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mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies

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Genomics, Proteomics & Bioinformatics 2020年第4期18卷 481-487页

作者： ya-wen zhang Cox Lwaka Tamba yang-Jun wen Pei Li wen-Long Ren Yuan-Li Ni Jun Gao Yuan-Ming zhang Crop Information Center College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Department of Mathematics Egerton UniversityEgerton 536-20115Kenya State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China Department of Epidemiology and Medical Statistics School of Public HealthNantong UniversityNantong 226019China College of Informatics Huazhong Agricultural UniversityWuhan 430070China

Previous studies have reported that some important loci are missed in single-locus genome-wide association studies(GWAS),especially because of the large phenotypic error in field *** solve this issue,multi-locus GWAS methods have been ***,only a few software packages for multi-locus GWAS are ***,we developed an R software named mr MLM *** software integrates mr MLM,FASTmr MLM,FASTmr EMMA,p LARm EB,p KWm EB,and ISIS EM-BLASSO methods developed by our *** are four components in mr MLM v4.0.2,including dataset input,parameter setting,software running,and result *** fread function in *** is used to quickly read datasets,especially big datasets,and the do Parallel package is used to conduct parallel computation using multiple *** addition,the graphical user interface software mr *** v4.0.2,built upon Shiny,is also *** confirm the correctness of the aforementioned programs,all the methods in mr MLM v4.0.2 and three widely-used methods were used to analyze real and simulated *** results confirm the superior performance of mr MLM v4.0.2 to other methods currently *** positive rates are effectively controlled,albeit with a less stringent significance *** MLM v4.0.2 is publicly available at Bio Code(https://***/biocode/tools/BT007077)or R(https://***/web/packages/mr ***/***)as an open-source software.

关键词： Genome-wide association study Linear mixed model mrMLM Multi-locus genetic model R

Enantioselective Reduction of Achiral Ketones with NaBH_4/I_2 Catalyzed by (S)-Ferrocenyl Amino Alcohols

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Chinese Chemical Letters 2002年第10期13卷 931-932页

作者： Wei Yi CHEN Jun LU ya wen zhang Zong Xuan SHEN Department of Chemistry and Chemical Engineering Suzhou UniversitySuzhou 215006

The reduction reagents prepared from sodium borohydride, I-2 and a catalytic amount of chiral ferrocenyl amino alcohols 2a-e have been successfully applied to the enantioselective reduction of ketones. The optically a... 详细信息

关键词： S)-Ferrocenyl amino alcohol asymmetric reduction enantioselective catalysis NaBH4/I2 combination.

A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies

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Molecular Plant 2022年第4期15卷 630-650页

作者： Mei Li ya-wen zhang Ze-Chang zhang Yu Xiang Ming-Hui Liu ya-Hui Zhou Jian-Fang Zuo Han-Qing zhang Ying Chen Yuan-Ming zhang Crop Information Center College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Cotton Biology Anyang 455000China

Although genome-wide association studies are widely used to mine genes for quantitative traits,the effects to be estimated are confounded,and the methodologies for detecting interactions are *** address these issues,the mixed model proposed here first estimates the genotypic effects for AA,Aa,and aa,and the genotypic polygenic background replaces additive and dominance polygenic ***,the estimated genotypic effects are partitioned into additive and dominance effects using a one-way analysis of variance *** strategy was further expanded to cover QTN-by-environment interactions(QEIs)and QTN-by-QTN interactions(QQIs)using the same mixed-model ***,a three-variance-component mixed model was integrated with our multi-locus random-SNP-effect mixed linear model(mrMLM)method to establish a new methodological framework,3VmrMLM,that detects all types of loci and estimates their *** Monte Carlo studies,3VmrMLM correctly detected all types of loci and almost unbiasedly estimated their effects,with high powers and accuracies and a low false positive *** re-analyses of 10 traits in 1439 rice hybrids,detection of 269 known genes,45 known gene-by-environment interactions,and 20 known gene-by-gene interactions strongly validated *** analyses of known genes showed more small(67.49%),minor-allele-frequency(35.52%),and pleiotropic(30.54%)genes,with higher repeatability across datasets(54.36%)and more dominance *** addition,a heteroscedasticity mixed model in multiple environments and dimension reduction methods in quite a number of environments were developed to detect QEIs,and variable selection under a polygenic background was proposed for QQI *** study provides a new approach for revealing the genetic architecture of quantitative traits.

关键词： genome-wide association study QTN QTN-by-environment interaction QTN-by-QTN interaction compressed variance component mixed model rice

ⅢVmrMLM:The R and C++tools associated with 3VmrMLM,a comprehensive GWAS method for dissecting quantitative traits

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Molecular Plant 2022年第8期15卷 1251-1253页

作者： Mei Li ya-wen zhang Yu Xiang Ming-Hui Liu Yuan-Ming zhang College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China

Inmost existingmethods and softwares of genome-wide association studies(GWAS)fordetecting quantitative trait nucleotides(QTNs),QTN-by-environment interactions(QEls),and QTN-by-QTN interactions(QQIs),only the allele substitution effect and its interaction-related effects are detected and estimated,conditional on method-specific polygenic background control,leading to confounding in effect estimation and insufficient polygenic background control(Li et al.,2022;Supplemental Tables 1-3).

关键词： founding GWAS method

Synthetic Effect of Cr and Mo Elements on Microstructure and Properties of Laser Cladding NiCrxMoy Alloy Coatings

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Acta Metallurgica Sinica(English Letters) 2020年第10期33卷 1331-1345页

作者： wen-ya zhang Can-Ming Wang Jing-Xin Ji Xiao-Li Feng Hong-Zhi Cui Qiang Song Chun-Zhi zhang College of Materials Science and Engineering Shandong University of Science and TechnologyQingdao 266590China

NiCrxMoy(x=1,1.5;y=0,0.1,0.3)alloy coatings were prepared on the Q235 substrate by laser cladding under the protection of *** phase composition,microstructure,corrosion behavior,and mechanical properties of the NiCrxMoy alloy coatings were investigated using X-ray diffraction,scanning electron microscopy,transmission electron microscopy,electrochemical tests,X-ray photoelectron spectroscopy,microhardness,and nanoindentation *** the Cr content increased,the phase composition of the coatings changed from a single face-centered cubic(FCC)structure to a dual-phase structure coexisting with body-centered cubic(BCC)and FCC structures,while the addition of Mo promoted the precipitation ofσ*** appearance of a homogeneous dual-phase structure and some amount ofσphase played a positive role in the corrosion resistance of NiCrxMoy ***^3+ ions and Mo^6+ ions in the passive film enhanced the stability of the *** nanoindentation tests showed that the nanohardness(6.71 GPa)and elastic modulus(184.40 GPa)of BCC phase were higher than those of the FCC phase(5.19 GPa and 155.26 GPa,respectively).Overall,the BCC phase andσphase improved the mechanical properties of the coatings.

关键词： NiCrMo coating Laser cladding Corrosion behavior Mechanical properties Q235 substrate

Ultra-small hollow ternary alloy nanoparticles for efficient hydrogen evolution reaction

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National Science Review 2021年第7期8卷 185-197页

作者： Zhenxing Li Chengcheng Yu Yikun Kang Xin zhang yangyang wen Zhao-Kui Wang Chang Ma Cong Wang Kaiwen Wang Xianlin Qu Miao He ya-wen zhang Weiyu Song State Key Laboratory of Heavy Oil Processing College of New Energy and Materials Beijing Key Laboratory of Biogas Upgrading Utilization China University of Petroleum (Beijing) College of Science China University of Petroleum (Beijing) Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Institute of Functional Nano and Soft Materials (FUNSOM) Soochow University Beijing Key Laboratory and Institute of Microstructure and Property of Advanced Materials Beijing University of Technology Beijing National Laboratory for Molecular Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications PKU–HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry College of Chemistry and Molecular Engineering Peking University

Hollow nanoparticles with large specific surface area and high atom utilization are promising catalysts for the hydrogen evolution reaction(HER). We describe herein the design and synthesis of a series of ultra-small hollow ternary alloy nanostructures using a simple one-pot strategy. The same technique was demonstrated for hollow PtNiCu nanoparticles, hollow PtCoCu nanoparticles and hollow CuNiCo nanoparticles. During synthesis, the displacement reaction and oxidative etching played important roles in the formation of hollow structures. Moreover, our hollow PtNiCu and PtCoCu nanoparticles were single crystalline, with an average diameter of 5 nm. Impressively, ultra-small hollow PtNiCu nanoparticles,containing only 10% Pt, exhibited greater electrocatalytic HER activity and stability than a commercial Pt/C catalyst. The overpotential of hollow Pt Ni Cu nanoparticles at 10 mA cm-2was 28 mV versus reversible hydrogen electrode(RHE). The mass activity was 4.54 A mg Pt-1at-70 mV versus RHE, which is 5.62-fold greater than that of a commercial Pt/C system(0.81 A mg Pt-1). Through analyses of bonding and antibonding orbital filling, density functional theory calculations demonstrated that the bonding strength of different metals to the hydrogen intermediate(H*) was in the order of Pt > Co > Ni > Cu. The excellent HER performance of our hollow PtNiCu nanoparticles derives from moderately synergistic interactions between the three metals and H*. This work demonstrates a new strategy for the design of low-cost and high-activity HER catalysts.

关键词： ultra-small hollow nanostructure hydrogen evolution reaction density functional theory

A trefoil-shaped macrocycle with [12]-imidazolium cations

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Chinese Chemical Letters 2022年第10期33卷 4567-4571页

作者： Le zhang Li-Ying Sun Jin-Ping Chang Hui-Yu Xie ya-wen zhang Yi-Fan zhang Ying-Feng Han Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education College of Chemistry and Materials ScienceNorthwest UniversityXi'an 710127China

A trefoil-like two-dimensional(2D)C_(3v) symmetric organic[12]-imidazolium cation H_(12)-2(PF_(6))_(12) featuring three[4]-imidazolium macrocycles was synthesized in three *** reaction of a dodecakis H_(12)-1(PF_(6))_(12) imidazolium salt with Ag_(2)O resulted in the formation of a hexanuclear AgI dodecacarbene assembly[Ag_(6)(1)](PF_(6))_(6).Upon UV irradiation,the photodimerization of the cinnamic ester pendants of[Ag_(6)(1)](PF_(6))_(6) led to the generation of a trefoil-like complex[Ag_(6)(2)](PF_(6))_(6) containing three closed *** of metal ions allowed for the synthesis of the target *** complexes were fully characterized by NMR spectroscopy(^(1)H,^(13)C{^(1)H}and 2D NMR)and high-resolution electrospray ionization mass spectrometry(HR-ESI-MS).

关键词： Trefoil-shaped macrocycle N-Heterocyclic carbenes Photochemical reaction Imidazolium

Boosting the water gas shift reaction on Pt/CeO_(2)-based nanocatalysts by compositional modification: Support doping versus bimetallic alloying

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Journal of Energy Chemistry 2022年第4期31卷 241-249页

作者： Kun Yuan Xiao-Chen Sun Hai-Jing Yin Liang Zhou Hai-Chao Liu Chun-Hua yan ya-wen zhang Beijing National Laboratory for Molecular Sciences(BNLMS) State Key Laboratory of Rare Earth Materials Chemistry and ApplicationsPKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic ChemistryCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China Beijing National Laboratory for Molecular Sciences(BNLMS) State Key Laboratory for Structural Chemistry of Stable and Unstable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871China

The water gas shift reaction is of vital significance for the generation and transition of energy due to the application in hydrogen production and industries such as ammonia synthesis and fuel *** influence of support doping and bimetallic alloying on the catalytic performance of Pt/Ce O_(2)-based nanocatalysts in water gas shift reaction was reported in this *** lanthanide ions and 3d transition metals were respectively introduced into the Ce O_(2)support or Pt to form Pt/Ce O_(2):Ln(Ln=La,Nd,Gd,Tb,Yb)and Pt M/Ce O_(2)(M=Fe,Co,Ni)*** sample of Pt/Ce O_(2):Tb showed the highest activity(TOF at 200℃=0.051 s^(-1))among the Pt/Ce O_(2):Ln and the undoped Pt/Ce O_(2)***,the sample of Pt Fe/Ce O_(2)exhibited the highest activity(TOF at 200℃=0.12 s^(-1))among Pt M/Ce O_(2)*** results of the multiple characterizations indicated that the catalytic activity of Pt/Ce O_(2):Ln catalysts was closely correlated with the amount of oxygen vacancies in doped ceria ***,the different activity of Pt M/Ce O_(2)bimetallic catalysts was owing to the various Pt oxidation states of the bimetals dispersed on *** study of the reaction pathway indicated that both the samples of Pt/Ce O_(2)and Pt/Ce O_(2):Tb catalyzed the reaction through the formate pathway,and the enhanced activity of the latter derived from the increased concentration of oxygen vacancies along with promoted water *** for the sample of Pt Fe/Ce O_(2),its catalytic mechanism was the carboxyl route with a higher reaction rate due to the moderate valence of Pt along with improved CO activation.

关键词： Pt/CeO_(2)catalysts Water–gas shift reaction Support doping Bimetallic alloying

A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an F_(2)population

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Plant Communications 2022年第3期3卷 127-141页

作者： Pei Li Guo Li ya-wen zhang Jian-Fang Zuo Jin-yang Liu Yuan-Ming zhang Crop Information Center College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Institute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjing 210014China

Theoretical and applied studies demonstrate the difficulty of detecting extremely over-dominant and smalleffect genes for quantitative traits via bulked segregant analysis(BSA)in an F_(2)*** address this issue,we proposed an integrated strategy for mapping various types of quantitative trait loci(QTLs)for quantitative traits via a combination of BSA and whole-genome *** this strategy,the numbers of read counts of marker alleles in two extreme pools were used to predict the numbers of read counts of marker *** observed and predicted numbers were used to construct a new statistic,G_(w),for detecting quantitative trait genes(QTGs),and the method was named *** method was significantly better than existing BSA *** the goal was to identify extremely over-dominant and smalleffect genes,another reserved DNA/RNA sample from each extreme phenotype F_(2)plant was sequenced,and the observed numbers of marker alleles and genotypes were used to calculate G_(w)to detect QTGs;this method was named *** simulated and real rice dataset analyses,dQTG-seq2 could identify many more extremely over-dominant and small-effect genes than BSA and QTL mapping ***2 may be extended to other heterogeneous mapping *** significance threshold of G_(w)in this study was determined by permutation *** addition,a handbook for the R software ***,which is available at https://***/web/packages/***/***,has been provided in the supplemental materials for the users’*** study provides a new strategy for identifying all types of QTLs for quantitative traits in an F_(2)population.

关键词： F_(2) bulked segregant analysis dQTG-seq extremely over-dominant gene small-effect gene rice