1

The publication of scientific

data

B. NEMERY, MD, PhDDept. of Public Health and Primary Care

KU Leuven

ben.nemery@med.kuleuven.be

Source

• “Successful scientific writing. A step-by-

step guide for the biological and medical sciences” (2nd edition)

J.R. Matthews, J.M. Bowen, R.W. Matthews.

Cambridge University Press, 2000

Source

• “How to write and publish a scientific

paper” (7th edition)

Robert DAY & Barbara GASTEL

Cambridge University Press, 2012

ISBN 978-1-107-67074-7 Paperback

Source

• “How to write, publish, & present in the

health sciences. A guide for clinicians & laboratory researchers” (7th edition)

Thomas A. LANG

American College of Physicians, ACP

Press, Philadelphia, 2010

ISBN 978-1-934465-14-1

Source

• “Academic writing. A resource for

researchers.” (3d edition)

Kristin BLANPAIN

ACCO, Leuven (Belgium), 2012

ISBN 978-90-334-8856-6

Source

Sterk P.J., Rabe K.F.

“The joy of writing a paper”

Breathe, 2008, 4, 225-232

2

Kotz D, Cals JW. “Effective writing and

publishing scientific papers” J Clin Epidemiol

• 2013 Apr;66(4):397 Part I: how to get started

• 2013 Jun;66(6):585 Part II: title and abstract

• 2013 Jul;66(7):702 Part III: introduction

• 2013 Aug;66(8):817 Part IV: methods

• 2013 Sep;66(9):945 Part V: results

• 2013 Oct;66(10):1064 Part VI: discussion

• 2013 Nov;66 (11):1197: Part VII: tables and figures

• 2013 Nov;66(11):1198 Part VIII: references

• 2013 Dec;66(12):1319 Part IX: authorship

• 2014 Jan;67(1):3 Part X: choice of journal

• 2014 Feb;67(2):123 Part XI: submitting a paper

Source

• International Committee of Medical

Journal Editors (ICMJE)

http://www.icmje.org/about.html

Source

• Vandenbroucke et al. Strengthening the

Reporting of Observational Studies in Epidemiology (STROBE): Explanation and

Elaboration. PLoS Medicine, 2007, 4(10):

e297. doi:10.1371/journal.pmed.0040297

• http://www.strobe-statement.org/

OUTLINE

• General introductionSome overlap with lecture on “scientific integrity”

• How to publish your research

– Writing an article

– Publishing an article

Why publish?

• Best science is useless if it is not published

• Publication depends on the quality and novelty/importance of the work– Peer-review process

• Validity of work depends on potential for replication of published findings

• Evaluation of researcher (“Publish or perish”)– How much? How good? Work cited?

– Most difficult part of research activity!

Scientific publishing

Kravitz DJ, Baker CI. Toward a new model of scientific publishing: discussion and a proposal.

Frontiers in Computational Neuroscience. Dec 2011, 5, Article 55

• Current system: redundancy, inconsistency, sluggishness, opacity, cost

• Proposal: guaranteed publication

– Anonymous (double blind) review focused on scientific merit (not publication worthiness) + feedback to revise (retract)

– Post-publication review by editorial board + rating

– Public discussion in a forum

3

Types of scientific publications

• “Full article”– Clinical, experimental, epidemiological data

• Case report• Review article

– Narrative review– Systematic review

• Letter to the editor• Editorial• Congress abstract

• Conference proceeding• Book chapter

Writing an Editorial

Fontanarosa PB. Guidelines for writing effective editorials. JAMA 2014, 311, 2179-80.

• 1200-1300 words, ~10 references

1. Introductory paragraph: statement of problem

2. Summary of study: design, numbers, numerical data; not too specialized

3. Key strong points and limitations

4. Balanced discussion in context of other research

5. Implications and next steps

6. Strong evidence-based conclusion with take-home message (not a “licence to preach”

Supplements, … When?

• “substantial findings”

– original data

– valid data

– answer to a research question or hypothesis

– don’t delay publication until you have “all”

answers

– beware of the LPU (“least publishable unit”)

and “salami-publication”

Original data

• “Not previously published”– except as conference abstract

+ legitimate exceptions: e.g. urgent public health warnings, reports, dissertations, …

• Cave:! full symposium proceedings

! preliminary electronic publication of data

! previous publication in national journal (non English)

! publication in the media (“Ingelfinger rule” NEJM 1969)

� always inform the editor when you submit the article

Original data

• Never submit a paper to two journals

simultaneously!

• If you submit related data to two different

journals, always inform the editor (and include the related manuscript)

4

Duplicate publication

• Duplicate (redundant) publication = Scientific misconduct

– Waste of resources

– May cause problems for meta-analyses

• Sanctions:– Publication of retraction (damage to reputation!)

– Ban from publishing in same or other journals

De Angelis C.D. Duplicate publication, multiple problems. JAMA, 2004, 292, 1745-6.

Duplicate publication

Dear Dr. ...

further to [...] the decision to reject your paper, I have the unpleasant task to inform you that editorial measure have to be taken in regard to

intended duplicate publication.

It was only due to the careful attention of a reviewer that duplicate publication could be prevented. He was aware of your published paper

in [symposium proceedings] .... This article totally duplicates the data of above manuscript. In your submission letter you wrote “neither the

manuscript nor any part of its essential substances, tables or figures have previously been published”. This is not true.

You and your co-authors ... are not allowed to submit any paper for consideration to the European Respiratory Journal for the next 3 years.

Duplicate publication

ERJ December 2011

Duplicate publicationAm J Respir Crit Care Med. 2002 Aug 15;166(4):625Thorax. 2002 Aug;57(8):751.

?

Duplicate publication

5

“Negative” results *

• “Positive” results are more likely to be

• submitted for publication

• accepted for publication

• accepted in high-profile journals

� “publication bias”

• cited

• Psychology: negative results are disappointing (humans & scientists are confirmation-biased)

• Sociology: reinforced by scientific community

(“publish or perish”)

* Fanelli D. Do pressures to publish increase scientists’ bias? An empirical support from US States data. PLoS One 2010, 5(4): e10271

“Negative” results

• Often never published (“file-drawer effect”)

• OK if invalid results (bad methodology, non-reproducible findings, low numbers, …)

• Try to publish as “negative” results

• Ethical duty (ICJME)

• Not impossible!

[“positive” results are not assessed with

same rigour and scrutiny as “negative”

results]

“Negative” results

• Publication of “negative” data is not

impossible • Lee K.P. et al. Predictors of publication: characteristics

of submitted manuscripts associated with acceptance at major biomedical journals. MJA 2006, 184, 621-6.

• 1107 manuscripts submitted to BMJ, Lancet, AIM

• 68 (6%) accepted, 777 (70%) rejected outright, 262 (24%) rejected after peer review

• Predictors of acceptance:

– methodological quality (RCT, ...)

– ...

– “statistically significant results”: no effect

“Negative” results

• Questionable “solutions”

• Reformulate hypothesis

• “HARKing” = Hypothesizing After the Results are Known

• Selecting only the positive findings

• Selective reporting

• Tweaking data or analyses to improve outcome

• Falsifying/fabricating data

6

Plagiarism

• Using (stealing) ideas, work, writings, figures, slides, … from others and presenting these as your own

= “Copy-and-paste” from others without attribution

If you wish to use someone else’s work:

• according to X, …; Y wrote that …

• Use “quotations marks” (or italics) for whole sentences or

paragraphs (+ mention source)

• For figures: “reproduced from …”; “adapted from …”; “modified from …” with permission from the author & publisher

• For slides: “slide received from …”; “slide courtesy of …”

If in doubt, err on the side of caution! Ask advice, be transparent

“How would you feel if it was your work being copied?”

Retracted publications

4121 (13.01.2016)

1951 (29.11.2011)

Retracted publications

7

retractionwatch.com/ retractionwatch.com/

The mission of the Center for Scientific Integrity, the parent organization of Retraction Watch, is to promote transparency and integrity in science and scientific publishing, and to disseminate best practices and increase efficiency in science.The goals of the Center fall under four broad areas:

• A database of retractions, expressions of concern and related publishing events, generated by the work of Retraction Watch. The database will be freely available to scientists, scholars and anyone else interested in analyzing the information.

• Long-form, larger-impact writing, including magazine-length articles, reports and books.• Scholarship on scientific integrity and incentives in science.• Aid and assistance to groups and individuals whose interests in transparency and accountability intersect

with ours, and who could benefit from shared expertise and resources.The Center is a 501(c)3 non-profit. Its work is funded by generous grants from the John D. and Catherine T. MacArthur Foundation and the Laura and John Arnold Foundation.Learn more about our Board of Directors here.

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retractionwatch.com/

Article Year of retraction Cites before retraction

Cites after retraction

Total cites

1. Visfatin: A protein secreted by visceral fat that mimics the effects of insulin. SCIENCE, JAN 21 2005Fukuhara A, Matsuda M, Nishizawa M, Segawa K, Tanaka M, Kishimoto K, Matsuki Y, Murakami M, Ichisaka T, Murakami H, Watanabe E, Takagi T, Akiyoshi M, Ohtsubo T, Kihara S, Yamashita S, Makishima M, Funahashi T, Yamanaka S, Hiramatsu R, Matsuzawa Y, Shimomura I.

2007 247 776 1023

2. Purification and ex vivo expansion of postnatal human marrow mesodermal progenitor cells. BLOOD, NOV 1 2001Reyes M, Lund T, Lenvik T, Aguiar D, Koodie L, Verfaillie CM.

2009 655 214 869

3. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. LANCET, FEB 28 1998Wakefield AJ, Murch SH, Anthony A, Linnell J, Casson DM, Malik M, Berelowitz M, Dhillon AP, Thomson MA, Harvey P, Valentine A, Davies SE, Walker-Smith JA.

2010 675 308 983

Top 10 most highly cited retracted papersReaders will see some familiar entries, such as the infamous Lancet paper by Andrew Wakefield that originally suggested a link between autism and childhood vaccines. You’ll note that many papers —including the #1 most cited paper — received more citations after they were retracted! (13.01.2016)

Proc Natl Acad Sci U S A. 2012,109,17028-33.

Proc Natl Acad Sci U S A. 2012,109,17028-33.

Honest mistakes!(no intention to deceive)

8

Plagiarism Plagiarism

Self-plagiarism = text recycling

Lancet 2011, 377, 2821-2

How?

• Writing article

• Submission process

• Publication process

Writing an article

• Title page

• Abstract

• Introduction

• Materials and methods

• Results

• Discussion

• Acknowledgements

• References

Publication of research

Balanced combination of

1. accurate reporting of research findings

2. convincing editor, reviewers and readers of the importance (novelty, implications) of the findings

� HONESTY: factual objective information

� RIGOUR: logical interpretations and conclusions

� STYLE: clarity and enthusiasm [“good story”1 ↔ “spin”2]

1 Plemmons D. A broader discussion of authorship. Sci Eng Ethics 2011, 17, 389-982 Horton R. The rhetoric of research. BMJ 1995, 310, 985-7

9

Writing an article

Uniform Requirements for Manuscripts

Submitted to Biomedical Journals

(“Vancouver style”)

International Committee of Medical

Journal Editors (ICMJE)

http://www.icmje.org/index.html

STROBE

• Vandenbroucke et al. Strengthening the

Reporting of Observational Studies in Epidemiology (STROBE): Explanation and

Elaboration. PLoS Medicine, 2007, 4(10):

e297. doi:10.1371/journal.pmed.0040297

• http://www.strobe-statement.org/

Title

• Working title(s) / final title– accurate (honest)

• neutral

• declarative (claim) or question

– Informative (sensitive + specific)• [A study of …]

• no abbreviations, no jargon

• specify animal species and other essential elements

– concise (max 100 characters)• + subtitle

– attractive

STROBE

1a. Indicate the study’s design with a

commonly used term in the title or the abstract

10

Authors

Responsible research publication

1. Soundness and reliability

2. Honesty

3. Balance

4. Originality

5. Transparency

6. Appropriate authorship and acknowledgement

7. Accountability and responsibility

8. Adherence to peer review and publication conventions

9. Responsible reporting of research involving humans or animals

Wager E, Kleinert S. (2011) Responsible research publication: international standards for authors. A position statement developed at the 2nd World Conference on Research Integrity. Singapore, July 22-24, 2010. Ch.50 in Mayer T & Steneck N (Eds) Promoting Research

Integrity in a Global Environment. Imperial College Press / World Scientific Publishing. Singapore (pp309-16)

Janssens, Peters, Smith, Jones, Taylor, Martin, Nowak, Müller, Nagy, Rossi,

Levi, Cohen, David, García, González, Martinez, Hernández, Silva, Diaz, Wang, Zhang, Chen, Sato, Suzuki, Tanaka, Nguyen, Kim, Lee, Park, Patel,

Das, Singh, Ahmed, Muhammad, Hussain, Touré, Diallo, Ndiaye, Samba, ...

orcid.org

Authors

! Spelling of names, first names, initial(s), degrees, affiliations, ...

Benoit

Authorship

1. Authorship conveys professional benefit

in that it allocates credit for scientific advances

2. Authorship conveys responsibility in that it implies the endorsement of the quality

and integrity of the work performed

Eggert LD. Best practices for allocating appropriate credit and

responsibility to authors of multi-authored articles. Front. Psychol. 2011, 2, doi 10.3389/fpsyg.2011.00196

11

Authors

• Who is an author?

– must agree to be a co-author (public responsibility)

– substantive (intellectual) contribution

– capable of defending the article

– some journals: “credits”

– some journals: “guarantor” of study

“Author” vs “contributor”

! “Gift authorship” and “Ghost authors”

“Contributor”

“Contribution is the activity of science that is

most relevant to publication because its disclosure can identify who is accountable

for what part of the research and allows the

reader to assign credit fairly”

Drummond RENNIE et al. JAMA 1997,278, 579-85

Authors

“This qualitative study [showed] that a

research paper rarely represents the full range of opinions of those scientists whose

work it claims to report”

Richart HORTON. JAMA 2002, 287, 2775-8

Multiple “authors”

http://sciencewatch.com/multiauthor-papers-onward-and-upward

http://sciencewatch.com/multiauthor-papers-onward-and-upward

2011 ATLAS Collaboration (Aad et al.) Phys. Lett. B 3,179

2010 ATLAS Collaboration (Aad et al.) Phys. Lett. B 3,221

2009 LIGO Sci. Collaboration, … (Abbott et al.) Nature 657

2008 CMS Collaboration (Chatrchyan et al.) J. Instrumentation 3,101

2007 CMS Collaboration (Bayatian et al.) J. Phys. G.-Nucl. Part. Phys. 2,011

2006 ALEPH, … (Schael et al.) Phys. Reports 2,517

2005 Antiretroviral Ther … (Costagliola et al.)Clin. Infect. Diseases 859

2004 MEGA study Group (Nakamura et al.) Circulation J. 2,459

2003 CDF II Collaboration (Acosta et al.) Phys. Rev. D 818

Who is an author? (ICMJE)

Authorship credit should be based on

1) substantial contributions to conception or design, or acquisition or analysis or interpretation of data;

2) drafting the article or revising it critically for important intellectual content;

3) final approval of the version to be published.

4) agreement to be accountable for all aspects of the work (i.e. confidence in integrity of contributions of co-authors)

Authors should meet conditions 1, 2, 3 and 4. [+ all those who meet criterion 1 should have the opportunity

to meet 2 and 3]

12

Who is (not) an author?

International Committee of Medical Journal Editors (ICMJE)

http://www.icmje.org/index.html

• Acquisition of funding, collection of data, or general supervision of the research group,

alone, does not justify authorship.

• All persons designated as authors should qualify for authorship, and all those who qualify should

be listed.

• Each author should have participated sufficiently

in the work to take public responsibility for appropriate portions of the content.

In practice ...

• Author: significant intellectual contribution

– “doing the work”, designing the study, interpretation, writing the paper, ...

• Technical contributions

– Laboratory measurements

– Data input

– Software development

– Textual editing

– ...

• Recruiting patients, providing tissues or cells, ...

• Provision of space, reagents, animals (“quid pro quo”)

• “Political reasons” (status)

– (All) members of the research team (“quid pro quo”)

– Senior members

– Obtaining funds

– Authority (“big name”)

co-author if substantial

intellectual/creative/interpretative contribution;

if not: acknowledge specific role

not co-author;

acknowledge or thank,

if needed

In principle

Authorship declaration Authorship declaration

Authors

• First author

– generally: the one with the “greatest” contribution

– recently: “joint first authors” or “equal contribution”

“Joint first authors”

Conte M.L. et al. Increased co-first authorships in biomedical and clinical

publications: a call for recognition. FASEB J. 2013, 27, 3902-4

Biomedical journals Clinical journals

13

Joint first authors ...

Nat Genet 2012, 43, 768-75

http://www.nature.com/authors/policies/authorship.htmlNature journals also allow two coauthors to be specified as having contributed equally to the

work being described (most often used for co-first authors), but prefer authors to use the "author contributions" style for reader clarity.

“Joint first authors”

Dubnansky E., Bishr Omary M. Acknowledging joint first authors of

published work: the time has come. Gastroenterology 2012, 143, 879-80

Never change the order of authors on your CV!

Authors

• First author

– generally: the one with the “greatest” contribution

– recently: “joint first authors” or “equal contribution”

• Last author

– usually: the real supervisor (PI) (↔ honorary author)

• Corresponding author

– for correspondence with editor (administrative)

– preferably: permanent author for future correspondence

• Guarantor (in multicentre studies)

– Responsibility for accuracy & integrity of the entire paper

Authors

• Co-authors 2 to n-1

– usually (not necessarily): ordered according to decreasing degree of contribution

• Group authorship

– “XYZ study group”, “ABC consortium”

– or: after one or more named authors

� members listed (alphabetically or not) in acknowledgements or appendix (+ often included in databases)

Authors

• Contributor

– if contribution, but not enough to be an author→ acknowledgements (must agree!)

• Gift author

– senior figures

• Internal (tradition, authority, respect, …) (“honorary author”)

• External (prestige, reputation, influence) (“guest author”)

– Colleagues: quid pro quo

• Ghost author

– “ignored” or “excluded” co-author

– professional writer → acknowledgements

Ghost authors

14

The “forgotten” author ...

Gift authorshipLancet, 2008, 372, 778

“Ghost authors”BMJ 2007;334:223 (3 February)

“Ghost authors”

Gift authors

15

Gift authorshipAuthors

• order of authors: agree beforehand!

Albert T., Wager E. How to handle authorship disputes: a guide for new researchers. The COPE report 2003. http://publicationethics.org/static/2003/2003pdfcomplete.pdf

Authors

Albert T., Wager E. How to handle authorship disputes: a guide for new researchers. The COPE report 2003. http://publicationethics.org/static/2003/2003pdfcomplete.pdf

• Follow institutional policy on authorship

• Start discussing authorship at the planning stage

• Decide authorship before starting writing

, 315

Institutional affiliations

• Hospital / institution / university

correct full names ! (translation?)

• Division / department

be consistent with previous publications

! Multiple affiliations

! Funding

Title page

• Corresponding author: – “permanent author”

• Funding sources

• Conflicts of interest• Key words

– from Index Medicus (MeSH)– no need to repeat words in title

• Running head (40 characters)• List of abbreviations

• Word count (+ number of figures & tables)

16

Abstract

• Abbreviated version of article – must be accurate and informative– results should be the most important part– consistent with body and conclusions of

article– usually no references– avoid unusual abbreviations– usually third person

• “structured abstracts”• often strict limitations of word count

Check (+ follow) journal’s instructions!

Abstract

– Abstract is very important

– It may be the only part of your article that will be assessed, not only by readers, but also by editors

Groves T., Abbasi K. Screening research

papers by reading abstracts. BMJ, 2004, 329, 470-471

“Please get the abstract right, because we may use it alone to assess your paper.”

STROBE

1b. Provide in the abstract an informative and balanced summary of what was done and what

was found

- present key results in numerical form (number of participants, estimates of associations, appropriate measures of variability and uncertainty)

- [it is] insufficient to state only that an exposure is or is not significantly associated with an outcome.

Avoid “empty clauses”

• “it is generally believed that

the treatment is effective”

• “there are some genetic

factors that ...”

• “the treatment is generally

believed to be effective”

• “genetic factors may ...”

Avoid “nominaliza8ons” (verb → noun)(-tion, -ment, - ance, -er, -or, -ent, -ity, -sion, -ness, -ance, -ence,-ist)

• “we made an assumption”

• “they conducted an investigation”

• “she applied the adjustments”

• “pain is an indicator of severity”

• “they provided supervision”

• “he stated his refusal to go”

weak verb needed

• “we assumed”

• “they investigated”

• “she adjusted”

• “pain indicates severity”

• “they supervised”

• “he refused to go”

17

How to save words1. Use plurals to eliminate articles

2. Hyphenate whenever grammatically defensible

3. Use abbreviations

4. Use prefixes instead of qualifying words

5. Avoid using empty words

6. Avoid using nominalizations

7. Remove prepositional phrases with adjectives

8. Avoid “circumlocutions”

9. Replace phrases with single more specific words

10. Use numerals (but not to begin sentences)

11. Prefer the active voice

12. Do not space between mathematical operators

13. Avoid multiple qualifications

14. Put common elements first in a list to avoid repetition

15. Use parallel constructions

Use of “positive” words

“novel”, “innovative”, “robust”,

“unprecedented”, “groundbreaking”, ...

• Don’t exaggerate!

18

Writing an article

“Split the thinking from the writing”

Sterk & Rabe, 2008

Writing an article

• IMRaD

– Introduction: ~1 page

– Methods: 2-3 pages

– Results: 2-3 pages

– Discussion: 2-4 pages

– Tables/figures: 3-6

– References: 20-35

Writing an article

• “Write for your readers, not for posterity”

• First draft: write as if you were explaining to a layperson (your mother)

• Sentences of 20-30 words, read without taking a new breath

• New idea = new paragraph!– Use “sign posts” (“However, …” “On the other hand, …”)

• Be enthusiastic!

Introduction

• Brief overview of general field & what is known – cite review articles & key references

– if applicable, cite your previous work

• remaining questions or gaps in our knowledge (be balanced)

• specify the questions or hypothesesaddressed and indicate the approach used

• (summarise the main findings)

! be concise

Introduction

Sterk & Rabe, 2008

STROBE

2. Explain the scientific background and

rationale for the investigation being reported

3. State specific objectives, including

prespecified hypotheses

19

Methods

WHAT ? WHY ? WHEN ?

HOW ? WHERE ? WHO ?

• Explain how evidence was obtained

• Should allow others to repeat the study:

clarity!

• subsections

Methods

• Subjects

– recruitment procedures & exclusion criteria

– specify (only) essential characteristics (age, gender, …)

– compliance with legal and ethical aspects

� check guidelines

– For RCT (CONSORT) www.consort-statement.org

– For observational studies (STROBE) www.strobe-statement.org

Methods

• Animals

– species, strain, sex, age/weight, origin (SPF)

– housing conditions, feed (starving), drink, …

– procedures for dosing, anaesthesia, euthanasia

– compliance with legal and ethical aspects

Methods

• Reagents

• media• consumables

• probes• antibodies

• technical equipmentbe specific, accurate and complete

(electronic supplement)

Methods

• Experimental procedures and protocols: – accurate

– “complete”: • very common techniques: refer to standard manual or

article – still specify standards and conditions of test

• complex protocols or techniques: sufficient detail to repeat the study

! Technique of X “with modifications” (be honest)

• novel technique: very complete description of all steps and conditions (figures, flow charts, …)

– indicate hazardous procedures

Methods

• All types of measurements made must be

given (even those that will not be reported in results)

20

Methods

• Data presentation and statistical analyses

– number of replicates

– expression of variation (SD or SEM)

– missing data

– transformation procedures

– statistical tests (specify Software and version

used)

– level of significance considered

STROBE

Results

Most important part of the article!

Results

Start by constructing tables and

figures

Results

• Begin with essential information: – characteristics of populations– completeness of data (flow diagram)– characteristics of excluded or lost subjects – survival of animals

– validation of techniques– …

• use subsections and titles if appropriate• present all relevant findings, including those

that do not fit your hypotheses(Electronic supplement)

Sloppy mistakes …

Anonymous. Must try harder. Too many sloppy mistakes are creeping into scientific papers. Lab heads must look more rigorously at the data – and at themselves (Editorial). Nature, 2012, 483, 509.

– Unrelated data panels

– Missing references

– Incorrect controls

– Undeclared cosmetic adjustments to figures

– Duplications

– Reserve figures and dummy text included

– Inaccurate and incomplete methods

– Improper use of statistics (e.g. technical replicates vs

independent experiments)

21

Sloppy mistakes …

Anonymous. Must try harder. Too many sloppy mistakes are creeping into scientific papers. Lab heads must look more rigorously at the data – and at themselves (Editorial). Nature, 2012, 483, 509.

Editors and referees cannot be expected to divine when only positive data are included and inconvenient results left out, but journals should encourage online presentation of the complete picture. And scientists should offer it. The complete picture is, after all, what this science of ours strives to provide.

Results

• Text– concise – systematic – neutral (FACTS)

– in general:• do not repeat the rationale for doing the study or

experiment (except very briefly)

• do not repeat the methodology

• do not interpret or discuss the data

– indicate clearly to which table or figure you refer (“Figure 2 presents …”)

– point out salient features of tables and figures

Results

• Figures and tables

– data either in a table or in a figure (do not duplicate)

– must be intelligible

• use adequate titles, headings, captions, footnotes

• legend must be comprehensive and sufficiently detailed for the figure to be understood on its own

• do not describe or discuss the data

• Use electronic supplement if necessary

Results

• Figures and tables

– each figure and table on a separate page (do not embed in text) (identify number!)

– do not include legends within figures, but give a separate list

! Reproducing figures from books, articles, ...:

ask permission from author and publisher (even for your own previous work)

STROBE Discussion

• Briefly repeat salient findings, novelty and interpretation (answer the question posed)

• address strengths and limitations of study

• compare with previously obtained data & explain possible differences

• propose interpretations

• suggest further avenues for research

• give possible implications

• summarise data and conclusions

22

Discussion

Sterk & Rabe, 2008

Proposal for structured discussion in medical research papers

Horton R. (The Lancet)

The hidden research paper.JAMA, 2002, 287, 2775-8

Discussion

• Be concise– subsections with titles

• do not over-interpret your findings

• discuss all findings

• distinguish facts and speculation

• give due credit to work of others

• address the questions and hypotheses stated in the introduction

• end with strong statement

STROBE

Hill AB. The environment and disease. Association or causation? Proc R Soc Med 1965, 58, 295-300

“It has long been known ...” – I didn’t look up the original references.

“A definite trend is evident ...” – These data are practically meaningless.

“Of great theoretical and practical importance ...” – Interesting to me.

“While it has not been possible to provide definite answers to these matters ...” –This was an unsuccessful experiment, but I still hope to get it published.

“Three of the samples were chosen for further study ...” – The others made no sense.

“Typical results are shown ...” –The best results are shown.

“The most reliable results are those obtained by Smith ...” – He was my fellow.

“It is believed that ...” – I think. “It is generally believed that ...” – My friends think so too.

“It is clear that much additional work will be required before a complete understanding

of the phenomenon is possible.” – I don’ understand it.

“Correct within an order of magnitude ...” – Wrong.

“It is hoped that this work will stimulate more work in this field.” –This is a lousy paper, but so are the others in this crummy area.

“Thanks are due to Joe Blow for assistance with the experimental work, and George

Fink for valuable discussion.” – Blow did the work, and Fink explained to me what it meant.

“A statistically oriented projection of the findings ...” – Wild guess.

“A highly significant area for exploratory study ...” – A totally useless topic suggested

by my PhD committee.

from Thurlbeck WM. Am Rev Respir Dis 1989, 139, 262-83

Acknowledgements

• Significant contribution– general support– fund raising– critical reading of manuscript– discussion at various stages

– collection of data! Ask permission

• Technical help• Funding sources

• Conflicts of interest

23

References

• Cite “all” relevant references– those supporting your hypothesis and data, as

well as those that do not agree– original articles whenever possible

– (avoid abstracts)

• Cite only relevant references

• Don’t over self-cite

• some journals limit the number of references

References

• never cite a reference that you have not seen yourself– check accuracy of citation

– check content

! Old articles, books, ...

! Articles in other languages

• if you have not seen the article: “according to X (ref), Y has published that …”

“Y showed that … [cited by X, (ref)]”

References

• Cite in body of text:– numbering (1), [2], 3

• according to order of appearance

• alphabetically by first author

– author name(s) and publication date• Smith, 1995

• Smith and Jones, 1995

• Smith et al., 1995

• unpublished observations (in text)

• personal communications (ask permission and give written proof)

References

• List of references

– only articles that are cited in the text

– be consistent

– be accurate

– check and recheck carefully

– conform to requirements of Journal

• Use ZOTERO (=free) or other system

(Refmanager, Endnote, …)

Successive drafts

• Order of writing sections is not final order

• submit drafts of your paper to supervisor and colleagues + co-authors– first check printed version (not just on-screen

version), number all pages

– use spell-check features, but cautiously

– check grammar and punctuation (ask linguistic advice if necessary)

– be prepared to shorten the paper

• submit the “final” draft to an internal review and all co-authors

Submitting an article

24

Where?

• International peer-reviewed journal

• scope & readership of the journal

• prestige of the journal• accessibility of the journal (“Open

access”?)

• chances of success (rejection rate)• speed of reviewing and publishing

• publication costs

• quality of photographs

Prestige of scientific journals

• Institute of Scientific Information

http://admin-

apps.isiknowledge.com/JCR/JCR?PointOfEn

try=Home&SID=N1KleK3DIfBLL5KCDGN

• Journal Citation Reports: impact factor

“number of citations in a given year to papers published in that journal in the preceding 2

years, divided by the number of papers the journal published in that same 2-year period”

25

Impact factor

• relative index (ratio)

• measure of citation, not a measure of quality

• depends on research field and subject area

• fluctuations with time (slow)

Amin M., Mabe M. Impact factors: use and abuse. Perspectives in Publishing, October 2000, 1-6

Seglen P.O. Why the impact factor of journals should not be used for evaluating research. BMJ, 1997, 314, 498-502

Prestige of scientific journals

• SCImago Lab

http://www.scimagojr.com/index.phpThe SCImago Journal & Country Rank is a portal that includes the journals

and country scientific indicators developed from the information

contained in the Scopus® database (Elsevier B.V.). These indicators can be used to assess and analyze scientific domains.

This platform takes its name from the SCImago Journal Rank (SJR)

indicator, developed by SCImago from the widely known algorithm

Google PageRank™. This indicator shows the visibility of the journals contained in the Scopus® database from 1996.

Prestige of scientific journals Nature

17 October 2013

26

“Diseased Science”

Casadell A., Fang F.C. Microbe, 2014, 9, 390-2

• “Impact Factor Mania” or “impactitis”

co-laureate of 2013 Nobel Prize in physiology or medicine

http://www.theguardian.com/commentisfree/2013/dec/09/how-journals-nature-science-cell-damage-science

http://www.theguardian.com/commentisfree/2013/dec/09/how-journals-nature-science-cell-damage-science

27

http://scholarlyoa.com/publishers/ http://scholarlyoa.com/publishers/

http://scholarlyoa.com/

OMICS Group Aims to Trick Researchers with Copycat Journal TitlesFebruary 19, 2015

OMICS Group continues to launch and publish scholarly journals whose

titles closely match those of established and respected journals, including journals published by scholarly societies. OMICS Group’s goal is to trick

researchers into thinking the OMICS journals are actually the legitimate

journals, so they can get the author fees from the authors.. …

http://scholarlyoa.com/

So-Called “Special” Issues of Journals: Big Money for Gold OA PublishersFebruary 24, 2015

Special issues of journals mean big money for gold (author-pays) OA

publishers. It’s a type of affinity marketing. The special issue guest editor typically invites his contacts and colleagues to contribute papers for a

special issue on a topic, and they all have to pay author fees to the

publisher. …

http://scholarlyoa.com/

The Journal of Chest is a fake and predatory journal, and I recommend that all researchers not submit papers to it or the hundreds of other journals published by OMICS Group.

16.06.2015Bohannon J.

28

Bohannon J.

Front Biosci (Elite Ed). 2010 Jun 1;2:1164-8. Telomere length and its associationswith oxidized-LDL, carotid artery distensibility and smoking. Nawrot TS, et al.

Submission of article

• Choose journal

• strictly follow “Instructions to Authors”

– electronic submission

– paper submission

! checklist

• include copies of relevant unpublished articles

• include required copyright transfer statements

• keep copies of everything

Submission of article

• cover letter

– specify type of submission (e.g. article, note, rapid communication, …)

– briefly state importance or context of the paper and justify choice of journal

– suggest impartial reviewers

– (indicate where you are prepared to make changes)

– state that all authors have read and approved the paper

– certify that the paper has not been submitted elsewhere (and/or indicate that portions of the paper have been published previously)

– indicate possible conflicts of interest

Reviewing process

• Manuscript identification (number)

• Internal review (first screen)

– rejection without review

Rejection without review

• usually rapid (< 1 week)

– Subject not relevant for journal

– Poor quality of paper (abstract)

– Mostly: “low priority”

• not original enough

• (unlikely to increase journal’s impact factor)

• …

� try elsewhere

� appeal ?

29

Reviewing process

• Manuscript identification (number)

• Internal review (first screen)

– rejection without review (“not interested”)

• Editor or assistant/associate editor invites

one or more reviewers to evaluate article

– proposed reviewers

– database of reviewers

– authors of articles in reference list

Reviewers

• “peer-review” to assess – scientific validity of article

– novelty of findings

– interpretation of findings

– implications

• give advice on suitability for publication – editor makes the decision

• generally anonymous

• must declare conflicts of interest

Review

• Brief summary of article

• General comments

• Major specific comments

• Minor comments

• should be fair and constructive

• should be rapid

Review

Hoppin F.G. Jr. How I review an original scientific article. Am. J. Respir. Crit. Care Med. 2002, 166,

1019-23

– What does it take to do a good review?

• Motivation: sense of responsibility

• Scientific expertise

• Helpful attitude: respect

• Time

Review

– How do I proceed• Acceptance: expert, time, already seen?• First reading + notations in margin

– Abstract, then full article: understand the science?

– Problems with the science (violations of logic!)– Problems with ethics

– Problems with presentation (lead the reader through your thinking)

• Second reading– Integrity of the science

– Novelty of the science– Presentation issues

– Recommendations to editor

Review

• The write-up– Comments to editors

» Summary

» Main criticisms/questions

» Recommendations

» Aspects not evaluated

» Help from other, conflict of interest

– Comments to authors: clarity, no praise, respect

» Summary

» Major comments (numbered): because …, suggestions

» Minor comments

30

Anonymous review

Review & confidentiality

Never disclose information obtained from reviewing an article

to a third party,

and certainly not to pharmaceutical companies

Review & confidentiality

Anonymous. The pitfalls and rewards of peer review. Lancet. 2008, 371, 447

Last week, a further firestorm gathered around the meta-analysis of rosiglitazone's cardiovascular risks, a paper that was originally published in the New England Journal of Medicine in May, 2007. […] “Doctor Accused of Leak to Drug Maker”, ran the headline in The New York Times on Jan 31. It had emerged that one of the peer reviewers had faxed a copy of the paper to a contact at GlaxoSmithKline (GSK), the maker of rosiglitazone, 18 days before publication. This clear and astonishing breach of reviewer confidentiality was made public by Republican Senator Charles E Grassley in a speech on drug safety before the US Senate last Wednesday.

Editorial decision

• Accepted as is

• Accepted conditional on revision

– “minor revision”

• Rejected in its present form, but revised

version will be considered

– “major revision”

• Rejected but resubmission encouraged

• Rejected and resubmission not accepted

Responding to reviewers

• Take the comments seriously

• Don’t take comments personally• If the reviewer did not understand you, it

generally means that you were not clear

• If you are upset, don’t react too quickly!• Respond to all comments point-by-point

– in general, follow the suggestions – argue reasonably against unjustified comments

• Respond within the requested time– ask for more time if necessary

31

Rejection Responding to reviewers

• Help the editor by

– repeating or summarising the reviewer comments

– indicating how you have made changes

• Submit a revised version

– identify clearly that it is a revised version

– include a version highlighting the changes

made

Revised version

• The revised version may

– be accepted without further review

– be reviewed again by the same or other

reviewers

– be returned for additional revision(s)

– be rejected

Accepted manuscript

• Galley proofs– correct on a photocopy first

– check very carefully using original manuscript

– use standard proofreaders’ symbols in margin• add complete list of corrections if necessary

– ask a non-scientist to proofread as well

– answer all queries of the publisher

– keep a copy of the corrections made

– return promptly

Accepted manuscript

• Galley proofs

– check all sections

• title, running title, names, affiliations, tables, figures, legends, references

– check numbers, units, dosages

• µg, ml, mL, subscripts, superscripts, special symbols, Greek letters, …

– check hyphenation

– check consistency of spelling

Publication

• Published ahead of print

• Published in final form

• Accompanying editorial

• Press release

– Increases impact of published article (and journal)

(Phillips et al. NEJM 1991, 325, 1180-3

Chew et al. J Roy Soc Med 2007, 100, 142-50)

– Cave exaggeration (Sumner et al. BMJ 2014, 349,

g7015)