and their effect on possible conclusions. • (b) The quality of the figures needs to be improved. • (c) The standard of English needs to be improved.

18. Comment of referee 2 • This is a nice paper. The problem is interesting, the simulations are well done, and the results are well presented. I have no doubt that readers will find it of interest. I have only two comments. The first still relates to the English, which still needs improvement before it can be accepted for publication. • The second to added three references. • To give the author an idea of the corrections needed, below I have made some editing of the Abstract.

19. Decision of editor [09-PONE-RA-09147] • Thank you for submitting your manuscript "Post-translational Modification of Phosphorylated KID from Molecular Dynamics Simulation" to PLoS ONE. After careful consideration, we believe that your study may have the potential to be published by PLoS ONE provided you revise your paper fundamentally, as described below. You must revise accordingly and explain your revisions in a covering letter if you wish for us to consider your paper further for publication

20. Decision of editor [09-PONE-RA-09147R1] • Thank you for submitting your manuscript "Molecular Dynamics Simulation of Phosphorylated KID Post-translational Modification" to PLoS ONE. After careful consideration, we believe that your study has the potential to be published by PLoS ONE provided you revise a few fundamental aspects of your paper, as described below. You must revise accordingly and EXPLAIN your revisions in a covering letter IN DETAIL if you wish for us to consider your paper further for publication.

21. Decision of editor [09-PONE-RA-09147R2] • Thank you very much for submitting your manuscript "Molecular Dynamics Simulation of Phosphorylated KID Post-translational Modification" for review by PLoS ONE. Unfortunately, the format in which you submitted your manuscript makes it very difficult to handle for me and for the referees.

22. Decision of editor [09-PONE-RA-09147R3] • Thank you very much for submitting your manuscript. After careful consideration, we have concluded that your manuscript has the potential to be published in PLoS ONE. However, since another referee still had some reservation about the writing style, I would request you to follow closely the suggestions for improvement outlined below. I realize that you have already made an effort at rewriting, but I believe that following the suggestions can only improve the paper. After I have received the revised version, I will make a decision without further refereeing.

23. PLoS ONE Decision of editor [09-PONE-RA-09147R4] • I am pleased to inform you that your manuscript has been deemed suitable for publication in PLoS ONE. • Thank you for this submission and please understand that this had to undergo several cycles of minor revision; comparing the current version to the initial submission, I must say that the paper has substantially improved in readability and clarity.

24. Rebuttal letter • Dear Prof. Langowski, • Manuscript ID 09-PONE-RA-09147R3 • Thank you very much for your kind suggestion to improve our manuscript. According to the referee’s request, we write this letter about our modification. • At first, we add three references relative to our research. (p16) • Then, we try our best to go over our manuscript. • The detail modification is as follow: • After post-translational modification by phosphorylation. (p2) • phosphorylated KID (pKID) (p2)

25. Comment of Reviewer1 • The manuscript by Qin and Chen addresses an important question in RNA folding, whether recognition of RNA is an induced fit or conformational sampling process. • I recommend the authors repeat all their simulations with the Arg52 to Gln mutation on U1A and see how their results are changed. • If these simulations show a significant difference in TS structure and folding kinetics, it would greatly strengthen this reviewer's confidence.

26. Comment of Reviewer 2 • The paper addresses an interesting problem. • This is a good and thoughtful paper and I am of the opinion that the investigator is knowledgeable and experienced in this type of simulations. • The work is solid, and I think it would find many interested readers. As the number of such papers is on the rise for proteins, I expect that the same will take place for RNA.

27. Decision Letter MS ID#: RNA/2009/020081MS TITLE: Induced Fit or Conformational Selection for RNA/U1A foldingDear Dr. chenWe are pleased to inform you that the above manuscript is acceptable forpublication. It may be worth putting together a couple of figures into a single panel. It makes reading easier.Best wishesEric Westhof

28. Introductory and Application Letters • Informal as to be impolite. • ‘Hi,’ or ‘Hi Petey,’ or ‘Hi Dr. Young’ • Overly formal • ‘My Very Dear Dr. Young’ or ‘Honored Professor’.

30. Introductory and Application Letters • The most effective letters of introduction or application are simple and direct. • You attach your resume and perhaps one other relevant brief document. • Letters of recommendation are sent later. • It is absolutely essential that you make no mistakes, even of a minor nature. • Edit your letter before you send it.

31. Introductory and Application Letters • Keep a file of letters you send and letters you receive. • These will serve you as a future resource for appropriate letter writing. • The danger of email correspondence is that you may write so quickly and send in email. • The best advice is to compose your letters in a word-processing program, copy and paste them into email.