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Genome and transcriptome analysis of the grapevine(Vitis vinifera L.) WRKY gene family

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Horticulture Research 2014年第1期1卷 227-242页

作者： Min Wang Alessandro Vannozzi Gang Wang Ying-Hai Liang Giovanni Battista Tornielli Sara Zenoni Erika Cavallini mario pezzotti Zong-Ming(Max)Cheng Fruit Crop Systems Biology Laboratory College of HorticultureNanjing Agricultural UniversityNanjing 210095China Dipartimento di Biotecnologie Universita`degli Studi di Verona37134 VeronaItaly Department of Agronomy FoodNatural resourcesAnimals and EnvironmentUniversity of Padova35020 LegnaroPDItaly

The plant WRKY gene family represents an ancient and complex class of zinc-finger transcription factors(TFs)that are involved in the regulation of various physiological processes,such as development and senescence,and in plant response to many biotic and abiotic *** the growing number of studies on the genomic organisation of WRKY gene family in different species,little information is available about this family in grapevine(Vitis vinifera L.).In the present study,a total number of 59 putative grapevine WRKY transcription factors(VvWRKYs)were identified based on the analysis of various genomic and proteomic grapevine *** to their structural and phylogentic features,the identified grapevine WRKY transcription factors were classified into three main *** order to shed light into their regulatory roles in growth and development as well as in response to biotic and abiotic stress in grapevine,the VvWRKYs expression profiles were examined in publicly available microarray *** analysis of these data revealed distinct temporal and spatial expression patterns of VvWRKYs in various tissues,organs and developmental stages,as well as in response to biotic and abiotic *** also extend our analysis to situations not covered by the arrays and to validate our results,the expression profiles of selected VvWRKYs in response to drought stress,Erysiphe necator(powdery mildew)infection,and hormone treatments(salicilic acid and ethylene),were investigated by quantitative real-time reverse transcription PCR(qRT-PCR).The present study provides a foundation for further comparative genomics and functional studies of this important class of transcriptional regulators in grapevine.

关键词： analysis Vitis vinifera

Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

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Horticulture Research 2016年第1期3卷 124-133页

作者： Danielle Costenaro da Silva Vítor da Silveira Falavigna Marianna Fasoli Vanessa Buffon Diogo Denardi Porto Georgios Joannis Pappas Jr mario pezzotti Giancarlo Pasquali Luís Fernando Revers Graduate Program in Cell and Molecular Biology Center for BiotechnologyUniversidade Federal do Rio Grande do SulPorto Alegre91501-970RSBrazil Dipartimento di Biotecnologie Universitàdegli Studi di VeronaVerona37134Italy Embrapa Uva e Vinho Bento Gonçalves95701-008RSBrazil Embrapa Semiárido Petrolina56302-970PEBrazil Department of Cell Biology Universidade de BrasíliaBrasília70910-900DFBrazil Syngenta Seeds Ltda UberlândiaMG38407-049Brazil Modesto CA 95354USA

The Dof(DNA-binding with one finger)protein family spans a group of plant transcription factors involved in the regulation of several functions,such as plant responses to stress,hormones and light,phytochrome signaling and seed *** we describe the Dof-like gene family in grapevine(Vitis vinifera L.),which consists of 25 genes coding for *** extensive in silico characterization of the VviDofL gene family was ***,the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray(cv Corvina)and real-time PCR(cv Pinot Noir)*** phylogenetic analysis comparing grapevine sequences with those of Arabidopsis,tomato,poplar and already described Dof genes in other species allowed us to identify several duplicated *** diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological ***,distinct expression patterns were identified between samples analyzed,corroborating such *** expression results indicate that several VviDofL genes perform their functional roles mainly during flower,berry and seed development,highlighting their importance for grapevine growth and *** identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.

关键词： involvement organs assessed

Relationship between antral distension and postprandial symptoms in functional dyspepsia

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World Journal of Gastroenterology 2006年第43期12卷 6982-6991页

作者： Nadia Pallotta Patrizio pezzotti Enrico Corazziari Department Scienze Cliniche Università degli Studi di Roma "La Sapienza" Rome Italy Agenzia di Sanità pubblica della Regione La zio Rome Italy

AIM: To investigate in patients with functional dyspepsia (FD) after an every-day meal whether (1) gastrointestinal (GI) and extra-GI symptoms had any relation with the degree of antral volume, (2) the onset of postprandial symptoms was associated with, and may predict, delayed gastric emptying. METHODS: In 94 symptomatic FD patients, antral volume variations and gastric emptying were assessed with ultrasonography after a 1050 kcal meal. Symptoms were evaluated with a standardized questionnaire. The association of GI and extra-GI symptoms with antral volumes and gastric emptying were estimated with logistic regression analysis. RESULTS: Forty percent of patients did not report any symptoms after a meal. Compared to the healthy controls, the antrum was more distended in patients throughout the entire observation period and 37 (39.4%) patients had delayed gastric emptying. Only postprandial drowsiness was associated with antral volume variations (AOR = 1.42; P < 0.001) and with delayed gastric emptying (AOR = 3.59; P < 0.03). CONCLUSION: In FD patients, GI symptoms are neither associated with antral distension nor with gastric emptying. Drowsiness is associated with antral distension and delayed gastric emptying. The onset of drowsiness is preceded by an increment of antral distension and the duration of the symptom appears to be related to the persistence of antral distension.

关键词： Antral distension Functional dyspepsia Gastric emptying, Ultrasonography

Relationship between gastrointestinal and extra-gastrointestinal symptoms and delayed gastric emptying in functional dyspeptic patients

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World Journal of Gastroenterology 2005年第28期11卷 4375-4381页

作者： N Pallotta P pezzotti E Calabrese F Baccini E Corazziari Dpt Scienze Cliniche Università degli Studi di Roma "La Sapienza" Reparto AIDS e Malattie Sessualmente Trasmesse Istituto Superiore di Sanità Rome Italy Dpt Scienze Cliniche

AIM: Delayed gastric emptying and an enlarged fasting gastric antrum are common findings in functional dyspepsia but their relationship with gastrointestinal (GI), and the frequently associated extra-GI symptoms remains *** study evaluated the relationship between GI and extra-GI symptoms, fasting antral volume and delayed gastric emptying in functional ***: In 108 functional dyspeptic patients antral volume and gastric emptying were assessed with ultrasonography (US). Symptoms were assessed with standardized questionnaire. The association of symptoms and fasting antral volume with delayed gastric emptying was estimated with logistic regression ***: Delayed gastric emptying was detected in 39.8% of the patients. Postprandial drowsiness (AOR 11.25; 95%CI 2.75-45.93), nausea (AOR 3.51; 95%CI 1.19-10.32), fasting antral volume (AOR 1.93; 95%CI 1.22-3.05), were significantly associated with delayed gastric emptying. Symptoms, mainly the extra-GI ones as postprandial drowsiness and nausea, combined with fasting antral volume predicted the modality of gastric emptying with a sensitivity and specificity of 78%.CONCLUSION: In functional dyspeptic patients, (1) an analysis of fasting antral volume and of symptoms can offer valuable indication on the modality of gastric emptying,and (2) it seems appropriate to inquire on postprandial drowsiness that showed the best correlation with delayed gastric emptying.

关键词： Functional dyspepsia Gastric emptying Ultrasonography

Chronic constipation in hemiplegic patients

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World Journal of Gastroenterology 2007年第29期13卷 3967-3972页

作者： F Bracci D Badiali P pezzotti G Scivoletto U Fuoco L Di Lucente A Petrelli E Corazziari Department of Clinical Sciences La Sapienza University Rome Italy ISS Ministry of Health Rome Italy IRCCS Foundation Santa Lucia Rome Italy

AIM: To assess the prevalence of bowel dysfunction in hemiplegic patients, and its relationship with the site of neurological lesion, physical immobilization and pharmacotherapy. METHODS: Ninety consecutive hemiplegic patients and 81 consecutive orthopedic patients were investigated during physical motor rehabilitation in the same period, in the same center and on the same diet. All subjects were interviewed ≥ 3 mo after injury using a questionnaire inquiring about bowel habits before injury and at the time of the interview. Patients’ mobility was evaluated by the Adapted Patient Evaluation Conference System. Drugs considered for the analysis were nitrates, angiogenic converting enzyme (ACE) inhibitors, calcium antagonists, anticoagulants, antithrombotics, antidepressants, anti-epileptics. RESULTS: Mobility scores were similar in the two groups. De novo constipation (OR = 5.36) was a frequent outcome of the neurological accident. Hemiplegics showed an increased risk of straining at stool (OR: 4.33), reduced call to evacuate (OR: 4.13), sensation of incomplete evacuation (OR: 3.69), use of laxatives (OR: 3.75). Logistic regression model showed that constipation was significantly and independently associated with hemiplegia. A positive association was found between constipation and use of nitrates and antithrombotics in both groups. Constipation was not related to the site of brain injury. CONCLUSION: Chronic constipation is a possible outcome of cerebrovascular accidents occurring in 30% of neurologically stabilized hemiplegic patients. Its onset after a cerebrovascular accident appears to be independent from the injured brain hemisphere, and unrelated to physical inactivity. Pharmacological treatment with nitrates and antithrombotics may represent an independent risk factor for developing chronic constipation.

关键词： Constipation Disphagia Stroke Pharmacotherapy

Micro-Raman Spectroscopy for Stress Evaluation of 3C-SiC Epitaxially Grown on Si Substrate by Hot Wall CVD

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材料热处理学报 2004年第5B期25卷 803-806页

作者： ZHUWen-liang ZHUJi-liang pezzottiGiuseppe CeramicPhysicsLaboratory＆ResearchInstituteforNanoscience RINKyotoInstituteofTechnologySakyo-kuMatsugasaki606-8585KyotoJapan DepartmentofElectronicsandInformationScience KyotoInstituteofTechnologySakyo-kuMatsugasaki606-8585KyotoJapan

A series of cubic SiC single crystals were heteroepitaxially grown by the hot-wall chemical vapor deposition (CVD) using a HMDS-C3H8-H2 system on 2 inch silicon substrates with the orientations of (100), (111), (110) and (211), respectively. Even though an initial carbonization was carried out to reduce the large lattice mismatch, residual stress could not be completely relieved, partly also due to the difference of their thermal expansion coefficients. Raman scattering studies for the specimens were performed to estimate the internal stress in the SiC epilayer and the substrate. Raman spectra were mapped out on the sample surface as well as on the cross section using an automated x-y stage with a spatial resolution capable of 100 nm. For all the samples, two Raman peaks corresponding to the transverse optical (TO) and longitudinal optical (LO) phonon modes were observed, even though the intensity varied with the polarization configurations. In the SiC epilayers, tensile stresses decrease away from the interface, while compressive stresses exist in the substrate, with the magnitudes dependent on the growth orientation. The lattice strains were discussed in terms of the elastic deformation theory for the comparison.

关键词：显微喇曼光谱学应力测定 3C-SiC 热壁CVD 外延生长

Towards an open grapevine information system

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Horticulture Research 2016年第1期3卷 43-50页

作者： A-F Adam-Blondon M Alaux C Pommier D Cantu Z-M Cheng GR Cramer C Davies S Delrot L Deluc G Di Gaspero J Grimplet A Fennell JP Londo P Kersey F Mattivi S Naithani P Neveu M Nikolski M pezzotti BI Reisch R Töpfer MA Vivier D Ware H Quesneville URGI UR1164 INRAUniversitéParis-SaclayVersailles78026France Department of Viticulture and Enology University of CaliforniaDavis95616CAUSA Department of Plant Sciences University of TennesseeKnoxville37996TNUSA Department of Biochemistry and Molecular Biology University of NevadaReno89557NVUSA CSIRO Agriculture and Food Waite CampusWIC West BuildingPMB2Glen OsmondSouth Australia5064Australia Universitéde Bordeaux ISVVEGFVUMR 1287Villenave d’OrnonF-33140France Department of Botany and Plant Pathology Oregon State UniversityCorvallis97331ORUSA Istituto di Genomica Applicata Udine33100Italy Instituto de Ciencias de la Vid y del Vino(CSIC Universidad de La RiojaGobierno de La Rioja)Logroño26006Spain Plant Science Department South Dakota State UniversityBioSNTRBrookings57007SDUSA United States Department of Agriculture-Agricultural Research Service-Grape Genetics Research Unit Geneva14456NYUSA European Molecular Biology Laboratory The European Bioinformatics InstituteWellcome Trust Genome CampusHinxtonCB101SDCambridgeUK Dipartimento QualitàAlimentare e Nutrizione Centro Ricerca ed Innovazione Fondazione Edmund MachVia E.Mach 1San Michele all'Adige38010Italia UMR Mistea INRAMontpellier34060France University of Bordeaux CBiBBordeaux33000France University of Bordeaux CNRS/LaBRITalence33405France Department of Biotechnology Universitàdegli Studi di VeronaVerona37134Italy Horticulture Section School of Integrative Plant ScienceCornell UniversityGeneva14456NYUSA JKI Institute for Grapevine Breeding Geilweilerhof Siebeldingen76833Germany Department of Viticulture and Oenology Institute for Wine BiotechnologyStellenbosch UniversityStellenbosch7602MatielandSouth Africa Cold Spring Harbor Laboratory Cold Spring Harbor11724NYUSA US Department of Agriculture-Agricultural Research Service NEA Robert W.Holley Center for Agriculture and HealthCornell UniversityIthaca14853NYUSA

Viticulture,like other fields of agriculture,is currently facing important challenges that will be addressed only through sustained,dedicated and coordinated *** the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature,in many domains of study,including grapevine research,there is a need to improve the findability,accessibility,interoperability and reusability(FAIR-ness)of these *** the heterogeneous nature of the data produced,the transnational nature of the scientific community and the experience gained elsewhere,we have formed an open working group,in the framework of the International Grapevine Genome Program(***),to construct a coordinated federation of information systems holding grapevine data distributed around the world,providing an integrated set of interfaces supporting advanced data modeling,rich semantic integration and the next generation of data mining *** achieve this goal,it will be critical to develop,implement and adopt appropriate standards for data annotation and *** development of this system,the GrapeIS,linking genotypes to phenotypes,and scientific research to agronomical and oeneological data,should provide new insights into grape biology,and allow the development of new varieties to meet the challenges of biotic and abiotic stress,environmental change,and consumer demand.

关键词： system gained sustained

Performance and calibration of quark/gluon-jet taggers using 140 fb^(-1) of pp collisions at √s=13 TeV with the ATLAS detector

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Chinese Physics C 2024年第2期48卷 1-25页

作者： G. Aad B. Abbott K. Abeling N.J. Abicht S.H. Abidi A. Aboulhorma H. Abramowicz H. Abreu Y. Abulaiti B.S. Acharya C. Adam Bourdarios L. Adamczyk S.V. Addepalli M.J. Addison J. Adelman A. Adiguzel T. Adye A.A. Affolder Y. Afik M.N. Agaras J. Agarwala A. Aggarwal C. Agheorghiesei A. Ahmad F. Ahmadov W.S. Ahmed S. Ahuja X. Ai G. Aielli A. Aikot M. Ait Tamlihat B. Aitbenchikh I. Aizenberg M. Akbiyik T.P.A. Åkesson A.V. Akimov D. Akiyama N.N. Akolkar K. Al Khoury G.L. Alberghi J. Albert P. Albicocco G.L. Albouy S. Alderweireldt M. Aleksa I.N. Aleksandrov C. Alexa T. Alexopoulos F. Alfonsi M. Algren M. Alhroob B. Ali H.M.J. Ali S. Ali S.W. Alibocus M. Aliev G. Alimonti W. Alkakhi C. Allaire B.M.M. Allbrooke J.F. Allen C.A. Allendes Flores P.P. Allport A. Aloisio F. Alonso C. Alpigiani M. Alvarez Estevez A. Alvarez Fernandez M. Alves Cardoso M.G. Alviggi M. Aly Y. Amaral Coutinho A. Ambler C. Amelung M. Amerl C.G. Ames D. Amidei S.P. Amor Dos Santos K.R. Amos V. Ananiev C. Anastopoulos T. Andeen J.K. Anders S.Y. Andrean A. Andreazza S. Angelidakis A. Angerami A.V. Anisenkov A. Annovi C. Antel M.T. Anthony E. Antipov M. Antonelli F. Anulli M. Aoki T. Aoki J.A. Aparisi Pozo M.A. Aparo L. Aperio Bella C. Appelt A. Apyan N. Aranzabal S.J. Arbiol Val C. Arcangeletti A.T.H. Arce E. Arena J-F. Arguin S. Argyropoulos J.-H. Arling O. Arnaez H. Arnold G. Artoni H. Asada K. Asai S. Asai N.A. Asbah J. Assahsah K. Assamagan R. Astalos S. Atashi R.J. Atkin M. Atkinson H. Atmani P.A. Atmasiddha K. Augsten S. Auricchio A.D. Auriol V.A. Austrup G. Avolio K. Axiotis G. Azuelos D. Babal H. Bachacou K. Bachas A. Bachiu F. Backman A. Badea P. Bagnaia M. Bahmani A.J. Bailey V.R. Bailey J.T. Baines L. Baines O.K. Baker E. Bakos D. Bakshi Gupta V. Balakrishnan R. Balasubramanian E.M. Baldin P. Balek E. Ballabene F. Balli L.M. Baltes W.K. Balunas J. Balz E. Banas M. Bandieramonte A. Bandyopadhyay S. Bansal L. Barak M. Barakat E.L. Barberio D. Barberis M. Barbero M.Z. Barel K.N. Barends T. Barillari M-S. Barisits T. Barklow P. Baron D.A. Baron Mo The ATLAS Collaboration

The identification of jets originating from quarks and gluons,often referred to as quark/gluon tagging,plays an important role in various analyses performed at the Large Hadron Collider,as Standard Model measurements and searches for new particles decaying to quarks often rely on suppressing a large gluon-induced *** paper describes the measurement of the efficiencies of quark/gluon taggers developed within the ATLAS Collaboration,using √s=13 TeV proton–proton collision data with an integrated luminosity of 140 fb^(-1) collected by the ATLAS *** taggers with high performances in rejecting jets from gluon over jets from quarks are studied:one tagger is based on requirements on the number of inner-detector tracks associated with the jet,and the other combines several jet substructure observables using a boosted decision tree.A method is established to determine the quark/gluon fraction in data,by using quark/gluon-enriched subsamples defined by the jet *** in tagging efficiency between data and simulation are provided for jets with transverse momentum between 500 GeV and 2 TeV and for multiple tagger working points.

关键词： ATLAS JET QUARK GLUON TAGGING