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Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches

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Current Zoology 2016年第6期62卷 603-616页

作者： Pierre-Alexandre gAgnAIRE oscar E. gAggIOTTI Universite Montpellier 2 Place Eugene Bataillon 34095 Montpellier Cedex 5 France ISEM - CnRS UMR 5554 SMEL 2 rue des Chantiers Sete 34200 France Scottish Oceans Institute University of St Andrews East Sands St Andrews KY16 9LB UK

Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype-phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.

关键词： local adaptation genome scans quantitative genetics genotype-phenotype association polygenic scores.

Can plasticity make spatial structure irrelevant in individual-tree models?

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Forestry Studies in China 2014年第3期16卷 134-146页

作者： oscar garcia University of northern British Columbia 3333 University WayV2N 4Z9 Prince GeorgeBCCanada

Background： Distance-dependent individual-tree models have commonly been found to add little predictive power to that of distance-independent ones. One possible reason is plasticity, the ability of trees to lean and to alter crown and root development to better occupy available growing space. Being able to redeploy foliage （and roots） into canopy gaps and less contested areas can diminish the importance of stem ground locations. Methods： Plasticity was simulated for 3 intensively measured forest stands, to see to what extent and under what conditions the allocation of resources （e.g., light） to the individual trees depended on their ground coordinates. The data came from 50 x 60 m stem-mapped plots in natural monospecific stands of jack pine, trembling aspen and black spruce from central Canada. Explicit perfect-plasticity equations were derived for tessellation-type models. Results： Qualitatively similar simulation results were obtained under a variety of modelling assumptions. The effects of plasticity varied somewhat with stand uniformity and with assumed plasticity limits and other factors. Stand-level implications for canopy depth, distribution modelling and total productivity were examined. Conclusions： generally, under what seem like conservative maximum plasticity constraints, spatial structure accounted for less than 10% of the variance in resource allocation. The perfect-plasticity equations approximated well the simulation results from tessellation models, but not those from models with less extreme competition asymmetry Whole-stand perfect plasticity approximations seem an attractive alternative to individual-tree models.

关键词： growth and yield Competition Perfect plasticity approximation (PPA) siplab

Integrated site-specific quantification of faecal bacteria and detection of DnA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

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Journal of Oceanology and Limnology 2018年第5期36卷 1629-1642页

作者： oscar Omondi DOnDE TIAn Cuicui XIAO Bangding Key Laboratory of Algal Biology of Chinese Academy of Sciences-Lake Restoration Research group Institute of Hydrobiology Chinese Academy of SciencesWuhan 430072China International College University of Chinese Academy of SciencesBeijing 100049China Egerton University Department of Environmental ScienceP.O.Box 536-20115Egerton-Kenya

The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued ef forts to improve the Faecal Contamination Source Tracking(FCST) techniques such as Microbial Source Tracking(MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DnA markers while accounting for seasonality and weather conditions' eff ects in tracking the major sources of faecal contamination in a freshwater system(Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DnA markers.

关键词： assay contamination faecal bacteria indicator source tracking water quality

Catenoidal Layers for the Allen-Cahn Equation in Bounded Domains

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Chinese Annals of Mathematics,Series B 2017年第1期38卷 13-44页

作者： oscar AgUDELO Manuel DEL PInO Juncheng WEI Department of Mathematics Zapadocescka Univerzita v PlzniPlzenCzech Republic Departamento de Ingenieria Matematica and CMM Universidad de ChileCasilla 170 Correo 3SantiagoChile Department of Mathematics University of British ColumbiaVancouver BC V6T 1Z2Canada

This paper presents a new family of solutions to the singularly perturbed Allen-Cahn equation α~2Δu + u(1- u^2) = 0 in a smooth bounded domain Ω R^3, with neumann boundary condition and α > 0 a small parameter. These solutions have the property that as α→ 0, their level sets collapse onto a bounded portion of a complete embedded minimal surface with finite total curvature intersecting ?Ω orthogonally and that is non-degenerate respect to ?Ω. The authors provide explicit examples of surfaces to which the result applies.

关键词： Allen-Cahn equation Critical minimal surfaces Critical catenoid Infinite dimensional gluing method neumann boundary condition

Effect of rhenium on the microstructure and mechanical behavior of Fe–2.25Cr–1.6W–0.25V-0.1C bainitic steels

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Journal of Materials Science & Technology 2017年第12期33卷 1487-1493页

作者： José Antonio Jiménez Manuel Carsí oscar Antonio Ruano Department of Physical Metallurgy Centro Nacional de lnvestigaciones MetalurgicasC.S.I.CAvda.Gregorio del Amo 828040 MadridSpain

A new ferritic creep resistant steel has been developed by eliminating nb and adding 1.5 mass % Re to a ferritic steel grade T/P23 with the aim of enhancing its mechanical properties at high *** ingots of both steels, new grade and ASTM T/P 23, were hot rolled at 900℃ and then submitted to a thermal treatment consisting of solubilization at 1050℃ and tempering at 700℃. Tempered bainitic microstructures obtained contain second phases reinforcing carbide particles, mainly M_6C and M_（23）C_6 at the boundaries of both, prior austenite grains and bainitic ferrite laths, as well as MC within the grains. Mechanical properties at temperatures ranging from 540 to 600℃ were studied by strain-ratechange tests in compression at strain rates between 10^（-7） and 10^（-4）s^（-1）. These tests showed high stress exponents（n ≥ 20） and activation energies（Q ≈ 400 k J/mol） for both alloys, which were associated with a dislocation movement mechanism with a strong interaction between dislocations and precipitates. On the other hand, a creep exponent of 5 was derived for the stress dependence of minimum creep rate from conventional-type creep tests at 600℃. Although this stress exponent is usually related to a dislocation climb controlled creep mechanism, remarkable microstructural degradation observed with increasing creep time makes difficult to elucidate the true deformation mechanism controlling creep.

关键词： Creep resistant steel T/P23 Thermal treatment Tempered bainite High temperature mechanical properties Creep

Operational definitions and measurement of externalizing behavior problems:An integrative review including research models and clinical diagnostic systems

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World Journal of Psychiatry 2023年第6期13卷 278-297页

作者： Lidia Torres-Rosado oscar M Lozano Manuel Sanchez-garcia Fermín Fernández-Calderón Carmen Diaz-Batanero Department of Clinical and Experimental Psychology University of HuelvaHuelva 21071Spain Research Center for natural Resources Health and EnvironmentUniversity of HuelvaHuelva 21071Spain

Measurement of externalizing disorders such as antisocial disorders,attentiondeficit/hyperactivity disorder or borderline disorder have relevant implications for the daily lives of people with these *** the Diagnostic and Statistical Manual of Mental Disorders(DSM)and the International Classification of Diseases(ICD)have provided the diagnostic framework for decades,recent dimensional frameworks question the categorical approach of psychopathology,inherent in traditional *** and instruments develop under the DSM or ICD framework preferentially adopt this categorical approach,providing diagnostic *** contrast,dimensional measurement instruments provide an individualized profile for the domains that comprise the externalizing spectrum,but are less widely used in *** paper aims to review the operational definitions of externalizing disorders defined under these different frameworks,revise the different measurement alternatives existing,and provide an integrative operational ***,an analysis of the operational definition of externalizing disorders among the DSM/ICD diagnostic systems and the recent Hierarchical Taxonomy of Psychopathology(HiTOP)model is carried ***,in order to analyze the coverage of operational definitions found,a description of measurement instruments among each conceptualization is *** phases in the development of the ICD and DSM diagnosis systems can be observed with direct implications for *** and DSM versions have progressively introduced systematicity,providing more detailed descriptions of diagnostic criteria and categories that ease the measurement instrument ***,it is questioned whether the DSM/ICD systems adequately modelize externalizing disorders,and therefore their *** recent theoretical approaches,such as the HiTOP model seek to overcome some of the criticism raised towards the classification ***,several issues

关键词： Externalizing disorders Measurement Diagnostic and Statistical Manual of Mental Disorders International Classification of Diseases Hierarchical Taxonomy of Psychopathology Psychopathology

Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： oscar gonzalez‑Recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor Alicia nieto‑Valle Monica Castro Almudena Fernandez Dpt.Mejora genetica Animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background genotype-by-sequencing has been proposed as an alternative to SnP genotyping arrays in genomic selection to obtain a high density of markers along the *** requires a low sequencing depth to be cost effective,which may increase the error at the genotype *** generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to *** aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks *** Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank *** LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)*** This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high *** may provide advantages in populations with no available SnP chip,or when a large density of markers with a wide range of allele frequencies is *** addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： genomic selection genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

Latitudinal pattern of the thermal sensitivity of running speed in the endemic lizard Liolaemus multimaculatus

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Integrative Zoology 2022年第4期17卷 619-637页

作者： oscar Aníbal STELLATELLI Laura EVEgA Carolina BLOCK Camila ROCCA Patricio BELLAgAMBA Juan Esteban DAJIL Félix Benjamín CRUZ Instituto de Investigaciones marinas y Costeras(IIMyC) Universidad Nacional de Mar del Plata-CONICETFacultad de Ciencias Exactas y NaturalesMar del PlataArgentina Municipalidad de general Pueyrredón Mar del PlataArgentina Instituto de Investigaciones en Biodiversidad y Medioambiente(InIBIOMA) Universidad Nacional del Comahue-CONICETSan Carlos de BarilocheArgentina

Physiological performance in lizards may be affected by climate across latitudinal or altitudinal *** the coastal dune barriers in central-eastern Argentina,the annual maximum environmental temperature decreases up to 2℃ from low to high latitudes,while the mean relative humidity of the air decreases from 50%to 25%.Liolaemus multimaculatus,a lizard in the family Liolaemidae,is restricted to these coastal *** investigated the locomotor performance of the species at 6 different sites distributed throughout its range in these dune *** inquired whether locomotor performance metrics were sensitive to the thermal regime attributable to *** thermal performance breadth increased from 7%to 82%with latitude,due to a decrease in its critical thermal minimum of up to 5℃ at higher *** from high latitude sites showed a thermal optimum,that is,the body temperature at which maximum speed is achieved,up to 4℃lower than that of lizards from the low *** relatively low temperatures,the maximum running speed of high-latitude individuals was faster than that of low-latitude *** parameters of locomotor performance were labile,decreasing as a function of *** results show populations of *** adjust thermal physiology to cope with local climatic *** suggests that thermal sensitivity responds to the magnitude of latitudinal fluctuations in environmental temperature.

关键词： latitude Liolaemus reptile running speed temperature thermal sensitivity

Serrated colorectal cancer: Molecular classification, prognosis, and response to chemotherapy

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World Journal of gastroenterology 2016年第13期22卷 3516-3530页

作者： oscar Murcia Miriam Juárez Eva Hernández-Illán Cecilia Egoavil mar giner-Calabuig maría Rodríguez-Soler Rodrigo Jover Unidad de gastroenterologia Hospital General Universitario de Alicante Instituto de Investigacion Sanitaria Isabial 03010 Alicante Spain

Molecular advances support the existence of an alternative pathway of colorectal carcinogenesis that is based on the hypermethylation of specific DnA regions that silences tumor suppressor genes. This alternative pathway has been called the serrated pathway due to the serrated appearance of tumors in histological analysis. new classifications for colorectal cancer(CRC) were proposed recently based on genetic profiles that show four types of molecular alterations: BRAF gene mutations, KRAS gene mutations, microsatellite instability, and hypermethylation of Cp g islands. This review summarizes what is known about the serrated pathway of CRC, including CRC molecular and clinical features, prognosis, and response to chemotherapy.

关键词： Colorectal cancer Methylator phenotype Serrated pathway Chemotherapy CIMP