Scientific Writing and Publication

Sagar Aryal31st March, 2017

Background (What you should know ?)

• Integral part of a researcher’sprofessional life.

• Getting a paper published can be avery tedious and time-consumingprocess.

• Challenging to start writing a newpaper and to remain motivatedduring the process.

Background (What you should know ?)• Scientific papers have to meet

certain requirements regarding howthe paper was written and the wayit is published.

• A scientific paper must be a validpublication

• Editors and publishers expect astandard form and structure ofsubmitted papers.

Background (What you should know ?)• The form may vary considerably by

type of paper (e.g. a case study ispresented in a different form from asurvey paper), but the basic buildingblocks are similar.

• Before writing, we should be clearabout the primary researchobjectives and key findings of thepaper.

How to get Started ?• Before wondering “How to Start?”,

think about “When and Where”

• What environment inspires you?

• Where are you most concentratedand least distracted?

• What day of the week and whattime of the day do you find mostfruitful for writing?

How to get Started ?

Set aside time for writing

INTERMEDIATE GOAL• Submit to Co-authors

FINAL GOAL• Submit to the Journal

How to get Started ?• Make use of writing sessions and

sufficient short and long breaks.

• Reward yourself for achievingintermediate- and long-term goals

PART I

SCIENTIFIC WRITING

Format of the Scientific Paper

• Title and abstract• Introduction• Methods• Results• Discussion• Conclusion• Acknowledgments• References

Title

Title• Fewest possible words that

adequately describe the contents ofthe paper.

• First Impression of the paper

• Electronic search databases usewords in the title and abstract toyield search results.

Title (Effective Titles)• identify the main issue of the paper;

• are accurate, clear, specific andcomplete;

• do not contain abbreviations unlessthey are well known by the targetaudience;

• attract readers.

Title (Effective Titles from Keywords)• Take a quiet moment to re-read

your paper and write down thekeywords of the different sections.

• Use the keywords and active verbsto formulate several potential titles.

• Try to write the most importantkeywords at the beginning of thetitle, as readers’ attention is focusedon the beginning.

Abstract

Abstract• Use the keywords of each section of

the paper to construct the abstract.

• Always state the objective of yourstudy at the beginning.

• Try to use short phrases, simplelanguage, and common wordcombinations, and avoid the passivevoice as much as possible.

AbstractCheck if the abstract covers the 4 Ws:

• Background: What is known andwhy is this study needed?

• Methods: What did you do?

• Results: What did you find?

• Conclusion: What does it mean?

Abstract• Does not contain any bibliography,

figures, tables, abbreviations.

• Generally written after the paper isprepared.

• Keywords are the important wordsfound in the research paper.

• Written below the abstract (3 to 6)

AbstractCritically revise abstract every time the main text

undergoes revisions.

Introduction

Introduction• Today many editors and reviewers

prefer short and focusedintroductions.

• The introduction does not have amaximum word count like theabstract but should be as concise aspossible, typically not more than 10to 15% of the full word count of thepaper.

IntroductionThe structure of an introduction canbe visualized as a funnel.

• The broadest part at the toprepresents the general context of thestudy topic (Background).

• It then narrows down to more topicalcontextual information.

• Ends with the specific rationale of thestudy and, vitally, the aim, purpose, orobjective.

IntroductionCheck if the introduction has afunnel shape with clear sections on:• General background (what is this all

about?);• What is known and what is

unknown about this specific subject(why was this study needed, andwhy is it important?);

• Primary research question (what didwe want to know?); and

• Study aim and design (what did wedo to answer the researchquestion?).

Methods

Methods• Includes basic information on study

design, setting and subjects, datacollection, data analysis, and ethicalapproval.

• It is quite common to use suchsubheadings to structure the section.

• In the case of research in humans, theauthority providing ethical clearanceneeds to be stated as well.

Methods

• Refer to previous publicationsfrom the same large researchproject, such as a study protocol,for additional information.

• Ask yourself, ‘‘Would a researcherbe able to re-produce the studywith the information I provide inthis paper?’’

MethodsMention the design of the present study

Methods

Explain:• when and where the study was

conducted• how the sample was recruited or

selected, and• which inclusion and exclusion

criteria were applied.

• Provide a sample size calculation forstudies to statistically test a specifichypothesis.

Methods• Match the part on data analysis

with the research questions.

• If you present a primary researchquestion in your introduction andone or more secondary questions,start by explaining the primaryanalysis, followed by the secondaryanalyses.

• Provide sufficient detail on thestatistical techniques you used.

Results

Results• Clear, concise and objective

description of the findings.

• Mostly written in past tense.

• Findings are presented withoutinterpretation.

• For every method (What you did),there should be a correspondingresult (What you found).

Results

• Findings in the results sectionshould match and answer theresearch questions from theintroduction, using the proceduresexplained in the methods section.

• Use tables and figures tosupport the main text of the resultssection.

Results

• Use more tables and figures tosupport the main text of the resultssection.

• Findings in the results section should match andanswer the research questions from the introduction,using the procedures explained in the methods section.

Tables and Figures

Tables and Figures• Tables and figures are an efficient

way of presenting findings froma study.

• If they are designed well, theyprovide more information thanwords.

• A paper’s key findings should bepresented in tables and figures, asreaders will look at them to get anoverview of the study results.

Tables and Figures• Importantly, they must be self-

explanatory; a reader should beable to fully understand theinformation without having to readthe text

• Most journals allow only a limitednumber of tables and figures to bepart of the print version of a paper(often around 5-6).

Tables and Figures• It is highly recommended to

design the layout of tables andfigures carefully;

• A clear and suitable layoutemphasizes the credibility of thestudy results, which is essential forthe peer-reviewing process.

Tables and Figures• Note that permission is needed if

you want to use a figure created bysomebody else.

• Both tables and figures should havea clear relation with the text of thepaper.

• They should be referred to in thetext in a chronological order startingwith 1 (e.g., ‘‘Table 1 shows .;’’‘‘We observed . (Figure 1)’’).

Tables and Figures

• The title of a table is usuallypresented at the top, whereas thatof a figure is usually placed at thebottom.

• Check whether the target journalrequires submitting tables orfigures as separate files andwhether figures must have aspecific file format (e.g., TIFF, JPEG,or PNG) to avoid unnecessary work.

Tables and Figures• Journals usually charge for

Colored Illustrations,

• So unless you do not mind spendingmoney on this, prepare black-and-white or gray-scale figures.

• Check whether the scales andfigures are distinguishable afterprinting.

Tables and Figures• When designing tables, use

horizontal lines to mark thetop and bottom and to separate thecolumn headings from the body, butno vertical lines as far aspossible.

• Use landscape page formatfor wide tables.

Discussion

DiscussionThe purpose of the discussion sectionis to:• Give the reader a summary of the

main findings,• To put them into context by

comparing with previous work and• Discussing future implications and

any shortcomings of the researchdesign.

Discussion

• Although the structure of theintroduction can be visualized as afunnel, the discussion can bevisualized as an inverted funnel.

• Thus, the introduction anddiscussion together form anhourglass shape.

Discussion

The discussion starts with:• The narrowest part by answering

the research question in thesummary of main findings,

• It then gradually widens out tocomparisons with other studies and

• the interpretation of the studyfindings in the wider context of thestudy topic.

Discussion• The discussion section should never

present any new results.

• Start by presenting the mainfindings, by answering the researchquestion in exactly the same way asyou stated it in the introductionsection.

• Do not waste words by repeatingresults in detail.

Discussion• Mention unexpected findings by

stating that they were unexpectedand did not relate to a priorhypothesis; such honesty willstrengthen your paper.

• Include a separate subsection aboutthe strengths and weaknesses ofthe study.

• Every study has its limitations, andyou should make sure to mentionthem.

Discussion• When comparing with other

studies, discuss the reasons fordifferences and similarities withyour results,

• Mention the limitations of thosestudies, but be respectful andobjective,

• Try to stress what your data adds tothe existing body of evidence.

DiscussionIt is appropriate to use• ‘‘may’’ or ‘‘might.’’• ‘‘Show,’’• ‘‘demonstrate,’’• ‘‘suggest’’

than using ‘‘prove,’’ which canhardly ever be used in research.

Discussion• Never, ever(!), just write that

further research is needed; this ispractically the same as telling peoplenot to forget to breathe.

• Formulate possible implications (forclinical practice and/or research,depending on the focus of the paper).

• Embrace the uniqueness of thisspecific study and always remember tostick to the original storyline of thepaper.

Discussion• End the discussion section with a

conclusion presenting your findingsin light of the evidence in the fieldand the specific strengths andlimitations of your research.

• Try to think of it as the one-liner(citable statement) that readersmust remember when havingseen your work.

Conclusion

Conclusion• Conclusion should be directly from

the data presented.

• No extra materials should beintroduced.

• The major function of conclusion isto make RECOMMENDATIONSbased on the results of the study.

Acknowledgment

Acknowledgment• Technical Help from Individuals

• Laboratory and Staffs

• Sources of special equipment

• Financial Assistance

(Grants, Fellowships)

References

References• Science moves forward by building

on the research work of others, so itis important to appropriately citeprevious work.

• Purpose is to enable the readers toconsult the original sources.

• Only references should be cited thathas been actually consulted.

References

• Organizing references can be timeconsuming.

• Most researchers work withreference management software,

• This allows them to organize, store,and download references of anytype (scientific papers, books, webpages, and other publication types)at all times.

References• Most of these software's

support automatic importingof references from databasessuch as PubMed.

• Any references added to acitation manager canbe easily inserted into thetext of the paper.

References• When pieces of text are moved

around during revisions, thereference management softwarewill automatically re-order thereferences.

• Papers that have been accepted butnot yet published can be cited as

‘‘in press.’’

ReferencesConsider choosing the reference which• Provides the highest level of evidence,• is open-access available,• has been most recently published, or• has been published in the journal to

which you are submitting yourmanuscript.

• The latter will demonstrate to editorsthat you know and read their journal.

Authorship

Authorship• Being an author of a scientific

paper and having a key role as anauthor can help your CAREER.

• It is therefore unsurprising thatauthorship is a highly debatedissue in meeting rooms andaround coffee machines atacademic departments.

Authorship

• The first author is the mostimportant position, followed by thelast author (supervisor) and thesecond author.

• The corresponding author is theprimary contact person forquestions related to the underlyingwork, during the editorial processand after publication.

AuthorshipCheck and follow ICMJE criteriaon contributorship andauthorship. Authors should have• contributed substantially to the

conception and design, dataanalysis and interpretation of data;

• contributed to writing the paper orrevising it critically for importantintellectual content; and

• given final approval of the version tobe published.

Authorship• Ask coauthors to critically review

and provide feedback with targetedquestions and set them deadlines torespond.

• Ask coauthors to meticulously checktheir names, initials, and affiliationsbefore submitting.

PART II

PUBLICATION

Choosing a Journal

Choosing a Journal• In a scientific paper, you try to tell a

story, but to whom?

• Your audience will largely dependon the journal you publish yourwork in.

• PubMed alone cites more than 20million papers.

• Choosing the right journal for yourwork is not easy.

Choosing a Journal• Acceptance rates vary from under 10%

for the most prestigious journals tomore than 80% for some journals.

• The impact factor of a journal reflectsthe average number of citations ofarticles published in the journal in thepast 2 years.

• The Impact Factor is calculated bydividing the number of citations in theJCR year by the total number ofarticles published in the two previousyears.

Choosing a Journal• The number of electronic journals

without printed formats is everincreasing as well as being able topublish papers very soon afteracceptance.

• Many scientific journals arenowadays open access.

• Although many journals(traditional and electronic) docharge some fees.

Choosing a Journal• There have been reported cases of

mock journals and fake publisherssending out e-mail invitationsto submit papers, while only beinginterested in pocketing publicationfees.

• Proper scientific journals will notnormally send such e-mails.

Choosing a Journal

• Think about a target journalbefore you start writing.

• Look at the journals’ web sites andauthor’s instruction.

• See if a journal actually publishesthe type of paper you intend towrite.

Choosing a Journal• Balance the desire to publish in high

impact factor journals with yourpreferred time to publication.

• Submitting a paper to a journal witha high rejection rate may giveyou useful reviewer reports butmay also delay your publicationprocess by several months asmultiple submissions may benecessary.

Choosing a Journal• If you want to publish in a specific

journal, be sure to read the journalguidelines.

• Discuss relevant target journals,prioritize them and rank a final listof 3-5 journals.

• This will enable you to focus on yourfirst journal of choice

Submitting a paper

Submitting a paper

• Each journal has its own specificrequirements for paper, which canbe found in the author instructionson the journal’s Web site.

• Every journal has slightly differentrequirements regarding aspects likethe maximum number of words,the reference style to use orwhether tables and figures shouldbe embedded in the paper orsubmitted separately.

Submitting a paper• The cover letter accompanies the

submission of your paper and may bethe first that an editor reads.

• Therefore, it should stress thesignificance of the paper for the fieldof research and the relevance to thespecific journal.

• The cover letter also confirmsadherence to the journal’s authorrequirements and contains anyadditional information that may be ofinterest to the editor.

Submitting a paper• Most journals want you to suggest

at least two or three potentialreviewers for your paper who areexperts in their field.

• A journal may contact these but willoften invite additional reviewersto receive at least two good-qualityreviews.

Submitting a paper• A journal’s online submission

system will guide you through thesubmission process step by step.

• Well prepared manuscripts can besubmitted within an hour or so,

• If you cannot finish the submissionin one go, the system usually allowsto save information and resumethe submission process later.

Submitting a paper

• Read your full paper from beginningto end carefully one more time.

Ask yourself:• Is the story line obvious, logical, and

interesting?• Is the text clear but also concise?• Have I been consistent in the use of

terms?• Is the language correct ?

Submitting a paper• Consider having your manuscript

proofread by a trusted peer.

• Such a peer is able to identify the‘‘blind spots’’ in the manuscript,which you and your coauthors haveoverlooked and to give valuablefeedback for final improvements ofthe manuscript.

• In case your mother tongue is notEnglish, it can be useful to have yourpaper checked by a native speaker or aprofessional language editing service.

Submitting a paper• Use the cover letter as an opportunity

to ‘‘sell your paper’’ to the editor, whowill ultimately decide on it.

Write a convincing cover letterincluding the following elements:• the paper’s title and your request to

submit for publication;• significance of the main findings for

the field;• relevance to the journal’s audience;• information required by the journal;

and• additional issues related to the paper.

Submitting a paper

• Once you have finished yoursubmission, you should archive allinformation from the submissionprocess.

• Monitor the status of yoursubmission regularly and contactthe journal if the status is unclear orwhen a decision is taking too long(example: when you have not heardfrom the journal in 2-3 months).

Responding to reviewers

Responding to reviewers

There are three types of editorialdecisions about submitted papers:

• Acceptance – RARE !!!

• Rejection (immediately by thejournal’s editor or after peerreview),

• Revision (usually with peerreview).

Responding to reviewers

• Receiving a ‘‘revise andresubmit’’ decision proves that ajournal is interested, which is goodnews.

• It means there is a good chance ofacceptation if you respondsatisfactorily to the reviewers’comments.

Responding to reviewers• Do not panic when receiving a‘‘reject after review’’decision!

• Be aware that papers are moreoften rejected than accepted.

• Reviewer reports will give you freeadvice on how to improve yourpaper.

Responding to reviewers

• Once you have received thedecision, read it, sleep on it, andread it again, reflecting on thereasons for rejection.

• Share the rejection decision withyour coauthors, and use theopportunity to further strengthenyour manuscript before submittingit to a different journal.

Responding to reviewers• When receiving a ‘‘revise and

resubmit’’ decision, read the reportcarefully and let it sink in beforewriting the response.

• Copy/paste all comments into a newdocument and respond to eachcomment according to the followingstructure:

• Author’s response: briefly respond tothe criticism

• Changes to the paper: state whetherand where in the paper you have maderevisions.

Responding to reviewers

• In your revised paper, mark thetext that has been changed sincethe previous version,

• For example, using the ‘‘trackchanges’’ option of your wordprocessor.

• Always be respectful toward thereviewers in your response to theircomments.

Responding to reviewers

• Provide solid arguments to supportyour point of view, includingreferences to evidence from yourown data or previously publishedwork.

• In any case, reviewers reading yourresponse and the revised papershould get the impression thatyou have taken their commentsseriously and that you have doneyour best to improve the paperaccordingly.

Responding to reviewers

• Add a word of thanks to eachreviewer for taking the time tosuggest improvements.

• In the end, you will find that hoped-for e-mail in your inbox headed‘‘accepted for publication.’’

• Cherish that moment and be sureto CELEBRATE IT!