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TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 974-988页

作者： Yiran Shan Qian Zhang Wenbo Guo Yanhong Wu yuxin miao Hongyi Xin Qiuyu Lian Jin Gu MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics DivisionDepartment of AutomationTsinghua UniversityBeijing 100084China UM-SJTU Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China

Sequencing-based spatial transcriptomics(ST)is an emerging technology to study in situ gene expression patterns at the whole-genome ***,ST data analysis is still complicated by high technical noises and low *** addition to the transcriptomic data,matched histopathological images are usually generated for the same tissue sample along the ST *** matched high-resolution histopathological images provide complementary cellular phenotypical information,providing an opportunity to mitigate the noises in ST *** present a novel ST data analysis method called transcriptome and histopathological image integrative analysis for ST(TIST),which enables the identification of spatial clusters(SCs)and the enhancement of spatial gene expression patterns by integrative analysis of matched transcriptomic data and *** devises a histopathological feature extraction method based on Markov random field(MRF)to learn the cellular features from histopathological images,and integrates them with the transcriptomic data and location information as a network,termed *** on TIST-net,SCs are identified by a random walk-based strategy,and gene expression patterns are enhanced by neighborhood *** benchmark TIST on both simulated datasets and 32 real samples against several state-of-the-art *** show that TIST is robust to technical noises on multiple analysis tasks for sequencing-based ST data and can find interesting microstructures in different biological *** is available at http://***/software/tist/and https://***/biocode/tools/BT007317.

关键词： Spatial transcriptomics Multimodal information integration Network-based analysis Spatial cluster identification Gene expression enhancement

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Flour-derived borocarbonitride enriched with boron-oxygen species for the oxidative dehydrogenation of propane to olefins

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Science China Chemistry 2023年第8期66卷 2389-2399页

作者： Dong Li Jingying Bi Zean Xie Lian Kong Bing Liu Xiaoqiang Fan Xia Xiao yuxin miao Zhen Zhao State Key Laboratory of Heavy Oil Processing China University of PetroleumBeijing102249China Institute of Catalysis for Energy and Environment College of Chemistry and Chemical EngineeringShenyang Normal UniversityShenyang110034China Department of Chemical Engineering School of Chemical and Material EngineeringJiangnan UniversityWuxi214122China

The preparation of porous materials by the simple and low-cost methods is one of the hot topics in materials ***,the porous carbon-incorporated BN(P-CBN)was synthesized from the low-cost flour by a fermentation combined with freezedrying technology and ammonolysis.P-CBN-x samples not only maintain the pores of the fermented dough,but also produce abundant oxygen-containing boron species(B-OH,O-O and B-O).Due to the unique structural advantages,P-CBN-x catalysts exhibit remarkably better catalytic performance than bulk BN for the oxidative dehydrogenation of propane(ODHP)to produce ***,P-CBN-23 obtains high C_(3)H_(8 )conversion of 62.1%and olefin yield of 42.7%.In-situ DRIFTS experiments and DFT calculations demonstrate the B-OO-B species in P-CBN-x framework is the most active species for the C3H8activation and the B-O…O-B species can be readily regenerated by O_(2),thus promoting the conversion of propane to olefin.

关键词： flour fermentation carbon-incorporated boron nitrides oxidative dehydrogenation propane

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An integrated approach to site-specific management zone delineation

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Frontiers of Agricultural Science and Engineering 2018年第4期5卷 432-441页

作者： yuxin miao David J.MULLA Pierre C.ROBERT Precision Agriculture Center Department of SoilWater and ClimateUniversity of Minnesota

Dividing fields into a few relatively homogeneous management zones(MZs) is a practical and costeffective approach to precision agriculture. There are three basic approaches to MZ delineation using soil and/or landscape properties, yield information, and both sources of information. The objective of this study is to propose an integrated approach to delineating site-specific MZ using relative elevation, organic matter, slope, electrical conductivity, yield spatial trend map, and yield temporal stability map(ROSE-YSTTS) and evaluate it against two other approaches using only soil and landscape information(ROSE) or clustering multiple year yield maps(CMYYM). The study was carried out on two no-till corn-soybean rotation fields in eastern Illinois, USA. Two years of nitrogen(N) rate experiments were conducted in Field B to evaluate the delineated MZs for site-specific N management. It was found that in general the ROSE approach was least effective in accounting for crop yield variability(8.0%–9.8%), while the CMYYM approach was least effective in accounting for soil and landscape(8.9%–38.1%), and soil nutrient and pH variability(9.4%–14.5%). The integrated ROSE-YSTTS approach was reasonably effective in accounting for the three sources of variability(38.6%–48.9%, 16.1%–17.3% and 13.2%–18.7% for soil and landscape, nutrient and pH, and yield variability, respectively), being either the best or second best approach. It was also found that the ROSE-YSTTS approach was effective in defining zones with high,medium and low economically optimum N rates. It is concluded that the integrated ROSE-YSTTS approach combining soil, landscape and yield spatial-temporal variability information can overcome the weaknesses of approaches using only soil, landscape or yield information,and is more robust for MZ delineation. It also has the potential for site-specific N management for improved economic returns. More studies are needed to further evaluate their appropriateness for precision N

关键词： economically optimum nitrogen rate fuzzy cluster analysis precision nitrogen management site-specific management soil landscape property yield map

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A New Critical Nitrogen Dilution Curve for Rice Nitrogen Status Diagnosis in Northeast China

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Pedosphere 2018年第5期28卷 814-822页

作者： HUANG Shanyu miao yuxin CAO Qiang YAO Yinkun ZHAO Guangming YU Weifeng SHEN Jianning YU Kang Georg BARETH International Center for Agro-Informatics and Sustainable Development College of Resources and Environmental Sciences China Agricultural University Beijing 100193 (China) Institute of Geography University of Cologne K5ln 50923 (Germany) Precision Agriculture Center Department of Soil Water and Climate University of Minnesota St. Paul 55108 (USA) National Engineering and Technology Center for Information Agriculture Nanjing Agricultural University Nanjing 210095 (China) Qixing Farm Jiansanjiang Jiamusi 156399 (China)

In-season diagnosis of crop nitrogen(N) status is crucial for precision N management. Critical N(N_c) dilution curve and N nutrition index(NNI) have been proposed as effective methods to diagnose N status of different crops. The N_c dilution curves have been developed for indica rice in the tropical and temperate zones and japonica rice in the subtropical-temperate zone, but they have not been evaluated for short-season japonica rice in Northeast China. The objectives of this study were to evaluate the previously developed N_c dilution curves for rice in Northeast China and to develop a more suitable N_c dilution curve in this region. A total of17 N rate experiments were conducted in Sanjiang Plain, Heilongjiang Province in Northeast China from 2008 to 2013. The results indicated that none of the two previously developed N_c dilution curves was suitable to diagnose N status of the short-season japonica rice in Northeast China. A new N_c dilution curve was developed and can be described by the equation N_c = 27.7 W^(-0.34) if W ≥ 1 Mg dry matter(DM) ha^(-1) or N_c = 27.7 g kg^(-1) DM if W < 1 Mg DM ha^(-1), where W is the aboveground biomass. This new curve was lower than the previous curves. It was validated using a separate dataset, and it could discriminate non-N-limiting and N-limiting nutritional conditions. Additional studies are needed to further evaluate it for diagnosing N status of different rice cultivars in Northeast China and develop efficient non-destructive methods to estimate NNI for practical applications.

关键词： japonica rice nitrogen nutrition index nitrogen use efficiency plant nitrogen concentration precision nitrogen mana-gement

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Testing a bell-shaped function for estimation of fully expanded leaf area in modern maize under potential production conditions

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The Crop Journal 2018年第5期6卷 527-537页

作者： Xiaoxing Zhen Hui Shao Weina Zhang Weige Huo William David Batchelor Peng Hou Enli Wang Guohua Mi yuxin miao Haigang Li Fusuo Zhang College of Resources and Environmental Sciences China Agricultural UniversityBeijing 100193China Biosystems Engineering Department Auburn UniversityAuburnAL 36849USA Institute of Crop Sciences Chinese Academy of Agricultural SciencesKey Laboratory of Crop Physiology and EcologyMinistry of AgricultureBeijing 100081China CSIRO Agriculture Flagship CanberraACT 2601Australia Department of Soil Water and ClimateMinnesota UniversitySt.PaulMN 55108USA

Accurate leaf area simulation is critical for the performance of crop growth models. Area of fully expanded individual leaves of maize hybrids released before 1995 (defined as old hybrids) has been simulated using a bell-shaped function (BSF) and the relationship between its parameters and total leaf number (TLNO). However, modern high-yielding maize hybrids show different canopy architectures. The function parameters calibrated for old hybrids will not accurately represent modern hybrids. In this study, we evaluated these functions using a dataset including old and modern hybrids that have been widely planted in China in recent years. Maximum individual leaf area (Y_0) and corresponding leaf position (X_0) were not predicted well by TLNO (R^2= 0.56 and R^2= 0.70) for modern hybrids. Using recalibrated shape parameters a and b with values of Y_0 and X_0 for modern hybrids, the BSF accurately predicted individual leaf area (R^2= 0.95–0.99) and total leaf area of modern hybrids (R^2= 0.98). The results show that the BSF is still a robust way to predict the fully expanded leaf area of maize when parameters a and b are modified and Y_0 and X_0 are fitted. Breeding programs have led to increases in TLNO of maize but have not altered Y_0 and X_0, reducing the correlation between Y_0, X_0, and TLNO. For modern hybrids, the values of Y_0 and X_0 are hybrid-specific. Modern hybrids tend to have less-negative values of parameter a and more-positive values of parameter b in the leaf profile. Growth conditions, such as plant density and environmental conditions, also affect the fully expanded leaf area but were not considered in the original published equations. Thus, further research is needed to accurately estimate values of Y_0 and X_0 of individual modern hybrids to improve simulation of maize leaf area in crop growth models.

关键词： Hybrids Leaf area Leaf number Plant density Environmental conditions

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ASD Field Spec3野外便携式高光谱仪诊断冬小麦氮营养

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农业工程学报 2018年第19期34卷 162-169页

作者：刘昌华方征陈志超周兰岳学智王哲王春阳 yuxin miao 河南理工大学测绘与国土信息工程学院焦作454000 中国农业大学资源与环境学院北京100193 Department of Soil Water and Climate University of Minnesota

氮素营养诊断关键在于氮营养指数(nitrogen nutrient index,NNI)预测。对于冬小麦氮营养指数预测模型而言,如何选取预处理方法和建模方法不一而足,不同预处理和模型选取对预测结果精度的影响程度目前还不清楚。该研究以ASD Field Spec3... 详细信息

氮素营养诊断关键在于氮营养指数(nitrogen nutrient index,NNI)预测。对于冬小麦氮营养指数预测模型而言,如何选取预处理方法和建模方法不一而足,不同预处理和模型选取对预测结果精度的影响程度目前还不清楚。该研究以ASD Field Spec3野外便携式高光谱仪采集乐陵市冬小麦冠层高光谱数据,采用10种光谱预处理方法并结合3种模型(偏最小二乘回归、BP神经网络和随机森林算法)建立多种冬小麦氮营养指数高光谱预测模型。对比模型预测精度表明最佳的高光谱建模方法为随机森林算法结合SG卷积平滑预处理所建模型(预测集R2=0.795,RMSE=0.125,RE=11.7%)精度高、可靠性强,是筛选出最佳的冬小麦氮营养指数高光谱预测模型。该研究结果对冬小麦氮营养指数高光谱预测建模具有科学价值,为筛选最优高光谱预处理方法和预测模型提供技术参考。

关键词：光谱分析氮诊断冬小麦模型氮营养指数

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HCCDB v2.0:Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 131-142页

作者： Ziming Jiang Yanhong Wu yuxin miao Kaige Deng Fan Yang Shuhuan Xu Yupeng Wang Renke You Lei Zhang Yuhan Fan Wenbo Guo Qiuyu Lian Lei Chen Xuegong Zhang Yongchang Zheng Jin Gu Eight-Year Program of Clinical Medicine Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics DivisionInstitute for Precision Medicine&Department of AutomationTsinghua UniversityBeijing 100084China Department of Liver Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Fuzhou Institute for Data Technology Fuzhou 350207China University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China International Cooperation Laboratory on Signal Transduction Eastern Hepatobiliary Surgery InstituteSecond Military Medical UniversityShanghai 200438China National Center for Liver Cancer Shanghai 201805China

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma(HCC).Integrated 15 transcriptomic datasets of HCC clinical samples,the first version of HCC database(HCCDB v1.0)was released in *** the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets,it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and *** four years having passed,the database now needs integration of recently published ***,the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial ***,we present HCCDB v2.0,an updated version that combines bulk,single-cell,and spatial transcriptomic data of HCC clinical *** dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples,thereby enhancing the reliability of transcriptomic meta-analysis.A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections,respectively.A novel single-cell level and 2-dimension(sc-2D)metric is proposed as well to summarize cell type-specific and dysregulated gene expression *** are all graphically visualized in our online portal,allowing users to easily retrieve data through a user-friendly interface and navigate between different *** extensive clinical phenotypes and transcriptomic data in the database,we show two applications for identifying prognosis-associated cells and tumor *** v2.0 is available at http://***/database/hccdb2.

关键词： Hepatocellular carcinoma Database Integrative analysis Single-cell RNA sequencing Spatial transcriptomics

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基于双波段作物长势分析仪的东北水稻长势监测

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农业工程学报 2011年第8期27卷 206-210页

作者：李修华李民赞崔笛苗宇新中国农业大学现代精细农业系统集成研究教育部重点实验室北京100083 中国农业大学资源与环境学院北京100083

为了实现水稻精细栽培和变量管理的目的,利用独立开发的双波段作物长势分析仪,进行了水稻生长监测的试验与分析。传感器分别在610与1220nm处测量太阳光与作物冠层反射光的强度,进而计算光谱反射率。利用双波段作物长势分析仪于2008年在... 详细信息

为了实现水稻精细栽培和变量管理的目的,利用独立开发的双波段作物长势分析仪,进行了水稻生长监测的试验与分析。传感器分别在610与1220nm处测量太阳光与作物冠层反射光的强度,进而计算光谱反射率。利用双波段作物长势分析仪于2008年在黑龙江省农垦总局建三江分局2处水稻试验田,在分蘖期与抽穗早期进行了氮肥胁迫试验,结果表明水稻叶片氮浓度及生物质干质量与RVI、NDVI都具有很高的相关性,但与NDVI的相关性比与RVI的更高。分蘖期的测量结果表明,NDVI与施肥量的相关性非常显著,R2大于0.94。但NDVI并不与施肥量成线性相关,过量的施氮量反而会引起NDVI值的降低。分蘖期、抽穗早期的NDVI值都与最终产量有着显著的相关,其中抽穗早期的NDVI与产量的决定系数(R2)达到了0.96。分析结果显示利用双波段作物长势分析仪监测水稻冠层,可达到控制投入和提高产量的目的,为水稻的精细栽培提供理论与技术支持。

关键词：监测氮肥作物 RVI NDVI 氮肥胁迫长势

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ORC低温发电系统试验站设计及优化

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中国科技纵横 2022年第2期 56-60页

作者：苗宇欣丹东克隆集团有限责任公司辽宁丹东 118000

本文主要介绍了ORC低温发电系统试验站构成,对ORC低温发电试验过程中的问题进行分析,综合评价试验效果,总结试验不足,从不同的专业角度给出更好的问题解决方案及改造建议,使系统进一步在功能上、结构上得到优化、提升,为实现设备大规模... 详细信息

本文主要介绍了ORC低温发电系统试验站构成,对ORC低温发电试验过程中的问题进行分析,综合评价试验效果,总结试验不足,从不同的专业角度给出更好的问题解决方案及改造建议,使系统进一步在功能上、结构上得到优化、提升,为实现设备大规模生产制造提供可靠、有效的数据支持.

关键词：低温余热回收双循环换热螺杆膨胀机系统优化

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产教融合视野下高校“双创”教育共同体的构建

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淮南职业技术学院学报 2021年第5期21卷 87-88页

作者：苗雨昕闽江师范高等专科学校福州350108

产教融合作为一种高校、科研、企业深入融合的新型教学模式,积极实现产教融合视野下高校“双创”教育共同体构建,对于培养新时代“双创”优秀人才、促进高校产教融合一体化发展、切实提升高校双创教育活动的规范性等诸多方面都具有无比... 详细信息

产教融合作为一种高校、科研、企业深入融合的新型教学模式,积极实现产教融合视野下高校“双创”教育共同体构建,对于培养新时代“双创”优秀人才、促进高校产教融合一体化发展、切实提升高校双创教育活动的规范性等诸多方面都具有无比重要的促进意义。分析了于产教融合视野下高校“双创”教育共同体构建存在的问题,提出了构建高校“双创”教育共同体的路径。

关键词：产教融合高校“双创” 教育共同体人才培养

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