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Scientific writing janssens 2016

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9/2/2016
1
Lisbon, September 2016
Dr. Barbara Janssens, Career Manager
Scientific Writing
www.wordle.net
www.slideshare.co...
9/2/2016
2
© Janssens Aug-16 - Scientific Writing
Van Dijk et al., Curr. Biol. 2014
DOI: http://dx.doi.org/10.1016/j.cub.2...
9/2/2016
3
© Janssens Aug-16 - Scientific Writing5
Job applications:
Straight to the top of the pile
 http://www.nature.c...
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Scientific writing janssens 2016

  1. 1. 9/2/2016 1 Lisbon, September 2016 Dr. Barbara Janssens, Career Manager Scientific Writing www.wordle.net www.slideshare.com/barbaja © Janssens Aug-16 - Scientific Writing2 The chicken and the egg Science Editing Publishing Science Career Advising
  2. 2. 9/2/2016 2 © Janssens Aug-16 - Scientific Writing Van Dijk et al., Curr. Biol. 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.04.039 Publication metrics and success on the academic job market © Janssens Aug-16 - Scientific Writing4
  3. 3. 9/2/2016 3 © Janssens Aug-16 - Scientific Writing5 Job applications: Straight to the top of the pile  http://www.nature.com/naturejobs/science/articles/10. 1038/nj7410-241a © Janssens Aug-16 - Scientific Writing6 Five top tips for your job application  1. Imagine YOU are the recruiter  2. Learn to present yourself in an “elevator pitch”  3. Actively network  4. Most important FIRST  5. Tell stories  http://youtu.be/FH0Hvk2tp-M
  4. 4. 9/2/2016 4 © Janssens Aug-16 - Scientific Writing Deese and Kaufman, J. Exp. Psychol. 1957, 54, 180-187. Murdock , J. Exp. Psychol. 1962, 64, 482-488. Serial position effect Recall Primacy Recency t 7 most important first! © Andrew Moore I’m hungry... Mustn’t forget to do the shopping... Drain needs unblocking!! Adapted from Andrew Moore © Janssens Aug-16 - Scientific Writing8 What scientists write  Papers  Curriculum vitae  Grants, Fellowships  Reports  Proposals  Web pages  Conferences  Lectures  Meetings  Posters  ...
  5. 5. 9/2/2016 5 © Janssens Aug-16 - Scientific Writing9 Think of your audience/reader  Poster – conference  Fellowship – review committee Personal selection – criteria (formal, CV, host)  Grant – reviewers Long-term planning  Job application – recruiter  Paper – journal peer review Imagine you are the recruiter/reviewer! © Janssens Aug-16 - Scientific Writing Scientific Writing  www.slideshare.net/Barbaja
  6. 6. 9/2/2016 6 © Janssens Aug-16 - Scientific Writing11 Scientific ...Writing <-> ...career  Writing, editing, career development  A career in science/publishing  About publishing and impact  Journals and impact  Titles and Abstracts  Tips on language/style  Writing a paper  IMRAD structure  How to get started & „sculpt“  How to submit with cover letter  Writing a job application  Publication ethics  Author (to be or not to be?)  Plagiarism (never copy-paste?)  Science Communication with the Public  http://www.slideshare.net/Barbaja  Cargill et al. Writing Scientific Research Articles  Nancy Fox The little book of scientific writing © Janssens Aug-16 - Scientific Writing  Peer reviewed publications  Publishers  Societies  Magazines  Scientific American, New Scientist, …  Spektrum der Wissenschaft (npg)  Public communication  Science in School  Cancer Prevention Service  Helmholtz Open Science Coordination  Science Open Publication landscape
  7. 7. 9/2/2016 7 © Janssens Aug-16 - Scientific Writing  PubMed/Medline  Google (Scholar)  Scopus (Elsevier)  CrossRef  BioMed experts  Open Access journals  ISI Web of Science (Thomson) Where do you find publications? © Janssens Aug-16 - Scientific Writing  Elsevier 2500 journals (Lancet, Cell), 33k books  John Wiley &sons/Wiley-VCH -> Wiley-Blackwell  Wiley 1500 journals, 16k ebooks  EMBO Press 4 journals  Nature (npg) 162 journals /Macmillan  Springer 2400 journals, 170k books  BioMedCentral 300 j  Springer Nature  Open Access:  PLoS  eLIFE  Etc etc… Publishers
  8. 8. 9/2/2016 8 © Janssens Aug-16 - Scientific Writing Elsevier 21% Npg Springer 12% Wiley 11% Other 56% % of articles 2015 Mergers and Acquisitions… http://scholarlykitchen.sspnet.org © Janssens Aug-16 - Scientific Writing16 Peer Review principle Submission Editorial Decision Reject Peer review Revision Editorial Decision Referee recommendation Accept
  9. 9. 9/2/2016 9 © Janssens Aug-16 - Scientific Writing17 Referee questions 1. 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? Do you peer-review?  Closed  Single blind (author doesn‘t know reviewer)  Double blind (reviewer also doesnt know author)  Triple blind (editor also doesnt know the author)  Open  Author, Editor and Reviewer all know eachother  Possibly published  Post-publication peer-review
  10. 10. 9/2/2016 10 Peerageofscience.org © Janssens Aug-16 - Scientific Writing19 © Janssens Aug-16 - Scientific Writing Transparent Process (EMBO press)
  11. 11. 9/2/2016 11 © Janssens Aug-16 - Scientific Writing21 Peer review process file (RPF) © Janssens Aug-16 - Scientific Writing The Editor writes…
  12. 12. 9/2/2016 12 © Janssens Aug-16 - Scientific Writing23 Most accessed – most cited © Janssens Aug-16 - Scientific Writing24 Impact Factor (IF) Devised by Eugene Garfield, founder of ISI (Chairman Emeritus of Thomson Scientific) 1955 Adapted from Matteo Cavalleri
  13. 13. 9/2/2016 13 © Janssens Aug-16 - Scientific Writing25 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.  www.webofknowledge.com - Thomson Reuters time Year 1 Year 2 Year 3 Articles published A1 A2 C12 Citations published Slide adapted from Matteo Cavalleri IF (Year 3) = C12 /(A1+A2) © Janssens Aug-16 - Scientific Writing26 All citations from all publications?  No  WOS is selective on coverage  covers 12,000 journals…  … from a total of 40-50,000  Coverage depends on topic  Ecology 65%  Geology 55%  Nursing 45%  Information sciences 33%  History 9%  Molecular Biology/Biochemistry (80)%  FT Krell, Eur J Sci Editing 2012, 38 (1). www.ease.org.uk
  14. 14. 9/2/2016 14 © Janssens Aug-16 - Scientific Writing27 Cites per paper in 2 years?  Since 2007: 5-year IF  Eigenfactor  Citations to 5 years  Considers from which journals cites come  Self-citations (from same journal) not considered  Article Influence  = Eigenfactor /(# articles in 5 years)  Average (mean) AI = 1.00 © Janssens Aug-16 - Scientific Writing28 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.
  15. 15. 9/2/2016 15 © Janssens Aug-16 - Scientific Writing29 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)  Only cited references from articles in the census period, and which refer to articles within the target period are counted  Only cited references indexed in the Scopus database are counted  www.scopus.com © Janssens Aug-16 - Scientific Writing30 The SJR Scimago Journal Ranking  SCImago Journal Rank (SJR) is a prestige metric based on the idea that ‘all citations are not created equal’.  the subject field, quality and reputation of the journal have a direct effect on the value of a citation.  http://www.scimagojr.com/
  16. 16. 9/2/2016 16 © Janssens Aug-16 - Scientific Writing31 Web of knowledge © Janssens Aug-16 - Scientific Writing32 JCR Journal citation reports
  17. 17. 9/2/2016 17 © Janssens Aug-16 - Scientific Writing IF = cites y3 / items y1+2 Items … Who cites? av. 1.0 © Janssens Aug-16 - Scientific Writing34 Pick a rising star?
  18. 18. 9/2/2016 18 © Janssens Aug-16 - Scientific Writing But watch out for Journal self-cites! (Energy Educ Sci Tech discontinued in 2012) © Janssens Aug-16 - Scientific Writing Self-citations vs Journal banned
  19. 19. 9/2/2016 19 © Janssens Aug-16 - Scientific Writing37 The author and the IF  It‘s not all up to senior scientists...  Chose the target journal and priorities  Market your article, not just the journal  Expert rating  Cited, accessed, bookmarked xx times  Press release, Higlights/columns, blogs  Talks and presentations  ... Perception counts more than the IF  ...“publish or perish“ © Janssens Aug-16 - Scientific Writing38 Albert Einstein  "Not everything that can be counted counts, and not everything that counts can be counted."
  20. 20. 9/2/2016 20 © Janssens Aug-16 - Scientific Writing39 Before writing…  What would you do?  Read read read...  Be critical! What is easy to understand? Well written?  Journal clubs!  Assemble data  Which journal/scope?  Which format?  Who will be author?  Check instructions to authors! © Janssens Aug-16 - Scientific Writing40 Select target journal Journal XXX XXX Publishes similar work? Scope/recent content? Quality/impact? Fast publication? Charges for pages, color, open access? Article format/length?
  21. 21. 9/2/2016 21 © Janssens Aug-16 - Scientific Writing41 Journal Author Name Estimator JANE  http://www.biosemantics.org/jane/ © Janssens Aug-16 - Scientific Writing42 Title  The first impression counts...  A strong title will attract readers/citations  Keep it short: 15 words  Clear, informative, raise curiosity  Interesting and easy to read  Main message of the paper  Remember Medline  Key words  Start with a „quick go“, remodel during writing process and rethink for some days when the whole manuscript is ready  Test: http://www.lulu.com/titlescorer
  22. 22. 9/2/2016 22 © Janssens Aug-16 - Scientific Writing43 Examples: compare  “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.”  “Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.” © Janssens Aug-16 - Scientific Writing44 Titles to avoid  Vague titles  Titles starting with  “Studies on..” “Implications of…”  “Involvement of…” “Observations on...” “Evidence for…”  “Investigations into...” “Insights in…” “Characterization of...”  “The involvement of this in that”  -> “This does that in signal transduction pathway xx”  Titles with jargon or abbreviations  Titles with “new” and “novel” (all research is new)
  23. 23. 9/2/2016 23 © Janssens Aug-16 - Scientific Writing45 Keywords  Donot repeat title words – these come up anyhow  Most cited versus never cited...  Try out in PubMed:  possibly your keywords should be obvious and short but bring less hits (and rather your than a competitor‘s article!) © Janssens Aug-16 - Scientific Writing46 Title syntax  “Preliminary canine and clinical evaluation of a new antitumor agent, streptovitacin.” (Clin. Res. 8:134, 1960)  „Evidence for women dreaming more often about food than men.“  ...
  24. 24. 9/2/2016 24 © Janssens Aug-16 - Scientific Writing Deese and Kaufman, J. Exp. Psychol. 1957, 54, 180-187. Murdock , J. Exp. Psychol. 1962, 64, 482-488. Serial position effect Recall Primacy Recency t 47 Write at beginning! Adapted from Andrew Moore I’m hungry... Mustn’t forget to do the shopping... Drain needs unblocking!! © Janssens Aug-16 - Scientific Writing48 Have a look at titles Never cited...........well cited Reviews Yoghurt fermentation at elevated temperatures by strains of Streptococcus thermophilus expressing a small heat-shock protein: Application of two- plasmid system for constructing food-grade strains of Streptococcus thermophilus New insights into mechanisms of growth and b- carotene production in Blakeslea trispora Research Articles Separation of catechin compounds from different teas Production and characterization of theromstable α- amylase by thermophilic Geobacillus stearothermophilus Molecular characteriazation of rpoB gene mutations in rifampicin-resistant Mycobacterium tuberculosis strains isolated from TB patients in Belarus Investigating pH and Cu(II) effects on lipase activity and enantioselectivity via kinetic and spectroscopic methods Metabolic flux analysis of the two astaxanthin- producing microorganisms Haematococcus pluvialis and Phaffia rhodozyma in the pure and mixed cultures Reviews Essential fatty acids: Biochemistry, physiology and pathology Metagenomics: An inexhaustible access to nature‘s diversity Production of biopharmaceuticals and vaccines in plants via the chloroplast genome Application of inkjet printing to tissue engineering Research Articles Arenicola marina extracullar hemoglobin: A new promising blood substitute Directed evolution of industrial biocatalyst 2-deoxy-D- ribose-5-phosphate aldolase Bio-electrosprays: The next generation of electrified jets A rapid, high content, in vivo model of glucocorticoid- induced osteoporosis
  25. 25. 9/2/2016 25 © Janssens Aug-16 - Scientific Writing More titles from JCS 1. Suppression of synaptotagmin II restrains phorbolester- induced downregulation of protein kinase C alpha by diverting the kinase from a degradative pathway to the recycling endocytic compartment 2. Identification of an alpha-tubulin mutant of fission yeast from gamma-tubulin-interacting protein screening: genetic evidence for alpha-/gamma-tubulin interaction 3. Genetic and molecular interactions of the Erv41p-Erv46p complex involved in transport between the endoplasmic reticulum and Golgi complex 4. Kendrin/pericentrin-B, a centrosome protein with homology to pericentrin that complexes with PCM-1 5. Regulatory mechanisms governing the oocyte-specific synthesis of the karyoskeletal protein NO145 6. Association of human ubiquitin-conjugating enzyme CDC34 with the mitotic spindle in anaphase 7. Inactivation of MAPK in mature oocytes triggers progression into mitosis via a Ca2+-dependent pathway but without completion of S phase 8. Repression of Wnt-5a impairs DDR1 phosphorylation and modifies adhesion and migration of mammary cells 1. Secreted antagonists of the Wnt signalling pathway 2. PKB/Akt: a key mediator of cell proliferation, survival and insulin responses? 3. Metalloproteinase inhibitors: biological actions and therapeutic opportunities 4. Clonal mesenchymal progenitors from human bone marrow differentiate in vitro according to a hierarchical model 5. SH3 domains: complexity in moderation 6. Cell adhesion and motility depend on nanoscale RGD clustering 7. Mechanisms of capacitative calcium entry 8. Release of an invasion promoter E- cadherin fragment by matrilysin and stromelysin-1 © Janssens Aug-16 - Scientific Writing50 Abstract © Janssens 2014 - Scientific Writing  Hardest part to write  Second most important part  Maximum 200 words (Medline truncates at 250 words)  What are the significant results?  Important methodology (in vitro vs. in vivo, human, model systems)  What are the conclusions/implications?  Start with writing these in bullet points and take time to re- re- and re-write this part with some distance  Write in PAST TENSE  NO citations, avoid non-standard abbreviations
  26. 26. 9/2/2016 26 © Janssens Aug-16 - Scientific Writing51 Optimize abstract  Be specific, not just one word  e.g. women's fiction not fiction.  Key phrases need to make sense within the title and abstract and flow well.  Focus on a maximum of three or four different keyword phrases rather than try to get across too many points.  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.  http://authorservices.wiley.com/bauthor/ © Janssens Aug-16 - Scientific Writing52 Language tips  Be cautious with imprecise words:  Several, some, many, affected, somewhat, quite, relatively  Don‘t add doubt unnecessarily. Could you replace...  Could -> can  Would -> will  Hopefully -> Possibly  Difficulty -> challenge
  27. 27. 9/2/2016 27 © Janssens Aug-16 - Scientific Writing53 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]  http://www.nlm.nih.gov/bsd/policy/structured_abstracts.html © Janssens Aug-16 - Scientific Writing54 Structured abstract  Developed in the late 1980s and early 1990s to assist health professionals in selecting clinically relevant and methodologically valid journal articles  Mainly medical  Makes text mining (search engines) easier  Could start to be used in life sciences (MedLine encourages)
  28. 28. 9/2/2016 28 © Janssens Aug-16 - Scientific Writing55 Graphical abstract  Started in chemical journals  VISUALISE the main message in ONE figure  Chemical reaction  Signal transduction pathway  Hypothesis  Structure  Etc… © Janssens Aug-16 - Scientific Writing56 LAY abstract  Sometimes asked at submission  Summary for non-expert  Here you CAN say why it is new  Always write this, it can be useful  In cover letter to convince Editor  After acceptance to highlight your work  To explain your friends and family
  29. 29. 9/2/2016 29 © Janssens Aug-16 - Scientific Writing57 Edit title/abstract  Title: short? Main message? What first? Provide 2 alternative titles to chose from  Mark key statements Do you get what it is about? What could be left out?  First and last sentence: strong?  Positive wording  Sentence length  …  What would you write in a “lay” abstract? © Janssens Aug-16 - Scientific Writing58 Scientific Writing  Introduction and basics  Mutual introductions  About journals and peer review  Online access and searches, IF  Before writing  Tips on language/style  Writing  IMRAD structure  How to get started & ‘sculpt’  How to submit with cover letter  Publication ethics  ----  Application writing  Science communication
  30. 30. 9/2/2016 30 © Janssens Aug-16 - Scientific Writing59 Style = Clarity  Write to be understood  Think of your audience  Make information accessible  Make reader feel comfortable  THINK what you want to say  Clear thinking = clear writing  Arrange your thoughts in a logical order (MIND MAP)  Errors don‘t always affect the meaning © Janssens Aug-16 - Scientific Writing60 Errors vs meaning © M. Cargill - Scientific Writing
  31. 31. 9/2/2016 31 © Janssens Aug-16 - Scientific Writing61 Errors vs meaning © M. Cargill © Janssens Aug-16 - Scientific Writing62 # languages… © Janssens 2014 - Scientific Writing  … different challenges!  Sentences too long/too short  False friends  Commas
  32. 32. 9/2/2016 32 © Janssens Aug-16 - Scientific Writing63 www.nature.com/scitable © Janssens Aug-16 - Scientific Writing64 www.nature.com/scitable
  33. 33. 9/2/2016 33 © Janssens Aug-16 - Scientific Writing65 www.nature.com/scitable © Janssens Aug-16 - Scientific Writing66 Sentence structure  Simple  Precise  Concise  Topic near the beginning!  Active tense where possible  KISS  Keep  It  Short and  Simple
  34. 34. 9/2/2016 34 © Janssens Aug-16 - Scientific Writing67 Sentence structure  Which sentence is easier to understand?  The primary site of contact with airborne allergens, irritants, pathogens and other proinflammatory agents is the pulmonary ephithelium  The pulmonary epithelium is the primary site of contact with airborne allergens, irritants, pathogens and other proinflammatory agents © Janssens Aug-16 - Scientific Writing68 Sentence structure  Often splitting in two is better, even if result is longer:  Wiley-VCH is a Weinheim, Germany, global STM publisher specialized in chemistry and life sciences, belonging to the Wiley-Blackwell group.  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.
  35. 35. 9/2/2016 35 © Janssens Aug-16 - Scientific Writing69 Paragraphs  Units of thought, not length  Provide visual relief  Contain related thoughts  Thoughts in logical order  Consistent organization  Use topic sentences  At beginning or end  Rarely in the middle (unless preceding is transitional) © Janssens Aug-16 - Scientific Writing I’m hungry... Mustn’t forget to do the shopping... Drain needs unblocking!! recency recall primacy t PI3K © Andrew Moore Serial Position Effect
  36. 36. 9/2/2016 36 © Janssens Aug-16 - Scientific Writing71 Which/that  Which/that: relative clauses  Defining clause: NO comma  That/which in UK, only that in US  No comma  Non defining clause: comma  , which ((by the way)) ….  Not essential to basic meaning  Comma before which  Land which/that is surrounded by water is an island.  Tasmania, which is surrounded by the waters of Bass Strait, is an island of great natural beauty. www.writeresearch.com.au © Janssens Aug-16 - Scientific Writing72 The comma: A matter of life and death?  “Panda: large black and white bear-like mammal, native to China. Eats, shoots and leaves.” [1]  Help the reader understand!/list information  Before the “and” is optional  To date, …  Use commas as you would salt and pepper: don’t overdo it! [1] Truss, L., Eats(,) Shoots and Leaves, Profile Books Ltd., UK 2003 Fay Wolter, BiotecVisions April 2011
  37. 37. 9/2/2016 37 © Janssens Aug-16 - Scientific Writinghttp://www.facebook.com/sujaybarc73 © Janssens Aug-16 - Scientific Writing74 Active vs passive (p.39)  Avoid passive (is, was, are, being...)  Use active: the subject of the sentence performs an action  The man was bitten by the dog - pass  The dog bit the man - active  Only use passive if you cannot use the „we“ form  Gel electrophoresis was used - pass  We used gel electrophoresis – active  Example from Adam Ruben  ACTIVE VOICE: We did this experiment.  PASSIVE VOICE: This experiment was done by us.  SEMI-PASSIVE VOICE: Done by us, this experiment was.  Yes, for the semi-passive voice, you’ll want to emulate Yoda. Yoda, you’ll want to emulate. A. Ruben dx.doi.org/10.1126/science.caredit.a1200033
  38. 38. 9/2/2016 38 © Janssens Aug-16 - Scientific Writing75 Anthropomorphism  = assigning actions that can only be performed by humans to non-living subjects. Subjects like method, theory, research, table, figure, etc. cannot determine, conclude, find, summarize, compare, or actively “act” as human subjects do www.biotecvisions.com Anthropomorphism Solution HPLC was able to determine the composition. We determined the composition by HPLC. The research found… The researchers found… Table 1 summarizes the results… The summary in Table 1. Figure 1 compares activities at 4°C and 37°C. Activities at 4°C and 37°C are compared in Table 1. Our hypothesis says… We hypothesize… © Janssens Aug-16 - Scientific Writing76 Some rules  Shun and avoid the employment of unnecessary, excess extra words.  Make certain all sentences are full and complete. If possible.  Avoid cliches like the plague.  Take pain's to spell and, punctuate correctly.  BE Consistent.  Don't approximate. Always be more or less precise.  Sedulously eschew obfuscatory hyperverbosity or prolixity.  Avoid pointless repetition, and don't repeat yourself unnecessarily.  Always try to remembr t he/E extreme importance of being accurit; ne at, and carfful.  Don't use no double negatives.  Don't never use no triple negatives.  All generalizations are bad.  Take care that your verb and subject is in agreement. From http://www.union.edu/PUBLIC/BIODEPT/wicked.html
  39. 39. 9/2/2016 39 © Janssens Aug-16 - Scientific Writing77 Some rules ii  A preposition is a bad thing to end a sentence with.  Don't use commas, which aren't necessary.  "Avoid overuse of 'quotation' marks."  Writing carefully, dangling participles must be avoided.  And don't start a sentence with a conjunction.  Reserve the apostrophe for it's proper use and omit it when its not necessary.  Avoid run-on sentences they are hard to read.  Proofread carefully to see if you any words out.  Never use that totally cool, radically groovy out-of-date slang.  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, they're worse than the Energizer Bunny, they babble incessantly, and these sentences, they just never stop.  From http://www.union.edu/PUBLIC/BIODEPT/wicked.html © Janssens Aug-16 - Scientific Writing78 If you don‘t know…  Google!!  Merriam Webster (US) or Oxford  www.merriamwebster.com  www.oed.com  Software ConcApp p.130  www.edict.com.hk/pub/concapp/  Build your own corpus (articles) of english journal articles  Search gives you CONTEXT of search words www.writeresearch.com.au
  40. 40. 9/2/2016 40 © Janssens Aug-16 - Scientific Writing79 Funny syntax...  “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.)  “….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)  “THF is a single heat-stable polypeptide isolated from calf thymus composed of 31 amino acids with a molecular weight of 3,200.”  “For sale, fine grand piano, by a lady, with three legs.”  “For sale, German Shepherd dog, obedient, well trained, will eat anything, very fond of children.” From Martin Welch, BIOCAM course © Janssens Aug-16 - Scientific Writing80 First letter… brain does the rest http://www.positscience.com/games-teasers/brain-teasers/teasers/scrambled-text
  41. 41. 9/2/2016 41 © Janssens Aug-16 - Scientific Writing © Janssens Aug-16 - Scientific Writing82 Now the manuscript
  42. 42. 9/2/2016 42 © Janssens Aug-16 - Scientific Writing83 Start 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) © Janssens Aug-16 - Scientific Writing84 Manuscript draft - IMRAD -  Title  Abstract  Introduction  Materials and Methods  Results  Discussion  Figures and Tables  Cover letter
  43. 43. 9/2/2016 43 © Janssens Aug-16 - Scientific Writing85 Writing order? © Janssens Aug-16 - Scientific Writing
  44. 44. 9/2/2016 44 © Janssens Aug-16 - Scientific Writing87 ...writing order  Figures and Tables  Title  Abstract  Results  Materials and Methods  Introduction  Discussion  Cover letter © Janssens Aug-16 - Scientific Writing88
  45. 45. 9/2/2016 45 © Janssens Aug-16 - Scientific Writing89 ...writing order  Figures and Tables  Title  Abstract  Results  Materials and Methods  Introduction  Discussion  Cover letter © Janssens Aug-16 - Scientific Writing90 Start with the data  This will cut your writer‘s block!  (Pictures of gels, graphs etc)  Order in Figures: write legends  What is the story?  (Title, abstract draft)
  46. 46. 9/2/2016 46 www.ScienceMatters.io Publish data first, then stories? © Janssens Aug-16 - Scientific Writing92 Figures  Should tell the story - quick readers will read the abstract and check the figures  Are the data comprehensive?  Not too many panels (6)  If too many data: provide as supporting material  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 figure  Include a concluding visual scheme, diagram, overview
  47. 47. 9/2/2016 47 © Janssens Aug-16 - Scientific Writing93 Figures II  Detail how many times the experiments were performed  Detail the number of animals/replicates  Provide clear statistical analyses  Should enable the reader to fully understand the figure  Ensure everything is described: abbreviations, symbols etc. © Janssens Aug-16 - Scientific Writing94 Figure or Table?  Table  Recording data (raw or processed)  Showing actual data values, precision  Multiple comparisons  Has a short title and footnotes  Figure  Showing trend or picture  Shape rather than numbers  Compare few elements  Has a legend with all details needed
  48. 48. 9/2/2016 48 © Janssens Aug-16 - Scientific Writing Keep source data! Statistics… © Janssens Aug-16 - Scientific Writing96 Clinical trial data online  Online archive of ALL trial data  Data protection issue…  …But it will come  Statistal analysis: some journals require author to pay for cost of second analysis if needed  Sometimes data need to be reanalysed decades after publication
  49. 49. 9/2/2016 49 © Janssens Aug-16 - Scientific Writing97 Image processing  Regulations by Rockefeller University Press  (now adopted by most journals)  No specific feature within an image may be enhanced, obscured, moved, removed, or introduced.  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.  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.  If the original data cannot be produced by an author when asked to provide it, acceptance of the manuscript may be revoked. http://www.councilscienceeditors.org/i4a/pages/index.cfm?pageid=3363 © Janssens Aug-16 - Scientific Writing MANIPULATION OF BLOTS B r i g t h n e s s a n d c o n t r a s t a d j u s t m e n t s . Rossner M , Yamada K M J Cell Biol 2004;166:11-15© 2004 Rockefeller University Press
  50. 50. 9/2/2016 50 © Janssens Aug-16 - Scientific Writing99 Figure 2: A B © Janssens Aug-16 - Scientific Writing100 Results  Follow the figures: Present the experiments performed in a logical and clear manner. Why did this lead to the next experiment?  Written in the PAST TENSE  Provide statistical analysis and clearly indicate significant data  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 discussion  Do not lose in technical details („we transfected and then purified cell extracts and then separated...“): these go to the M&M  Be SELECTIVE  Present your results ONCE, either in the text, OR a Table OR Figure
  51. 51. 9/2/2016 51 © Janssens Aug-16 - Scientific Writing101 Materials & Methods  Should be concise but complete  Written in PAST TENSE  DO NOT include any results!  A colleague should be able to repeat the experiment  All new reagents, sequences, etc should stated;  New method: provide ALL detail  Standard procedures: cite and only mention modifications  If too lengthy: decide afterwards if parts can be cut or removed to supporting information  Write 20 mL (not ml), 5 mm, 3 min (not mins), kDa (not Kda; molecular mass – not weight), M (not mole)  Check chemical nomenclature www.chem.qmw.ac.uk/iubmb © Janssens Aug-16 - Scientific Writing102 Funny M&M  “After standing in boiling water for an hour, I loaded the sample on a gel…..”  “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)  “Employing a straight platinum wire rabbit, sheep and human blood agar plates were inoculated….”  “Lying on top of the small intestine, we observed a small transparent thread”  “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
  52. 52. 9/2/2016 52 © Janssens Aug-16 - Scientific Writing103 Introduction  Entrance to manuscript  Make sure referees/readers continue to read  3 major stages: Country, city, house 1. Broad general statement, what is known, present tense (also non-expert understands) 2. Justification for study, research gap, need (interesting?) 3. Aim (start with this). State your principal results and conclusions in one sentence © Janssens Aug-16 - Scientific Writing104 Discussion  QUICKLY summarize the findings  This is not just the results presented in another format, they need to be discussed in the wider context of the field  What are the implications for future work?  Systematically compare findings with supporting and/or conflicting literature  Discuss implications and applications, future directions to take  Be clear, honest, don‘t over-interprete but also don‘t minimize  Are there any models/rules that can be established?  If it was a model system, what are the implications for the human system? Parallels, differences?  If primarily in vitro studies, what is the scope for further in vivo studies? Relation to published in vivo studies?
  53. 53. 9/2/2016 53 © Janssens Aug-16 - Scientific Writing105 ...writing order  Title  Abstract  Figures and Tables  Results  Materials and Methods  Introduction  Discussion  Cover letter © Janssens Aug-16 - Scientific Writing106 Last but not least: Cover letter  Convince the editor of the importance of your work  State in a few sentences what the paper is about (not abstract)  Why does it fit the scope of the journal?  Why is it novel?  Why will it be of interest to reviewers? If you state non-preferred reviewers, you may explain why  Write this for the EDITOR
  54. 54. 9/2/2016 54 © Janssens Aug-16 - Scientific Writing107 What the Editor wants?  OURS  Originality  Understandibility  Reliability  Suitability  Poorly written or conceived papers will be rejected editorially © Janssens Aug-16 - Scientific Writing108 Cover letter example  Dear 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 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,
  55. 55. 9/2/2016 55 © Janssens Aug-16 - Scientific Writing109 Cover letter quotes  “It gives me immense satisfaction to be able to share with you an additional application of….”  “We, the Arthurs of this mansucript …”  “The conception of Chapter 1..”  “We hope that paper should priority handing”  “I would like to express my honour to submit our hard work to your respected journal”  “Dear Sir, Thank you for the sweet reviewing process and find here the responce for the reviewers comments”  “After deep thinking of the comments, we made statement as follow:” Thanks to Lucie and Uta, EJLST and ELS Job application cover letter....  Different?  Tell STORIES – EXAMPLES of skills  STAR Situation Task Action Result  I‘m a very organised person.  For example I introduced Trello to organise our student conference 2016, which saved time and got us excellent feedback from invited speakers.
  56. 56. 9/2/2016 56 © Janssens Aug-16 - Scientific Writing111 Scientific Writing  Introduction and basics  introduction  About journals and peer review  Online access and searches, IF  Before writing  Tips on language/style  The manuscript - IMRAD  Publication ethics  Authorship  Plagiarism © Janssens Aug-16 - Scientific Writing112 Authors
  57. 57. 9/2/2016 57 © Janssens Aug-16 - Scientific Writing113 Authors  Author = significant contributor  Providing reagents, scientific/moral support = acknowledgement  First author =„paternity“ („the one without whom the work could not have been accomplished“)  Last author =„Senior author“ (often the group leader or head of Department)  Corresponding author (usually first and/or last) = assumes responsibility for writing, submiting, revising and answering questions after publication. Most prestigious.  „These authors have contributed equally“  Decide authors and order as early as possible  Which author you are will be important for your CV – but being an author in the first place is what matters © Janssens Aug-16 - Scientific Writing International Committee of Medical Journal Editors (ICMJE) recommends that authorship be based on the following four criteria: (1) substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; (2) drafting the work or revising it critically for important intellectual content; (3) final approval of the version to be published; (4) agreement to be accountable for all aspects of the work, thereby ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.114 Authors ICMJE
  58. 58. 9/2/2016 58 © Janssens Aug-16 - Scientific Writing115 Authors  FIRST AUTHOR: Weary graduate student who spent hours doing the work.  SECOND AUTHOR: Resentful graduate student who thinks he or she spent hours doing the work.  THIRD AUTHOR: Undergraduate just happy to be named.  FOURTH AUTHOR: Collaborator no one has ever met whose name is only included for political reasons.  FIFTH AUTHOR: Postdoctoral fellow who once made a chance remark on the subject.  SIXTH AUTHOR: For some reason, Vladimir Putin.  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 dx.doi.org/10.1126/science.caredit.a1200033 © Janssens Aug-16 - Scientific Writing116 Ghost or guest authors?  Ghost authors: individuals not named as authors but who contributed substantially to the work  Guest authors: named authors who have not met authorship criteria  Confidential survey of corresponding authors of 809 articles  156 articles (19%) had evidence of honorary authors  93 articles (11%) had evidence of ghost authors  Flanagin et al., Prevalence of Articles with Honorary Authors and Ghost Authors in Peer-Reviewed Medical Journals. J. Am. Med. Assoc. 1998, 280, 222-224.  http://dx.doi.org/10.1001/jama.280.3.222
  59. 59. 9/2/2016 59 © Janssens Aug-16 - Scientific Writing117 Author acknowledged  From PNAS, EMBO Press…  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. © Janssens Aug-16 - Scientific Writing118 Ethics/plagiarism  What is plagiarism?  The „Guttenberg syndrome“  Plagiarism is the representation of another person's words, ideas, or information as if they were one's own  ... Do not publish previously published work!  However you may reuse some of your own and „CITED“ [1] material  Check COPE - the Committee on Publishing Ethics (http://www.publicationethics.org.uk/about).  Check „copyright transfer agreement“
  60. 60. 9/2/2016 60 © Janssens Aug-16 - Scientific Writing119 Plagiarism  Definition (http://plagiarism.org)  Plagiarism is the representation of another person's words, ideas, or information as if they were one's own  Publishers policy  COPE - Committee on Publishing Ethics (www.publicationethics.org.uk/about)  CTA (copyright transfer agreement)  Crosscheck database (www.crossref.org/crosscheck/)  Non-for-profit use of DOI (Digital Object Identifier)  30 Billion websites  100 Million articles  100k Journals  iThenticate: to detect words http://ithenticate.com © Janssens Aug-16 - Scientific Writing120 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 for  financial consideration to the Contributor.  (iv) Nothing herein shall permit dual publication in violation of journal  ------------------------------- http://onlinelibrarystatic.wiley.com/central/cta/UKscta.pdf
  61. 61. 9/2/2016 61 © Janssens Aug-16 - Scientific Writing121 www.publicationethics.org.uk http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf © Janssens Aug-16 - Scientific Writing122 Types of Plagiarism http://publicationethics.org/files/COPE_plagiarism_discussion_%20doc_26%20Apr%2011.pdf
  62. 62. 9/2/2016 62 © Janssens Aug-16 - Scientific Writing123 Manuscript submission system http://scholarone.com © Janssens Aug-16 - Scientific Writing124 SIMILARITY REPORT
  63. 63. 9/2/2016 63 © Janssens Aug-16 - Scientific Writing125 30% = Plagiarism?  Individual for each article…  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 consideration  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 (http://plagiarism.org) © Janssens Aug-16 - Scientific Writing126 SIMILARITY REPORT
  64. 64. 9/2/2016 64 © Janssens Aug-16 - Scientific Writing127 ~(30)% similarity -> manual check Not cited High similarity Reject Ethical misconduct Inform Head of Institute and Funding Ban publicationReasonable similarity Cited Results, content Review Article Revise 250 words Methods, Introduction,Abstract Accept © Janssens Aug-16 - Scientific Writing  http://publicationethics.org/  Code of Conduct and Best Practice Guidelines  Flowcharts on how to handle ethical problems  Database of all cases, advice given and outcome COPE – commission of pulication ethics
  65. 65. 9/2/2016 65 © Janssens Aug-16 - Scientific Writing129 Further reading © Janssens Aug-16 - Scientific Writing130 Go to get a grant http://www.nature.com/naturejobs/science/articles/10.10 38/nj7385-429a
  66. 66. 9/2/2016 66 © Janssens Aug-16 - Scientific Writing  Editing  Nomenclature and terminology  Policies and processes  Peer review  Ethics  Publishing and promoting EASE Science Editors Handbook http://www.ease.org.uk/ © Janssens Aug-16 - Scientific Writing Training for Editors www.ease.org.uk
  67. 67. 9/2/2016 67 © Janssens Aug-16 - Scientific Writing  http://www.ismte.org/ ISMTE Intl. Soc. Managing & Technical Editors © Janssens Aug-16 - Scientific Writing Thank you! "Be yourself. Everyone else is already taken." - Oscar Wilde  For questions:  de.linkedin.com/in/janssens  www.dkfz.de/careers  www.slideshare.net/barbaja  www.facebook.com/phdcareers

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