Teknis Penulisan Artikel dan Korespondensi di Jurnal Ilmiah

Journal of Biosciences

ISSN:1978-3019 E-ISSN:2086-4094

Berry Juliandi Teknis Penulisan Artikel dan Korespondensi di Jurnal Ilmiah

Berry Juliandi

[email protected]

[email protected]

• Sekretaris, Departemen Biologi FMIPA IPB

• Kepala, Laboratorium Veterinary Stem Cells, Pusat

Penelitian Sumberdaya Hayati dan Bioteknologi IPB

• Chief Editor, HAYATI Journal of Biosciences

(Elsevier)

• Anggota, Akademi Ilmuwan Muda Indonesia (ALMI)


S1, Jurusan Biologi, FMIPA, IPB

S2, Program Studi Biologi, IPB

S3 dan Postdoc,

Lab. Molecular Neuroscience,

Nara Institute of Science & Technology,

Jepang

Postdoc,

Dept. Stem Cell Biology & Medicine,

Kyushu University, Jepang

Daur Penciptaan Ilmu Pengetahuan

Reference

Under translation and modification by Juliandi et al. and will be published by IPB Press on 2017

Choosing your target journal • Balance needed between several factors:

– Which metrics are important for you? (e.g. Impact Factor, SCI)

– If you aim too high, rejection could lead to delays in getting the work published

– Who do you really want to read this paper?

– Which journals do you cite most in the paper?

– Is the contribution of the paper of local/applied or more global/ theoretical significance?

• Talk about this and get advice early

Selecting target journals

• Check if the journal:

– normally publishes the kind of work you have done

– referees the papers

– publishes reasonably quickly

– has no page charges – or will waive them

– provides an affordable open-access option (if you need it)

– is NOT suspected ‘predatory journal’

Instructions to Contributors

• Find them early in the preparation period

• Seek out Overview, Scope or Aims section in particular to help decision re target choice

• Once chosen, check for downloadable template of required format for manuscript

• Note table/figure requirements in detail

• Submissions are often returned if instructions are ignored

Implications ...

• Once you have chosen your target journal, you are aiming to convince the editor and referees that your paper fulfils the criteria stated in the Aims and scope/Journal overview

• Analyse multiple examples from this journal to see how and where they signal both level and type of contribution in their writing.

The AIMRaD article: Abstract, Introduction,

Methods, Results and Discussion

Materials and

methods

Results

Abstract

Introduction

Discussion

• Abstract

• Introduction

• Materials and Methods

• Results

• Discussion

For many ‘molecular’ papers (AIRDaM)

Materials and

methods

Results

Abstract

Introduction

Discussion

• Abstract

• Introduction

• Results

• Discussion

• Materials and Methods

Structure of articles that combine Results and Discussion (AIM[RaD]XC)

Materials and

Methods

Abstract

Introduction

Conclusions

Result/

Results

etc.

Results

etc.

Results

discussion

• Abstract

• Introduction

• Materials and methods

• Combined Results and Discussion

• Conclusions

For theoretical/modelling/ computing/argument papers: AIBC

• Abstract

• Introduction

• Body of paper (with content-based subheadings)

• Conclusion

Development

of model/

validation, or

problem/

solution or

theory/

algorithm, etc.

Abstract

Introduction

Conclusion

Start from your Results/findings

• To begin a paper, focus on your results/ findings/ argument

• Everything in the paper must relate to the data and analysis you present

• Talk with co-authors and get agreement:

– Which data/analysis belong in the paper?

– What story do the data/evidence tell?

• The questions on the next slide help with this task

Your results

• What do my results/arguments ‘say’? • What do they mean in their context? (what

conclusions can be drawn from these results/findings?)

• Who needs to know this? (= audience for the paper)

• Why do they need to know? (what contribution do these results make to the field? – or why would it matter if researchers never read your paper?)

Presenting data

• What data are essential for the ‘story’ of the paper?

• Prepare tables and/or figures that present the key data that form your story

• Present data in the order that builds the story and refer to each data element in the text

• Check if the journal will accept other data as appendices/supplementary material

Key role of figures/tables in drafting

• Initial planning meeting held of co-author group

• Lead author (student) presents data figures/tables

• Beneath each are bullet-points stating the key findings shown in the figure/table

• Points are labelled according to where in the paper the information will be written (e.g. R, D)

• Team agrees on data, presentation and story

• Lead author then drafts paper in English

Tables are useful for …

Databases - recording data (raw or processed)

Explaining calculations or showing components of calculated data

Where the actual numbers are important

Where there are numerous individual comparisons to be made, in many directions

Figures are more useful where …

The overall picture is important

The results can be comprehended more rapidly through shape than through number

The comparisons between elements are relatively simple

Additional considerations

Be consistent with the styles of tables and

figures

Figures should tell the story with little

reference to the text

Keep the figure free from clutter (= many

different items, distracting reader from main

point/s)

Figure legends: beneath the figure Description or Declaration?

• Usually one descriptive line, tells you what the figure is about, e.g. “Shell thickness of PDA capsules as a function of the DMDES concentration.”

• Maybe one sentence about the method

• Explain key results or observations

• Key – explain the different treatments for different points

• Explain statistical and other notation

• Check that the figure ‘stands alone’ (do not need the reader to consult the rest of the text in order to understand them) – check target journal examples for specific guidelines

Tables Design the table around the point you wish

to illustrate most strongly

Keep tables free of clutter

Don’t box tables, use horizontal lines as separators

Use space to distinguish columns

Define abbreviations in the table using footnotes and the title legend

Sort data to best show the main correlations

Materials and Methods • Stated purpose is that the work can be

repeated

• Additional purpose is to establish the credibility of the results

• Cite methods if they are previously published

• Describe in full if readers lack access to the original publication (e.g. it is only published in Bahasa Indonesia)

• All novel methods must be described, but avoid excessive detail (use supplementary material?)

Organising the M&M effectively (1)

• Readers come to the Methods from many directions; make it easy for them to find what they are looking for

• It can be useful to use similar or identical subheadings or order of information for the Results and the M&M

• For the reviewer, it can be useful to include an overview of the experimental design first

• Investigate your example paper to see if the authors have used these strategies

Organising the M&M effectively (2)

• Consider using introductory phrases to explain why a method was used, e.g.

To generate an antibody to GmDmt1;1, a 236-bp DNA fragment coding for 79 N-terminal amino acids was amplified using the PCR. (Kaiser et al. 2003)

• Or use the first sentence in a paragraph to introduce the

method and then give details, e.g. Mineralisable N was estimated using an anaerobic

incubation assay as described by Keeney (1982). This involved …

Argument ‘stages’ of an Introduction

1. Statements about the field, providing the reader with a setting or context for the problem to be reported and claiming its centrality or importance

2. More specific statements about the aspects of the problem already studied by other researchers, laying a foundation of information already known

3. Statements that indicate the need for more investigation, a gap, need for extension, or research niche for the present study

4. Statements giving the purpose or objective of the author’s study OR its main activity OR findings

5. Optional statement(s) that give a value or benefit for carrying out the study

6. A map of the rest of the article (some fields, and reviews)

Task:

• Read the introduction of your example article and decide if all stages are present, and where each one begins and ends. (It is possible that stages may be repeated or come in different order to that suggested above!)

• Tip: identify Stage 4 first, then look for Stage 3 (gap, need). Then identify Stage 1 and where it moves into Stage 2. Are there repeated sets of Stages 1, 2, 3?

Stage 4: Format?

• Look at the last paragraph of the Introduction in your example paper

• Does it contain a statement of aim/ objective? A statement of principal activity (what the study did, or the paper does)? A summary of results?

• Look at verb tenses – how do they reflect the specific focus of the Stage 4?

• Will your ms follow the same pattern?

Stage 3: The research ‘gap’ or ‘niche’

• There are special ‘signal’ words that often appear in this Stage.

• One type of signal points to an upcoming contrast (eg ‘however’)

• Another type indicates a problem or a lack.

• Check in your example article for words that serve these purposes.

• Consider the relative strength of the wordings, in terms of the significance of filling the gap/niche.

Strategic questions on Introductions

• Does Stage 1 match the interests of the target readers (journal editor/referees)?

• Does the start of Stage 1 reflect the points made at the end of the Discussion/Conclusion?

• Does every component of Stage 4 have a Stage 3 gap/need somewhere in the Introduction?

• Is all the Stage 2 literature review necessary to justify why the study was done?

• Could a referee answer ‘yes’ to the questions ‘Is this work new?’ and ‘Is this work significant?’

Suggested process for drafting an introduction (after Results „story‟ is clear)

• Begin with Stage 4

• Draft Stage 3 next – the ‘gap’

• Then think about how to begin Stage 1 – the setting (think about your audience)

• Next arrange the information you have collected from the literature into Stage 2

• Then, combine the stages and add any additional sentences needed to connect them into a coherent Introduction.

Discussion: Making meaning

• The Discussion relates to the Introduction

– the aim/purpose statement

– the evidence leading to the ‘gap’, and

– the ‘Universe’ where the Introduction began

• It highlights the key points from the Results ‘story’

• Does your target journal allow a separate ‘Conclusion’? If not, use the last paragraph of the Discussion to conclude.

Information elements to include

1. Reference to the main hypothesis, aims (purpose) or research questions of the study

2. Review of the most important findings, whether they support the original hypothesis, and/or agree with the findings of others

3. Possible explanations or speculations about the results

4. Limitations that restrict the generalisability of the findings

5. Implications of the study

6. Recommendations for further research or practical applications

Discussions, cont.

• First 4-5 of these often repeated for each group of Results

• Concentrate on ‘take home messages’ (THMs)

• Use a subheading or a topic sentence to show where each THM begins

• Check for link between ‘take home’ message/s and paper title

Why are Abstracts important?

• Often the only thing busy readers read – its job is to get readers to download your paper

• May be all that is available to some readers

• What about ‘additional keywords’? – Choose words your target audience might use to

search under; avoid general words (e.g. growth)

– Check if they are used in other papers in your field (or in the database index, if available)

– Strategic repetition of words in title/abstract can maximise search engine results

– Editors use your keywords to select reviewers

Abstracts: Typical information elements

B = some background information

P = the principal activity (or purpose) of the study and its scope

M = some information about the methodology used in the study

R = the most important results of the study

C = a statement of conclusion or recommendation

Abstracts, cont.

This list can sometimes be compressed (in a so-called reduced abstract) to:

P + M = purpose and method of the study

R = results

C = conclusion (and recommendations)

Thinking about titles

• Title is the first thing a reader reads

• Can be a Noun Phrase (NP), a sentence, or sometimes a question

• Can be in two parts, separated by a colon or a dash

• Should provide as much information as possible but be concise

• Important to avoid ambiguity if using long and complex noun phrases

The Title: examples describing the same work

Effects of added calcium on salinity tolerance of tomato

Calcium addition improves salinity tolerance of tomato

Calcium addition has differential effects on salinity tolerance of three varieties of tomato

Calcium addition has differential effects on salinity tolerance of three varieties of tomato grown in solution culture

Calcium addition improves salinity tolerance of tomato by increasing the K/Na ratio in plant tissues

Enhancing the salinity tolerance of tomato: calcium addition increases the K/Na ratio in plant tissues

The Editor‟s Role (PART 1)

The editor is responsible for maintaining the

reputation and competitiveness of the journal.

The editor is responsible for the initial decision as to

whether a submitted manuscript will be sent to

reviewers.

Sometimes the editor returns the manuscript to the

author at this stage.

Follow Guide For Author

What does the editor want to publish?

• Important - significant and important research work

• Interesting - appropriate and interesting work for readers of the journal

• Quality - experimental and statistical methods are valid

• Meaningful - literature review, discussion and conclusions are relevant and correctly interpreted

• Clear - understandable and readable

• Presentable - presentation undertaken with care (spelling, grammar etc.) and instructions to authors followed closely

The contributor‟s covering letter

• Often now this is a message typed into an online form

• State that the paper is in the field of the journal

• Emphasize that the paper is new & original and fits the

journal‟s desired emphasis (use key terms from the Aims and

Scope section on the webpage)

• Highlight specific points which may raise questions for the

editor e.g. –

– Your belief that a longer paper is justified, not two

short ones

– Photographs are necessary rather than drawings

What are reviewers asked to do?

• Manuscripts are commonly sent to at least two peer referees

• Each journal has its own set of instructions for reviewers – sometimes these are available on the journal‟s website

• Check to see if this is the case for the journal you are targeting

What are reviewers asked to do?

(cont.)

• In addition to „ticking the boxes‟, reviewers are

asked to write their comments about any

problems with the manuscript or any suggestions

for improvement that need to be followed before

the manuscript can be considered suitable for

publication in the journal

• Reviewers return their comments to the editor

Recommendation

Accept without alteration

Accept after minor revision

Review again after major revision

Reject

The Editor‟s Role (PART 2)

The editor receives the reports from the referees and decides what response will be made to the author/s

If the first two referees disagree, sometimes the editor will send the manuscript to a third referee for an additional opinion

The editor then writes to the corresponding author, telling her/him of the decision

Dealing with comments of editors and

reviewers

1. If paper is accepted

2. If paper is rejected

3. If paper needs revision

• Respond quickly

• Try to make all the changes

• Don‟t start any unnecessary arguments

Paper accepted +/- revision

Who gets rejected?

• Survey of scientists who had published at least 10 papers in 5 top ecology journals between 1990-1999*

• 22% of papers eventually accepted had been rejected at least once

• Every author had at least one paper rejected

• Senior scientists & scientists with more publications had higher rejection rate

• EVERYONE

*Cassey & Blackburn (2003) Trends in Ecology and Evolution 18:375-376

Why a paper might be rejected:

• high ranking journals need to reject a high proportion of submitted manuscripts even if the reviews are (mostly) positive

• the paper may not fit the scope of the journal

• referees may not read or understand the paper thoroughly enough to appreciate it (remember: the review process is unpaid work for busy people)

• something may have annoyed the referee – they are unpredictable: can be helpful or (sometimes) rude

• the recommendations from the referee to the editor may be clear or unclear

Paper rejected

Determine why the manuscript is rejected:

• Not suitable for the journal – submit to another journal

• Problems with design or method – try to publish the good parts

• Research not new or „important‟ enough – submit to lower ranking journal

• If submitting the same manuscript, make changes recommended by reviewers

You are asked to revise the paper:

Rules of thumb

• Rare that the referee is completely right and the author completely wrong

• Object is to accommodate the referee by addressing their comments without compromising the message of the paper

• Always show the editor you are doing the right thing – be polite

• If editor‟s comments are not clear, get advice locally or email journal to get clarification

“Based on the comments and recommendations of the two

reviewers (included) and my own reading of the manuscript, it is

my view that some revision is required before this paper would be

acceptable for publication. If you wish, you can send me a revised

version of the manuscript, with a covering letter outlining how the

reviewers‟ comments have been addressed. I have also included

an annotated copy of the manuscript with some corrections to

grammatical, typographical and formatting errors. Please attend to

these as well in the manuscript revision.”

Example: letter from editor to author after

review

“Please find enclosed a revised version of the manuscript, a

letter outlining how the reviewers‟ comments have been

addressed and the annotated copy of the first version. Sorry

for the delay, but some … measurements were required… .

The manuscript has been thoroughly revised in order to

address the valuable suggestions of the editor and the two

reviewers.”

Example: response from author to editor after

revision

Your response document to editor

• Make it very easy for the editor to see what you have done

• Heading: Referee 1

• Then copy all the comments, one by one, perhaps in italic

type

• Underneath each one, in plain type, say what you have

done in response

– If you have not followed the referee‟s suggestion/ advice in some

cases, give your reasons

• Then do the same for Referee 2

Main types of comments from referees

1. The aims of the study are not clear

2. The theoretical premise or “school of thought” on which the work is based is challenged.

3. The experimental design or analysis methods are challenged

4. You are asked to supply addition data or information that would improve the paper

5. You are asked to remove information or discussion

6. The conclusions are considered incorrect, weak or too strong

7. The referee has unspecific negative comments – e.g. poorly designed / written / organised

What to do:

check the aims are clearly stated in the

Introduction

check the aims are consistent with the

experimental design

check that the Discussion refers back to the

aims

1. The aims of the study are not

clear

R: “The purpose of the research is not clear”

A: “Regarding the purpose of the research, a

sentence has been added at the end of the

introduction…viz „This should provide a better

basis for understanding and

predicting…change…”

1. The aims of the study are not clear

EXAMPLES:

2. The theoretical premise or “school of thought” on

which the work is based is challenged

What to do: check that the Introduction shows the diversity of

theories (cite the literature) and demonstrate that you are testing one of these theories

if you are challenging accepted wisdom, use theory, references and structure (e.g. section headings)

include caveats in the discussion

3. Experimental design or analysis methods are

challenged

What to do:

defend the design or analysis on its merits

refer to previously published examples using the

design or analysis

include additional information on the design or

analysis if available

3. Experimental design or analysis methods are challenged

EXAMPLES:

R: “I think it is not appropriate to conclude that „without

employing such a technique, [method] is qualitative”

A: .“…without proof that [method] is quantitative, it should be

considered qualitative. A sentence has been added to state

this explicitly in the text.”

R: “No explanation is given for the [pre-treatment]

procedure”

A: “Two paragraphs are added justifying the use of [the

procedure]. Two recent references are included which show

that the procedure [works].

4. You are asked to supply additional data or

information that would improve the paper

What to do: do it if you can

if you cannot, consider whether you are expected to make major or minor corrections by the editor.

if you think the paper will not be improved with the suggested additions, make your case to the editor

4. You are asked to supply addition data or


EXAMPLES:

R: “One possible approach is to run replicate

analyses…see [suggested reference]”

A: “Taking the ideas of [suggested reference], we ran

duplicate measurements…” [new data included]



EXAMPLES:

R: “It would also be valuable to have [experimental

results] calculated for the [duration of experiment].

Can this information be calculated from the data

collected?”

A: “Unfortunately, [extra experimental results]

cannot be extracted from our data. A study

concerning the long term effects of [experimental

conditions] has been published elsewhere

[reference].”



EXAMPLES:

R: “I think it would help if the authors were to suggest where we should go from here. In the final sentence it is suggested that analyses of this type provide the insights needed for a more targeted approach in the future. What might this more targeted approach be?”

A: “We have revised the manuscript in accordance with the suggestions…”

5. You are asked to remove information or

discussion

What to do: do it if you can, without changing the „story‟

ask a colleague to make suggestions on where to make cuts

if you don‟t want to cut, see if one referee is on your side and make your case to the editor

5. You are asked remove information or discussion

EXAMPLES:

R: “…section contains unnecessary repetition of

previous work”

A: “As (other) reviewer points out, …sufficient

explanation is required to make sense of and

interpret the results.”

R: “This area of research is well known and does

not need this exhaustive review section.”

A: “We have reduced the size of this section and

referred to critical reviews by [references]”

6. The conclusions are considered incorrect,

weak or too strong

What to do: make sure the discussion is tied to the aims at the beginning

of the paper

reassess the literature you have cited and make a case to the editor if there is adequate supporting literature

check that all your statements are justified & the strength is appropriate

include caveats in the discussion

6. The conclusions are considered incorrect, weak or

too strong

EXAMPLES:

R: “…you need to say what magnitude differences you

believe to be significant, and provide some

justification…”

A: “We accepted the comment completely.” [new data and

supporting statistical analysis presented]

6. The conclusions are considered incorrect, weak

or too strong

EXAMPLES:

R: “…the paper is far too descriptive and speculative…”

A: “After doing some statistics, much of the „cloud‟ surrounding the

descriptive analysis…has disappeared…. The paper was also

shortened and some too speculative paragraphs were omitted”

6. The conclusions are considered incorrect, weak or too

strong

EXAMPLES:

R: “This is hardly astonishing. A similar accumulation was reported by [References]”

A: “The comments of the reviewer were profoundly appreciated and taken into consideration. Two references referred to by the reviewer were included…”

6. The conclusions are considered incorrect, weak

or too strong

EXAMPLES:

R: “I do not believe the conclusion that [specific conclusion] is a valid one, based on the data presented.”

A: “Regarding the conclusion that [specific conclusion], we changed the text in the abstract, results and discussion. We omitted the conclusions on the possible role of [conditions] but we would like to keep Figure 8a, just to maintain [conditions] as a working hypothesis for future studies.”

7. The referee has unspecific negative comments

eg. poorly designed / written / organised

What to do: show the referees‟ comments to a peer and discuss

them

think about what the referee has a specific problem with; restate it and respond

point out to the editor all the work you have done to improve the paper

build up a body of positives – eg. “ I have addressed point 1 by….”



EXAMPLES:

R: “The English is not good and needs to be greatly improved.”

A: “Grammatical points of the language were reviewed to improve

readability….None of the authors is an English native speaker. …we tried

to improve it as far as we could.”

R: “The logic and circumstantial evidence for [results] is very clear up to

p.16:line5. The next section…was difficult for me to wade through…I

can not offer any suggestions to simplify this section.”

A: “I take this as a comment”



R1: “… improves our understanding and is interesting to a wider audience. That said, it must be stated that the paper needs substantial improvement in language and also in correcting sloppy formatting such as typos in the title, inconsistency of spelling and use of abbreviations, presentation of units, quotations in incorrect order etc.”

R2: “The scientific content of the manuscript is poor and results do not represent any innovative progress…”

E: “Probably none of these [design & analysis] shortcomings are, by themselves, grounds for rejection. However, their combined effect, and the fact that the reviewers found very little positive to say about this paper, leads me to recommend rejection”

Re-submit (same journal), with letter to editor

Point out supportive comments by referees and disagree-ments between them (try to get editor on your side)

List the main changes individually, referring to referees‟ reports (copy each individual referee’s comment (e.g. in BOLD text) and address each comment directly underneath (e.g. in plain text)

Say you have also corrected minor errors (e.g. English)

Defend your conclusions if referee is factually wrong

Say you believe the paper is important research and is now acceptable

Hope for the best!

Terima Kasih! https://www.journals.elsevier.com/hayati-journal-of-biosciences http://www.sciencedirect.com/science/journal/19783019


ISSN:1978-3019 E-ISSN:2086-4094

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Teknis Penulisan Artikel dan Korespondensi di Jurnal Ilmiah