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Building Expertise on FAIR Through Evolving Bring your Own Data(ByOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé Lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis Luiz Olavo Bonino da Silva santos Ronald Cornet Bruna dos santos Vieira Nawel Lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de Ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.Wilkinson Egon L.Willighagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly Department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands Department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands Department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands Department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands Department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The Leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring your Own Data"workshops(ByODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The ByOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused ByODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused ByODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused ByODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these ByODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The ByODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the ByODs and describe examples of early ByODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making ByODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring your Own Data Workshop ByOD

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Antibacterial enhancement of antibiotic activity by Enterolobium contortisiliquum(Vell.)Morong

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Asian Pacific Journal of Tropical Biomedicine 2017年第10期7卷 945-949页

作者： Zildene de Sousa Silveira Nair Silva Macêdo Thiago sampaio de Freitas Ana Raquel Pereira da Silva joycy france.y sampaio dos santos Maria Flaviana Bezerra Morais-Braga José Galberto Martins da Costa Raimundo Nonato Pereira Teixeira Jean Paul Kamdem Henrique Douglas Melo Coutinho Francisco Assis Bezerra da Cunha Laboratorio de Bioprospeccao do Semioarido Universidade Regional do CaririCratoBrazil Laboratorio de Microbiologia e Biologia Molecular Universidade Regional do CaririCratoBrazil Laboratorio de Pesquisas de Produtos Naturais Universidade Regional do CaririCratoBrazil Departamento de Ciencias biologicas Universidade Regional do Cariri-URCACratoCEP:63105-000Brazil Programa de Pos-graduacao em Bioprospeccao Molecular Universidade Regional do Cariri–URCACratoBrazil

Objective: To identify the main chemical classes of compounds from aqueous extract of Enterolobium contortisiliquum(E. contortisiliquum) seed bark and to evaluate its antibacterial activity, as well as its potential to increase the activity of antibiotics against strains of Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia ***: Different classes of compounds in the aqueous extract of E. contortisiliquum were evaluated based on the visual changes in the coloration and the formation of precipitate after the addition of specific reagents. The antibacterial activity of the extract and its potential to increase of antibiotic activity of antibiotics drugs, gentamicin and norfloxacin was determined by using the microdilution ***: Our results demonstrated that the following secondary metabolites were presented in E. contortisiliquum seed bark: flavones, flavonols, xanthones, flavononols,chalcones, aurones, flavones and catechins. The extract itself had very low antibacterial activity against all bacterial strains tested(MIC ≥ 1024 μg/m L), but there was an increase in the antibiotic activity of gentamicin and norfloxacin when combined in the subinhibitory concentration(i.e., MIC/8).Conclusions: Our data suggests that E. contortisiliquum seed bark may be an alternative source for new drugs with the potential to increase antibiotic activity against different strains of bacteria.

关键词： Antibiotic activity Enhancement Synergism Chemical compounds Bioactivity

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BEIJING METROPOLIS' TO THE CONQUEST OF ITS NEW STATUS

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Journal of Geographical Sciences 1997年第1期7卷 21-32页

作者： Marie～Josee \ dos santos Department of Geography University of Paris IV, Sorbonne, france

In this paper, we analyse the main strategy for the development of Beijing as it was presented by the last Master Plan: “Beijing should be, by the middle of the 21st century an international modern metropolis of the first world rank”. At first, we summarize the current Chinese studies and urban changes that are being carried out in Beijing, both in spatial and function aspects. Further, we underline the necessity to Beijing to become a powerful economically modernized metropolis. We emphasize with three main reasons in order to explain this necessity: the new “socialist economic market” in China, the inter urban competition among Chinese cities, and the comparison with the current metropolises of the first world rank. Finally, after a summary about the internalization process of London, Paris, New york and Tokyo, we present a simplified analysis of the urban internalization process. According to this analysis, we conclude that Beijing must combine two status: a powerful economically modernized metropolis and the Asian Cultural Capital status, so that could project Beijing into the next century as one of the elite metropolis in the world.

关键词： Beijing urban functions world city.

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Direct measurement of electrocaloric effect in P(VDF-TrFE-CFE)film using infrared imaging

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Journal of Materiomics 2023年第2期9卷 256-260页

作者： Ashwath Aravindhan Pierre Lheritier Alvar Torello Uros Prah youri Nouchokgwe Asmaa El Moul Xavier Chevalier Fabrice Domingues dos santos Emmanuel Defay Veronika Kovacova Materials Research and Technology Department Luxembourg Institute of Science and Technology(LIST)41 Rue du BrillL-4422BelvauxLuxembourg University of Luxembourg 2 Avenue de l’UniversiteEsch-sur-AlzetteL-4365Luxembourg Arkema e Piezotech CRRA Rue Henri Moissan69493Pierre Benite CedexFrance

Poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene)P(VDF-TrFE-CFE)is a relaxor ferroelectric polymer,which exhibits a temperature-independent electrocaloric effect at room *** this work,the electrocaloric effect in P(VDF-TrFE-CFE)film was directly analysed using infrared imaging.P(VDF-TrFE-CFE)64.8%/27.4%/7.8%(in mole)film of(15±1)mm thickness was deposited on polyethylene naphthalate *** ECE of P(VDF-TrFE-CFE)film was measured from 15 to 35C at different electric fields.A maximum adiabatic temperature change(DTad)of 3.58 K was measured during the cooling cycle at a field of 100 V/mm at 30*** element analysis of temperature dissipation through the sample estimated that the actual temperature change within P(VDF-TrFE-CFE)film was 4.3 *** the thermal mass of the substrate,a substantial ECE was observed in P(VDF-TrFE-CFE)*** electrocaloric terpolymer composition could be of interest for electrocaloric cooling applications.

关键词： Direct measurement Electrocaloric effect P(VDF-TrFE-CFE) Relaxor ferroelectric polymer Infrared imaging Finite element analysis

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Dental impact of anti-fibroblast growth factor 23 therapy in X-linked hypophosphatemia

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International Journal of Oral Science 2023年第4期15卷 691-700页

作者： Elis J.Lira dos santos Kenta Nakajima Julien Po Ayako Hanai Volha Zhukouskaya Martin Biosse Duplan Agnès Linglart Takashi Shimada Catherine Chaussain Claire Bardet UniversitéParis Cité Institut des maladies musculo-squelettiquesLaboratory Orofacial PathologiesImaging and Biotherapies URP2496 and FHU-DDS-NetDental Schooland Plateforme d’Imagerie du Vivant(PIV)MontrougeFrance R&D Division Kyowa KirinCo.Ltd3-6-6 Asahi-machiMachida-shiTokyoJapan UniversitéParis Cité Institut ImagineINSERM UMR 1163ParisFrance AP-HP Reference Center for Rare Disorders of the Calcium and Phosphate MetabolismDental Medicine DepartmentBretonneau HospitalGHN-UniversitéParis CitéParisFrance Paris-Saclay University AP-HPINSERM U1185DMU SEAEndocrinology and Diabetes for ChildrenReference Center for Rare Diseases of the Calcium and Phosphate MetabolismOSCAR filièreEndoRareand BOND ERNsBicêtre Paris Saclay HospitalLe Kremlin-BicêtreFrance Medical Affairs Department Kyowa KirinCo.Ltd1-9-2 OtemachiChiyoda-kuTokyoJapan

Elevated fibroblast growth factor 23(FGF23)in X-linked hypophosphatemia(XLH)results in rickets and phosphate wasting,manifesting by severe bone and dental ***,a FGF23-neutralizing antibody,an alternative to conventional treatment(phosphorus and active vitamin D analogs),showed significant improvement in the long bone ***,we examined whether FGF23 antibody(FGF23-mAb)also improved the dentoalveolar features associated with ***-week-old male Hyp mice were injected weekly with 4 or 16 mg·kg−1 of FGF23-mAb for 2 months and compared to wild-type(WT)and vehicle(PBS)treated Hyp mice(n=3–7 mice).Micro-CT analyses showed that both doses of FGF23-mAb restored dentin/cementum volume and corrected the enlarged pulp volume in Hyp mice,the higher concentration resulting in a rescue similar to WT ***23-mAb treatment also improved alveolar bone volume fraction and mineral density compared to vehicle-treated *** revealed improved mineralization of the dentoalveolar tissues,with a decreased amount of osteoid,predentin and *** periodontal ligament attachment was also observed,evidenced by restoration of the acellular *** preclinical data were consistent with the retrospective analysis of two patients with XLH showing that burosumab treatment improved oral *** together,our data show that the dentoalveolar tissues are greatly improved by FGF23-mAb treatment,heralding its benefit in clinics for dental abnormalities.

关键词： doses vitamin treatment

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Paraneoplastic leukemoid reaction in pancreatic cancer: A case report

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World Journal of Gastrointestinal Oncology 2015年第10期7卷 259-262页

作者： Mélanie dos santos Karine Bouhier Manh-Thong Dao Department of Gastroenterology CHU de Caen

Paraneoplastic leukemoid reaction is a rare syndrome defined by a leukocyte count exceeding 50 Giga/Liter(G/L), mostly described with progressive lung or renal carcinoma. We report a case of a 68-year-old man with recurrent pancreatic carcinoma presenting a leukemoid reaction with a white blood cell count of 63.87 G/L without identified infectious, iatrogenic or hematologic causes. His overall condition quickly degraded and he died three weeks after the discovery of the leukemoid reaction. This is the first case in French literature of leukemoid reaction in a patient with pancreatic carcinoma with poor prognostic value.

关键词： Leukemoid reaction Pancreatic neoplasms Paraneopla

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Microbial enzymatic stoichiometry and the acquisition of C, N,and P in soils under different land-use types in Braziliansemiarid

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Soil Ecology Letters 2023年第3期5卷 101-108页

作者： Erika Valente de Medeiros Érica de Oliveira Silva Gustavo Pereira Duda Mario Andrade Lira Junior Uemeson Josédos santos Claude Hammecker Diogo Paes da Costa Fabio Fernando Araujo Arthur Prudêncio de Araujo Pereira Lucas William Mendes Ademir Sergio Ferreira Araujo Laboratory of Microbiology and Enzymology-LEMA Federal University of Agreste PernambucoGaranhuns 55292-270Brazil Federal Rural University of Pernambuco Rua Dom Manuel de Medeiross/nDois Irmãos52171-900RecifeBrazil Soil-Agrosystem-Hydrosystem Interaction Lab-LISAH Place Pierre Viala234060 MontpellierFrance Universidade do Oeste Paulista Presidente PrudenteSPBrazil Departamento de Ciência Do Solo Universidade Federal Do CearáFortalezaCEBrazil Center for Nuclear Energy in Agriculture University of Sao PauloPiracicabaSPBrazil Soil Quality Lab Agricultural Science CenterFederal University of PiauíTeresinaPI 60049-550Brazil

This study hypothesized that different land-use affect the microbial enzymatic stoichiometry and C-,N-,and P-acquisition in Brazilian semiarid ***,the enzymesβ-glucosidase(C-acquiring enzyme),urease(N-acquiring enzyme),and acid phosphatase(P-acquiring enzyme)were assessed in soil samples collected at 0−5 and 5−10 cm depth from a tropical dry forest,a protected area with Angico,a protected area with Ipê,scrub area,and an agricultural area with *** values of C-,N-,and P-acquiring enzymes were used to calculate the enzymatic C:N,C:P,and N:P *** values of C:P and N:P ratios were higher at 0−5 cm depth,while no significant variation,between soil depth,was observed for C:N *** values of C-and N-acquiring enzymes were higher at 0−5 cm in tropical dry forest areas and Angico forest,*** all land use types,the values of vectors L and A were higher than 1°and 45°,*** study showed that both land-use and soil depth influence the enzymatic stoichiometry,showing higher values of C-and N-acquiring enzymes in native and protected forests at soil surface.

关键词： C:N:P stoichiometry tropical forests soil depth Luvisols

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Chronic hepatitis B liver disease in patients living in the Amazon region: S gene mutations and genotypes characterization

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World Journal of Cardiovascular Diseases 2013年第8期3卷 506-511页

作者： Deusilene Vieira Marie Gauthier Larissa Deadame de Figueiredo Nicolete Alcione Oliveira dos santos Carina Picelli Eduardo Honda Glaucia Paranhos-Baccala Guy Vernet Juan Miguel Villalobos Salcedo Research Center for Tropical Medicine CEPEM/Tropical Pathology Research InstituteFiocruz RondoniaRio de JaneiroBrazil Emerging Pathogens Laboratory Fondation MerieuxIFR 128 BioSciences GerlandLyonFrance

The Amazon region is considered to be a high endemic area for Hepatitis B Virus (HBV) infections, Rondônia state having the highest prevalence. The aim of this study was to identify molecular genotypes and mutations in the S gene region of HBV viral genomes from 20 patients using a DNA microarray. Results: Serological tests showed that 88% of patients were HBeAg negative, 82% had anti-HBe antibodies and 33% were co-infected with Hepatitis Delta Virus. Sixteen percent of the patients were considered cirrhotic, and 11% have been transfused. The microarray technique identified the genotypes A (4 patients), D (7 patients) and F (7 patients) in 18 samples. Mutations were detected in all 3 genotypes and, overall, A159G, which has been associated with a reduced antigenicity of the virus, was detected most frequently. In genotype A, G119E was the most frequently detected mutation followed by mutations A159G, F134y, W172C, y161F and T143S. A159G was detected in all genotype D and F samples followed by mutations T143S, y161F, N131T, T114S and G119E in genotype D and mutations T143S, y161F, N131T, T114S and G119E in genotype F. Conclusion: The analysis of mutations repartition among genotypes suggests that some of them are preferentially or exclusively associated with genotype A, D or F. This type of tool is adapted for clinical and therapy monitoring of patient as well as for molecular epidemiology research on HBV.

关键词： Hepatitis B Virus Mutant Detection DNA Microarray Amazon Region

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A large epeiric methanogenic Bambuí sea in the core of Gondwana supercontinent?

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Geoscience Frontiers 2021年第1期12卷 203-218页

作者： Sergio Caetano-Filho Pierre Sansjofre Magali Ader Gustavo M.Paula-santos Cristian Guacaneme Marly Babinski Carolina Bedoya-Rueda Matheus Kuchenbecker Humberto L.S.Reis Ricardo I.F.Trindade Universidade de Sao Paulo Instituto de GeocienciasRua do Lago562-Sao Paulo05508-080Brazil MNHN Sorbonne UniversiteCNRS UMR 7590Institut de Mineralogiede Physique des Materiaux et de Cosmochimie75005ParisFrance Universite de Paris Institut de Physique du Globe de ParisCNRSF-75005ParisFrance Universidade Estadual de Campinas Instituto de GeocienciasRua Carlos Gomes250-Campinas13083-855Brazil Universidade Federal dos Vales do Jequitinhonha e Mucuri Instituto de Ciencia e TecnologiaLaboratorio de Estudos TectonicosRodovia MGT 367Km 583-Diamantina39100-000Brazil Universidade Federal de Ouro Preto Departamento de Geologia-Escola de MinasLaboratiorio de Modelagem TectonicaCampus Morro do Cruzeiro-Ouro Preto35400-000Brazil Universidade de Sao Paulo Instituto de AstronomiaGeofísica e Ciencias AtmosfericasRua do Matao1226-Sao Paulo05508-090Brazil

Carbon isotope compositions of both sedimentary carbonate and organic matter can be used as key proxies of the global carbon cycle and of its evolution through time,as long as they are acquired from waters where the dissolved inorganic carbon(DIC)is in isotope equilibrium with the atmospheric ***,in shallow water platforms and epeiric settings,the influence of local to regional parameters on carbon cycling may lead to DIG isotope variations unrelated to the global carbon *** may be especially true for the terminal Neoproterozoic,when Gondwana assembly isolated waters masses from the global ocean,and extreme positive and negative carbon isotope excursions are recorded,potentially decoupled from global *** improve our understanding on the type of information recorded by these excursions,we investigate the pairedδ^13Ccarb andδ^13Corg evolution for an increasingly restricted late Ediacaran-Cambrian foreland system in the West Gondwana interior:the basal Bambui *** succession represents a 1~(st)-order sedimentary sequence and records two majorδ^13Ccarb excursions in its two lowermost lower-rank *** basal cap carbonate interval at the base of the first sequence,deposited when the basin was connected to the ocean,hosts antithetical negative and positive excursions forδ^13Ccarb andδ^13Corg,respectively,resulting inΔ^13C values lower than 25‰.From the top of the basal sequence upwards,an extremely positiveδ^13Ccarb excursion is coupled toδ^13Corg,reaching values of+14‰and-14‰,*** positive excursion represents a remarkable basin-wide carbon isotope feature of the Bambui Group that occurs with only minor changes inΔ^13C values,suggesting change in the DIC isotope *** argue that this regional isotopic excursion is related to a disconnection between the intrabasinal and the global carbon *** extreme carbon isotope excursion may have been a product of a disequilibria between the basin DIC and atmospheric CO2

关键词： Methanogenesis Ediacaran Cambrian Carbon isotopes Sao Francisco Basin Bambui Group

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Identification,Structure Analyses and Expression Pattern of the ERF Transcription Factor Family in Coffea arabica

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Journal of Botanical Research 2021年第1期3卷 32-45页

作者： Silvia Graciele Hülse de Souza Tiago B.dos santos Douglas S.Domingues Anne Bernadac Mondher Bouzayen Luiz F.P.Pereira Giuliano Degrassi Valéria Carpentieri-Pípolo Laboratory of Molecular Biology Universidade Paranaense PO box 87502-210UmuaramaPRBrazil Instituto Agronômico do Paraná Laboratório de Biotecnologia VegetalCP 481PO box 86001-970LondrinaPRBrazil Department of Botany Instituto de BiociênciasUniversidade Estadual PaulistaUNESPRio ClaroSPBrazil Laboratoire de Genomique et Biotechnologie des Fruits UMR 990 INRA/INP-ENSAT Chemin de BorderougePO box 10731326 Castanet Tolosan CedexFrance Empresa Brasileira de Pesquisa Agropecuária Embrapa CaféParque Estação BiológicaBrasíliaDFPO box 70770-901Brazil International Centre for Genetic Engineering and Biotechnology(ICGEB) 1Industrial Biotechnology GroupBuenos AiresRepública Argentina Empresa Brasileira de Pesquisa Agropecuária Embrapa TrigoPO box 99001-970Passo FundoRSBrazil

Members of the ERF Family of Transcription Factors play an important role in plant development and gene expression that regulates responses to biotic and abiotic *** work identified 36 ERF family genes in Coffea arabica within the AP2/ERF full domain,using the EST-based genomic resource of the Brazilian Coffee Genome *** ERF family genes were classified into nine of the ten existing groups through phylogenetic analysis of the deduced amino acid sequences and comparison with the sequences of the ERF family genes in *** addition to the AP2 domain,other conserved domains were identified,typical of members of each *** in silico analysis and expression profiling showed high levels of expression for libraries derived from tissues of fruits,leaves and flowers as well as for libraries subjected to water *** results suggest the participation of the ERF family genes of *** in distinct biological functions,such as control of development,maturation,and responses to water *** results of this work imply in the selection of promising genes for further functional characterizations that will provide a better understanding of the complex regulatory networks related to plant development and responses to stress,opening up opportunities for coffee breeding programs.

关键词： AP2/ERF Coffee Ethylene Transcription factor

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