DoDo’’s and Dons and Don’’ts ts of Scientific Writingof Scientific Writing

Assembled by Dr. Ismail HassanAssembled by Dr. Ismail Hassan

What is a Scientific Paper ?What is a Scientific Paper ?What is a Scientific Paper ?What is a Scientific Paper ?

A scientific paper is a written and A scientific paper is a written and published report describing original published report describing original research resultsresearch results

33

What is What is your personal reasonyour personal reason for for publishing?publishing?

• However, editors, reviewers, and the However, editors, reviewers, and the research community don’t care about research community don’t care about these reasons. these reasons.

…???

Get promoted?

Get

funding?

PhD

degree?

Writing a Research PaperWriting a Research PaperWriting a Research PaperWriting a Research Paper

• No single best wayNo single best way• Varies from paper to paperVaries from paper to paper• Wait till data analyzedWait till data analyzed• Background readingBackground reading

- not too extensivenot too extensive- make notes; make notes of make notes; make notes of

notesnotes- write down sentences or write down sentences or

parts of them parts of them - not during not during ““writing timewriting time””

Write with the Reader in MindWrite with the Reader in Mind

Who is the reader?Who is the reader?• Editor, reviewersEditor, reviewers• Scientists and professionals Scientists and professionals • StudentsStudents

Assumptions:Assumptions:• They are all busy, with little spare timeThey are all busy, with little spare time• They prefer to read clear and concise They prefer to read clear and concise articlesarticles

First DraftFirst DraftFirst DraftFirst Draft

• Write as quickly as possible• As if thinking out loud• Get everything down• Ignore spelling, grammar, style• Skip troublesome words• Correct and rewrite only when the whole text is on paper• Do not split the manuscript among the co-authors

Writing: Narrative FlowWriting: Narrative FlowWriting: Narrative FlowWriting: Narrative Flow• Telling a story• Reader follows from start to end• Writing is sequential: logic is the glue• Sentences hold hands• Smooth transitions

Bad WritingBad WritingBad WritingBad Writing

•If multiple mistakes in spelling and

syntax, reviewer suspects similar

sloppiness in the lab

RewritingRewritingRewritingRewriting

• Secret of writing is rewriting • Secret of rewriting is re-thinking

JournalJournal

• Choose before writingChoose before writing

• General vs. sub-especialty General vs. sub-especialty journaljournal

Journal selectionJournal selectionJournal selectionJournal selection

Strategies to choose the journal:•Where many of the papers cited were published?• Where do cited scientists publish their work?• Read the “scope” paragraph in the “I for A”• Read the table of contents of potential journals• Examine several articles in potential journals

Try to Avoid:Try to Avoid:

• Long complicated sentencesLong complicated sentences• Pretentious languagePretentious language• RepetitionRepetition• Meaningless phrases Meaningless phrases • Irrelevant materialIrrelevant material• Cluttering a paragraphCluttering a paragraph• Citing too many referencesCiting too many references

Long Complicated SentencesLong Complicated Sentences

A long and complicated example:A long and complicated example:

Various management strategies, such as the Various management strategies, such as the development of sanctuaries, closed seasons, development of sanctuaries, closed seasons, minimum size-limit for harvesting of 75mm minimum size-limit for harvesting of 75mm carapace length (CL) lobsters, enforcing a no-take carapace length (CL) lobsters, enforcing a no-take status on ovigerous females and issuing quotas status on ovigerous females and issuing quotas according to a total allowable catch (TAC) have according to a total allowable catch (TAC) have been introduced over the years but catch-rates been introduced over the years but catch-rates have steadily declined since the 1950s to the have steadily declined since the 1950s to the present catch of around 2500 tons - an effect present catch of around 2500 tons - an effect attributed not only to over-exploitation but to attributed not only to over-exploitation but to decreased lobster growth-rates and large-scale decreased lobster growth-rates and large-scale environmental changes in the BCLME.environmental changes in the BCLME.

Long Complicated SentencesLong Complicated Sentences

Can be broken down to three parts:Can be broken down to three parts:

Various management strategies, such as the Various management strategies, such as the development of sanctuaries, closed seasons, development of sanctuaries, closed seasons, minimum size-limit of harvesting of 75 mm minimum size-limit of harvesting of 75 mm carapace length (CL), enforcing a no-take status carapace length (CL), enforcing a no-take status on ovigerous females and issuing quotas on ovigerous females and issuing quotas according to a total allowable catch (TAC), have according to a total allowable catch (TAC), have been introduced over the yearsbeen introduced over the years but catch-rates but catch-rates have steadily declined since the 1950s to the have steadily declined since the 1950s to the present catch of around 2500 tons - present catch of around 2500 tons - an effect an effect attributed not only to over-exploitation but to attributed not only to over-exploitation but to decreased lobster growth-rates and large-scale decreased lobster growth-rates and large-scale environmental changes in the BCLMEenvironmental changes in the BCLME..

Much better is:Much better is:

Management strategies introduced since the Management strategies introduced since the 1950s include: lobster sanctuaries, closed 1950s include: lobster sanctuaries, closed fishing seasons, minimum size-limits, no take-fishing seasons, minimum size-limits, no take-of ovigerous females, and a quota system.of ovigerous females, and a quota system.

Catches have continued to decline, reaching Catches have continued to decline, reaching 2500 tons by 2006.2500 tons by 2006.

The decline is attributed to over-exploitation The decline is attributed to over-exploitation and decreased lobster growth rates resulting and decreased lobster growth rates resulting from large scale environmental changes in the from large scale environmental changes in the BCLME.BCLME.

Pretentious LanguagePretentious Language

• Using pretentious language will not make you Using pretentious language will not make you sound sound more intelligent – it will simply make you more intelligent – it will simply make you unintelligibleunintelligible

• Commonly used words instead of obscure words Commonly used words instead of obscure words The study was conducted…The study was conducted… The study was done…The study was done…

Avoid RepetitionAvoid Repetition

• Discussion in the Results sectionDiscussion in the Results section

• Results in the Discussion sectionResults in the Discussion section

• Information can be in the Information can be in the Introduction Introduction OR Discussion – not in OR Discussion – not in both!both!

Meaningless PhrasesMeaningless Phrases

• The results are given in Figure1, where it is shown that The results are given in Figure1, where it is shown that temperature was temperature was directly proportional to metabolic rate… directly proportional to metabolic rate…

Rather writeRather write

Temperature was directly proportional to metabolic rate Temperature was directly proportional to metabolic rate (Fig.1)..(Fig.1)..

• In order to determine... In order to determine... OROR to determine… to determine…

• Use parenthesis (brackets) for statistical resultsUse parenthesis (brackets) for statistical results Fruit size was significantly greater in trees growing alone Fruit size was significantly greater in trees growing alone (t=3.65, df=2, p<0.05).(t=3.65, df=2, p<0.05).

Irrelevant MaterialIrrelevant Material

Irrelevant material lengthens a paper Irrelevant material lengthens a paper without adding to its substance:without adding to its substance:

Focus, focus, focusFocus, focus, focus Stick to the facts; speculate sparinglyStick to the facts; speculate sparingly DonDon’’t get side-trackedt get side-tracked You donYou don’’t need to include t need to include ALLALL your data or your data or analyses!analyses!

Cluttering a ParagraphCluttering a Paragraph

DonDon’’t have more than one main idea or t have more than one main idea or theme in a paragraph? It is better in such theme in a paragraph? It is better in such cases to rather write two or more linked cases to rather write two or more linked paragraphs.paragraphs.

DonDon’’t overkill with too many citations. Just t overkill with too many citations. Just cite the most important, most recent or, cite the most important, most recent or, where available, review papers? where available, review papers?

(However, in a review paper it may be (However, in a review paper it may be appropriate to have an appropriate to have an extensive/complete list of references)extensive/complete list of references)

The DoThe Do’’s:s:

• Read the Read the ““Instructions to AuthorsInstructions to Authors”” – stick – stick to it!to it!• Maintain the focus of the paper – be clear Maintain the focus of the paper – be clear and and conciseconcise• Use the appropriate tenseUse the appropriate tense• Use passive instead of active voiceUse passive instead of active voice• Maintain balance between text length and Maintain balance between text length and

numbers of figures/tablesnumbers of figures/tables• Be consistent in format (choice of words, Be consistent in format (choice of words, font, font, numbering, punctuation, numbering, punctuation, abbreviation, abbreviation, spacing, citation)spacing, citation)

Use the Appropriate TenseUse the Appropriate Tense

• AbstractAbstract Past tense when describing and giving Past tense when describing and giving resultsresults Present tense for conclusionsPresent tense for conclusions

• IntroductionIntroduction Past or present tense Past or present tense

• Methods & Results Methods & Results Past tense (What you did and what you Past tense (What you did and what you found)found)

• Discussion Discussion Past and/or present tensePast and/or present tense

Use Passive not Active VoiceUse Passive not Active Voice

• ActiveActive We used ANOVA to compare distances We used ANOVA to compare distances moved.moved. I sampled 50 sites. I sampled 50 sites.

• But better is But better is PassivePassive ANOVA was used to compare distances ANOVA was used to compare distances moved.moved. Fifty sites were sampled.Fifty sites were sampled.

Other Suggestions:Other Suggestions:

• When you are done and think it is perfect.....itWhen you are done and think it is perfect.....it ’’s not!s not!

• Forget about the article for a week and then read it Forget about the article for a week and then read it again!again!

• Give it to an experienced colleague to read and ask Give it to an experienced colleague to read and ask him/her to be brutal!him/her to be brutal!

• Remember…there are as many different styles as Remember…there are as many different styles as there there are researchers…but they all need to get past are researchers…but they all need to get past the the journal editor and the reviewers!journal editor and the reviewers!

Practically….how to start Practically….how to start writing?writing?

SequenceSequenceSequenceSequence

•Figures, tables• Methods and Results• Discussion and Introduction• Abstract and Title

StructureStructureStructureStructure

• Biggest problems come first• A scaffold of headings and subheadings• IMRAD: each on a separate sheet - In the first draft: random order, telegraphic style

- Afterwards: the ideas must be numbered and an order generated

FiguresFiguresFiguresFigures

• Do before writing• Redraw, redraw, •No caption• Reduce to 1 column in journal

- Reduced xerox copy to check out- Original should be <3x final

FiguresFiguresFiguresFigures• Axes

- Minimize tick marks

- Don’t number each tick

• Lettering- Uniform, lower case- Minimize, avoid bold- After reduction, 2-3 mm high

• Legend- Gives message

TablesTablesTablesTables

• Single unit, understood without text•Exceed 1 sheet: redraw, rotate all 90º

• Avoid narrow/broad; •If small: move data to text

Methods SectionMethods SectionMethods SectionMethods Section

• Enough information for an experienced investigator to repeat

your work• Avoid tiresome detail• Cut-and-paste from previous work of the author(s), not

somebody else’s• It is the first section of the paper in which subheadings should

be used

Results SectionResults SectionResults SectionResults Section

• Refer to data (Fig. X, Table Y)• Don’t repeat numbers in Tables• Can state numbers from Figures if

precision is required• A lot of numbers, make Table

IntroductionIntroductionIntroductionIntroduction

2-3 paragraphs, <450 words• First paragraph

- Introduce broad area

• Second paragraph- Explicit rationale

• Last paragraph- Hypothesis

Discussion SectionDiscussion SectionDiscussion SectionDiscussion Section

• First paragraph- State major findings

- Paraphrase abstract

• Last paragraph- “In summary…” (2-3 sentences)- “In conclusion…” (biggest message, return to Intro, avoid speculation, avoid “need more work”

Discussion SectionDiscussion SectionDiscussion SectionDiscussion Section

• Middle paragraphs- Base each on a major result

• Always focus on your results• Never discuss prior work without reference to your work• Refer Tables and Figures

AbstractAbstractAbstractAbstract

• Précis writing• Informative, not descriptive• Some numbers, but not in excess• Determines if paper will be read

TitleTitleTitleTitle

• Max info in least words• <12 words• <100 characters• The title is a label• Should almost never contain abbreviations•State results

AuthorshipAuthorshipAuthorshipAuthorship

• Decided as early as possible• Should include persons who:

- Can defend the intellectual content,

including data and conclusions- Must be willing to concede publicly any

errors- In the case of fraud be willing to state

publicly the nature and extent, and

account for its occurrence

Authorship: CriteriaAuthorship: CriteriaAuthorship: CriteriaAuthorship: Criteria

• All the following criteria should be

met:- Generate at least part of the intellectual content (conception

or design, data analysis and interpretation)- Drafting, reviewing or revising critically for important

intellectual content- Final approval of the version to be published

Authorship: OrderAuthorship: OrderAuthorship: OrderAuthorship: Order

• Some journals use the alphabetical order• Most of them assume an order based on each author’s importance to the study

- The first author is primarily responsible for collecting and analyzing data, and writing - The last one, an established investigator, assumes the overall responsibility for the study- The middle authors are listed according to their order of importance to the study

Authorship: Authorship: ResponsibilitiesResponsibilitiesAuthorship: Authorship: ResponsibilitiesResponsibilities

The authors must comply with the following rules when submitting the manuscript for publication:

• The manuscript is not under consideration elsewhere and the research will not be submitted elsewhere until a final decision has been made by the journal• The manuscript is a trustful, original work without fabrication, fraud or plagiarism• The authors have made an important scientific contribution and are familiar with the primary data• The authors have read the manuscript and take responsibility for its content, and understand that if the paper, or part of it, is found to be faulty or fraudulent, they share responsibility

Authorship: Conflict of Authorship: Conflict of InterestInterestAuthorship: Conflict of Authorship: Conflict of InterestInterest

• All funding sources supporting the work and all institutional or

corporate affiliations of the authors must be acknowledged• The authors must certify that they have no commercial

association that might pose a conflict of interest in connection

with the submitted paper

Class activity:

Let’s look at your chosen papers. Tell us a little about why you chose them and what they are about. Let’s see how they are organized and how best to go about reading them.

Let’s hear about your own projects:

Give us a short, ten-minute summary of what you intend to do. In such situations you must assume that the audience is interested but not informed. Thus, the introductory sentences are most critical.

What elseWhat else

• Cover letterCover letter

• Figures presentationFigures presentation

• Endnote templateEndnote template

• Author responseAuthor response

Cover letterCover letter• Dear Editor:Please find enclosed our manuscript entitled “RNF138 is an E3 ubiquitin ligase that displaces Ku to promote DNA end resection and regulate DNA repair pathway

choice” that we wish to be considered for publication in Nature Cell Biology.•  • DNA double strand breaks (DSBs) are repaired mainly by non-homologous end joining (NHEJ) or homologous recombination. The cell cycle stage and resection of the DSB ends

are two key mechanisms that are believed to license DSB repair for the homologous recombination pathway. Moreover, Ku70/80 binds to DSBs in all cell cycle stages and is likely actively displaced from DSB ends to free the DNA ends for DNA end resection and thus homologous recombination to occur. However, exactly how such coordination occurs in vivo is largely unknown.

•  • In this paper, using a high throughput screen to identify E3 ubiquitin ligases that regulate homologous recombination pathway, we identified a novel E3 ubiquitin ligase, RNF138,

as a previously unknown regulator of homologous recombination. RNF138 is part of a small family of poorly characterized E3 ubiquitin ligases and is reported to be involved in Wnt signaling. We found that RNF138 is recruited to sites of DSBs and contains a robust DNA binding activity that is specific for single-stranded DNA or double-stranded DNA with 5’- or 3’- single-stranded overhangs but does not bind blunt-ended double-stranded DNA. When RNF138 is depleted from cells, DNA end resection is strongly inhibited thereby preventing the error-free homologous recombination pathway from being utilized and stimulating repair by the error-prone NHEJ pathway. We explored the mechanism(s) responsible for the inhibition of DNA end resection and found that the inhibition is upstream of CtIP and Exo1 nuclease activities, resulting in the inhibition of ATR activation. A further exploration of the mechanism revealed that RNF138 ubiquitylates the Ku80 protein and destabilizes its binding to DNA ends. Ku80 is part of a protein complex that binds the broken ends of DSBs and promotes repair by NHEJ. By destabilizing Ku80 binding, RNF138 promotes DNA end resection and the initiation of the homologous recombination repair pathway. This is the first report identifying an E3 ubiquitin ligase that regulates DSB repair choice in human cells.

•  • Highlights of our paper include:•  • A high throughput screen identified a novel E3 ubiquitin called RNF138 as a new positive regulator of homologous recombination pathway.• Depletion of RNF138 impairs homologous recombination, stimulates NHEJ pathway and sensitizes cells to DNA damaging agents such as IR and CPT. •  We are aware of Dr. Steve Jackson’s story (Cambridge-UK) on RNF138 and we have just learned from him that he just submitted his paper on RNF138 to NCB. In light of this and

because our manuscript is very complementary to his and that we are aware of his work we request coordinating submission of the two manuscripts.  •  • •  • Suggested reviewers: •  • 1- Dr. Roger Greenberg• Department of Cancer Biology• Abramson Family Cancer Research Institute• The Perelman School of Medicine at the University of Pennsylvania• 421 Curie Boulevard• 513 BRB II/III• Philadelphia, PA 19104-6160• Office: 215-746-2738• Fax: 215-573-2486• Lab: 215-746-7799• Email: rogergr@mail.med.upenn.edu•  

Typos and inconsistencyTypos and inconsistency

• ColorsColors

• FontsFonts

• StylesStyles

• SizeSize

SpellingsSpellings