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BnVIR:bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

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Molecular Plant 2022年第5期15卷 779-782页

作者： Zhiquan yang Congyuan Liang LuLu Wei Shengbo Wang Feifan Yin Dongxu Liu Liang Guo yongming Zhou qing-yong yang National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China

Dear Editor,Genetic variations,which range from single nucleotide polymor-phisms(SNPs)and short insertion/deletions(InDels)to large-scale structural variations(SVs),are the basis of phenotypic diversity.Understanding the effect of genetic variations on traits is critical for uncovering the genetic architecture of various phe-notypes.

关键词： agronomic traits InDel

BnlR:A multi-omics database with various tools for Brassica napus research and breeding

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Molecular Plant 2023年第4期16卷 775-789页

作者： Zhiquan yang Shengbo Wang Lulu Wei Yiming Huang Dongxu Liu Yupeng Jia Chengfang Luo Yuchen Lin Congyuan Liang Yue Hu Cheng Dai Liang Guo yongming Zhou qing-yong yang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510405China

In the post-genome-wide association study era,multi-omics techniques have shown great power and poten-tial for candidate gene mining and functional genomics research.However,due to the lack of effective data integration and multi-omics analysis platforms,such techniques have not still been applied widely in rape-seed,an important oil crop worldwide.Here,we report a rapeseed multi-omics database(BnlR;http:/l ***/BnlR),which provides datasets of six omics including genomics,transcriptomics,variomics,epigenetics,phenomics,and metabolomics,as well as numerous"variation-gene expression-phenotype"associations by using multiple statistical methods.In addition,a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these datasets.BnlR is the most comprehensive multi-omics database for rapeseed so far,and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

关键词： Brassica napus multi-omics database candidate gene mining functional genomics

Genome-and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

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Molecular Plant 2021年第3期14卷 470-487页

作者： Shan Tang Hu Zhao Shaoping Lu Liangqian Yu Guofang Zhang Yuting Zhang qing-yong yang yongming Zhou Xuemin Wang Wei Ma Weibo Xie Liang Guo National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhanChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhanChina Department of Biology University of Missouri-St.LouisSt.LouisMO 63121USA Donald Danforth Plant Science Center St.LouisMO 63132USA School of Biological Sciences Nanyang Technological UniversitySingapore 637551Singapore

Seed oil content(SOC)is a highly important and complex trait in oil crops.Here,we decipher the genetic basis of natural variation in SOC of Brassica napus by genome-and transcriptome-wide association studies using 505 inbred lines.We mapped reliable quantitative trait loci(QTLs)that control SOC in eight environments,evaluated the effect of each QTL on SOC,and analyzed selection in QTL regions during breeding.Six-hundred and ninety-two genes and four gene modules significantly associated with SOC were identified by analyzing population transcriptomes from seeds.A gene prioritization framework,POCKET(prioritizing the candidate genes by incorporating information on knowledge-based gene sets,effects of variants,genome-wide association studies,and transcriptome-wide association studies),was implemented to determine the causal genes in the QTL regions based on multi-omic datasets.A pair of homologous genes,BnPMT6s,in two QTLs were identified and experimentally demonstrated to negatively regulate SOC.This study provides rich genetic resources for improving SOC and valuable insights toward understanding the complex machinery that directs oil accumulation in the seeds of B.napus and other oil crops.

关键词： Brassica napus seed oil content QTL GWAS TWAS gene module

Dynamic SLAM Visual Odometry Based on Instance Segmentation:A Comprehensive Review

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Computers, Materials & Continua 2024年第1期78卷 167-196页

作者： Jiansheng Peng qing yang Dunhua Chen Chengjun yang yong Xu yong Qin College of Automation Guangxi University of Science and TechnologyLiuzhou545000China Department of Artificial Intelligence and Manufacturing Hechi UniversityHechi547000China

Dynamic Simultaneous Localization and Mapping(SLAM)in visual scenes is currently a major research area in fields such as robot navigation and autonomous driving.However,in the face of complex real-world envi-ronments,current dynamic SLAM systems struggle to achieve precise localization and map construction.With the advancement of deep learning,there has been increasing interest in the development of deep learning-based dynamic SLAM visual odometry in recent years,and more researchers are turning to deep learning techniques to address the challenges of dynamic SLAM.Compared to dynamic SLAM systems based on deep learning methods such as object detection and semantic segmentation,dynamic SLAM systems based on instance segmentation can not only detect dynamic objects in the scene but also distinguish different instances of the same type of object,thereby reducing the impact of dynamic objects on the SLAM system’s positioning.This article not only introduces traditional dynamic SLAM systems based on mathematical models but also provides a comprehensive analysis of existing instance segmentation algorithms and dynamic SLAM systems based on instance segmentation,comparing and summarizing their advantages and disadvantages.Through comparisons on datasets,it is found that instance segmentation-based methods have significant advantages in accuracy and robustness in dynamic environments.However,the real-time performance of instance segmentation algorithms hinders the widespread application of dynamic SLAM systems.In recent years,the rapid development of single-stage instance segmentationmethods has brought hope for the widespread application of dynamic SLAM systems based on instance segmentation.Finally,possible future research directions and improvementmeasures are discussed for reference by relevant professionals.

关键词： Dynamic SLAM instance segmentation visual odometry

A Convenient Heterogeneous Reduction of Knoevenagel Product by Hantzsch Ester and Its Development into Reductive Alkylation of Malononitrile

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Chinese Journal of Chemistry 2014年第7期32卷 650-653页

作者： yong-qing yang Zheng Lu School of Pharmacy Jiangsu UniversityZhenjiangJiangsu 212013China

Poor solubility of Hantzsch ester is used as indicator in the reduction of methylidene malononitrile.The Knoevenagel reaction is integrated to develop a reductive alkylation of malononitrile with aryl and aliphatic al... 详细信息

关键词： heterogeneous reduction Hantzsch ester Knoevenagel condensation reductive alkylation

Biogenic volatile organic compounds dominated the near-surface ozone generation in Sichuan Basin,China,during fall and wintertime

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Journal of Environmental Sciences 2024年第7期141卷 215-224页

作者： Dasheng Huang qing Li Yan Han Shi-yong Xia Jiawei Zhou Hanxiong Che Keding Lu Fumo yang Xin Long yang Chen Research Center for Atmospheric Environment Chongqing Institute of Green and Intelligent TechnologyChinese Academy of SciencesChongqing 400714China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China College of Resources and Environment Chongqing SchoolUniversity of the Chinese Academy of Sciences(UCAS Chongqing)Chongqing 400714China College of Environmental and Chemical Engineering Chongqing Three Gorges UniversityChongqing 404199China Key Laboratory for Urban Habitat Environmental Science and Technology School of Environment and EnergyPeking University Shenzhen Graduate SchoolLishui RoadNanshan DistrictShenzhen 518055China SKL-ESPC and BIC-ESAT College of Environmental Sciences and EngineeringPeking UniversityBeijing 100871China College of Architecture&Environment Sichuan UniversityChengdu 610065China

The complex air pollution driven by both Ozone(O_(3))and fine particulate matter(PM2.5)sig nificantly influences the air quality in the Sichuan Basin(SCB).Understanding the O_(3)for mation during autumn and winter is necessary to understand the atmospheric oxidative capacity.Therefore,continuous in-site field observations were carried out during the late summer,early autumn and winter of 2020 in a rural area of Chongqing.The total volatile organic compounds(VOCs)concentration reported by a Proton-Transfer-Reaction Time-of Flight Mass Spectrometry(PTR-ToF-MS)were 13.66±9.75 ppb,5.50±2.64 ppb,and 9.41±5.11 ppb in late summer,early autumn and winter,respectively.The anthropogenic VOCs(AVOCs)and biogenic VOCs(BVOCs)were 8.48±7.92 ppb and 5.18±2.99 ppb in late sum mer,3.31±1.89 ppb and 2.19±0.93 ppb in autumn,and 6.22±3.99 ppb and 3.20±1.27ppb in winter.A zero-dimensional atmospheric box model was employed to investigate the sensitivity of O_(3)-precursors by relative incremental reactivity(RIR).The RIR values of AV OCs,BVOCs,carbon monoxide(CO),and nitrogen oxides(NOx)were 0.31,0.71,0.09,and-0.36 for late summer,0.24,0.59,0.22,and-0.38 for early autumn,and 0.30,0.64,0.33 and-0.70 for winter,and the results showed that the O_(3)formation of sampling area was in the VOC-limited region,and O_(3)was most sensitive to BVOCs(with highest RIR values,>0.6)This study can be helpful in understanding O_(3)formation and interpreting the secondary formation of aerosols in the winter.

关键词： VOCs PTR-MS Model Ozone

Ultra‑Efficient and Cost‑Effective Platinum Nanomembrane Electrocatalyst for Sustainable Hydrogen Production

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Nano-Micro Letters 2024年第6期16卷 95-110页

作者： Xiang Gao Shicheng Dai Yun Teng qing Wang Zhibo Zhang Ziyin yang Minhyuk Park Hang Wang Zhe Jia Yunjiang Wang yong yang Department of Mechanical Engineering College of EngineeringCity University of Hong KongTat Chee AvenueKowloon TongKowloonHong KongPeople’s Republic of China State Key Laboratory of Nonlinear Mechanics Institute of MechanicsChinese Academy of SciencesBeijingPeople’s Republic of China School of Engineering Science University of Chinese Academy of SciencesBeijingPeople’s Republic of China Laboratory for Microstructures Institute of MaterialsShanghai UniversityShanghaiPeople’s Republic of China School of Materials Science and Engineering Jiangsu Key Laboratory for Advanced Metallic MaterialsSoutheast UniversityNanjingPeople’s Republic of China Department of Materials Science and Engineering College of EngineeringCity University of Hong KongTat Chee AvenueKowloon TongKowloonHong KongPeople’s Republic of China

Hydrogen production through hydrogen evolution reaction(HER)offers a promising solution to combat climate change by replacing fossil fuels with clean energy sources.However,the widespread adoption of efficient electrocatalysts,such as platinum(Pt),has been hindered by their high cost.In this study,we developed an easy-to-implement method to create ultrathin Pt nanomembranes,which catalyze HER at a cost significantly lower than commercial Pt/C and comparable to non-noble metal electrocatalysts.These Pt nanomembranes consist of highly distorted Pt nanocrystals and exhibit a heterogeneous elastic strain field,a characteristic rarely seen in conventional crystals.This unique feature results in significantly higher electrocatalytic efficiency than various forms of Pt electrocatalysts,including Pt/C,Pt foils,and numerous Pt singleatom or single-cluster catalysts.Our research offers a promising approach to develop highly efficient and cost-effective low-dimensional electrocatalysts for sustainable hydrogen production,potentially addressing the challenges posed by the climate crisis.

关键词： Platinum Hydrogen evolution reaction Lattice distortion Heterogeneous strain

Significantly Enhanced Energy Storage Performances of PEI-based Composites Utilizing Surface Functionalized ZrO_(2) Nanoparticles for High-Temperature Application

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Chinese Journal of Polymer Science 2024年第3期42卷 322-332,I0006页

作者： qing-qing Liu Qiu-Hao Lin Xiao-Dong Qi Nan Zhang Ting Huang Jing-Hui yang yong Wang School of Chemistry Southwest Jiaotong UniversityChengdu 610031China Key Laboratory of Advanced Technologies of Materials Ministry of Education of ChinaSouthwest Jiaotong UniversityChengdu 610031China

Polymer dielectrics with a high energy density and an available energy storage capacity have been playing an important role in advanced electronics and power systems. Nevertheless, the use of polymer dielectrics in harsh environments is limited by their low energy density at high temperatures. Herein, zirconium dioxide(ZrO_(2)) nanoparticles were decorated with amino group utilizing 4,4-methylenebis(phenyl isocyanate)(AMEO) and successfully incorporated into polyetherimide(PEI) matrix. The dielectric properties, breakdown strength, and energy storage performances of PEI/ZrO_(2)-AMEO nanocomposites were investigated from 25 ℃ to 150 ℃. It is found that the combination of moderate bandgap ZrO_(2) with modest dielectric constant and polar groups at interface with deep trap can offer an available strategy to simultaneously increase the dielectric constant and breakdown strength of polymer dielectrics. As a result, the composites containing ZrO_(2)-AMEO exhibit excellent energy storage performance at elevated temperatures. Specially, the PEI-based composites with 3 vol% ZrO_(2)-AMEO display a maximum discharged energy density(U_(d)) of 3.1 J/cm^(3) at 150 ℃, presenting 90% higher than that of neat PEI. This study may help to better develop the polymer-based dielectric composite applied at elevated temperatures.

关键词： Polyetherimide High temperature dielectric ZrO_(2) Interface

Advanced organic electrode materials for aqueous rechargeable batteries

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Science China Chemistry 2024年第1期67卷 137-164页

作者： Gaojing yang Yaxun Zhu Qi Zhao Zhimeng Hao yong Lu qing Zhao Jun Chen Frontiers Science Center for New Organic Matter Key Laboratory of Advanced Energy Materials Chemistry(Ministry of Education)College of ChemistryNankai UniversityTianjin 300071China

Organic electrode materials take advantages of potentially sustainable production and structural tunability compared with present commercial inorganic electrode materials.However,their applications in traditional rechargeable batteries with nonaqueous electrolytes suffer from the premature failure and safety concerns.In comparison,aqueous rechargeable batteries based on organic electrode materials have received extensive attentions in recent years for low-cost and sustainable energy storage systems due to their inherent safety.This review aims to provide a comprehensive summary on the recent progress in advanced organic electrode materials for aqueous rechargeable batteries.We start from the overview of working principles and general design strategies of organic electrode materials in aqueous rechargeable batteries.Then the research advances of organic electrode materials in various aqueous rechargeable batteries are highlighted in terms of charge carriers(monovalent ions,multivalent ions,and anions).We emphasized the characteristics of organic electrode materials in various charge carriers.Finally,the critical challenges and future efforts of aqueous organic rechargeable batteries are discussed.More organic electrode materials with better electronic conductivity and fast reaction kinetics are still needed to build advanced aqueous batteries for commercial applications.

关键词： organic electrode materials aqueous batteries organic batteries rechargeable batteries