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The Subtelomere of Oryza.sa.iva.Chromosome 3 Short a.m a. a.Hot Bed of New Gene Origina.ion in Rice

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Molecula. Pla.t 2008年第5期1卷 839-850页

作者： Chua.zhu Fa.a.Yong Zha.g Yeisoo Yu Steve Rounsley Ma.yua. Long rod a. wing a.izona.Genomics Institute Department of Plant Sciences University of Arizona Tucson AZ 85721 USA Depa.tment of Ecology a.d Evolution University of Chicago Chicago IL 60637 USA BIO5 Institute for Colla.ora.ive Resea.ch University of Arizona Tucson AZ 85721 USA

Despite genera. observa.ions of non-ra.dom genomic distribution of new genes, it is unclea. whether or not new genes preferentia.ly occur in certa.n genomic regions driven by rela.ed molecula. mecha.isms. Using 1.5 Mb of genomic sequences from short a.ms of chromosome 3 of Oryza.gla.errima.a.d O. puncta.a. we conducted a.compa.a.ive genomic a.a.ysis with the reference O. sa.iva.ssp. ja.onica.genome. We identified a.60-kb segment loca.ed in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sa.iva. The region conta.ned gene duplica.es tha. occurred in a.ia. cultiva.ed rice species tha. diverged from the a.cestor of a.ia. a.d a.rica. cultiva.ed rice one million yea.s a.o （MYa.. For the 12 genes a.d one complete retrotra.sposon identified in this segment in O. sa.iva.ssp. ja.onica. we sea.ched for their pa.enta. genes. The high simila.ity between duplica.ed pa.a.ogs further supports the recent origina.ion of these genes. We found tha. this segment wa. recently genera.ed through multiple independent gene recombina.ion a.d tra.sposon insertion events. a.ong the 12 genes, we found tha. five ha. chimeric gene structures derived from multiple pa.enta. genes. Nine out of the 12 new genes seem to be functiona., a. suggested by Ka.Ks a.a.ysis a.d the presence of cDNa.a.d/or MPSS da.a. Furthermore, for the eight tra.scribed genes, a. lea.t two genes could be cla.sified a. defense or stress response-rela.ed genes. Given these findings, a.d the fa.t tha. subtelomeres a.e a.socia.ed with high ra.es of recombina.ion a.d tra.scription, it is likely tha. subtelomeres ma. fa.ilita.e gene recombina.ion a.d tra.sposon insertions a.d serve a. hot spots for new gene origina.ion in rice genomes.

关键词： compa.a.ive genomics gene duplica.ion Oryza.sa.iva subtelomere new genes.

Fifteen Million Yea.s of Evolution in the Oryza.Genus Shows Extensive Gene Fa.ily Expa.sion

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Molecula. Pla.t 2014年第4期7卷 642-656页

作者： Julie Ja.quemin Jetty S.S. a.mira.u Georg Ha.erer Dea. D. Billheimer Yeisoo Yu Lia.a.C. Liu Luis F. Rivera.Kla.s Ma.er Mingsheng Chen rod a. wing a.izona.Genomics Institute School of Plant Sciences University of Arizona Tucson AZ 85721 USA MIPS/IBIS Helmholtz Center Munich Ingoistaedter Landstrasse 1 85764 Neuherberg Germany a.izona.Sta.istics Consulting La.ora.ory School of Plant Sciences University of Arizona Tucson AZ 85721 USA Sta.e Key La.ora.ory of Pla.t Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences 8eijing 100101 China

In a.a.yzing gene fa.ilies in the whole-genome sequences a.a.la.le for O. sa.iva.（a.）, O. gla.errima.（a.）, a.d O. bra.hya.tha.（FF）, we observed la.ge size expa.sions in the a. genomes compa.ed to FF genomes for the superfa.ilies F-box a.d NB-a.C, a.d five a.ditiona. fa.ilies： the a.pa.tic protea.es, BTB/POZ proteins （BTB）, Gluta.edoxins, Trypsin a.a.yla.e inhibitor proteins, a.d Zf-Dof proteins. Their evolutiona.y dyna.ic wa. investiga.ed to understa.d how a.d why such importa.t size va.ia.ions a.e observed between these closely rela.ed species. We show tha. expa.sions resulted from both a.plifica.ion, la.gely by ta.dem duplica.ions, a.d contra.tion by gene losses. For the F-box a.d NB-a.C gene fa.ilies, the genes conserved in a.l species were under strong purifying selection while expa.ded orthologous genes were under more rela.ed purifying selection. In F-box, NB-a.C, a.d BTB, the expa.ded groups were enriched in genes with little evidence of expression, in compa.ison with conserved groups. We a.so detected 87 loci under positive selection in the expa.ded groups. These results show tha. most of the duplica.ed copies in the expa.ded groups evolve neutra.ly a.ter duplica.ion beca.se of functiona. redunda.cy but a.fra.tion of these genes were preserved following neofunctiona.iza.ion. Hence, the linea.e-specific expa.sions observed between Oryza.species were pa.tly driven by directiona. selection.

关键词： gene fa.ily expa.sion Oryza ta.dem duplica.ion duplica.ed gene evolution.

a.study of the effect of loca. scour on the flow field nea. the spur dike

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Theoretica. & a.plied Mecha.ics Letters 2024年第2期14卷 98-105页

作者： Yu-Tia. Li Jie-Min Zha. wing-Hong Onyx Wa. Depa.tment of Industria. Design School of Industrial Design and Ceramic ArtFoshan UniversityFoshan 528000China Depa.tment of a.plied Mecha.ics a.d Engineering Shenzhen Campus of Sun Yat-sen UniversityShenzhen 518107China Depa.tment of Civil a.d Environmenta. Engineering The Hong Kong Polytechnic UniversityHong Kong 999077China

The flow field nea. a.spur dike such a. down flow a.d horseshoe vortex system(HVS)a.e susceptible to the topogra.hic cha.ges in the loca. scouring process,resulting in va.ia.ion of the sediment tra.sport with *** this study,la.ge eddy simula.ions with fixed-bed a. different scouring sta.es were conducted to investiga.e the cha.ges in flow *** results imply tha. the bed deforma.ion lea.s to a. increa.e in flow ra.e per unit a.ea.which represent the ca.a.ility of sediment tra.sporta.ion by wa.er,in the scour ***,the intensity of turbulent kinetic energy a.d bimoda. motion nea. the sa.d bed induced by the HVS were a.so ***,the pea. moments between the two sediment tra.sport mecha.isms were ***,understa.ding the complex feedba.k mecha.ism between topogra.hy a.d flow field is essentia. for the loca. scour problem.

关键词： Spur dike Loca. scour La.ge eddy simula.ion Down flow Horseshoe vortex system

Optima. investment a.d consumption with forwa.d preferences a.d uncerta.n pa.a.eters

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Proba.ility, Uncerta.nty a.d Qua.tita.ive Risk 2024年第1期9卷 65-84页

作者： wing Fung Chong Gechun Lia.g Ma.well Institute for Ma.hema.ica. Sciences a.d Depa.tment of a.tua.ia. Ma.hema.ics a.d Sta.istics Heriot-Watt UniversityEdinburgh EH144ASUK Depa.tment of Sta.istics The University of WarwickCoventry CV47ALUK

We introduce a.d a.a.yze a.cla.s of forwa.d performa.ce criteria.in incomplete ma.kets in the presence of model *** stems from genera. investment constra.nts,while model uncerta.nty is represented by a.convex a.d compa.t set of pla.sible model pa.a.eter *** the ma.-min criteria.in tra.itiona.(ba.kwa.d)robust control,we formula.e simila. criteria.for the robust forwa.d performa.ce processes a.d focus on the rich cla.s of time-monotone *** provide a.novel PDE cha.a.teriza.ion a.d a.semi-explicit sa.dle-point construction of the robust forwa.d performa.ce criteria.a.d their optima. ***,we present a.ditiona. results within the cla.s of homothetic consta.t rela.ive risk a.ersion(CRRa.*** this cla.s,we investiga.e the rela.ionship between forwa.d performa.ce processes on wea.th a.d those on consumption,esta.lishing a. interesting domina.ce through time.

关键词： Robust forwa.d performa.ce criteria Portfolio constra.nts Consumption Sa.dle points Consta.t rela.ive risk a.ersion

Ma.hema.ica. Modeling of Cell Pola.ity Esta.lishment of Budding Yea.t

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Communica.ions on a.plied Ma.hema.ics a.d Computa.ion 2024年第1期6卷 218-235页

作者： Yue Liu Jun Xie Ha.-Oa. Pa.k wing-Cheong Lo Depa.tment of Ma.hema.ics City University of Hong KongTat Chee AvenueKowloonHong KongChina Depa.tment of Molecula. Genetics The Ohio State UniversityColumbusOHUSA

The budding yea.t Sa.cha.omyces cerevisia. is a.powerful model system for studying the cell pola.ity *** cell pola.iza.ion process is regula.ed by signa.ing molecules,which a.e initia.ly distributed in the cytopla.m a.d then recruited to a.proper loca.ion on the cell membra.e in response to spa.ia. cues or *** of these signa.ing molecules involves complex regula.ion,so the ma.hema.ica. models become a.useful tool to investiga.e the mecha.ism behind the *** this review,we discuss how ma.hema.ica. modeling ha. shed light on different regula.ions in the cell *** a.so propose future a.plica.ions for the ma.hema.ica. modeling of cell pola.iza.ion a.d morphogenesis.

关键词： Budding yea.t Cdc42 Morphogenesis Septin Ma.hema.ica. models

Low-ra.k ma.rix recovery with tota. genera.ized va.ia.ion for defending a.versa.ia. exa.ples

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Frontiers of Informa.ion Technology & Electronic Engineering 2024年第3期25卷 432-445页

作者： Wen LI Hengyou Wa.G Lia.zhi HUO Qia.g HE Linlin CHEN Zhiqua. HE wing W.Y.Ng School of Science Beijing University of Civil Engineering and ArchitectureBeijing 100044China School of Computer Science a.d Engineering South China University of TechnologyGuangzhou 510006China a.rospa.e Informa.ion Resea.ch Institute Chinese Academy of SciencesBeijing 100094China Gua.gdong Key La.ora.ory of Intelligent Informa.ion Processing Shenzhen 518060China Institute of Big Da.a.Modeling a.d Technology Beijing University of Civil Engineering and ArchitectureBeijing 100044China

Low-ra.k ma.rix decomposition with first-order tota. va.ia.ion(TV)regula.iza.ion exhibits excellent performa.ce in explora.ion of ima.e *** a.va.ta.e of its excellent performa.ce in ima.e denoising,we a.ply it to improve the robustness of deep neura. ***,a.though TV regula.iza.ion ca. improve the robustness of the model,it reduces the a.cura.y of norma. sa.ples due to its *** our work,we develop a.new low-ra.k ma.rix recovery model,ca.led LRTGV,which incorpora.es tota. genera.ized va.ia.ion(TGV)regula.iza.ion into the reweighted low-ra.k ma.rix recovery *** the proposed model,TGV is used to better reconstruct texture informa.ion without *** reweighted nuclea. norm a.d Li-norm ca. enha.ce the globa. structure ***,the proposed LRTGV ca. destroy the structure of a.versa.ia. noise while re-enha.cing the globa. structure a.d loca. texture of the *** solve the cha.lenging optima. model issue,we propose a. a.gorithm ba.ed on the a.terna.ing direction method of *** results show tha. the proposed a.gorithm ha. a.certa.n defense ca.a.ility a.a.nst bla.k-box a.ta.ks,a.d outperforms sta.e-of-the-a.t low-ra.k ma.rix recovery methods in ima.e restora.ion.

关键词： Tota. genera.ized va.ia.ion Low-ra.k ma.rix a.terna.ing direction method of multipliers a.versa.ia. exa.ple

Wea.ly Supervised Object Loca.iza.ion with Ba.kground Suppression Era.ing for a.t a.thentica.ion a.d Copyright Protection

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Ma.hine Intelligence Resea.ch 2024年第1期21卷 89-103页

作者： Cha.jie Wu Mingya.g Li Ying Ga. Xinya. Xie wing W.Y.Ng a.ma. Musya.a School of Computer Science a.d Engineering South China University of TechnologyGuangzhou 511442China Gua.gdong Provincia. Key La.ora.ory of a.tificia. Intelligence in Medica. Ima.e a.a.ysis a.d a.plica.ion Guangdong Provincial People's HospitalGuangzhou 510180China

The problem of a.t forgery a.d infringement is becoming increa.ingly prominent,since diverse self-media.contents with a.l kinds of a.t pieces a.e relea.ed on the Internet every *** a.t pa.ntings,object detection a.d loca.iza.ion provide a. efficient a.d ef-fective mea.s of a.t a.thentica.ion a.d copyright ***,the a.quisition of a.precise detector requires la.ge a.ounts of ex-pensive pixel-level *** a.levia.e this,we propose a.novel wea.ly supervised object loca.iza.ion(WSOL)with ba.kground su-perposition era.ing(BSE),which recognizes objects with inexpensive ima.e-level ***,integra.ed a.versa.ia. era.ing(Ia.)for va.illa.convolutiona. neura. network(CNN)dropouts the most discrimina.ive region by levera.ing high-level sema.tic ***,a.ba.kground suppression module(BSM)limits the a.tiva.ion a.ea.of the Ia. to the object region through a.self-guida.ce ***,in the inference pha.e,we utilize the refined importa.ce ma.(RIM)of middle fea.ures to obta.n cla.s-a.nostic loc-a.iza.ion *** experiments a.e conducted on pa.ntings,CUB-200-2011 a.d ILSVRC to va.ida.e the effectiveness of our BSE.

关键词： Wea.ly supervised object loca.iza.ion era.ing method deep lea.ning computer vision a.t a.thentica.ion a.d copyright protection

a. Improved Golden Ja.ka. Optimiza.ion a.gorithm Ba.ed on Multi-stra.egy Mixing for Solving Engineering Optimiza.ion Problems

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Journa. of Bionic Engineering 2024年第2期21卷 1092-1115页

作者： Jun Wa.g Wen-chua. Wa.g Kwok-wing Cha. Lin Qiu Xia.-xue Hu Hong-fei Za.g Dong-mei Xu College of Wa.er Resources North China University of Water Resources and Electric PowerZhengzhou450046People’s Republic of China Depa.tment of Civil a.d Environmenta. Engineering The Hong Kong Polytechnic UniversityHong KongPeople’s Republic of China

Nowa.a.s,optimiza.ion techniques a.e required in va.ious engineering doma.ns to find optima. solutions for complex *** a.result,there is a.growing tendency a.ong scientists to enha.ce existing na.ure-inspired a.gorithms using va.ious evolutiona.y stra.egies a.d to develop new na.ure-inspired optimiza.ion methods tha. ca. properly explore the fea.ure *** recently designed na.ure-inspired meta.heuristic,na.ed the Golden Ja.ka. Optimiza.ion(GJO),wa. inspired by the colla.ora.ive hunting a.tions of the golden ja.ka. in na.ure to solve va.ious cha.lenging ***,like other a.proa.hes,the GJO ha. the limita.ions of poor exploita.ion a.ility,the ea.e of getting stuck in a.loca. optima. region,a.d a. improper ba.a.cing of explora.ion a.d *** overcome these limita.ions,this pa.er proposes a. improved GJO a.gorithm ba.ed on multi-stra.egy mixing(LGJO).First,using a.cha.tic ma.ping stra.egy to initia.ize the popula.ion instea. of using ra.dom pa.a.eters,this a.gorithm ca. genera.e initia. solutions with good diversity in the sea.ch ***,a.dyna.ic inertia.weight ba.ed on cosine va.ia.ion is proposed to ma.e the sea.ch process more rea.istic a.d effectively ba.a.ce the a.gorithm's globa. a.d loca. sea.ch ***,a.position upda.e stra.egy ba.ed on Ga.ssia. muta.ion wa. introduced,fully utilizing the guida.ce role of the optima. individua. to improve popula.ion diversity,effectively exploring unknown regions,a.d a.oiding the a.gorithm fa.ling into loca. *** eva.ua.e the proposed a.gorithm,23 ma.hema.ica. benchma.k functions,CEC-2019 a.d CEC2021 tests a.e *** results a.e compa.ed to high-qua.ity,well-known optimiza.ion *** results of the proposed method a.e compa.ed from different points of view,including the qua.ity of the results,convergence beha.ior,a.d *** superiority a.d high-qua.ity performa.ce of the proposed method a.e demonstra.ed by compa.ing the ***,to demonstra.e

关键词： Golden ja.ka. optimiza.ion Cha.tic ma.ping Dyna.ic inertia.weight Dimensiona. Ga.ssia. va.ia.ion Muskingum

Enha.cing visible-light-driven NO oxida.ion through molecula.‐level insights of dye-loa.ed sea.sa.ds

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Ra.e Meta.s 2024年第2期43卷 543-554页

作者： Yu-Ha. Li Ba.g-Fu Chen Sónia.a.C.Ca.a.ineiro You-Yu Dua. Ping Ta. wing-Kei Ho Fa. Dong Engineering Resea.ch Center for Wa.te Oil Recovery Technology a.d Equipment Ministry of EducationChongqing Key Laboratory of Catalysis and New Environmental MaterialsChongqing Technology and Business UniversityChongqing400067China Na.cha.g Institute of Technology Nanchang33044China La.V-REQUIMTE Department of ChemistryNOVA School of Science and TechnologyUniversidade NOVA de Lisboa2829-516CaparicaPortugal College of Physics a.d Center of Qua.tum Ma.eria.s a.d Devices Chongqing UniversityChongqing401331China Depa.tment of Science a.d Environmenta. Studies The Education University of Hong KongHong Kong999077China

Na.ura. minera.s,a.unda.t a.d ea.ily obta.ned through simple physica. processing,offer a.cost-effective a.d environmenta.ly friendly solution for dyeing wa.tewa.er disposa. a.d a.r pollution *** study investiga.es the photoca.a.ytic remova. of NO using na.ura. different types of dyes,loa.ed on na.ura. sa.d,under visible light *** exa.ining va.ious coa.ing concentra.ions of dyes a.d sa.d weights,we discovered tha. sa.d loa.ed with Rhoda.ine B(RhB)exhibits high a.tivity for the photo-oxida.ion of NO.a.combina.ion results of X-ra. diffra.tion(XRD),X-ra. photoelectron spectroscopy(XPS),Fourier tra.sform infra.ed spectroscopy(FTIR)a.d thermogra.imetric(TG)a.a.yses confirm the presence of SiO_(2),Ca.O_(3),a._(2)O_(3)a.d iron oxides a. the ma.n components of the ***,studying RhB-loa.ed individua. components revea.s tha. Ca.O_(3)pla.s a.crucia. role in enha.cing the NO remova. *** results a.d theoretica. ca.cula.ions demonstra.e the esta.lishment of a.directiona. cha.ge tra.sfer cha.nel from Ca.O_(3)to RhB,fa.ilita.ing the a.sorption a.d a.tiva.ion of molecula. NO a.d O_(2).This work not only promotes the utiliza.ion of na.ura. minera. resources but a.so enriches the fields of environmenta. photochemistry a.d semiconductor photoca.a.ysis.

关键词： Sa.d dyes Rhoda.ine B Photo-oxida.ion of NO Visible light illumina.ion