Scientific Writing: Preparing a hypothesis-driven research paper

Mar 8th - May 10th 2018 (Thursdays, 09.30-12.30h)

Organizer: Filipa Nunes (iMM Career Development service) Venue: Egas Moniz Building FMUL/IMM ECTS: 1 Vacancies: 20 The goal of the course is for students to be able to write a full hypothesis-driven research paper based on data that are provided to them (which should be considered as real and genuine data). The students will build and write each section of the research paper (Introduction, Materials and Methods, Results and Discussion) and will learn how to navigate through the steps involved in producing and publishing a research paper. To apply please visit: https://fenix.medicina.ulisboa.pt/ APPLICATION DEADLINE FEBRUARY 20TH, 2018 Fees: FMUL/CAML PhD Students Free CAML Applicants (IMM/FMUL/CHLN) Free Other Applicants Not Available More information available at: http://www.fm.ul.pt/camlcourses If you have any questions please contact: camlphd@fm.ul.pt Course organized under Doctoral Programme of the Lisbon Academic Medical Centre (FMUL/IMM/HSM-CHLN)

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Preparingahypothesis-drivenresearchpaperHands-onclass

ProfessorMarciaTriunfol,PhD(CVintheendofthedocument)

COURSESYLABUSDescriptionThis is a hands-on course in which students write a full hypothesis-drivenresearch paper. Forwriting the paper, students use data that are provided tothemandwhichshouldbeconsideredasrealandgenuinedata.Emphasisareonbuilding each section of the research paper according to the IMRAD(Introduction, Material and Methods, Results and Discussion) format and onlearninghowtonavigatethroughthestepsinvolvedinproducingandpublishinga research paper. Even though the focus of the course is the production of aresearchpaper,manyof the lessons learned in this course canbeapplied to athesis.OrganizationThe group is divided in small groups of no more than 5 students each. Eachgroup produces an entire hypothesis-driven research paper throughout thecourse. The data used to produce the research paper is provided to students.Thesedataarenotrealbutareplausibleandshouldbeconsideredasgenuine.Thedataprovidedwillbeontopicsoftheirinterest/knowledge.TheresearchpapershouldbewritteninEnglish.ItshouldbenotedthatEnglishgrammarandusagearenotthefocusofthiscourse.Thecourseisdividedin9classes(1perweek,ideally)of3hourseach.TopicsThiscoursewillcoverthefollowingtopics:

• Thestructureoftheresearchpaper• Thenarrativeofeachsectionoftheresearchpaper• Buildingthefirstdraftofaresearchpaper• Writingtheresearchpaper• UsingPubmedtosearchthescientificliterature• Buildingtablesandfigures• Plagiarism• Reproducibilityinscience• Authorshipinscience• Usingreferencescorrectly• Choosingtherightjournal

MaterialsandNecessaryResources

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Studentsshouldbringtheirlaptops.Studentsshouldhaveaccesstotheinternetthroughoutthecourse.Studentsshouldhaveaccesstodatabasesofresearchpapers(PUBMED)andalsotoscientificjournals.Theentirebibliographyofthiscoursewillbeprovideddigitally.FinalEvaluationStudentswillbeevaluatedasfollows:

• Theresearchpaperwrittenduringthecourse(upto6.0points).• Quiz based on the content presented in class or provided in the

bibliographyofthecourse(upto4.0points).Class1TheresearchpaperInthisfirstclass,wetalkabouttheresearchpaper,understandthehistorybehindtheIMRADformat,thenatureoftheresearchpaperandtheresponsibilitiesoftheauthor.AbriefintroductiononhowtousePUBMEDispresened.Next,studentsaresplitingroupsofnomorethanfivepeople.Eachgroupreceivesasetofdataandashorttextexplaininghowthedatawascollected.Studentsspendtheentireclasstogetfamiliarwiththedataandthescientifictopic,they use PUBMED to find reviews on the subject and share information andknowledgeaboutthetopicamongparticipantsinthesamegroup.Bibliographyforthisclass:SollaciLB,PereiraMG.Theintroduction,methods,results,anddiscussion(IMRAD)structure:afifty-yearsurvey.JMedLibrAssoc.2004Jul;92(3):364-7.PubMedHelp:NCBIHelpManual,availableathttps://www.ncbi.nlm.nih.gov/books/NBK3830/VollmerWM.Responsibilitiesofauthorship.Chest.2007Dec;132(6):2042-5.Class2Whatisascientificquestion,howtodefinethescientificquestionofyourstudyandbuildthehypothesisFindingtherightjournalforyourpaperIn this class, studentsdefine the scientific questionof the study, according to thedatatheyhavereceivedinthepreviousclass.Theydefinetheroleeachoneinthegroupwillhaveduringtheprocessofwritingthepaper.Studentssearchforthebestpossiblejournalfortheirresearchpaper.

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BibliographyforthisclassLipowskiEE.Developinggreatresearchquestions.AmJHealthSystPharm.2008Sep1;65(17):1667-70.MeadowsKA.Soyouwanttodoresearch?2:developingtheresearchquestion.BrJCommunityNurs.2003Sep;8(9):397-403.BrianHaynesR.Formingresearchquestions.JClinEpidemiol.2006Sep;59(9):881-6.HarveyBJ,LangTA.Hypothesistesting,studypower,andsamplesize.Chest.2010Sep;138(3):734-7.WelchSJ.Avoidingcommonproblemsduringonlinesubmissionofmanuscripts.Chest.2007May;131(5):1591-4.ThompsonPJ.Howtochoosetherightjournalforyourmanuscript.Chest.2007Sep;132(3):1073-6.Class3Theroleoftablesandfiguresintheresearchpaper10questionstoproduceyourfirstdraftInthisclassstudentspreparethefiguresandtablesforthedatatheyhavereceivedandaccordingtotheanalysisdonebythestatistician(ifnecessary).Theyworkonthefirstdraftoftheirpaper.BibliographyforthisclassRougierNP,DroettboomM,BournePE. Ten simple rules for better figures. PLoSComputBiol.2014Sep11;10(9):e1003833.LangTA.Whenapictureneeds1,000words.Chest.2009Jun;135(6):1688-91.HamiltonCW.Onthetable:formandfunction.Chest.2009Apr;135(4):1087-1089.Class4WritingtheResultssectionoftheresearchpaperandpresentingtablesandfiguresUnderstandinghowtousethesection“SupplementaryMaterial”In this class, students write the Results section of their research paper. Theprofessorprovidesassistancetoeachgroupindividually.Bibliographyforthisclass:BrowneJE.Gettingstartedwithresearch"Writing-uptheresultsofyourresearch".Ultrasound.2014Feb;22(1):70-2.WagnerPD.Writingupyourresearchresultsforpublication.Chest.2009Aug;136(2):639-642.

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Class5Writing the Introduction section of the research paper, considering the mainbuildingblocksofthesection:

• Scenario• Previousstudies• Knowledgegap• Researchquestion

Inthisclass, studentswrite the Introductionsectionof theirresearchpaper. Theprofessorprovidesassistancetoeachgroupindividually.Bibliographyforthisclass:FooteM.Howtomakeagoodfirstimpression:aproperintroduction.Chest.2006Dec;130(6):1935-7.CalsJW,KotzD.Effectivewritingandpublishingscientificpapers,partIII:introduction.JClinEpidemiol.2013Jul;66(7):702.Class6Writing the Discussion section of the research paper, considering the mainbuildingblocksofthesection:

• Summaryofmainfindings• Contextualizationofmainfindingsaccordingtotheliterature• Study’slimitations• Study’scontribution• Futuresteps

In this class, students write the Discussion section of their research paper. Theprofessorprovidesassistancetoeachgroupindividually.Bibliographyforthisclass:CalsJW,KotzD.Effectivewritingandpublishingscientificpapers,partVI:discussion.JClinEpidemiol.2013Oct;66(10):1064HessDR.Howtowriteaneffectivediscussion.RespirCare.2004Oct;49(10):1238-41.Class7Writing the Abstract of the research paper, considering the different types ofabstract:

• Graphicalabstract• Structuredabstract

WritingtheTitleoftheresearchpaper,consideringdifferenttypesoftitles:

• Descriptive• Questionmark• Informative

In this class, students write the Abstract and Title of their research paper. Theprofessorprovidesassistancetoeachgroupindividually.

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Bibliographyforthisclass:CalsJW,KotzD.Effectivewritingandpublishingscientificpapers,partII:titleandabstract.JClinEpidemiol.2013Jun;66(6):585.FooteM.Someconcreteideasaboutmanuscriptabstracts.Chest.2006May;129(5):1375-7.vonElmE.Writingtheabstract:completenessandaccuracymatter.EurJAnaesthesiol.2011Jul;28(7):483-4.Pferschy-WenzigEM,PferschyU,WangD,MocanA,AtanasovAG.DoesaGraphicalAbstractBringMoreVisibilitytoYourPaper?Molecules.2016Sep18;21(9).pii:E1247.Checkhttp://www.wikihow.com/Make-a-Graphical-Abstract-for-Scientific-PublicationClass8Finishing-up:

• Writingthecoverletter• Finishingtheresearchpaper

Inthisclass,studentswritethecoverletterthatshouldbesenttogetherwiththeirresearchpaperduringthesubmissionprocess.BibliographyforthisclassPehWC,NgKH.WritingalettertotheEditor.SingaporeMedJ.2010Jul;51(7):532-5.Class9Submittingyourpaperandthepeer-reviewprocess+promotingthepaperinthescientificcommunityandinthesocietyatlarge

• Thepeer-reviewprocess(blind,double-blindandopenreviews)• Pressrelease• Embargo• Researchgateandotherplatforms• Talkingtojournalists• Internationalmeetings

Inthisclass,studentswill learnaboutthedifferenttypesofreviewprocesses,andwhattodowhenreceivingtheacceptance(ornot!)letterfromthejournal.BibliographyforthisclassWelchSJ.Avoidingcommonproblemsduringonlinesubmissionofmanuscripts.Chest.2007May;131(5):1591-4.

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NeillUS.Howtowriteaneffectiverefereereport.JClinInvest.2009May;119(5):1058-60.WoolleyKL,BarronJP.Handlingmanuscriptrejection:insightsfromevidenceandexperience.Chest.2009Feb;135(2):573-7.

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Marcia Triunfol, Ph.D. mtriunfol@gmail.com

Rua Heliodoro Salgada 75 RC Esq Lisbon, Portugal

+351-934-174-565

EDUCATION 2016- Become a journalist: Report the News (2 modules, final grade over 9.5). Michigan State University via Coursera. 1999-2001- Post-doc at the National Institutes of Health (NCI), USA 1995-1999- Ph.D. in Human Genetics. Johns Hopkins University (USA) and Universidade Federal Fluminense (Brazil) 1991-1993- M.S. in Genetics. Universidade Federal do Rio de Janeiro (Brazil) 1987-1990- B.S. in Biology. Genetics. Universidade Federal do Rio de Janeiro (Brazil) CURRENT ACTIVITIES Scientific advisor at Humane Society International. Since August 2016. Professor of the subject “Science Writing” for the Graduate Program in Health Sciences at the Albert Einstein Hospital, São Paulo, Brazil. Since 2014. Founder and current CEO of Publicase (www.publicase.com.br), a science communication company in Brazil. Since 2008. Freelance Science Writer and Journalist for high-impact journals and media outlets. Since 2002. Member of the American Association of Science Writers (United States, since 2014). PRODUCTION AS A SCIENCE WRITER AND JOURNALIST News

Marcia Triunfol. New data back early hypothesis for infectious microcephaly. The Lancet Infectious Disease, Volume 16, No. 9, p1008–1009, September 2016

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Marcia Triunfol. Zika Infects Adults Neural Progenitors Too. The Scientist, August 18, 2016. http://www.the-scientist.com/?articles.view/articleNo/46841/title/Zika-Infects-Adults-Neural-Progenitors-Too/ Marcia Triunfol. Sofosbuvir Shows Anti-Zika Activity In Vitro The Scientist, July 19, 2016. http://www.the-scientist.com/?articles.view/articleNo/46585/title/Sofosbuvir-Shows-Anti-Zika-Activity-In-Vitro/

Marcia Triunfol. Chloroquine Protects Against Zika In Vitro. The Scientist, May 12, 2016. http://www.the-scientist.com/?articles.view/articleNo/46076/title/Chloroquine-Protects-Against-Zika-In-Vitro/

Marcia Triunfol. Microcephaly in Brazil: confidence builds in Zika connection. The Lancet Infectious Disease. Volume 16, No5, p527–528, May 2016 Marcia Triunfol and Udani Samaraseka. Concern over Zika virus grips the world. The Lancet 387: 10018 (2016) Marcia Triunfol. A new mosquito-borne threat to pregnant women in Brazil. Lancet Infectious Disease 16: 156 (2016) Marcia Triunfol. Human embryonic stem-cell research re-approved in Brazil. Lancet Oncology 9:616 (2008)

Marcia Triunfol. Latin America Science Moves into the Spotlight. Cell 131: 1213-1216 (2007).

Marcia Triunfol and Jeffrey Mervis. Miguel Nicolelis Profile: Brazil Institute Charts a New Hemisphere for Neuroscience. Science 303: 1131-1132 (2004) Book review Marcia Triunfol. Lucifer in the Sky with Dinosaurs. Science 298: 1178 (2002) Marcia Triunfol. More Bark than Bites. Science 297: 342 (2002)

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Press Release (short list)

Ever-changing moods may be toxic to the brain of bipolar patients

(http://www.eurekalert.org/pub_releases/2016-05/pcc-emm052816.php) No kissing or singing in the rain (http://www.eurekalert.org/pub_releases/2013-10/pcc-nko091413.php) Prions and cancer: A story unfolding (http://www.eurekalert.org/pub_releases/2012-06/pcc-pac062512.php) A sip of resveratrol and a full p53: Ingredients for a successful cell death (http://www.eurekalert.org/pub_releases/2012-11/pcc-aso111312.php) A potential novel drug-target for colorectal cancer treatment comes from the brain (http://www.eurekalert.org/pub_releases/2011-04/pcc-apn042611.php A prognostic and predictive biomarker for nonsmall cell lung cancer (http://www.eurekalert.org/pub_releases/2010-06/pcc-apa060110.php) The female nose always knows: Do women have more olfactory neurons? (http://www.eurekalert.org/pub_releases/2014-11/pcc-tfn110514.php) Try a little tenderness and your brain will tell (http://www.eurekalert.org/pub_releases/2012-09/pcc-tal090212.php) Book authorship Author of the book Folha Explica: Os Clones (Cloning), Marcia L. Triunfol. Part of a collection of reference books on different topics published by PubliFolha in Brazil. TV/Documentary Script Co-author of the script for the episode 100 Greatest Discoveries in Science: Genetics, for Discovery Science Television in 2004. (http://www.imdb.com/title/tt1674786/combined) Website Writer for Tropika, a website on tropical and neglected diseases created and supported by WHO (From March 2008 to January 2009) What you see is not what you get (for NCBI’s Bookshelf- 2005) http://www.ncbi.nlm.nih.gov/books/NBK100133/ Fact sheet about Chromosomes for the National Human Genome Research Institute (NIH, USA). http://www.genome.gov/26524120

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Fact sheet about Cloning for the National Human Genome Research Institute (NIH, USA). http://www.genome.gov/25020028 (Winner of the NIH Plain Language Award in 2008) Fact sheet about DNA for the National Human Genome Research Institute (NIH, USA). http://www.genome.gov/25520880 (Winner of the NIH Plain Language Award in 2008) Tropical microbicide prevents HIV transmission (For AAAS’s AIDScience website) http://aidscience.org/articles/aidscience029.asp The speed of HIV spread (For AAAS’s AIDScience website) (http://aidscience.org/Articles/AIDScience034.asp) Barebacking and bug chasers: expressions of an HIV subculture (For AAAS’s AIDScience website) http://aidscience.org/Articles/aidscience030.asp Articles in Spanish Marcia Triunfol. "La evolución es cosa de tu cabeza", Revista Cómo Ves? 4(45): 30-33 (in Spanish) Mexico. Marcia Triunfol. "Peligro, peligro...Will Robinson", Gaceta Biomédicas, September 2002 (in Spanish) Mexico. (Biomedical newsletter of UNAM- Mexico). FUN WRITING THE BARK: SURFBOARDING IN BRAZIL. HTTPS://THEBARK.COM/CATEGORY/AUTHOR/MARCIA-TRIUNFOL PREVIOUS APPOINTMENTS AS A SCIENCE EDITOR Scientific Editor at the National Center for Biotechnology Information (NIH, USA) (2005-2006), Bethesda, USA. Associate editor at Science Magazine at the American Association for the Advancement of Science (2002 to 2004), Washington DC, USA. PREVIOUS EXPERIENCE AS AN EDUCATOR Senior Project Associate at Project 2061 at the American Association for the Advancement of Science–AAAS (2004 - 2005), Washington DC, USA As a Senior Project Associate, my job included writing clarifications for key ideas in genetics, doing a literature review of issues related to genetics education and students’ ideas on genetics, describing phenomena to illustrate scientific ideas and findings, and finding or creating new representations to help with the understanding of several concepts in

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genetics. Associate editor at Science Magazine at the American Association for the Advancement of Science (2001), Washington DC, USA

Science Controversies On-line Partnership in Education (SCOPE): SCOPE was an educational website that explored controversial issues in science. My job resulted in the following research paper: Marcia Triunfol and P. J. Hines. Dynamics of List-server Discussion on Genetically Modified Foods. Public Understanding of Science 13: 155-175 (2004)

Visiting Professor of the subject “The History of Genomic Medicine” at the Graduate Program on History of Health Sciences, Fundação Oswaldo Cruz, (2001), Rio de Janeiro, Brazil

EXPERIENCE AS A BENCH SCIENTIST OBS: Lachtermacher and/or Rocha = Triunfol 1999-2001 - National Cancer Institute (NIH), Frederick, MD. PIs: Dr. Michael Dean and Dr. Stephen O´Brien

The human ATP binding cassette gene ABCA13, located on chromosome 7p12.3, encodes a 5058 amino acid protein with an extracellular domain encoded in part by a 4.8 kb conserved exon. Prades, C., Arnould, I., Annilo, T., Shulenin, S., Chen, Z.Q., Orosco, L., Triunfol, M., et al. Cytogenet. Genome. Res. 98:160-168. 2002 Identification and characterization of a cluster of five new ATP-Binding Cassette transporter genes on human chromosome 17q24: A new sub-group within the ABC sub-family. Schriml LM, Arnould I, Prades C, Lachtermacher-Triunfol M et al. GeneScreen 1:157-164.2001. Human duplex sex determination PCR. Gold B, Bergeron J, Lachtermacher-Triunfol M, Dean M. Biotechniques 31(1):28-30. 2001.

1996-1998- Johns Hopkins University (Kennedy Krieger Institute), Baltimore, MD. PIs: Dr. Kirby Smith and Dr. Hugo Moser

One-step PCR strategy for identification of mutations by SSCP and DNA sequencing. Lachtermacher MBR, Seuanez HN, Moser HW and Smith KD. Biotechniques 29 (2): 234-236. 2000 Determination of 30 X-linked Adrenoleukodystrophy mutations, including 15 not previously described. Lachtermacher MBR, Seuanez HN, Moser AB, Moser HW and Smith KD. Human Mutation 15(4):348-353. 2000 Accurate DNA-based diagnostic and carrier testing for X-linked Adrenoleukodystrophy. Bohem CD, Cutting GR, Lachtermacher MBR,

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Moser HW, and Chong SS. Molecular Genetics and Metabolism 66 (2):128-36. 1999.

1995-1996- Instituto Nacional do Câncer, Rio de Janeiro, Brazil PI: Dr. Hector Seunaez

The human chromosome 3 gene cluster ACY1-CACNL1-ZNF64-ATP2B2 is conserved in Ateles peniscus chamek (Platyrrhini, Primates). Seuanez H, Lachtermacher MBR (Triunfol), Canavez F, and Moreira MA. Cytogenetics Cell Genetics 77 (3-4): 314-7. 1997. Molecular monitoring after allogeneic BMT in a Brazilian boy with X-linked Adrenoleukodystrophy. Rocha (Triunfol) MB, Seuanez H, and Tabak D. Brazilian Journal of Genetics 19(02): 123. Abstract # 126. 1996. Rapid identification of blast origin by PCR amplification three years after allogeneic BMT. Rocha (Triunfol) MB, Seuanez H, and Tabak D. Brazilian Journal of Genetics 19(02): 124. Abstract # 127. 1996.

1993-1994- Southwest Foundation for Biomedical Research, San Antonio, TX PI: Dr. Jeff Rogers

The effects of age, body weight and genetic variation on bone density of the spine and radius in Baboons (Papio hamadryas) measured using dual energy X-ray absorptiometry. Roger J, Mahaney MC, Wittman NJ, Hodgson WJ, Rocha (Triunfol) MB, Parry P, and Kammerer CM. Journal of Bone and Mineral Research 10 (1): S442. 199

1991-1993- National Cancer Institute, Rio de Janeiro, Brazil PI: Dr. Hector Seuanez

DNA fingerprinting in three species of Neotropical primates. Rocha (Triunfol) M.B, Seuanez H, and Muniz J. American Journal of Primatology 40: 83-93. 1996.

Other interesting things about me Co-author of U.S. Patent Application No. 60/405,006 August 20, 2002. NIH (DHHS) Ref. No. E-304-2000/0-US-01. For: ABCA13 NUCLEIC ACIDS AND PROTEINS, AND USES THEREOF Curator of the meeting “First Brazilian Colloquium on High-Impact Research and Publication” held in April 2010 at the Albert Einstein Hospital in São Paulo, Brazil.

Founder and Executive Director of DNA Goes to School, a non-profit organization in Brazil that had the mission of educating and informing the

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public about ethical issues and scientific advances in the biomedical field. (1998 to 2010). See selected list of accomplishments below:

• 2004- Production of a science event at the First Week of Science and Technology in Brazil. The event generated the following paper: Have you eaten any DNA today? Science communication during Science and Technology Week in Brazil

• 2006- Production of an exhibition on cancer prevention exhibited at

the São Paulo subway system that attracted international attention. See Cancer Communication Targets Commuters. Lancet Oncology vol 8, issue 4: 294-295 (2007)

• 2006-Production of the Brazilian Portuguese version of Cold Spring Harbor Laboratory’s award-winning educational on-line resource DNA from the Beginning.

• Languages and skills Fluent: Portuguese (mother tongue), Spanish (intermediate level) and English (near native fluency). Proficient in PhotoShop, InDesign, MS Office, Social Media