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| 1 | Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform显示文摘DNA markers play important roles in plant breeding and genetics.The Insertion/Deletion(InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision.However,the canonical way of searching for InDel markers is time-consuming and laborintensive.We developed an end-to-end computational solution(InDel Markers Development Platform,IMDP) to identify genome-wide InDel markers under a graphic pipeline environment.IMDP constitutes assembled genome sequences alignment pipeline(AGA-pipe) and next-generation resequencing data mapping pipeline(NGS-pipe).With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11.Using NGS-pipe,we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4.Combining AGApipe and NGS-pipe,we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern.Polymerase chain reaction(PCR)analysis of subgroup-specific markers indicated that the precision reached 90%(86 of 95).Finally,to make them available to the public,we have integrated the InDels/markers information into a website(Rice InDel Marker Database,RIMD,http://gffzz71b3756633b74a6ehkp9w6qkx69cv660x.ffgz.tsg.suse.edu.cn/).The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers,in addition it can be used in other species with reference genome sequences and NGS data. | Yang L Xiao Cui Rui Li Piaopiao Huang Jie Zong Danqing Yao Gang Li Dabing Zhang Zheng Yuan | 2015 | Journal of Integrative Plant Biology2015，57，11： | 9 |
| 2 | Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing显示文摘Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields. | Xinyao Xia Piaopiao Zhang Linlin He Xingxing Gao Weijun Li Yuanyuan Zhou Zongxin Li Hui Li Long Yang | 2019 | Journal of Integrative Plant Biology2019，61，6： | 3 |
| 3 | Point attention network for point cloud semantic segmentation显示文摘We address the point cloud semantic segmentation problem through modeling long-range dependencies based on the self-attention mechanism.Existing semantic segmentation models generally focus on local feature aggregation.By comparison,we propose a point attention network(PA-Net)to selectively extract local features with long-range dependencies.We specially devise two complementary attention modules for the point cloud semantic segmentation task.The attention modules adaptively integrate the semantic inter-dependencies with long-range dependencies.Our point attention module adaptively integrates local features of the last layer of the encoder with a weighted sum of the long-range dependency features.Regardless of the distance of similar features,they are all correlated with each other.Meanwhile,the feature attention module adaptively integrates inter-dependent feature maps among all local features in the last layer of the encoder.Extensive results prove that our two attention modules together improve the performance of semantic segmentation on point clouds.We achieve better semantic segmentation performance on two benchmark point cloud datasets(i.e.,S3DIS and Scan Net).Particularly,the Io U on 11 semantic categories of S3DIS is significantly boosted. | Dayong REN Zhengyi WU Jiawei LI Piaopiao YU Jie GUO Mingqiang WEI Yanwen GUO | 2022 | Science China(Information Sciences)2022，65，9： | 2 |
| 4 | Trace elements of Carboniferous–Permian coal from the Adaohai Mine, Daqingshan Coalfield, Inner Mongolia, China显示文摘A total of 48 samples of Carboniferous–Permian coal was taken from the Adaohai Mine, Daqingshan Coalfield, Inner Mongolia, China. Cu2 coal is the major coalseam of the Daqingshan Coalfield. The samples were analyzed by the ?nductively coupled plasma–mass spectrometer method.The results indicate the content of V, Cr, Cu, Zn, Ga, Se, Ag,Cd, In, Ba, Pb and U of the Cu2 coals from Adaohai Mine is higher than that of the common Chinese coals. Compared to the world hard coals, the content of V, Cu, Zn, Ga, Se, Sr, Ag,Cd, In, Ba and U is relatively high. Compared to the clark values of the crust, only elements Se, Ag, Pb and Bi are enriched in the coal. Most of the elements in coal benches are lower than in those in roofs and partings. The statistical analysis and clustering analysis showed that the modes of trace elements occurrence for the Cu2 coal correlated positively with the minerals. The values of Sr/Ba show that the coal forming environment was influenced both by sea water and fresh water. | Piaopiao Duan Yanheng Li Teng Guan | 2015 | Chinese Journal Of Geochemistry2015，34，3： | 1 |
| 5 | A comparative investigation on absorption performances of three expanded graphite-based complex materials for toluene显示文摘 | Shande Li Shuanghong Tian Yunfeng Feng Jiajia Lei Piaopiao Wang Ya Xiong | 2010 | Journal of Hazardous Materials2010，，1： | 1 |
| 6 | The interpolating element-free Galerkin method for elastic large deformation problems显示文摘This paper presents an interpolating element-free Galerkin(IEFG) method for solving the two-dimensional(2D) elastic large deformation problems. By using the improved interpolating moving least-squares method to form shape function, and using the Galerkin weak form of 2D elastic large deformation problems to obtain the discrete equations, we obtain the formulae of the IEFG method for 2D elastic large deformation problems. As the displacement boundary conditions can be applied directly, the IEFG method can acquire higher computational efficiency and accuracy than the traditional element-free Galerkin(EFG)method, which is based on the moving least-squares approximation and can not apply the displacement boundary conditions directly. To analyze the influences of node distribution, scale parameter of influence domain and the loading step on the numerical solutions of the IEFG method, three numerical examples are proposed. The IEFG method has almost the same high accuracy as the EFG method, and for some 2D elastic large deformation problems the IEFG method even has higher computational accuracy. | WU Qiang PENG PiaoPiao CHENG YuMin | 2021 | Science China(Technological Sciences)2021，64，2： | 1 |
| 7 | EUS elastography for diagnosis of solid pancreatic masses: a meta-analysis显示文摘 | Mei Mei Jingmei Ni Dan Liu Piaopiao Jin Leimin Sun | 2012 | Gastrointestinal Endoscopy2012，，： | 1 |
| 8 | Enhanced optical nonlinearity in a silicon–organic hybrid slot waveguide for all-optical signal processing显示文摘Silicon photonic integrated devices used for nonlinear optical signal processing play a key role in ultrafast switching,computing,and modern optical communications.However,current devices suffer from limited operation speeds and low conversion efficiencies due to the intrinsically low nonlinear index of silicon.In this paper,we experimentally demonstrate enhanced optical nonlinearity in a silicon–organic hybrid slot waveguide consisting of an ultranarrow slot waveguide coated with a highly nonlinear organic material.The fabricated slot area is as narrow as 45 nm,which is,to the best of our knowledge,the narrowest slot width that has been experimentally reported in silicon slot waveguides.The nonlinear coefficient of the proposed device with a length of 3 mm is measured to be up to 1.43×10^(6) W^(-1)km^(-1).Based on the nanostructure design,the conversion efficiencies of degenerate four-wave mixing showed enhancements of more than 12 dB and 5 dB compared to those measured for an identical device without the organic material and a silicon strip waveguide,respectively.As a proof of concept,all-optical canonical logic units based on the prepared device with two inputs at 40 Gb/s are analyzed.The obtained logic results showed clear temporal waveforms and wide-open eye diagrams with error-free performance,illustrating that our device has great potential for use in high-speed all-optical signal processing and high-performance computing in the nodes and terminals of optical networks. | YONGHUA WANG SU HE XIAOYAN GAO PIAOPIAO YE LEI LEI WENCHAN DONG XINLIANG ZHANG PING XU | 2022 | Photonics Research2022，10，1： | 1 |
| 9 | Injective coloring of planar graphs with girth 5显示文摘A coloring of a graph G is injective if its restriction to the neighbour of any vertex is injective.The injective chromatic number x_(i)(G)of a graph G is the least k such that there is an injective k-coloring.In this paper,we prove that for each planar graph with g≥5 and Δ(G)≥20,xi(G)≤Δ(G)+3. | Yuehua BU Piaopiao YE | 2022 | Frontiers of Mathematics in China2022，17，3： | 0 |
| 10 | Decoupling gene functions from knockout effects by evolutionary analyses显示文摘Genic functions have long been confounded by pleiotropic mutational effects.To understand such genetic effects,we examine HAP4,a well-studied transcription factor in Saccharomyces cerevisiae that functions by forming a tetramer with HAP2,HAP3 and HAP5.Deletion of HAP4 results in highly pleiotropic gene expression responses,some of which are clustered in related cellular processes(clustered effects)while most are distributed randomly across diverse cellular processes(distributed effects).Strikingly,the distributed effects that account for much of HAP4 pleiotropy tend to be non-heritable in a population,suggesting they have few evolutionary consequences.Indeed,these effects are poorly conserved in closely related yeasts.We further show substantial overlaps of clustered effects,but not distributed effects,among the four genes encoding the HAP2/3/4/5 tetramer.This pattern holds for other biochemically characterized yeast protein complexes or metabolic pathways.Examination of a set of cell morphological traits of the deletion lines yields consistent results.Hence,only some deletion effects of a gene support related biochemical understandings with the rest being often pleiotropic and evolutionarily decoupled from the gene’s normal functions.This study suggests a new framework for reverse genetic analysis. | Li Liu Mengdi Liu Di Zhang Shanjun Deng Piaopiao Chen Jing Yang Yunhan Xie Xionglei He | 2020 | National Science Review2020，7，7： | 0 |
| 11 | Improvement Strategy of Street Vitality based on Continuity of Street-side Interface:A Case Study of Minde Road in Nanchang City显示文摘From the perspective of continuous perception and interaction between people and street–sideinterface,the relationship between continuity of street–side interface and street vitality is discussed in thepaper.Taking Minde Road in Nanchang City as an example,the continuity of the interface of Minde Roadis analyzed from the two elements of architectural interface and environmental interface,and the infl uenceof street interface continuity on behavior psychology and activities of people in the street is studied.Themethod of reforming and utilizing street–side interface and enhancing continuity of street–side interface isput forward to realize the improvement of street vitality. | LONG Piaopiao | 2020 | Journal of Landscape Research2020，12，6： | 0 |
| 12 | Dual attention autoencoder for all-weather outdoor lighting estimation显示文摘Accurate outdoor illumination estimation is not easy due to extremely complicated sky appearance and the mutual interference of the sun and sky. In view of these challenges, we present a new deep approach for the estimation of all-weather outdoor illumination. The key to our approach is a novel dual attention autoencoder(DAA) with two independent branches to compress the sun and sky lighting information from an input HDR panorama, respectively. This enables more accurate lighting estimation as evidenced by our experiments since the mutual interference between the sun and sky can be precluded effectively. In DAA,we design the adaptive feature pyramid and the attention module to promote its accuracy in compression.We further develop a sun-sky predictor, a masked network, to learn the sun and sky lighting conditions from an Fo V-limited image. Comprehensive qualitative and quantitative experiments verify the effectiveness of our proposed approach and show its superiority over the state of the arts. | Piaopiao YU Jie GUO Longhai WU Cheng ZHOU Mengtian LI Chenchen WANG Yanwen GUO | 2021 | Science China(Information Sciences)2021，64，11： | 0 |
| 13 | Deep graph learning for spatially-varying indoor lighting prediction显示文摘Lighting prediction from a single image is becoming increasingly important in many vision and augmented reality(AR)applications in which shading and shadow consistency between virtual and real objects should be guaranteed.However,this is a notoriously ill-posed problem,especially for indoor scenarios,because of the complexity of indoor luminaires and the limited information involved in 2D images.In this paper,we propose a graph learning-based framework for indoor lighting estimation.The core is a new lighting model(DSGLight)based on depth-augmented spherical Gaussians(SGs)and a graph convolutional network(GCN)that infers the new lighting representation from a single low dynamic range(LDR)image of limited field-of-view.Our lighting model builds 128 evenly distributed SGs over the indoor panorama,where each SG encodes the lighting and the depth around that node.The proposed GCN then learns the mapping from the input image to DSGLight.Compared with existing lighting models,our DSGLight encodes both direct lighting and indirect environmental lighting more faithfully and compactly.It also makes network training and inference more stable.The estimated depth distribution enables temporally stable shading and shadows under spatially-varying lighting.Through thorough experiments,we show that our method obviously outperforms existing methods both qualitatively and quantitatively. | Jiayang BAI Jie GUO Chenchen WANG Zhenyu CHEN Zhen HE Shan YANG Piaopiao YU Yan ZHANG Yanwen GUO | 2023 | Science China(Information Sciences)2023，66，3： | 0 |
| 14 | A Modified Characteristics Finite Element Method for the Electroneutral Micro-Fluids显示文摘In this paper,a numerical method for the electroneutral micro-fluids based on thefinite element method will be given.In order to deal with the non-linearity of the equation,the modified characteristics method will be used to deal with the tempo-ral derivates term and the convective term.In this way,the non-linear equation can be linearlized.Then,we will give the unconditional stability and optimal error estima-tion.At last,some numerical results are given to show the effectiveness of our method.From the stability analysis we can see that the method is unconditionally stable.The numerical results show that our method is robust. | Zhiyong Si Piaopiao Dong Yunxia Wang | 2022 | Advances in Applied Mathematics and Mechanics2022，14，2： | 0 |
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