Scientific writing janssens 2017

Brussels, April 2017
Dr. Barbara Janssens, Career Manager
Scientific Writing
www.slideshare.com/barbaja

© Janssens 2017 - Scientific Writing2
The chicken and the egg
Science Editing
Publishing
Science Career
Advising

© Janssens 2017 - 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
Become PI
Leave Academia

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

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
6
most important first!
© Andrew Moore
I’m hungry...
Mustn’t forget
to do the shopping...
Drain needs
unblocking!!

Job applications:
Straight to the top of the pile
 http://www.nature.com/naturejobs/science/articles/10.
1038/nj7410-241a

Scientific Writing
 www.slideshare.net/Barbaja

Scientific ...Writing <-> ...career
 Writing, editing, career development
 A career in science/publishing
 About publishing and impact
 Journals and impact
 Titles and Abstracts
 Writing a grant/paper
 IMRAD structure
 How to get started & „sculpt“
 How to submit with cover letter
 Publication ethics
 Tips on language/style
 Writing an application
 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
 http://www.biotecvisions.com

3 days or 1 hour
 Where do we go shopping today?
 Focus on
 Postdoc Careers e.g. in publishing
 Publishing, peer review, IF
 Titles and abstracts
 Language and style
 Manuscript and Figures
 Ethics & Authorships
 Writing a paper or a CV
 Writing a grant or fellowship

What scientists write
 Papers
 Curriculum vitae
 Grants, Fellowships
 Reports
 Proposals
 Web pages
 Conferences
 Lectures
 Meetings
 Posters
 ...

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

 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

 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

Elsevier
21%
Npg Springer
12%
Wiley
11%
Other
56%
% of articles
Mergers and Acquisitions…
http://scholarlykitchen.sspnet.org

Peer Review principle
Submission
Editorial
Decision
Reject
Peer review
Revision
Editorial
Decision
Referee
recommendation
Accept

Transparent Process (EMBO press)

The Editor writes…

Peer review process file (RPF)

Most accessed – most cited

Impact Factor (IF)
 Devised by Eugene Garfield, founder of ISI (Chairman
Emeritus of Thomson Scientific)
1955
Slide by
Matteo Cavalleri

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)

Citation lifetime

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

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

Citation distribution

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.

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
30
 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/

Bibliometrics....
32
 Web of Knowledge
http://isiwebofknowledge.com
 Scopus
http://www.scopus.com
 Faculty of 1000 (post-publication peer review)
http://f1000.com/
 Australian journal ranking A*, A, B, C
http://www.arc.gov.au/era
A* - one of the best in its field A - very high quality B -
solid, though not outstanding reputation C - journals
that do not meet the criteria of the higher tiers

JCR Journal citation reports
34

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

Self-citations vs Journal banned

Plos one articles
37
0
5000
10000
15000
20000
25000
2009 2010 2011 2012
Plos One Articles

Plos one citations
38
0
20
40
60
80
100
120
140
160
180
0 1000 2000 3000 4000 5000
Citations2011
Articles 2009-2010

Compare journals
39
 Plos One IF 3.7 H index 101
 Nature
 IF 38.6 h 768
 10,000 items for 5,000 articles
 most cited: 1,621 but 600 zero cites (magazine)
 Nature Scientific Reports 2.9
 Biology Open (Company of Biologists) no IF
 Open Biology (Royal Society) 3.6

Energy Educ Sci Tech

Journal self-cites
(Energy Educ Sci Tech)

IF without self-cites

When you cite... -> References
 The references must comply to house style
 Ensure that they are cited in numerical order and that
every reference is cited
 The work cited should be fair and balanced
 Ensure that credit is given to the original discoveries,
including back-to-back publications
 Use a reference manager (e.g. Endnote) and correctly
format the citations and ref list
 Do you read before you cite?
 misprint distribution in citations -> 20% copied
 http://arxiv.org/pdf/cond-mat/0401529.pdf

The author and the IF
 Chose the target journal and priorities
 Optimize title and keywords
 Market the 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“

The DOI
 Cite per DOI (Digital object identifier)
 = Publisher/MSnumber
 http://dx.doi.org
 http://doi.wiley.com/10.1002/biot.2009xxxxx
 Link refers to abstract – send this instead of / before the PDF!
 Market your work!
 Press release
 Higlights/columns
 Talks and presentations
 ... Perception counts more than the IF
 ...“publish or perish“

Your real impact factor

Albert Einstein
 "Not everything that can be counted counts, and not
everything that counts can be counted."

Before writing…
 What would you do?
 Read read read...
 Assemble data
 Which journal/scope?
 Which format?
 Who will be author?
 Check instructions to authors!

Read… but how?
 How do you find articles?
 How do you read them?
 How can you be critical?
 If a paper is difficult to follow/understand: ask yourself
how you like the writing…
 How do you keep track of articles?
 Web of Science
 Self archiving
 Mendeley http://www.mendeley.com/

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?

Journal Author Name Estimator JANE
 http://www.biosemantics.org/jane/

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?

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

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)

Keywords
 Donot repeat title words – these come up anyhow
 Most cited versus never cited...
 Try out in Medline:
 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.“
 ...

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
Write at beginning!
© 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

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
 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

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

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)

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

Edit an abstract
 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’
 ----
 Application writing
 Science communication

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)
https://de.slideshare.net/BarbaraJanssens2

Errors vs meaning
© M. Cargill - Scientific Writing73

Errors vs meaning
© M. Cargill74
Complex Grammar!
Verb modality
Verb tense

# languages…
 … different challenges!
 Sentences too long/too short
 False friends
 Commas

www.nature.com/scitable

Sentence structure
79
 Simple
 Precise
 Concise
 Topic near the beginning!
 Active tense where possible
 KISS
 Keep
 It
 Short and
 Simple

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.

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

Word usage from a to z
 Above ("the above method," "mentioned above," etc.) –
 Affect, effect -- Affect is a verb and means to influence. Effect, as a verb, means to bring about; as a
noun, effect means result.
 All of, both of -- Just "all" or "both" will serve in most instances.
 Alternate, alternative -- Be sure which you mean.
 And or But (to begin a sentence) -- You have been told not to do this in grade school. But …
 Apparently (apparent) -- means obviously, clearly, plainly evident, but also means seemingly or
ostensibly as well as observably. Ambiguity results. Use obvious(ly), clear(ly), seeming(ly),
evident(ly), observable or observably, etc., as needed to remove doubt.
 Appear, appears -- Seem(s)? "He always appears on the scene, but never seems to know what to
do." "Marley's ghost appeared but seemed harmless."
 As -- Dialectal when used in place of that or whether; do not use as to mean because or inasmuch as.
 At the present time, at this point in time -- Say "at present" or "now" if necessary at all.
 But (to begin a sentence) -- Go right ahead (see "And" and "However").
 By means of -- Most often, just "by" will serve and save words.
 Case -- "In the case of Scotch whiskey,...." For "in this case," try "in this instance.“
 Compare with, compare to -- Compare with means to examine differences and similarities; compare
to means to represent as similar.
 http://www.ag.iastate.edu/aginfo/word_usage.php

Word usage from c to h
 Comprise -- comprise meant to contain, include, or encompass (not to constitute or compose)
 Correlated with, correlated to -- things may be related to one another, but are correlated with one another.
 Different from, different than -- One thing differs from another, although you may differ with your colleagues.
 Due to does NOT mean because of. "Due to the fact that..." is an attempt to weasel out.
 During the course of, in the course of -- Just use "during" or "in."
 Either....or, neither...nor -- Apply to no more than two items or categories.
 Etc. -- Use at least two items or illustrations before "and so forth" or "etc."
 Experience(d) -- To experience something is sensory; inanimate, unsensing things (lakes, soils, enzymes,
streambeds, farm fields, etc.) do not experience anything.
 Following -- "After" is more precise if "after" is the meaning intended. "After [not following] the procession,
the leader announced that the ceremony was over.”
 High(er), low(er) -- Much too often used, frequently ambiguously or imprecisely, for other words such as
greater, lesser, larger, smaller, more, fewer; e.g., "Occurrences of higher concentrations were lower at
higher levels of effluent outflow." One interpretation is that greater concentrations were fewer or less
frequent as effluent volume(s) increased, but others also are possible.
 However -- Place it more often within a sentence or major element rather than at the beginning or end.
"But" serves better at the beginning.

Word usage from i to p
 In order to -- For brevity, just use "to"; the full phrase may be used, however, [in order] to achieve
useless padding.
 Irregardless -- No, regardless. But irrespective might do.
 It should be mentioned, noted, pointed out, emphasized, etc. -- Such preambles often add nothing but
words. Just go ahead and say what is to be said.
 It was found, determined, decided, felt, etc. -- Are you being evasive? Why not put it frankly and
directly?
 Less(er), few(er) -- "Less" refers to quantity; "fewer" to number.
 Majority, vast majority -- See if most will do as well or better. Look up "vast."
 Myself -- Not a substitute for me. "This paper has been reviewed by Dr. Smith and myself" -> me
 Partially, partly -- Compare the meanings (see also impartially). Partly is the better, simpler, and more
precise word when partly is meant.
 Percent, percentage -- Not the same; use percent only with a number.
 Predominate, predominant -- Predominate is a verb. Predominant is the adjective; as an adverb,
predominantly (not "predominately").
 Prefixes -- (mid, non, pre, pro, re, semi, un, etc.) -- Usually not hyphened in US usage except before a
proper name (pro-Iowa) or numerals (mid-60s) or when lack of a hyphen makes a word ambiguous

Word usage from p to z
 Principle, principal -- They're different; make sure which you mean.
 Prior to, previous to -- Use before, preceding, or ahead of. There are prior and subsequent events
that occur before or after something else, but prior to is the same kind of atrocious use that attempts
to substitute "subsequent to" for "after."
 Proven -- Although a proven adjective, stick to proved for the past participle. "A proven guilty person
must first have been proved guilty in court."
 Provided, providing -- Provided (usually followed by "that") is the conjunction; providing is participle.
 Reason why -- Omit why if reason is used as a noun. The reason is...; or, the reason is that..
 Since -- has a time connotation; use "because" or "inasmuch as" when either is intended meaning.
 Small in size, rectangular in shape, blue in color, tenuous in nature, etc. -- Redundant.
 That and which – ,(comma) which ((by the way))
 To be -- Frequently unnecessary. "The differences were [found] [to be] significant."
 Varying -- distinguish from various or differing. varying amounts or conditions, you are implying
individually changing amounts or conditions rather than a selection of various or different ones.
 Where -- Use when you mean where, but not for "in which," "for which," etc.
 Which is, that were, who are, etc. -- Often not needed. For example, "the data that were related to
age were analyzed first" means that the data related to age were analyzed first. While -- Preferably
not if, while writing, you mean and, but, although, or whereas.

Recognize
Usage
Errors

Recognize Grammar Errors
RO
rising. However
FP
rashes and sores, and
RO
cavity. Otherwise,
FRAG
. Examples include
RO
correct. Therefore,
MM
, we retested the circuit
FP
voltages and contact
http://writing.engr.psu.edu/exercises

Recognize punctuation errors
http://writing.engr.psu.edu/exercises

misplaced or dangling modifiers and
pronoun antecedent problems
 The difficulty here is that you, as the author, know exactly to which each has reference
even though not explicitly stated. Your reader, however, doesn't have this advantage,
and the result may be confusing, misleading, or funny. EXAMPLES:
 Modifier problems
 "Using multiple-regression techniques, the animals in Experiment I were...
 "Based only on this doubtful inference, we find the conclusions not supported."
 "The determinations were made on samples using gas chromatography."
 "In assessing the damage, the plants exhibited numerous lesions."
 "The spiders were inadvertently discovered while repairing a faulty growth chamber."
 "Settling in the collected effluent, we observed what was determined to be..."
 Ambiguous pronoun antecedents
 "The flavor was evaluated by an experienced taste panel, and it was deemed obnoxious."
 "All samples in Lot II were discarded when the authors found that they were contaminated
with alcohol, rendering them unstable." [and unable to think clearly?]
 "The guidelines were submitted to the deans, but they subsequently were ignored.

, 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

which/that (p. 137)
1 Lime which raises the pH of the soil to a level more suitable for crops is injected into the
soil using a pneumatic injector.
2 Manipulation which involves adding or deleting genetic information is referred to as
genetic engineering.
3 Non-cereal phases which are essential for the improvement of soil fertility break disease
cycles and replace important soil nutrients.
4 Senescence which is the aging of plant parts is caused by ethylene that the plant
produces.
5 Opportunities that arise from the economically buoyant nature of domestic wine
production must be identified and carefully assessed.
6 Seasonal cracking which is a notable feature of this soil type provides pathways at least
6mm wide and 30 cm deep that assist in water movement into the subsoil.
7 Plants which experience waterlogging early in their development would be expected to
have a much shallower root system than non-waterlogged plants.
8 Yellow lupin which may tolerate waterlogging better than the narrow-leafed variety has
the potential to improve yields in this area.
9 Lucerne is a drought-hardy perennial legume which produces high-quality forage.
1 Lime, which raises the pH of the soil to a level more suitable for crops, is injected into
the soil using a pneumatic injector.
2 Manipulation which involves adding or deleting genetic information is referred to as
genetic engineering.
3 Non-cereal phases, which are essential for the improvement of soil fertility, break
disease cycles and replace important soil nutrients.
4 Senescence, which is the aging of plant parts, is caused by ethylene that the plant
produces.
5 Opportunities that arise from the economically buoyant nature of domestic wine
production must be identified and carefully assessed.
6 Seasonal cracking, which is a notable feature of this soil type, provides pathways at
least 6mmwide and 30cm deep that assist in watermovement into the subsoil.
7 Plants which experience waterlogging early in their development would be expected to
have a much shallower root system than non-waterlogged plants.
8 Yellow lupin, which may tolerate waterlogging better than the narrow-leafed variety, has
the potential to improve yields in this area.
9 Lucerne is a drought-hardy perennial legume which produces high-quality forage.

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

English punctuation
© Janssens 2014 - Scientific Writing95 http://files.nothingisreal.com/publications/Tristan_Miller/advice.pdf

Some tips
 Avoid vague terms such as ‘trends’
 Be very precise and clear
 “The cells increased following treatment with” – what
characteristic of the cells increased: size, number?
 Data = results; datum = result; use the correct verb
form (also criteria/criterion etc.)
 Careful with embedded phrases
 Avoid separating subject and verb

http://www.facebook.com/sujaybarc © Janssens 2014 - Scientific Writing97

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

Writing language and style (p. 136)
___ propagule pressure is widely recognized as ___ important factor that
influences ___ invasion success. ___ previous studies suggest that ___
probability of ___ successful invasion increases with ___ number of propagules
released, with ___ number of introduction attempts, with ___ introduction rate,
and with ___proximity to ___ existing populations of invaders.
Moreover, ___ propagule pressure may influence ___ invasion dynamics after
___ establishment by affecting ___ capacity of ___ non-native species to adapt
to their new environment.
Despite its acknowledged importance, ___ propagule pressure has rarely been
manipulated experimentally and ___ interaction of ___ propagule pressure with
___ other processes that regulate ___ invasion success is not well understood.
___ Propagule pressure is widely recognized as an important
factor that influences ___ invasion success. ___ Previous studies
suggest that the probability of ___ successful invasion increases
with the number of propagules released, with the number of
introduction attempts, with ___ introduction rate, and with ___
proximity to ___ existing populations of invaders.
Moreover, ___ propagule pressure may influence ___ invasion
dynamics after ___ establishment by affecting the capacity of ___
non-native species to adapt to their new environment.
Despite its acknowledged importance, ___ propagule pressure
has rarely been manipulated experimentally and the interaction of
propagule pressure with ___ other processes that regulate ___
invasion success is not well understood.
(Britton-Simmons & Abbott 2008, p. 68)

Past vs present tense
 Past tense: for a completed study
 what was done and found
 Present tense: for what is always true or always there
 An example is….
 Modal tense: doubt
 This may influence…

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

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…

Use links
 Transition words
 And, so, therefore, however, in conclusion, nevertheless
 Do not use several words where one will do
 As a means of
 Ask the question
 At the present time
 During the time that
 In order that
 With regard to
 Prior to
 With the exception of
 ...

Rather not use ...
 Seems/appears
 Uncritical
 Undermined
 Confounded
 Inappropriate
 Purported
 Caution
 Limitations
• Restricted
• Unsupported
• Limited
• Compromised
• Somewhat
• Superficial
• Of doubtful value
• Unlikely

Also negative ...
 Unclear
 Uncertain
 Potentially biased
 Controversial
 Debatable
 Unexpected
• Uncontrolled
• Anomalous
Surprising
• Unusual
• Confusing
• Negative

Avoid redundancy
 Present moment in time
 Fewer in number
 Estimate at about
 Whether or not
 Try and endeavour
 True facts

.. Do not be arrogant...
 As is well-known
 It is obvious that
 It will be self-evident that
 Of course
 A not inconsiderable body of evidence...
 Starting sentences with “obviously” or “as everyone knows”
demonstrates your intellectual superiority. If possible, start
sentences with, “As super-intelligent beings like myself know,”
or “Screw your stupidity; here’s a fact-bomb for you.” A. Ruben

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.

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

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

Scientific Writing
 Mutual introductions
 Before writing
 Writing
 IMRAD structure
 How to get started & ‘sculpt’
 ----------------------------------------
 Application writing
 Science communication

Now the manuscript

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

Writing order?

...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)

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

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

Keep source data! Lies, damn lies and
statistics
http://www.slideshare.net/lemberger/editorial-process

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

Figure quality
 resolution should be at least 400 dpi
 to be printed either to fit the width of one column (8
cm) or to fit the width of the page (17 cm)
 Avoid extreme height-to-width ratios (“noodles” and
“skyscrapers”)
 Resizing: Increasing the resolution of an image will
result in a proportionally smaller image size
 20 x 30 cm 96 dpi -> 400 dpi 5 x 7 cm
 do not embed TIFF files in DOC files; JPEG files will not
be compressed

Look at figures in sample articles
 Figure layout
 Information in Figure
 Legend 5 elements
 Title summarizing what it is about
 Details of results
 Additional explanation
 Description of units or statistical annotation
 Explanation of other symbols or units

Chart Resolution
 Excel: scale the chart to at least 400% of the expected
printing size
 Select the chart, copy
 PowerPoint: Edit-“Paste special…“: paste as PNG file

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

Stick to the figure guidelines...

Figure 2:
© Janssens/Mavris 2014 - Scientific Writing135
A B

IMRAD revisited
 Title
 Abstract
 Results
 Introduction
 Discussion
 Cover letter

Results book p. 33
 Format: results or results plus discussion
 Locate figures and tables
 Comments on results
 Use of tense in results
 Past for already completed
 Present for facts and ongoing
 modal

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

Methods book p. 37
 Provide info for other scientists
 Credibility for your work
 Organise this section with headings
 Use of passive and active tense, avoid top heavy
passive
 What to cite
 Textbook not necessary
 Published (recent) yes

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

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

Introduction , book p. 42
 Entrance to manuscript
 Make sure referees continue to read
 3 major stages: Country, city, house
 Broad general statement, what is known, present
 Justification for study, research gap, need
 Aim (start with this)

Introduction
 Provides the background to the study
 Can be written in PRESENT TENSE (= existing knowledge)
 Details the results from relevant published studies (difference
between we demonstrated – it was demonstrated – it has been
demonstrated – it is known)
 Explains what is still unknown
 Describes why the work was carried out and what the aim of the
study was
 Enables a non-expert to understand the rationale
 Try to cite relevant review articles rather than going back to all
basic papers
 State your principal results and conclusions in one sentence
 Decision about what is interesting or not can be left to the
reader

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

Discussion chapter 9 p.59
 Repeat key message
 Elements
 Most important findings
 Explanations
 Limitations
 Implications
 recommencations

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?

References
 The references must comply to house style
 Ensure that they are cited in numerical order and that
every reference is cited
 The work cited should be fair and balanced
 Ensure that credit is given to the original discoveries,
including back-to-back publications
 Use a reference manager (e.g. Endnote) and correctly
format the citations and ref list
 Do you read before you cite?
 misprint distribution in citations -> 20% reads
 http://arxiv.org/abs/condmat/0212043

All sections - Keep it short
 600-700 words = one typeset page - excluding figures. (12000
words = 20 pages)
 Introduction < 1000 words
 Concluding section < 300 words
 Shorten:
 Latest publications of relevance
 Keep details to minimum
 Concentrate on bullet points, 3 key arguments
 Cover only as much historical background as is necessary for
the contextualization of the topic for a broad readership.
 Avoid detailed lists of genes, gene products, acronyms etc. ->
Table

Keep within the page limit

Scientific Writing
 introduction
 Before writing
 The manuscript - IMRAD
 Authorship
 Plagiarism

Authors

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

Authors ICMJE
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.

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

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

Author acknowledged
 From PNAS:
 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“

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

www.publicationethics.org.uk

Types of Plagiarism
© Janssens 2014 - Scientific Writing162 http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf

SIMILARITY REPORT

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)

Not cited = PLAGIARISM
 "The Ghost Writer„ : writer turns in another's work, word-for-word, as his or her own.
 "The Photocopy„ : writer copies significant portions of text straight from a single source,
without alteration.
 "The Potluck Paper„ : writer tries to disguise plagiarism by copying from several different
sources, tweaking the sentences to make them fit together while retaining most of the
original phrasing.
 "The Poor Disguise„: writer has retained the essential content of the source, but has
altered the paper's appearance slightly by changing key words and phrases.
 "The Labor of Laziness„: writer takes the time to paraphrase most of the paper from
other sources and make it all fit together, instead of spending the same effort on original
work.
 "The Self-Stealer„: writer "borrows" generously from his or her previous work, violating
policies concerning the expectation of originality adopted by most academic institutions.
 http://plagiarism.org

Cited but still plagiarism
 "The Forgotten Footnote„: writer mentions an author's name for a source, but neglects to
include specific information on the location of the material referenced. This often masks
other forms of plagiarism by obscuring source locations.
 "The Misinformer„: writer provides inaccurate information regarding the sources, making
it impossible to find them.
 "The Too-Perfect Paraphrase„: writer properly cites a source, but neglects to put in
quotation marks text that has been copied word-for-word, or close to it. Although
attributing the basic ideas to the source, the writer is falsely claiming original
presentation and interpretation of the information.
 "The Resourceful Citer„: writer properly cites all sources, paraphrasing and using
quotations appropriately. The catch? The paper contains almost no original work! It is
sometimes difficult to spot this form of plagiarism because it looks like any other well-
researched document.
 "The Perfect Crime„: Well, we all know it doesn't exist. In this case, the writer properly
quotes and cites sources in some places, but goes on to paraphrase other arguments
from those sources without citation. This way, the writer tries to pass off the paraphrased
material as his or her own analysis of the cited material.
 http://plagiarism.org

 Software implemented by most publishers (Nature, Wiley-
Blackwell, Elsevier, Springer, Taylor & Francis,…)
 Prevent ethical misconduct
 Publisher checks but is not judge
 Author has full responsibility
 Test 2009: 10% of submitted articles contain plagiarism
 (Nature 466, 167 (2010) | doi:10.1038/466167a)
 Workflow
 Journal policy: run iThenticate
 Submission or Revision/Acceptance
 Original research and review articles
 % similarity is no proof -> manual check needed
 Low similarity -> 10 minutes
 High similarity -> 1-4 hours
iThenticate http://ithenticate.com
iThenticate

~(30)% similarity -> manual check
Not cited High similarity Reject
Ethical misconduct
Inform Head of
Institute and Funding
Ban publicationReasonable similarity
Cited
Results, content
ReviewArticle Revise
250 words
Methods,
Introduction,Abstract
Accept

...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

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 for 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,

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,

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

 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

 http://www.ismte.org/
ISMTE
Intl. Soc. Managing & Technical Editors

 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

Now submit
 http://mc.mscentral.com/btj
 Take time! You will need to provide
 Names and emails of authors
 Names and emails of referees
 4 preferred referees
 Evt non-preferred: best state WHY – this choice will be respected
 Title, abstract and keywords
 Lay abstract/practical applications
 Cover letter
 Conflict of interest statement

Submit online:
 http://mc.manuscriptcentral.com/btj

Then be patient
 The editors will try to get back to you as soon as
possible
 Immediate decision within 1 week
 Peer review within 4 weeks is fast!
 You may inquire after 6 weeks

After decision
 Always sleep over the referee comments
 Reply correctly, especially if „rebuttal“
 Carefully revise and make a point-by-point answer to
referee comments – especially if some requests
cannot be fulfilled, come up with a plausible
explanation!
 The revised version has to be PERFECT – it will save
a lot of time for all parties involved.

Handle rejections
 Sleep over it!
 You can point out mistakes to the editor
 Rebuttal is not a frustration outlet

Editing
 Language vs peer review/editing
 Badly written -> reject
 Poor language -> language polishing
 Small mistakes -> copy-editor
 Shashok K. Content and communication: How can
peer review provide helpful feedback about the
writing?
 BMC Medical Research Methodology 2008, 8:3,
doi:10.1186/1471-2288-8-3.
http://www.biomedcentral.com/1471-2288/8/3

… Accepted
 Celebrate!
 Cite per DOI (Digital object identifier)
 = Publisher/MSnumber
 http://dx.doi.org
 http://doi.wiley.com/10.1002/biot.2009xxxxx
 Publication times….
 Author
 Signed copyright transfer agreement
 Final figures/text
 Galley proof corrections
 Publisher
 Copy-editing
 Typesetting
 Online publication
 Issue and/or print: pages assigned

Writing funding proposals
Cargill p.139

Grant/fellowship writing
 http://learnerassociates.net/proposal

Grant draft
 Title
 Abstract/Overview
 Introduction/Problem/Question
 Methods/Resources
 Research goals and objectives/Milestones
 Discussion/Perspectives/Evaluation
 Cover letter
Imagine you are the recruiter/reviewer

Think like a grant reviewer
 Formalities
 Filter - Assign to reviewer
 Person CV
 Title/summary
 Review
 Project – figures - milestones
 Host, feasibility, …
 Interview
 Presentation, knowledge
 Potential (fit into a team)
 Ranking

Tips for grant writing
 Follow guidelines
 Start early, look at examples
 Be clear, easy to read
 Get to the point
 Convince with content, not with statements
 Don’t criticize others (who will review?)
 Be realistic – don’t ask too little/too much
 Ask feedback

Go to get a grant
 http://www.nature.com/naturejobs/science/articles/10.
1038/nj7385-429a

Best practice in science writing
 Title and abstract clear, precise and attractive
 Before writing discuss journals and authorships
 Structure, writing order, styles specific to IMRAD
 Style, tenses, word usage, clear thinking, clear writing,
mindmap, be critical
 Cite appropriately, avoid plagiarism

Boring scientific literature
 http://dx.doi.org/10.1111/j.0030-1299.2007.15674.x

Websites

 http://www.slideshare.net/barbaja
 http://www.wiley.com/authors
 http://www.biotecvisions.com
 http://www.writeresearch.com.au
 http://www.writing.engr.psu.edu/exercises/
 http://www.bioc.cam.ac.uk/teaching/partii/both/ScientificWri
ting.pdf
 http://www.freelancers.co.uk/
 http://www.inter-biotec.com/services/services.html
 http://www.union.edu/PUBLIC/BIODEPT/wicked.html
 http://www.lib.umich.edu/hsl/resources/writing

Scientific Writing tips

Recommended References
 Alley, M., The Craft of Scientific Writing
 Fox, N., The Little Book of Science Writing, 2014
 Shashok, K., Content and communication: How can peer
review provide helpful feedback about the writing? BMC
Medical Research Methodology 2008, 8:3,
http://dx.doi.org/10.1186/1471-2288-8-3
 Cargill, M., O’Connor, P., Writing scientific research
articles. Blackwell Publishing, Chichester 2009, ISBN 978-
1-4051-8619-3.
 Ruben, A., How to Write Like a Scientist. Sciencecareers
2012, March 23,

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