Tossi Talk

8/8/2019 Tossi Talk

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Dipartimento di Scienze della Vita

Depar t ment o f L i fe Sc iences U

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Depar t ment o f L i fe Sc iences

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AnatomyAnatomy of of aa scientificscientific publicationpublication …………..

………….. and some.. and some adviceadvice onon howhow toto writewrite oneone

Prof. Alessandro Tossi [email protected]

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NATURAL & LIFE SCIENCESNATURAL & LIFE SCIENCES – – MAIN TYPES OF SCIENTIFIC PUBLICATIONMAIN TYPES OF SCIENTIFIC PUBLICATION

•• text bookstext books

•• specialized texts / handbooksspecialized texts / handbooks

•• chapters in thematic bookschapters in thematic books

•• congress proceedingscongress proceedings

•• articles on internetarticles on internet

•• patentspatents

•• technical reporttechnical report

online sourcesonline sources PubMed Central / MEDLINE

Chemical Abstracts Service

Other databases (ISI, Scopus)

University electronic libraryservices

Journal Publishers web pa e

scientific journal

•• pos erpos er

•• peer reviewed scientific articlespeer reviewed scientific articles

Google / Google scholar

TYPES OF SCIENTIFIC JOURNALTYPES OF SCIENTIFIC JOURNALSS

•• multidisciplinary (multidisciplinary (egeg. Nature, Science, PNAS). Nature, Science, PNAS)

•• monodisciplinarymonodisciplinary ((egeg. Biochemistry, J. Biological Chem.). Biochemistry, J. Biological Chem.)

•• sectorialsectorial ((egeg. Peptide Research, Antimicrobial Agents &. Peptide Research, Antimicrobial Agents & Chemo.TherChemo.Ther.).)

•• online (online (eses.. BioMedCentralBioMedCentral, PLOS), PLOS)

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TYPES OF SCIENTIFIC ARTICLESTYPES OF SCIENTIFIC ARTICLES

•• Review articleReview article

•• Full articleFull article

•• Communication / Letter / NoteCommunication / Letter / Note

•• CommentComment

•• EditorialEditorial

ANATOMY OF A SCIENTIFIC ARTICLEANATOMY OF A SCIENTIFIC ARTICLE

1)1) TitleTitle

2)2) AuthorsAuthors

3)3) AffiliationsAffiliations

4)4) Date of receipt and acceptanceDate of receipt and acceptance 5)5) Corresponding authorCorresponding author

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6)6) Abstract or SynopsisAbstract or Synopsis - simple

- compound (Objectives, Methods, Conclusions)

7)7) Key WordsKey Words

8)8) AbbreviationsAbbreviations

9)9) IntroductionIntroduction

10)10) Materials & MethodsMaterials & Methods ↑↓↑↓↑↓↑↓↑↓↑↓↑↓↑↓

ANATOMY OF A SCIENTIFIC ARTICLE (cont.)ANATOMY OF A SCIENTIFIC ARTICLE (cont.)

Figure with captionsFigure with captions

TablesTables

11)11) ResultsResults

12)12) DiscussionDiscussion

13)13) ConclusionsConclusions

14)14) AcknowledgmentsAcknowledgments

15)15) ReferencesReferences

16)16) Supplementary materialsSupplementary materials (only online)

RisultsRisults & discussion& discussion

(AppendixAppendix)

}

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writing a scientific publication ….. when and why

• Don‘t waitDon‘t wait until you have absolutely all the data … you never will

• At some stage you just must sit down and start writingsit down and start writing

• some good reasonsreasons for publishing results.

- ,,

- increases knowledgeknowledge in your area

- puts you on the researchresearch landscapelandscape

- its absolutely necessarynecessary forfor youryour carreercarreer

- its absolutely necessarynecessary toto obtainobtain fundingfunding

- its necessarynecessary forfor youryour self self--esteemesteem

- it generally is requiredrequired of of youyou inin anyany casecase

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the publication process

1)1) choose an appropriate journalchoose an appropriate journal (based on subject, impact etc.)

2)2) submit manuscriptsubmit manuscript (+ figures & supplementary material) to editor

3)3) editor 1editor 1stst decision:decision: is subject/quality suitable for the journal?

- If NONO, sends it back you choose another journal (maybe rewrite)

- If YESYES, sends it to 2 to 4 independent peer reviewerspeer reviewers

-

- accept as isaccept as is (very rare)

- accept with minor modificationaccept with minor modification answer reviewers comments

make suggested modifications

-- qualified accept with major modificationqualified accept with major modification new experiments

answer reviewer’s comments

extensive rewriting

- refuserefuse choose other journal, rewrite using reviewer critiques

– – – –

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Role of junior authors

• be insistentbe insistent – senior authors are often too busy to work on a paper

•• be patientbe patient – – senior authors have more experience, their requests

even if irritating usually make sense

•• prepare clear methods section:prepare clear methods section: (know what you did)

• prepare good quality figures and tablesprepare good quality figures and tables (follow journal instructions)

•• carry out an extensive literature searchcarry out an extensive literature search

•• keep a hard copy of each referenced paperkeep a hard copy of each referenced paper (for quick consultation)

•• quicklyquickly carry outcarry out focusedfocused experiments if necessaryexperiments if necessary

•• keep careful track of manuscript versionskeep careful track of manuscript versions

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GettingGetting startedstarted -- thinkthink aboutabout howhow toto organiseorganise thethe paperpaper::

• Title: precise and informative attract readers on Pubmed

• Abstract: provide all key information attract readers on Pubmed

• Introduction: what you did and why

• Materials/Methods: how you did it

• Results: your data

• Discussion: your interpretation of the data

• Conclusions: what we learned from your work

PAGE 8

organiseorganise your data first and then decide how to use ityour data first and then decide how to use it::

• prepare a complete set of figures and tablesfigures and tables

• collect all the necessary information on methodsinformation on methods used

• decide on the list andlist and placement of authorsplacement of authors (according to your

area’s hierarchical traditions), and then each author’s tasks

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• writing has to be simplesimple,, clearclear,, and toto thethe pointpoint..- not too compressed and no jargon or excessive abbreviation

- avoid a flowery literary stile and hyperbolae (extreemly is out).

• use the present tensepresent tense for known facts or results(... membranes are composed of phospholipids...)

• use the past tensepast tense for the results you are presenting, as you

writing

have completed the experiments (... the membrane wasdepolarised on treatment with the peptide ...)

• use the future tensefuture tense for prospective experiments

( .... experiments are required to determine if this is due tomembrane damage ...)

•• avoidavoid using first person ( we measured x x was measured )

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THE TITLE

• this should be descriptive of the paper

• make it appealing if possible (good bait on Pubmed)

• avoid acronyms (especially yours), symbols and trite oroverused terms (e.g. DON’t use novel )

THE ABSTRACT

• state the principal objectivesprincipal objectives of the investigation.

PAGE 10

• briefly describe key methodskey methods employed.•• summarizesummarize the main resultsmain results and principal conclusionsprincipal conclusions.

- it is normally a single paragraph, typically < 250 words.

- use the past tense (describes done experiments)

- only cite references if necessary (use full reference)- reduce acronyms and symbols to a minimum

- include only keykey quantitative parameters

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KEYWORDS

• 3 to 6. Must relate to the content of the paper.• they provide a profile of your paper for data banks.

• they are generally required by journals, which may or may not

provide a selection of keywords to choose from.

INTRODUCTION

• provides the justification of the work done.

• gives a brief overview on the state of the art in your area and

puts your work into context.

• cites relevant literature pertaining to your area that provides a

background or motivation for your work

• ends by briefly indicating what your intentions are and how your

work fills a gap in current knowledge

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MATERIALS / METHODS

• write this in the pastpast tense.

• include just just enough detail for a competent workercompetent worker to repeat experiments

[….3 mg of protein were dissolved in phosphate buffer (pH 7.5)….. ]

• include information on reagents, tissues or strains, methods employed,instrumentation [ … reagent grade methanol was from Sigma (DE)… ]

•• be precise but not pedanticbe precise but not pedantic – affects reviewer’s assessment of your work

PAGE 12

• do NOTNOT include results in this section.

•• keep it lightkeep it light – use supplementary materialssupplementary materials / appendixappendix for detailed

theoretical approaches, instrumental methods etc.

• provide details on data analysisdata analysis and statistical methodsstatistical methods used

• can shorten by citing references to published methodsreferences to published methods, – try to balance

concisenessconciseness and informationinformation provided

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RESULTS

• Present data in clear figures and tables, with concise explanationsin the text.

• Be selective – only relevant data and not too much detail (you can

always use the supplementary materials section).

• Try to combine the data into the minimum amount of figures and

tables but don’t make them too complicated. Use multi-panel

figures or indented panels logically .

supplementarysupplementarymaterialmaterial

A B

C D

Be carefulBe careful

with figurewith figure

manipulationmanipulation

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RESULTS (cont.)

• Present results clearly and brieflybriefly commentcomment - leave extensiveinterpretation/hypotheses for the Discussion section.

• comment each result so as to provide a smoothsmooth transitiontransition to the

next experiment (logical progression

optimized flow).• Don’t state the obvious – its irritating

• -

reader. (Provide concise and competent description of howcomplex results were derived and refer to a more exhuastive

supplementary section or appendix for a more complete

treatment) .

• Provide a list of the abbreviations and symbols you use.

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CONCLUSIONS

• May be the last paragraph of the discussion section or appear asa separate section.

• Start with a few phrases to summarize the work donesummarize the work done.

• List the main “lessons learnedlessons learned” or “knowledge gainedknowledge gained”• Presents future perspectivesfuture perspectives.

- N.B. it is NOTNOT a repetition of the Abstract.

- the abstract and conclusions are often the only sections that arecarefully read so make the best use of them to define your work.

AKNOWLEDGEMENTS

• Be polite - thank people for material, technical assistance or help

with the manuscript

• Be clever – thank funding agencies

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Usage

IN TEXT IN REFERENCE LISTIN TEXT IN REFERENCE LIST

Superscript NSuperscript N°° normally in ordernormally in orderof appearanceof appearance

Bracketed NBracketed N°° normally in ordernormally in order

REFERENCES

• Each journal has its OWN format for literature referencesEach journal has its OWN format for literature references

•• Programs like Endnote can help organise themPrograms like Endnote can help organise them

First author normally inFirst author normally in& publ. year alphabetical order& publ. year alphabetical order

NumberedNumbered referencereference: (1) (1,4,8) (1, 4: (1) (1,4,8) (1, 4--8)8)

NamedNamed referencereference (Perry, 2008); (Perry and Roche, 2008); (Perry(Perry, 2008); (Perry and Roche, 2008); (Perry etet al., 2008)al., 2008)

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Reference formats

•• extended single ref.extended single ref.with titlewith title

•• single ref. no titlesingle ref. no title

•• aggregated, no titleaggregated, no title

(often mixed with methods(often mixed with methods

references)references)

1 Harder et.al., (2001). J. Biol. Chem. 276, 5707

2 Jia et al. (2001) Gene 263, 211

•• compressedcompressed

Which ever you choose, you MUST be consistentWhich ever you choose, you MUST be consistent

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EvaluatingEvaluating aa publicationspublications recordrecord

•• NN°° of of publicationspublications

•• ImpactImpact factorfactor of of publicationspublications

•• PlacementPlacement asas authorauthor

°° --

(Thompson(Thompson webweb of of science) orscience) or ScopusScopus ((ElsevierElsevier))

•• HH--indexindex-- a scholar with an index of h has published n papers h of a scholar with an index of h has published n papers h of

of which have been cited by others at least h timesof which have been cited by others at least h times

-- reflects both the number of publications andreflects both the number of publications and

the number of citations per publicationthe number of citations per publication

-- highly dependent on the age of the scholarhighly dependent on the age of the scholar

h ≈ age in serviceh ≈ age in service

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Common forms of data presentation at conferences

– keynote lecture (45 – 1 hr)

– invited lecture (20 min each, usually 5 per session)

– poster (poster session) – invited poster oral presentation (5 min)

– book of abstracts (½ page abstract)

– conference proceedings (2 pages in book) – conference special issue (article or review)(limited)

Preparation process

• Send abstract (deadline 3 - 6 months before)

• Prepare poster (1-2 weeks before)

• Prepare proceedings (1-2 weeks before)

• Prepare article for special issue (1-3 months after)

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Preparing a poster

its only one of many and people have little time to read it … so…

Maximum parsimony

Minimum amount of LARGE text

Maximum clarity

Pleasant & effective graphics

, .

Presenting a poster

Accept your posters location

Provide an envelope for address cards

Or provide some A3 copies of the poster

Stand next to it during your poster session

Send information if requested

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YOUR TARGET (5 main types of poster readers)

• The genuinely interested readerThe genuinely interested reader (RARE, comes anyway and reads it all)

• The browserThe browser (comes because he/she selected it from the abstracts)

• The drifterThe drifter (drifts past and gets hooked by graphics or title)

• The collaredThe collared (you drag him/her to the poster, or block a wanderer)

• The judging committeeThe judging committee (for best poster)

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ANATOMY OF A THESISANATOMY OF A THESIS

Cover :Cover : Normally hardback, withNormally hardback, with

Inside cover:Inside cover: copy of front covercopy of front cover

Index:Index: page Npage N°° of of chapters, sections, subsectionschapters, sections, subsections

(Index of figures and tables)(Index of figures and tables) (optional)(optional) Synopsis in EnglishSynopsis in English

Synopsis in own languageSynopsis in own language

institutioninstitution

facultyfaculty

Chapter 1:Chapter 1: introductionintroduction

Thesis aimsThesis aims

Chapter 2:Chapter 2: materials and methodsmaterials and methods

Chapter 3:Chapter 3: resultsresults

Discussion and conclusionsDiscussion and conclusions

BibliographyBibliography :: full reference listfull reference list

AppendicesAppendices (optional)(optional)

coursecourse

authorauthor

titletitle

date & academic yeardate & academic year

supervisorsupervisor

coco--supervisorssupervisors

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IndexIndex

-- prepare a tentative versionprepare a tentative version before you start writingbefore you start writing – – its very helpfulits very helpful

-- reflects the hierarchical organisation of the thesisreflects the hierarchical organisation of the thesis

-- orginiseorginise in CHAPTERS, SECTIONS and SUBSECTIONSin CHAPTERS, SECTIONS and SUBSECTIONS

1 INTRODUCTION …………………………………..........1

1.1 The immune system…………………………........31.1.1 Innate immunity…………………………... 4

1.2.3 Adaptive immunity………………………... 7

1.2 Antimicrobial peptides…………………………...8

1.2.1 Roles in immunity and expression……… 8

1.2.2 Structure…………………………………… 10

1.2.3 Mode of action……………………………….11

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Synopsis in EnglishSynopsis in English -- needed if your thesis is in your own languageneeded if your thesis is in your own language

-- useful for your CV (abroad)useful for your CV (abroad)

Synopsis in own languageSynopsis in own language -- recognises your National System if thesis is in Englishrecognises your National System if thesis is in English

-- useful for your CV (at home)useful for your CV (at home)

-- nice for your family to know what you are doingnice for your family to know what you are doing

Chapter 1Chapter 1:: INTRODUCTIONINTRODUCTION

-- Describe the state of the art in your areaDescribe the state of the art in your area

-- Provide general and background knowledge connected with itProvide general and background knowledge connected with it

-- Describe and discuss known techniques, hypotheses and algorithmsDescribe and discuss known techniques, hypotheses and algorithms

Thesis aims:Thesis aims: -- What you intended to doWhat you intended to do

-- Why it was importantWhy it was important

-- What you hoped to findWhat you hoped to find

objectivesobjectives

relevancerelevance

newnew knowledgeknowledge

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Chapter 2Chapter 2:: MATERIALS & METHODSMATERIALS & METHODS

-- detailed experimental protocols (legacy for your lab)detailed experimental protocols (legacy for your lab)

-- some figures & tables (calibration data, yields, quality control)some figures & tables (calibration data, yields, quality control)

-- information on strains, tissues, algorithms etc.information on strains, tissues, algorithms etc.

-- data and statistical analysesdata and statistical analyses

Chapter 3:Chapter 3: RESULTSRESULTS

-- your datayour data

-- your interpretation of data itemsyour interpretation of data items

Discussion and conclusions:Discussion and conclusions: 1 or 2 pages. Global data interpretation,1 or 2 pages. Global data interpretation,

hypotheses, knowledge advance and futurehypotheses, knowledge advance and future

perspectivesperspectives

Bibliography:Bibliography: -- full reference listfull reference list

-- Exhaustive but not excessiveExhaustive but not excessive

-- DO NOTDO NOT leave it till the endleave it till the end – – ongoing with thesis preparationongoing with thesis preparation

AppendicesAppendices -- databases, computer code, mathematical treatments etc.databases, computer code, mathematical treatments etc.

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Thank you and good work

Tossi Talk

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