28 August 2012Ganesha Associates1 Basic Skills for Scientific Research and Publishing. Segment 8. Getting a scientific article published

Ganesha Associates 128 August 2012

Basic Skills for Scientific Research and Publishing.

Segment 8. Getting a scientific article published


What is scientific publishing ?

• Scientific publishing is the process by which scientific progress is communicated to the community.

• So it is an essential part of the scientific process

• If it isn’t published, it isn’t science…

• …and you’ve wasted a lot of the tax-payer’s money

• Scientific publishing is a commercial enterprise


Publishing drives the scientific process

New consensus view

Old consensus view


• Attribution of priority via peer review– It’s new (probably), you were the first !

• Verification via peer review– Your conclusions are clear and plausible, your methodology

appropriate– But your conclusions may still later be proved to be incorrect…

• Communication– Replication, integration into the consensus view– Permanent archive

• Evaluation !!– $$$$$– CAPES Qualis

Getting published is important for you because…


Which journal will you publish in ? (Field: developmental neuroscience)– Tier A: high profile, broad readership journals such as Nature,

Science and Cell

– Tier B: the “highest quality” specialized journals, or less high quality broader journals such as Neuron, Nature Neuroscience, Genes & Development, and Development. If going for breadth, PNAS, Current Biology, EMBO Journal

– Tier C: “safe bet” journals, such as Developmental Biology, J. Neuroscience, BioMedCentral journals

– Tier D: the “just publish it” titles, such as Mechanisms of Development, Experimental Brain Research. Some authors would never publish in these journals – they would just as soon put their work in a drawer


– “If I have a paper which I believe demonstrates a fundamental advance in our understanding of neural differentiation – what path do I take ?”

– “….there are two underlying pressures determining the place to publish: the prestige of the journal and the need to be first.”

– “….if the aim is to ‘establish turf’, if someone else comes out before you in any ‘respectable journal where you trust the quality of the science, then you have lost your ability to stake your claim to that particular piece of ‘turf’.

– If there is more time, authors may go from one top tier journal to another before choosing to go to the next level.”

Which journal will you publish in ? (Field: developmental neuroscience)


Which journal will you publish in ? (Field: cell biology)


The mycology journal ‘ecosystem’– Important journals - Mycology Dept, UFPE (2006)

• Journal of Invertebrate Pathology• Phytopathology• Plant Pathology• Mycological Research• Plant Disease• Applied and Environmental Microbiology• Current Microbiology• Genetics and Molecular Biology• Molecular Plant Pathology• Medical Mycology• Mycopathology• Applied Soil Ecology• ………..and at least 10 more journals!

– Note only three titles contain a reference to mycology !


Ecosystems


Journal hierarchies

• General discoveries of high fundamental importance– Nature

• Discoveries of high fundamental importance within a specialist discipline or field– Journal of Neuroscience

• Confirmatory studies– Generalisation to other species– Qualification of boundary conditions– Brain Research

• Me-too studies, esoteric fields– Brain and Cognition


Implications of discipline-specific journal ecosystems

• Identify the most important journals in your field • Check the impact factor• Remember, every journal has a well-defined role• So read the ‘Aims and Scope’ statements for

each journal carefully• At the same time, make a copy of the journals’

‘Instructions for Authors’, they will be different too


Cell: Aims and Scope

• Cell publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease.

• The basic criterion for considering papers is whether the results provide significant conceptual advances into, or raise provocative questions and hypotheses regarding an interesting biological question.


Genomics: Aims and Scope

• The goal of Genomics is to promote the understanding of the structure, function, and evolution of genomes in all kingdoms of life and the application of genome sciences and technologies to challenging problems in biology and medicine. The scope of the journal is broad and we welcome original, full-length, and timely papers in all of the following areas: – Comparative genomics analysis that yields valuable insights into

conserved and divergent aspects of function, regulation, and evolution– Bioinformatics and computational biology with particular emphasis on

data mining and improvements in data annotation and integration– Functional genomics approaches involving the use of large-scale and/or

high-throughput methods to understand genome-scale function and regulation of transcriptomes and proteomes

– Identification of genes involved in disease and complex traits, including responses to drugs and other xenobiotics

– Significant advances in genetic and genomics technologies and their applications, including chemical genomics


Gastroenterology: Aims and Scope

• Gastroenterology publishes novel clinical and basic studies on all aspects of the digestive system, including the liver and pancreas, as well as nutrition.

• The types of articles Gastroenterology publishes include original papers, review articles, case reports, and special category manuscripts.


Agricultural and Forest Meteorology

• Agricultural and Forest Meteorology is an international journal for the publication of original articles and reviews on the inter-relationship between meteorology and the fields of plant, animal and soil sciences, ecology, and biogeochemistry. Emphasis is on basic and applied scientific research relevant to practical problems in agriculture, forestry, and natural ecosystems. Articles must appeal to an international audience. Theoretical models should be tested against experimental data. Special issues devoted to single topics are also published.


Inside a primary journal: Cell

• Cell was launched in 1974 as the journal of exciting biology.

• Now a part of Elsevier’s Cell Press, a family of ten journals,

• Cell’s Ph.D.-trained scientific editors work with authors, reviewers, and editorial board members with the goal of publishing 26 issues of the most interesting discoveries in biology every year


Cell’s editorial structure

• In-house Editor– Employed by the journal’s publisher to carry out

administrative and copy-editing roles• Editor-in-Chief

– Major figure in the field• Editorial Board

– Represent all of the major sub-fields, act as advisors to the Editor-in-Chief. Usually recognised experts in their respective fields

• Referees– Selected by the Editorial Board, usually an expert in

the specific area covered by the manuscript


Editorial evaluation process - Cell

• All submissions are initially evaluated in depth by the Editor-in-Chief or sent to an appropriate member of the Editorial Board.

• Papers that do not conform to the general criteria for publication will be returned to the authors without detailed review, typically within 3-5 days.

• Otherwise, manuscripts will be sent to reviewers who have agreed in advance to assess the paper rapidly.

• The editors will make every effort to reach decisions on these papers within 3 weeks of the submission date.

• Accepted papers will be published within 3 months of acceptance.


What is the Editor looking for ?

• Plausibility– Is the experimental design robust ?– How effectively have the alternative

hypotheses been excluded ?• Topicality

– Is the work original– Is it interesting ?– Is it relevant ?– Is it useful ?


The most likely outcome of the editorial process is rejection

• Nature, Science, Cell and other top ranking journals have rejection rates of over 95%

• Most high quality journals have a rejection rate of over 80%

• Most journals with an Impact Factor >1 have a rejection rate > 66%

• All Editors want their journals to be better than their rivals.

• So they select only the best articles to publish.• Some manuscripts may not even be sent for full peer

review• Authors of accepted papers will often be asked for

revisions and reductions in length


Define: Triage

A system for allocating scarce resources; it provides the maximum resources to individuals of highest priority, and few or no resources to individuals of lowest priority.

Derived from practices used to prevent medical systems from being overwhelmed when there are many sick or injured.


Triage quality varies

• Journal of Biological Chemistry, Biochemistry, and Biochimica Biophysica Acta all have rejection rates > 80%

• Impact Factors of 7.4, 5.1. 2.5• 21%, 34%, 55% of published articles receive 1

or 0 citations• High Impact Factor journals have higher false

negative rates – they reject a lot that is good• Low Impact Factor Journals have higher false

positive rates – they publish a lot that is not good


The importance of rejection rates


How to avoid rejection ?

Author

Journal staff

Editor-in-Chief

Referees

Publication

Rejection

Rejection

Rejection


Major reasons for rejection - Editors

• Subject falls outside of the aims and scope of the journal

• Subject is not of sufficient importance or novelty for publication in the journal so it will not appeal to a broad audience

• Manuscript not written in the appropriate style or format for the journal

• Manuscript too long• Manuscript incomplete• Quality of English not perfect


The role of peer review

– History– Anonymous– Multiple, to avoid bias– Validation/accreditation– Selecting the best– Or de-selecting the worse ?– Alternatives

• Nature• PLos One


The role of peer review

• A peer is someone who is of the same or equal standing as another. Thus peer review is review performed by individuals considered to be professional equals.

• The process forces authors to meet the standards of their discipline and achieve scientific objectivity.

• Publications and awards that have not undergone peer review are likely to be regarded with suspicion by scholars and professionals in many fields.

• Peer review is important to achieve clear, precise writing. This is just as true for professional scientists as it is for students.

• Peer review can result in acceptance, conditional acceptance or rejection


Peer review – the pros

– A peer is someone who is of the same or equal standing as another. Thus peer review is review performed by individuals considered to be professional equals.

– The process forces authors to meet the standards of their discipline and achieve scientific objectivity.

– Publications and awards that have not undergone peer review are likely to be regarded with suspicion by scholars and professionals in many fields.

– Peer review is important to achieve clear, precise writing. This is just as true for professional scientists as it is for students.

– Peer review can result in acceptance, conditional acceptance or rejection


Peer review – the cons

– A peer is likely to be a competitor. How objective are they going to be ?

– Most articles get published and the quality of articles published in high impact titles such as Nature is highly variable.

– Authors are encouraged by the publishing process to exaggerate their claims and even be selective of the data being published, leading to bias

– Negative findings are rarely published, leading to further bias when judging the effectiveness say of new medical technologies

– “There is increasing concern that most current published research findings are false” John Ioannidis, PLoS 2005


This paper describes clinical and cytogenetic finding in a child with retinoblastoma who had an aggressive fatal course. The authors postulate that this may be related to changes in chromosome 6. However, it is difficult to see how the findings here either promote or negate that hypothesis. In addition several other problems should be addressed:

a. Abstract, line 9: could (not should)

b. Abstract: define IO

c. Staging details at the time of initial diagnosis are inadequate. Were scans done of the head? chest? abdomen? pelvis? bone?

d. One assumes that the right eye was normal at initial diagnosis but this is not stated.

Reviewer comments - example


e.Staging details at the time of initial relapse are inadequate. Were scans done of the head? chest? abdomen? pelvis? bones?

f. What was the csf cytology at the time of initial relapse?

g. What cytologic studies were performed on the ocular, marrow and other tumors at the initial relapse to prove that this was retinoblastoma?

h. What is MADIT?

i. If the authors are going to postulate that chromosome 6 abnormalities are important then other publications require more careful review and more detailed presentation of findings. How does one more case advance the hypothesis?

Reviewer comments – example, cont’d


Author’s Hypothesis:

This case represents a particularly aggressive form of retinoblastoma which can be diagnosed by the observation of a rare chromosomal abnormality

Referees Hypotheses:

The initial treatment of the retinoblastoma was ineffective

But assuming it wasn’t:

Several chromosomal abnormalities described – no evidence that specific chromosomal defect chosen was connected with the disease severity

Reviewer Comments – main problems


A Referee’ Check List

• Taken from the journal Respiratory Care• Structured to focus on each section of the

manuscript


PLoS One• PLoS ONE is an international, peer-reviewed, open-

access, online publication. PLoS ONE welcomes reports on primary research from any scientific discipline. It provides: – Open-access—freely accessible online, authors retain copyright – Fast publication times – Peer reviewed by expert, practicing researchers – Post-publication tools to indicate quality and impact – Community-based dialogue on articles – Worldwide media coverage

• “All papers that make a valuable contribution to the scientific literature, that are replicable, that are clearly written, and whose conclusions are supported by the data deserve publication.”


Neuroscience Peer-Review Consortium• The NPRC was created to reduce the inefficiency that arises

when an author submits a manuscript to a journal after the same manuscript has been reviewed and rejected by another journal.

• In many cases, publication of good manuscripts —which may have been rejected solely because of space or scope limitations— is delayed as editors from each journal attempt to find reviewers, send the reviews, and wait for the reviews to be returned. Often the same reviewer is asked to review the same manuscript multiple times.

• The NPRC streamlines this process by allowing reviews solicited by one journal to be forwarded and re-used by other member journals.

• However, ultimate control of manuscript submission remains in the hands of authors as reviews are forwarded only when the author requests this service.


Introduction

• Is the background information adequate to introduce the research problem ?

• Are the references adequate ?• Are specific study objectives or

hypotheses stated ?• Is the writing in this section clear and

concise ?


Methods• Are there outcome variables described for each

study objective or hypothesis ?• Are there appropriate descriptions of how

calculated values were determined ?• Are outcome variables that do not relate to the

objectives or hypotheses avoided ?• Are the measurement procedures appropriate

for the study objectives or hypotheses ?• Is there enough detail to judge validity and for

readers to replicate the study ?• Were appropriate statistical methods chosen for

this study design ?• Is the writing in this section clear and concise ?


Results

• Are there complete data for each procedure or test described in the Methods section ?

• Do the data, or descriptions on the data, appear to be valid ?

• Are data that do not relate to the study objectives or hypotheses avoided ?

• Are the tables and illustrations adequate ?• Does the text avoid presenting the same data as

the Tables and Illustrations ?• Is the writing clear and concise ?


Discussion

• Is there an explanation of how the results address the problem statement or hypothesis ?

• Are theoretical and practical aspects of the results discussed ?

• Do you agree with the interpretation of the results ?• Is there a comparison of this study with previously

published studies ?• Are the references adequate ?• Is there a discussion of the limitations of the study ?• Is there a section that clearly states the authors

conclusions ?• Is the writing of this section clear and concise ?


Major reasons for rejection - Referees

• Inappropriate or incomplete statistics• Over-interpretation of results• Inappropriate instrumentation• Sample too small or unbiased• Text too difficult to follow• Insufficient problem statement• Inaccurate or inconsistent data reported• Incomplete, inaccurate, or outdated literature review• Insufficient data presented• Defective tables or figures


Main reasons for rejection - Brasil

• Submitted to the wrong journal• Journal aims and scope not followed• Purpose of the work unclear• Work does not relate to current areas of

research interest• Too long• English


Ten simple rules to help you get published– Read many papers, and learn from both the good and the

bad work of others. It is never too early to become a critic– The more objective you can be about your work, the better

that work will ultimately become.– Good editors and reviewers will be objective about your

work.– If you do not write well in the English language, take lessons

early; it will be invaluable later.– Learn to live with rejection.

– Philip E. Bourne, PLoS – http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/jo

urnal.pcbi.0010057

http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0010057



Ten simple rules to help you get published

– The ingredients of good science are obvious - novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion

– Start writing the paper the day you have the idea of what questions to pursue

– Become a reviewer early in your career.– Decide early on where to try to publish your paper.– Quality is everything

– Philip E. Bourne, PLoS – http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/jo

urnal.pcbi.0010057




Some more suggestions to help you get published

– Choosing a problem• Something that you have a personal interest in• is based on a current experimental paradigm recognized by the

international scientific community• for which experimental resources are available, affordable• and for which you have intellectual support, e.g. experimental design,

data interpretation, etc– Mestrado/Doutorado projects

• Choose a supervisor with a good research track record• Specify the research problem during the first year• Try to shape first year course work around these specific needs• Pay more attention to experimental design, not just statistics• Don’t attempt one big experiment, but plan several• Seek progress reviews at regular intervals

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28 August 2012Ganesha Associates1 Basic Skills for Scientific Research and Publishing. Segment 8. Getting a scientific article published