Scientific Writing Barbara Janssens 2012


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Scientific Writing Workshop: Abstracts, Articles, Grants, Cover Letters, Press releases

The goal of the scientific writing workshop is to effectively write peer-reviewed articles in English, but also grant proposals, cover letters and columns or press releases for a broader public. We will cover
· Background to peer review and publishing

· Manuscript structure

· Language and style techniques

· Abstract and title writing

· Science communication

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Scientific Writing Barbara Janssens 2012

  1. 1. SCIENTIFIC WRITING Heidelberg, March 2012 Scientific Writing Dr. Barbara Janssens, PhD Career Manager 1
  2. 2. SCIENTIFIC ...WRITING <-> ...CAREER 1.  Writing, editing, career development ○  A career in science ○  Editor ○  Career ○  About publishing and impact ○  Before writing 2.  Publication ethics 3.  Writing a paper ○  IMRAD structure ○  How to get started & „sculpt“ ○  Titles and abstracts ○  How to submit with cover letter 4.  Tips on language/style 5.  Writing an application 6.  Science Communication with the Public http://www.biotecvisions.comMY CVÒ  Master Biotechnology (Ghent, Belgium, 1997)Ò  Erasmus in Uppsala, SwedenÒ  PhD cell-cell adhesion/migration (Ghent 2002)Ò  Postdoc (+ 2 kids) in Paris (Institut Curie) on Rho/ARF GTPase cell biology (2002-2005)Ò  Editor at Wiley-Blackwell (2005-2010) É  Heidelberg 2005: 1-year Editorial Trainee position at Wiley-VCH in Weinheim; launch of BTJ in 2006 É  More than editing: peer review, marketing, controlling, accounting, customer service, journal production, strategics, research, BIBLIOMETRICS É  Managing/Executive Editor of BTJ and Publishing Editor for biotech portfolioÒ  Teaching scientific writing since 2008Ò  PhD Career Manager at DKFZ Heidelberg in 2011 2
  3. 3. EDITOR: JOHN WILEY & SONSÒ  Founded in 1807Ò  Over 5000 employees in USA, Europe, Canada, Asia, AustraliaÒ  2007: Wiley-Blackwell STMS É  science technical medicalÒ  Products include É  1500 peer reviewed journals É  3 M articles É  6500 books (also online) É  Major reference works, databases, lab manuals, WIREs,… É  Online open: author pays for non- subscribers EDITOR: LIFE SCIENCE JOURNALS USA EUROPE USA Asia 3
  4. 4. EDITOR: BIOTECH JOURNALS Weinheim 上海市
 (Germany) (China) Hoboken (NY, USA) Oxford / Chichester (UK)EDITOR: MAGAZINEÒ  Since June 2009Ò  Hottest news & discussionsÒ  Fully interactive PDFÒ  Printed in WB biotech portfolioÒ  Columns É  GettingPublished É  BiotecCareers 4
  6. 6. A JOB IN SCIENCE… X 40 Richard Bolles, What Color Is Your Parachute? LIFE/WORK PLANNING L/W-PÒ  France: Daniel Porot It´s easier to act yourself É into a new way of thinking, than it is to think yourself É into a new way of acting.Ò  Germany: John Webb Richard N Bolles É É  www.lwp-seminare.deÒ  US: Richard N. Bolles É 6
  7. 7. 2 DAYS OR 2 HOURSÒ  Where do we go shopping today?Ò  Focus on É  Publishing and ethics? É  Writing a paper? É  Writing a CV? É  Language and style?WHAT SCIENTISTS WRITEž  Papersž  Curriculum vitaež  Grantsž  Reportsž  Proposalsž  Web pagesž  Conferencesž  Lecturesž  Meetingsž  Postersž  ... 7
  8. 8. WHY SCIENTISTS WRITEž  „Your research is not complete until you publish it“ (Ibn al Haytham, 1021) —  Make a permanent and accessible record of your findings —  Avoid others repeat unnecessarilyž  Publish or perish....ž  Publico ergo sum!ž  Stuff your CV (you need papers to get grants) —  More papers = more eminent scientist (Hirsch factor)WHERE DO YOU FIND IT?Ò  Journals, scopes, readership: who reads and cites your papers?...Ò  Think of your audience!!!Ò  Search sites ×  PubMed/Medline ×  Google Scholar ×  Scopus (Elsevier) ×  CrossRef ×  BioMed experts ×  Open Access journals ×  ISI Web of Science (Thomson) – IFÒ  Downloads vs citations 8
  9. 9. IMPACT FACTOR (IF) Devised by Eugene Gar field, founder of ISI (Chairman Emeritus of Thomson Scientific) 1955  Slide byMatteo 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. Citations   C12   published   Articles   A1   A2   time   published   Year  1   Year  2   Year  3   C12 IF (Year 3) = A1 + A2 Slide adapted from Matteo Cavalleri 9
  10. 10. 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)Ò  Only cited references from articles in the census period, and which refer to articles within the target period are countedÒ  Only cited references indexed in the Scopus database are counted 10
  11. 11. BIBLIOMETRICS.... Web of Knowledge Scopus Faculty of 1000 (post-publication peer review) Australian journal ranking A*, A, B, C              BEFORE WRITING... 11
  12. 12. BEFORE WRITING…ž  What would you do?ž  Read read read...ž  Assemble data1.  Which journal/scope?2.  Which format?3.  Who will be author?4.  Check instructions to authors!READ… BUT HOW?Ò  How do you find articles?Ò  How do you read them?Ò  How can you be critical? É  If a paper is difficult to follow/understand: ask yourself how you like the writing…Ò  How do you keep track of articles? É  Web of Science É  Self archiving É  Mendeley 12
  14. 14. CHOSE TARGET JOURNAL Journal XXX XXX Publishes similar work? Scope/recent content? Quality/impact? Fast publication? Charges for pages, color, open access? Article format/length?TIMING 14
  15. 15. SCIENTIFIC WRITING 1.  Introduction and basics ○  introduction ○  About journals and peer review ○  Online access and searches, IF ○  Before writing 2.  Publication ethics ○  Authorship ○  Plagiarism 3.  Writing ○  IMRAD structure ○  How to get started & „sculpt“ ○  How to submit with cover letter ---------------------------------------- 4.  Tips on language/style 5.  Practical abstract/title writing 6.  Science communicationAUTHORS 15
  16. 16. AUTHORSÒ  Author = significant contributorÒ  Providing reagents, scientific/moral support = acknowledgementÒ  First author =„paternity“ („the one without whom the work could not have been accomplished“)Ò  Last author =„Senior author“ (often the group leader or head of Department)Ò  Corresponding author (usually first and/or last) = assumes responsibility for writing, submiting, revising and answering questions after publication. Most prestigious.Ò  „These authors have contributed equally“Ò  Decide authors and order as early as possibleÒ  Which author you are will be important for your CV – but being an author in the first place is what mattersAUTHORSÒ  FIRST AUTHOR: Weary graduate student who spent hours doing the work.Ò  SECOND AUTHOR: Resentful graduate student who thinks he or she spent hours doing the work.Ò  THIRD AUTHOR: Undergraduate just happy to be named.Ò  FOURTH AUTHOR: Collaborator no one has ever met whose name is only included for political reasons.Ò  FIFTH AUTHOR: Postdoctoral fellow who once made a chance remark on the subject.Ò  SIXTH AUTHOR: For some reason, Vladimir Putin.Ò  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 16
  17. 17. GHOST AUTHORS?Ò  Ghost authors: individuals not named as authors but who contributed substantially to the workÒ  Honorary authors: named authors who have not met authorship criteriaÒ  Confidential survey of corresponding authors of 809 articles É  156 articles (19%) had evidence of honorary authors É  93 articles (11%) had evidence of ghost authorsFlanagin et al., Prevalence of Articles with Honorary Authors and Ghost Authors in Peer-Reviewed Medical Journals. J. Am. Med. Assoc. 1998, 280, 222-224. ACKNOWLEDGEDÒ  FromPNAS: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. 17
  18. 18. ETHICS/PLAGIARISMÒ  What is plagiarism?Ò  The „Guttenberg syndrome“Ò  Plagiarism is the representation of another persons words, ideas, or information as if they were ones ownÒ  ... Do not publish previously published work!Ò  However you may reuse some of your own and „CITED“ [1] materialÒ  Check COPE - the Committee on Publishing Ethics (Ò  Check „copyright transfer agreement“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 forfinancial consideration to the Contributor.(iv) Nothing herein shall permit dual publication in violation of journal------------------------------- 18
  19. 19. PLAGIARISM CHECKS É  EVE2, OrCheck, CopyCheck, and WordCHECK, to name a few É  eTBLAST and Déjà vu É É É É Implemented for all W-B journalsSIMILARITY REPORT 19
  20. 20. 30% = PLAGIARISM?Individual for each article…a)  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 considerationb)  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 ( CITED = PLAGIARISM  "The Ghost Writer„ : writer turns in anothers 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 papers 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. Ò 20
  21. 21. CITED BUT STILL PLAGIARISMÒ  "The Forgotten Footnote„: writer mentions an authors 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.Ò  "The Misinformer„: writer provides inaccurate information regarding the sources, making it impossible to find them.Ò  "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.Ò  "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.Ò  "The Perfect Crime„: Well, we all know it doesnt 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.orgSCIENTIFIC WRITING 1.  Introduction and basics ○  Mutual introductions ○  About journals and peer review ○  Online access and searches, IF ○  Before writing 2.  Publication ethics 3.  Writing ○  IMRAD structure ○  How to get started & „sculpt“ ○  How to submit with cover letter ---------------------------------------- 4.  Tips on language/style 5.  Practical abstract/title writing 6.  Science communication 21
  22. 22. NOW THE MANUSCRIPTSTART 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) 22
  23. 23. WRITE AT BEGINNING! Serial position effect Drain needs Recall unblocking!! Mustn’t forget to do the shopping... I’m hungry... t Primacy Recency Deese and Kaufman, J. Exp. Psychol. 1957, 54, 180-187.�© Andrew Moore Murdock , J. Exp. Psychol. 1962, 64, 482-488.� FIRST LETTER… BRAIN DOES THE REST Ò 23
  24. 24. MANUSCRIPT DRAFT- IMRAD -Ò  TitleÒ  Abstract1.  Introduction2.  Materials and Methods3.  Results4.  Discussion5.  Figures and TablesÒ  Cover letterWRITING  ORDER?   24
  25. 25. ...WRITING ORDER1.  Figures and TablesÒ  TitleÒ  Abstract2.  Results3.  Materials and Methods4.  Introduction5.  DiscussionÒ  Cover letter...WRITING ORDERÒ  Figures and TablesÒ  TitleÒ  Abstract2.  Results3.  Materials and Methods4.  Introduction5.  DiscussionÒ  Cover letter 25
  26. 26. START WITH THE DATAÒ  This will cut your writer‘s block!Ò  (Pictures of gels, graphs etc)Ò  Order in Figures: write legendsÒ  What is the story?Ò  (Title, abstract draft)FIGURESÒ  Should tell the story - quick readers will read the abstract and check the figuresÒ  Are the data comprehensive?Ò  Not too many panels (6)Ò  If too many data: provide as supporting materialÒ  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 figureÒ  Include a concluding visual scheme, diagram, overview 26
  27. 27. FIGURES IIÒ  Detail how many times the experiments were performedÒ  Detail the number of animals/replicatesÒ  Provide clear statistical analysisÒ  Should enable the reader to fully understand the figureÒ  Ensure everything is described: abbreviations, symbols etc.FIGURE OR TABLE?Ò  Table É  Recording data (raw or processed) É  Showing actual data values, precision É  Multiple comparisons É  Has a short title and footnotesÒ  Figure É  Showing trend or picture É  Shape rather than numbers É  Compare few elements É  Has a legend with all details needed 27
  28. 28. KEEP SOURCE DATA! FIGURE QUALITYÒ  resolution should be at least 400 dpiÒ  to be printed either to fit the width of one column (8 cm) or to fit the width of the page (17 cm)Ò  Avoid extreme height-to-width ratios (“noodles” and “skyscrapers”)Ò  Resizing: Increasing the resolution of an image will result in a proportionally smaller image size É  20 x 30 cm 96 dpi -> 400 dpi 5 x 7 cm É  do not embed TIFF files in DOC files; JPEG files will not be compressed 28
  29. 29. CHART RESOLUTIONÒ  Excel: scale the chart to at least 400% of the expected printing sizeÒ  Select the chart, copyÒ  PowerPoint: Edit-“Paste special…“: paste as PNG file PIMAGE PROCESSING Regulations by Rockefeller University Press (now adopted by most journals) Ò  No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. Ò  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. Ò  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. Ò  If the original data cannot be produced by an author when asked to provide it, acceptance of the manuscript may be revoked. 29
  30. 30. MANIPULATION OF BLOTS Brigthness and contrast adjustments.© 2004 Rockefeller University Press Rossner M , Yamada K M J Cell Biol 2004;166:11-15 STICK  TO  THE  FIGURE  GUIDELINES...   30
  31. 31. ...WRITING ORDER1.  Figures and TablesÒ  TitleÒ  Abstract2.  Results3.  Materials and Methods4.  Introduction5.  DiscussionÒ  Cover letterTITLEž  The first impression counts...ž  A strong title will attract readers/citationsž  Keep it short: 15 wordsž  Clear, informative, raise curiosityž  Interesting and easy to readž  Main message of the paperž  Remember Medlinež  Key wordsž  Start with a „quick go“, remodel during writing process and rethink for some days when the whole manuscript is readyÒ  Test: 31
  32. 32. EXAMPLES: COMPAREÒ  “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.”Ò  “Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.”Ò  “Preliminary canine and clinical evaluation of a new antitumor agent, streptovitacin.” (Clin. Res. 8:134, 1960)Ò  „Evidence for women dreaming more often about food than men.“TITLES TO AVOIDÓ  Vague titlesÓ  Titles starting with Ó  „Studies on..“ „Implications of…“ Ó  „Characterization of...“ „Involvement of…“ Ó  „Observations on...“ „Evidence for…“ Ó  „Investigations into...“ „Insights in…“ Ó  “The involvement of protein x in signal transduction pathway y” —  -> „Protein x does y in this signal transduction pathway “ PÓ  Titles with jargon or abbreviationsÓ  Titles with „new“ and „novel“ (all research is new) 32
  33. 33. KEYWORDSÒ  Donot repeat title words – these come up anyhowÒ  Most cited versus never cited...Ò  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 SYNTAXÒ  “Preliminary canine and clinical evaluation of a new antitumor agent, streptovitacin.”(Clin. Res. 8:134, 1960)Ò  „Evidence for women dreaming more often about food than men.“Ò  ... 33
  34. 34. HAVE A LOOK AT TITLES Reviews Reviews + Yoghurt fermentation at elevated temperatures by Essential fatty acids: Biochemistry, physiology and - strains of Streptococcus thermophilus expressing a small heat-shock protein: pathology Application of two-plasmid system for + Metagenomics: An inexhaustible access to constructing food-grade strains of nature‘s diversity Streptococcus thermophilus - New insights into mechanisms of growth and b- carotene production in Blakeslea trispora Production of biopharmaceuticals and vaccines in plants via the chloroplast genome +/- +/- Research Ar ticles Separation of catechin compounds from different Application of inkjet printing to tissue engineering + teas +/- Production and characterization of theromstable Research Ar ticles α-amylase by thermophilic Geobacillus stearothermophilus Arenicola marina extracullar hemoglobin: A new promising blood substitute +/- - Molecular characteriazation of rpoB gene mutations in rifampicin-resistant Mycobacterium tuberculosis strains isolated Directed evolution of industrial biocatalyst 2- deoxy-D-ribose-5-phosphate aldolase + - from TB patients in Belarus +/- Investigating pH and Cu(II) effects on lipase Bio-electrosprays: The next generation of activity and enantioselectivity via kinetic electrified jets - and spectroscopic methods +/- Metabolic flux analysis of the two astaxanthin- A rapid, high content, in vivo model of producing microorganisms Haematococcus glucocorticoid-induced osteoporosis pluvialis and Phaffia rhodozyma in the pure and mixed cultures Never cited...........well citedABSTRACTž  Hardest part to writež  Second most important partž  Maximum 200 words (Medline truncates at 250 words)ž  What are the significant results?ž  Important methodology (in vitro vs. in vivo, human, model systems)ž  What are the conclusions/implications?ž  Start with writing these in bullet points and take time to re- re- and re-write this part with some distancež  Write in PAST TENSEž  NO citations, avoid non-standard abbreviations 34
  35. 35. © Andrew Moore Drain needs recall unblocking!! PI3K Mustn’t forget to do the shopping... I’m hungry... t primacy recencyOPTIMIZE ABSTRACTÒ  Be specific, not just one word É  e.g. womens fiction not fiction.Ò  Key phrases need to make sense within the title and abstract and flow well.Ò  Focus on a maximum of three or four different keyword phrases rather than try to get across too many points.Ò  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. 35
  36. 36. 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] ABSTRACTÒ  Developed in the late 1980s and early 1990s to assist health professionals in selecting clinically relevant and methodologically valid journal articlesÒ  Mainly medicalÒ  Makes text mining (search engines) easierÒ  Could start to be used in life sciences (MedLine encourages) 36
  37. 37. GRAPHICAL ABSTRACTÒ  Startedin chemical journalsÒ  VISUALISE the main message in ONE figure É  Chemical reaction É  Signal transduction pathway É  Hypothesis É  Structure É  Etc…LAY ABSTRACTÒ  Sometimes asked at submissionÒ  Summary for non-expertÒ  Here you CAN say why it is newÒ  Always write this, it can be useful É  In cover letter to convince Editor É  After acceptance to highlight your work É  To explain your friends and family 37
  38. 38. EDIT AN ABSTRACTÒ  Mark key statements É  Doyou get what it is about? É  What could be left out?Ò  Firstand last sentence: strong?Ò  Positive wordingÒ  Sentence lengthÒ  Suggest one or two alternative titlesÒ  What would you write in a „lay“ abstract?EDITORIAL CORRECTIONS 38
  39. 39. ...WRITING ORDER1.  Figures and TablesÒ  TitleÒ  Abstract2 .  Results3 .  Materials and Methods4.  Introduction5.  DiscussionÒ  Cover letter 39
  40. 40. RESULTSÒ  Follow the figures: Present the experiments performed in a logical and clear manner. Why did this lead to the next experiment?Ò  Written in the PAST TENSEÒ  Provide statistical analysis and clearly indicate significant dataÒ  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 discussionÒ  Do not lose in technical details („we transfected and then purified cell extracts and then separated...“): these go to the M&MÒ  Be SELECTIVEÒ  Present your results ONCE, either in the text, OR a Table OR FigureMATERIALS & METHODSÒ  Should be concise but completeÒ  Written in PAST TENSEÒ  DO NOT include any results!Ò  A colleague should be able to repeat the experimentÒ  All new reagents, sequences, etc should stated;Ò  New method: provide ALL detailÒ  Standard procedures: cite and only mention modificationsÒ  If too lengthy: decide afterwards if parts can be cut or removed to supporting informationÒ  Write 20 mL (not ml), 5 mm, 3 min (not mins), kDa (not Kda; molecular mass – not weight), M (not mole)   Check chemical nomenclature 40
  41. 41. FUNNY M&MÒ  “After standing in boiling water for an hour, I loaded the sample on a gel…..”Ò  “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)Ò  “Employing a straight platinum wire rabbit, sheep and human blood agar plates were inoculated….”Ò  “Lying on top of the small intestine, we observed a small transparent thread”Ò  “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 ORDERÒ  TitleÒ  Abstract1.  Figures and Tables2.  Results3.  Materials and Methods4 .  Introduction5.  DiscussionÒ  Cover letter 41
  42. 42. INTRODUCTIONÒ  Provides the background to the studyÒ  Can be written in PRESENT TENSE (= existing knowledge)Ò  Details the results from relevant published studies (difference between we demonstrated – it was demonstrated – it has been demonstrated – it is known)Ò  Explains what is still unknownÒ  Describes why the work was carried out and what the aim of the study wasÒ  Enables a non-expert to understand the rationaleÒ  Try to cite relevant review articles rather than going back to all basic papersÒ  State your principal results and conclusions in one sentenceINTRODUCTION Ò  Donot keep the reader in suspense: Tell the audience at the start that the butler did it. [Which they already know anyway, because they’ve read the abstract……..] Ò  Decisions about what is or is not interesting should be left up to the reader. 42
  43. 43. ...WRITING ORDERÒ  TitleÒ  Abstract1.  Figures and Tables2.  Results3.  Materials and Methods4.  Introduction5 .  DiscussionÒ  Cover letterDISCUSSIONÒ  QUICKLY summarize the findingsÒ  This is not just the results presented in another format, they need to be discussed in the wider context of the fieldÒ  What are the implications for future work?Ò  Systematically compare findings with supporting and/or conflicting literatureÒ  Discuss implications and applications, future directions to takeÒ  Be clear, honest, don‘t over-interprete but also don‘t minimizeÒ  Are there any models/rules that can be established?Ò  If it was a model system, what are the implications for the human system? Parallels, differences?Ò  If primarily in vitro studies, what is the scope for further in vivo studies? Relation to published in vivo studies? 43
  44. 44. REFERENCESÒ  The references must comply to house styleÒ  Ensure that they are cited in numerical order and that every reference is citedÒ  The work cited should be fair and balancedÒ  Ensure that credit is given to the original discoveries, including back-to-back publicationsÒ  Use a reference manager (e.g. Endnote) and correctly format the citations and ref listNOW THINK LIKE REFEREE1. 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? 44
  45. 45. KEEP IT SHORT É  600-700 words = one typeset page - excluding figures. (12000 words = 20 pages) É  Introduction < 1000 words É  Concluding section < 300 wordsÒ  Shorten: É  Latest publications of relevance É  Keep details to minimum É  Concentrate on bullet points, 3 key arguments É  Cover only as much historical background as is necessary for the contextualization of the topic for a broad readership. É  Avoid detailed lists of genes, gene products, acronyms etc. -> TableKEEP  WITHIN  THE  PAGE  LIMIT   45
  46. 46. ...WRITING ORDERÒ  TitleÒ  Abstract1.  Figures and Tables2.  Results3.  Materials and Methods4 .  Introduction5.  DiscussionÒ  Cover letterLAST BUT NOT LEAST: COVER LETTERÒ  Convince the editor of the importance of your workÒ  State in a few sentences what the paper is about (not abstract)Ò  Why does it fit the scope of the journal?Ò  Why is it novel?Ò  Why will it be of interest to reviewers? If you state non- preferred reviewers, you may explain whyÒ  Write this for the EDITOR 46
  47. 47. COVER LETTER = Getting through the first editorial assessment... ...or will not be sent out for peer reviewWHAT THE EDITOR WANTS?Ò  OURS É  Originality É  Understandibility É  Reliability É  SuitabilityÒ  Poorlywritten or conceived papers will be rejected editorially 47
  48. 48. COVER LETTER EXAMPLEDear 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 EXAMPLEDear 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 deser t 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, 48
  49. 49. COVER LETTER QUOTESÒ  “It gives me immense satisfaction to be able to share with you an additional application of….”Ò   “We, the Arthurs of this mansucript …”Ò  “The conception of Chapter 1..”Ò  “We hope that paper should priority handing”Ò   “I would like to express my honour to submit our hard work to your respected journal”Ò  “Dear Sir, Thank you for the sweet reviewing process and find here the responce for the reviewers comments”Ò   “After deep thinking of the comments, we made statement as follow:” Thanks to Lucie and Uta, EJLST and ELSNOW SUBMIT   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 49
  50. 50. SUBMIT ONLINE:Ò 50
  51. 51. THEN BE PATIENTÒ  The editors will try to get back to you as soon as possible É  Immediate decision within 1 week É  Peer review within 4 weeks is fast! É  You may inquire after 6 weeksAFTER DECISIONÒ  Always sleep over the referee commentsÒ  Reply correctly, especially if „rebuttal“Ò  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!Ò  The revised version has to be PERFECT – it will save a lot of time for all parties involved. 51
  52. 52. EDITINGÒ  Language vs peer review/editing É  Badly written -> reject É  Poor language -> language polishing É  Small mistakes -> copy-editorÒ  Shashok K. Content and communication: How can peer review provide helpful feedback about the writing? É  BMC Medical Research Methodology 2008, 8:3, doi:10.1186/1471-2288-8-3. http:// 52
  53. 53. … ACCEPTED   Celebrate!   Cite per DOI (Digital object identifier) ○  = Publisher/MSnumber   Publication times…. Ø  Author Ø  Signed copyright transfer agreement Ø  Final figures/text Ø  Galley proof corrections Ø  Publisher Ø  Copy-editing Ø  Typesetting Ø  Online publication Ø  Issue and/or print: pages assignedSTYLE = CLARITYÒ  Writeto be understoodÒ  Think of your audienceÒ  Make information accessibleÒ  Make reader feel comfortableÒ  THINK what you want to say É  Clear thinking = clear writingÒ  Arrange your thoughts in a logical order (MIND MAP) 53
  54. 54. #  LANGUAGES…  Ò  …  different  challenges!  Ò  Sentences  too  long/too   short  Ò  False  friends  Ò  Commas  SENTENCE STRUCTUREÒ  SimpleÒ  PreciseÒ  ConciseÒ  Topic near the beginning!Ò  Active tense where possibleÒ  KISS Ð  Keep   Ð  It   Ð  Short  and   Ð  Simple   54
  55. 55. SENTENCE STRUCTUREÒ  Which sentence is easier to understand? É  The primary site of contact with airborne allergens, irritants, pathogens and other proinflammatory agents is the pulmonary ephithelium É  The pulmonary epithelium is the primary site of contact with airborne allergens, irritants, pathogens and other proinflammatory agentsSENTENCE STRUCTUREÒ  Often splitting in two is better, even if result is longer: É  Wiley-VCH is a Weinheim, Germany, global STM publisher specialized in chemistry and life sciences, belonging to the Wiley-Blackwell group. É  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. 55
  56. 56. PARAGRAPHSž  Units of thought, not lengthž  Provide visual reliefž  Contain related thoughtsž  Thoughts in logical orderž  Consistent organizationž  Use topic sentences —  At beginning or end —  Rarely in the middle (unless preceding is transitional) © Andrew Moore Drain needs recall unblocking!! PI3K Mustn’t forget to do the shopping... I’m hungry... t primacy recency 56
  57. 57. SOME TIPSÒ  Avoid vague terms such as trendsÒ  Be very precise and clearÒ  “The cells increased following treatment with” – what characteristic of the cells increased: size, number?Ò  Data = results; datum = result; use the correct verb form (also criteria/criterion etc.)Ò  Careful with embedded phrases É  Avoid separating subject and verbENGLISH  PUNCTUATION 57
  58. 58. MORE TIPSÒ  Be cautious with imprecise words: É  Several, some, many, affected, somewhat, quite, relativelyÒ  Don‘t add doubt unnecissarily. Could you replace... É  Could -> can É  Would -> will É  Hopefully -> Possibly É  Difficulty -> challenge 58
  59. 59. PAST VS PRESENT TENSEÒ  Past tense: for a completed study É  what was done and foundÒ  Present tense: for what is always true or always there É  An example is….Ò  Modal tense: doubt É  This may influence…ACTIVE VS PASSIVE É  Avoid passive (is, was, are, being...) É  Use active: the subject of the sentence performs an action Ð  The man was bitten by the dog - pass Ð  The dog bit the man - active É  Only use passive if you cannot use the „we“ form Ð  Gelelectrophoresis was used - pass Ð  We used gel electrophoresis – active É  Example from Adam Ruben Ð  ACTIVE VOICE: We did this experiment. Ð  PASSIVE VOICE: This experiment was done by us. Ð  SEMI-PASSIVE VOICE: Done by us, this experiment was. Ð  Yes, for the semi-passive voice, you’ll want to emulate Yoda. Yoda, you’ll want to emulate. A. Ruben 59
  60. 60. WHICH/THATÒ  Which/that: relative clauses Ð  Defining clause: NO comma ×  That/which in UK, only that in US ×  No comma Ð  Non defining clause: comma ×  ,which ((by the way)) …. ×  Not essential to basic meaning ×  Comma before whichØ  Land which/that is surrounded by water is an island.Ø  Tasmania, which is surrounded by the waters of Bass Strait, is an island of great natural beauty. THE COMMA: A MATTER OF LIFE AND DEATH?Ò  “Panda: large black and white bear-like mammal, native to China. Eats, shoots and leaves.” [1]Ò  Help the reader understand!/list informationÒ  Before the “and” is optionalÒ  To date, …Ò  Use commas as you would salt and pepper: don’t overdo it!Ò  [1] Truss, L., Eats(,) Shoots and Leaves, Profile Books Ltd., UK 2003Ò  Fay Wolter, BiotecVisions April 2011 60
  61. 61. ANTHROPOMORPHISM= assigning actions that can only be performed by humans to non-living subjects. Subjects like method, theor y, research, table, figure, etc. cannot determine, conclude, find, summarize, compare, or actively “act” as human subjects do Anthropomorphism   Solu�on   HPLC  was  able  to  determine   We  determined  the   the  composi�on.   composi�on  by  HPLC.   The  research  found…   The  researchers  found…   Table  1  summarizes  the   The  summary  in  Table  1.   results…   Figure  1  compares  ac�vi�es   Ac�vi�es  at  4°C  and  37°C  are   at  4°C  and  37°C.   compared  in  Table  1.   Our  hypothesis  says…   We  hypothesize… USE LINKSž  Transition words —  And, so, therefore, however, in conclusion, neverthelessž  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 —  ... 61
  62. 62. RATHER NOT USE ...Ò  Seems/appears Ò  RestrictedÒ  Uncritical Ò  UnsupportedÒ  Undermined Ò  LimitedÒ  Confounded Ò  CompromisedÒ  Inappropriate Ò  SomewhatÒ  Purported Ò  SuperficialÒ  Caution Ò  Ofdoubtful valueÒ  Limitations Ò  UnlikelyALSO NEGATIVE ...Ò  Unclear Ò  UncontrolledÒ  Uncertain Ò  AnomalousÒ  Potentially biased SurprisingÒ  Controversial Ò  UnusualÒ  Debatable Ò  ConfusingÒ  Unexpected Ò  Negative 62
  63. 63. AVOID REDUNDANCYÒ  Present moment in timeÒ  Fewer in numberÒ  Estimate at aboutÒ  Whether or notÒ  Try and endeavourÒ  True facts.. DO NOT BE ARROGANT...Ò  As is well-knownÒ  It is obvious thatÒ  It will be self-evident thatÒ  Of courseÒ  A not inconsiderable body of evidence...Ò  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 63
  64. 64. SOME RULESÒ  Shun and avoid the employment of unnecessary, excess extra words.Ò  Make certain all sentences are full and complete. If possible.Ò  Avoid cliches like the plague.Ò  Take pains to spell and, punctuate correctly.Ò  BE Consistent.Ò  Dont approximate. Always be more or less precise.Ò  Sedulously eschew obfuscatory hyperverbosity or prolixity.Ò  Avoid pointless repetition, and dont repeat yourself unnecessarily.Ò  Always try to remembr t he/E extreme importance of being accurit; ne at, and carfful.Ò  Dont use no double negatives.Ò  Dont never use no triple negatives.Ò  All generalizations are bad.Ò  Take care that your verb and subject is in agreement.SOME RULES IIÒ  A preposition is a bad thing to end a sentence with.Ò  Dont use commas, which arent necessary. ,Ò  "Avoid overuse of quotation marks." "Ò  Writing carefully, dangling participles must be avoided.Ò  And dont start a sentence with a conjunction.Ò  Reserve the apostrophe for its proper use and omit it when its not necessary.Ò  Avoid run-on sentences they are hard to read.Ò  Proofread carefully to see if you any words out.Ò  Never use that totally cool, radically groovy out-of-date slang.Ò  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, theyre worse than the Energizer Bunny, they babble incessantly, and these sentences, they just never stop.From 64
  65. 65. IF YOU DON‘T KNOW…Ò  Google!!Ò  Merriam Webster É  www.merriamwebster.comÒ  Linguee for German to EnglishÒ  Software ConcApp É É  Build your own corpus (articles) of english journal articles É  Search gives you CONTEXT of search words FUNNY SYNTAX...Ò  “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.)Ò  “….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)Ò  “THF is a single heat-stable polypeptide isolated from calf thymus composed of 31 amino acids with a molecular weight of 3,200.”Ò  “For sale, fine grand piano, by a lady, with three legs.”Ò  “For sale, German Shepherd dog, obedient, well trained, will eat anything, very fond of children.” From Martin Welch, BIOCAM course 65
  66. 66. NOW YOU CAN WRITE… A CV?Ò  Think of your audienceÒ  Write to be understoodÒ  Most important firstPICK OUT THE RIGHT CVÒ  You have 10 minutes to read 20 CVsÒ  Which criteria do you use?Ò  What attracts you in a cover letter?Ò  When do you spot what is important?Ò  -> YOUR listÒ  -> THE list of writing tips 66
  67. 67. WHEN IS A CV NOT SELECTED?Ò  No cover letterÒ  No motivationÒ  UnclearÒ  Not interestingÒ  No extra skillsÒ  Not matching job descriptionÒ  Perfect but boring (standard without extra)Ò  The person behind this CV does not appealÒ  …CV TIPS IÒ  Deliver information at first glance É  Trigger interest É  Emphasize specific skills É  Criteria from job ad can be found back in examples É  Cover letter focused on position É  Picture not required but IF, it will be seen… É  Clear motivationÒ  Easy to read – content and layout, uncongested É  Clearstructure É  CV not too long not too short       67
  68. 68. CV TIPS IIÒ  Be É  precise and concise É  specific and concrete É  honest but not over-honest É  yourselfÒ  Show that É  you know the needs (search for company info in any possible way) É  you are mature (know what you are talking about) É  you can learn what you don’t know É  you can deal positively with problemsCV TIPS IIIÒ  State É  work experience É  international experience É  relevant awards and prizes É  extra activities (especially social ones) É  examples of additional skillsÒ  But É  No information without examples É  No gaps without explaining É  No unnecessary details É  No spelling mistakes 68
  69. 69. RECOGNIZE YOUR SKILLS – STAR TECHNIQUEÒ  Situation The setting, the aim, the obstacles, the persons involved.Ò  Task What did you and your team want to achieve? What problem did you face? What was your particular role?Ò  Action What did you do? How did you do it?Ò  Result What was the outcome? What did you achieve? What was the value of your contribution? What did you learn from the experience?HOW TO TURN YOUR CV INTO A „RESUME“ 69
  70. 70. CV DO‘S AND DON‘TSÒ  Do Ò  Don‘t É  Give evidence for everything É  Start every sentence with „I…” you claim you’ve done without variation É  Be specific about everything É  Copy-paste the website you state É  Be concise but not terse É  Push open doors (they already É  Avoid jargon if not relevant know that “publishing is a great É  Use active verbs. career option”) (“I do” not “It was done”) É  Repeat exactly the same É  Use strong verbs information from your CV in the (“Initiate”, “Devise”, cover letter “Perform”,) É  Insert doubt É  Show your enjoyment and É  Be over-modest satisfaction in relevant É  Use long words or sentences activities where shorter means the same É  Add some concrete details wherever it helpsCOVER LETTER: STRUCTURE1.  Reference to previous contact/job ad2.  Information about yourself3.  Your specific contribution to the position4.  Suggest next steps É  I will be available XXX to discuss with you É  I can start from XXX 70
  72. 72. WEBSITESÒÒÒ  http://www.biotecvisions.comÒÒÒÒÒÒÒ READING 72
  73. 73. QUESTIONS? Contact me:Ò  Barbara.janssens@gmail.comÒ WHAT DID YOU BUY?Ò  Today É  Xxx É  Xxx É  Xxx É  Xxx É  Xxx É  Xxx É  Xxx É  Xxx É  xxx 73
  74. 74. RECOMMENDED REFERENCESÒ  Shashok, K., Content and communication: How can peer review provide helpful feedback about the writing? BMC Medical Research Methodology 2008, 8:3,Ò  Cargill, M., O’Connor, P., Writing scientific research articles. Blackwell Publishing, Chichester 2009, ISBN 978-1-4051-8619-3.Ò  Ruben, A., How to Write Like a Scientist. Sciencecareers 2012, March 23, science.caredit.a1200033 74