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1、1,Workshop on Scientific Writingin Medicine and Life Sciences科技论文写作研讨会Shantou University, November 2010Session 2- Writing a Manuscript,Patrick Choy, PhD, MD, FAHA, FIACS (蔡镇潮 ) Professor Emeritus in Biochemistry, Medical Genetics, Immunology and Pathology Special Advisor to the President and Dean of
2、 Medicine University of Manitoba,2,Acknowledgement,I acknowledge the help that I obtained from the “Biomedical English Writing and Reading Workshops for Students in China”, co-authored by Bill Orr and Yulin Li. I highly recommend it to students who want to write their first paper in English. I thank
3、 our colleagues in China for their submission of manuscripts to the focused issue of the 2000 Mol Cell Biochem (MCB) which I co-edited with Dr. Ricky Man, as well as the 2007 and 2010 focused issues of Biochem Cell Biol (BCB), which I co-edited with Dr. Frieda Law. The experience from reviewing thes
4、e manuscripts has been invaluable to me in preparing this workshop.,3,Papers Published in MCB, 2000Based on a Symposium in Hong Kong,Co-edited by Patrick Choy Ricky Man,4,Papers Published in BCB 2007Based on the First International Symposium in Shantou,Co-edited by: Patrick Choy Frieda Law,5,Papers
5、Published in BCB 2010Based on the Second International Symposium in Shantou,Co-edited by: Patrick Choy Frieda Law,6,International Symposium 2009,7,East-West Alliance Meeting 2010,8,Why do we need to publish papers,Publication is the accepted way for a scientist to communicate his/her work to colleag
6、ues and the general public. The publication of peer-reviewed papers indicate that the work has been found to be acceptable by peers. The number of publications and the quality of these publications, are indicative of the productivity of a scientist. In some institutions, the publication of a peer-re
7、viewed paper is a requirement for a PhD degree.,9,Sample Paper in BCB, August 2010,The paper is published in English with an abstract in French (Langlais et le franais sont des langues officielles; 英語和法語是加拿大的官方語言 ) The paper has undergone the Journals usual peer-review process. The e-mail address of
8、 the corresponding author is listed. The Journal is published by the National Research Council of Canada.,10,Characteristics of a Good Paper (I)(in the eyes of a reviewer),It does not take a major effort to read and understand the manuscript. The paper has a clear objective of the study, a reasonabl
9、e approach, good tabulation of results, and a fair discussion on how the work has advanced our knowledge.,11,Characteristics of a Good Paper (II)(in the eyes of a reviewer),There are no typographic or grammatic errors. A sloppily prepared paper is a poor reflection of the work done by the author. Th
10、e work is focused on a limited number of themes. The paper has a succinct review on the work done by others, and a clear rationale for carrying out the current study. The author has provided a strong justification for the experimental approach he/she used in the study. The work was done in full comp
11、liance with local regulatory committees/agencies.,12,Characteristics of a Good Paper (III)(In the eyes of a reviewer),The results are presented in a logical and sequential fashion. The paper has a thorough discussion on each segment of the results obtained. The overall contribution of the study to t
12、he understanding of the subject has been clearly articulated. The references are current, and organized in an acceptable fashion. The figures and tables are carefully constructed and the data are clearly explained in the legends. The units used are consistent throughout the study.,13,How to select a
13、 journal for your paper?,High Impact Factor? High Acceptance Rate? Good Self-Assessment is Important,14,How to select a journal for your paper (II),Decide between a general biomedical journal, or a specialized journal. General biomedical journals include Science, Nature, Cell, PNAS, Life Science, et
14、c. Specialized journals include Biochemistry, Am. J. Physiology, JPET, Neuroscience, etc. The choice of a journal is based on (a) the quality of the work, in comparison with the prestigious nature of the journal, (b) acceptance rate. The choice of a journal is also based on its (a) SCI rating, (b) e
15、ditorial board, (c) fast track review, (d) fast publication, (e) page charge- especially for color plates, (g) free reprints.,15,SCI Impact Factor (I),The SCI rating is organized by the ISI Web of Knowledge, which has indexed over 11,000 science and social science journals. It varies among disciplin
16、es (e.g. regenerative medicine and neuroscience are hot topics, but theoretical biology is not a hot topic) The impact factor refers to the average number of citations per paper in a journal. It has no bearing on the quality of the particular paper. The impact factor can be manipulated by a journal,
17、 e.g. a higher impact factor can be achieved by publishing more review articles.,16,SCI Impact Factor (II)(Examples),17,Other Matrices to Measure Impact,The open-access journal Public Library of Science ONE (PLoS One) announced in 2009 that other ways are available to calculate impact (alternative i
18、mpact data) of an article. On Jan 18, 2009, the managing editor of PLoS One in Research Triangle Park announced the new articles-level matrices which posts usage data, page views, citations from Scopus and CrossRef, social networking links, press coverage, comments, and user ratings. This new assess
19、ment has been accepted and used by some institutions.,18,What is next?,After you have selected a journal to submit your paper to, the next thing you have to do is obtain a printed copy of the journal. Read a few papers, and try to assess whether your work is suitable for submission to the journal. W
20、hen you have found the appropriate journal for submission, go to the Instruction to Authors. Follow the format outlined in the Instruction to Authors closely. A paper will be rejected by the editor if the author has not prepared the paper according to the prescribed format.,19,Instruction to Authors
21、 (I)(Every Journal has its own specific instruction to authors),Example: The Journal of Biological Chemistry (www.jbc.org) Resources for Authors Authors should review the following information before beginning a manuscript submission: Instructions to Authors: A description of JBCs style and format r
22、equirements for manuscripts for review. Online Submission Instructions: Iinformation on the online submission process and requirements. JBC Editorial Policies: An overview of JBCs publication policies. Papers in Press and Open Access information Acceptable biological and chemical abbreviations Abbre
23、viations of units of measurement and of physical and chemical quantities,20,Instruction to Authors (II),Instructions for Authors for JBC General requirements How to submit Initial manuscript submissionRevised manuscript submissionReport submission (formerly known as Accelerated publication)Final sub
24、mission of an accepted manuscript Organization of the manuscript Text, References, Tables and figures, RGB workflow, Supplemental data Publication charges, Page charges, Color figures, Halftones, Reprints, NIH-funded articles Author Choice option Chemical and mathematical usage, Enzyme activity data
25、, Protein and nucleic acid sequences, Genomic and proteomic studies, Structural studies, Database accession hyperlinks for JBC Online,21,Instruction to Authors (III),Organization of the manuscript for J. Biol. Chem. Formatted for standard 8.5-by-11-inch paper Single spacing throughout Two-column pag
26、e format, including Abstract through Discussion sections. Title section as well as references, footnotes, figure legends and tables at the end of the manuscript are in single-column format. One-inch left and right margins and 0.25-inch spacing between columns Text typed in 11-point Times New Roman M
27、anuscript is to be arranged in the following order: (a) title, author(s), complete name(s) of institution(s) and running title (b) abstract, (c) introduction, (d) experimental procedures, (e) results, (f) discussion (g) references, (h) footnotes, (i) figure legends, (j) tables, (k) figures(l) supple
28、mental data 7. Number all pages, including those with figures. Note: Any paper submitted without page numbers will be deleted, and you will be asked to resubmit with pages numbers.,22,The first steps to put the paper together,After reading through the Instruction to Authors, you need to: Put all dat
29、a into figures and tables, and have them in front of you. Look at them carefully, and arrange them in a logical sequence. Develop a plan to interpret your data, and how your data and interpretation will fit into the bigger story.,23,Now, You are ready to write the paper,Get plenty of coffee (or tea)
30、. Find a quiet place free of distraction. Turn off the cell phone Organize the data, and put the figures and tables in front of you. Jot down the framework on how you want to present your study. Decide on a tentative title.,24,How to Start Writing a Paper (1),Writing a paper is not an easy task. The
31、re is no such thing as “writing is difficult for me, but it is easy for you”. It is difficult for every one of us. Do not start writing if you do not know what you want to write about. Do not start writing if you cannot put the task as your first priority. Often, you will make excuses and stop writi
32、ng just because concentrating on writing is a difficult undertaking. One can always find something easier to do.,25,How to Start Writing a Paper (II),There is no such thing as a perfect paper. You have to accept the limitation of your own study. Put all data that you have obtained for this study in
33、proper figures and tables, and arrange them in a logical sequence. Careful analysis of the results obtained will allow you (or your group) to have an idea on whether the objective has been achieved. It is unlikely that the available data will provide you with all the answers to your objective/questi
34、ons. Based on the data obtained, you may have to modify your objectives (e.g. limit the scope or ask a slightly different question) in order to complete the study.,26,How to Start Writing a Paper (III)(Start with Methods and Material),When you have decided to write the paper, the easiest way to appr
35、oach it is to start with the Methods and Material section. This section should cover all the methods you used to obtain the data in the figures and tables. It is very straight forward, and a lot of methodologies can actually be transferred from your previous publications or theses. 3. For standard m
36、ethods, you can just quote the reference, e.g. protein was measured by Bradford (reference). Others need more detail.,27,How to Start Writing a Paper (IV) (Start with Methods and Materials),Make sure that you define the source of material, e.g. Bovine Serum Albumin was obtained from Sigma (is that S
37、igma China, or Sigma St. Louis, Mo) If the material was provided by your colleague, include the name and e-mail address of the colleague, and preferably, his/her publication describing the synthesis/production of the material. If animals were used in the study, make sure to include in this section t
38、hat your study had received the approval of the local animal care committee. Include patient consent if samples from patients were included in your study.,28,Now You Have Finished the Materials and Methods Section,Completed Materials and MethodsResults,29,Results (I)Purpose and Organization,The purp
39、ose of the results section is to explain the data summarized in your figures and tables. The results section should be organized in a logical sequence, so that the reader will be able to follow your logic of presentation. It does not, and should not, follow the chronological sequence of the work don
40、e in your laboratory. The results section should be organized into several sub-sections. A brief description on why and how the work was being done in each sub-section is desirable. You should also highlight the significant points found in each figure and/or table described in the sub-section.,30,Re
41、sults (II)How to put things together,Put all your data in figures and tables (you do not have to use all of them). It is easy to write the results section when you have all the data in front of you. Arrange the figures and tables in the sequence that you want to present them, and write a short descr
42、iption on each of them. Normally, 4-6 sentences for each figure will be adequate. Start your results section by “ Our initial study was to demonstrate that xxxx”. Try to provide a short rationale for the next study, e.g. “Based on this finding, our next experiment was designed to (answer the questio
43、n).”,31,Results (III)Common Mistakes on the Description of Experiments,Inadequate description of the experiment presented in figures and tables. It is not adequate to say “Rats were fed with different diets, and the results are presented in Fig. 1”. Inadequate attention given to the Results section.
44、 There are often some mistakes in identifying the proper figure/table described in the Results section. This can be very frustrating for the reviewer. Make sure what you state in the results section agrees with what you said in the figure/table legend. Reviewers take these mistakes seriously.,32,Res
45、ults (IV)Common Mistakes on Experimental Design,Lack of proper control, especially in clinical studies involving patients (e.g. washout periods?) Lack of proper statistical analysis. You cannot do valid statistics based on n=2. Lack of proper information on statistic analysis. The statement that “st
46、atistical analysis was performed by HP software 12345” is not acceptable. What is actually comparing with what? Chi square? T-test? Lack of a time-course study. Example: “Rats were fed with a special diet, and blood sample was analyzed after 7 days.” Why 7 day? You need a time course to justify the
47、time point of your study.,33,Results (V)Common Mistakes on Data Presentation,Do not use different units in your tables and figures. For example, cholesterol is measured in the US as mg/dL, and in other parts of the world in mmol/L. You must use only one unit throughout your study. If you had defined
48、 the level of significance as p0.05, it would not be a good idea to present some analysis as p0.01 and p0.001. (It is not clear why some authors choose to do it this way). In morphological presentation, it is useful to state how many experiments you had done, and how many times you saw what you depi
49、ct in the figure.,34,Now You Have Finished the Results,Results Completed Introduction Section,35,The Introduction (I),The Introduction is not a real introduction of the subject. Readers who are not familiar with the subject will not read your paper. The purpose of the Introduction is to explain why the study was being conducted. The background information should be short but comprehensive. The existing gap of knowledge is the reason why you are doing the current study. The objective and the hypothesis of the current study should be well-defined in the Introduction. The approach should b