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META-R:A software to analyze data from multi-environment plant breeding trials

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The Crop Journal 2020年第5期8卷 745-756页

作者： Gregorio Alvarado Francisco M.rodríguez Angela pacheco Juan Burgueño JoséCrossa Mateo Vargas paulino pérez-rodríguez Marco A.Lopez-Cruz Biometrics and Statistics Unit International Maize and Wheat Improvement Center(CIMMYT)MexicoDF 6-64106600Mexico Centro de Investigación en Matemáticas(CIMAT)A.C. Jalisco S/NCol.ValencianaGuanajuatoGto 40236023Mexico Universidad Autónoma Chapingo Carretera Federal México-Texcoco km 38.5TexcocoMéxico 6356230Mexico Colegio de postgraduados Carretera México-Texcoco Km.36.5MontecilloTexcoco 6356231Mexico Department of plant Soil and Microbial SciencesMichigan State University1066 Bogue StEast LansingMI 48824USA

META-R(multi-environment trial analysis in R)is a suite of R scripts linked by a graphical user interface(GUI)designed in Java *** objective of META-R is to accurately analyze multi-environment plant breeding trials(METs)by fitting mixed and fixed linear models from experimental designs such as the randomized complete block design(RCBD)and the alpha-lattice/lattice ***-R simultaneously estimates the best linear and unbiased estimators(BLUEs)and the best linear and unbiased predictors(BLUps).Additionally,it computes the variance-covariance parameters,as well as some statistical and genetic parameters such as the least significant difference(LSD)at 5%significance,the coefficient of variation in percentage(CV),the genetic variance,and the broad-sense *** parameters are very important in the selection of top performing genotypes in plant ***-R also computes the phenotypic and genetic correlations among environments and between traits,as well as their statistical *** genetic correlations between environments or traits can be visualized in a biplot graph or a tree diagram(dendrogram).Genetic correlations are very important for identifying environments with similar behavior or making indirect selection and identifying the most highly associated ***-R performs multi-environment analyses by using the residual maximum likelihood(REML)method;these analyses can be done by environment,across environments by grouping factors(stress conditions,nitrogen content,etc.)and across environments;the analyses across environments can be done with a pre-defined degree of heritability.

关键词： environments breeding variance

Genomic prediction of the performance of hybrids and the combining abilities for line by tester trials in maize

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The Crop Journal 2022年第1期10卷 109-116页

作者： Ao Zhang paulino pérez-rodríguez Felix San Vicente Natalia palacios-Rojas Thanda Dhliwayo Yubo Liu Zhenhai Cui Yuan Guan Hui Wang Hongjian Zheng Michael Olsen Boddupalli M.prasanna Yanye Ruan Jose Crossa Xuecai Zhang College of Biological Science and Technology Shenyang Agricultural UniversityShenyang 110866LiaoningChina b International Maize and Wheat Improvement Center(CIMMYT) El BatanTexcoco 56237Mexico CIMMYT-China Specialty Maize Research Center Shanghai Academy of Agricultural SciencesShanghai 200063China Colegio de postgraduados Estado De MéxicoMexico Crop Breeding and Cultivation Research Institute Shanghai Academy of Agricultural SciencesShanghai 200063China International Maize and Wheat Improvement Center(CIMMYT) P.O.Box 1041Village MarketNairobi 00621Kenya

The two most important activities in maize breeding are the development of inbred lines with high values of general combining ability(GCA)and specific combining ability(SCA),and the identification of hybrids with high yield *** selection(GS)is a promising genomic tool to perform selection on the untested breeding material based on the genomic estimated breeding values estimated from the genomic prediction(Gp).In this study,Gp analyses were carried out to estimate the performance of hybrids,GCA,and SCA for grain yield(GY)in three maize line-by-tester trials,where all the material was phenotyped in 10 to 11 multiple-location trials and genotyped with a mid-density molecular marker *** showed that the prediction abilities for the performance of hybrids ranged from 0.59 to0.81 across all trials in the model including the additive effect of lines and *** the model including both additive and non-additive effects,the prediction abilities for the performance of hybrids were improved and ranged from 0.64 to 0.86 across all *** prediction abilities of the GCA for GY were low,ranging between-0.14 and 0.13 across all trials in the model including only inbred lines;the prediction abilities of the GCA for GY were improved and ranged from 0.49 to 0.55 across all trials in the model including both inbred lines and testers,while the prediction abilities of the SCA for GY were negative across all *** prediction abilities for GY between testers varied from-0.66 to 0.82;the performance of hybrids between testers is difficult to *** offers the opportunity to predict the performance of new hybrids and the GCA of new inbred lines based on the molecular marker information,the total breeding cost could be reduced dramatically by phenotyping fewer multiple-location trials.

关键词： Maize Genomic selection Line-By-Tester General combining ability Specific combining ability

Elasto-viscoplastic consistent tangent operator concept-based implicit boundary element methods

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Science China(Technological Sciences) 2000年第2期43卷 154-164页

作者：刘勇梁利华 GlaucioH.paulino 1. Institute of Superplasticity and plasticity Zhejiang University of Technology 310014 Hangzhou China 2. Department of Civil and Env. Eng. University of California 95616-5294 Davis CA USA 3. Department of Mechanical Engineering Zhejiang University of Technology 310014 Hangzhou China

An elasto-viscoplastic consistent tangent operator (CTO) concept-based implicit algorithm for nonlinear boundary element methods is presented. Both kinematic and isotropic strain hardening are considered. The elasto-viscoplastic radial return algorithm (RRA) and the elasto-viscoplastic CTO and its related scheme are developed. In addition, the limit cases (e.g. elastoplastic problem) of vis-coplastic RRA and CTO are discussed. Finally, numerical examples, which are compared with the latest FEM results of Ibrahimbegovic et al. and ABAQUS results, are provided.

关键词： boundary element method elasto-viscoplasticity consistent tangent operator (CTO) implicit algorithm computational mechanics.

Heart failure with preserved ejection fraction in the elderly: pathophysiology, diagnostic and therapeutic approach

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Journal of Geriatric Cardiology 2019年第5期16卷 421-428页

作者： Ernesto Ruiz Duque Alexandros Briasoulis paulino A Alvarez Cardiomyopathy Section Cardiology Division University of Iowa

Heart failure with preserved ejection fraction(HFpEF)is a clinical syndrome characterized by symptoms and sings of heart failure with elevated left ventricular filling pressures at rest or during *** is the most common type of heart failure in the elderly and its prevalence increases with age and is higher in females at any given *** is frequently accompanied of comorbid conditions such as diabetes mellitus,obesity,atrial fibrillation and renal *** diagnosis relies in the integration of clinical information,laboratory data and interpretation of cardiac imaging and hemodynamic findings at rest and during *** that have a specific treatment such as coronary artery disease,valvular disease,cardiac amyloidosis and constrictive pericarditis should be considered and evaluated as *** management of comorbidities,optimization of blood pressure control and volume status using diuretics as needed are among the current treatment *** are no specific therapies that have shown to decrease mortality in *** symptomatic patients with history of hospital admission for decompensated heart failure,the implantation of a wireless pulmonary artery pressure monitor should be ***,given the high mortality of this condition,goals of care discussion should be initiated early and involvement of palliative care medicine should be considered.

关键词： Echocardiography Ejection fraction Heart failure pharmacology The elderly

EFFECTS OF SpECTRAL DEpENDENCE IN pASS-THROUGH pHOTON-BASED BIOMEDICAL TRANSILLUMINATION

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Journal of Innovative Optical Health Sciences 2009年第3期2卷 235-244页

作者： paulino VACAS-JACQUES MARIJA STROJNIK GONZALO pAEZ Centro de Investigaciones en Optica Apartado Postal 1-94837000LeonGuanajuatoMexico

We have proposed an interferometric setup for biomedical analysis in transillumination *** dependence of optical properties must be considered for selecting source and sam*** expansion of the sample optical properties,around the central wavelength of emission,serves to account for spectral *** spectral values depend on the central moments of the source,and specific constants associated to the optical properties of the *** matching wavelength characteristics of source and sample,a first-order approximation is *** such case,the expected values are exactly the optical properties evaluated at the central ***,in the first-order approximation,the transillumination interferometer yields the integrated attenuation of the sample at the central wavelength of *** verify the latter assertion by performing a wavelength-dependent Monte Carlo analysis to calculate the response of the transillumination *** attenuation coefficients,for imaging and characterization scenarios,are in agreement with the value computed at the central wavelength of the source.

关键词： Transillumination wavelength-dependent Monte Carlo tissue characterization tissue imaging.

Ballistic response of armour plates using Generative Adversarial Networks

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Defence Technology（防务技术） 2022年第9期18卷 1513-1522页

作者： S.Thompson F.Teixeira-Dias M.paulino A.Hamilton Institute for Infrastructure and Environment(IIE) School of EngineeringThe University of Edinburgh Alexander Graham Bell BuildingThe King's BuildingsEdinburghEH93FGUnited Kingdom School of Engineering Faculty of ScienceEngineering and Built EnvironmentDeakin University Waurn PondsVictoria3220Australia Data Science and AI EngineeringGroup Chief Information O CeLloyds Banking Group69 Morrison StEdinburghEH38BWUnited Kingdom

It is important to understand how ballistic materials respond to impact from projectiles such that informed decisions can be made in the design process of protective armour systems. Ballistic testing is a standards-based process where materials are tested to determine whether they meet protection, safety and performance criteria. For the V50ballistic test, projectiles are fired at different velocities to determine a key design parameter known as the ballistic limit velocity(BLV), the velocity above which projectiles perforate the target. These tests, however, are destructive by nature and as such there can be considerable associated costs, especially when studying complex armour materials and systems. This study proposes a unique solution to the problem using a recent class of machine learning system known as the Generative Adversarial Network(GAN). The GAN can be used to generate new ballistic samples as opposed to performing additional destructive experiments. A GAN network architecture is tested and trained on three different ballistic data sets, and their performance is compared. The trained networks were able to successfully produce ballistic curves with an overall RMSE of between 10 and 20 % and predicted the V50BLV in each case with an error of less than 5 %. The results demonstrate that it is possible to train generative networks on a limited number of ballistic samples and use the trained network to generate many new samples representative of the data that it was trained on. The paper spotlights the benefits that generative networks can bring to ballistic applications and provides an alternative to expensive testing during the early stages of the design process.

关键词： Machine learning Generative Adversarial Networks GAN Terminal ballistics Armour systems

Effects of climate changes on distribution of Eremanthus erythropappus and ***(Asteraceae)in Brazil

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Journal of Forestry Research 2020年第2期31卷 353-364页

作者： Lucas Fernandes Rocha Isaias Emilio paulino do Carmo Joema Souza rodrigues povoa Dulcineia de Carvalho Departamento de Ciencias Florestais Universidade Federal de LavrasLavrasMG CEP 37200-000Brazil Institute of Biosystems Engineering Poznan University of Life SciencesWojska Polskiego 5060-637 PoznanPoland

phylogeographic patterns of endemic species are critical keys to understand its adaptation to future climate ***,based on chloroplast DNA,we analyzed the genetic diversity of two endemic and endangered tree species from the Brazilian savanna and Atlantic forest(Eremanthus erythropappus and Eremanthus incanus).We also applied the climate-based ecological niche modeling(ENM)to evaluate the impact of the Quaternary climate(last glacial maximum*21 kyr Bp(thousand years before present)and Mid-Holocene*6 kyr Bp)on the current haplotype ***,we modeled the potential effect of future climate change on the species distribution in 2070 for the most optimistic and pessimistic *** primer/enzyme combination(SFM/HinfI)revealed polymorphism with very low haplotype diversity,showing only three different *** haplotype 1 has very low frequency and it was classified as the oldest,diverging from six mutations from the haplotypes 2 and *** *** populations are structured and differ genetically according to the areas of *** general,the populations located in the north region are genetically different from those located in the *** genetic structuring was observed for *** ENM revealed a large distribution during the past and a severe decrease in geographic distribution of *** and *** from the LGM until present and predicts a drastic decline in suitable areas in the *** reduction may homogenize the genetic diversity and compromise a relevant role of these species on infiltration of groundwater.

关键词： Ecological niche modeling Genetic diversity Climate change Chloroplast DNA

plant proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal proteins

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Genomics, proteomics & Bioinformatics 2016年第6期14卷 357-370页

作者： Obed Ramirez-Sachez paulino perez-rodriguez Luis Delaye Axel Tiessen Genetic Engineering Department CINVESTAV Unidad IrapuatoIrapuatoCP 36821Mexico Colegio de postgraduados Campus MontecilloTexcocoCP 56230Mexico

protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylo- genetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues （aa）, average protein sizes in plant genomes are smaller than those of animals and fungi. proteins unique to plants are -81 aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by -10 exons of small size [-176 nucleotides （nt）]. Streptophyta have on average only -5.7 exons of medium size （-230 nt）. Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons （〉 400 nt）. Among subcellular compartments, membrane proteins are the largest （-520 aa）, whereas the smallest proteins correspond to the gene ontology group of ribosome （-240 aa）. plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have -34% more but -20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.

关键词： Digital proteome Eukarya Evolution Viridiplantae polypeptide length

Investigation on Muscle Mechanical properties under Compression Loading for Human Body Model Improvement

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Investigation on Muscle Mechanical Properties under Compress...

作者： AYUOL，paulino Onyaw Mayik 湖南大学

学位级别：硕士

本研究的主要目标是探究关于人体肌肉力学性能以及爆炸对人体的影响。肌肉解剖结构研究发现,肌肉有三种类型;一种是肌肉。骨骼肌,平滑肌和心肌。相同的研究证明,肌肉占体重的40%,由70-80%的水,3%的脂肪和10%的胶原蛋白组成。研究了有关... 详细信息

本研究的主要目标是探究关于人体肌肉力学性能以及爆炸对人体的影响。肌肉解剖结构研究发现,肌肉有三种类型;一种是肌肉。骨骼肌,平滑肌和心肌。相同的研究证明,肌肉占体重的40%,由70-80%的水,3%的脂肪和10%的胶原蛋白组成。研究了有关肌肉产生力的机理的理论;他们的实验研究集中在生物力学和力学上,这些理论在肌肉组件中实现,如收缩组件（CC）,串联弹性组件（SEC）和平行弹性组件。另一方面,爆炸伤调查证实,塞波以超音速传播,并随压力,密度和速度而变化。生物学研究表明,爆炸波会以多种方式造成伤害,这些伤害可分为三类。初级伤害,次级伤害和高级伤害。在获得了人腓肠肌,牛和猪后腿的肌肉样品的立方体形状的样品组织后,用福尔马林固定组织不超过24小时以防止组织溶解。实验时,通过MTS E45万能试验机来使用不同的加载率（0.05%,0.50%和5%）和不同的纤维方向（0°,45°和90°）的载荷对样本进行压缩实验。进行有限元仿真时,选择一阶Ogden超弹性材料本构模型和三阶准线性粘弹性（QLV）材料本构模型来对人体肌肉组织的被动行为进行建模。立方体形代表动作说明的3-D模型被证明为骨骼肌组织。Hyper Mesh软件用于实现八个几何节点并创建组件。沿着不同物种具有不同纤维取向的实验曲线的平均值被用作优化材料参数的客观曲线。建立了具有人体模型可用材料参数的仿真结果,并表明由于种类,负载率和纤维取向而导致的肌肉压缩特性的显着差异,并且所有仿真结果均与实验响应良好吻合。

关键词：骨骼肌人类胃肠反向分析有限元仿真参数标识