Professor Abdelazeem Eldawlatly Writing Scientific Paper Manual for Writing Scientific Paper WorkshopSUBJECT INTRODUCTION “PROGRAM -MODULE#! -MODULE#2 -MISTAKES TO AVOID -HOW 10 KEEP REFEREES HAPPY -HOW 10 GET YOUR PAPER REJECTED -SOME EXAMPLES FROM SIA ON REVIEWERS DECISIONS “REFERENCES, Table of Contents PAGE 20 a 26 Page [1INTRODUCTION Writing a scientific paper in a foreign language is tough work. When the time comes to write it, many feel left to their own devices. However, writing a scientific paper involves not only literary abilities. It is above all a matter of organization, It's not a talent but experience, This writing workshop is designed to help you step-by-step through the process of creating a research paper. Specific exercises will support the process of organizing your work and getting your thoughts down on paper; revision techniques will help you to improve the quality of your writing. Peer review - a crucial part of the writing process = ‘will help to strength the writing of both reviewers and writers. This writing workshop is project-based: you will work on your ‘own publication project using your existing data. Prior to attending, you will need to identify your target journal and bring along the guidelines for authors. This workshop is specially designed for non-native speakers. It will be run in English, General information ‘The workshop is imeractive, with participants encouraged to think and discuss why, where, when and how to publish and who their readers arc, The workshop is tailored as far as possible to the needs of the group and the outline above may be altered accordingly. ‘The facilitator will contact participants before the course to gain an understanding of their levels of experience in writing scientific publications, to discover if they have experienced any particular barriers to writing, and iff they have any specific rnceds or skill gaps they wish to address, Each participant will be asked to bring a current writing project to develop during the workshop. Tf this is not possible, the facilitator will make alternative arrangements with the participant to ensure s/he gains practical experience during the ‘workshop, Objectives Learning and training an appropriate strategy for writing a scientific paper in English Developing autonomy and empowering critical thinking ‘Training coherence and logic in argumentative writing Finding individual solutions for specific problems. Write the best paper you ever have written Bring the paper through the review process Content 1, The critical element ofa scientific paper 2, When should I think about writing up my results as a paper? 3. Working toward a paper 4. Choosing the right journal 5, Practical writing tips 6. Submission and the long wait for the reviews 7. Dealing with the eyeling process of the journal 8, Practical examples Format Interactive lecture covering points 1-6 Discussion and computer based practical examples covering points 7-8 Page |2Writing a Scientific Paper Workshop Material Module | (Ref#2) Writing is often viewed as a difficult task, and is frequently left to the last minute out of dislike, lack of confidence or lack of know-how. However, writing can be fun, and the fruits of your labor can have substantial benefits, Physicians tend to be perfectionists and have a good eye for detail. They often wish to share insights into theit work, gained from research or clinical practice. Often they are not trained in the art of communicating these insights on paper, despite having che ability to present their work at meetings in front of their peers. Obviously writers whose first language is not English may require more help than thers. However, language should always be “a precision tool, conforming to simple rules and conveying meaning logically”, One must remember at all times that the purpose of the paper is communication, and for this reason a “house style” is used, because the aim of such writing is not only to make yourself understood, but to make sure that you are not ‘misunderstood, So, assuming that you are writing a full-length paper, which is reporting a clinical trial, how do you start? Woy did you start? ‘What did you do? What did you find? ‘What does it mean anyway? In other words, Introduction, Patients and methods, Results, and Discussion. At this point it is necessary to get your data on to paper. There are many different ways of writing a first draft; use the one that suits you best. You may prefer to write the paper by hand, and then transeribe on to the computer but you may prefer to type dircetly on to the computer. Don't stop to edit at this stage—just write, You can edit later. It is important to keep the flow going. Do not be afraid of simple, everyday words, Readers will thank you, not to mention editors and referees. Keep it simple, and keep it as short as possible; imagine that you are going to have to pay £1 for every word you use. Instructions to authors Before writing, itis imperative to obtain the “Instructions to Authors’. These instructions will detail the total character, word for page length for the manuscript, total number of figures and tables allowed and total character or word count for the abstract. The precise format for the abstract will be provided, and typically includes a background, methods, results and conclusion sections. Many journals use different formats; thus, itis critical to obtain these instructions before starting to write, Another important aspect of the ‘Instructions to Authors’ is the actual typeset format used to prepare the manuscript document. While the majority of journals stil require the document to be double spaced with specific margins (typically 1 inch) and specific sections, some journals have now adopted a single-spaced approach or even double-column single-spaced approach, Journals also have requirements regarding the use of abbreviations and references. Last, each journal has specific format requirements for figures. Many journals require the images to be JPEG or TIFF images, with specific requirements for mage resolution if they are color (i.e. 600 dpi) versus black and white (i.e. 300 dpi); however, some journals do allow images, from PowerPoint files or as PDF images. Therefore, attention to these details will save time, energy and frustration on your part since submission using an incorrect format will ensure either automatic rejection or annoyance on the part of the reviewers, withthe later potentially leading to a less than favorable review. Manuscript writing order ‘The key to writing a good manuscript isto rll a story! This is often best accomplished by writing the manuscript out of order from the journals prescribed order for the sections as certain sections are more logical and easy to write first, while others are easier to write after the bulk of the manuscript has been written, I recommend starting with the figures and tables, as the figures and tables should tell the whole story, as well as a good story. After the figures and tables are determined, create the ttle page, carefully including all ofthe information required by the journal. Be sure to include all middle initials of authors if they are used by the authors, as well as correct institution information. After the ttle page, the methods (or materials and methods) section should be written, as tis is simple to do and a Togical lead into the results section. Next, complete the results section Page 13‘and organize this section using subheadings. This should be simple to write with the figures and tables in hand, While om your mind, after preparing the results section, it is convenient to write the figure legends. The introduction, followed by discussion should be written next. After you have all these data committed to paper (or rather, electronically), the introduction and discussion sections are less daunting to write. After all of the above sections are completed, it is time to write the abstract. A common mistake is to write the abstract frst, before the results section, However, you will have a better sense of what to include in the abstract, as well as what to emphasize, after the majority of the paper is written. Remember, the abstract should include all pertinent data from the manuscript and accurately portray what isin the manuscript, Finally, do not forget the acknowledgements and references sections, Order For Writing A Manuscript Figures and Tables t Methods t Results Figures Legends Introduction t Discussion ' Abstract ' Acknowledgements t References Page 14Abstract ‘The best time to write the abstract is after the manuscript is completed, The length of the abstract will be clearly stated by the joumal and it is prudent to adhere to the length requirements, Sentence writing should be concise and succinct in the abstract, given the length requirements. Additionally, be careful to adhere to the formatting guidelines, as each journal has unique Subheadings that must be used. In general, the abstract should provide an overview of the paper that makes sense when read alone and when read with the paper. The abstract should provide enough information for the casual reader to understand what the manuscript is about. Include information from each section of the manuscript in the abstract, being careful to include, highlight or emphasize important data and take home messages, as often the abstract is the only part of the manuscript that is read. The abstract should not contain information that is not included in the manuscript. However, there may be some data in the manuscript that is not necessary 10 include in the abstract if it is not germane to the overall conclusion of the paper. Introduction ‘The Introduction should be just that: an introduction to the topic and why you thought that the topic was worth investigating. It usually fills about half an A4 page. Grab the readers’ attention with the introduction. Awaken the readers" interest and prepare them to understand the manuscript as well as its context to the scientific area being studied. Limit the introduction sections to no more than three paragraphs. In the first paragraph, clearly state the clinical problem being addressed and its significance within the medical community. In the second paragraph, state what is known and then what is not known about the clinical problem. In the third paragraph, relate what is not known about the clinical problem to your study, providing clear support for why your study is important and being conducted. Then, cleatly state the goals or aims of the study, along with the hypothesis, Ifthe introduction is too long or confusing, the reader will lose interest and not read the rest ofthe manuscript Patients and methods ‘The Patients and Methods section should describe the comparability of the groups that you studied (sex [please not “gender”, which is a grammatical term)), age, severity-as objectively as possible, current treatment, and so on) and give a brief resume of your statistical methods. Remember to mention the program that you used to analyze the data because the statistical adviser may wish to check the calculations, and programs do differ in some ways. Normally this section should fill about 2-2% pages. The methods section conveys to the reader wiat experiments or interventions were performed to address the hypothesis or question that was formed for the study. Methods should be described in enough detail so thatthe reader can judge whether the findings reported in the results section are reliable. Additionally, enough detail should be provided to allow the reader to reproduce the experiment. If the methods have been described in a previous publication, it is acceptable and advised to reference that publication and only briefly describe the method, However, if deviations from the published methodology occurred, this should be clearly stated and described. If a new methodology is described, be sure to explain what experiments were conducted to test or validate the new methodology. The methods section should be subdivided into descriptive subheadings based on logical topics. Results In the Results section consider using tables as much as possible, Ifyou can tabulate results, or put them into figures, do so, However, remember that one of the most common faults is to tabulate your results and then describe them in detail in the text, Don’t, Use one or the other. The ideal results section would read, “The results are shown in Tables 1-4”. As Figures are often used as well as tables to illustrate results I will mention them here. They are, of course, partly a matter of the journal's chosen style, but there are rules. First of all, three-dimensional graphs are never acceptable in scientific publishing. Each figure and table should stand on its own without reference to the text, This means that all abbreviations should be spelt out ‘cach time that they are used in the specific legend, or as a footnote. And please explain units of measurement. A word about statistical analysis. A p-value does not equal truth; there is no substitute for common sense and, if something does not make sense, it probably isn’t true. Never say that something is “NS”, meaning not significant (always give an exact p value). People will have more respect for someone who says “We did not study enough patients, but the result looks promising” than {or someone who tries to blind them with statistics. A good rough guide as to whether data are normally distributed or not is to see whether the SD is more than half the mean. If itis, they are skewed. Avoid the SEM; prefer the 95% confidence interval (Cl) of the mean instead. Do not use the ‘sign, Use a parametric test for normally distributed data, and a non- Parametric lst for skewed data, Always report whole numbers together with percentages, never percentages alone, Theage | 5Teason Tor tis that for numbers of Jess than 20, percentages are misleading, The resulls secion should ella story and emphasize the take-home message, The results section should state the findings of the experiments and not contain conjecture. The later is best left forthe discussion section, Avoid repeating introductory material and minimize experimental details since experimental details belong in the methods section. Avoid lengthy analyses and comparisons to other studies, as those also belong in the discussion section, Furthermore, remember the difference between data and results. Data ae the facts obtained from the experiments and observations, results are statements that interpret the data, Arrange the results section in a logical fashion, ether chronologically, mostto-least important, in vitro to in vivo, ete, using descriptive subheadings. For each subheading section, I find it helpful o state the purpose of the experiment(s) being performed to guide the reader seamlessly through these sections. After stating the purpose, the data are provided ina clear, concise and logical manner. At the end of each subheading section, a statement is provided that summarizes and interprets the data, that is, provides the results (eg. these data suggest that, ."). This technique isa very effective and efficient approach to convey data and results to readers. The results section should also clearly direct the reader to the related figures and tables that support the data, In addition, it is important to avoid overlap between the text in the results section and the figures and tables. If data are described in a table or figure, there is no need to also list those data points in the text, as this is redundant. In summary, well Jaid-out and well-written results section should be simple to read and should provide a clear story of the data forthe reader 9 Interpret and make independent assessments and judgments Figure legends After writing the results section, itis simple to prepare the figure legends, as these two sections are very similar. Use brief sentences to describe the figure. Different journals have unique requirements regarding the format, For example, some journals prefer including a tile sentence for each figure legend that is description, while others do not. It is prudent to review publications from that journal to determine how figure legends are formatted, Figure legends should be free-standing from the text of the manuscript, mesning that a reader should be able to fully understand the experiment and data provided in the figure by reading just the figure legend, and not having to refer to the text of the manuscript. Describe all aspects of the figure, and if the figure has multiple panels, each panel must be described separately. Minimize experimental details, as that is the purpose of the methods section. All abbreviations, lines, bars, arrows and symbols must be described. Provide statistical information; ifthe figure contains statistical notations such as asterisks, the P-values for these statistical notations should be provided in the figure legend. Discussion ‘The Discussion is difficult to write, because there is such a temptation to mention and discuss everything that you have found. Pick out only your major points (particularly if they are controversial) to explain and elaborate, Again, avoid the passive voice. “The skin was incised" is, for example, shorter and clearer than “An incision was made through the skin”. Use simple words:"do “is better than "perform"you are not a seal) or “carry out"(you are not removing a corpse); and the use of nouns as adjectives should be avoided as it makes a paper difficult to read, I is always a bonus for the reader if you avoid clichés — prefer “clinically” to “in the clinical situation", and “daily” to “on a daily basis” - and also vogue words such as “determine” and “enhance”. Many authors fear writing manuscripts because of the discussion section. However, if the discussion section is deconstructed to just five paragraphs, it can actually be fun to write. Inthe first paragraph, summarize the results section and answer the question or hypothesis stated in the introduction, Place the data in the context of the bigger clinical problem. Examples of sentences that signal the answer include: “This study indicates that ..”, or ‘The results of this study show that. ..” Examples of sentences that link the results to the answer they support include: “In our experiments, we showed that...” or In our subjects, we found that...” or “The evidence provided in this study shows that, ..”The second and third paragraphs require the most thought and insight to write, First, use these two paragraphs to compare and contrast your data to existing literature. An example is: ‘though our results may differ from those of Chen et al. we used a different method to ascertain compliance with therapy,” or ‘while our results are opposite to those of Kao ef al. we used a different rat strain with our studies.” Second, explain unexpected findings. For example, “We were surprised to find that @ normal WBC was predictive of morbidity following endovascular interventions.” Third, describe patterns, principles, and relationships that the results show. Fourth, address if the results have theoretical or practical implications. Do the results relate to other situations or other spocies? Do the results help us to understand the broader topic? By addressing these issues, you will have provided the reader ‘with additional insight into your study and how to place your results in context of the greater scientific field of study. In the fourth paragraph, address limitations and/or weaknesses of the study, Let’s be candid ~ there is no point in ignoring the limitations of your study, All studies have weaknesses and/or limitations and if you do not address them; you are leaving Page 16YyourselT open to crlicism by the reviewers, Thus, address the limitations and discuss why these limitations or weaknesses exist and how they may affect interpretation of the data, The fifth and final paragraph should be the concluding paragraph, Provide a brief and global summary of the results and what it all means in context of the larger clinical problem discussed in the introduction. Signal the end using phrases such as, “In conclusion, ‘or ‘In summary". Indicate the importance of the work by stating the applications of the work, recommendations suggested from the work, implications of the work or speculations about the importance of the work, Remember, do not overstate the conclusion, and understate it. When writing the discussion section, several errors are common. First, and do not restate the results. This is a crutch that many authors use if they do not know what else to put in the discussion section, Second, understate the conclusions rather than overstate them. Overstating conclusions is a certain way to annoy reviewers and readers. Third, be focused with your writing. Long, tangential thoughts make for sloppy and difficult to read discussion sections. Fourth, write clear and logical paragraphs with introductory and concluding sentences, Acknowledgements ‘The beauty of the acknowledgements section is its simplicity and importance, This is where most journals require the listing of support from funding agencies. Also, acknowledge individuals that contributed to the work but did not meet criteria for authorship. Gifts of special reagents, animals, software, etc., can be described here, Administrative support can be acknowledged. OF note, many journals now require that authorization be obtained from all individuals named in the acknowledgements section, so be sure to read the ‘Instructions to Authors’ on this matter. Last, some joumals ask for conflict of interest information or additional disclosure information in this section, or specifically have separate sections addressing those topics. References Ensure key statements of fact are referenced. It is not necessary to reference large numbers of papers that all make the same point. However, those that are cited should be entirely relevant, as recent as possible and of the best-quality studies undertaken. As a rule, cite only the original research articles, not review papers. If itis expedient to cite a review paper, be hhonest and state this. For example, you could state “In a review by Milleret al...” Make sure that references are done in the format required by the journal. Not doing so annoys both the editors and reviewers. Choosing a journal When choosing a joumal, consider the journal's impact factor, the readership and the journal’s reputation for efficieney and fair review. Like it or not, the impact factor is still important when it comes to securing grants and promotion. A journal is ‘more likely to accept your paper if it will appeal to its readership. For example, studies on Australian snake bite management are more likely to be published in Australian journals. Joumals differ in their efficiency. Consider your own previous experience and that of your colleagues. Last, do not be aftaid to aim for @ good journal and do not underestimate the value of ‘your paper. Never submit a paper to two joumals simultaneously. Too long Keeping to the word limit can be a challenge. Although the journals usually have some tolerance of papers that exceed the suggested word count, it is not uncommon to be asked to trim the paper, even before peer review. A particularly common criticism is that the discussion is too long, To see where a paper can be trimmed, check: are results duplicated in tables and text, or results and discussion? Is there discussion of previous literature that is not strictly necessary? Is there excessive discussion about secondary outcomes or excessive speculation about mechanisms and the implications of the study? Remember to keep the paper focused on the rescarch question and the primary outcome, Review process {Aficr submission, your paper will be checked by the joural office for format and completeness. I there is some potential for Publication, it will be sent for peer review. Alternatively, the editor might reject the paper immediately. The peer-review process is not perfect and itis best to approach it with a postive and patient attitude. Do not be disheartened by pages of Page 17ommenis and questions, These are offen of considerable use in improving the paper. When the reviewer” comments are received, respond to all their questions and comments. Editors look favorably on a reply letter with the reviewers’ comments listed and, below each comment, a description of how the paper has been revised in response, You can disagree with a comment, but you have to provide a clear reason why you disagree. Some comments are just suggestions and might not need to be adopted. Do not ignore any questions and pay particular attention to any comments or questions posed by the editor as they are the ones who make the final decision. Thank the reviewers for their constructive comments and be polite and respectful in your reply. Your paper will inevitably be better after review and some reviewers spend many hours trying to help you produce a better paper. Good editors will filter out unhelpful comments from reviewers, but ifsome do slip through do not respond with sarcasm or rudeness. If you are rejected, then do not be despondent. It might be thatthe joumal does not think your paper fits theie journal or that there is simply no page space available. I you have been rejected and the reviewers and editor have clearly misunderstood your pape, then you may appeal tothe editor. If your study question is clear, originel and relevant, and your methodology is valid, then your paper will eventually be published somewhere. If you take care to ‘write the paper well, then it wil be published sooner and in a beter journal. ‘One paper or two? Duplicate submission and duplicate publication (generally unacceptable unless editors are notified in special circumstances) and acceptable secondary publications of the same materials are clearly set out in the Uniform Requirements, for Manuscripts Submitted to Biomedical Journals by the International Committee of Medical Journal Editors. The more frequent issue for emergency researchers is that in some projects large amounts of data are collected and it might be that some secondary outcomes are important enough to warrant their own paper. There must be a balance between including large amounts of data about secondary outcomes in a single paper and the temptation to split the results among multiple papers. If the Tatter is excessive this is known as ‘slicing the salami” publication. A publication combining as many components as possible will have a bigger scientific impact. In principle, separation of data between papers is acceptable, but this must be acknowledged in each paper. Some journals expect all such related papers to be submitted to the same journal. Bort Introduction 1. Why is your research important? 2. What is known about the topic? 53, What are your hypotheses? 4. What are your objectives? Materials and Methods 1. What materials did you use? 2. Who were the subjects of your study? 3, What was the design of your research? | What procedure did you fllow? Results 1. What ate your most significant results? 2, What are your supporting rsulls? Discussion and Conclusions 1. What are the studies major findings? 2. What isthe significancelimplication of ‘he results? Bord Tortured English Meaning Excessive inerposodadipoe tissue Fat Maki of the lo was present the eg moved Inthe authors opinion Tink (Om acount ofthe fet at because One out of every two Hale Surges procedure Operation Exogenous nutrient elements Food Page 18Bors Poor word choice Better word choice Acquire Get Uaiize Use Altempted “ried Ascertain Make sure Next Big, large full Purchase Buy Remainder Rett Box A (ROTATY Page 19