UNIVERSITY OF ZAGREB PhD Programme:

School of Medicine Biomedicine and Health Sciences

Course: Structure, methodology and functioning of scientific work II

Hand-outs (reminder)

“Useful scientific research has its beginning, end and published result”. (Michael Faraday)
“To publish or to parish”
Science has a cumulative character, every new “peace of knowledge” enlarges previous one
and changes (revises) it.
Nowadays it is more and more important to publish in internationally visible journals i.e.
those indexed in international bibliographic and citation databases.
Only those papers published in high quality peer reviewed journals that are indexed in Current
Contents (CC) or MEDLINE (and recently other databases like Scopus) are internationally
visible and have a potential of being citied.
Moreover, scientific productivity today very often means counting only these indexed
publications and measure of their impact. Thus not only number of published articles is
important but also the quality of journals in which they are published. The journals are ranked
according to their impact factors. Bibliographic and citation databases accessible and
searchable by use of user friendly programmes offer a lot of additional options for
scientometric analysis enabling everybody to evaluate the scientific production of an
individual, group of individuals, department, institution, country etc.
All of that is globally available with free access in case of popular Entrez PubMed service
provided by US National Library of Medicine (available at http://www.ncbi.nlm.nih.gov
formerly MEDLINE or Index Medicus), or a limited access for those paying subscription like
in case of databases encompassed in Web of Science (Thomson Reuters) or SciVerse Scopus
(Elsevier, available at http://www.info.sciverse.com/scopus/).
Unfortunately, such publication productivity in Central and Eastern European countries is far
below that of Western European countries and United States of America.
The scientific process can be fun and it can be exciting, but it also carries a great
responsibility.
Read carefully Singapore Statement on Research Integrity (attached and available at:
http://www.singaporestatement.org) and think about every one of listed responsibilities.
Which one says that you ought to report any case doubtful to include falsified or fabricated
data? Which one referees to retraction of papers?
Office of Research Integrity (ORI) belongs to U.S. Department of Health and Human
Services. In many other countries such offices do not exist.
Please visit ORI web page at http://ori.hhs.gov/ and find out what is misconduct in research,
how and to whom should be reported.
Question:
What is expected from a scientist in Germany or in any South European country in case if
(s)he get know that one colleague from the same institution has submitted a paper for
publication based on falsified data? To whom (s)he should report?

Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 1

Art vs. Science
• Both look at the world in a new way
• Science deliberately builds on the past in order to accumulate knowledge
• Therefore, scientific knowledge must be communicated so that others may most
effectively continue this process. This requires:
o Honesty
o Sufficiency
o Accuracy
o Selectivity
Publication vs. Presentation

Publication Presentation
Conciseness +
Timelines +
Personal, Informal +
Completeness +
Peer-reviewed +
Retrivable +

Report or article consists of the following sections

• Title
• Abstract
• Introduction
• Patients and Methods / Material and Methods (including Statistical methods)
• Results
• Discussion (including Limitations if they are not a separate section)
• Conclusions
• References
There are often some additional sections (depending of the journal and publication
type) e.g.:
• Keywords
• Acknowledgments
• Authors’ contributions
• Disclosures/conflict of interest
• Funding/financial disclosure
• Trial registration
• Appendix/Supplementary data – data available in electronic form only
• Pre-publication history – versions of manuscript that preceded published version
together with reviewers’ responses and authors’ replies to them

Title
• Functions
o Attract and inform reader
o Identify and classify the paper
• Suggestions
Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 2
 o Make it substantive – a mini-abstract (informative)
o Give the scope of the study
o Stay within space limitations
o Avoid jargon and “waste words”

Abstract
• Structured or not-structured
o Brief statement of purpose
o General description of procedures
o Concise, specific summary of results
o Brief statement of relevant conclusions
o Avoid promises, undefined terms
o Stay within space limitations

If journal does not require structured abstract, it needs to be structured (but not formally).
If structured abstract is required, the structure has different elements in different journals
(examples of different journals like Croat Med J. BMJ, The Lancet and JAMA are given
below, try to find structure required by other journals and particularly your home country
journals)

Abstract structure as required by different journals:

Components of abstract as required by Croatian Medical Journal (CMJ):
1. Aim
2. Methods
3. Results
4. Conclusion

Components of abstract as required by British Medical Journal (BMJ):

1. Objective
2. Design
3. Settings
4. Methods or Participants
5. Intervention (if applicable)
6. Main outcome measures
7. Results
8. Conclusion
9. Trial registration (it applicable)

Components of abstract in The Lancet:

1. Background
2. Methods
3. Findings
4. Interpretation
5. Funding

Components of abstract in JAMA:

1. Importance
2. Objectives
3. Design, Setting, and Participants
4. Main Outcomes and Measures
5. Results
Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 3
 6. Conclusions and Relevance
7. Trial Registration

Precious results have to be given in abstract, too. Why?

Introduction
• The most important thing is to justify why this particular study was done
• Show a clear, logical connection between hypothesis (or research questions) and design
and methods
• Cite only the most relevant references

Methods
• Provide enough information to allow the reader
o Replicate the study
o Evaluate its value and relevance
• In Presentation
o Highlight only the most important aspects
o Leave details for the discussion period

Statistical analysis (included in section Methods)

• Use tests that reflect the hypothesis or research question(s)
• Document any unusual test or procedure
• Provide enough information so that the appropriateness of tests and procedures can be
evaluated

Results
• Be selective, emphasizing
o Data that speak directly to the hypothesis or question
o Relevant unexpected findings
• Use well-planned, digestible (self explanatory) visual aids
• Provide results of statistical tests correctly (avoid for example “orphan p”)

Discussion
• Restrict to what is relevant to the results obtained
• Include relevant limitations
• Avoid lengthy speculations
• Suggestion
o Include suggestions for future research

References
• Use an appropriate format (style)
• Be sure that there is an exact correspondence between citations in the text and
references at the end
o Do not use uncited references
o Be sure that all references cited appear in the reference section
• Proofread for accuracy
Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 4
 • Proofread ones again

References are listed at the end but citied primarily in Introduction and Discussion. Methods
(including the statistical methods used) are briefly referenced if necessary (particularly non-
standard procedures) in the methodological section.

Major Referencing Styles

• APA Style (APA – American Psychological Association)
• ACS Style (ACS - American Chemical Society)
• ASA Style (ASA – American Sociological Association)
• CSE (CSE – Council of Science editors)
• IEEE (IEEE - Institute of Electrical and Electronics Engineers)
• MLA Style (MLA - Modern Language Association of America)
• Harvard
• Vancouver Style

Detailed description can be found for example at:

• Vancouver Community College Library (VCC)
http://library.vcc.ca/research/research_apamla.cfm
• University of Queensland, Australia - Referencing Styles
http://www.library.uq.edu.au/infoskil/styles2.html
• Purdue OWL – Purdue Online Writing Lab - Research and Citation Resources -
https://owl.english.purdue.edu/owl/section/2/

Vancouver style
Vancouver is a generic term for a style of referencing widely used in the health sciences,
using a numbered reference list.
There is no official manual of the Vancouver style, but the US National Library of Medicine's
style guide is now considered the most authoritative manual on this type of referencing.

International Committee of Medical Journal Editors (ICMJE)

http://www.icmje.org
Please visit http://www.icmje.org where you can find standards agreed by medical
journal editors (not only regarding referencing style but manuscript preparation and
how to send it to the editors, ethical issues, disclosure of interest, and other.
Please go through the following pages of the Uniform Requirements for Manuscripts
Submitted to Biomedical Journals (URM):
• Statement of Purpose:
o About the Uniform Requirements
o How to Use the Uniform Requirements
• Ethical Considerations in the Conduct and Reporting of Research
o Authorship and Contributorship
o Peer Review
o Conflict of Interest
o Privacy and Confidentiality
o Protection of Human Subjects and Animals in Research

Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 5

• Publishing and Editorial Issues
o Obligation to Publish Negative Studies
o ……
o ……
o Obligation to Register Clinical Trials (please visit http://www.clnicaltrials.gov)
• Manuscript Preparation
o Preparing a Manuscript for Submission to a Biomedical Journal
o Sending the Manuscript to the Journal
• References
o References Cited in this Document
o Other Sources of Information Related to Biomedical Journals

Please visit:
World Association of Medical Editors (WAME) http://www.wame.org
Declaration of Helsinki http://www.healthscience.net/resources/declaration-of-helsinki

Manuscript
• Put it aside for awhile
• Check carefully for technical errors
o Data
o References
o Spelling – use Spell Check but do not rely exclusively on it
• Adhere to journal guidelines regarding all (length, referencing style, etc.)
o Read carefully journal’s Guidelines again and again
• Solicit peer review!

Editorial Reviw (functions)

• Peer Review
• Gatekeeping
• Teaching/Learning

Editorial Structure (types or roles)

• Editorial Staff (e.g., Science, Academic Medicine)
• Editorial Board (honorary vs. active)
• Individual Consultants
• Internal Referrals

How to select journal and reviewers (initially)

• Appropriateness of the paper for the particular journal
• Selection of reviewers (they must be independent from authors and their institutions)
o Areas of Expertise
o General Standards

Editorial Decision
• Decision could be
Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 6
 o Accepted without changes (almost impossible)
o Modify without Necessity to Review it again (minor changes)
o Modify with and Review Again (usually same reviewers)
o Rejected
• “Arbitration” and opportunity for revision may depend on rejection ratio
• Feedback to authors and reviewers

Revising the manuscript

• Respond to all editorial concerns.
• Be deferential; the editor has the gun!
• Reviewers are not infallible

Resubmition (to other journal after being not accepted in the first one)
• Take the advantage of the previous reviews (Clever people are learning!)
• Don’t send manuscript looking like a resubmission (Don’t tell them that you were
refused, advertise your paper according to the scope of chosen journal)
• Keep in mind that you could get the same reviewer!

Evaluating published papers

• Do not assume that a study is good because it was published
• Even at best, all studies have limitations
• Beware of the tendency to focus only on results and conclusions and to trust them!
• The most critical part of a research paper is the Method section

Bibliographic and citation databases

• Bibliographic or citation database?
• With or without full texts
• Multidisciplinary or not
• Including descriptors (classification) or not

Let’s classify databases that you know according to above criteria!

MEDLINE (previously Index Medicus) available for free through Entrez PubMed
programme (interface)
Current Contents (CC) – 7 editions : Agriculture, Biology & Environmental Sciences
(ABES); Social & Behavioral Sciences (SBS); Clinical Medicine (CM); Life Sciences (LS);
Physical, Chemical & Earth Sciences (PCES); Engineering, Computing & Technology (ECT);
Arts & Humanities (AH)
Web of Knowledge (WoK) and its “subset” Web of Science (WoS) (Thomson Reuters,
previously Institute of Scientific Information, Philadelphia) available limited and only
through subscription at http://www.isiknowledge.com (when you are logged in note at the
right side label that you are subscribed through Ministry of Science Education and Sports of
the Republic of Croatia
You can select and search different citation bases (Science Citation Index - EXPANDED,
Social Sciences Citation Index, Arts & Humanities Index, Current Contents, MEDLINE
(different user interface than Entrez Pub Med which is freely available), Journal Citation
Reports – impact factors

Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 7

Scopus (Elsevier) only with subscription at http://www.scopus.com/home.url
Pay attention what you will see in the upper right corner (Brought to you by
Ministry of Science, Education and Sports)
MEDLINE and Current Contents are bibliographic databases, Google Scholar, WoS (WoK)
and Scopus are citations databases because with every indexed publication you can access
all its references and citations (of course only those indexed in the same citation database).
Links to many bibliographic databases, citation bases as well as to guided tutorials and demos
you can find at:
The Central Medical Library of the School of Medicine University of Zagreb
http://smk.mef.hr
Rudjer Bošković Institute Library http://lib.irb.hr/web

A series of short but excellent and readable (“digestible”), well written articles with examples
were published by Thomas M. Annesley during the last three years (2010-2012) in the journal
Clinical Chemistry under the common title Guide to Scientific Writing. Strongly
recommended for reading!
Here are some attractive titles:
− “It was a cold and rainy night”: Set the Scene with a Good Introduction
− The Abstract and the Elevator Talk: A Tale of Two Summaries
− Who, What, When, Where, How, and Why: The Ingredients in the Recipe for a Successful
Methods Section
− Show Your Cards: The Results Section and the Poker Game
− Bring Your Best to the Table
− Put Your Best Figure Forward: Line Graphs and Scattergrams
− Bars and Pies Make Better Desserts than Figures
− The Discussion Section: Your Closing Argument
− Giving Credit: Citations and References
− Passing the Paternite´ Test
− How to Write a Rave Review
− Top 10 Tips for Responding to Reviewer and Editor Comments
− Now You Be the Judge
− Seven Reasons Not to Be a Peer Reviewer—And Why These Reasons Are Wrong

Pay attention also to the article entitled

− An appeal to medical journal editors: the need for a full description of laboratory methods
and specimen handling in clinical study reports
(authors Rifai N, Annesley TM and co-authors) published in several journals. That is
sometimes a case that identical article is re-published by many journals because each journal
wants to inform its readership about important standards (guidelines) agreed by group of
journal editors, compare articles published by Drazen JM and co-authors entitled
− Toward more uniform conflict disclosures: the updated ICMJE conflict of interest
reporting form
that was proceeded by the first version entitled
− Uniform format for disclosure of competing interests in ICMJE journals

Structure, methodology and functioning of scientific work II – Hand-outs 18-5-2013 8