1. Scientific Writing Masterclass
Infectious Diseases
Module
MMLS
November 2011
Calvin & Hobbes, copyright Bill Watterson

2. Introduction
• Students
– Master level,
non-native
English.
• Masterclass
– Apply advanced
theory
– Intense and
practical

3. • …the purpose of writing is to inflate weak
ideas, obscure poor reasoning, and inhibit
clarity. With a little practise, writing can be
an intimidating and impenetrable fog!

4. Masterclass outline
• What is scientific writing?
• The grind
– Rules & conventions
– Punctuation & grammar
• The style
– Learn to recognise and have it!
• Get intimate
– Writing with intent, know your audience

5. What is scientific writing
• Form of formal academic writing.
• Primary purpose is to disseminate
information to a defined audience.
• Three major factors influencing scientific
writing
! Grammatical rules
! Scientific conventions
! Audience

6. The Grind
Rules versus Style
Correct English (spelling, Flexibility in expression (grammar,
punctuation, grammar) should personal style).
ALWAYS be used.
Foundation for brilliant writing! Defined by: House styles, context,
purpose, audience

7. The Grind: Punctuation
Which is correct (A or B)?
Periods
A. Dr. Prof. B.Sc Mr.
B. Dr Prof BSc Mr
Both- be consistent. Abbreviations &
suspensions

8. Quick Lesson

9. The Grind: Punctuation
• Commas
A. Neutralising antibodies are not measured in
convalescent patients, nor in patients in the
acute phase.
B. Neutralising antibodies are not measured in
convalescent patients nor in patients in the acute
phase.
Before coordinating conjunctions (for, and, nor,
but, or, yet etc) joining two independent clauses.

10. The Grind: Punctuation
• Commas
A. The human immunodeficiency virus, one
of the simplest of viral constructs still
evades true understanding.
B. The human immunodeficiency virus, one
of the simplest of viral constructs, still
evades true understanding.
Commas instead of parenthetical elements

11. The Grind: Punctuation
• Commas
A. Currently, infectious diseases remain the
leading cause of deaths worldwide.
B. Currently infectious diseases remain the
leading cause of deaths, worldwide.
After introductory elements(However,
Unfortunately, Surprisingly, Finally, In
conclusion, To summarise etc).

12. (A) , (B) ;
You did your best , / ; let’s hope you pass the exam.
Separating independent clauses. You did your best.
Let’s hope you pass the exam.
An effect of the Ebola virus is bleeding , / ; especially in
the mucosa.
Not independent clauses. Use a comma!
Is the following usage of semicolons A. Correct or B.
Incorrect ?
Combine 6.7 ml 30 % acrylamide (60:1); 10 ml 5X
tris/glycine buffer; 33.3 ml H2O; 250 μl 10%
ammonium persulfate and lastly, 60 μl TEMED.
Both are acceptable – using the colon as a
supercomma

13. The Grind: Grammar
• Adverbs: A. Correct or B. Incorrect?
The bacteria were harvested quick. ly.
B. Incorrect. An adverb requires inflection.
Adverb position- which is correct?
A. The virus rapidly multiplied.
B. The virus multiplied rapidly.
Answer: both. Changing adverb position
changes the emphasis

14. Quick Lesson
Adverb position
• Front position: links to previous sentence, or is not the
main focus.
– However, the virus multiplied.
• Mid position
– The virus rapidly multiplied.
• End position
– The virus multiplied rapidly.
 Words in the last position generally receive the
most emphasis.

15. Quick Lesson
Adverbs: Be aware of the placement to
avoid ambiguities
• The patient failed almost all the
tests.(failed most but passed a few)
• The patient almost failed all the tests. (but
just passed the tests)
• Children who laugh, rarely are shy.
• Children who laugh rarely are shy.

16. The Grind: Commonly misused
words
There were about/approximately 200
participants in the study.
However, ‘approximately’ is more suited to
formal writing.
The level of IL-6 was about/approximately
4.0 g/L.
Answer: B. Use approximately for mass
nouns.

17. •If a bacterial culture is spilled, the
affected/effected area must be disinfected
immediately.
•The affects/effects of contamination are health
related.
•Affect= verb (to influence)
•Effect= noun (the result)
•A virus that/which has lost virulency is
harmless.

18. Quick Lesson: That/Which
• That introduces restrictive clauses (essential)
while which introduces non-restrictive (non-
essential) clauses.
• If the information is left out, is the meaning of the
sentence changed?
• A virus that/which has lost virulency is harmless
Essential information: use THAT
Unessential information: use WHICH
Throw out the ‘which’ and it will not be missed.

19. The Grind: Commonly misused
words
• Since/Because chocolate is so delicious, I can eat
an entire block.
• Why is editing important? Since/Because it
produces higher quality work.
• There are so many exercises since/because
grammar is an important skill.
• Since/Because can be used at the beginning of
sentences
• Because – in the middle of sentences.
• Because- to introduce new information

20. The Grind: Commonly misused
words
• The actual/current figures from the report.
• You might lose/loose your pants.
• If your pants are too lose/loose you might lose
your pants.
The monkey realised he was bigger than/then the
dog.
The monkey than/then threatened the dog
• The diagnostic test had been applied since/from
2008.
• The gel was run since/from two o’clock.

21. Quick Lesson- Since/From/For
Describe an event with a point in time reference.
• Since
– perfect tenses: „has had, have been, has
been, had been.‟
• From
– other tenses (past, future): ‘was, will be‟.
– For periods of time with a defined start and
end.
• The vaccine had been commercially available
since 1998.
• The vaccine was produced in chickens from
2000

22. Quick Lesson: Since/From/For
• Period of time: use ‘For’ for all tenses
– „This class runs for 2 hours.
– The masterclass ran for longer than expected.
– The writing course had been given for two
years.

23. END OF PUNCTUATION!
• See study guide.
• Use reference books.
• Don’t trust all that you read!
• Practise punctuating.
--PAUSE--

24. Good Scientific Writing

25. Style
Recognise Edit Write, write,
good style ↓ write & edit,
↓ Read, take edit, edit
Learn to initiative. ↓
identify it. Be your own
Understand strictest critic.
what makes it
good, or bad.
Vaccine advise
Masterclass Masterclass & own report & own
initiative initiative

26. Good Scientific Writing
• Plain language
Six key
movement: ‘To improve
features communication by
*Understandable eliminating
* Clear and unnecessarily complex
simple language from
* Credible academia,
* Efficient government, law and
business.’
* Follows
• Encouraged by many
convention
journals.

27. Style Guide
Document & House Style
Define your Audience
Personal Writing Style
Flexibility,

28. Type of Document & House Style
• Type of document.
• Employer, journal, association,
university.
• Font, layout, UK/US English,
abbreviations.

29. American vs British Spelling
• „Though the tough cough and hiccough plough
him through’
• British English is irregular
– Borrowed words
– Shift in pronunciation
– Spelling reform not successful
• Webster’s American Dictionary of the English
language.

30. British Spelling American Spelling
Flavour Flavor
Colour Color
Neighbour Neighbor
Metre Meter
Litre Liter
Titre Titer
Organise Organize
Analyse Analyze
Hydrolyse Hydrolyze
Amoeba Ameba
Foetal Fetal
Paediatric Pediatric
Analogue Analog
Dialogue Dialog
Pedagogue Pedagog
Personal preference, geographic location,
employer preference, publisher’s
instructions.

31. Have a purpose when writing
• Identify your motivation
Explain, inform, argue, educate, justify, request,
report, document, investigate, debate,
summarise, evaluate, recommend, propose,
review, advise.
• What is the context?
Essay, literature review, abstract,
research report, project proposal.
• Combine the motivation and the context to
clarify for yourself WHY you are writing

32. Jargon ∝ Audience
Efficient Fog of
communication impenetrability
• Define your audience
• The audience and context determines
the amount of jargon
• Jargon is only a problem when it is
inappropriate for the intended audience.

33. Aspect Lay audiences Managerial audiences Expert audiences
Focus/
Purpose Decision-making
Reporting, dissemination
purpose
Human interest of information.
> Informative,
> real life application. >Accurate reporting
Interpretive in the
> Overall and reasoning.
related context.
features
Explain specialised Use specialised terms
Jargon Limited
terms, use glossary with minimal explanation
Analogies, relate Intermediate level of Detailed, concepts can
Information
concepts to easily detail, explain the be explained using
level
relatable contexts concepts references
Present selected results
Present detailed results
Scientific data Results are paraphrased and give summaries or
and interpretation
overviews
Use illustrations to Use appropriate figures, Provide data in figures,
Graphics
explain concepts tables or graphs tables or graphs

34. Surgeons make cancer cells fluoresce for removal
analogy, Intraoperative tumor-specific fluorescence
Trying to remove every last cancer cell during imaging in ovarian cancer by folate receptor-α
recognisable Writing for non-scientists
surgery can be a bit like playing blind man's bluff:
context
targeting: first in-human results
they are often the same colour as healthy cells, so
surgeons risk leaving behind cancer cells which The prognosis in advanced-stage ovarian cancer
simplified
can regrow. But that could change thanks to a remains poor. Tumor-specific intraoperative
technique that makes ovarian cancer cells glow. fluorescence imaging may improve staging and
Currently, adding largely rely on touch to
Quote, surgeons personality, varies debulking efforts in cytoreductive surgery and
determine where an ovarian tumour starts and
writing style thereby improve prognosis. The overexpression of
ends. "You have no real clue where the borders folate receptor-α (FR-α) in 90–95% of epithelial
Simplifying data,
recognisable
are," says Gooitzen van Dam (...). ovarian cancers prompted the investigation of
paraphrasing jargon
Van Dam and his colleagues took advantage of the intraoperative tumor-specific fluorescence
terminology
fact that the vast majority of ovarian cancer cells imaging in ovarian cancer surgery using an FR-α–
over-express a receptor for folate on their cell targeted fluorescent agent. In patients with
surface while normal cells do not. They attached a ovarian cancer, intraoperative tumor-specific
fluorescent label to folate molecules and fluorescence imaging with an FR-α–targeted
administered them to women via an intravenous fluorescent agent showcased the potential
drip 2 hours before surgery to remove their applications in patients with ovarian cancer for
tumours. improved intraoperative staging and more radical
Human interest emphasis,the cancer
The labelled folate was taken up by cytoreductive surgery.
cells but not normal cells, so surgeons could use a
broader focus
camera that detects fluorescence to see the
tumours. The team now plan to see whether the
method boosts patient survival rates.

35. Cancer drug thwarts malaria Activation of a PAK-MEK signalling pathway in
IN THE wake of World Malaria Day on Monday Human interest, impact on society
malaria parasite-infected erythrocytes
Catchy title
comes news that certain anti-cancer drugs might Merozoites of malaria parasites invade red blood
also work against the malarial parasite.inhibitors cells (RBCs), where they multiply by schizogony,
Kinase are a new class of
There were 780,000 deaths and 225 milliondrugs undergoing development through ring,
anticancer
cases of malaria in 2009. With resistance to trophozoite and schizont stages that are
existing anti-malarial drugs growing all the time, responsible for malaria pathogenesis. Here, we
Selective information
new weapons against the disease are a priority. report that a protein kinase-mediated signalling
Simple language colleagues have
Now C. Doerig (...) and pathway involving host RBC PAK1 and MEK1,
discovered that Plasmodium falciparum, the which do not have orthologues in the
parasite that causes malaria, co-opts two red Plasmodium kinome, is selectively stimulated in
blood cell proteins called kinases. Many new Plasmodium falciparum-infected (versus
cancer treatments also target kinases, and when uninfected) RBCs, as determined by the use of
the team exposed malaria-infected red blood phospho-specific antibodies directed against the
Simple and catchy activated forms of these enzymes.
cells and liver cells to some of these "kinase
inhibitors", they killed the bug but not the cells. Pharmacological interference with host MEK and
"Our discovery opens up new ways to potentially PAK function using highly specific allosteric
combat malaria," says Doerig, although he inhibitors in their known cellular IC50 ranges
cautions that the work is very preliminary. results in parasite death. Furthermore, MEK
However, the team is in discussions with inhibitors have parasiticidal effects ...on the
pharmaceutical companies to test more kinase rodent malaria parasite Plasmodium berghei,
inhibitors, especially those that have proved safe indicating conservation of this subversive
in clinical trials but didn't make the grade as strategy in malaria parasites. These findings have
cancer drugs. profound implications for the development of
novel strategies for antimalarial chemotherapy.

36. Inhibition of TLR8- and TLR4-induced Type I IFN induction by alcohol is
different from its effects on inflammatory cytokine production in monocytes
Prolonged alcohol consumption is a significant Alcohol
co-factor in the progression of chronic viral ism
infections including hepatitis C and HIV, which are Related to
disease
both single-stranded RNA viruses. progression
Toll like receptor 8 (TLR8), a pattern recognition
receptor expressed in monocytes, senses viral Virus presence
single stranded RNA as a danger signal and
leads to the induction of Type I interferon (IFN) as Leads to
well as the pro-inflammatory cytokine, tumor immune
system
necrosis factor alpha (TNF alpha)
reponse
Alcohol
These novel results suggest first, that alcohol has supresses
a profound inhibitory effect on Type I IFN virus
induction regardless of intracellular (TLR8) or cell activated
Alcohol
immune
(?binge
surface-derived (TLR4) danger signals. Second,
system
drinking &
both acute and prolonged alcohol exposure can response
chronic
inhibit antiviral Type I IFN pathway activation. alcohol abuse)

37. Too much alcohol dulls more than your wits. It also weakens
Alcohol your immune system and could make you much more
ism vulnerable to viruses, including HIV.
Related to To see how alcohol affects resistance to infection, Gyongyi
disease Szabo (...) and colleagues exposed monocytes – white blood
progression cells involved in the front-line defence against infection – to
chemicals that mimic viruses and bacteria. Half of the cells
Virus presence were also soused in the levels of alcohol that a person might
have in their blood after quaffing four or five alcoholic drinks
daily for a week.
Leads to Alcohol blunted the monocytes' defences. When the over-the-
immune limit cells were exposed to a virus mimic, they produced only a
quarter as much of the virus-fighting signalling molecule called
system
type-1 interferon as teetotal monocytes made.
reponse
Alcohol "Interferon is pivotal, the first response to any viral infection,"
supresses says Szabo. "There's no viral elimination without it."
Szabo says that the results fit with evidence from medical
virus
records that chronic heavy drinkers with HIV die sooner than
activated
Alcohol non-drinkers. They also fit with earlier studies showing that the
immune immune system of heavy drinkers might be less vigilant
(?binge
system against cancer.
drinking &
response Szabo says heavy drinkers should beware of damaging their
chronic immune systems.
alcohol

38. Style Guide
Document & House Style
Define your Audience
Personal Writing Style
Flexibility,

39. Personal Writing Style
• Learn the rules before playing with them!
• There is often more than one correct way to
say something.
• Elements of style: use them as your
weapons!
– Simple sentences
– Active Voice
– Renovating long sentences
– Writing paragraphs

40. Simple sentences
WHAT?
• Strict definition: one independent clause (idea)
• Practical definition: limit ideas, length
Short Simple sentence (strict definition) We are studying.
Simple long sentence (strict definition) We are studying punctuation, grammar,
scientific writing, elements of style and
paragraphs.
Simple sentence (practical definition) We are learning about punctuation,
grammar, scientific writing, elements of
style and paragraphs.

41. Simple Sentences
WHY?
• Effective Communication
• Punchy, Powerful, Energy.
• Long sentences are difficult to write well.
• Badly written sentences are confusing.

42. Simple Sentences
How?
• Use punctuation
• Split up sentences
• Use active voice
• Remove unnecessary words
• Simplify terminology
• Limit the number of ideas in one sentence

43. Remove unnecessary words
• In order to write elegantly, you do not need many
words.
• It was reported that more girls were born in
industrialised countries.
• The fact that I have three boys undermines this
finding.
• My days, which are busy, are enjoyable.
• My children who are energetic, are a handful.
• Moreover,
• Furthermore,
• Indeed,

44. Activation of a PAK-MEK signalling pathway in malaria parasite-
infected erythrocytes
Merozoites of malaria parasites invade red blood cells (RBCs), where
they multiply by schizogony, undergoing development through ring,
trophozoite and schizont stages that are responsible for malaria
pathogenesis. Here, we report that a protein kinase-mediated signalling
pathway involving host RBC PAK1 and MEK1, which do not have
orthologues in the Plasmodium kinome, is selectively stimulated in
Plasmodium falciparum-infected (versus uninfected) RBCs, as
determined by the use of phospho-specific antibodies directed against
the activated forms of these enzymes. Pharmacological interference with
host MEK and PAK function using highly specific allosteric inhibitors in
their known cellular IC50 ranges results in parasite death. Furthermore,
MEK inhibitors have parasiticidal effects ...on the rodent malaria parasite
Plasmodium berghei, indicating conservation of this subversive strategy
in malaria parasites. These findings have profound implications for the
development of novel strategies for antimalarial chemotherapy.

45. Simple sentences
Merozoites of malaria parasites invade red blood cells
(RBCs), where they multiply by schizogony, undergoing
development through ring, trophozoite and schizont
stages that are responsible for malaria pathogenesis.
Too many ideas in one sentence: Redundancy – undergoing
RBC invasion, multiplication, development
development stages, pathogenesis
Overload of terminology. * TRY TO EDIT THIS
All relevant information? SENTENCE!
Dangler
Passive- undegoing development
Merozoites of malaria parasites invade red blood cells
(RBCs), where they reproduce by schizogony. During
reproduction, they develop through the ring, trophozoite
and schizont stages that are responsible for malaria
pathogenesis.

46. • . Here, we report that a protein kinase-mediated
signalling pathway involving host RBC PAK1 and MEK1,
which do not have orthologues in the Plasmodium
kinome, is selectively stimulated in Plasmodium
falciparum-infected (versus uninfected) RBCs, as
determined by the use of phospho-specific antibodies
directed against the activated forms of these enzymes

47. Passive and Active Voice
Sunflowers, a Vincent van Gogh
painting by painted
Vincent van Sunflowers
Gogh
Emphasis on the object Emphasis on the subject

48. Active Voice
• Modern scientific writing embraces active
voice!
• Strong verbs
• Clear meaning
• Shorten sentence
Subject – Verb - Object

49. Active: Subject - verb - object
I shot the sheriff
Passive: Object - verb (modified) - subject
The sheriff was shot by me.

50. How to rescue passive sentences
• Seek and change the adverb into the verb
– Examination
– Analysis
The, an
– Investigation
– a
The,Performance
– Are going to …
Investigation into the recent deaths is being carried
out by private detectives.
Investigate
Private detectives are investigating the recent
deaths

51. Renovating Long Sentences
• Remove unnecessary words
• Remove repetition
• Keep subject and verb together
• Avoid danglers
• Punctuate
• Reduce prepositions
• Unstack wordy terminology

52. Rescuing long sentences
• In patients with ovarian cancer, intraoperative redundan
tumor-specific fluorescence imaging with an FR- simplify
α–targeted fluorescent agent showcased the Vague, unsu
potential applications in patients with ovarian Get to the p
cancer for improved intraoperative staging and Ideas over
more radical cytoreductive surgery.
• Using an FR-α-specific fluorescent imaging
system may benefit patients with ovarian cancer.
Visual detection of cancerous cells during surgery
may improve intraoperative staging and aid more
radical cytoreductive surgery.

53. Paragraphs
• the topic sentence comes at or near the beginning;
• the succeeding sentences explain or establish or
develop the statement made in the topic sentence; and
• the final sentence either emphasizes the thought of the
topic sentence or states some important consequence.
• (strunk)

54. • Be positive, not negative.
• Since Hemingway wasn’t the cheeriest guy in the world, what does he mean by be
positive? Basically, you should say what something is rather than what it isn‟t.
• This is what Michel Fortin calls using up words:
• By stating what something isn‟t can be counterproductive since it is still directing the
mind, albeit in the opposite way. If I told you that dental work is painless for example,
you‟ll still focus on the word “pain” in “painless.”
• • Instead of saying “inexpensive,” say “economical,”
• Instead of saying “this procedure is painless,” say “there‟s little discomfort” or “it‟s
relatively comfortable,”
• And instead of saying “this software is error-free” or “foolproof,” say “this software is
consistent” or “stable.”
• He was not very often on time.He usually came late.He did not think that studying
Latin was much use.He thought the study of Latin useless.The Taming of the
Shrew is rather weak in spots. Shakespeare does not portray Katharine as a very
admirable character, nor does Bianca remain long in memory as an important
character in Shakespeare's works.The women in The Taming of the Shrew are
unattractive. Katharine is disagreeable, Bia

55. • Grammatical Variation
• Don’t overuse any one element

56. Syntax
• Elements of style Strunk
• http://www.bartleby.com/141/