Scientific Writing: A step forward Arash Etemadi, MD Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences aetemadi@tums.ac.ir

Why Writing Is Important? No publication, no project Make information available for others No publication, no promotion Yardstick of productivity No publication, no funding What have you done for me lately?

Intrinsic Causes of Writing Problems Internal Censors Fears of Failure Perfectionism Procrastination

Intrinsic Blocks to Writing (I) Inability to Start Writing “First, there is the difficulty of writing at all” D. Brande Becoming a Writer Perfectionism, self-consciousness, procrastination

How to Start Daily 30 minutes to one hour Do not pay attention to structure, grammar, spelling

Stimulus Control Few regular places to work Close the door Unplug the phone No e-mail Arrange the site But do not clean up the office

(II) Inability to Finish Writing Multiple revisions Multiple analyses “Each time I think I am finished, I see there is a lot more to do” Similar roots as inability to start (perfectionism) Different people Lack of insight

TUMS workshops on scientific writing Level 1: Basics Level 2: Focus on international publications Level 3: Specialized writing

An overview

The traditional IMRaD Introduction Metods Results Discussion

A full paper consists of: Title Authors and Affiliation Abstract Introduction Methods Results Discussion Acknowledgments (optional) References

Target your paper at a particular journal Familiarise yourself thoroughly with potential journals what sort of papers do they publish? (original articles, briefs, reviews, commentaries, iconoclastic pieces?) What is the “culture” of the journal? National or international focus? Write for that journal

If for a general medical journal.. Mostly read by clinicians, so “practical”, useful, papers highly regarded.

If a specialist journal... Cut to the chase! Do not waste time with elementary ABC introductory sections -- it is being read by people who know the field locate your paper precisely in what has gone before

Design well Decide politics Choose journal Read instructions to authors/papers Set framework Prepare drafts Distribute Polish Submit

What is the gestational period for a clinical science publication? START PROTOCOL/IRB 2-4 months STUDIES/ EXPERIMENTS 4-24 months WRITE AND SUBMIT 14-44 Months! 2-4 months REWRITE AND RESUBMIT 2-4 months 2-4 months WAIT 2-4 months PUBLISHED! BEST GUESS

Order of writing? Results Methods Introduction Discussion Abstract References

Order of writing? Methods Results Introduction Discussion Abstract References

Getting Started Do you have enough data for a manuscript? Do you have a complete story to tell? Write a list of the figures and tables that you would include in your paper Write a brief, skeleton outline of the paper (1-2 pages) and show it, along with the list of figures, to your coworkers and discuss

TIPS…. Be enthusiastic about your data and your story Be sure you convey what “problem” you have addressed in your study Be sure to describe the area of research you are studying as fascinating and important

First Steps Analyze your data critically Do statistical analyses Prepare figures make graphs take photographs, get prints, label Prepare tables Be sure your data is internally consistent Show the final data figures (and tables) to your co-authors for comment

Effective Data Presentation Figures are almost always better than tables Look at published figures (in papers that have data similar to yours) to get ideas about how to compose graphs, and how to frame and label blots, gels and photomicrographs Learn how to use graphics programs (Sigma Plot or Excel) Learn to use Adobe Photoshop Photomicrographs - color is expensive!

Instructions to the Authors Guidelines for writing the paper Usually found in January issue of journal Almost always found on the web site for the journal

Mechanics of Writing- Title, Abstract and Introduction Title- be as specific as possible; include design Abstract is a summary of the paper (therefore write last); check for a word limit; structure it. Introduction – Importance, a brief review of the literature, information gaps, statement of hypothesis Introduction- about 3 to 4 paragraphs

Mechanics of Writing - Methods Use subheadings to organize Details - use sufficient detail for another investigator to be able to reproduce your results Reference methods used previously Be precise with respect to measurements and definitions Statistics

Mechanics of Writing-Results Tell a story Use the most logical sequence to present the data (not necessarily the order in which you did the experiments) Just report the data - do not include interpretation or comparison to literature No duplication of data

Guidelines for Writing Results - The Study as it was Conducted Specify the dates of the study Provide a schematic summary Describe the characteristics of each group Indicate if the sample is representative Indicate if randomization was successful Describe duration and nature of follow up For observations based on judgment, provide assessment of consistency

Guidelines for Writing Results: The Study Outcomes Present the results for all primary endpoints Report statistical findings in detail Report actual p values , 95% CI , etc. Report the main findings in figures or tables - you don’t need to also report them in the text Report confounders

Mechanics of Writing- Discussion Construct parallel to results Interpretation of data Relate your results to the findings of other investigators Summary paragraph at end - include significance of results Avoid redundancy with results and introduction sections

Good discussions--- Address every key finding of the study Present the finding in terms of what is known State why this study is different State why the results concur/ disagree with current knowledge Justify differences Point out future directions/ continued knowledge gaps

References Aim for about 30 references Use recent review papers where appropriate to decrease the number Get a hard copy of every reference in the manuscript and make sure the referenced paper says what you say it does! Don’t use abstracts! Proof-read the reference list especially carefully as one of your reviewers may be cited! Use End Note or other bibliographic software Use the Internet

A Few Rules The first time you use an abbreviation, define it When you give the commercial source for a reagent, the first time you cite the source include the location of the company (city and state) Make sure the subject and verb agree in every sentence No contrac. or exclamation points!

A Few Rules - continued Look for redundancy within the manuscript Try not to use “it” or “they” - be specific! No jargon Two shorter sentences are frequently much more effective than a long, complex sentence “Data” is plural not singular, i.e., “the data are…” NOT “ the data is…”

A Few Rules - continued Capitalize people’s names, i.e., Golgi apparatus Never, ever plagiarize! (even from yourself!) Use numbers when expressing measurements, except when the number would begin a sentence

Common Errors in Manuscripts The Title is misleading/ does not set limits Gives away the punch line The Abstract reports different measures/ methods results are not the same as the paper conclusions are not the same

The Introduction question, hypothesis, study objectives are not specified, or are confused importance, novelty, originality of the study not shown presentation is not intriguing (ie, the introduction is boring)

The Methods Probably the most important section reported methods not used details are missing so you cannot understand entire methods are omitted

Common Errors When Reporting RESULTS Errors of Omission: Not accounting for all study subjects Not naming which statistical tests were used for specific analyses Not presenting the results in clinically relevant terms

Errors in the Analysis Lack of power Failure to adjust for multiple comparisons Analysis by treatment received and not by intention to treat Errors in Interpretation Not recognizing the limits/meaning of p Clinical significance ignored in the face of statistics

The Discussion logic is loose is too expansive, wanders is biased, omits key findings key results are poorly explained references are outdated speculation is not identified implications/ importance are overstated limitations are not described

The Conclusions simply restate the results do not answer the study question do not set limits for application

General Tips Just START !! Follow the instructions for authors Apply research analytical principles Adhere to scientific and writing ethics Be patient - centered and not numbers centered Write with vigor and write vividly

General Tips Write for readers and not to please peer reviews - readers read to learn; reviewers, to improve Avoid self plagiarism Update the literature review Have a clinical colleague read your draft Seek out criticism

More reading Hall GM, ed. How to write a paper. London: BMJ Publishing Group. Peat J. Scientific Writing Easy when you know how. BMJ Publishing Group. 2002. The Vancouver Group. Uniform requirements for manuscripts submitted to biomedial journals. www.icmje.org

Finding and choosing an appropriate journal Where to look for the journal: Personal experience Colleagues’ experience Library Citations Online

Appropriate Journal General versus Specialty International versus Local High versus Low impact LOOK AT THE JOURNAL LOOK AT THE AUDIENCE

1. What type of paper you wrote ? research report (“original article”) review paper special article editorial case report letter to the editor

2. Is the paper really worth being published? Is the message new, or new to a particular audience? Search the literature to make sure you are not repeating history ++ Determine the odds that a particular journal will appreciate the newness and importance of your manuscript in the context of the existing medical literature

3. Be realistic This is your first manuscript or you have already a real track of publications on the topic ? Are the co-authors or the Institution were you are based recognized in the field ? Are you an Iranian author submitting to a national, a European or an American journal ? Reviews are mostly only by invitation but national journals can be quite open

4. Know your journal targets? Impact factor and prestige Normal content of one of the journal issues Which kind of manuscripts are published ? What are the preferred formats ? Style and recent trends in the journal Who is the editor-in-chief ? Can you contact him ? Who are the members of the editorial-board ? They are very aware of the journal’s publication policy…you can try to contact some of them with questions

1. Impact Factor: Oncology 1998 1999 2000 2001 2002 J Natl Cancer Institute 10.730 12.945 14.159 14.240 14.500 J of Clinical Oncology 8.228 7.963 8.773 8.530 9.868 Cancer Research 8.370 8.614 8.460 8.302 8.318 Clinical Cancer Research 2.941 3.442 4.643 5.076 5.991 Oncogene 6.192 6.517 6.490 6.737 5.979 Gene Chromosome Cancer 3.804 4.902 4.534 4.416 4.199 Int Jrnl Cancer 3.283 3.545 3.918 4.233 4.056 Cancer 3.660 3.362 3.611 3.909 3.941 Annals of Oncology 2.867 3.195 3.249 3.153 3.114

2. Normal content of the journal ? Is the topic within the scope of the journal? Is the topic represented in the journal frequently, or only rarely? Would the journal offer the best match of audience and topic? What formats are acceptable to the journal?

3. Style and recent trends Do look at a recent issue of the journal you plan to submit to Do read the Instruction to authors of the journal (links to 3500 journals’ Instructions at www.mco.edu/lib/instr/libinsta.html) Be aware of word/figure/table limits Use the appropriate reference and citation styles Help Editors and Referees (and yourself) – Number all pages

4. Editor in chief and editorial board Who is the editor-in-chief ? If you can contact him, query the editor be specific sell your product Editorial board members?

5. Ask your mentor He may belong to a specific editorial board He senses new opportunities Launching of a new journal Accurate format to sell your product Provides a more realistic point of view

6. What is your own agenda when publishing ? Colleagues Prestige journal vs. rapid publication National visibility vs international fame Issues of timeliness and in-depth track do matter

7. Timeliness and friendliness of the submission process Hot topic? You can query about the average reviewing time (assistant of the editors) Is there an online submission process? Can you track your manuscript status online

Target your paper at a particular journal Familiarise yourself thoroughly with potential journals what sort of papers do they publish? (original articles, briefs, reviews, commentaries, iconoclastic pieces?) What is the “culture” of the journal? National or international focus? Write for that journal

Anatomy of a submission Compose a title page determine who is the first author (you) vs. the senior author (last in the list of authors) Be sure to cite the source of funding for the project

Study design and ethical approval Data analysis Authorship Conflicts of interest Peer review Redundant publication (and duplicate submission) Plagiarism and fraud Dealing with misconduct

An “author” is generally considered to be someone who has made substantive intellectual contributions to a published study, and biomedical authorship continues to have important academic, social, and financial implications. Some journals now request and publish information about the contributions of each person named as having participated in a submitted study, at least for original research. Editors are strongly encouraged to develop and implement a contributorship policy, as well as a policy on identifying who is responsible for the integrity of the work as a whole (guarantorship).

Authorship credit should be based on 1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) drafting the article or revising it critically for important intellectual content; and 3) final approval of the version to be published. Authors should meet conditions 1, 2, and 3.

Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. All persons designated as authors should qualify for authorship, and all those who qualify should be listed. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. The order of authorship on the byline should be a joint decision of the co-authors. Authors should be prepared to explain the order in which authors are listed.

All contributors who do not meet the criteria for authorship should be listed in an acknowledgments section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, or a department chair who provided only general support. Financial and material support should also be acknowledged. Groups of persons who have contributed materially to the paper but whose contributions do not justify authorship may be listed under a heading such as “clinical investigators” or “participating investigators”

When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript. These individuals should fully meet the criteria for authorship defined above. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name. An example: GEMINI

Conflicts of interest Conflicts of interest comprise those which may not be fully apparent and which may influence the judgment of author, reviewers, and editors. They have been described as those which, when revealed later, would make a reasonable reader feel misled or deceived. They may be personal, commercial, political, academic or financial. “Financial” interests may include employment, research funding, stock or share ownership, payment for lectures or travel, consultancies and company support for staff.

(1) Such interests, where relevant, must be declared to editors by researchers, authors, and reviewers. (2) Editors should also disclose relevant conflicts of interest to their readers. If in doubt, disclose. Sometimes editors may need to withdraw from the review and selection process for the relevant submission.

Redundant publication/ duplicate submission Redundant publication occurs when two or more papers, without full cross reference, share the same hypothesis, data, discussion points, or conclusions. Duplicate submission is when the same manuscript has been sent to journal while still under evaluation by another.

(1) Published studies do not need to be repeated unless further confirmation is required. (2) Previous publication of an abstract during the proceedings of meetings does not preclude subsequent submission for publication, but full disclosure should be made at the time of submission. (3) Re-publication of a paper in another language is acceptable, provided that there is full and prominent disclosure of its original source at the time of submission. (4) At the time of submission, authors should disclose details of related papers, even if in a different language, and similar papers in press.

What is fraud? Fabrification: Invention of data or cases Falsification: Wilful distortion of data Ignoring outliers? Not admitting that some data are missing. Post hoc analyses that are not admitted? Not including data on side effects in a clinical trial

What is fraud? Plagiarism: Copying of data or papers But by how much? Stealing ideas? Redundant publication Gift authorship. Not attributing other authors. Not publishing research Not disclosing a conflict of interest

Plagiarism Plagiarism ranges from the unreferenced use of others’ published and unpublished ideas, including research grant applications to submission under “new” authorship of a complete paper, sometimes in a different language. It may occur at any stage of planning, research, writing, or publication: it applies to print and electronic versions. All sources should be disclosed, and if large amounts of other people’s written or illustrative material is to be used, permission must be sought.

Dealing with misconduct (1) The general principle confirming misconduct is intention to cause others to regard as true that which is not true. (2) The examination of misconduct must therefore focus, not only on the particular act or omission, but also on the intention of the researcher, author, editor, reviewer or publisher involved. (3) Deception may be by intention, by reckless disregard of possible consequences, or by negligence. It is implicit, therefore, that “best practice” requires complete honesty, with full disclosure. (4) Codes of practice may raise awareness, but can never be exhaustive.

Investigating misconduct (1) Editors should not simply reject papers that raise questions of misconduct. They are ethically obliged to pursue the case. However, knowing how to investigate and respond to possible cases of misconduct is difficult. (2) COPE is always willing to advise, but for legal reasons, can only advise on anonymised cases. (3) It is for the editor to decide what action to take.

Serious misconduct Less serious misconduct Sanctions, blacklists

Feedback Ask your co-authors to read the manuscript critically Give the paper to informed colleagues (1or 2 max) to read A real friend will give you lots of ideas for improvement Read your own paper as if you were a reviewer, with the figures in front of you as you read it

Final Preparations for Submission Proof-read, proof-read, proof-read! Make sets of figures for submission but also keep a set of original figures for your files Make copies of the submitted manuscript, including the figures, for every author Write a cover letter, short and direct, addressed to the editor Make a list of suggested reviewers, if this is requested by the journal

Dr. Michael Holtzman, American Journal of Respiratory Cell and Molecular Biology, Editorial Office American Thoracic Society 1740 Broadway, New York, NY 10019-4374 Tel 212-315-6440 Fax 212-315-6456 Dear Dr. Holtzman, Please find enclosed an original manuscript entitled, “……………………...” by [authors]. The material presented in this paper is original and has not been submitted for publication elsewhere. No part of the research presented in this manuscript has been funded by tobacco industry sources. We verify that all the authors have read the manuscript and approve its submission. To aid the review process, may we suggest the reviewers listed on the following page. We hope that you will find our manuscript acceptable for publication in the American Journal of Respiratory Cell and Molecular Biology. Thank you for your attention. Sincerely ……. Corresponding author

List of Potential Reviewers 1) Dr. Joe Smith Duke University Medical Center Cell Biology 438 Nanaline Duke/Box 3709 Durham, NC 27710 Phone: 919-684-8040 Fax: 919-684-8106 e-mail: j.smitht@cellbio.duke.edu 2)Dr. Virginia Jones Vanderbilt University Pathology 1310 24th Ave S. Nashville, TN 37212-2637 Phone: 615-327-4751 X 5499 Fax: 615-321-6305 e-mail: jonesv@aol.com 3)Dr. Tony D. Soprano Southampton General Hospital Child Health Level G (803) Center Block Tremona Rd. Southampton, SO16 6YD United Kingdom Phone: 44-23 8079 6161 Fax: 44-23 8079 6378 e-mail: adp@soton.ac.uk 4) Dr. David Mitchell Department of Pediatrics Milton S. Hershey Medical Center H085 Hospital Hershey, PA 17033 Phone: 717-531-5925 Fax: 717-531-8985 e-mail: dsp4@psu.edu 5)Dr. Arnold Smith University of Missouri-Columbia Department of Molecular Microbiology and Immunology M616 Medical Sciences Building DC 04400 Columbia, MO 65212 Phone: 573-882-8989 Fax: 573-882-4287 e-mail: SmithAL@missouri.edu

COVERING LETTER Polite Why Journal chosen Importance of paper Concessions Brief

Submitting the Paper Frequently done on-line via PDF files If required, send the number of hard copies of the manuscript and figures required by the journal Send a disk with files for the manuscript and figures, if required Get the copyright form used by the journal signed by all authors, if required Send all of this material by a reliable method, so that your precious manuscript is not lost in the mail!!

Peer review Articles submitted to peer-reviewed journals (manuscripts) are reviewed by experts who advise the editor on whether they should be published and what changes are necessary.

Editorial decision Accepted as it is (rare) Accepted on the condition of certain amendments (back to cycle) Reconsidered if reviewers’ comments met (back to cycle) Rejected

Peer Review - Functions To Protect i) The author from publishing & ii) The subscriber from reading Material of insufficient quality

Problems with peer review Slow Expensive A lottery Ineffective Biased Easily abused Can’t detect fraud Works for improving studies not selecting which to publish

Dealing with the Journal’s Response Absolute Rejection Don’t take it personal Don’t write or call the editors (unless you know them well !) Editorial rejection: send it out the next day to another journal Reviewers comments: Fix the easy ones Fix the glaring ones Unlikely to get much better sitting on your desk Send it out the next day

Dealing with the Journal’s Response Conditional acceptance (rejection) It is yours to lose First cool down (24-48 hours) Within 1-2 weeks decide on responses Make real changes, say you have done great changes (describe, highlight,etc) Look for clues from the editor as to the extent of the revision needed. Avoid arguments Thank sincerely, but avoid being obsequious

Responding to reviews Swallow your pride! You don’t have to accept all, but don’t over-reject Ask editor about conflicting comments However unreasonable the reviewers may seem: be polite! Distinguish conditional acceptance from offer to reconsider (and from rejection of course!) Appeals (for rejection)

Resubmission Letter Dr. Brian F. McCabe Editor, Annals of Otology, Rhinology and Laryngology Department of Otolaryngology-Head and Neck Surgery The University of Iowa Hospitals and Clinics Iowa City, IA 52242 Dear Dr. McCabe, Please find enclosed a revised manuscript entitled, "Surfactant protein A in rabbit sinus and middle ear mucosa" by………. We have addressed the comments of the reviewers as detailed below: 1)We have changed the title of the paper as suggested by the reviewer. 2)We have expanded the description of the animals used in the study (page 4, paragraph 1). All the animals except the pathogen-free, were naturally infected with Pasteurella multocida. The antibiotic treated animals were chosen randomly. The infections were observed postmortem and pathogen was identified by culture by the Animal Care Unit. 3)The lengths of the micron bars in Figures 5-8 have been added to the legends. A magnification bar has been added to Figure 10. We hope that you will now find our manuscript suitable for publication in the Annals of Otology, Rhinology and Laryngology. Thank you very much for your prompt review. Sincerely,