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Genomic selection in plant breeding:Key factors shaping two decades of progress

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Molecular Plant 2024年第4期17卷 552-578页

作者： Admas Alemu Johanna Astrand Osval A.Montesinos-López Julio Isidro y sanchez Javier fernandez-Gónzalez Wuletaw Tadesse Ramesh R.Vetukuri Anders S.Carlsson Alf Ceplitis JoséCrossa Rodomiro Ortiz Aakash Chawade Department of Plant Breeding Swedish University of Agricultural SciencesAlnarpSweden Lantmannen Lantbruk SvalövSweden facultad de Telematica University de ColimaColimaColima 28040Mexico Centro de Biotecnología y Genómica de Plantas(CBGP UPM-INIA)Universidad Politécnica de Madrid(UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo-UPM28223 MadridSpain International Center for Agricultural Research in the Dry Areas(ICARDA) RabatMorocco International Maize and Wheat Improvement Center(CIMMYT) Km 45Carretera México-VeracruzTexcocoMéxico 52640Mexico

Genomic selection,the application of genomic prediction(GP)models to select candidate individuals,has significantly advanced in the past two decades,effectively accelerating genetic gains in plant breeding.This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period.We delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP accuracy.Special emphasis was placed on optimizing training population size.We explored its benefits and the associated diminishing returns beyond an optimum size.This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms.The density and distribution of single-nucleotide polymorphisms,level of linkage disequilibrium,genetic complexity,trait heritability,statistical machine-learning methods,and non-additive effects are the other vital factors.Using wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various traits.The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits.We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets,effective training population optimization methods and support from other omics approaches(transcriptomics,metabolomics and proteomics)coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy,making genomic selection an effective tool in plant breeding.

关键词： genomic selection genetic gain genomic prediction optimization deep learning training population optimization

Thedual pathogenesisofpenileneoplasia: The heterogeneous morphology of human papillomavirus-relatedtumors

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Asian Journal of Urology 2022年第4期9卷 349-358页

作者： Alcides Chaux Diego f.sanchez Maria Jose fernandez-Nestosa Sofia Canete-Portillo Ingrid M.Rodriguez Giovanna A.Giannico Antonio L.Cubilla Department of Scientific Research School of Postgraduate Studies Norte UniversityAsuncionParaguay InstitutodePatologiae Investigacion AsuncionParaguay Polytechnic School National University of AsuncionSan LorenzoParaguay Department of Pathology University of Alabama at BirminghamBirminghamALUSA School of Medicine National University of AsuncionSan LorenzoParaguay Department of Pathology Microbiologyand ImmunologyVanderbilt University Medical CenterNashvilleTNUSA

Objective:Penile neoplasia,usually of squamous histogenesis,is currently classfied into human papillomavirus(HPV)-related or-dependent and non-HPV-related or-indepen dent.There are distinct morphological differences among the two groups.New research studies on penile cancer from Northern countries showed that the presence of HPV is corre lated with a better prognosis than virus negative people,while studies in Southern countries had not confirmed,perhaps due to differences in staging or treatment.Methods:We focused on the description of the HPV.related carcinomas of the penis.The approach was to describe common clinical features followed by the pathological features of each entity or subtype stressing the characteristics for differential diagnosis,HPV genotypes,and prognostic features of the invasive carcinomas.Similar structure was followed for penile intraepithelial neoplasia,except for prognosis because of the scant evidence available.Results:Most of HPV-related lesions can be straightforwardly recognized by routine hematoxylin and eosin stains,but in some cases surrogate p16 immunohistochemical staining or molecular methods such as in situ hybridization or polymerase chain reaction can be utilized.Currently,there are eight tumor invasive variants associated with HPV,as follows:basaloid,warty,warty-basaloid,papillary basaloid,clear cell,medullary,lymphoepithelioma-like,and giant condylomas with malignant transformation.Conclusion:This review presents and describes the heterogeneous clinical,morphological,and genatypic features of the HPV-related subtypes of invasive and non-invasive penile neoplasia.

关键词： Penile neoplasia Squamous cell carcinoma Human papillomavirus Carcinoma in situ Penile intraepithelial neoplasia

Machine learning-based zero-touch network and service management:a survey

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Digital Communications and Networks 2022年第2期8卷 105-123页

作者： Jorge Gallego-Madrid Ramon sanchez-Iborra Pedro M.Ruiz Antonio f.Skarmeta Department of Information and Communication Engineering University of Murcia30100MurciaSpain Department of Engineering and Applied Techniques University Center of Defense30729San Javier Air Force BaseSpain

The exponential growth of mobile applications and services during the last years has challenged the existing network infrastructures.Consequently,the arrival of multiple management solutions to cope with this explosion along the end-to-end network chain has increased the complexity in the coordinated orchestration of different segments composing the whole infrastructure.The Zero-touch Network and Service Management(ZSM)concept has recently emerged to automatically orchestrate and manage network resources while assuring the Quality of Experience(QoE)demanded by users.Machine Learning(ML)is one of the key enabling technologies that many ZSM frameworks are adopting to bring intelligent decision making to the network management system.This paper presents a comprehensive survey of the state-of-the-art application of ML-based techniques to improve ZSM performance.To this end,the main related standardization activities and the aligned international projects and research efforts are deeply examined.from this dissection,the skyrocketing growth of the ZSM paradigm can be observed.Concretely,different standardization bodies have already designed reference architectures to set the foundations of novel automatic network management functions and resource orchestration.Aligned with these advances,diverse ML techniques are being currently exploited to build further ZSM developments in different aspects,including multi-tenancy management,traffic monitoring,and architecture coordination,among others.However,different challenges,such as the complexity,scalability,and security of ML mechanisms,are also identified,and future research guidelines are provided to accomplish a firm development of the ZSM ecosystem.

关键词： Zero-touch network and service management(ZSM) Next generation networks(NGN) Artificial intelligence(AI) Machine learning(ML)

Corneal topography in keratoconus: state of the art

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Eye and Vision 2016年第1期3卷 37-48页

作者： f.Cavas-Martinez E.De la Cruz sanchez J.Nieto Martinez f.J.fernandez Canavate D.G.fernandez-Pacheco Department of Graphical Expression Technical University of CartagenaC/Doctor Fleming s/nCartagena 30202MurciaSpain faculty of Sports Science C/Santa Alicia s/nSantiago de la Ribera30720 MurciaSpain

The morphological characterization of the cornea using corneal topographers is a widespread clinical practice that is essential for the diagnosis of keratoconus.The current state of this non-invasive exploratory technique has evolved with the possibility of achieving a great number of measuring points of both anterior and posterior corneal surfaces,which is possible due to the development of new and advanced measurement devices.All these data are later used to extract a series of topographic valuation indices that permit to offer the most exact and reliable clinical diagnosis.This paper describes the technologies in which current corneal topographers are based on,being possible to define the main morphological characteristics that the keratoconus pathology produces on corneal surface.finally,the main valuation indices,which are provided by the corneal topographers and used for the diagnosis of keratoconus,are also defined.

关键词： Placido disc Detection system Topographer Diagnosis

Risk factors for suicidal behaviour in late-life depression:A systematic review

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World Journal of Psychiatry 2022年第1期12卷 187-203页

作者： Veronica fernandez-Rodrigues Yolanda sanchez-Carro Luisa Natalia Lagunas Laura Alejandra Rico-Uribe Andres Pemau Patricia Diaz-Carracedo Marina Diaz-Marsa Gonzalo Hervas Alejandro de la Torre-Luque Department of Psychology Universidad Complutense de MadridMadrid 28223Spain Department of Psychiatry Universidad Autonoma de MadridMadrid 28046Spain Centre for Biomedical Research in Mental Health(CIBERSAM) Madrid 28029Spain Department of Legal Medicine Psychiatry and PathologyUniversidad Complutense de MadridMadrid 28046Spain of Psychology La Rioja International UniversityLogrono 26006Spain Institute of Psychiatry and Mental Health San Carlos Clinical HospitalMadrid 28040Spain

BACKGROUND Suicide is a leading cause of preventable death worldwide,with its peak of maximum incidence in later life.Depression often puts an individual at higher risk for suicidal behaviour.In turn,depression deserves particular interest in old age due to its high prevalence and dramatic impact on health and wellbeing.AIM To gather integrated evidence on the potential risk factors for suicide behaviour development in depressive older adults,and to examine the effects of depression treatment to tackle suicide behaviour in this population.METHODS A systematic review of empirical studies,published from 2000 onwards,was conducted.Suicidal behaviour was addressed considering its varying forms(i.e.,wish to die,ideation,attempt,and completed suicide).RESULTS Thirty-five papers were selected for review,comprising both clinical and epidemiological studies.Most of studies focused on suicidal ideation(60%).The studies consistently pointed out that the risk was related to depressive episode severity,psychiatric comorbidity(anxiety or substance use disorders),poorer health status,and loss of functionality.Reduced social support and loneliness were also associated with suicide behaviour in depressive older adults.finally,the intervention studies showed that suicidal behaviour was a robust predictor of depression treatment response.Reductions in suicidal ideation were moderated by reductions in risk factors for suicide symptoms.CONCLUSION To sum up,common and age-specific risk factors seem to be involved in suicide development in depressive older adults.A major effort should be made to tackle this serious public health concern so as to promote older people to age healthily and well.

关键词： Late-life depression Suicide behaviour Disability Chronic disease Loneliness

Crop phenotyping in a context of global change:What to measure and how to do it

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Journal of Integrative Plant Biology 2022年第2期64卷 592-618页

作者： Jose Luis Araus Shawn Carlisle Kefauver Omar Vergara-Díaz Adrian Gracia-Romero fatima Zahra Rezzouk Joel Segarra Maria Luisa Buchaillot Melissa Chang-Espino Thomas Vatter Rut sanchez-Bragado JoséArmando fernandez-Gallego Maria Dolores Serret Jordi Bort Integrative Crop Ecophysiology Group Plant Physiology SectionFaculty of BiologyUniversity of BarcelonaBarcelonaSpain AGROTECNIO Center LleidaSpain Plant Ecophysiology and Metabolism Lab ITQB NovaPlant Sciences DivisionOeirasPortugal Programa de Ingeniería Electrónica Facultad de IngenieríaUniversidad de IbaguéIbaguéColombia

High-throughput crop phenotyping,particularly under field conditions,is nowadays perceived as a key factor limiting crop genetic advance.Phenotyping not only facilitates conventional breeding,but it is necessary to fully exploit the capabilities of molecular breeding,and it can be exploited to predict breeding targets for the years ahead at the regional level through more advanced simulation models and decision support systems.In terms of phenotyping,it is necessary to determined which selection traits are relevant in each situation,and which phenotyping tools/methods are available to assess such traits.Remote sensing methodologies are currently the most popular approaches,even when lab-based analyses are still relevant in many circumstances.On top of that,data processing and automation,together with machine learning/deep learning are contributing to the wide range of applications for phenotyping.This review addresses spectral and red-green-blue sensing as the most popular remote sensing approaches,alongside stable isotope composition as an example of a lab-based tool,and root phenotyping,which represents one of the frontiers for field phenotyping.further,we consider the two most promising forms of aerial platforms(unmanned aerial vehicle and satellites)and some of the emerging data-processing techniques.The review includes three Boxes that examine specific case studies.

关键词： crop phenotyping deep learning models photosynthesis platforms remote sensing roots satellites sensors stable isotopes

Study on the performance of thin-film VCSELs on composite metal substrate

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frontiers of Optoelectronics 2023年第4期16卷 1-11页

作者： William Anderson Lee sanchez Shreekant Sinha Po‑Yu Wang Ray‑Hua Horng Institute of Electronics Yang Ming Chiao Tung UniversityHsinchu 30010China

Thin film p-side up vertical-cavity surface-emitting lasers(VCSELs)with 940 nm wavelength on a composite metal(Copper/Invar/Copper;CIC)substrate has been demonstrated by twice-bonding transfer and substrate removing techniques.The CIC substrate is a sandwich structure with a 10µm thick Copper(Cu)layer/30µm thick Invar layer/10µm thick Cu layer.The Invar layer was composed of Iron(fe)and Nickel(Ni)with a proportion of 70:30.The thermal expansion coefcient of the composite CIC metal can match that of the GaAs substrate.It results that the VCSEL layers can be successfully transferred to CIC metal substrate without cracking.At 1 mA current,the top-emitting VCSEL/GaAs and thin-flm VCSEL/CIC had a voltage of 1.39 and 1.37 V,respectively.The optical output powers of VCSEL/GaAs and VCSEL/CIC were 21.91 and 24.40 mW,respectively.The 50µm thick CIC substrate can play a good heat dissipation function,which results in improving the electrical and optical characteristics of thin flm VCSELs/CIC.The VCSEL/CIC exhibited a superior thermal management capability as compared with VCSEL/GaAs.The obtained data suggested that VCSELs on a composite metal substrate not only afected signifcantly the characteristics of thin film VCSEL,but also improved considerably the device thermal performance.

关键词： Thin film VCSELs GaAs substrate Composite metal CIC substrate Twice-bonding transfer Electrical properties Heat dissipation

Physiological strategies of moult-migrating Black-necked Grebes(Podiceps nigricollis)in a polluted staging site according to blood chemistry

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Avian Research 2023年第3期14卷 453-459页

作者： Juan A.Amat Nico Varo Marta I.sanchez Andy J.Green Damaso Hornero-Mendez Juan Garrido-fernandez Cristina Ramo Departamento de Ecología y Evolucion Estacion Biologica de Donana(EBD-CSIC)41092SevillaSpain Independent researcher 41010SevillaSpain Departamento de Biología de la Conservacion y Cambio Global Estacion Biologica de Donana(EBD-CSIC)41092SevillaSpain Departamento de fitoquímica de Alimentos Instituto de la Grasa(IG-CSIC)41013SevillaSpain

After breeding,Black-necked Grebes(Podiceps nigricollis)perform a moult-migration to autumn hypersaline staging sites,where they moult the flight feathers and forage on superabundant brine shrimp(Artemia spp.)before leaving for wintering areas.During the stay in moulting sites,the grebes experience changes in organs and muscle size(atrophy,hypertrophy),and almost double their body mass,which has been suggested to act as an insurance against a collapse in prey availability in late autumn.During two years we collected blood samples from hundreds of individuals at one of the most important European moulting sites(the Odiel marshes,SW Spain),which is a highly polluted area due to mining drainage and chemical industry.We assessed the potential effect of moulting stage,day of the year and body condition on 16 blood biochemical parameters.Because of the changes in prey availability and body composition of grebes,we expected some physiological adjustments during moult.Elevated levels of cholesterol suggested that birds in active moult increased foraging effort to face the costs of moulting.There was increased amount of lactate dehydrogenase,corresponding to periods of breast muscle atrophy.Birds in active moult augmented protein ingestion,likely to account for the requirements of feather growth.We also show that the probability of fasting due to low prey availability increased late in the moulting season,as demonstrated by an increase in plasmaβ-hydroxy-butyrate.

关键词： Blood biochemistry Eared grebe fasting feather replacement Odiel marshes Waterbird

Unclonable human-invisible machine vision markers leveraging the omnidirectional chiral Bragg diffraction of cholesteric spherical reflectors

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Light(Science & Applications) 2022年第11期11卷 2583-2601页

作者： Hakam Agha Yong Geng Xu Ma Deniz IsInsu Avsar Rijeesh Kizhakidathazhath Yan-Song Zhang Ali Tourani Hriday Bavle Jose-Luis sanchez-Lopez Holger Voos Mathew Schwartzo Jan P.f.Lagerwall University of Luxembourg Department of Physics&Materials Science1511 LuxembourgLuxembourg University of Luxembourg Interdisciplinary Centre for SecurityReliability and Trust(SnT)1855 LuxembourgLuxembourg University of Luxembourg University of LuxembourgDepartment of EngineeringL-1359 LuxembourgLuxembourg New Jersey Institute of Technology College of Architecture and DesignUniversity HeightsNewarkNJUSA

The seemingly simple step of molding a cholesteric liquid crystal into spherical shape,yielding a Cholesteric Spherical Reflector(CSR),has profound optical consequences that open a range of opportunities for potentially transformative technologies.The chiral Bragg diffraction resulting from the helical self-assembly of cholesterics becomes omnidirectional in CSRs.This turns them into selective retroreflectors that are exceptionally easy to distinguish-regardless of background--by simple and low-cost machine vision,while at the same time they can be made largely imperceptible to human vision.This allows them to be distributed in human-populated environments,laid out in the form of QR-code-like markers that help robots and Augmented Reality(AR)devices to operate reliably,and to identify items in their surroundings.At the scale of individual CSRs,unpredictable features within each marker turn them into Physical Unclonable functions(PUfs),of great value for secure authentication.Via the machines reading them,CSR markers can thus act as trustworthy yet unobtrusive links between the physical world(buildings,vehicles,packaging...).and its digital twin computer representation.This opens opportunities to address pressing challenges in logistics and supply chain management,recycling and the circular economy,sustainable construction of the built environment,and many other fields of individual,societal and commercial importance.

关键词： spherical steric chiral