Scientific writing janssens 2016

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Lisbon, September 2016
Dr. Barbara Janssens, Career Manager
Scientific Writing
www.wordle.net
www.slideshare.com/barbaja
© Janssens Aug-16 - Scientific Writing2
The chicken and the egg
Science Editing
Publishing
Science Career
Advising

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© Janssens Aug-16 - Scientific Writing
Van Dijk et al., Curr. Biol. 2014
DOI: http://dx.doi.org/10.1016/j.cub.2014.04.039
Publication metrics and success on
the academic job market

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Job applications:
Straight to the top of the pile
 http://www.nature.com/naturejobs/science/articles/10.
1038/nj7410-241a
Five top tips for your job application
 1. Imagine YOU are the recruiter
 2. Learn to present yourself in an “elevator pitch”
 3. Actively network
 4. Most important FIRST
 5. Tell stories
 http://youtu.be/FH0Hvk2tp-M

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Deese and Kaufman, J. Exp. Psychol. 1957, 54, 180-187.
Murdock , J. Exp. Psychol. 1962, 64, 482-488.
Serial position effect
Recall
Primacy Recency
t
7
most important first!
© Andrew Moore
I’m hungry...
Mustn’t forget
to do the shopping...
Drain needs
unblocking!!
Adapted from Andrew Moore
What scientists write
 Papers
 Curriculum vitae
 Grants, Fellowships
 Reports
 Proposals
 Web pages
 Conferences
 Lectures
 Meetings
 Posters
 ...

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Think of your audience/reader
 Poster – conference
 Fellowship – review committee
Personal selection – criteria (formal, CV, host)
 Grant – reviewers
Long-term planning
 Job application – recruiter
 Paper – journal peer review
Imagine you are the recruiter/reviewer!
Scientific Writing
 www.slideshare.net/Barbaja

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Scientific ...Writing <-> ...career
 Writing, editing, career development
 A career in science/publishing
 About publishing and impact
 Journals and impact
 Titles and Abstracts
 Tips on language/style
 Writing a paper
 IMRAD structure
 How to get started & „sculpt“
 How to submit with cover letter
 Writing a job application
 Publication ethics
 Author (to be or not to be?)
 Plagiarism (never copy-paste?)
 Science Communication with the Public
 http://www.slideshare.net/Barbaja
 Cargill et al. Writing Scientific Research Articles
 Nancy Fox The little book of scientific writing
 Peer reviewed publications
 Publishers
 Societies
 Magazines
 Scientific American, New Scientist, …
 Spektrum der Wissenschaft (npg)
 Public communication
 Science in School
 Cancer Prevention Service
 Helmholtz Open Science Coordination
 Science Open
Publication landscape

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 PubMed/Medline
 Google (Scholar)
 Scopus (Elsevier)
 CrossRef
 BioMed experts
 Open Access journals
 ISI Web of Science (Thomson)
Where do you find publications?
 Elsevier 2500 journals (Lancet, Cell), 33k books
 John Wiley &sons/Wiley-VCH -> Wiley-Blackwell
 Wiley 1500 journals, 16k ebooks
 EMBO Press 4 journals
 Nature (npg) 162 journals /Macmillan
 Springer 2400 journals, 170k books
 BioMedCentral 300 j
 Springer Nature
 Open Access:
 PLoS
 eLIFE
 Etc etc…
Publishers

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Elsevier
21%
Npg Springer
12%
Wiley
11%
Other
56%
% of articles 2015
Mergers and Acquisitions…
http://scholarlykitchen.sspnet.org
Peer Review principle
Submission
Editorial
Decision
Reject
Peer review
Revision
Editorial
Decision
Referee
recommendation
Accept

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Referee questions
1. Is the subject matter suitable for publication in XXX?
2. Does the manuscript contain new and significant
information to justify publication?
3. Is the technical quality of the paper adequate for
publication?
4. Are the interpretations and conclusions justified by
the results?
5. Is the summary (abstract) informative and concise?
6. Is the English satisfactory?
7. Do the references adequately refer to related work?
Do you peer-review?
 Closed
 Single blind (author doesn‘t know reviewer)
 Double blind (reviewer also doesnt know author)
 Triple blind (editor also doesnt know the author)
 Open
 Author, Editor and Reviewer all know eachother
 Possibly published
 Post-publication peer-review

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Peerageofscience.org
Transparent Process (EMBO press)

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Peer review process file (RPF)
The Editor writes…

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Most accessed – most cited
Impact Factor (IF)
Devised by Eugene Garfield, founder of ISI (Chairman
Emeritus of Thomson Scientific)
1955
Adapted from Matteo Cavalleri

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Impact Factor (IF)
 IF = average number of times articles from the journal
published in the past two years have been cited in the
JCR year.
 www.webofknowledge.com - Thomson Reuters
time
Year
1
Year
2
Year
3
Articles
published
A1 A2
C12
Citations
published
Slide adapted from Matteo Cavalleri
IF (Year 3) = C12 /(A1+A2)
All citations from all publications?
 No
 WOS is selective on coverage
 covers 12,000 journals…
 … from a total of 40-50,000
 Coverage depends on topic
 Ecology 65%
 Geology 55%
 Nursing 45%
 Information sciences 33%
 History 9%
 Molecular Biology/Biochemistry (80)%
 FT Krell, Eur J Sci Editing 2012, 38 (1). www.ease.org.uk

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Cites per paper in 2 years?
 Since 2007: 5-year IF
 Eigenfactor
 Citations to 5 years
 Considers from which journals cites come
 Self-citations (from same journal) not considered
 Article Influence
 = Eigenfactor /(# articles in 5 years)
 Average (mean) AI = 1.00
The h factor
 A scientist has index h if h of [his/her] Np papers have at
least h citations each,
 and the other (Np - h) papers have at most h citations
each.

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The SNIP
 Since 2010 SNIP = Source Normalized Impact per Paper
 SNIP (Journal)= RIP/CP
 RIP = Raw Impact per Paper
 CP = Citation Potential
 (average number of references in the articles that cite a given journal)
 Only cited references from articles in the census period,
and which refer to articles within the target period are
counted
 Only cited references indexed in the Scopus database are
counted
 www.scopus.com
The SJR Scimago Journal Ranking
 SCImago Journal Rank (SJR) is a prestige metric
based on the idea that ‘all citations are not created
equal’.
 the subject field, quality and reputation of the journal
have a direct effect on the value of a citation.
 http://www.scimagojr.com/

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Web of knowledge
JCR Journal citation reports

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IF = cites y3 / items y1+2
Items
…
Who cites?
av. 1.0
Pick a rising star?

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But watch out for Journal self-cites!
(Energy Educ Sci Tech discontinued in 2012)
Self-citations vs Journal banned

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The author and the IF
 It‘s not all up to senior scientists...
 Chose the target journal and priorities
 Market your article, not just the journal
 Expert rating
 Cited, accessed, bookmarked xx times
 Press release, Higlights/columns, blogs
 Talks and presentations
 ... Perception counts more than the IF
 ...“publish or perish“
Albert Einstein
 "Not everything that can be counted counts, and not
everything that counts can be counted."

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Before writing…
 What would you do?
 Read read read...
 Be critical! What is easy to understand? Well written?
 Journal clubs!
 Assemble data
 Which journal/scope?
 Which format?
 Who will be author?
 Check instructions to authors!
Select target journal
Journal XXX XXX
Publishes similar work?
Scope/recent content?
Quality/impact?
Fast publication?
Charges for pages, color,
open access?
Article format/length?

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Journal Author Name Estimator JANE
 http://www.biosemantics.org/jane/
Title
 The first impression counts...
 A strong title will attract readers/citations
 Keep it short: 15 words
 Clear, informative, raise curiosity
 Interesting and easy to read
 Main message of the paper
 Remember Medline
 Key words
 Start with a „quick go“, remodel during writing process and
rethink for some days when the whole manuscript is ready
 Test: http://www.lulu.com/titlescorer

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Examples: compare
 “The X-ray crystal structure of the complex formed
between a recognition domain on a sensor histidine
kinase (CheA) and its cognate response-regulator
(CheY) reveals insights into the mechanism of signal
transduction in bacterial chemotaxis.”
 “Structure of the CheY-binding domain of histidine
kinase CheA in complex with CheY.”
Titles to avoid
 Vague titles
 Titles starting with
 “Studies on..” “Implications of…”
 “Involvement of…” “Observations on...” “Evidence for…”
 “Investigations into...” “Insights in…” “Characterization
of...”
 “The involvement of this in that”
 -> “This does that in signal transduction pathway xx”
 Titles with jargon or abbreviations
 Titles with “new” and “novel” (all research is new)

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Keywords
 Donot repeat title words – these come up anyhow
 Most cited versus never cited...
 Try out in PubMed:
 possibly your keywords should be obvious and short but
bring less hits (and rather your than a competitor‘s
article!)
Title syntax
 “Preliminary canine and clinical evaluation of a new
antitumor agent, streptovitacin.” (Clin. Res. 8:134, 1960)
 „Evidence for women dreaming more often about food
than men.“
 ...

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Deese and Kaufman, J. Exp. Psychol. 1957, 54, 180-187.
Murdock , J. Exp. Psychol. 1962, 64, 482-488.
Serial position effect
Recall
Primacy Recency
t
47
Write at beginning!
Adapted from Andrew Moore
I’m hungry...
Mustn’t forget
Drain needs
unblocking!!
Have a look at titles
Never cited...........well cited
Reviews
Yoghurt fermentation at elevated temperatures by
strains of Streptococcus thermophilus expressing
a small heat-shock protein: Application of two-
plasmid system for constructing food-grade strains
of Streptococcus thermophilus
New insights into mechanisms of growth and b-
carotene production in Blakeslea trispora
Research Articles
Separation of catechin compounds from different teas
Production and characterization of theromstable α-
amylase by thermophilic Geobacillus
stearothermophilus
Molecular characteriazation of rpoB gene mutations in
rifampicin-resistant Mycobacterium tuberculosis
strains isolated from TB patients in Belarus
Investigating pH and Cu(II) effects on lipase activity
and enantioselectivity via kinetic and
spectroscopic methods
Metabolic flux analysis of the two astaxanthin-
producing microorganisms Haematococcus
pluvialis and Phaffia rhodozyma in the pure and
mixed cultures
Reviews
Essential fatty acids: Biochemistry, physiology and
pathology
Metagenomics: An inexhaustible access to nature‘s
diversity
Production of biopharmaceuticals and vaccines in plants
via the chloroplast genome
Application of inkjet printing to tissue engineering
Research Articles
Arenicola marina extracullar hemoglobin: A new
promising blood substitute
Directed evolution of industrial biocatalyst 2-deoxy-D-
ribose-5-phosphate aldolase
Bio-electrosprays: The next generation of electrified jets
A rapid, high content, in vivo model of glucocorticoid-
induced osteoporosis

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More titles from JCS
1. Suppression of synaptotagmin II restrains phorbolester-
induced downregulation of protein kinase C alpha by
diverting the kinase from a degradative pathway to the
recycling endocytic compartment
2. Identification of an alpha-tubulin mutant of fission yeast
from gamma-tubulin-interacting protein screening: genetic
evidence for alpha-/gamma-tubulin interaction
3. Genetic and molecular interactions of the Erv41p-Erv46p
complex involved in transport between the endoplasmic
reticulum and Golgi complex
4. Kendrin/pericentrin-B, a centrosome protein with
homology to pericentrin that complexes with PCM-1
5. Regulatory mechanisms governing the oocyte-specific
synthesis of the karyoskeletal protein NO145
6. Association of human ubiquitin-conjugating enzyme
CDC34 with the mitotic spindle in anaphase
7. Inactivation of MAPK in mature oocytes triggers
progression into mitosis via a Ca2+-dependent pathway
but without completion of S phase
8. Repression of Wnt-5a impairs DDR1 phosphorylation and
modifies adhesion and migration of mammary cells
1. Secreted antagonists of the Wnt signalling
pathway
2. PKB/Akt: a key mediator of cell
proliferation, survival and insulin
responses?
3. Metalloproteinase inhibitors: biological
actions and therapeutic opportunities
4. Clonal mesenchymal progenitors from
human bone marrow differentiate in vitro
according to a hierarchical model
5. SH3 domains: complexity in moderation
6. Cell adhesion and motility depend on
nanoscale RGD clustering
7. Mechanisms of capacitative calcium entry
8. Release of an invasion promoter E-
cadherin fragment by matrilysin and
stromelysin-1
Abstract
© Janssens 2014 - Scientific Writing
 Hardest part to write
 Second most important part
 Maximum 200 words (Medline truncates at 250 words)
 What are the significant results?
 Important methodology (in vitro vs. in vivo, human, model
systems)
 What are the conclusions/implications?
 Start with writing these in bullet points and take time to re-
re- and re-write this part with some distance
 Write in PAST TENSE
 NO citations, avoid non-standard abbreviations

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Optimize abstract
 Be specific, not just one word
 e.g. women's fiction not fiction.
 Key phrases need to make sense within the title and
abstract and flow well.
 Focus on a maximum of three or four different keyword
phrases rather than try to get across too many points.
 Finally, always check that the abstract reads well,
remember the primary audience is still the researcher not a
search engine, so write for readers not robots.
 http://authorservices.wiley.com/bauthor/
Language tips
 Be cautious with imprecise words:
 Several, some, many, affected, somewhat, quite,
relatively
 Don‘t add doubt unnecessarily. Could you replace...
 Could -> can
 Would -> will
 Hopefully -> Possibly
 Difficulty -> challenge

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Structured abstract
 BACKGROUND: Infections due to methicillin-resistant Staphylococcus aureus have
become increasingly common in hospitals worldwide. S aureus continues to be a cause
of nosocomial bacteremia. METHODS: We analyzed the clinical significance (mortality)
of MRSA and methicillin-susceptible S aureus bacteremia in a retrospective cohort study
in a 2900-bed tertiary referral medical center. Survival and logistic regression analyses
were used to determine the risk factors and prognostic factors of mortality. RESULTS:
During the 15-year period, 1148 patients were diagnosed with nosocomial S aureus
bacteremia. After controlling potential risk factors for MRSA bacteremia on logistic
regression analysis, service, admission days prior to bacteremia, age, mechanical
ventilator, and central venous catheter (CVC) were independent risk factors for MRSA.
The crude mortality rate of S aureus bacteremia was 44.1%. The difference between the
mortality rates of MRSA (49.8%) and MSSA bacteremia (27.6%) was 22.2% (P < .001).
Upon logistic regression analysis, the mortality with MRSA bacteremia was revealed to
be 1.78 times higher than MSSA (P < .001). The other predicted prognostic factors
included age, neoplasms, duration of hospital stay after bacteremia, presence of
mechanical ventilator, and use of CVC. CONCLUSIONS: Resistance to methicillin was
an important independent prognostic factor forpatients with S aureus bacteremia.
PMID: 18313513 [PubMed - indexed for MEDLINE]
 http://www.nlm.nih.gov/bsd/policy/structured_abstracts.html
Structured abstract
 Developed in the late 1980s and early 1990s to assist
health professionals in selecting clinically relevant and
methodologically valid journal articles
 Mainly medical
 Makes text mining (search engines) easier
 Could start to be used in life sciences (MedLine
encourages)

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Graphical abstract
 Started in chemical journals
 VISUALISE the main message in ONE figure
 Chemical reaction
 Signal transduction pathway
 Hypothesis
 Structure
 Etc…
LAY abstract
 Sometimes asked at submission
 Summary for non-expert
 Here you CAN say why it is new
 Always write this, it can be useful
 In cover letter to convince Editor
 After acceptance to highlight your work
 To explain your friends and family

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Edit title/abstract
 Title: short? Main message? What first?
Provide 2 alternative titles to chose from
 Mark key statements
Do you get what it is about?
What could be left out?
 First and last sentence: strong?
 Positive wording
 Sentence length
 …
 What would you write in a “lay” abstract?
Scientific Writing
 Introduction and basics
 Mutual introductions
 About journals and peer review
 Online access and searches, IF
 Before writing
 Writing
 IMRAD structure
 How to get started & ‘sculpt’
 How to submit with cover letter
 ----
 Application writing
 Science communication

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Style = Clarity
 Write to be understood
 Think of your audience
 Make information accessible
 Make reader feel comfortable
 THINK what you want to say
 Clear thinking = clear writing
 Arrange your thoughts in a logical order (MIND MAP)
 Errors don‘t always affect the meaning
Errors vs meaning
© M. Cargill - Scientific Writing

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Errors vs meaning
© M. Cargill
# languages…
© Janssens 2014 - Scientific Writing
 … different challenges!
 Sentences too long/too short
 False friends
 Commas

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www.nature.com/scitable

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Sentence structure
 Simple
 Precise
 Concise
 Topic near the beginning!
 Active tense where possible
 KISS
 Keep
 It
 Short and
 Simple

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Sentence structure
 Which sentence is easier to understand?
 The primary site of contact with airborne allergens,
irritants, pathogens and other proinflammatory agents is
the pulmonary ephithelium
 The pulmonary epithelium is the primary site of contact
with airborne allergens, irritants, pathogens and other
proinflammatory agents
Sentence structure
 Often splitting in two is better, even if result is longer:
 Wiley-VCH is a Weinheim, Germany, global STM
publisher specialized in chemistry and life sciences,
belonging to the Wiley-Blackwell group.
 Wiley-VCH is a publishing house located in Weinheim,
Germany. As a part of the global Wiley-Blackwell
scientific/technical/medical (STM) program, it is
specialized in Chemistry and Life Science publications.

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Paragraphs
 Units of thought, not length
 Provide visual relief
 Contain related thoughts
 Thoughts in logical order
 Consistent organization
 Use topic sentences
 At beginning or end
 Rarely in the middle (unless preceding is transitional)
I’m hungry...
Mustn’t forget
Drain needs
unblocking!!
recency
recall
primacy
t
PI3K
© Andrew Moore
Serial Position Effect

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Which/that
 Which/that: relative clauses
 Defining clause: NO comma
 That/which in UK, only that in US
 No comma
 Non defining clause: comma
 , which ((by the way)) ….
 Not essential to basic meaning
 Comma before which
 Land which/that is surrounded by water is an island.
 Tasmania, which is surrounded by the waters of Bass
Strait, is an island of great natural beauty.
www.writeresearch.com.au
The comma: A matter of life and death?
 “Panda: large black and white bear-like mammal,
native to China. Eats, shoots and leaves.” [1]
 Help the reader understand!/list information
 Before the “and” is optional
 To date, …
 Use commas as you would salt and pepper: don’t
overdo it!
[1] Truss, L., Eats(,) Shoots and Leaves, Profile Books Ltd., UK 2003
Fay Wolter, BiotecVisions April 2011

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© Janssens Aug-16 - Scientific Writinghttp://www.facebook.com/sujaybarc73
Active vs passive (p.39)
 Avoid passive (is, was, are, being...)
 Use active: the subject of the sentence performs an action
 The man was bitten by the dog - pass
 The dog bit the man - active
 Only use passive if you cannot use the „we“ form
 Gel electrophoresis was used - pass
 We used gel electrophoresis – active
 Example from Adam Ruben
 ACTIVE VOICE: We did this experiment.
 PASSIVE VOICE: This experiment was done by us.
 SEMI-PASSIVE VOICE: Done by us, this experiment was.
 Yes, for the semi-passive voice, you’ll want to emulate Yoda. Yoda,
you’ll want to emulate.
A. Ruben
dx.doi.org/10.1126/science.caredit.a1200033

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Anthropomorphism
 = assigning actions that can only be performed by
humans to non-living subjects. Subjects like method,
theory, research, table, figure, etc. cannot determine,
conclude, find, summarize, compare, or actively “act”
as human subjects do
www.biotecvisions.com
Anthropomorphism Solution
HPLC was able to determine
the composition.
We determined the
composition by HPLC.
The research found… The researchers found…
Table 1 summarizes the
results…
The summary in Table 1.
Figure 1 compares activities
at 4°C and 37°C.
Activities at 4°C and 37°C are
compared in Table 1.
Our hypothesis says… We hypothesize…
Some rules
 Shun and avoid the employment of unnecessary, excess extra words.
 Make certain all sentences are full and complete. If possible.
 Avoid cliches like the plague.
 Take pain's to spell and, punctuate correctly.
 BE Consistent.
 Don't approximate. Always be more or less precise.
 Sedulously eschew obfuscatory hyperverbosity or prolixity.
 Avoid pointless repetition, and don't repeat yourself unnecessarily.
 Always try to remembr t he/E extreme importance of being accurit; ne
at, and carfful.
 Don't use no double negatives.
 Don't never use no triple negatives.
 All generalizations are bad.
 Take care that your verb and subject is in agreement.
From
http://www.union.edu/PUBLIC/BIODEPT/wicked.html

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Some rules ii
 A preposition is a bad thing to end a sentence with.
 Don't use commas, which aren't necessary.
 "Avoid overuse of 'quotation' marks."
 Writing carefully, dangling participles must be avoided.
 And don't start a sentence with a conjunction.
 Reserve the apostrophe for it's proper use and omit it when its not necessary.
 Avoid run-on sentences they are hard to read.
 Proofread carefully to see if you any words out.
 Never use that totally cool, radically groovy out-of-date slang.
 Avoid those long sentences that just go on, and on, they never stop, they just
keep rambling, and you really wish the person would just shut up, but no, they
just keep on going, they're worse than the Energizer Bunny, they babble
incessantly, and these sentences, they just never stop.
 From http://www.union.edu/PUBLIC/BIODEPT/wicked.html
If you don‘t know…
 Google!!
 Merriam Webster (US) or Oxford
 www.merriamwebster.com
 www.oed.com
 Software ConcApp p.130
 www.edict.com.hk/pub/concapp/
 Build your own corpus (articles) of english journal articles
 Search gives you CONTEXT of search words
www.writeresearch.com.au

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Funny syntax...
 “A large mass of literature has accumulated on the cell
walls of staphylococci.” (From a MS submitted to the editor
for publication in J. Bacteriol.)
 “….He presented evidence that women who smoke are
likely to have pulmonary abnormalities and impaired lung
function at the annual meeting of the American Lung
Association.” (From a Press release)
 “THF is a single heat-stable polypeptide isolated from calf
thymus composed of 31 amino acids with a molecular
weight of 3,200.”
 “For sale, fine grand piano, by a lady, with three legs.”
 “For sale, German Shepherd dog, obedient, well trained,
will eat anything, very fond of children.”
From Martin Welch, BIOCAM course
First letter… brain does the rest
http://www.positscience.com/games-teasers/brain-teasers/teasers/scrambled-text

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Now the manuscript

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Start To WRITE…
• “The time to begin writing an article is when you have
finished it to your satisfaction. By that time you begin to
clearly and logically perceive what it is you really want
to say.” (Mark Twain, 1902)
• 1) Have something to say
2) Say it
3) Stop as soon as you have said it (Billings, J., An
address to our medical literature. Brit. Med. J. 1881, xx,
262-268)
• NOT instant messaging, tweeting, status updating...
(that‘s marketing AFTER your publication)
Manuscript draft
- IMRAD -
 Title
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Figures and Tables
 Cover letter

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43
Writing order?

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44
...writing order
 Title
 Abstract
 Results
 Introduction
 Discussion
 Cover letter

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45
...writing order
 Title
 Abstract
 Results
 Introduction
 Discussion
 Cover letter
Start with the data
 This will cut your writer‘s block!
 (Pictures of gels, graphs etc)
 Order in Figures: write legends
 What is the story?
 (Title, abstract draft)

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46
www.ScienceMatters.io
Publish data first, then stories?
Figures
 Should tell the story - quick readers will read the
abstract and check the figures
 Are the data comprehensive?
 Not too many panels (6)
 If too many data: provide as supporting material
 Think: what do I need to convince the reviewer? What
is the minimum to satisfy a reader without “losing the
forest because of the trees”? e.g. No need to repeat
all different conditions as a proper figure
 Include a concluding visual scheme, diagram,
overview

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47
Figures II
 Detail how many times the experiments were
performed
 Detail the number of animals/replicates
 Provide clear statistical analyses
 Should enable the reader to fully understand the
figure
 Ensure everything is described: abbreviations,
symbols etc.
Figure or Table?
 Table
 Recording data (raw or processed)
 Showing actual data values, precision
 Multiple comparisons
 Has a short title and footnotes
 Figure
 Showing trend or picture
 Shape rather than numbers
 Compare few elements
 Has a legend with all details needed

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48
Keep source data! Statistics…
Clinical trial data online
 Online archive of ALL trial data
 Data protection issue…
 …But it will come
 Statistal analysis: some journals require author to pay
for cost of second analysis if needed
 Sometimes data need to be reanalysed decades after
publication

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49
Image processing
 Regulations by Rockefeller University Press
 (now adopted by most journals)
 No specific feature within an image may be enhanced,
obscured, moved, removed, or introduced.
 Adjustments of brightness, contrast, or color balance are
acceptable if they are applied to the whole image and as long as
they do not obscure, eliminate, or misrepresent any information
present in the original.
 The grouping of images from different parts of the same gel, or
from different gels, fields, or exposures must be made explicit by
the arrangement of the figure (e.g., dividing lines) and in the text
of the figure legend.
 If the original data cannot be produced by an author when
asked to provide it, acceptance of the manuscript may be
revoked.
http://www.councilscienceeditors.org/i4a/pages/index.cfm?pageid=3363
MANIPULATION OF BLOTS
B
r
i
g
t
h
n
e
s
s
a
n
d
c
o
n
t
r
a
s
t
a
d
j
u
s
t
m
e
n
t
s
.
Rossner M , Yamada K M J Cell Biol 2004;166:11-15© 2004 Rockefeller University Press

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Figure 2:
A B
Results
 Follow the figures: Present the experiments performed in a
logical and clear manner. Why did this lead to the next
experiment?
 Written in the PAST TENSE
 Provide statistical analysis and clearly indicate significant data
 Cite relevant literature but only the FACTS to understand (as
previous studies showed XXX [23] we tested the cells with
XXX). Comparing is for the discussion
 Do not lose in technical details („we transfected and then
purified cell extracts and then separated...“): these go to the
M&M
 Be SELECTIVE
 Present your results ONCE, either in the text, OR a Table OR
Figure

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Materials & Methods
 Should be concise but complete
 Written in PAST TENSE
 DO NOT include any results!
 A colleague should be able to repeat the experiment
 All new reagents, sequences, etc should stated;
 New method: provide ALL detail
 Standard procedures: cite and only mention modifications
 If too lengthy: decide afterwards if parts can be cut or
removed to supporting information
 Write 20 mL (not ml), 5 mm, 3 min (not mins), kDa (not
Kda; molecular mass – not weight), M (not mole)
 Check chemical nomenclature www.chem.qmw.ac.uk/iubmb
Funny M&M
 “After standing in boiling water for an hour, I loaded the
sample on a gel…..”
 “Blood samples were taken from 48 informed and
consenting patients….. the subjects ranged in age from 6
months to 22 years.” (Pediatr. Res. 1972, 6, 26)
 “Employing a straight platinum wire rabbit, sheep and
human blood agar plates were inoculated….”
 “Lying on top of the small intestine, we observed a small
transparent thread”
 “In this experiment, one third of the mice were cured by the
test drug, one third were unaffected by the drug and
remained moribund, and the third mouse got
away.”(Reputedly from a MS submitted to Infection and
Immunity)
From Martin Welch, BIOCAM course

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52
Introduction
 Entrance to manuscript
 Make sure referees/readers continue to read
 3 major stages: Country, city, house
1. Broad general statement, what is known, present tense
(also non-expert understands)
2. Justification for study, research gap, need (interesting?)
3. Aim (start with this). State your principal results and
conclusions in one sentence
Discussion
 QUICKLY summarize the findings
 This is not just the results presented in another format, they
need to be discussed in the wider context of the field
 What are the implications for future work?
 Systematically compare findings with supporting and/or
conflicting literature
 Discuss implications and applications, future directions to take
 Be clear, honest, don‘t over-interprete but also don‘t minimize
 Are there any models/rules that can be established?
 If it was a model system, what are the implications for the
human system? Parallels, differences?
 If primarily in vitro studies, what is the scope for further in vivo
studies? Relation to published in vivo studies?

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...writing order
 Title
 Abstract
 Results
 Introduction
 Discussion
 Cover letter
Last but not least: Cover letter
 Convince the editor of the importance of your work
 State in a few sentences what the paper is about (not
abstract)
 Why does it fit the scope of the journal?
 Why is it novel?
 Why will it be of interest to reviewers? If you state
non-preferred reviewers, you may explain why
 Write this for the EDITOR

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54
What the Editor wants?
 OURS
 Originality
 Understandibility
 Reliability
 Suitability
 Poorly written or conceived papers will be rejected
editorially
Cover letter example
 Dear Dr. Brown,
 Please find attached the manuscript „Arbuscular mycorrhizal associations of
the southern Simpson Desert“. This manuscript examines the mycorrhizal
status of plants growing on the different soils of the dune-swale systems of the
Simpson Desert. There have been few studies of the ecology of the plants in
this desert and little is known about how mycorrhizal assocaitions are
distributed amonst the desert plants of Australia. We report the arbuscular
mycorrhizal status of 47 plant species for the first time. The manscript has
been prepared according to the journal‘s Instructions fo Authors. We believe
that this new work is within the scope of your jounal and hope that you will
consider this manuscript for publication in the Australian Journal of Botany.
 We await your response and the comments of reviewers.
 Yours sincerely,

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55
Cover letter quotes
 “It gives me immense satisfaction to be able to share with
you an additional application of….”
 “We, the Arthurs of this mansucript …”
 “The conception of Chapter 1..”
 “We hope that paper should priority handing”
 “I would like to express my honour to submit our hard
work to your respected journal”
 “Dear Sir, Thank you for the sweet reviewing process and
find here the responce for the reviewers comments”
 “After deep thinking of the comments, we made statement
as follow:”
Thanks to Lucie and Uta, EJLST and ELS
Job application cover letter....
 Different?
 Tell STORIES – EXAMPLES of skills
 STAR
Situation
Task
Action
Result
 I‘m a very organised person.
 For example I introduced Trello to organise our student
conference 2016, which saved time and got us excellent
feedback from invited speakers.

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56
Scientific Writing
 Introduction and basics
 introduction
 About journals and peer review
 Online access and searches, IF
 Before writing
 The manuscript - IMRAD
 Authorship
 Plagiarism
Authors

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57
Authors
 Author = significant contributor
 Providing reagents, scientific/moral support = acknowledgement
 First author =„paternity“ („the one without whom the work could
not have been accomplished“)
 Last author =„Senior author“ (often the group leader or head of
Department)
 Corresponding author (usually first and/or last) = assumes
responsibility for writing, submiting, revising and answering
questions after publication. Most prestigious.
 „These authors have contributed equally“
 Decide authors and order as early as possible
 Which author you are will be important for your CV – but being
an author in the first place is what matters
International Committee of Medical Journal Editors (ICMJE)
recommends that authorship be based on the following four
criteria:
(1) substantial contributions to the conception or design of
the work; or the acquisition, analysis, or interpretation of data
for the work;
(2) drafting the work 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,
thereby ensuring that questions related to the accuracy or
integrity of any part of the work are appropriately
investigated and resolved.114
Authors ICMJE

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58
Authors
 FIRST AUTHOR: Weary graduate student who spent hours
doing the work.
 SECOND AUTHOR: Resentful graduate student who thinks he
or she spent hours doing the work.
 THIRD AUTHOR: Undergraduate just happy to be named.
 FOURTH AUTHOR: Collaborator no one has ever met whose
name is only included for political reasons.
 FIFTH AUTHOR: Postdoctoral fellow who once made a chance
remark on the subject.
 SIXTH AUTHOR: For some reason, Vladimir Putin.
 LAST AUTHOR: Principal investigator whose grant funded the
project but who hasn’t stood at a lab bench in decades, except
for that one weird photo shoot for some kind of pamphlet, and
even then it was obvious that he or she didn’t know where to
find basic things.
A. Ruben
dx.doi.org/10.1126/science.caredit.a1200033
Ghost or guest authors?
 Ghost authors: individuals not named as authors but who contributed
substantially to the work
 Guest authors: named authors who have not met authorship criteria
 Confidential survey of corresponding authors of 809 articles
 156 articles (19%) had evidence of honorary authors
 93 articles (11%) had evidence of ghost authors
 Flanagin et al., Prevalence of Articles with Honorary Authors and Ghost
Authors in Peer-Reviewed Medical Journals. J. Am. Med. Assoc. 1998, 280,
222-224.
 http://dx.doi.org/10.1001/jama.280.3.222

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Author acknowledged
 From PNAS, EMBO Press…
 Author contributions: A.B. designed research; A.B.,
M.G.K., and J.-E.S. performed research; A.B., M.G.K.,
and J.-E.S. analyzed data; and A.B., M.G.K., and J.-
E.S. wrote the paper.
Ethics/plagiarism
 What is plagiarism?
 The „Guttenberg syndrome“
 Plagiarism is the representation of another person's
words, ideas, or information as if they were one's own
 ... Do not publish previously published work!
 However you may reuse some of your own and
„CITED“ [1] material
 Check COPE - the Committee on Publishing Ethics
(http://www.publicationethics.org.uk/about).
 Check „copyright transfer agreement“

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60
Plagiarism
 Definition (http://plagiarism.org)
 Plagiarism is the representation of another person's words, ideas, or
information as if they were one's own
 Publishers policy
 COPE - Committee on Publishing Ethics
(www.publicationethics.org.uk/about)
 CTA (copyright transfer agreement)
 Crosscheck database (www.crossref.org/crosscheck/)
 Non-for-profit use of DOI (Digital Object Identifier)
 30 Billion websites
 100 Million articles
 100k Journals
 iThenticate: to detect words http://ithenticate.com
Copyright Transfer Agreement CTA
 ……………
 a. Contributors may re-use unmodified abstracts for any non-
commercial purpose. For on-line uses of the abstracts, Wiley-Blackwell
encourages but does not require linking back to the final published
versions.
 b. Contributors may re-use figures, tables, data sets, artwork, and
selected text up to 250 words from their Contributions, provided the
following conditions are met:
 (i) Full and accurate credit must be given to the Contribution.
 (ii) Modifications to the figures, tables and data must be noted.
 Otherwise, no changes may be made.
 (iii) The reuse may not be made for direct commercial purposes, or for
 financial consideration to the Contributor.
 (iv) Nothing herein shall permit dual publication in violation of journal
 -------------------------------
http://onlinelibrarystatic.wiley.com/central/cta/UKscta.pdf

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61
www.publicationethics.org.uk
http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf
Types of Plagiarism
http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf

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62
Manuscript submission system
http://scholarone.com
SIMILARITY REPORT

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63
30% = Plagiarism?
 Individual for each article…
 When the sources are not cited
 High similarity = ethical misconduct -> reject
 Depending on response by author, the Editor may
 inform the head of the research institute and/or
 ban the author from publication for 1-3 years.
 reasonable similarity -> revise -> further consideration
 When the sources are correctly cited
 high degree of flexibility towards e.g. methods and
introduction (up to 250 words, see CTA), but
 If results or conclusions are copied -> reject
 mosaic-type (patchwork) article -> reject
 A review type article -> at least revise
 Hidden plagiarism is still possible (http://plagiarism.org)
SIMILARITY REPORT

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64
~(30)% similarity -> manual check
Not cited High similarity Reject
Ethical misconduct
Inform Head of
Institute and Funding
Ban publicationReasonable similarity
Cited
Results, content
Review Article Revise
250 words
Methods,
Introduction,Abstract
Accept
 http://publicationethics.org/
 Code of Conduct and Best Practice Guidelines
 Flowcharts on how to handle ethical problems
 Database of all cases, advice given and outcome
COPE – commission of pulication ethics

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65
Further reading
Go to get a grant
http://www.nature.com/naturejobs/science/articles/10.10
38/nj7385-429a

9/2/2016
66
 Editing
 Nomenclature and terminology
 Policies and processes
 Peer review
 Ethics
 Publishing and promoting
EASE Science Editors Handbook
http://www.ease.org.uk/
Training for Editors www.ease.org.uk

9/2/2016
67
 http://www.ismte.org/
ISMTE
Intl. Soc. Managing & Technical Editors
Thank you!
"Be yourself. Everyone else is already taken."
- Oscar Wilde
 For questions:
 de.linkedin.com/in/janssens
 www.dkfz.de/careers
 www.slideshare.net/barbaja
 www.facebook.com/phdcareers

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