class: center, middle # Write to be read ## Principles and methods for writing a scientific paper Dr Bernard Pochet, 2023 - CC-BY     .center[] --- .right[] In science, research and literature are linked  --- .right[] And don't forget the processes  --- .right[] Especially the editorial process  --- .right[] ### Write to be read … barriers? - The **title**: short, attractive, representative of the text/research - **Authors**, their affiliation - **Abstract**: abstract structure? - **Keywords**: thesaurus? - **Language**: do you speak/write/read English? - The **text**: - The quality of the scientific approach - The structure of the text: IMRaD,... - The **quality of the writing**: - readability - clarity - precision - style --- .center[] --- .right[] ### A paper Is:  - A problem and a solution; - A new and original answer (compared to what we already know); - Only one message. ### Although not what was planned at the beginning of the research... --- .right[]         # Anatomy of a research paper ---  ---  ---  --- .right[] ## Introductory part ### Elements: - **Title** (+ current title & translated title); - **author(s)** + affiliation (use institutional standardization); - **structured abstract**; - **Keywords**: use a thesaurus. ### Special attention must be paid to the quality of these informations - it is also the metadata of the paper - each element is listed “as it” in most bibliographic databases --- .right[] ## The title - Short (between 5 and 25 words); - Clear (so unambiguous); - Summary (= summary of the abstract); - Must attract the reader; - Informative or synthetic; - In the form of a question or statement. --- .right[] ## A structured abstract  --- .right[] ## Or a graphical abstract  --- .right[] ### The body of the text: IMRaD model/structure  --- .right[] ### The body of the text: IMRaD model/structure  --- .right[] ### The body of the text: IMRaD model/structure  --- .right[] ### The body of the text: IMRaD model/structure  --- .right[] ### The body of the text: IMRaD model/structure  --- .right[] ## The body of the text: Introduction ### Must: - indicate the problem (what exactly are we talking about?); - refer to published literature (what we already know?); - present the hypothesis(s) (what is asked?).   ### Objectives: - highlight the value of the work presented in the article; - justify the choice of hypotheses and scientific approach. --- .right[] ## The body of the text: Material (and methods) **Description** (specify, unless already well described in the literature) **of the experimental protocol**. ## Objectives: - allow the evaluation of the the result’s quality; - allow another researcher to: - reproduce the results obtained, - use the same method in further experimentation. --- .right[] ## The body of the text: Results #### No interpretation, only results! ### Illustrations - not to be redundant (graphs, tables and text); - readable independently of the text: - quality of the title (above for tables & below for graphics) and legends (always below), - multilingual; - numbered and always called (Table x or Figure y) before in the text. --- .right[] ### The body of the text: Results (sample)    _{Total polyphenols contents of spices using different roasting temperatures (roasting time: 15 min) and different roasting times (roasting temperature: 140 °C), respectively — Teneurs en polyphénols totaux des épices respectivement à différentes températures de torréfaction (temps de torréfaction : 15 min) et à différents temps de torréfaction (température de torréfaction : 140 °C).} --- .right[] ## The body of the text: Discussion/conclusions ### Must: - relate the results to the starting hypothesis; - recall the originality and interest of the article (and research); - highlight the practical consequences of this research; - no bibliographic references. It is the discussion of the author's work, not that of other works; - be critical, present the limits of the research conducted (without denigrating the work); - possibly explain unexpected results or observations.   ### It is an essential part. Sentences can be cited in articles and books. --- .right[] ## A review (or systematic review) ### →  For a review paper; ### →  For an application for research funding; ### →  For a research paper (part of the introduction); ### →  For a thesis. --- .right[] ## A Review ### 1. Demonstrates the value of your work. ### 2. Show that you're proficient in the topic. ### 3. Express your agreement and disagreement. --- .right[] ## A review - may use another structure #### Introduction: - subject, limitations, and scope of the research; - presentation of the structure of the "Literature" section; - presentation of the methodology of the extended literature search. #### Literature: - discussion on the different sources selected; - organization: evolution over time, points of view and schools, different aspects. #### Conclusions (or "implications" and "future"): - contributions of the literature (what is already known); - areas of agreement and controversy (incl. Your voice); - questions still awaiting answers (by You). --- .right[] ## A revue - can also be structured as a research article #### Introduction - subject, limitations, and scope of the research. #### Material & methods - presentation of the methodology of the extended literature search. #### Results - findings (structured presentation of the literature) by sources, area of knowledge, timeline, ... #### Discussion - contributions of the literature (what is already known); - areas of agreement and controversy (incl. Your voice); - questions still awaiting answers (by You). --- .right[] ## The bibliography   .center[**All documents used must be cited in the text, with reference to the bibliography.**] .center[] .center[**All documents in the bibliography must be cited at least once in the text.**] --- .right[] ## The bibliography ### References must be: - recent - exhaustive (but not redundant – a selection of the most representative) - accessible (not « submitted » or « local document not published ») - scientific (should this be specified?) #### And don’t forget the use of the right tool to manage documents and bibliography! ---  --- .right[] ## Appendices / annexes - some publishers accept appendices; - it's getting easier with electronic publishing; - with open science, it's called open data: - whith data management plan - in dataverse.uliege.be (for instance) --- .right[] ## Writing a paper : first steps #### 1. before all: **literature search**; #### 2. the **article type** (research, review, research note, method...); #### 3. the list of **authors** (!); #### 4. the choice of the **journal** (tools...); #### 5. define the **subject** of the article (one question - one answer); #### 6. **authorizations** (for illustrations). --- .right[] ##The authors ### A decision must be taken **before** starting the work (research and writing). ### The author: - plays a central role in determining hypothesis; - contributes to obtaining, analyzing and interpreting results; - participates in writing a significant part of the article; - not to be confused with thanks.   #### The place of an author in the list is also important (first, last...) --- .right[] ## The CRediT taxonomy ### 14 roles: - Conceptualization - Data curation - Formal Analysis - Funding acquisition - Investigation - Methodology - Project administration - Resources - Software - Supervision - Validation - Visualization - Writing – original draft - Writing – review & editing --- .right[] ## The journal choice (recall) ### before 1950 - researcher read/used two or three titles - peer reviewing process was not yet used ### after WW2 - increase of the number of publications (mainly in English) - IF created to help librarians to choose titles - the IF has been guide to authors to choose (prestigious) titles to read and where to publish ... with all the biases that are now well identified - evaluation systems of researchers and research have integrated IF in evaluation process - DORA's declaration on research evaluation is gradually changing the situation --- .right[] ## The journal choice (recall) ### Currently With the multiplication of bibliographic databases and specialized search engines, the developement of Open Access, We choose our readings: - less on the basis of titles where they are published - but on the basis of a bibliographic search ### Continue to choose titles with IF to publish is for: - the ego of researchers (based on the notion of prestige, not quality) - competition between research teams (and universities) - respond to the "diktats" of some evaluation committees --- .right[] ## The journal choice (recall) ### It is necessary to: - reappropriate the publishing process - reduce the costs (in public money) ### Open Access is a solution (green or gold way) knowing that with the evolution of the models, increase of the quality of: - the evaluation - the publishing processes --- .right[] ## The journal choice (recall) ### Points of attention: - predatory journals (which have appeared since the invention of APCs) and "borderline" journals such as Frontiers in or MDPI - the amount of APCs and the transforming models that will continue to link universities to big publishers who will make even more money (we refuse to sign these agreements) - the intrinsic quality of journals: process, visibility, editing... --- .right[] ## The journal choice - Open access! (or at least fair publisher): - avoid hybrid journals ("Open Choise"), - avoid predatory journals/publishers. - International recognition; - Databases and citations; - Peer reviewing and validation process; - Audience (generalist vs. specialist, language...); - diffusion (eJournal, frequency, process duration); - Edition (author's guide). **OA = between 2 et 5 times more citations!** ---  ---  ---  ---  ---  ---  ---  --- .right[] ## Authorizations ### For: - tables; - graphics (including maps!); - drawing or photograph. ### You must have permission to reproduce (unless in open access, e.g. CC, or public domain) contact with rights holders (editor, authors...) can take a long time... --- .right[] ## And the law in Belgium? ### Open Access decree of the Wallonia-Brussels Federation (May 2018) **Authors always have to deposit articles in Open Access, immediately after acceptance of the article by the publisher.**   If the publisher requires it, the decree allows the article to be deposited in Open Access with an embargo that cannot exceed: - 6 months for the fields of science, technology and human or veterinary medicine; - 12 months for the humanities and social sciences. --- .right[] ## And the law in Belgium? ### Belgian copyright law (July 2018). If: - the research behind the article have been financed at least half by public funds; - a point of contact is located in Belgium (author, publisher, research or funding institution…).   **Authors have the right to deposit their journal articles in Open Access, regardless of the contract signed with the publisher!**   Only the author's version (final revised version without layout) accepted for publication is concerned. --- .right[] ## Writing ### The basic - write to communicate, not to impress; - keep your audience in mind; - write in your own voice: express yourself; - organize the information carefully; - follow the instructions; - set aside blocks of time for writing; - write quickly and leave gaps if necessary; - revise, revise, revise. --- .right[] ## Writing ### Your text - write readable (words, sentences & paragraphs); - be understandable and direct; - remove jargon; - use concrete words; - add enough details (but not to much); - credit sources adequately. --- .right[] ## Writing ### The right tools - use a mental map to structure your ideas; - write without editing! - use an editor (instead of a word processor) to write without distraction; - why not to learn Markdown… ### Don't try to get it right the first time and resist the temptation to edit as you go. → You will tend to get stuck and waste time. --- .right[] ## Take care of the readability of your text ### Readability depends on: - the complexity of the words used - the length of the sentences ### There should be only one idea per paragraph! ### If a reader has to reread a sentence to understand it, it is probably poorly written… --- .right[] ## Be precise ### It is essential to avoid using the terms: - few, - many, - a lot, - some - … Their meaning are subjective → You must give a quantity, a proportion, a percentage. Say how many! --- .right[] ## Some simple tips to improve your writing (to write stronger sentence) ### 1. Avoid contractions don’t → do not can’t → cannot shouldn’t → should not… ### 2. Avoid “there is” or “there are” There are many issues that students face at university → Students face issues at university --- .right[] ## Some simple tips to improve your writing (to write stronger sentence) ### 3. Avoid “really”, “very”, “a lot”, “so” A lot of students think university is very hard → 50% of students find it hard to study at university ### 4. Prefer the active voice Healthcare reforms were implemented by Obama → Obama implemented healthcare reforms ### 5. Use strong verbs He made objection to nationalization → He objected to nationalization --- .right[] ## Ethics ### Predatory publishers and fake journals ### Experimental ethics - ethics commission; - protocol number. ### Peer reviewing process - open / single blind / double blind; - contacts (between the authors and reader) are forbidden. --- .right[] ## Ethics ### Fraud - plagiarism and self-plagiarism; - data production; - data manipulation and falsification. ### Conflict of interest - financial and Commercial; - contractual; - patent. --- .right[] ## Ethics ### Authorship - who did what? - ghost authors (rewriting company). - think CRediT nomenclature --- .right[] ## The fighting course ### Submit your paper - via email or on a dedicated site; - With a cover letter: - a brief description of the work, its purpose, and interest in the journal, - the originality of the manuscript, - the subject of the manuscript fit with the scope of the journal; - declaration on the honor of lack of conflict of interest (funding, for example); - declaration on honor that all co-authors authorize the submitting of the paper; - description of each co-author's role. ### It is strictly forbidden to submit the same paper to two different journals at the same time! --- .right[] Think the process…  --- .right[] ## The fighting course ### After preliminary reading (and opinion of the editorial board) - rejection; - request for additions before the beginning of peer review process. ### After peer review - acceptance (rarely with the first version); - minor revisions (form); - major revisions (content); - rejection. ### Delay = several months (up to one year!) reviewers + corrections by authors + management of a large number of articles --- .right[] ## The main reasons for rejection (or major revision) are as follows: - there's plagiarism; - the content is not original; - there are too many language mistakes (spelling, grammar, ...); - poor quality of illustrations; - objectives (hypothesis\[s\]) are not defined; - the interest is too local; - the experimental design is too poor; - there are inconsistencies in the data; - the conclusions are hasty or erroneous; - the results are too partial ("further study should..."); - the bibliography is poor or too old and does not give a current vision of the problem. --- .right[]           .center[**These slides have been written in *Markdown* in an .html file using *remark.js* technology**] .center[(press ctrl-u to view source code)]   .center[**Thanks for your participation!**]