Scientific Writing Masterclass

Infectious Diseases Module

MMLS

November 2011

Calvin & Hobbes, copyright Bill Watterson

Introduction

• Students– Master level,

non-native English.

• Masterclass– Apply advanced

theory– Intense and

practical

• …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!

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

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

The Grind

Rules versus Style

Correct English (spelling, punctuation, grammar) should

ALWAYS be used.

Foundation for brilliant writing!

Flexibility in expression (grammar, personal style).

Defined by: House styles, context, purpose, audience

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

Quick Lesson

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.

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

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).

(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

The Grind: Grammar

• Adverbs: A. Correct or B. Incorrect?

The bacteria were harvested quick.

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

ly.

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.

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.

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.

• 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.

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.

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

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.

Quick Lesson- Since/From/ForDescribe 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

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.

END OF PUNCTUATION!

• See study guide.• Use reference books.• Don’t trust all that you read!• Practise punctuating.

--PAUSE--

Good Scientific Writing

StyleRecognise good style ↓Learn to identify it.Understand what makes it good, or bad.

Masterclass

Edit ↓Read, take initiative.

Masterclass & own initiative

Write, write, write & edit, edit, edit ↓Be your own strictest critic.

Vaccine advise report & own initiative

Good Scientific Writing

• Plain language movement: ‘To improve communication by eliminating unnecessarily complex language from academia, government, law and business.’

• Encouraged by many journals.

Six key features*Understandable* Clear and simple* Credible* Efficient* Follows convention

Style Guide

Document & House Style

Define your Audience

Personal Writing Style

Flexibility,

Type of Document & House Style

• Type of document.• Employer, journal, association,

university.• Font, layout, UK/US English,

abbreviations.

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.

British Spelling American Spelling

FlavourColourNeighbour

FlavorColorNeighbor

MetreLitreTitre

MeterLiterTiter

OrganiseAnalyseHydrolyse

OrganizeAnalyzeHydrolyze

AmoebaFoetalPaediatric

AmebaFetalPediatric

AnalogueDialoguePedagogue

AnalogDialogPedagog

Personal preference, geographic location, employer preference, publisher’s instructions.

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

Jargon ∝ Audience

• 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.

Efficient communication

Fog of impenetrability

Focus/ Purpose

> Overall features

Human interest

> real life application.

Decision-making purpose

> Informative, Interpretive in the related context.

Reporting, dissemination of information.

>Accurate reporting and reasoning.

Aspect Lay audiencesManagerial audiences

Expert audiences

Jargon LimitedExplain specialised terms, use glossary

Use specialised terms with minimal explanation

Information level

Analogies, relate concepts to easily relatable contexts

Intermediate level of detail, explain the concepts

Detailed, concepts can be explained using references

Scientific data Results are paraphrasedPresent selected results and give summaries or overviews

Present detailed results and interpretation

GraphicsUse illustrations to explain concepts

Use appropriate figures, tables or graphs

Provide data in figures, tables or graphs

Writing for non-scientistsSurgeons make cancer cells fluoresce for removal Trying to remove every last cancer cell during surgery can be a bit like playing blind man's bluff: they are often the same colour as healthy cells, so surgeons risk leaving behind cancer cells which can regrow. But that could change thanks to a technique that makes ovarian cancer cells glow.Currently, surgeons largely rely on touch to determine where an ovarian tumour starts and ends. "You have no real clue where the borders are," says Gooitzen van Dam (...).Van Dam and his colleagues took advantage of the fact that the vast majority of ovarian cancer cells over-express a receptor for folate on their cell surface while normal cells do not. They attached a fluorescent label to folate molecules and administered them to women via an intravenous drip 2 hours before surgery to remove their tumours.The labelled folate was taken up by the cancer cells but not normal cells, so surgeons could use a camera that detects fluorescence to see the tumours. The team now plan to see whether the method boosts patient survival rates.

Intraoperative tumor-specific fluorescence imaging in ovarian cancer by folate receptor-α targeting: first in-human results

The prognosis in advanced-stage ovarian cancer remains poor. Tumor-specific intraoperative fluorescence imaging may improve staging and debulking efforts in cytoreductive surgery and thereby improve prognosis. The overexpression of folate receptor-α (FR-α) in 90–95% of epithelial ovarian cancers prompted the investigation of intraoperative tumor-specific fluorescence imaging in ovarian cancer surgery using an FR-α–targeted fluorescent agent. In patients with ovarian cancer, intraoperative tumor-specific fluorescence imaging with an FR-α–targeted fluorescent agent showcased the potential applications in patients with ovarian cancer for improved intraoperative staging and more radical cytoreductive surgery.

analogy, recognisable context

simplified

Quote, adding personality, varies writing style

Simplifying data, paraphrasing jargon

recognisable terminology

Human interest emphasis, broader focus

Cancer drug thwarts malariaIN THE wake of World Malaria Day on Monday comes news that certain anti-cancer drugs might also work against the malarial parasite.There were 780,000 deaths and 225 million cases of malaria in 2009. With resistance to existing anti-malarial drugs growing all the time, new weapons against the disease are a priority.Now C. Doerig (...) and colleagues have discovered that Plasmodium falciparum, the parasite that causes malaria, co-opts two red blood cell proteins called kinases. Many new cancer treatments also target kinases, and when the team exposed malaria-infected red blood cells and liver cells to some of these "kinase inhibitors", they killed the bug but not the cells."Our discovery opens up new ways to potentially combat malaria," says Doerig, although he cautions that the work is very preliminary. However, the team is in discussions with pharmaceutical companies to test more kinase inhibitors, especially those that have proved safe in clinical trials but didn't make the grade as cancer drugs.

Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytesMerozoites 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.

Selective informationSimple language

Simple and catchy

Human interest, impact on societyCatchy titleKinase inhibitors are a new class of anticancer drugs

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 co-factor in the progression of chronic viral infections including hepatitis C and HIV, which are both single-stranded RNA viruses.

Toll like receptor 8 (TLR8), a pattern recognition receptor expressed in monocytes, senses viral single stranded RNA as a danger signal and leads to the induction of Type I interferon (IFN) as well as the pro-inflammatory cytokine, tumor necrosis factor alpha (TNF alpha)

These novel results suggest first, that alcohol has a profound inhibitory effect on Type I IFN induction regardless of intracellular (TLR8) or cell surface-derived (TLR4) danger signals. Second, both acute and prolonged alcohol exposure can inhibit antiviral Type I IFN pathway activation.

Alcoholism

Related to disease

progression

Virus presence

Leads to immune system reponseAlcohol

supresses virus activated

immune system

response

Alcohol (?binge drinking &

chronic alcohol abuse)

supresses immune

system = drinkers beware!

Alcoholism

Related to disease

progression

Virus presence

Leads to immune system reponseAlcohol

supresses virus activated

immune system

response

Alcohol (?binge drinking &

chronic alcohol abuse)

supresses immune system

= drinkers beware!

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

Style Guide

Document & House Style

Define your Audience

Personal Writing Style

Flexibility,

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

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.

Simple Sentences

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

Simple Sentences

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

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,

Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytesMerozoites 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.

Simple sentencesMerozoites 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: RBC invasion, multiplication, development stages, pathogenesisOverload of terminology.All relevant information?DanglerPassive- undegoing development

Redundancy – undergoing

development

* TRY TO EDIT THIS SENTENCE!

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.

• . 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

Passive and Active Voice

Sunflowers, a painting by Vincent van Gogh

Vincent van Gogh painted Sunflowers

Emphasis on the object Emphasis on the subject

Active Voice

• Modern scientific writing embraces active voice!

• Strong verbs• Clear meaning• Shorten sentence

Subject – Verb - Object

Active: Subject - verb - object

I shot the sheriff

Passive: Object - verb (modified) - subject

The sheriff was shot by me.

How to rescue passive sentences

• Seek and change the adverb into the verb– Examination– Analysis– Investigation – Performance– Are going to …

The, an

The, a

Investigation into the recent deaths is being carried out by private detectives.

Investigate

Private detectives are investigating the recent deaths

Renovating Long Sentences

• Remove unnecessary words• Remove repetition• Keep subject and verb together• Avoid danglers• Punctuate• Reduce prepositions• Unstack wordy terminology

Rescuing long sentences

• In patients with ovarian cancer, intraoperative tumor-specific fluorescence imaging with an FR-α–targeted fluorescent agent showcased the potential applications in patients with ovarian cancer for improved intraoperative staging and 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.

redundancysimplify

Get to the pointIdeas overload!

Vague, unsuitable

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)

• 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

• Grammatical Variation• Don’t overuse any one element

Syntax

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