writing and publishing a scientific research paper pdf

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• Scientific Writing and Publishing

Scientific Writing and Publishing

A comprehensive manual for authors.

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• Denys Wheatley , University of Aberdeen
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Book description

Knowing how to prepare, write and publish high-quality research papers can be challenging for scientists at all stages of their career. This manual guides readers through successfully framing and presenting research findings, as well as the processes involved in publishing in learned journals. It draws on the author's wealth of practical experience, from working in academic research for over 40 years and teaching scientific writing in over 20 countries, to gaining insights as a journal editor. Well-written and logical, it provides clear step-by-step instructions to enable readers to become more effective at writing articles, and navigating difficulties related to journal submission, the review process, editing and publication. It comprehensively covers themes such as publication ethics, along with current topics including Open Access publishing and pre-print servers. This is a useful, user-friendly guide for graduate students, early career scientists, and more experienced researchers, particularly in the life and medical sciences.

‘Denys Wheatley has addressed an important issue - the writing up of findings. His manual is comprehensive, concise, and timely. It is truly an excellent piece of work. The manual will not only benefit native speakers wishing to publish scientific papers, but also non-native speakers. I will make this manual mandatory reading for all young scientists in my department before they attempt to write up their results.’

Wolfgang H. Goldmann - Friedrich-Alexander-Universität, Erlangen-Nürnberg, Germany

‘Professor Denys Wheatley’s Manual is a must-read for any Ph.D. student, researcher or scientist writing and publishing scientific papers. Not only is it the perfect primer for a first-time scientific writer, but also a complete guide for professionals. As a French-speaking biochemist, I did not encounter any difficulties in understanding this manual, and that is why it is certainly a stepping-stone for my research career.’

Nadia Bouktit - University A Mira of Béjaïa, Algeria

‘This much-needed book is clear, succinct and comprehensive, it gives the inexperienced (and indeed the more experienced) scientific author sound practical guidance at every step in the process, from planning and drafting the manuscript … It is this comprehensiveness and common-sense practicality that distinguishes it from other guides to scientific writing. I would happily recommend it to research students and post-docs, and I wish it had been available when I first embarked on a career in science.’

Mark P. Henderson - Formerly at Napier University, Edinburgh

‘‘If I had known that before …’. It meets the high needs in writing good scientific papers and getting them published … A ‘must read’ for young scientists as well as for instructors.’

Laurent Jaeken - Karel de Grote University College, Antwerp University Association, Antwerp, Belgium

‘This is a very useful document … Thank you for this wonderful and highly useful material.’

Kelath Murali Manoj - Satyamjayatu: The Science and Ethics Foundation, Kerala, India

‘Your manual on Scientific Writing and Publishing is really brilliant! … From my 50-year experience in science, it is very much needed for young and even middle-aged scientists.’

Jekaterina Erenpreisa - Full Member of the Latvian Academy of Science, Head Tumour Cell Biology Laboratory, Latvian Biomedical Research and Study Centre, Riga, Latvia

‘I certainly believe such a guide is sorely needed.’

Tom Ireland - Editor, The Biologist, Managing Editor, Royal Society of Biology

‘I have considered this Manual carefully and conclude it is a valuable and very much needed.’

James S. Clegg - Molecular and Cellular Biology, University of California, Davis, USA

‘This manual … is long overdue; it will be an extremely useful guide and reference … at all levels from beginning students to experienced investigators.’

Cynthia Jensen - University of Auckland, New Zealand

‘The book is well organized, clearly edited … it is easy to find in it the required information.’

Attila Miseta - Dean of the Medical University, Pécs, Hungary

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Scientific Writing and Publishing pp i-ii

• Get access Check if you have access via personal or institutional login Log in Register

Scientific Writing and Publishing - Title page pp iii-iii

• A Comprehensive Manual for Authors

Copyright page pp iv-iv

Contents pp v-x, acknowledgements pp xi-xii, introduction pp 1-15, writing and publishing a scientific paper pp 3-15.

• An Overview

1 - General Features of a Scientific Paper pp 16-27

• Structure and Format

2 - The Typical Scientific Paper pp 28-54

• A Published Paper with Annotations

3 - Results pp 55-64

• Presenting Your Findings

4 - Discussion pp 65-75

• The Place to Argue Your Case

5 - The Introduction pp 76-82

• The First Major Section of a Paper

6 - Materials and Methods pp 83-92

7 - the abstract pp 93-98.

• The Summary of the Main Findings

8 - The ‘Smaller’ Sections That Complete a Paper pp 99-110

9 - figures and tables pp 111-126, 10 - presubmission pp 127-133, 11 - submission of manuscripts pp 134-145, 12 - peer review pp 146-155.

• The Crux of the Problem in Publishing Papers

13 - The Last Stages of the Editorial Process pp 156-161

• Decisions, Revisions and Final Editing

14 - From Acceptance to Publication pp 162-169

Appendix 14.1 - flow chart pp 168-168, appendix 14.2 - description of the types of files commonly used pp 168-169, 15 - copyright pp 170-175, 16 - ethics and scientific integrity pp 176-187, 17 - epilogue pp 188-191, further reading pp 192-195, index pp 196-200, altmetric attention score, full text views.

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• Biochem Res Int
• v.2022; 2022

Essential Guide to Manuscript Writing for Academic Dummies: An Editor's Perspective

Syed sameer aga.

1 Department of Basic Medical Sciences, Quality Assurance Unit, College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGHA), King Abdulaziz Medical City, Jeddah 21423, Saudi Arabia

2 Molecular Diseases & Diagnostics Division, Infinity Biochemistry Pvt. Ltd, Sajad Abad, Chattabal, Srinagar, Kashmir 190010, India

Saniya Nissar

Associated data.

No data were used in this review.

Writing an effective manuscript is one of the pivotal steps in the successful closure of the research project, and getting it published in a peer-reviewed and indexed journal adds to the academic profile of a researcher. Writing and publishing a scientific paper is a tough task that researchers and academicians must endure in staying relevant in the field. Success in translating the benchworks into the scientific content, which is effectively communicated within the scientific field, is used in evaluating the researcher in the current academic world. Writing is a highly time-consuming and skill-oriented process that requires familiarity with the numerous publishing steps, formatting rules, and ethical guidelines currently in vogue in the publishing industry. In this review, we have attempted to include the essential information that novice authors in their early careers need to possess, to be able to write a decent first scientific manuscript ready for submission in the journal of choice. This review is unique in providing essential guidance in a simple point-wise manner in conjunction with easy-to-understand illustrations to familiarize novice researchers with the anatomy of a basic scientific manuscript.

1. Background

Communication is the pivotal key to the growth of scientific literature. Successfully written scientific communication in the form of any type of paper is needed by researchers and academicians alike for various reasons such as receiving degrees, getting a promotion, becoming experts in the field, and having editorships [ 1 , 2 ].

Here, in this review, we present the organization and anatomy of a scientific manuscript enlisting the essential features that authors should keep in their mind while writing a manuscript.

2. Types of Manuscripts

Numerous types of manuscripts do exist, which can be written by the authors for a possible publication ( Figure 1 ). Primarily, the choice is dependent upon the sort of communication authors want to make. The simplest among the scientific manuscripts is the “Letter to an Editor,” while “Systematic Review” is complex in its content and context [ 3 ].

Types of manuscripts based on complexity of content and context.

3. Anatomy of the Manuscript

Writing and publishing an effective and well-communicative scientific manuscript is arguably one of the most daunting yet important tasks of any successful research project. It is only through publishing the data that an author gets the recognition of the work, gets established as an expert, and becomes citable in the scientific field [ 4 ]. Among the numerous types of scientific manuscripts which an author can write ( Figure 1 ), original research remains central to most publications [ 4 – 10 ].

A good scientific paper essentially covers the important criteria, which define its worth such as structure, logical flow of information, content, context, and conclusion [ 5 ]. Among various guidelines that are available for the authors to follow, IMRAD scheme is the most important in determining the correct flow of content and structure of an original research paper [ 4 , 11 – 13 ]. IMRAD stands for introduction, methods, results, and discussion ( Figure 2 ). Besides these, other parts of the manuscript are equally essential such as title, abstract, keywords, and conclusion ( Figure 3 ).

Generalized anatomy of manuscript based on IMRAD format.

Three important contents of the title page—title, abstract, and keywords.

IMRAD scheme was introduced in the early 1900 by publishers to standardize the single format of the scientific manuscript and since then is the universal format used by most the publishing houses [ 6 , 14 – 17 ]. In the next sections, the contents and criteria of each of them are explained in detail. A list of the most common mistakes, which the author makes in these sections, is also provided in the tabulated form [ 18 ] ( Table 1 ).

Common mistakes authors make in their manuscripts.

• The title is the most important element of the paper, the first thing readers encounter while searching for a suitable paper [ 1 ]. It reflects the manuscript's main contribution and hence should be simple, appealing, and easy to remember [ 7 ].
• A good title should not be more than 15 words or 100 characters. Sometimes journals ask for a short running title, which should essentially be no more than 50% of the full title. Running titles need to be simple, catchy, and easy to remember [ 19 , 20 ].
• Keeping the titles extremely long can be cumbersome and is suggestive of the authors' lack of grasp of the true nature of the research done.
• It usually should be based on the keywords, which feature within the main rationale and/or objectives of the paper. The authors should construct an effective title from keywords existing in all sections of the main text of the manuscript [ 19 ].
• Having effective keywords within the title helps in the easy discovery of the paper in the search engines, databases, and indexing services, which ultimately is also reflected by the higher citations they attract [ 1 ].
• It is always better for the title to reflect the study's design or outcome [ 21 ]; thus, it is better for the authors to think of a number of different titles proactively and to choose the one, which reflects the manuscript in all domains, after careful deliberation. The paper's title should be among the last things to be decided before the submission of the paper for publication [ 20 ].
• Use of abbreviations, jargons, and redundancies such as “a study in,” “case report of,” “Investigations of,” and passive voice should be avoided in the title.

5. Abstract

• The abstract should essentially be written to answer the three main questions—“What is new in this study?” “What does it add to the current literature?” and “What are the future perspectives?”
• A well-written abstract is a pivotal part of every manuscript. For most readers, an abstract is the only part of the paper that is widely read, so it should be aimed to convey the entire message of the paper effectively [ 1 ].

Two major types of abstract—structured and unstructured. Structured abstracts are piecemealed into five different things, each consisting of one or two sentences, while unstructured abstracts consist of single paragraph written about the same things.

• An effective abstract is a rationalized summary of the whole study and essentially should contain well-balanced information about six things: background, aim, methods, results, discussion, and conclusion [ 6 , 19 ].

Three C concept followed while writing the manuscript.

• An abstract should be written at the end, after finishing the writing of an entire manuscript to be able to stand-alone from the main text. It should reflect your study completely without any reference to the main paper [ 19 ].
• The authors need to limit/write their statements in each section to two or three sentences. However, it is better to focus on results and conclusions, as they are the main parts that interest the readers and should include key results and conclusions made thereof.
• Inclusion of excessive background information, citations, abbreviations, use of acronyms, lack of rationale/aim of the study, lack of meaningful data, and overstated conclusions make an abstract ineffective.

6. Keywords

• Keywords are the important words, which feature repeatedly in the study or else cover the main theme/idea/subject of the manuscript. They are used by indexing databases such as PubMed, Scopus, and Embase in categorizing and cross-indexing the published article.
• It is always wise to enlist those words which help the paper to be easily searchable in the databases.
• Keywords can be of two types: (a) general ones that are provided by the journal or indexing services called as medical subject headings (MeSH) as available in NCBI ( https://www.ncbi.nlm.gov/mesh/ ) and (b) custom ones made by authors themselves based on the subject matter of the study [ 6 , 20 ].
• Upon submission, journals do usually ask for the provision of five to ten keywords either to categorize the paper into the subject areas or to assign it to the subspecialty for its quick processing.

7. Introduction

• (i) The whole idea of writing this section is to cover two important questions—“What are the gaps present in the current literature?” and “Why is the current study important?”
• (ii) Introduction provides an opportunity for the authors to highlight their area of study and provide rationale and justification as to why they are doing it [ 20 , 22 , 23 ].
• (iii) An effective introduction usually constitutes about 10–15% of the paper's word count [ 22 ].
• The first paragraph of the introduction should always cover “What is known about the area of study?” or “What present/current literature is telling about the problem?” All relevant and current literature/studies, i.e., original studies, meta-analyses, and systematic reviews, should be covered in this paragraph.
• The second paragraph should cover “What is unknown or not done about this issue/study area?” The authors need to indicate the aspects of what has not been answered about the broader area of the study until now.
• The third paragraph should identify the gaps in the current literature and answer “What gaps in the literature would be filled by their current study?” This part essentially identifies the shortcoming of the existing studies.
• The fourth paragraph should be dedicated to effectively writing “What authors are going to do to fill the gaps?” and “Why do they want to do it?” This paragraph contains two sections—one explains the rationale of the study and introduces the hypothesis of the study in form of questions “What did authors do? and Why they did do so?” and the second enlists specific objectives that the authors are going to explore in this study to answer “Why this study is going to be important?” or “What is the purpose of this study?”.

Funnel-down scheme followed while writing the introduction section of manuscript, moving from broader to specific information.

• (v) Introduction is regarded as the start of the storyline of manuscript, and hence, the three Cs' scheme ( Figure 5 ) becomes more relevant while writing it: the context in terms of what has been published on the current idea/problem around the world, content as to what you are going to do about the problem in hand (rationale), and conclusion as to how it is going to be done (specific objective of the study) [ 1 , 23 ].
• (vi) Introduction is the first section of the main manuscript, which talks about the story; therefore, while writing it authors should always try to think that “would this introduction be able to convince my readers?” [ 25 ]. To emphasize on the importance of the study in filling the knowledge gap is pivotal in driving the message through [ 23 ].
• (vii) Introduction should never be written like a review, any details, contexts, and comparisons should be dealt within the discussion part [ 16 ].
• (viii) While choosing the papers, it is wise to include the essential and recent studies only. Studies more than 10 years old should be avoided, as editors are inclined towards the recent and relevant ones only [ 20 , 22 ].
• (ix) In the last paragraph, enlisting the objectives has a good impact on readers. A clear distinction between the primary and secondary objectives of the study should be made while closing the introduction [ 22 ].
• (i) It is regarded as the skeleton of the manuscript as it contains information about the research done. An effective methods section should provide information about two essential aspects of the research—(a) precise description of how experiments were done and (b) rationale for choosing the specific experiments.
• Study Settings: describing the area or setting where the study was conducted. This description should cover the details relevant to the study topic.

Different guidelines available for perusal of the authors for writing an effective manuscript.

• Sample Size and Sampling Technique: mentioning what number of samples is needed and how they would be collected.
• Ethical Approvals: clearly identifying the study approval body or board and proper collection of informed consent from participants.
• Recruitment Methods: using at least three criteria for the inclusion or exclusion of the study subjects to reach an agreed sample size.
• Experimental and Intervention Details: exhaustively describing each and every detail of all the experiments and intervention carried out in the study for the readers to reproduce independently.
• Statistical Analysis: mentioning all statistical analysis carried out with the data which include all descriptive and inferential statistics and providing the analysis in meaningful statistical values such as mean, median, percent, standard deviation (SD), probability value (p), odds ratio (OR), and confidence interval (CI).

Methods and the seven areas which it should exhaustively describe.

• (iii) Methods should be elaborative enough that the readers are able to replicate the study on their own. If, however, the protocols are frequently used ones and are already available in the literature, the authors can cite them without providing any exhaustive details [ 26 ].
• (iv) Methods should be able to answer the three questions for which audience reads the paper—(1) What was done? (2) Where it was done? and (3) How it was done? [ 11 ].
• (v) Remember, methods section is all about “HOW” the data were collected contrary to “WHAT” data were collected, which should be written in the results section. Therefore, care should be taken in providing the description of the tools and techniques used for this purpose.
• (vi) Writing of the methods section should essentially follow the guidelines as per the study design right from the ideation of the project. There are numerous guidelines available, which author's must make use of, to streamline the writing of the methods section in particular (see Table xx for details).
• (vii) Provision of the information of the equipment, chemicals, reagents, and physical conditions is also vital for the readers for replication of the study. If any software is used for data analysis, it is imperative to mention it. All manufacturer's names, their city, and country should also be provided [ 6 , 11 ].
• The purpose of the results section of the manuscript is to present the finding of the study in clear, concise, and objective manner to the readers [ 7 , 27 , 28 ].
• Results section makes the heart of the manuscript, as all sections revolve around it. The reported findings should be in concordance with the objectives of the study and be able to answer the questions raised in the introduction [ 6 , 20 , 27 ].
• Results should be written in past tense without any interpretation [ 6 , 27 ].

Interdependence between methods and results of the manuscript.

• It is always better to take refuge in tables and figures to drive the exhaustive data through. Repetition of the data already carried in tables, figures, etc., should be avoided [ 4 , 6 , 20 ].
• Proper positioning and citations of the tables and figures within the main text are also critical for the flow of information and quality of the manuscript [ 6 , 11 ].
• Results section should carry clear descriptive and inferential statistics in tables and/or figures, for ease of reference to readers.
• Provision of the demographic data of the study participants takes priority in the results section; therefore, it should be made as its first paragraph. The subsequent paragraphs should introduce the inferential analysis of the data based on the rationale and objectives of the study. The last paragraphs mention what new results the study is going to offer [ 6 , 11 , 20 ].
• authors should not attempt to report all analysis of the data. Discussing, interpreting, or contextualizing the results should be avoided [ 20 ].

10. Discussion

• (i) The main purpose of writing a discussion is to fill the gap that was identified in the introduction of the manuscript and provide true interpretations of the results [ 6 , 11 , 20 ].

Pyramid scheme followed while writing the discussion section of manuscript, moving from the key results of the study to the specific conclusions.

• (iii) Discussion section toggles between two things—content and context. The authors need to exhaustively describe their interpretation of the analyzed data (content) and then compare it with the available relevant literature (context) [ 1 , 29 ]. Finally, it should justify everything in conclusion as to what all this means for the field of study.
• (iv) The comparison can either be concordant or discordant, but it needs to highlight the uniqueness and importance of the study in the field. Care should be taken not to cover up any deviant results, which do not gel with the current literature [ 30 ].
• (v) In discussion it is safe to use words such as “may,” “might,” “show,” “demonstrate,” “suggest,” and “report” while impressing upon your study's data and analyzed results.
• (vi) Putting results in context helps in identifying the strengths and weakness of the study and enables readers to get answers to two important questions—one “what are the implications of the study?” Second “how the study advance the field further?” [ 1 , 30 ].
• The first paragraph of the discussion is reserved for highlighting the key results of the study as briefly as possible [ 4 , 6 ]. However, care should be taken not to have any redundancy with the results section. The authors should utilize this part to emphasize the originality and significance of their results in the field [ 1 , 4 , 11 , 20 ].
• The second paragraph should deal with the importance of your study in relationship with other studies available in the literature [ 4 ].
• Subsequent paragraphs should focus on the context, by describing the findings in comparison with other similar studies in the field and how the gap in the knowledge has been filled [ 1 , 4 ].
• In the penultimate paragraph, authors need to highlight the strengths and limitations of the study [ 4 , 6 , 30 ].
• Final paragraph of the discussion is usually reserved for drawing the generalized conclusions for the readers to get a single take-home message.
• (viii) A well-balanced discussion is the one that effectively addresses the contribution made by this study towards the advancement of knowledge in general and the field of research in particular [ 7 ]. It essentially should carry enough information that the audience knows how to apply the new interpretation presented within that field.

11. Conclusion

• It usually makes the last part of the manuscript, if not already covered within the discussion part [ 6 , 20 ].
• Being the last part of the main text, it has a long-lasting impact on the reader and hence should be very clear in presenting the chief findings of the paper as per the rationale and objectives of the study [ 4 , 20 ].

Crux of the conclusion section.

12. References or Bibliography

• Every article needs a suitable and relevant citation of the available literature to carry the contextual message of their results to the readers [ 31 ].
• Inclusion of proper references in the required format, as asked by the target journal, is necessary.

A Google Scholar screenshot of different styles of formatting of references.

• Depending upon the journal and publishing house, usually, 30–50 citations are allowed in an original study, and they need to be relevant and recent.

13. Organization of the Manuscript Package

Ideally, all manuscripts, no matter where they have to be submitted, should follow an approved organization, which is universally used by all publication houses. “Ready to submit” manuscript package should include the following elements:

• (i) Cover letter, addressed to the chief editor of the target journal.
• (ii) Authorship file, containing the list of authors, their affiliations, emails, and ORCIDs.
• (iii) Title page, containing three things—title, abstract, and keywords.
• Main text structured upon IMRAD scheme.
• References as per required format.
• Legends to all tables and figures.
• Miscellaneous things such as author contributions, acknowledgments, conflicts of interest, funding body, and ethical approvals.
• (v) Tables as a separate file in excel format.
• (vi) Figures or illustrations, each as a separate file in JPEG or TIFF format [ 32 ].
• (vii) Reviewers file, containing names of the suggested peer reviewers working or publishing in the same field.
• (viii) Supplementary files, which can be raw data files, ethical clearance from Institutional Review Board (IRBs), appendixes, etc.

14. Overview of an Editorial Process

Each scientific journal has a specific publication policies and procedures, which govern the numerous steps of the publication process. In general, all publication houses process the submission of manuscripts via multiple steps tightly controlled by the editors and reviewers [ 33 ]. Figure 12 provides general overview of the six-step editorial process of the scientific journal.

An overview of the journal's editorial process.

15. Summary

The basic criteria for writing any scientific communication are to know how to communicate the information effectively. In this review, we have provided the critical information of do's and don'ts for the naive authors to follow in making their manuscript enough impeccable and error-free that on submission manuscript is not desk rejected at all. but this goes with mentioning that like any other skill, and the writing is also honed by practicing and is always reflective of the knowledge the writer possesses. Additionally, an effective manuscript is always based on the study design and the statistical analysis done. The authors should always bear in mind that editors apart from looking into the novelty of the study also look at how much pain authors have taken in writing, following guidelines, and formatting the manuscript. Therefore, the organization of the manuscript as per provided guidelines such as IMRAD, CONSORT, and PRISMA should be followed in letter and spirit. Care should be taken to avoid the mistakes, already enlisted, which can be the cause of desk rejection. As a general rule, before submission of the manuscript to the journal, sanitation check involving at least two reviews by colleagues should be carried out to ensure all general formatting guidelines are followed.

Acknowledgments

The authors would like to thank all academicians and researchers who have actively participated in the “Writing Manuscript Workshops” at the College of Medicine, KSAU-HS, Jeddah, which prompted them to write this review.

Data Availability

Conflicts of interest.

The authors declare no conflicts of interest.

Authors' Contributions

Both authors have critically reviewed and approved the final draft and are responsible for the content and similarity index of the manuscript. SSA conceptualized the study, designed the study, surveyed the existing literature, and wrote the manuscript. SN edited, revised, and proofread the final manuscript.

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A critical question in Space Biology is how will astronauts adapt to long-term spaceflight missions to Moon, Mars, and beyond? On November 25, twenty-nine scientific papers – including several from NASA’s GeneLab project – will offer answers to this question. These papers will be published in five  Cell Press  journals including  Cell, Cell Reports, iScience, Cell Systems , and  Patterns . They have been contributed by over 200 investigators from dozens of academic, government, aerospace, and industry groups, representing the largest set of astronaut data and space biology data ever produced, including longitudinal multi-omics profiling, single-cell immune and epitope mapping, novel radiation countermeasures, and detailed biochemical profiles of 59 astronauts who represent more than 10% of all humans who have ever been in space.

Some of the groundbreaking work reported in these papers utilized the GeneLab platform and its repository of spaceflight omics data, which are used to generate novel discoveries and develop new hypotheses for determining systemic biological responses occurring in spaceflight. Space biologists around the world are increasingly reliant on these omics data (epigenomics, transcriptomics, proteomics, metagenomics, and metabolomics) to maximize the knowledge gained from rare spaceflight experiments.

Below is a summary of the four GeneLab-related papers authored by the GeneLab team and its Analysis Working Group (AWG) members, investigators.

• RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques,  Lai Polo, S., et al , iScience
• Multi-Omics Analysis Reveals Mitochondrial Stress as a Central Hub   for Spaceflight Biological Impact , da Silveira, W.,  Cell
• Comparative Transcriptomics Identifies Altered Neuronal and Metabolic Function as Common Adaptations to Microgravity and Hypergravity in Caenorhabditis elegans, Willis et al., iScience
• A Longitudinal Epigenetic Aging and Leukocyte Analysis of Simulated Space Travel: The Mars-500 Mission, Nwanaji-Enwerem, J., Cell Reports

To view all 29 scientific papers published in the five Cell Press journals including Cell, Cell Reports, iScience, Cell Systems, and Patterns go to:  https://www.cell.com/c/the-biology-of-spaceflight

Writing and publishing a scientific paper

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• Volume 8 , article number  8 , ( 2022 )

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This text is designed to give the reader a helping hand in writing a scientific paper. It provides generic advice on ways that a scientific paper can be improved. The focus is on the following ethical and non-technical issues: (1) when to start writing, and in what language; (2) how to choose a good title; (3) what should be included in the various sections (abstract, introduction, experimental, results, discussion, conclusions, and supporting information (supplementary material); (4) who should be considered as a co-author, and who should be acknowledged for help; (5) which journal should be chosen; and (6) how to respond to reviewers’ comments. Purely technical issues, such as grammar, artwork, reference styles, etc., are not considered.

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“Work, finish, publish” (Michael Faraday) [ 1 ]. Footnote 1

Introduction

The task of writing a scientific paper usually befalls young researchers quite early in their bachelor, masters or PhD degree programs. In most cases, the candidates know very little about the publishing process, which involves a complex combination of historical traditions and modern innovations. Guidebooks are of course available, but these tend to focus on purely technical issues, and miss the interpersonal nuances that are so daunting for the beginner. In any case, the technical issues are normally not the main problem for computer-literate students, so I avoid them in this document. Instead I present my personal views on the overall process, and leave it to the reader to evaluate them.

Long experience has taught me that there are many ways of writing a successful paper, but nevertheless some general principles can be identified. In what follows, all my suggestions are informed by my experience as the editor-in-chief of two international journals, the Journal of Solid State Electrochemistry for 25 years, and ChemTexts—The Textbook Journal of Chemistry for 7 years. I have also been the editor of the series Monographs in Electrochemistry , as well as various reference books and textbooks.

Looking back at history, the communication of scientific results in specialist journals is a rather recent development: its origins date back to the second half of the seventeenth century. In 1665, the Journal des sçavans started in France, while the Philosophical Transactions of the Royal Society began in Great Britain. Before that time, it was common to publish new findings in books. However, the increasing pace of scientific developments, as well as the increasing number of people who were devoting their lives to science, required a more efficient and faster form of communication. For this to be achieved, journals proved to be very successful. The history of scientific journals cannot be traced here, but I recommend the book The Scientific Journal by Alex Csiszar [ 2 ].

Scientific communication requires a common language that is shared by the author and the reader. Michael D. Gordin has described in his book Scientific Babel [ 3 ] how, over the last few centuries, scientific communication has gradually shifted from Latin to English. The author also pays detailed attention to the French, German and Russian languages, which played important roles in the nineteenth and twentieth centuries. These languages retain their importance for scientists, because they contain the foundational texts of many important branches of science.

When to start writing a manuscript

It is trivial to say that one should write a manuscript only when one has new results to communicate. But new results do not appear suddenly and without ambiguity. Rather, they tend to accumulate gradually over time, and require repeated contextualisation to be fully appreciated. This begs the question, at what point should one publish?

Answering this question is difficult. Students certainly need to discuss the matter with their supervisors, who have the necessary experience and far-sightedness. Beginners often wildly underrate or overrate their data. Realistically, however, all scientific publication is a compromise between “publishing too late” and “publishing too early”.

“Publishing too late” (or never) is a well-known fault of some overcautious individuals, who withhold their data from public scrutiny because they are not satisfied with its accuracy and completeness. Although this demonstrates their high ethical standards as regards their personal participation in the scientific process, it also reveals an indifference to the social value of their data and the financial costs to others of having to reproduce their results. In the final analysis, tax-payers’ money that is spent on unpublished work is wasted money, and this raises questions of probity. (In the case of industrial research, contractual confidentiality may also restrict publication, but that is a problem I cannot discuss here.)

“Publishing too early” is a fault of some reckless individuals who have scant regard for the integrity of the scientific process. The institutional pressure to publish papers and the competition for scarce funds are the main causes of this. Nowadays, pollution of the scientific literature by worthless, irreproducible or sloppy work is an increasing and serious problem. Here I can only plead with colleagues of all ages: please do not be tempted by the short-term advantages of overpublication. The benefits are illusory, and the damage is untold. With the advent of mass data storage, published papers are effectively immortal, and sooner or later bad work (and its creators) will be found out.

Of course, “publishing too early” is most tempting for the beginner, and the problem becomes critical when the supervisor is also overambitious. If the supervisor pressurizes the student to publish uncooked results, then the student has a big problem! Now, many universities have introduced ‘thesis committees’ consisting of the primary supervisor plus two or three additional members. These committees can provide valuable advice with respect to timeliness of publishing and they may also mitigate conflicts between the student and their main supervisor, if they happen to occur.

Personally, I have been an ombudsman at my university, and I am pleased to say that such conflicts can be resolved amicably by careful and trustful discussions between all parties. But I fear that global science has a problem with this issue.

The whole question of when to start writing cannot be answered by a simple prescription, and depends to a large extent on the personalities of the individuals concerned. My personal advice is to start writing as soon as the main results become discernible. Writing down the first tranche of clear and reliable results is a useful discipline which indicates what has been achieved and what experiments remain to be done. If you delay writing until you think that all the required experiments have been completed, then you will be sadly disappointed. You will discover that much has been omitted, and then you will have to start again with certain crucial experiments. It goes without saying that co-authors should be involved very early in the writing.

In what language should the paper be written?

What language to use is rather obvious. If you want to be understood worldwide, then you must publish in English. In 2021, there were around 1.35 billion people, scattered over many countries, who spoke English as a first or second language. If you are not a native English speaker, then I strongly recommend that you start to write in English. Do not write in your native language with the vague notion of translating it later into English. This is always bad policy, because you will certainly find it more difficult to translate your text into English than to compose it from scratch. Assuredly, this demands a reasonable command of English. But there are practical steps that you can take to help you along the way.

To achieve a sufficient command of English, you should read as many well-written(!) scientific papers in English as possible. For technical English, try to focus on papers written by native English speakers. However, do not limit yourself to scientific papers, but also read English stories and novels, or any other writings, that can expand your knowledge of English. You should also try to distinguish the different styles (scientific, colloquial, etc.) and avoid mixing them in your own writing.

At this point I suggest the book The Chemist’s English [ 4 ] written by Robert Schoenfeld, and his paper “Say it in English, please” [ 5 ]. Schoenfeld was editor-in-chief of the Australian Journal of Chemistry . One trick that I have found very effective for improving my written English is to translate the draft manuscript back into my native language (in my case German). For many years I did this for publications in Angewandte Chemie , a journal that is published both in English and German, and these back translations frequently revealed the weaknesses in my English.

Concerning written text, I have some further advice which is not specific to the English language: first of all, write clearly and understandably! The eminent physicist Carl Wagner (1901–1976) famously wrote “Any fool can think and write something complicated” (“Jeder Dumme kann etwas Kompliziertes denken und schreiben”) [ 6 ]. Always remember these wise words! Whenever you write a very complicated phrase, ask yourself, do you really understand what you have written? Very often, complicated constructions are the result of an insufficient understanding, or represent an attempt at “hedging” i.e. attempting to disguise the omission of certain facts which might otherwise conflict with the overall claims being made.

In the same book, Wagner also wrote “It is a very special art to speak understandably about subjects when they are not yet completely known”. With regard to clear and understandable language, I should also like to give a serious warning regarding the misuse of certain words and phrases that express uncertainty: “possibly”, “probably”, “may be an indication of”, “seems to be”, “cannot be excluded”, “it is reasonable to assume”, etc. It is possible that these constructions may be justified in certain circumstances, but more often than not they hide a lack of understanding, and trigger alarm bells in the minds of readers. Whenever you write these phrases, ask yourself, are they necessary, are they well-reasoned? I have seen manuscripts full of such vague phrases, and it was clear that they were more or less worthless!

For the language of a paper to be intelligible, it is also necessary that a well-defined terminology is used. The terms have to be internationally accepted (e.g. by IUPAC) and have to be used consistently. It is not good to operate with several synonyms, but one and the same should be used throughout.

The structure of a scientific paper

Usually, scientific papers are structured in the following subsections: (1) title, (2) name of authors and their affiliation(s), (3) keywords, (4) graphical abstract, (5) abstract, (6) introduction, (7) experimental part, (8) results and discussion, (9) conclusions, (10) acknowledgements, (11) references, (12) list of figure captions, (13) figures. Most journals offer publication of ‘supporting information’ (or ‘supplementary material’): these supplements are not part of the main paper, but usually constitute a depository for data, figures, tables, mathematical derivations, etc. which the reader may like to consult for a deeper understanding, which, however, are not vital for a general understanding of the paper. I always prefer to put as much as possible into the main paper, and restrict supplementary information to items which are really of less significance. Many journals provide templates, which you should use. In these templates, the order of items may differ from that given above. You should always adhere strictly to the guidelines of the journal. Some details relating to the subsections of a paper are described below.

The title is the entrance door to your paper. Reading the title, many people make the decision whether to enter the document or walk away. According to Thomson’s Web of Science , about 27% of natural science papers are uncited after 5 years, most likely because they are unread, or undiscovered by search engines. To attract interest, the title of a paper needs to be as short as possible, but as long as necessary. It should also contain some searchable terms for easy computer recognition. Certainly, the title also needs to indicate the very essence of the paper. Prior to the advent of computers, it was customary to use titles like “Studies in phosphorus chemistry. Part XII.”! What on earth does that tell you? Nothing about the specific contents, that’s for sure. Luckily, the time of such absurdities is over.

Phrasing the title of a scientific paper is hard work, and usually the final choice will emerge only after long consideration. It is my personal view that authors should think about the title at the very beginning of writing a manuscript. Since the title reveals the essence, a well-chosen title can set the tone for the entire manuscript. And it goes without saying that the title can still be modified many times as the manuscript mutates into its final form.

The keywords

Most journals request a list of keywords. These are important for the classification of the paper in information systems. Think about the terms that best characterise the content of your paper. However, try to avoid newly created terms or abbreviations. Although an overlap between title terms and keywords is unavoidable, the latter should provide additional information.

The abstract

Following the title, the abstract is the most important device for attracting the attention of readers. Personally, I have always advocated writing the first draft of the abstract before writing the remainder of the text. This forces the author to identify the principal achievements at an early stage. Like the title, the abstract needs to be as short as possible and as long as necessary. Its function is to summarize all the main results. I know that many experienced colleagues disagree with my suggestion of writing the first draft of the abstract before writing the main body of the text. However, my suggestion is not meant to be an apodictic rule. You must find out what best suits you.

Drafting the title and abstract at an early stage presupposes that you already have a clear picture of your achievement. If you do not have that clear picture, then a good suggestion is to arrange all your diagrams and tables in a logical sequence, and then write the text around that.

The abstract needs to contain as much quantitative information as possible. If you have new and significant data, give them in the abstract!

The introduction

The introduction should state the motivation and the aim of the presented research and refer to all relevant literature. If the paper is intended for a specialised journal, avoid rehashing simple textbook knowledge, as you can assume that expert readers will already be acquainted with it. In more general journals, some wider introductory remarks may be necessary.

When you discuss earlier works in your field, do not focus purely on their shortcomings. Make sure that you acknowledge their achievements. Be fair in your presentation. Cite all relevant papers, at least the most important ones. Do not overcite your own papers.

At the end of the introduction, state what you have achieved and what you will present in the paper. Do not repeat the abstract. This is important for the entire paper: avoid repetitions!

The experimental part

This part should contain sufficient experimental details (chemicals, instruments, methods, etc.) for your work to be reproduced in another laboratory. If certain procedures or techniques have previously been published by you, or others, you may refer to those papers without repeating the details. However, the reference has to be accessible. I have seen papers in which the author wrote “the technique is described in Ref. X”. When reading Ref. X, I found the remark “the technique is described in Ref. Y”, and so forth until I gave up searching! This is unacceptable.

The results and discussions

In the past, many journals have demanded that the results and discussion be reported separately. Some journals still demand this. Especially in the case of highly multidisciplinary work it is necessary to present first the results of the different disciplines, followed by a joint discussion referring to all the disciplines. However, if possible, I advocate providing the results and discussion simultaneously, since the combined text is easier to understand.

The most important point in writing the results and discussion section is logical consistency . The most frequently seen weakness appears when authors forego logical consistency and instead provide a chronological history of their experiments. This is often copied from laboratory notebooks. One then finds phrases like “first we thought that x may be the reason for y, and we performed the following experiments… then it turned out that y has nothing to do with x, and we supposed that z might cause the observed effect. Then we did this, and later we did that, and in the end…”. Such historical summaries are extremely tedious for the reader, and may even be misleading.

In results and discussion , it is essential to illustrate the results with clear reference to figures and tables, and to arrange the results within a logical framework. Figures, having captions, and tables, having headings, should be understandable without reading the detailed text.

The conclusions

The most frequent fault is the copying of an abstract, or the minor modification of an abstract, without any reference to the context of the results. The abstract does not require justification of the work: the conclusions certainly do. The conclusions have to provide new insight into a field of research, and this must be explained. The best writers will also indulge in some speculations about future work. These should open the readers’ eyes to novel and unexpected applications of the findings.

When you have finished writing a manuscript, leave it for some time untouched, and then read it again after some days or weeks. You will discover that a fresh reading reveals flaws, repetitions, typos, etc., which you missed the first time around. You should also use that time to circulate the document among trusted friends and colleagues who may act as internal reviewers before external submission. You will be surprised what typos your friends find! The blindness of authors to their own typos is legendary. The modern spellcheckers of computer systems do not prevent all typos, but they are helpful. (They may even introduce further errors, if you are not attentive).

Who should be co-authors and who should be acknowledged for help?

The ethical guidelines of most scientific funding organisations (e.g. Deutsche Forschungsgemeinschaft (DFG)/German Research Council [ 7 ]) demand that everybody who has a distinct share, be it intellectual or experimental, in a paper has to be listed as a co-author. Any “honorary” co-authorship is not allowed! This is a clear statement, but a lot of questions may arise in specific cases. Since I cannot say it in a better way, I cite here from the DFG guidelines:

Guideline 14: Authorship An author is an individual who has made a genuine, identifiable contribution to the content of a research publication of text, data or software. All authors agree on the final version of the work to be published. Unless explicitly stated otherwise, they share responsibility for the publication. Authors seek to ensure that, as far as possible, their contributions are identified by publishers or infrastructure providers such that they can be correctly cited by users. Explanations: The contribution must add to the research content of the publication. What constitutes a genuine and identifiable contribution must be evaluated on a case-by-case basis and depends on the subject area in question. An identifiable, genuine contribution is deemed to exist particularly in instances in which a researcher—in a research-relevant way—takes part in the development and conceptual design of the research project, or the gathering, collection, acquisition or provision of data, software or sources, or the analysis/evaluation or interpretation of data, sources and conclusions drawn from them, or the drafting of the manuscript. If a contribution is not sufficient to justify authorship, the individual’s support may be properly acknowledged in footnotes, a foreword or an acknowledgement. Honorary authorship where no such contribution was made is not permissible. A leadership or supervisory function does not itself constitute co-authorship.

At some educational institutions, the rules for submitting a PhD thesis demand a certain number of submitted or published papers. Unfortunately, this occasionally leads to a sharing of authorship among two or more candidates, so that each of them reaches the desired number, although neither of them has a proper share in all the papers. This is unethical and is strongly condemned.

A very crucial point is that all co-authors must give their clear consent to the submission of the manuscript. Nowadays, most journals send emails to the co-authors informing them about the submission. However, this does not liberate principal authors from the moral imperative of sending their co-authors copies of the manuscript in advance of publication and asking for their consent! Similar advice applies to acknowledgements. Who would be happy about an acknowledgement in a paper that they disagree with?

Which journal should be chosen?

The manuscript should be submitted to a journal which is devoted to the branch of science concerned. Usually there are several journals available so authors need rational criteria for making a choice. Experienced authors typically decide on the basis of publishers’ reputations (journal citation metrics) or personal connections (networks of esteem). Nowadays, scientific information systems even make it possible to unearth obscure papers published in “wrong” journals, on the basis of the title, keywords and abstract. However, indifference to journal choice is not recommended as a career strategy!

Citation metrics have a history of about 200 years [ 8 ]. However the modern infatuation with citation metrics has been driven by their uncritical adoption by research organisations and promotion committees in making decisions about funding and promotion.

In 2012, the San Francisco Declaration on Research Assessment (DORA; https://sfdora.org ) criticized the use of “impact factors” for evaluating the merits of scientists. Since then, the criticism has intensified (see, e.g., [ 9 , 10 , 11 , 12 , 13 ]). Authors are now in a serious conflict situation: should they follow the metrics, or should they choose a journal according to other quality measures? This question is difficult to answer.

What are other quality measures? In my view, one of the most important is the quality of its reviewers and their reports. Those reports are the best which are competent, fair and helpful. Journals which provide such reports should certainly be considered. But these high-quality journals can only be identified by long experience.

Ultimately, neither the Impact Factor nor the CiteScore of a journal is an unambiguous measure of the quality of a single paper. So students should not feel upset when their papers appear in low index journals, nor should they feel triumphant when their papers appear in high index journals.

In all cases authors should beware of publishing in predatory journals ( https://en.wikipedia.org/wiki/Predatory_publishing ). Open access predatory journals publish manuscripts without serious review. They publish only for money.

Now, a final word about “open access” publishing: this is certainly the best way to disseminate scientific information; however, only if the journals operate a strict peer review. Some scientific publishers (e.g. Springer Nature, https://www.springernature.com/gp/open-research/institutional-agreements ) also have international agreements with universities and institutions to pay the costs of publishing.

How to respond to reviews of submitted manuscripts

It is very interesting to learn how the “peer review system” emerged and I suggest that students read about it in a paper by Csiszar in Nature [ 14 ]. Nowadays, when a manuscript is submitted to a reputable journal, it will first be read by members of the editorial board, who decide whether it should be sent out to referees (reviewers) or sent back to the authors. If serious deficiencies are identified then it is senseless to bother reviewers.

When you receive the reviews of your manuscript, normally at least two or three, you need to know what to do with them. In any event, you should be self-critical: if you get the report “publish as is” or a similar positive evaluation, do not image that your manuscript is perfect. Possibly the reviewer was not competent or was very sloppy in assessing your manuscript. Believe the positive evaluations only when you get two or three of them!

The other extreme may be a report saying “this is a very weak manuscript that should not be published”, without giving specific criticism. Such a report is not helpful and the editor must take the blame for accepting it and passing it to the author. Harsh criticisms require detailed justification, just as extraordinary claims require extraordinary proof.

Fortunately, most reviewers take their job very seriously and deliver clear and detailed reports. You, the author, should always presume that the reviewers are trying to help you to improve your manuscript. They are not your enemy, but on your side, and they are fair. If you do identify clear signs of unfairness, then you should turn to the editor and ask for further reports. It often happens that the first reaction of an author is “oh, this reviewer has completely misunderstood me” and then starts to write a long rebuttal to the editor, explaining all the misunderstandings! However, since reviewers are experts in their field, the author should realize that a likelier explanation of a poor review is the poor quality of the manuscript!

Of course, it really may be true that a reviewer has misunderstood a manuscript. However, in most cases, it is my experience as an editor that the misunderstandings result from deficiencies of the manuscript, such as confusing phrases. Therefore, it is my advice to ask yourself how this misunderstanding could have happened. Do not blame the reviewer; think about your own text!

When you prepare the revised manuscript, follow carefully the advice of the reviewers. In the revised manuscript, you should highlight all the revised parts, which makes it easy for the editor and reviewers to see how you have responded. Your revised manuscript also needs to be accompanied by a detailed document (rebuttal) in which you list the changes and give your explanations for the revisions. Certainly, you are not obliged to do everything as requested by the reviewers. If you have good arguments against the reviewer’s proposals, bring them forward, and it will be up to the editor and reviewers to accept or to reject them.

It goes without saying that it is unacceptable to submit a rejected manuscript to another journal (sometimes even the same journal) without any revisions. This is profoundly disrespectful. When a manuscript has been rejected by a journal, you are of course free to submit it elsewhere, but you need to pay attention to the previous reviews.

Conclusions

Writing a scientific paper is an art as well as a science. With all its dry scientific data and equations, it must nevertheless provide an exciting and fascinating story, in which the leitmotif is present in all parts. It should never be boring.

Publishing scientific results is a very serious task and authors must adhere to the highest ethical standards. It is neither a game nor a routine. Always remember that a published paper will remain forever attached to your name. Do not try to split your work into several pieces to increase the number of your publications. The scientific community is already overwhelmed by a flood of second-rate “minimalist” papers. Reviewers are also inundated with reviewing requests. One solid and comprehensive paper is worth much more than five short papers with tedious repetitions.

It is on record that when a young aspirant asked Faraday the secret of his success as a scientific investigator, he replied: “The secret is comprised in three words—work, finish, publish.”

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Acknowledgements

The following colleagues have provided very valuable suggestions: Antonio Doménech-Carbó (Valencia), György Inzelt (Budapest), Sigurd Lenzen (Hannover), Michael Hermes (Berlin), Heike Kahlert (Greifswald), Uwe Schröder (Greifswald) and my wife Gudrun Scholz. I am grateful for general advice from Stephen Fletcher (Loughborough), and especially thankful to him for his elegant language editing. Wilhelmine Klamt (Greifswald) is acknowledged for having drawn the graphic abstract.

Open Access funding enabled and organized by Projekt DEAL.

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Scholz, F. Writing and publishing a scientific paper. ChemTexts 8 , 8 (2022). https://doi.org/10.1007/s40828-022-00160-7

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DOI : https://doi.org/10.1007/s40828-022-00160-7

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