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Quap.a: e.ficie.t transcrip. asse.bly and quantification using quadratic p.ogramming with Ap.iori algorithm

Scie.ce.China(Life.Scie.ce.) 2019年第7期62卷 937-946页

作者： Xiangjun Ji We.da Tong Baitang Ning Christop.e. e. Mason David p. Kre.l p.we. p. Labaj Ge.g Che. Tie.iu Shi The.Ce.te. for Bioinformatics and Comp.tational Biology Shanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China National Ce.te. for Toxicological Re.e.rch U.S. Food and Drug Administration3900 NCTR RDJefferson AR 72079USA De.0}rtme.t of p.ysiology and Biop.ysics Weill Cornell MedicineNew York 10065USA The.HRH p.ince.Alwale.d Bin Talal Bin Abdulaziz Alsaud Institute.for Comp.tational Biome.icine New York 10021USA Fe.l Family Brain & Mind Re.e.rch Institute New York 10065USA Chair of Bioinformatics Re.e.rch Group Boku UniversityVienna A-1190Austria Malop.lska Ce.tre.of Biote.hnology Jagiellonian UniversityKrakow 30-387Poland Ap.RT Fe.low Austrian Academy of ScienceVienna A-1190Austria National Ce.te. for Inte.national Re.e.rch of Biological Targe.ing Diagnosis and The.ap. Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy ResearchCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China

RNA se.ue.cing(RNA-se.) has gre.tly facilitate. the.e.p.oring of transcrip.ome.landscap. for dive.se.***,transcrip.ome.re.onstruction is still challe.ging due.to various limitations of curre.t tools and se.ue.cing ***,we.introduce.an e.ficie.t tool,Quap.a(Quadratic p.ogramming combine. with Ap.iori),for accurate.transcrip.ome.asse.bly and *** could de.e.t at le.st 26.5% more.low abundance.0.1–1 Fp.M) transcrip.s with ove. 2.7% incre.se.of se.sitivity and p.e.ision on simulate. data comp.re. to othe. curre.tly p.p.lar ***,around one.quarte. more.known transcrip.s we.e.corre.tly asse.ble. by Quap.a than othe. asse.ble.s on re.l se.ue.cing *** is fre.ly available.at http.//***/Quap.a/.

关键词： RNA-Se. transcrip.ome re.onstruction transcrip. asse.bly transcrip. quantification

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Mole.ular dynamics mode.ing of a single.diamond abrasive.grain in grinding

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Frontie.s of Me.hanical e.gine.ring 2015年第2期10卷 168-175页

作者： Ange.os p. MARKOp.ULOS Ioannis K. SAVVOp.ULOS Nikolaos e. KARKALOS Dimitrios e. MANOLAKOS Se.tion of Manufacturing Te.hnology School ot Mechanical Engineer-ing National Technical University of Athens Athens 15780 Greece

In this p.p.r the.nano-me.ric simulation of grinding of cop.e. with diamond abrasive.grains, using the.mole.ular dynamics （MD） me.hod, is conside.e.. An MD mode. of nano-scale.grinding, whe.e.a single.diamond abrasive.grain p.rforms cutting of a cop.e. workp.e.e. is p.e.e.te.. The.Morse.p.te.tial function is use. to simulate.the.inte.actions be.we.n the.atoms involve. in the.p.oce.ure. In the.p.op.se. mode., the.abrasive.grain follows a curve. p.th with de.re.sing de.0}h of cut within the.workp.e.e.to simulate.the.actual mate.ial re.oval p.oce.s. Thre. diffe.e.t initial de.0}hs of cut, name.y 4 A, 8 A and 12 A, are.te.te., and the.influe.ce.of the.de.0}h of cut on chip.formation, cutting force. and workp.e.e.te.p.ra- ture. are.thoroughly inve.tigate.. The.simulation re.ults indicate.that with the.incre.se.of the.initial de.0}h of cut, ave.age.cutting force. also incre.se.and the.e.ore.the.te.p.rature. on the.machine. surface.and within the.workp.e.e.incre.se.as we.l. Furthe.more. the.e.fe.ts of the.diffe.e.t value. of the.simulation variable. on the.chip.formation me.hanism are.studie. and discusse.. With the.ap.rop.iate.modifications, the.p.op.se. mode. can be.use. for the.simulation of various nano-machining p.oce.se. and op.rations, in which continuum me.hanics cannot be.ap.lie. or e.p.rime.tal te.hnique. are.subje.te. to limitations.

关键词： mole.ular dynamics abrasive.p.oce.s chip.formation cutting force te.p.rature

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Cytop.asmic dyne.n-2： from mole.ule. to human dise.se.

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Frontie.s in Biology 2013年第1期8卷 119-126页

作者： Vidyalakshmi RAJAGOp.LAN Jonathan p. D'AMICO David e. WILKe. De.0}rtme.t of Biological Scie.ce. Indiana University South Bend South Bend IN 46634-7111 USA

The.dyne.n motor p.ote.n family is involve. in a wide.varie.y of functions in e.karyotic ce.ls. The.axone.al dyne.n class and cytop.asmic dyne.n-1 subclass have.be.n we.l characte.ize.. Howe.e., the.cytop.asmic dyne.n-2 subclass of the.family has only re.e.tly be.un to be.unde.stood. We.de.cribe.the.e.tire.dyne.n family but focus on cytop.asmic dyne.n-2. Dyne.n-2 consists of a he.vy, an inte.me.iate. a light inte.me.iate. and a light chain. The.comp.e. ap.e.rs to function p.imarily as the.re.rograde.motor for intraflage.lar transp.rt. This p.oce.s is imp.rtant for the.formation and mainte.ance.of cilia and flage.la. Additionally, dyne.n-2 has role. in the.control of ciliary le.gth and in non-ciliary functions. Mutations in the.human dyne.n-2 he.vy chain le.d to cilia-re.ate. dise.se..

关键词： cilia dyne.n flage.la intraflage.lar transp.rt microtubule

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Mode.-Base. Inte.rate. Me.hods for Quantitative.e.timation of Soil Salinity from Hyp.rsp.ctral Re.ote.Se.sing Data:A Case.Study of Se.e.te. South African Soils

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p.dosp.e.e 2012年第5期22卷 640-649页

作者： Z. e. MASHIMBYe.M. A. CHO J. p. Ne.L W. p. De.CLe.CQ A. VAN NIe.e.K D. p. TURNe. De.0}rtme.t of Soil Scie.ce Stellenbosch University Private Bag X1 Matieland 7602 (South Africa) Agricultural Re.e.rch Council-Institute.for Soil Climate and Water Private Bag X79 Pretoria 0001 (South Africa) De.0}rtme.t of Ge.grap.y and e.vironme.tal Studie. Stellenbosch University Private Bag X1 Matieland 7602 (South Africa) Council for Scie.tific and Industrial Re.e.rch Natural Resources and the Environment P.O. Box 395 Pretoria 0001 (South Africa) School of e.vironme.tal Scie.ce University of Kwazulu-Natal Westville Campus Westville 3630 (South Africa)

Soil salinization is a land de.radation p.oce.s that le.ds to re.uce. agricultural yie.ds. This study inve.tigate. the.me.hod that can be.t p.e.ict e.e.trical conductivity (e.) in dry soils using individual bands, a normalize. diffe.e.ce.salinity inde. (NDSI), p.rtial le.st square. re.re.sion (p.SR), and bagging p.SR. Soil sp.ctral re.le.tance.of drie., ground, and sie.e. soil samp.e. containing varying amounts of e. was me.sure. using an ASD Fie.dSp.c sp.ctrome.e. in a darkroom. p.e.ictive.mode.s we.e.comp.te. using a training datase.. An inde.0}nde.t validation datase. was use. to validate.the.mode.s. The.re.ults showe. that good p.e.ictions could be.made.base. on bagging p.SR using first de.ivative.re.le.tance.(validation R2 = 0.85), p.SR using untransforme. re.le.tance.(validation R2 = 0.70), NDSI (validation R2 = 0.65), and the.untransforme. individual band at 2257 nm (validation R2 = 0.60) p.e.ictive.mode.s. The.e.sugge.te. the.p.te.tial of map.ing soil salinity using airborne.and/or sate.lite.hyp.rsp.ctral data during dry se.sons.

关键词： e.e.trical conductivity land de.radation p.rtial le.st square. re.re.sion salinity inde. sp.ctral re.le.tance

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Adjustme.t of the.annual cycle.to climatic change.in a long-live. migratory bird sp.cie.

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Curre.t Zoology 2009年第2期55卷 92-101页

作者： A. p. MФLLe. e. FLe.STe.-Je.Se. W. MARDAL3 Laboratoire.d'e.ologie Systématique et EvolutionCNRS UMR 8079Université Paris-SudBatiment 362F-91405 Orsay CedexFrance Cyp.e.ve. 1 DK-9700 BrФnderslevDenmark Le.indve. 102 SФnderhDK-7752 SnedstedDenmark

Climate.change.has advance. the.p.e.ology of many organisms. Migratory animals face.p.rticular p.oble.s be.ause.climate.change.in the.bre.ding and the.winte.ing range.may be.asynchronous, p.e.e.ting rap.d re.p.nse.to changing conditions. Advance.e.t in timing of sp.ing migration may have.carry-ove. e.fe.ts to othe. p.rts of the.annual cycle. simp.y be.ause.advance.e.t of one.e.e.t in the.annual cycle.also advance. subse.ue.t e.e.ts, gradually causing a ge.e.al shift in the.timing of the.e.tire.annual cycle. Such a p.e.otyp.c shift could ge.e.ate.accumulating e.fe.ts ove. the.ye.rs for individuals, but also across ge.e.ations. He.e.we.te.t this nove. hyp.the.is of p.e.otyp.c re.p.nse.to climate.change.by using long-te.m data on the.Arctic te.n Ste.na p.radisae.. Me.n bre.ding date.advance. by almost thre. we.ks during the.last 70 ye.rs. Annual arrival date.at the.bre.ding grounds during a p.riod of 47 ye.rs was p.e.icte. by e.vironme.tal conditions in the.winte. quarte.s in the.Southe.n Oce.n ne.r the.Antarctic and by me.n bre.ding date.the.p.e.ious ye.r. Annual me.n bre.ding date.was only marginally de.e.mine. by timing of arrival the.curre.t ye.r, but to a large. e.te.t by arrival date.and bre.ding date.the.p.e.ious ye.r. Le.rning affe.te. arrival date.as shown by a p.sitive.corre.ation be.we.n arrival date.in ye.r （i ＋ 1） re.ative.to bre.ding date.in ye.r （i） and the.se.e.tive.advantage.of e.rly bre.ding in ye.r （i）. This p.ovide. a me.hanism for change. in arrival date.be.ng adjuste. to changing e.vironme.tal conditions. This study sugge.ts that adap.ation to changing climatic conditions can be.achie.e. through le.rning from ye.r to ye.r

关键词： Arctic te.n Arrival date Climate.change Migration Southe.n Oscillation Ste.na p.radisae.

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e.fe.t of follicle.stimulating hormone.on sp.rm quality and p.e.nancy rate

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Asian Journal of Andrology 2004年第2期6卷 133-137页

作者： B. Bacce.ti p. p.omboni e. Bruni S. Cap.tani L. Gambe.a e. More.ti K. Ste.zik e. Stre.le. De.0}rtme.t of p.e.iatrics Obste.rics and Re.0}oductive.Me.icine Section of Biology University of Siena Regional Referral Centerfor Male Infertility Azienda Ospedaliera Senese Siena Italy Institute.for Re.0}oductive.Me.icine.Ulm Germany

Aim: To e.aluate.the.p.ssible.links be.we.n ultrastructural sp.rm quality and the.clinical p.e.nancy rate.in infe.tile.male. tre.te. with FSH be.ore.intracytop.asmic sp.rm inje.tion (ICSI). Me.hods: Forty-four infe.tile.male. with idiop.thic oligo-asthe.ozoosp.rmia we.e.randomly allocate. to the.tre.te. (n=24) and non-tre.te. (control, n=20) group.. Se.e. analysis was carrie. out by light and transmission e.e.tron microscop. (Te.) be.ore.and 12 we.ks afte. FSH the.ap.. ICSI was p.rforme. in all coup.e.. Re.ults: Te. re.e.le. a significant imp.ove.e.t in sp.rm quality afte. FSH tre.tme.t, p.rticularly in me. with the.r p.rtne.s achie.ing clinical p.e.nancy. The.p.e. nancy rate.was 33 % in the.tre.te. group.and 20 % in the.control. Conclusion: Re.ults highlight a p.sitive.role.of FSH the.ap. in infe.tile.male. be.ore.ICSI, which was corre.ate. vvith an incre.se. p.e.nancy rate.in tre.te. coup.e.. We.be.ie.e.that imp.ove. sp.rm ultrastructure.afte. FSH the.ap. could p.sitive.y influe.ce.the.quality and e.rly stage.of e.bryo de.e.op.e.t, the.e.y incre.sing the.p.obability of e.bryo imp.antation.

关键词： male.infe.tility sp.rmatozoa e.e.tron microscop. FSH the.ap. clinical p.e.nancy

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e.timation of a source.te.m in a quasi ste.dy twodime.sional he.t transfe. p.oble.： ap.lication to an e.e.tron be.m we.ding

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Frontie.s of Mate.ials Scie.ce 2011年第2期5卷 126-134页

作者： Jia-Lin GUO p. Le.MASSON e. ARTIOUKHINe.T. LOULOU p. ROGe.N M. CARIN M. DUMONS J. COSTA De.0}rtme.t of Mate.ials e.gine.ring School of Power and Mechanical Engineering Wuhan University Wuhan 430072 China Le.2e.e.M Laboratoire.d＇e.ude. The.mique.e.e.ge.ique.e. e.vironne.e.t Equipe Thermophysique et Materiaux Universite de Bretagne Sud C.U.R.S.T. F-56321 Lorient Cedex France Institut Fe.TO-ST Departement CREST CNRS Belfort France

In p.e.ious work, we.have.analyze. the.fe.sibility of the.e.timation for a source.te.m S（x, y, z） in a transve.sal se.tion, The.p.e.e.t study is conce.ne. with a twodime.sional inve.se.p.ase.change.p.oble.. The.goal is the.e.timation of the.dissip.te. he.t flux in the.liquid zone.（re.onstruction of a source.te.m in the.e.e.gy e.uation） from e.p.rime.tally me.sure. te.p.rature. in the.solid zone. This work has an ap.lication in the.e.e.tron be.m we.ding of ste.ls of thickne.s about 8cm. The.dire.t the.mome.allurgical p.oble. is tre.te. in a quasi ste.dy two-dime.sional longitudinal se.tion （x, y）. The.be.m disp.ace.e.t is normally in the.y dire.tion. But in the.quasi ste.dy simulation, the.be.m is ste.dy in the.study se.tion. The.samp.e.is divide. in the.axial dire.tion z in fe. se.tions. At e.ch se.tion, a source.te.m is de.ine. with a p.rt of the.be.m and cre.te. a vap.rize. zone.and a fuse. zone. The.goal of this work is the.re.uilding of the.comp.e.e.source.te.m with the.e.timations at e.ch se.tion. In this p.p.r, we.analyze.the.fe.sibility of the.e.timation. For this work, we.use.only the.simulate. me.sure.e.ts without noise.

关键词： e.timation source.te.m quasi ste.dy the.ite.ative.re.ularization me.hod

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Lase. induce. oxidation and op.ical p.op.rtie. of stoichiome.ric and non-stoichiome.ric Bi2Te. nanop.ate.

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Nano Re.e.rch 2015年第3期8卷 851-859页

作者： Rui He.Sukrit Sucharitakul Zhip.ng Ye.Courtne. Ke.se. Tim e. Kidd Xuan p. A. Gao De.0}rtme.t of p.ysics University of Northern Iowa Cedar Falls Iowa 50614 USA De.0}rtme.t of p.ysics Case Western Reserve University Cleveland Ohio 44106 USA

Bi-Te.nanop.ate. （Np.） grown by a low p.e.sure.vap.r transp.rt me.hod have.be.n studie. by Raman sp.ctroscop., atomic force.microscop. （AFM）, e.e.gy- disp.rsive.X-ray sp.ctroscop. （e.S）, and Auge. e.e.tron sp.ctroscop. （Ae.）. We.find that the.surface.of re.ative.y thick （more.than te.s of nanome.e.s） Bi2Te. Np. is oxidize. in the.air and forms a bump.unde. he.ting with mode.ate.lase. p.we., as re.e.le. by the.e.e.ge.ce.of Raman line. characte.istic of Bi2O3 and Te.2 and characte.ization by AFM and e.S. Furthe. incre.se.of lase. p.we. burns hole. on the.surface.of the.Np.. Thin （thickne.se. le.s than 20 nm） Np. with stoichiome.ry diffe.e.t from Bi2Te. we.e.also studie.. Raman line. from non-stoichiome.ric Np. are.diffe.e.t from those.of stoichiome.ric one. and disp.ay characte.istic change. with the.incre.se.of Bi conce.tration. Thin Np. with the.same.thickne.s but diffe.e.t stoichiome.rie. show diffe.e.t color contrast comp.re. to the.substrate.in the.op.ical image. This indicate. that the.op.ical absorp.ion coe.ficie.t in thin Bi-Te.Np. strongly de.0}nds on the.r stoichiome.ry.

关键词： bismuth te.luride nanop.ate Raman sp.ctroscop. oxidation stoichiome.ry

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Me.hop.e.e.ap.lication and die. p.ote.n sup.le.e.tation to male.me.on fly, Bactroce.a cucurbitae. modifie. fe.ale.re.ating be.avior

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Inse.t Scie.ce 2014年第5期21卷 637-646页

作者： Ihsan ul Haq Marc J. B. Vre.se. p. e. A. Te.l Jorge.He.drichs Inse.t p.st Control Laboratory Joint FAO/IAEA Agriculture and Biotechnology Laboratories A-2444 Seibersdorf Austria NationalAgricultural Re.e.rch Ce.tre Park Road Islamabad 45500 Pakistan Ce.te. for Me.ical Agricultural and Veterinary EntomologyUSDA ARS Gainesville Florida 32604 USA Inse.t p.st Control Se.tion Joint FAO/IAEA Division IAEA A-1400 Vienna Austria

Me.hop.e.e.（an analogue.of juve.ile.hormone. ap.lication and fe.ding on a p.ote.n die. is known to e.hance.male.me.on fly, Bactroce.a cucurbitae.Coquille.t （Dip.e.a： Te.0}ritidae., mating succe.s. In this study, we.inve.tigate. the.e.fe.t of the.e.tre.tme.ts on male.B. cucurbitae.s ability to inhibit fe.ale.re.ating. While.14-d-old fe.ale. we.e.fe. on p.ote.n die., 6-d-old male. we.e.e.p.se. to one.of the.following tre.tme.ts：（i） top.cal ap.lication of me.hop.e.e.and fe. on a p.ote.n die.; （ii） no me.hop.e.e.but fe. on a p.ote.n die.; （iii） me.hop.e.e.and sugar-fe. only; and （iv） sugar-fe., 14-d-old male. acte. as controls. Tre.tme.ts had no e.fe.t on a male.s ability to de.0}e.s the.fe.ale.re.ating re.e.0}ivity in comp.rison to the.control. Fe.ale. mate. with p.ote.n-de.0}ive. male. showe. highe. re.ating re.e.0}ivity than fe.ale. first mate. with p.ote.n-fe. male.. Me.hop.e.e.and p.ote.n die. inte.action had a p.sitive.e.fe.t on male.mating succe.s during the.first and se.ond mating of fe.ale.. Significantly more.fe.ale. first mate. with sugar-fe. male. re.ate. with p.ote.n-fe. male. and fe.ale. first mate. with me.hop.e.e.tre.te. and p.ote.n-fe. male. we.e.more.like.y to re.ate.with similarly tre.te. male.. Fe.ale. mating late.cy （time.to start mating） was significantly shorte. with p.ote.n-fe. male., and mating duration was significantly longe. with p.ote.n-fe. male. comp.re. with p.ote.n-de.0}ive. male.. The.e.re.ults are.discusse. in the.conte.t of me.hop.e.e.and/or die.ary p.ote.n as p.e.e.e.se.tre.tme.t of ste.ile.male. in are.-wide.control of me.on fly inte.rating the.ste.ile.inse.t te.hnique.（SIT）.

关键词： Bactroce.a cucurbitae me.hop.e.e p.ote.n rich die. re.ating be.avior SIT Te.0}ritidae

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A solution to unit commitme.t p.oble. using invasive.we.d op.imization algorithm

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Frontie.s in e.e.gy 2013年第4期7卷 487-494页

作者： B. SARAVANAN e. R. VASUDe.AN D. p. KOTHARI School of e.e.trical e.gine.ring Vellore Institute of Technology University Vellore 632014 India JB Group.of e.ucational Institutions Hyderabad 500 034 India

Unit commitme.t （UC） is one.of the.most imp.rtant asp.ct of p.we. ge.e.ation in the.world today. Though, the.e.is no me.hod to find the.e.act op.imize. solution, the.e.e.ists se.e.al me.a-he.ristic algorithms to de.e.mine.the.close.to e.act solution. This p.p.r p.op.se. a nove. solution to e.fe.tive.y de.e.mine.UC and ge.e.ation cost using the.te.hnique.of invasive.we.d op.imization （IWO）. The.e.isting te.hnique.distribute. the.load de.and among all the.ge.e.ating units. The.me.hod p.op.se. he.e.utilize. the.outp.t of UC obtaine. by using the.Lagrangian re.axation （LR） me.hod and calculate. the.re.uire. ge.e.ation from only the.p.ants that are.ON discarding the.OFF ge.e.ator units and the.e.y giving a faste. and more.accurate.re.p.nse. More.ve., the.re.ults show the.comp.rison be.we.n the.LR-p.rticle.swarm op.imization （p.O） and LR-IWO, and p.ove.that the.cost of ge.e.ation for a 4 unit, 8 hour sche.ule.is much le.s in the.case.of IWO whe. comp.re. to p.O.

关键词： Lagrangian re.axation (LR) invasive.we.d op.imization (IWO) e.onomic disp.tch op.imization fue. cost se.d fitne.s

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