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Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane

The Crop Journal 2023年第6期11卷 1805-1815页

作者： Ricardo JoséGonzaga Pimenta Alexandre Hild Aono Roberto Carlos Villavicencio Burbano Marcel Fernando da Silva Ivan Antônio dos Anjos Marcos Guimarães de Andrade Landell Marcos Cesar Gonçalves luciana rossini pinto Anete Pereira de Souza Centre for Molecular Biology and Genetic Engineering University of CampinasCampinasBrazil Gustavo Galindo Velasco Campus Littoral Polytechnic Superior SchoolGuayaquilEcuador Advanced Centre for Technological Research in Sugarcane Agribusiness Agronomic Institute of CampinasRibeirão PretoBrazil Plant Protection Research Centre Biological InstituteSão PauloBrazil Department of Plant Biology Institute of BiologyUniversity of CampinasCampinasBrazil

Sugarcane mosaic virus(SCMV)is the main etiological agent of sugarcane mosaic disease,which affects sugarcane and other grass *** the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize,the genetic basis of this trait in sugarcane is largely ***,a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane *** single-nucleotide polymorphisms(SNPs)explained up to 29.9%of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy,precision,recall,and F1 scores(the harmonic mean of precision and recall).Both marker sets were validated in additional sugarcane genotypes,in which the SNPs explained up to 23.6%of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%.Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane,explaining why this major resistance source has not been identified in this ***,using sugarcane RNA-Seq data,markers associated with resistance to SCMV were annotated,and a gene coexpression network was constructed to identify the predicted biological processes involved in *** network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses,photosynthesis,and the regulation of transcription and translation in resistance to *** results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance.

关键词： Saccharum SCMV GWAS Machine learning RNA-Seq

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Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane

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The Crop Journal 2023年第6期

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Nicotinic cholinergic receptors in esophagus:Early alteration during carcinogenesis and prognostic value

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World Journal of Gastroenterology 2016年第31期22卷 7146-7156页

作者： Marina Chianello Nicolau Luis Felipe Ribeiro pinto Pedro Nicolau-Neto Paulo Roberto Alves de Pinho Ana rossini Tatiana de Almeida Simao Sheila Coelho Soares Lima Departamento de Bioquímica Instituto de Biologia Roberto Alcantara GomesUniversidade do Estado do Rio de Janeiro Programa de Carcinogênese Molecular Instituto Nacional de CancerCoordenacao de Pesquisa Gastroenterologia Hospital Universitário Pedro ErnestoUniversidade do Estado do Rio de Janeiro

AIM: To compare expression of nicotinic cholinergic receptors(CHRNs) in healthy and squamous cell carcinoma-affected esophagus and determine the prognostic ***: We performed RT-q PCR to measure the expression of CHRNs in 44 esophageal samples from healthy individuals and in matched normal surrounding mucosa, and in tumors from 28 patientsdiagnosed with esophageal squamous cell carcinoma(ESCC). Next, we performed correlation analysis for the detected expression of these receptors with the habits and clinico-pathological characteristics of all study participants. In order to investigate the possible correlations between the expression of the different CHRN subunits in both healthy esophagus and tissues from ESCC patients, correlation matrices were generated. Subsequently, we evaluated whether the detected alterations in expression of the various CHRNs could precede histopathological modifications during the esophageal carcinogenic processes by using receiver operating characteristic curve analysis. Finally, we evaluated the impact of CHRNA5 and CHRNA7 expression on overall survival by using multivariate ***: CHRNA3, CHRNA5, CHRNA7 and CHRNB4, but not CHRNA1, CHRNA4, CHRNA9 or CHRNA10, were found to be expressed in normal(healthy) esophageal mucosa. In ESCC, CHRNA5 and CHRNA7 were overexpressed as compared with patient-matched surrounding non-tumor mucosa(ESCC-adjacent mucosa; P < 0.0001 and P = 0.0091, respectively). Positive correlations were observed between CHRNA3 and CHRNB4 expression in all samples analyzed. Additionally, CHRNB4 was found to be differentially expressed in the healthy esophagus and the normalappearing ESCC-adjacent mucosa, allowing for distinguishment between these tissues with a sensitivity of 75.86% and a specificity of 78.95%(P = 0.0002). Finally, CHRNA5 expression was identified as an independent prognostic factor in ESCC; patients with high CHRNA5 expression showed an increased overall survival, in comparison with those

关键词： Nicotinic cholinergic receptors Esophagus Esophageal squamous cell carcinoma Tobacco Alcohol Gene expression

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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

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