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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 *** article provides a holistic overview of key factors that have influenced GP in plant breeding during this *** delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP *** emphasis was placed on optimizing training population *** explored its benefits and the associated diminishing returns beyond an optimum *** was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization *** 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 *** wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various *** 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 *** 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

Systemic Inflammation Response Index and weight loss as prognostic factors in metastatic pancreatic cancer: A concept study from the PANTHEIA-SEOM trial

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World Journal of Gastrointestinal Oncology 2024年第2期16卷 386-397页

作者： Vilma Pacheco-Barcia Sara Custodio-Cabello Fatima Carrasco-Valero Magda Palka-Kotlowska Axel Mariño-Mendez Alberto Carmona-Bayonas javier Gallego A J Muñoz Martín Paula Jimenez-Fonseca Luis Cabezon-Gutierrez Department of Medical Oncology Hospital Universitario de TorrejonMadrid 28850Spain Department of Internal Medicine Hospital Universitario de TorrejonMadrid 28850Spain Department of Medical Oncology Hospital Universitario Central de AsturiasOviedo 33011Spain Department of Medical Oncology Hospital Universitario Morales MeseguerUniversity of MurciaMurcia 30001Spain Department of Medical Oncology Hospital General Universitario de ElcheElche 03202Spain Department of Medical Oncology Hospital General Universitario Gregorio MarañónUniversidad Complutense MadridMadrid 28007Spain Universidad Francisco de Vitoria Madrid 28223Spain

BACKGROUND The prognostic value of the Systemic Inflammation Response Index(SIRI)in advanced pancreatic cancer is recognized,but its correlation with patients´nutritional status and outcomes remains *** To study the prognostic significance of SIRI and weight loss in metastatic pancreatic *** The PANTHEIA-Spanish Society of Medical Oncology(SEOM)study is a multicentric(16 Spanish hospitals),observational,longitudinal,non-interventional initiative,promoted by the SEOM Real World-Evidence work *** pilot study sought to analyze the association between weight loss and inflammatory status as defined by *** cohort stems from a proof-of-concept pilot study conducted at one of the coordinating *** with pathologically confirmed metastatic pancreatic adenocarcinoma,treated from January 2020 to January 2023,were *** index was calculated using the product of neutrophil and monocyte counts,divided by lymphocyte counts,obtained within 15 days before initiation *** study evaluated associations between overall survival(OS),SIRI and weight *** A total of 50 patients were included.66%of these patients were male and the median age was 66 *** sites:36%liver,12%peritoneal carcinomatosis,10%lung,and 42%multiple *** the first line palliative chemotherapy treatments:50%received gemcitabine plus nab-paclitaxel;28%,modified fluorouracil,leucovorin,irinotecan and oxaliplatin,and 16%were administered gemcitabine.42%had a weight loss>5%in the three months(mo)preceding diagnosis.21 patients with a SIRI≥2.3×10^(3)/L exhibited a trend towards a lower median OS compared to those with a SIRI5%weight loss before diagnosis,the median OS was 6 mo,in contrast to 19 mo for those who did not experience such weight loss(P=0.003).Patients with a weight loss>5%showed higher SIRI *** difference was statistically significant(P<0.000).For pat

关键词： Pancreatic cancer Nutrition Prognostic factor Inflammation Advanced cancer Systemic inflammatory response index Weight loss

Bendamustine and rituximab as frontline therapy in extranodal marginal zone lymphoma:a single-institution experience

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Oncology Research 2024年第6期32卷 1031-1036页

作者： CONSTANTINE N.LOGOTHETIS NATHAN P.HORVAT TONY KURIAN CELESTE BELLO JULIO CHAVEZ LEIDY ISENALUMHE BIJAL SHAH LUBOMIR SOKOL HAYDER SAEED javier PINILLA SAMEH GABALLA Department of Internal Medicine University of South FloridaTampaFL33602USA College of Medicine University of South Florida MorsaniTampaFL33602USA H.Lee Moffitt Cancer Center and Research Institute TampaFL33612USA

Extranodal marginal zone lymphoma(EMZL)encompasses 70%of cases of marginal zone *** bendamustine and rituximab(BR)were derived from trials involving other indolent non-Hodgkin’s *** one trial has evaluated frontline BR prospectively in *** retrospective study reports outcomes among EMZL patients receiving frontline ***-five patients were included with a median age of 69 years(40–81).Five(20.0%)patients had stage Ⅰ/Ⅱ disease,and 20(80.0%)had stage Ⅲ/Ⅳ *** median number of cycles was 6.0(3.0–6.0).Maintenance rituximab was administered to 10(41.7%)*** response rate(ORR)was 100.0%(60.0%complete response,40.0%partial response).Medians of overall survival and progression-free survival were not *** estimated 2-year progression-free survival was 85.2%and overall survival was 100.0%.Four(16.6%)patients had infections related to treatment;3(12.0%)transformed to diffuse large B-cell lymphoma;5(20.8%)had a relapse or progression of EMZL;and 3(12.0%)died unrelated to *** is an efficacious and well-tolerated front-line regimen for EMZL with response data consistent with existing literature.

关键词： Extranodal marginal zone lymphoma Bendamustine Rituximab Front-line therapy

A new oxidative pathway of nitric oxide production from oximes in plants

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Molecular Plant 2024年第1期17卷 178-198页

作者： Pedro Lopez-Gomez javier Buezo Marina Urra Alfonso Cornejo Raquel Esteban Jorge Fernandez de los Reyes Estibaliz Urarte Estefania Rodriguez-Dobreva Alejandro Chamizo-Ampudia Alejandro Eguaras Sebastian Wolf Daniel Marino Victor Martinez-Merino Jose F.Moran Institute for Multidisciplinary Research in Applied Biology(IMAB) Department of SciencesPublic University of Navarre(UPNA)Avda.de Pamplona 12331192 MutilvaSpain Institute for Advanced Materials and Mathematics(INAMAT2) Department of SciencesPublic University of Navarre(UPNA)Campus de Arosadia31006 PamplonaSpain Department of Plant Biology and Ecology University of the Basque Country(UPV/EHU)Sarriena s/nApdo.64448080 BilbaoSpain Center for Plant Molecular Biology(ZMBP) University of TubingenGeschwister-Scholl-Platz72074 TubingenGermany Institute of Natural Resources and Agrobiology of Salamanca(IRNASA) Department of Plant-Microorganism InteractionsSpanish National Research Council(CSIC)Cordel de Merinas40-5237008SalamancaSpain Department of Biochemistry Area of Molecular BiologyVeterinary FacultyUniversity of LeonCampus de Vegazanas/n.24071 LeonSpain

Nitric oxide(NO)is an essential reactive oxygen species and a signal molecule in *** several studies have proposed the occurrence of oxidative NO production,only reductive routes for NO production,such as the nitrate(NO_(3)^(-))-upper-reductase pathway,have been evidenced to date in land ***,plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3−,evidencing the existence of a metabolic pathway for oxidative production of *** hypothesized that oximes,such as indole-3-acetaldoxime(IAOx),a precursor to indole-3-acetic acid,are intermediate oxidation products in NO *** detected the production of NO from IAOx and other oximes catalyzed by peroxidase(POD)enzyme using both 4-amino-5-methylamino-2′,7′-difluorescein fluorescence and *** stimulated the reaction,while superoxide dismutase inhibited ***,mouse NO synthase can also use IAOx to produce NO at a lower rate than *** provided a full mechanism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory *** showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO,while in vivo supplementation of IAOx and other oximes increased the number of lateral roots,as shown for NO donors,and a more than 10-fold increase in IAOx dehydratase ***,we found that in vivo supplementation of IAOx increased NO production in Arabidopsis thaliana wild-type plants,while prx33-34 mutant plants,defective in POD33-34,had reduced *** data show that the release of NO by IAOx,as well as its auxinic effect,explain the superroot ***,our study reveals that plants produce NO utilizing diverse molecules such as oximes,POD,and flavins,which are widely distributed in the plant kingdom,thus introducing a long-awaited oxidative pathway to NO production in plants.T

关键词： ammonium oxidation auxin nitric oxide oxime peroxidase root phenotype

Distribution and Relation of Primes with Tesla Numbers 3, 6, and 9

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Journal of Applied Mathematics and Physics 2024年第4期12卷 1021-1027页

作者： javier Mendoza-Navarrete Huetzin Perez Ismael Ojeda Victor Verdugo Gabriel Luna Sandoval Ricardo Jimenez Garcia Jaime Alvarez Departametno de Matemá ticas CBTis 256 DGETI Cabo San Lucas M&#233xico DCI Departamento de Fisica Mé dica Universidad de Guanajuato Leon M&#233xico Divisió n de Ingenieria en Sistemas Computacionales Tecnol&#243gico Nacional de M&#233xico ITES Los Cabos Cabo San Lucas M&#233xico Departamento de Ingenieria Industrial en Manufactura Universidad Estatal de Sonora Navojoa M&#233xico Departamento de Elé ctrica-Electr&#243nica Tecnol&#243gico Nacional de M&#233xico Campus Mexicali Mexicali M&#233xico Guanajuato M&#233xico

This work presents a different approach to twin primes, an approach from the perspective of the Tesla numbers and gives a refresh and new observation of twin primes that could lead us to an answer to the Twin Prime Conjecture problem. We expose a peculiar relation between twin primes and the generation of prime numbers with Tesla numbers. Tesla numbers seem to be present in so many domains like time, vibration and frequency [1], and the space between twin primes is not the exception. Let us say that twin primes are more than just prime numbers plus 2 or minus 2, and Tesla numbers are more involved with twin primes than we think, and hopefully, this approach give us a better understanding of the distribution of the twin pairs.

关键词： Tesla Numbers Prime Number Twin Prime Numbers Twin Pair

Multi-omic study to unmask genes involved in prostate cancer development in amulti-case family

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Cancer Communications 2024年第3期44卷 443-447页

作者： Lucia Chica-Redecillas Sergio Cuenca-Lopez Eduardo Andres-Leon Laura Carmen Terron-Camero Blanca Cano-Gutierrez Jose Manuel Cozar Jose Antonio Lorente Fernando Vazquez-Alonso Luis javier Martinez-Gonzalez Maria Jesus Alvarez-Cubero GENYO Centre for Genomics and Oncological ResearchPfizerUniversity of GranadaAndalusian Regional GovernmentPTS GranadaGranadaGranadaSpain Department of Biochemistry Molecular Biology III and ImmunologyFaculty of MedicineUniversity of GranadaPTS GranadaGranadaGranadaSpain Bioinformatics Unit Institute of Parasitology and Biomedicine“López-Neyra”Spanish National Research CouncilGranadaGranadaSpain Nursery Service.University Hospital Clínico San Cecilio GranadaGranadaSpain Urology Department University Hospital Virgen de las NievesGranadaGranadaSpain Legal Medicine and Toxicology Department Faculty of MedicineUniversity of GranadaPTS GranadaGranadaGranadaSpain Ibs Biosanitary Research InstituteGranadaGranadaSpain

Dear Editor,Hereditary prostate cancer(PC)comprises 5%-10%of all PC *** increased risk of PC in menwith a family his-tory of the disease is well known and is commonly caused by germline mutations,leading to clinical guidelines men-tioning various genes for identifying high-risk ***,the complex inheritance patterns involvingmul-tiple single nucleotide polymorphisms(SNPs)make it a genetically heterogeneous disease,with genetic testing still in its early stages.

关键词： cancer clinical cases

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Acknowledgements

Advances in Polar Science 2024年第1期35卷 142-142页

作者： Carolina Acosta Hospitaleche javier N.Gelfo Carolina Acosta Hospitaleche and javier N.Gelfo

Acknowledgement to reviewers for Vol.35 No.1 issue The editors of this special volume,along with the Editorial Board and Editorial Office of Advance in Polar Science,wish to express deep gratitude for the time invested and the meticulous revisions carried out by Enrique Bostelmann(Chile),Michael Burns(USA),Rodolfo Coria(Argentina),Jun Ebersole(USA),Jürgen Kriwet(Austria),Guillermo M.López(Argentina),James Parham(USA),Juan Saad(Argentina),Leonardo Salgado(Argentina),Sergio Soto Acuña(Chile),Washington Jones(Uruguay)and seven anonymous reviewers from Argentina,China,Germany,Poland,and USA.

关键词： knowledge invested Saa

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Foreword

Advances in Polar Science 2024年第1期34卷 2-2页

作者： javier N.Gelfo Carolina Acosta Hospitaleche

Motivated by the spirit ignited during the I Provincial Scientific Congress on Antarctica in the city of Ushuaia,in Tierra del Fuego,Antártida e Islas del Atlántico Sur Province,Argentina,convened in October 2022,we proudly introduce this special volume entitled“Past and present climatic change in Antarctica:geological proxies and biological processes”.

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Multi-gigahertz mode-locked femtosecond Yb:KLuW waveguide lasers

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Photonics Research 2022年第11期10卷 2584-2589页

作者： JI EUN BAE XAVIER MATEOS MAGDALENA AGUILÓ FRANCESC DÍAZ javier GARCÍA AJATES CAROLINA romero javier RODRÍGUEZ VÁZQUEZ DE ALDANA FABIAN ROTERMUND Department of Physics Korea Advanced Institute of Science and Technology(KAIST)34141 DaejeonRepublic of Korea Universitat Rovira i Virgili(URV) Fı´sica i Cristal·lografia de Materials i Nanomaterials(FiCMA)43007 TarragonaSpain Grupo de Investigación en Aplicaciones del Láser y Fotónica University of Salamanca37008 SalamancaSpain

We demonstrate multi-gigahertz continuous-wave mode-locking of a Yb:KLuW waveguide laser. A femtosecondlaser-inscribed Yb:KLuW channel waveguide in an extended laser cavity delivers a fundamentally mode-locked laser near 1030 nm. A tunable few-centimeter-long cavity containing a single-walled carbon nanotube saturable absorber as mode-locker generates self-starting femtosecond pulses with average output powers exceeding210 mW at repetition rates of 2.27, 2.69, and 3.55 GHz. The laser cavity, which includes a wedged waveguide,is extended by using a lens pair that controls the laser fluence on the saturable absorber for reliable mode-locked operation without instability. The presented laser performance, mode-locked up to 3.55 GHz, highly suggests the potential of crystalline Yb:KLuW waveguides for realizing high-power ultrafast lasers with higher GHz repetition rates in a quasi-monolithic cavity.

关键词： waveguide femtosecond mode