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GenoDrawing:An Autoencoder Framework for Image Prediction from SNP Markers

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Plant Phenomics 2023年第4期5卷 816-824页

作者： Federico Jurado-Ruiz David Rousseau Juan A.Botía maria josé aranzana Center for Research in Agricultural Genomics(CRAG) 08193 BarcelonaCerdanyolaSpain Universitéd'Angers LARISINRAe UMR IRHS49000 AngersFrance Department of Information and Communication Engineering University of Murcia30071 MurciaSpain IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species,providing an abundance of genotypic data for genomic *** selection and neural networks(NNs),particularly deep learning,have been developed to predict complex traits from dense genotypic ***,an NN model to extract features from images in an unsupervised manner,has proven to be useful for plant *** study introduces an autoencoder framework,GenoDrawing,for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism(SNP)array,potentially useful in predicting traits that are difficult to *** demonstrates proficiency in its task using a small dataset of shape-related *** indicate that the use of SNPs associated with visual traits has substantial impact on the generated images,consistent with biological *** using substantial SNPs is crucial,incorporating additional,unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important *** proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping,particularly beneficial for small to medium breeding companies to predict economically substantial heritable *** GenoDrawing has limitations,it sets the groundwork for future research in image prediction from genomic *** studies should focus on using stronger models for image reproduction,SNP information extraction,and dataset balance in terms of phenotypes for more precise outcomes.

关键词： Auto Drawing prediction

Prunus genetics and applications after de novo genome sequencing:achievements and prospects

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Horticulture Research 2019年第1期6卷 1222-1246页

作者： maria joséaranzana Véronique Decroocq Elisabeth Dirlewanger Iban Eduardo Zhong Shan Gao Ksenija Gasic Amy Iezzoni Sook Jung Cameron Peace Humberto Prieto Ryutaro Tao Ignazio Verde Albert G.Abbott Pere Arús IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UBCampus UABEdifici CRAGCerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain UMR 1332 BFP INRAUniversity of BordeauxA3C and Virology Teams33882 Villenave-d’Ornon CedexFrance Allergy Research Center Zhejiang University310058 HangzhouChina Clemson University ClemsonSC 29634USA Department of Horticulture Michigan State University1066 Bogue StreetEast LansingMI 48824-1325USA Department of Horticulture Washington State UniversityPullmanWA 99164-6414USA Biotechnology Laboratory La Platina Research StationInstituto de Investigaciones AgropecuariasSanta Rosa11610 La PintanaSantiagoChile Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria(CREA)-Centro di ricerca Olivicoltura Frutticoltura e Agrumicoltura(CREA-OFA)RomeItaly University of Kentucky 106 T.P.Cooper HallLexingtonKY 40546-0073USA

Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST *** public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits *** this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome *** the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs ***,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus *** include phenology,fruit quality,allergens,disease resistance,tree architecture,and ***,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop ***,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

关键词： Prunus breeding achievements

The apple REFPOP—a reference population for genomics-assisted breeding in apple

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Horticulture Research 2020年第1期7卷 364-379页

作者： Michaela Jung Morgane Roth maria joséaranzana Annemarie Auwerkerken Marco Bink Caroline Denancé Christian Dujak Charles-Eric Durel Carolina Font i Forcada Celia M.Cantin Walter Guerra Nicholas P.Howard Beat Keller Mariusz Lewandowski Matthew Ordidge Marijn Rymenants Nadia Sanin Bruno Studer Edward Zurawicz François Laurens Andrea Patocchi Hélène Muranty Molecular Plant Breeding Institute of Agricultural SciencesETH Zurich8092 ZurichSwitzerland Breeding Research group Agroscope 8820 WädenswilSwitzerland IRTA(Institut de Recerca i Tecnologia Agroalimentàries) 08140 Caldes de MontbuiBarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UAB08193 BellaterraBarcelonaSpain Better3fruit N.V. 3202 RillaarBelgium Biometris Wageningen University and Research6708 PB WageningenThe Netherlands Hendrix Genetics Research Technology and Services B.V.PO Box 1145830AC BoxmeerThe Netherlands IRHS Universitéd’AngersINRAEInstitut AgroSFR 4207 QuaSaV49071 BeaucouzéFrance ARAID(Fundación Aragonesa para la Investigación y el Desarrollo) 50018 ZaragozaSpain Research Centre Laimburg 39040 AuerItaly Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Institute of Biology and Environmental Sciences University of Oldenburg26129 OldenburgGermany Research Institute of Horticulture 96-100 SkierniewicePoland School of Agriculture Policy and DevelopmentUniversity of ReadingWhiteknights RG66AR ReadingUK Laboratory for Plant Genetics and Crop Improvement KU Leuven B-3001 LeuvenBelgium GAFL INRAE84140 MontfavetFrance

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection ***-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic *** we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple *** population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of *** on the genotypic data,linkage disequilibrium was low and population structure was *** well-studied phenological traits of horticultural importance were *** found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,*** decreasing SNP density,the detection of significant marker–trait associations varied depending on trait *** of the trait,10,000 SNPs sufficed to maximize genomic prediction *** confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

关键词： breeding planted utilize

An integrated approach for increasing breeding efficiency in apple and peach in Europe

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Horticulture Research 2018年第1期5卷 825-838页

作者： Francois Laurens maria joséaranzana Pere Arus Daniele Bassi Marco Bink Joan Bonany Andrea Caprera Luca Corelli-Grappadelli Evelyne Costes Charles-Eric Durel Jehan-Baptiste Mauroux Hélène Muranty Nelson Nazzicari Thierry Pascal Andrea Patocchi Andreas Peil Bénédicte Quilot-Turion Laura Rossini Alessandra Stella Michela Troggio Riccardo Velasco Eric van de Weg IRHS INRAAgrocampus-OuestUniversitéd’AngersSFR 4207 QuaSaVUniversitéBretagne Loire42 rue Georges MorelBeaucouzé49071France IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UABBellaterraBarcelonaSpain Universitàdegli Studi di Milano-DiSAA Via Celoria 2Milan20133Italy Biometris Wageningen University and ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands IRTA-Mas Badia Mas BadiaLa Tallada17134Spain Parco Tecnologico Padano Via EinsteinLoc.Cascina CodazzaLodi26900Italy Dipartimento di Scienze Agrarie Alma Mater Studiorum-Universitàdi BolognaBolognaItaly UMR AGAP INRAMontpellier34398France GAFL INRAMontfavet84143France Agroscope Research Division Plant BreedingSchloss 1Wädenswil8820Switzerland Julius Kühn-Institute(JKI) Federal Research Centre for Cultivated Plants Institute for Breeding Research on Fruit CropsPillnitzer Platz 3aDresden01326Germany Research and Innovation Center Fondazione Edmund MachSan Michele all’AdigeTrentoItaly CREA-VE Center of Viticulture and Enologyvia XXVIII Aprile 26Conegliano(TV)31015Italy Plant Breeding Wageningen University and ResearchDroevendaalsesteeg 1P.O.Box 386Wageningen6700AJThe Netherlands Hendrix Genetics Research Technology&ServicesBoxmeer5830 ACThe Netherlands

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and *** bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private *** complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for *** breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank *** also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection *** FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the *** review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

关键词： breeding germplasm breed

Complementary roles of glial cells in generating region-specific neuroinflammatory responses and phagocytosis in Parkinson’s disease

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Neural Regeneration Research 2025年第10期20卷 2917-2918页

作者： Leyre Ayerra maria S.Aymerich Universidad de Navarra Facultad de CienciasDepartamento de Bioquímica y GenéticaPamplonaSpain CIMA-Universidad de Navarra PamplonaSpain IdiSNA Instituto de Investigación Sanitaria de NavarraPamplonaSpain

Neuroinflammation is associated with Parkinson’s disease:Reactive gliosis and neuroinflammation are hallmarks of Parkinson’s disease(PD),a multisystem neurodegenerative disorder characterized by a progressive loss of dopaminergic *** has long been considered a mere consequence of neuronal loss,but whether it promotes PD or is a key player in disease progression remains to be *** leukocyte antigen.

关键词： inflammation leukocyte generating

Calcium-sensitive protein MLC1 as a possible modulator of the astrocyte functional state

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Neural Regeneration Research 2025年第7期20卷 2008-2010页

作者： Elena Ambrosini Angela Lanciotti maria Stefania Brignone Department of Neuroscience Istituto Superiore di SanitàRomeItaly

Astrocytes,the main population of glial cells in the central nervous system(CNS),exert essential tasks for the control of brain tissue homeostasis,supporting neuron and other glial cell activity from the developmental stage to adult *** maintain the optimal functionality of the brain,astroglial cells are particularly committed to reacting to every change in tissue homeostatic conditions,from mild modifications of the physiological environment,a process called astrocyte activation,to the more severe alterations occurring in pathological situations causing astrocyte reactivity or reactive astrogliosis(Escartin et al.,2021).During these reactive states,astrocytes mount an active,progressive response encompassing morphological,molecular,and interactional remodeling,leading to the acquisition of new functions and the loss of others,whose intensity,duration,and reversibility are dependent on the nature of the stimulus and regulated in a context-specific manner.

关键词： alterations modulator maintain

Treatment of spinal cord injury with biomaterials and stem cell therapy in non-human primates and humans

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Neural Regeneration Research 2025年第2期20卷 343-353页

作者： Ana Milena Silva Olaya Fernanda Martins Almeida Ana maria Blanco Martinez Suelen Adriani Marques PhD Program in Pathological Anatomy Federal University of Rio de JaneiroRio de JaneiroBrazil Biomedical Science Institute Federal University of Rio de JaneiroRio de JaneiroBrazil Graduate Program in Pathological Anatomy Federal University of Rio de JaneiroRio de JaneiroBrazil Graduate Program in Pathological Anatomy(PPGAP/UFRJ) Department of Neurobiology/Institute of BiologyCampus do GragoatáNiteróiRio de JaneiroBrazil

Spinal cord injury results in the loss of sensory,motor,and autonomic functions,which almost always produces permanent physical ***,in the search for more effective treatments than those already applied for years,which are not entirely efficient,researches have been able to demonstrate the potential of biological strategies using biomaterials to tissue manufacturing through bioengineering and stem cell therapy as a neuroregenerative approach,seeking to promote neuronal recovery after spinal cord *** of these strategies has been developed and meticulously evaluated in several animal models with the aim of analyzing the potential of interventions for neuronal repair and,consequently,boosting functional *** the majority of experimental research has been conducted in rodents,there is increasing recognition of the importance,and need,of evaluating the safety and efficacy of these interventions in non-human primates before moving to clinical trials involving therapies potentially promising in *** article is a literature review from databases(PubMed,Science Direct,Elsevier,Scielo,Redalyc,Cochrane,and NCBI)from 10 years ago to date,using keywords(spinal cord injury,cell therapy,non-human primates,humans,and bioengineering in spinal cord injury).From 110 retrieved articles,after two selection rounds based on inclusion and exclusion criteria,21 articles were ***,this review arises from the need to recognize the experimental therapeutic advances applied in non-human primates and even humans,aimed at deepening these strategies and identifying the advantages and influence of the results on extrapolation for clinical applicability in humans.

关键词： bioengineering biomaterials cell therapy humans non-human primates spinal cord injury stem cell therapy

Challenges and improvement strategies in the hospitalization of chronic multimorbid patients

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World Journal of Clinical Cases 2025年第3期13卷 35-41页

作者： Andres Fontalba-Navas Francisco Pozo Muñoz Rogelio Garcia Cisneros maria jose Garcia Larrosa maria del Mar Callejon Gil Ignacio Garcia Delgado maria Belen Jimenez Martinez Antequera Hospital Northern Málaga Integrated Healthcare AreaAntequera 29200AndalusiaSpain Department of Public Health and Psychiatry University of MálagaMálaga 29010Spain Antequera Hospital Northern Málaga Antequera Integrated Healthcare AreaAntequera 29200MálagaSpain

BACKGROUND Addressing the growing challenge of hospitalizing chronic multimorbid patients,this study examines the strain these conditions impose on healthcare systems at a local level,focusing on a pilot *** diseases and complex patients require comprehensive management strategies to reduce healthcare burdens and improve patient *** proven effective,this pilot model has the potential to be replicated in other healthcare settings to enhance the management of chronic multimorbid *** To evaluate the effectiveness of the high complexity unit(HCU)in managing chronic multimorbid patients through a multidisciplinary care model and to compare it with standard hospital *** The study employed a descriptive longitudinal approach,analyzing data from the Basic Minimum Data Set(BMDS)to compare hospitalization variables among the HCU,the Internal Medicine Service,and other services at Antequera Hospital throughout *** HCU,designed for patients with complex chronic conditions,integrates a patient-centered model emphasizing multidisciplinary care and continuity *** The study employed a descriptive longitudinal approach,analyzing data from the BMDS to compare hospitalization variables among the HCU,the Internal Medicine Service,and other services at Antequera Hospital throughout *** HCU,designed for patients with complex chronic conditions,integrates a patient-centered model emphasizing multidisciplinary care and continuity *** This study demonstrates the effectiveness of the HCU in managing patients with complex chronic diseases through a multidisciplinary *** coordinated care provided by the HCU results in improved patient outcomes,reduced unnecessary hospitalizations,and better management of patient *** superiority of the HCU compared to standard care is evident in key outcomes such as fewer readmissions and higher patient satisfaction,reinforcing its value as a model of ca

关键词： High complexity unit Chronic multimorbidity Patient-centered care Integrated care Healthcare management

Predicting the aquatic risk of realistic pesticide mixtures to species assemblages in Portuguese river basins

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Journal of Environmental Sciences 2015年第5期27卷 12-20页

作者： Emília Silva Michiel A.Daam maria josé Cerejeira Centro de Engenharia dos Biossistemas (CEER) Instituto Superior de Agronomia (ISA) University of Lisbon (UL) Tapada da Ajuda1349-017 Lisbon Portugal

Although pesticide regulatory tools are mainly based on individual substances, aquatic ecosystems are usually exposed to multiple pesticides from their use on the variety of crops within the catchment of a river. This study estimated the impact of measured pesticide mixtures in surface waters from 2002 and 2008 within three important Portuguese river basins（＇Mondego＇, ＇Sado＇ and ＇Tejo＇） on primary producers, arthropods and fish by toxic pressure calculation. Species sensitivity distributions（SSDs）, in combination with mixture toxicity models, were applied. Considering the differences in the responses of the taxonomic groups as well as in the pesticide exposures that these organisms experience, variable acute multi-substance potentially affected fractions（ms PAFs） were obtained. The median msP AF for primary producers and arthropods in surface waters of all river basins exceeded 5%, the cut-off value used in the prospective SSD approach for deriving individual environmental quality standards. A ranking procedure identified various photosystem II inhibiting herbicides, with oxadiazon having the relatively largest toxic effects on primary producers, while the organophosphorus insecticides, chlorfenvinphos and chlorpyrifos, and the organochloride endosulfan had the largest effects on arthropods and fish, respectively. These results ensure compliance with European legislation with regard to ecological risk assessment and management of pesticides in surface waters.

关键词： Pesticides Mixtures Risk assessment Multi-substance potentially affected fraction Surface waters