Scientific Writing – How can I prepare a goodManuscript ? –

Strategy to Publish in Reputable International Journals

Bogor, September 2019

Prof. (em.) Ulrike Lindequist

University Greifswald

Institute for Pharmacy

lindequi@uni-greifswald.de

1

Why are publications important for a scientist?

• You don´t research for you alone!

• Your research is mostly financed by public resources!

• You have to leave a record of research to the community!

• You have responsibility for the community and to legalize the research!

• Publications are one way to cope with the responsibilities!

• You can receive feedback on results, ideas etc.!

• You can attract interest from others in the area of research!

• You will join an international conversation and become a member of the international researchcommunity!

• Important criterium for success of a scientist and your carrier!

Specialities of writing in natural sciences

• Clear structure

• Concrete results

• Basing on facts

• Correct statistics

• Logic, clarity of style

• Readability

• Ensure against plagiarism

(Plagiarism: using data, idea or words that originated in work by another person without

appropriately acknowledging their source)

Where should this paper be published?Criteria for selection of the journal

• Scope and aims of the journal

• Peer review system

• Reputation of the journal; Journal impact

• Time line

• Charges

• Open access or not

• Balance between the international value of your work and the impact of the journal

• Avoid unserious journals!

(strong advertisement, bad quality, no peer review system, short time of existence, no

impact factor…, their number is increasing)

Journal Impact

Journal impact factor for a given year: average number of times articles published

in the journal in the two previous years have been cited in that year

Journal Impact Factor (year x) = Cites to recent articles (Year x-1 + Year x-2) /

Number of recent articles (Year x-1 + Year x-2)

Other: Journal Immediacy Index; Journal Cited Half-Life…

Comparing journals from different fields of research is not meaningful!

Non-english papers are excluded!

Printed journal of open access?

Print versus Open access

Limited number of readers Open for all interestedpersons

Low or no expenses Mostly high expenses

Risk of unserious journals

Who is your audience?

-People working in areas related to yours

As Gate keeper:

-Journal editor

-Reviewers (referees)

-Community (in case of popular papers)

Types of publications

• Original research articles

• Short communications

• Reviews

• Letters to the editor

• Book reviews

• Commentaries

Types of publications: Original research articles

• The paper presentates the results of your own (experimental) research work

• Your research bases on analysis of literature

„Telling a compelling story“

Types of publications: Short communications

• Limited length and number of figures and tables

• Fast publication

Types of publications: Reviews

• Assembly, critical appraisal and synthesis of all relevant studies on a specific topic

• Focus on peer-reviewed publications about a specific problem

• Use rigorous, standardized methods for selecting and assessing articles

• May or may not include a meta-analysis which is a quantitative summary ofthe results

• A good review sets the trend and direction of future research on the

subject matter being reviewed.

Original research articles: structure

• Title

• Abstract

• Methods and Materials

• Results

• Discussion (possibly together with results)

• Conclusions

• Acknowledgements

• References

• (Supplemental Material)

Original research articles: structureA) Everything in the article must relate and be

connected to the data presented in the results section.

B) 1. Introduction begins with a broad focus.

3. Introduction ends with a focus exactly

parallel to that of the results.

2. between these two points background

information.

C) Methods section, showing how results were

obtained

D) Discussion begins with the same breadth of

as the results – but it ends at the same breadth

as the starting point of the introduction.

(Cargill and O`Connor 2009)

Original research articles: Questions to focus the draftingprocess (Cargill, O´Connor)

• What do my results say?

• What do these results mean in their context?

• Who needs to know about these results?

• Why do they need to know?

Original research articles: Title

• Title: as short and meaningful as possible

• Clear identification of the research focus

• Should arouse readers curiosity and interest

• Most important word(s) should placed at the beginning:

„Calcium addition improves salinity of tomato.“ better than

„Effects of calcium addition on salinity tolerance of tomato.“

• In searchable databases

Very important for detection of the paper by possible reader!

Cargill and O´Connor

Original research articles: Title

• As noun phrase (a number of words around one important head noun: „Systems of weed control in peanuts“

brief and effective, but enough information?

• As statement (sentence with a subject and a verb): „Calcium addition improvessalinity tolerance of tomato.“

give more explicit information about results of the study, only for

papers that address a specific question, not for complex answers

• As question: „Which insect introductions succeed and which fail?“For more complex answers

Cargill and O´Connor

Original research articles: Title

• Most important word(s) should placed at the beginning:

„Calcium addition improves salinity of tomato.“ better than

„Effects of calcium addition on salinity tolerance of tomato.“

• Avoid misunderstanding

„soybean seedling growth suppression“ – „suppression of soybean seedling growth“

• When nouns are used as adjectives, they are always used in the singular

„ (food for dogs) – dog food“

„ (disturbance by herbivores) – herbivore disturbance

Cargill and O´Connor

Original research articles: Key words

• In searchable databases

Very important for detection of the paper by possible reader!

• Use prominent key words

• Number of key words is limited depending on the journal

Thereafter possibly List of Abbreviations

Original research articles: Abstract• In searchable databases (together with title and key words)

• The only part that is available to all readers

• For busy readers maybe the only part of the paper they read

• Limited number of words

• Content: -some background information

-principal activity or purpose of the study and its scope

-some information about the methods used

-the most important results

-statement of conclusion or recommendation (Cargill and O´Connor)

• Graphical abstract

• Highlights

Original research articles: Introduction

Opening: Introduces the problem the paper is targeting

What is the context, and what are the characters we arestudying?

Background: What information does the reader need to understand thespecific work the authors did? Why it is important?

comprehensive literature search necessary

Challenge: What are the specific hypothesis/questions/goals of thecurrent work? (Schimel)

From general to more specific information!

Original research articles: Materials and Methods

What did you use and what did you do?

• Listing chemicals, equippment etc. incl. source

• Listing biogenic materials (place and date of collection, collector, taxonomicdetermination, voucher number, place of storage)

• Exact determination of methods (similar like a cookbook)

• Statistics

• Mainly passive sentences

• Avoid „I“ and „We“.

Original research articles: Results• Clear and value-free presentation of experimental results incl. statistics

• What is really necessary?

• Tables and figures should „stand-alone“

• Numeration of tables and figures

• Do not repeat in words all the results from the tables or figures!

• All tables and figures have to be cited in the text.

Tense:

Past tense is used when the sentence focuses on the completed study. What was done and found.

Present tense is used to describe an „always true“ situation and when the sentence focuses on a document („here is an example from Müller et al….“).

Modal verbs (could, may..) in comments, especially in „that…“ clauses

Tables or Figures (Cargill and O,Connor)

Most useful Table Figure

When working with number shape

When concentrating on individual data value overall pattern

When accurate values are more important less important

For the same results only table or figure!

Figures

Most useful for

• Showing an overall trend

• Comprehension of the story through „shape“ rather than the actual numbers

• Allowing simple comparisons between only a few elements

• Legend and foot notes below the figure

• Indicate if color should be used for any figures in print (can be expensive)

Types of Figures

• Fotos

• Overview Charts

• Chemical structures

• Pie charts: highlighting proportions of a total

or whole

Schwämme29%

Rotalgen8%

Braunalgen4%

Grünalgen1%

Mikroorganismen23%

Andere Tiere1%

Echino-dermaten

6%Tunikaten

5%

Nesseltiere19%

From PhD thesis Christian Bäcker

Types of Figures

Figure 2. Representative example of the oxygen consumption rate in THP-1 and Jurkat cells. From PhD thesis N. Schultze

0

5

10

15

20

25

30

35

KT03

KT13

KT15

KT19

KT26

KT28

KT29

KT30

KT31

KT32

KT33 A

50

Fungal isolates

Dia

met

er o

f in

hib

itio

n z

one

(in m

m w

ith d

isc)

Freshwater cultures Seawater cultures

Fig. 3.18. Antibacterial activity of EtOAc extracts against Staphylococcus aureus

(2 mg/disc; A50=Ampicillin 50 µg/disc; n=4; Data are expressed as Mean+SD)

From PhD thesis Kusti Tarman

• Column and bar charts: comparing the values of different categories whenthey are independent from each other

• Line charts: display of a sentence of variables in time or space or otherdependent relationships

Often occurring weaknesses of Figures

• Not the right proportion (best for the eye 3 : 2)

• Wrong figure type

• Figure unnecessarily cluttered with lines, numbers etc.

• Poorly chosen axis scale division

• Not correct description of axis

• The overall picture or trend is not obvious enough.

• Weak legend

Example Figures

What is better ?From Cargill and O´Connor, p. 26

Comparison

5.2:

-removal of error bars and replacement with LSD bar

-decreased cluttering

-expanded y axis

-more detail about the significance level in the legend

-no box

-x-axis more descriptively titled

-title changed from a descriptive statement to a story-telling statement

From Cargill and O´Connor, p. 26

TablesMost useful for

• Recording data

• Explaining calculations or showing components of calculated data

• Showing the actual data values and their precision

• Allowing multiple comparisons between elements in many directions

• Legends upper the table

• Foot notes below the table

Often occurring weaknesses of Tables

• Weak title

• Inclusion of unnecessary or redundant data

• Not arranged to highlight the most significant results

• Not sorted to show important relationships between elements

• To much cluttering

• To many decimals (presents false accuracy, better round back)

• No explanation of abbreviations etc.

• Missing of units

Example Tables

From Cargill and O´Connor, p. 26What is better ?

Comparison

5.3:

-title changed from a descriptive to a story-telling statement

-samples are sorted to better highlight the gradient of soil clay content

-mean and standard deviation values have been rounded back

(which prevents presentation of false accuracy and reduces clutter)

From Cargill and O´Connor, p. 26

Original research articles: Discussion (Cargill and O´Connor)

• Restatement of the most important findings:

Do they support the original hypothesis?

How do they contribute to answer the research questions?

Do they meet the research objectives?

Do they agree with the findings of other researchers?

• Explanations and/or speculations for/about the findings, especially contradictory results,

supported by literature references

• Limitations of the study

• Implications of the study (generalization: what the results mean in a context of a broaderfield)

• Recommendations for future research and/or practical work

Some journals allow to combine discussion with results.

Original research articles: Conclusion

Resolution must map back to the introduction

Take home message

Acknowledgement

References (text and list of references)

• All references mentioned in the List of References are cited in the text and vice versa.

• Unique style according to the author guide lines.

• Correct and unique abbreviation of journal titles.

Original research articles: Supplemental material

Additional information like

spectra

calibration curves

single values of biological tests etc.

Succession of writing?

• Table or Figures with results

• Basing on the results development of a „story“

• Material and Methods

• Introduction

• Text to results

• Discussion and conclusion

• Abstract

Possible mistakes: Out of scope

• Study carefully the guide for authors of journals and select the mostsuitable journal

• Avoid non established journals which offer very easy acceptanceconditions and which show overdone advertisement

Possible mistakes: Too preliminary

• In vitro assays with single concentration or very high concentration

• Single dose studies with very few animals, no dose-response studies

• No proper control

• No characterization of the test sample (e.g. fingerprinting of the testextract)

A paper must be based on a thorough and extensive study.

Possible mistakes: Lack of novelty

• Repetition of well-known data

• Use of non-specific pharmacological test methods or of phytochemicalscreening methods

• Use of pharmacological assays or clinical trials which are not internationally recognized as valid and relevant

• Identification of only well-known ubiquitious compounds with no orlittle relation to activity

The study must represent a novel approach (not: using another extract ofthe same organism, or in case of antimicrobial activity, some othermicroorganisms)

Possible mistakes: Simple in vitro assays

• In vitro antioxidant activity

Antioxidant activity is present in all plants etc. Screening with in vitro assays has little meaning if no clear evidence is given for in vivo activity.

• Antimicrobial activity

Measuring only inhibition zones and no MIC values,

No information on type of activity (-cidal or growth inhibition)

Possible mistakes: Lack of exact taxonomic identificationand declaration

• Complete name of organisms (genus and species) in italics

Atropa belladonna

• Only genus: not in italics

Atropa species

• Genus can be abbreviated

• Author name of the plant (at first mention)

• Accepted taxonomic name: for plants www.ipni.org (International Plant Name

Index) or www.theplantlist.org, for algae www.algaebase.org, for fungi

www.mycobank.org

Possible mistakes: Lack of characterization of investigatedextracts

Extracts have to be at least characterized by:

origin

solvent

mode of preparation

mode of storage (part of Materials and Methods)

chemical fingerprinting e.g. by TLC or HPLC (mostly part of results)

Often occurring English language errors

• Incorrect usage of singular/plural forms: Leaves was (were); results suggests(suggest)

• Over-complex grammatical structures: prefer short sentences

• Incorrect choice of prepositions: depending of (on), similar with (to)

• Non-standard usage of the articles a/an and the: a/an for more generalstatements, the for more specific statements

Often occurring English language errors

• Non-standard selection of modal verbs: would versus will; could versus can

• Non-conventional selection of tense:

Past tense is used when the sentence focuses on the completed study. What was done and found?

Present tense is used to describe an „always true“ situation and when the sentencefocuses on a document („here is an example from Müller et al….“).

Key points

• Good science is the most important thing, but

• The science needs to be clearly understandable.

(Cargill and O´Connor)

Submitting the manuscript

• Manuscript has been „spell-checked“ and „grammar-checked“, best by a native

speaker.

• All necessary files (text, figures, tables, possibly supplementary material) have

been uploaded.

• Cover letter to the editor

• Permission has been obtained for use of copyrighted material from other sources

(including the Internet)

Important to consider: Policy and ethics

• International, national and institutional biodiversity rights. Each country has itsown rights on its biodiversity.

• Animal studies: In the Methods section must be stated that the research was conducted in accordance with the internationally accepted principles forlaboratory animal use and care.

• Human studies: In the Methods section must be stated that the research followedguidelines of the Declaration of Helsinki and Tokyo for humans, and was approved by the institutional human experimentation committee or equivalent, and that informed consent was obtained.

Important to consider: Authors

• Each author has substantial contributed to the publication. Many journals require

that for each author the contribution should be mentioned.

• One author has been designated as the corresponding author.

• All authors must disclose any financial and personal relationships with other

people or organizations that could inappropriately influence (bas) their work.

Relevant relationships have to be declared.

• All authors have to support the submission.

Bias

• Any tendency to influence the results of a trial (or their interpretation) other than

the experimental intervention

• A bias in a systematic review caused by incompleteness of the search, such as

omitting non-English language sources

Some Advices• Follow the author guidelines exactly

• Look for articles in the recent issues of the journal regarding data presentation

• Cite articles from the selected journal

• If you are not enough experienced in English language use a native speaker or a

professional language service

• Mark trade names®™

• It is not allowed to submit a manuscript to more than 1 journal in parallel!

Referee criteria

Blind or double blind review processes

• Scientific content

• Novelty

• Interest for readers

• Fitting into the scope of the journal

• Presentation (Language, formal aspects)

Typical questions on evaluation forms (Cargill and O`Connor)

• Is the contribution new?

• Is the contribution significant?

• Is it suitable for the publication in the journal?

• Is the organization acceptable?

• Do the methods and the treatment of results conform to accepted standards?

• Are all conclusions firmly based in the data presented?

• Is the length of the paper satisfactory?

• Are all the figures and tables necessary?

• Does the title clearly indicate the content of the paper?

• Are the references complete?

• Very often classification: excellent, very good, good…..poor

• Does the manuscript fall into the …% of manuscripts you have read during the last 12 months?

What is to do after requirement for revision?

• Be thankful to the reviewers and editor

• Revise the critical points as far as you can accept it

• If you can not accept the criticism, argue objective against it

• Often a native speaker or professional language service can be helpful.

What is to do after rejection?• Rejection is normal and every researcher knows it.

• Nevertheless you need a high frustration tolerance!

What is to do?

• Read the reasons and try to understand it!

• Discuss it with experienced colleagues!

• Probably revise it!

• Submit it to a different journal or resubmit it after revision!

What is to do after acceptance?• Check the draft very carefully

• Check the draft in time (mostly only 48 h)

• Send the checked draft back to the editor or the publisher

Publications as Criteria for Scientific Carrier

• Quality of publication (not „Publish or perish“)

• Image of the journal (Impact factor)

• Number of citations (H-index)

• Number of publications

• Position at the list of authors (corresponding author?)

Literature

• Author guidelines of each journal

• JEP: Rules of 5

• Cargill M, O´Connor P. Writing scientific research articles. Wiley Blackwell, 2009

• Schimel J: Writing science. How to prepare papers that get cited and proposalsthat get funded. Oxford University Press, 2012

Exercise

Act as reviewer and evaluate the manuscripts