周五下午文献阅读与写作

Howtoreadapaper:Thethree-pass Tricksfor ture Howtowritea Principlesforfigure Publishing HowtosubmitNGSdatato Case:HowtopublishinPLoS PapersofRNA- Case1:PlosONE Case2:NSMBPartI.HowtoreadaThethree-pass Thefirst givesyouageneralideaaboutthe Thesecond letsyougraspthepaper'scontent,butnotits Thethird helpsyouunderstandthepaperinThefirst Thefirstpassisaquickscantogetabird's-eyeviewoftheYoucanalsodecidewhetheryouneedtodoanymorepasses.Thispassshouldtakeaboutfivetotenminutesandconsistsofthefollowingsteps: Carefullyreadthe ,and Readthesectionandsub-sectionheadings,but Glanceatthemathematicalcontent(ifany)todetermine Readthe Glanceoverthereferences,mentallytickingofftheonesalreadyThefirst Attheendofthefirstpass,youshouldbeabletoanswerthe Category:Whattypeofpaperisthis?Ameasurementpaper?ysisofanexistingsystem?Adescriptionofa Context:Whichotherpapersisitrelatedto?Whichbaseswereused yzethe Correctness:Dotheassumptionsappeartobe Contributions:Whatarethepaper'smain Clarity:IsthepaperwellThesecond Readthepaperwithgreatercare,butignoredetailssuchasIthelpstojotdownthekeypoints,ortomakecommentsinthemargins,asyouread.Thispassshouldtakeuptoanhourforanexperiencedreader. Lookcarefullyatthefigures,diagramsandotherillustrationsinthepaper.Payspecialattentiontographs.Aretheaxesproperlylabeled?Areresultsshownwitherrorbars,sothatconclusionsarestatisticallysignificant?Commonmistakeslikethesewillseparaterushed,hoddyworkfromthetrulyexcellent. Remembertomarkrelevantunreadreferencesforfurtherreading(thisisagoodwaytolearnmoreaboutthebackgroundoftheThesecond Afterthispass,youshouldbeabletograspthecontentofthe Sometimesyouwon'tunderstandapaperevenattheendofpass,Youcannowchoose setthepaperaside, youdon'tneedtounderstandmaterialtobesuccessfulinyour returntothepaperlater,perhapsafterreading persevereandgoontothethirdThethirdnTofullyunderstandapaper,particularlyifyouarereviewer,requiresathirdpass.Thispasscantakemanyhoursforbeginnersandmorethananhourortwoevenforanexperiencedreader.nThispassrequiresgreatattentiontodetail.Youshouldidentifychallengeeveryassumptioninevery Attheendofthispass,youshouldbeabletoreconstructtheentirestructureofthepaperfrommemory,aswellasbeabletoidentifyitsstrongandweakpoints.Tricksfor ture Hoffmann,R.,Valencia,A.Agenenetworkfornavigatingthe ture.Genetics36,664PartII.Howtowritea Askyourselfbefore Whydidyoustart? Whatdidyoudo? Whatdidyoufind? WhatdoesitHowtowritea Contentisessential内容是基 Presentationiscritical表达是关 Writeyourmanuscriptsothatit lsaclearstoryitmusthavea Youwantpeopletolearnaboutyourworkmakeiteasyforthem论 Makeiteasyforreviewersand 格式便于编辑和审稿人读评 Usethespellcheckerand rchecker使用拼写检查和语法查来避免拼写和语法 Structureofascientific Title+ + Materialsand Results& Accuracy准确：准确地反 的内 Brevity简洁：中文最好不超过20个汉字，英文最好不超过12 Clarity清楚：清晰地反映文章的具体内容和特色 力求简洁有效、点突 尽可能将表 内容 词放在题名开 慎重使用缩略 避免使用化学式、上下角标、特殊符号(数字符号、希腊字母等)等 避免使用ThoughtsonRegardingStudyExampleof Bad:Actionofantibioticson Bad:Preliminaryobservationsontheeffectofcertainantibioticsvariousspeciesof Good:ActionofStreptomycinonMycobacterium Better:InhibitionofgrowthofMycobacteriumtuberculosisExampleofBad:LinearprogrammingmethodofoptimizationofsystemsofdifferentialGood:LinearprogrammingmethodforoptimizationofBad:Formulationofequationsofverticalmotionoffiniteelementformforvehicle-bridgein ctionsystemGood:Finiteelementbasedformulationsforvehicle-bridgein systemconsideringverticalmotionExampleof Simplestraightforwardtitle单标 ProteinassociationstudiedbyNMR BiosynthesisoftheTerpenePhenalinolactoneinStreptomycessp.Tü6071: ysisoftheGeneClusterandGenerationof Whoarethe 国际医学期编 (ICMJE)有关作者资格的界 课题的构思与设计，资料的分析和解 文稿的写作或对其中重要学术内容作重大修 参与最后定稿，并同意投稿 以上3项条件应全部具备方可成为作 作者的排列顺序应由所有作者共同决 每位作者都应该能够 的全部内容向公众负 Correspondingauthorandfirst 的执笔人或主要撰写者应该是第一作者(first 通信作者(correspondingauthor)通常是实际统筹处复审稿意见等工作的主导者，也常是稿件所涉及研究工。通信作者 多位列 作 的最后，但其贡献不亚的第一作q通信作者标注：CorrespondingauthorTowhomcorrespondenceshouldbeaddressedq如果两个以上的作者在地位上是相同的，可以采jointfirstauthor(共同第一作者）的署名方式，并标注TheseauthorscontributedequallytotheworkMaterialand Enoughinformationmustbegivensothattheexperimentscouldreproduced必须给出足够信息确保 讨 nClarityandbrevity:disyofdatawithlogicaldevelopmentshowinghowyourfindingssatisfyyourobjectives简明扼要，合理展示数据， Numbershouldbemeaningful(wherepossiblegiveillustrativeexamplesandcomparethosewithknownresultsfromli ture数 Useappropriatestatistics,error ysis,checkforaccuracyandinternalconsistency合理运用统计，误差分析； Payconsiderableattentiontobestwaytopresentdatausetablesandfigures)合理运用图表Results 不要因追求美术效果而将图形做得过于花哨(立体效果等n 坐标图的标值应尽量取0.1–00之间的数值；坐标轴的说明应清楚,量和单位 的放大倍数应使用图示法(标尺 结 在的问题及不 Theoreticalorpracticalimplicationsimportance理论或实际的应用 Backgroundforunderstandingthediscussion必要背景阐 Whatyoudidfoundthoughtandwhatitmeansforthediscipline验过程、结果 给出评 Howyourresultswereuniqueordifferentfrompreviousresearch与 Technicalassistance技术支持 FinancialAssistance Helpfuldiscussions有益的讨论 致谢的开始就用“Wethank”,不要使用“WewishtothankWewouldliketothank”,等 如果说“IwishtothankJonesfor…”则是在浪费单词,并且也可能蕴含着我希望感谢JohnJones的帮助,但这种帮助并不那么大 nIncludethemainscientificpublicationsonwhichyourworkisbasedtypically20-50papersincludereviewarticlesasappropriate主要文献，一般20-50篇，适当综述文献nMakesurethelistisuptodate保证所引文献的前沿nChecktheformat根据期要求调整格 Sci Ren,S.L.,Rousseau,R.,Internationalvisibilityscientificjournals,Scientometrics,2002,53: Ren,S.&Rousseau,R.Internationalvisibilityofscientificjournals.Scientometrics,2002,53(3):389–405 S.Ren,R.Rousseau,Scientometrics53,389 ProcNatlAcadSci Ren,S.&Rousseau,R.(2002)Scientometrics53,Principlesforfigure Uinformspacingan Consistant Legend Simplifyand Grid NoWhenpresentedwithavisualstimulusinwhichasmallnumberofelementsisdifferent(color,shape,etc),yourbrainrapidlyremapstheattentionalcaptureofeachelement.Adjacentsimilarelementsinhibiteachother’ssalienceandyourattentionisquicklyfocusedontheelementsthataredifferent.UinformspacinganKeepthesize,spacingandalignmentfixedofasmanyelementsaspossible.Anyvariationinthefigurewillbeinterpretedasimportanttoitsmessage.Splicingisanadjacencyrelationshiptheemphasisshouldtherefore ontheconnectionsbetweenexons.Recallthepreviousslideaboutsalience.Bylimitingvariationofnon-criticalelements,youareemphasizingthevisualweightofthecoremessage.ConsistantAvoidchangingaxisscales.Youcansavethereaderfromhavingtochecktheconsistencyofyouraxesbyshowingasingleaxisformultiplepanels.LegendOrderelementsinthelegendconsistentlywiththeirappearanceinthefigure.Astackofelementswillbeperceivedmorevisuallybalancedwhendarkertonesareatthebottom.Wherepossible,usethesameshapeinthelegendandthefigure(e.g.donotusesquaresymbolsinalegendforafigurethatusescircles).Useeithershapeorcolor,notCircleandsquarecanappearsimilar.Useempty/filled(orsmall/large)glyphstocategorizedataemptyorsmall–filledorlarge–UsetheBrewerpalettesforBlacktextondarkcolorsisillegibleduetoinsufficientluminositycontrast.Wherepossiblekeepbackgroundcolorslightanddesaturated.Onlyusecolorwhereitisunavoidable.Variationinshape,strokeandgreytoneisusuallysufficienttoprovidecontrast.SimplifySimplifyandThereadermustworkhardtooverlooktheunnecessaryvariationinthearrows.NoticehowtheweightandsizeofarrowsintheCNEEVOLUTIONpanelisirrelevant,butusedtoencoderateofevolutionintheEVOLUTIONRATEpanel.Thetimeaxisalreadyindicatestheflowoftime,makingallotherarrowsredundant.Noticehowtheredesignedfigureusesalignmentandconsistencytoenhancethesalienceofcriticalelements. SimplifyandTheuseofvisuallycomplexelementsobscuresthefigure’smessagewhenpatternsinspatialrelationshipsareimportant.Here,becauseallthearrowspointinthesamedirection,theyarenotuseful.Again,alignmentandsimplificationincreasesthesalienceofimportantpatterns(e.g.relationshipofelementstoARE)andattenuatesunimportantcharacteristics,suchassizeoftheelementsandabsolutedistancebetweenthem(itisunclearwhetherthearrows’sizeanddistanceismeaningfulintheoriginalfigure).SimplifyandTextlabelsshouldbeshortenedtoemphasizeuniqueness.Inthiscase,eachlabelsharesthe“-cldn”suffixwhichdoesnotneedtoberepeated.ThereaderwillfindalignedtexteasiertoSimplifyandResisttheurgetodecorateyourfigure.Asimpleandconcisepresentationwillbevaluedbythereader.Witheachunnecessaryvariationthevalueofthefigureisdecreased.SimplifyandGridTheuseofagridlayoutcangreatlyimproveafigure.Left,elementsareorganizedhaphazardly.Right,removingthedependenceonboxesandcalloutsbyusingagridmodel.Clutterisreduced.No3Dviewssufferfromocclusionandimprecision.Withoutdroplinestoeach youcannotuniquelydetermineapoint’sposition.Inthe3Dplots(A,C)theaxesPC1/PC2arereversedrelativeto(B,D).Didyouseethisimmedia NoThesetwofiguresdemonstratethebenefitsofapplyingsomeofthedesignrulesmentionedonthepreviousslides.PartIII.Publishing作者投作者投编辑初录改后录改后录用、再Publishing Whoisreviewingyour 专家评 ‘Peer’means‘someonelike ‘Peerreview’:areviewbyanotherscientistinyour Editor-in-Chief:aninternationallyfamousscientistwhodecidesoneachmanuscriptChosea 稿件 是否适合期所规定的范围“作者须知”中有关 范围的说作者本人经常阅读 的 期的声引证指标(影响因子、总被引频次期在科学界 的看法 对非英语国家的作者 是否收取版面Chosea 阅读“作者须知”或“投稿指南 和范 各栏 采取何种体例格式?如：页边距、纸张大小、参考文献的体例、图 履行何种形式 评 多长时间后能决定可否录Preparationbefore Last Readcarefullythemanuscriptincludingthecoverletter)一定要细阅稿件（包括投稿信 Askoneormorecolleaguestoreadyourpaperbeforesubmission(tocheckthespellingmistakesorinaccurate 可能,请英语国家的合作者或 是否符合西方人的思Preparationbefore Howtowriteacover Conciseandclear,lessthanonepage.简短明了、重点突出 好不要超过一 Whattoinclude?投稿信的基本内 Significanceofyourresearch文章内容的重要性本 Reviewers推荐的审稿人或