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外文资料--Qualitative Analysis of a Delayed and Stage-Stuctured Predator-Prey System (2).PDF

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外文资料--Qualitative Analysis of a Delayed and Stage-Stuctured Predator-Prey System (2).PDF

NIPAHVIRUSCLASSIFICATIONVIAFRACTALDIMENSIONSHANNONENTROPYTODDHOLDEN,NGADURA,ECHEUNG,PSCHNEIDER,GTREMBERGER,JR,NELHAM,DSUNIL,DLIEBERMAN,ANDTCHEUNGPHYSICSANDBIOLOGYDEPARTMENTSCUNYQUEENSBOROGHCOMMUNITYCOLLEGEBAYSIDE,NY11364USACONTACTEMAILTHOLDENQCCCUNYEDUABSTRACTNIPAHVIRUSGLYCOPROTEINANDNUCLEOPROTEINSEQUENCESWERESTUDIEDUSINGFRACTALDIMENSIONANDSHANNONENTROPYTHENUCLEOTIDEATOMICNUMBERFLUCTUATIONFORMSTHEBASISOFTHEPHYLOGENYSTUDYTHECLASSIFICATIONREPRODUCESTHEMAINRESULTSOFTRADITIONALPHYLOGENYANALYSIS,BUTWITHBETTERABILITYTODISTINGUISHCLOSELYRELATEDSTRAINSTHEFRACTALDIMENSIONCORRELATIONWITHTHEGCPAIRCONTENTINTHEGLYCOPROTEINSEQUENCEANDDINUCLEOTIDEENTROPYINTHENUCLEOPROTEINSUGGESTSDIFFERENTEVOLUTIONARYMECHANISMSORSTRATEGIESEXTENSIONTOOTHERFLUVIRUSSUGGESTSTHATLOWFRACTALDIMENSIONALITYINTHENUCLEOPROTEINSEQUENCECOULDBEAMARKERFORTHENIPAHANDSPANISHFLULIKEVIRUSESKEYWORDSCOMPONENTNIPAHVIRUS;GLYCOPROTEIN;NUCLEOPROTEIN;SHANNONDINUCLEOTIDEENTROPY;FRACTALDIMENSION;CORRELATIONIINTRODUCTIONCLOSELYRELATEDVIRUSESCANBECLASSIFIEDBYACOLLECTIONOFPHYLOGENETICMARKERSWITHNUMBERSDETERMINEDFROMMATHEMATICALOPERATIONSONDNASEQUENCEINCASESWHERESUCHMARKERSDIFFERSIGNIFICANTLYFROMWHATWOULDBEEXPECTEDFORRANDOMMUTATIONS,WECANGETANIDEAOFHOWMUCHNATURALSELECTIONHASINFLUENCEDTHEEVOLUTIONOFAPARTICULARSEQUENCENIPAHVIRUSISAZOONOTICINFECTIOUSVIRUSRESPONSIBLEFOROUTBREAKSAMONGPIGFARMERSINASIAPHYLOGENYANDREPLICATIONVIAACELLTOCELLSPREADINGMECHANISMWASREPORTED1FATALENCEPHALITISCASESWEREALSOREPORTED2HERE,WEANALYZETHEVIRUSGLYCOPROTEINANDNUCLEOPROTEINSEQUENCESUSINGNUCLEOTIDEENTROPY,DINUCLEOTIDEENTROPY,ANDFRACTALDIMENSIONWEEXAMINETHERELATIONSHIPOFTHEABOVEMENTIONEDPHYLOGENETICMARKERSTOSHEDLIGHTONWHETHERTHEREISSELECTIONPRESSURERESULTINGINSYSTEMICNUCLEOTIDEFLUCTUATIONTRENDANDITSCORRELATIONWITHSEQUENCEFUNCTIONALITYTHENUCLEOTIDEBASEPAIRCHANGESOVERAGENESEQUENCECANBEVIEWEDASAFLUCTUATIONAND,CONSEQUENTLY,CANBEINVESTIGATEDWITHTOOLSTHATINCLUDECORRELATIONANDFRACTALDIMENSIONANALYSISFORTHISSTUDY,THENUMERICALSEQUENCEREPRESENTINGTHENUCLEOTIDESINAGENESEQUENCEWASGENERATEDUSINGTHEPROTONNUMBEROFEACHNUCLEOTIDENUCLEOTIDEFLUCTUATIONHASBEENSTUDIEDUSINGOTHERASSIGNMENTSCHEMES3,4,5THEUSEOFPROTONNUMBERWASMOTIVATEDPARTLYBYTHEOBSERVATIONOFMASSFRACTALDIMENSIONINTHEXRAYDATAOFPROTEINSANDRIBOSOMES6,ANDUSINGAPROTONASSIGNMENTSCHEMEMAYREVEALPROTONSENSITIVITYINTHEUNDERLYINGGENETICSEQUENCETOTHEFOLDINGINDUCEDMASSFRACTALARECENTCOMPARISONOFHUMANANDCHIMPANZEEGENOMESREVEALEDTHATITISPOSSIBLETOMEASURETHEACCELERATIONRATEOFTHEACCELERATEDREGIONSOFTHEHUMANGENOME7FRACTALANALYSISOFTHESEACCELERATEDREGIONSSHOWEDTHATTHEDIFFERENCESINFRACTALDIMENSIONCANBEUSEDASAMARKEROFEVOLUTION8ADDITIONALIMPLICATIONSOFEVOLUTIONANDPOSITIVESELECTIONHAVEBEENDISCUSSEDINRECENTLITERATURE9IIMETHODSAGENETICSEQUENCETHENIPAHVIRUSSTRAINSEQUENCESWEREDOWNLOADEDFROMGENBANKUSINGTHEACCESSIONNOSINREFERENCE1ADDITIONALFLUSEQUENCES,SARSCOVSEQUENCES,16SRRNA,12SRRNA,ETC,WEREDOWNLOADEDSIMILARLYDUETOTHELIMITEDSPACEINTHISPAPER,WEASKINTERESTEDREADERSTOCONTACTUSFORFURTHERDOWNLOADINFORMATIONBHIGUCHIFRACTALMETHODTHEATCGSEQUENCEWASCONVERTEDTOANUMERICALSEQUENCEBYASSIGNINGTHEATOMICNUMBER,THETOTALNUMBEROFPROTONS,INEACHNUCLEOTIDEA70,T66,C58,G78THEASSIGNEDNUMBERISPROPORTIONALTOTHENUCLEOTIDEMASSIGNORINGISOTOPESTHEATANDCGPAIRSINDOUBLESTRANDEDDNAHAVETHESAMEVALUEOF136AMONGTHEVARIOUSFRACTALDIMENSIONMETHODS,THEHIGUCHIFRACTALMETHODISWELLSUITEDFORSTUDYINGSIGNALFLUCTUATIONANDHASBEENAPPLIEDTONUCLEOTIDESEQUENCES10THENUMERICALSEQUENCEICOULDBEUSEDTOGENERATEADIFFERENCESERIESIJIIFORDIFFERENTLAGSTHENONNORMALIZEDAPPARENTLENGTHOFTHESERIESCURVEISSIMPLYLKΣ|IJII|FORALLPAIRSWHEREJIEQUALSKTHENUMBEROFTERMSINAKSERIESVARIESANDNORMALIZATIONMUSTBEUSED11IFIIISAFRACTALFUNCTION,THENAPLOTOFLOGLKVERSUSLOG1/KWILLBEASTRAIGHTLINEWITHTHESLOPEEQUALTOTHEFRACTALDIMENSIONHIGUCHIINCORPORATEDACALIBRATIONDIVISIONSTEPDIVISIONBYKSUCHTHATTHEMAXIMUMTHEORETICALVALUEISCALIBRATEDTOTHETOPOLOGICALVALUEOF2ANDAMINIMUMVALUEOF1THEHIGUCHIFRACTALALGORITHMUSEDINTHISPROJECTWASCALIBRATEDWITHTHEWEIERSTRASSFUNCTIONTHISFUNCTIONHASTHEFORMWXΣANHCOS2ΠANXFORALLTHENVALUES0,1,2,3THEFRACTALDIMENSIONOFTHEWEIERSTRASSFUNCTIONWASGIVENBY2HWHEREHTAKESONANARBITRARYVALUEBETWEENZEROANDONETHEPROJECTWASPARTIALLYSUPPORTEDBYSEVERALCUNYGRANTS9781424447138/10/25002010IEEECSHANNONENTROPYCALCULATIONTHESHANNONENTROPYOFASEQUENCECANBEUSEDTOMONITORTHELEVELOFFUNCTIONALCONSTRAINTSACTINGONTHEGENE12ASEQUENCEWITHARELATIVELYLOWNUCLEOTIDEVARIETYWOULDHAVEALOWSHANNONENTROPYMORECONSTRAINTINTERMSOFTHESETOF16POSSIBLEDINUCLEOTIDEPAIRSASEQUENCE’SENTROPYCANBECOMPUTEDASTHESUMOFPILOGPIOVERALLSTATESIANDTHEPROBABILITYPICANBEOBTAINEDFROMTHEEMPIRICALHISTOGRAMOFTHE4NUCLEOTIDESOR16DINUCLEOTIDEPAIRSTHEMAXIMUMENTROPYISTWOBITSPERMONONUCLEOTIDEWITHFOURPOSSIBILITIES22THEMAXIMUMDINUCLEOTIDEENTROPYIS4BINARYBITSPERPAIRFOR16POSSIBILITIES24IIIRESULTSANDDISCUSSIONAGLYCOPROTEINSEQUENCENUCLEOTIDEFLUCTUATIONTHEFRACTALDIMENSIONANDSHANNONDINUCLEOTIDEENTROPYOFTHEGLYCOPROTEINSEQUENCESOFTHENIPAHVIRUSSTRAINSAREDISPLAYEDINFIG1THEDATACLUSTERSINTOTHREEGROUPSTHEBANGLADESHSTRAINHASTHEHIGHESTENTROPYWHILETHECAMBODIASTRAINHASTHELOWESTENTROPYTRADITIONALPHYLOGENYANALYSISPUTTHEBANGLADESHSTRAINWITHTHELARGESTDISTANCEANDTHECAMBODIASTRAINATTHESMALLESTDISTANCEFIGURE1BOFREFERENCE1THELARGESTGROUPCLUSTERSATLOWERFRACTALDIMENSIONVALUESANDTHEDETAILSAREDISPLAYEDINFIG2THEUMMC2STRAIN,SEREMBANSTRAIN,UMMC1STRAIN,ANDCDCSTRAINFORMSASUBGROUPHAVINGSIMILARFRACTALDIMENSIONANDENTROPYVALUESCONSISTENTWITHTRADITIONALPHYLOGENYANALYSISRESULTOURANALYSISSPLITSTHEMALAYSIASTRAINCROSSAWAYTHEUM0128ANDSUNGAIBULOHSTRAINSSQUAREWHILETHETRADITIONALPHYLOGENYANALYSISGROUPSTHESETHREESTRAINSTOGETHERITAPPEARSTHATTHECLASSIFICATIONVIAFRACTALDIMENSIONANDENTROPYMAYHAVESLIGHTLYBETTERABILITYTODISTINGUISHCLOSELYRELATEDSTRAINSASCOMPAREDTOTHETRADITIONALPHYLOGENYANALYSISMETHODUSEDINREFERENCE138963897389838993939013902390339043905197519819851991995FIGURE1THEXAXISREPRESENTSFRACTALDIMENSIONANDTHEYAXISREPRESENTSSHANNONDINUCLEOTIDEENTROPYDIAMONDBANGLADESHSTRAIN,SQUARECAMBODIASTRAIN,TRIANGLESTAMBUNSTRAIN,MALAYSIASTRAIN,UM0128STRAIN,SUNGAIBULOHSTRAIN,UMMC2STRAIN,SEREMBANSTRAIN,UMMC1STRAIN,ANDCDCSTRAIN390223902339024390253902639027390283902939033903139032197731977419775197761977719778FIGURE2THEXAXISREPRESENTSFRACTALDIMENSIONANDTHEYAXISREPRESENTSSHANNONDINUCLEOTIDEENTROPYDIAMONDTAMBUNSTRAIN,CROSSMALAYSIASTRAIN,SQUAREUM0128STRAINANDSUNGAIBULOHSTRAIN,TRIANGLEUMMC2STRAIN,SEREMBANSTRAIN,UMMC1STRAIN,ANDCDCSTRAINTHEFRACTALDIMENSIONOFTHESEQUENCESISFOUNDTOBEASSOCIATEDWITHTHEGCDINUCLEOTIDEPAIRCONTENTTHECLASSIFICATIONOFTHESTRAINSINTOTHREECLUSTERSASDISPLAYEDINFIG1SHOWSUPINFIG3ASWELLTHEFRACTALDIMENSIONANDGCCONTENTCLASSIFICATIONNOTONLYPRODUCESTHREECLUSTERS,BUTALSOSUGGESTSACORRELATIONWITHR2OFABOUT09WITHN10ITWASREPORTEDTHATTHENIPAHVIRUSCANUSETHEMONOCYTESTOCROSSTHEBLOODBRAINBARRIERCAUSINGFATALENCEPHALITISTHEEFFECTIVENESSOFATTACHMENTTOTHEMONOCYTESCOULDDEPENDONTHEGCCONTENTANDPRODUCEEVOLUTIONARYPRESSUREY02708X05025R208923003150032003250033003350034003450035003550036003650037197519819851991995FIGURE3THEXAXISREPRESENTSFRACTALDIMENSIONANDTHEYAXISREPRESENTSGCCONTENTN10BNUCLEPROTEINSEQUENCENUCLEOTIDEFLUCTUATIONTHEFRACTALDIMENSIONANDSHANNONDINUCLEOTIDEENTROPYOFTHENUCLEOPROTEINSEQUENCESOFTHENIPAHVIRUSSTRAINSAREDISPLAYEDINFIG4THEDATACLUSTERSINTOTWOGROUPSTHEBANGLADESHSTRAINHASTHEHIGHESTENTROPYWITHTHERESTOFTHENINESTRAINSNEAREACHOTHERATLOWERENTROPYVALUESTRADITIONALPHYLOGENYANALYSISPUTTHEBANGLADESHSTRAINHAVINGTHELARGESTDISTANCE,ANDCAMBODIASTRAINASTHENEARBYNEIGHBORINGSEQUENCETHEFIGURE4DISTANCEBETWEENBANGLADESHSTRAINDIAMONDANDTHECAMBODIASTRAINSQUAREISALSOTHESMALLEST,CONSISTENTWITHTHETRADITIONPHYLOGENYANALYSISRESULTINFIGURE1AOFREFERENCE1THECLOSENESSOFTHEMALAYSIASTRAINCROSSWITHTHEOTHERSEQUENCESSTARINFIG4ISALSOCONSISTENTWITHTHERESULTOFREFERENCE1ASTHETOPTHREESTRAINSHAVINGTHELARGESTDISTANCESRESPECTIVELY,ANDPUTTHEREMAININGSTRAINSTOGETHERHAVINGTHELEASTDISTANCEOURANALYSISSPLITSTHETAMBUNSTRAINTRIANGLEINFIG4FROMTHEREMAININGSTRAINSASTHESTRAINHAVINGTHELOWESTFRACTALDIMENSIONAREGRESSIONANALYSISOFTHE9STRAINSEXCLUDINGTHEBANGLADESHSTRAINSHOWSCORRELATIONWITHR2AT09FIG5THEEVOLUTIONARYMECHANISMOFTHENUCLEOPROTEINSEQUENCEISDIFFERENTFROMTHATOFTHEGLYCOPROTEINSEQUENCEITWASREPORTEDTHATTHETAMBUNSTRAINHAVECAUSEDTHEHIGHESTFATALITY2,ANDTHEASSOCIATIONWITHLOWFRACTALDIMENSIONALITYWOULDBEANINTERESTINGISSUEANEXTENSIONTOINCLUDEOTHERVIRUSNUCLEOPROTEINSEQUENCESWASPERFORMEDANDTHERESULTISDISPLAYEDINFIGURE639053906390739083909391391139123913391439151996199822002FIGURE4THEXAXISREPRESENTSFRACTALDIMENSIONANDTHEYAXISREPRESENTSSHANNONDINUCLEOTIDEENTROPYDIAMONDBANGLADESHSTRAIN,TRIANGLETAMBUNSTRAIN,SQUARECAMBODIASTRAIN,CROSSMALAYSIASTRAIN,STARUM0128STRAIN,SUNGAIBULOHSTRAIN,UMMC2STRAIN,SEREMBANSTRAIN,UMMC1STRAIN,ANDCDCSTRAINY03998X47048R2088063905439056390583906390623906439066390681996199719981999FIGURE5THEXAXISREPRESENTSFRACTALDIMENSIONANDTHEYAXISREPRESENTSENTROPYN9386538738753883885389389539390539139153921941961982202FIGURE6THEXAXISREPRESENTSFRACTALDIMENSIONOFTHENUCLEOPROTEINSEQUENCEANDTHEYAXISREPRESENTSSHANNONDINUCLEOTIDEENTROPYDIAMONDNIPHAVIRUS;CROSSSARSCOV;SQUARESWINEFLU,AVIANFLU,SPANISHFLU,ANDH2N2NETHERLANDSFLU;TRIANGLEH2N2KOREAFLU,H3N2CHEONGJUFLU,ANDH3N2NEWYORKFLU;CROSS16SRRNAGORILLA,CHIMP,NEANDERTHALS,ANDHUMAN;CIRCLE12SRRNAGORILLA,CHIMP,NEANDERTHALS,ANDHUMANTHERELATEDHENDRAVIRUSNUCLEOPROTEINSEQUENCEHASFRACTALDIMENSION1991ANDENTROPY3915BITS,NOTSHOWNUSINGTHE16SRRNAAND12SRRNASEQUENCESPREADSASGUIDES,THEEVOLUTIONARYPRESSUREEXPERIENCEDBYTHESTUDIEDVIRUSNUCLEOPROTEINSEQUENCESWOULDBEOFTHESAMEORDEROFMAGNITUDEASTHESTUDIEDRIBOSOMALRNASEQUENCESAMONGTHESWINEFLU,AVIANFLU,SPANISHFLU,ANDH2N2NETHERLANDSFLUCLUSTER,THEHIGHESTFATALITYSPANISHFLU13,14ALSOHASTHELOWESTFRACTALDIMENSION197,SIMILARTOTHEHIGHESTFATALITYASSOCIATEDWITHTHELOWESTFRACTALDIMENSIONNIPAHVIRUSTAMBUNSTRAIN2THESARSCOVCLOSENESSTOTHENIPAHCLUSTERCOULDBEINDICATIVEOFITSBATORIGIN15FUTURESTUDYCANINCLUDETHOSEVIRUSESTHATHAVEINTERNALRIBOSOMEENTRYSITES,FOREXAMPLE,THERHINOVIRUS16IVCONCLUSIONTHEFRACTALDIMENSIONANDSHANNONENTROPYWEREUSEDTOANALYZETHENUCLEOTIDEFLUCTUATIONOFTHEGLYCOPROTEINANDNUCLEOPROTEINSEQUENCESINTHENIPAHVIRUSTHECLAS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