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VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 320-331页

作者： Dongfang Wang j.n gu MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics Division & Center for Synthetic and Systems BiologyDepartment of Automation Tsinghua University

Single-cell RNA sequencing(scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data(VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.

关键词： Single cell RNA sequencing Deep variational autoencoder Dimension reduction Visualization Dropout

激光去除AH32钢漆层的数值模拟及实验研究

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光电子·激光 2025年第1期36卷 93-99页

作者：张鑫王涛冯伟峰顾志同河北工业大学机械工程学院

采用有限元模拟软件建立激光去除AH32钢表面环氧树脂漆层的数值模型，并在其表面加载脉冲激光清洗过程。探究了不同激光参数对激光去除AH32船用钢表面漆层的温度场影响。模拟结果表明，漆层表面最高温度随光斑中心的移动而变化，其扫描... 详细信息

采用有限元模拟软件建立激光去除AH32钢表面环氧树脂漆层的数值模型，并在其表面加载脉冲激光清洗过程。探究了不同激光参数对激光去除AH32船用钢表面漆层的温度场影响。模拟结果表明，漆层表面最高温度随光斑中心的移动而变化，其扫描轨迹呈彗星状；漆层表面最高温度随光斑直径和扫描速度的增大而减小，随激光重复频率和激光功率的增大而增大，并通过实物清洗实验验证此规律，观察其清洗后的表面形貌，得到当激光功率为28W,光斑直径为0.05 mm,重复频率为50 kHz,扫描速度为1 000 mm/s时，不仅能完全把漆层去除，而且不会损伤基底材料。研究结果为激光清洗船用钢表面漆层提供理论依据和实验参照。

关键词：激光清洗数值模拟 AH32船用钢表面形貌

Evaluating the historical,clinical,and cultural value of the Tian Hui Yi j.an

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j.urnal of Traditional Chinese Medicine 2024年第1期44卷 220-221页

作者： YU Linyong gu Man China Academy of Chinese Medical Sciences Beijing 100700China Institute for History of Medicine and Medical Literature China Academy of Chinese Medical SciencesBeijing 100700China

Tian Hui Yi j.an was compiled by the Tianhui Medical Manuscripts Compilation Group,which includes scholars from the Institute for History of Medicine and Medical Literature of the China Academy of Chinese Medical Sciences(CACMS),Chengdu University of Traditional Chinese Medicine,Chengdu Institute of Cultural Relics and Archaeology,and j.ngzhou Cultural Relics Protection *** was published by the Cultural Relics Press in November *** volume includes images of eight medical manuscripts,along with the Team's annotations,and photographs of a lacquered figurine with meridian-channels and words on its surface.

关键词： surface Chengdu Tian

Effects of thermally pretreated temperature on bio-hydrogen production from sewage sludge

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j.urnal of Environmental Sciences 2006年第1期18卷 6-12页

作者： XIAO ben-yi LIU j.n-xin Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China

Hydrogen can be obtained by anaerobic fermentation of sewage sludge. Therefore, in this paper the effects of thermally pretreated temperatures on hydrogen production from sewage sludge were investigated under different pre-treatment conditions. In the thermal pretreatment, some microbial matters of sludge were converted into soluble matters from insoluble ones. As a result, the suspended solid（SS） and volatile suspended solid（VSS） of sludge decreased and the concentration of soluble COD（SCOD） increased, including soluble carbohydrates and proteins. The experimental results showed that all of those pretreated sludge could produce hydrogen by anaerobic fermentation and the hydrogen yields under the temperatures of 121℃ and 50℃ were 12.23 ml/g VS（most） and 1.17 ml/g VS （least）, respectively. It illuminated that the hydrogen yield of sludge was affected by the thermally pretreated temperatures. Additionally, the endurance of high hydrogen yield depended on the translation of microbial matters and inhibition of methanogens in the sludge. The temperatures of 100℃ and 121℃ （treated time, 30 min） could kill or inhibit completely the methanogens while the others could not. To produce hydrogen and save energy, 100℃ was chosen as the optimal temperature for thermal pretrcatment. The composition changes in liquid phase in the fermentation process were also discussed. The SCOD of sludge increased, which was affected by the pretreatment temperature. The production of volatile fatty acids in the anaerobic fermentation increased with the pretreatment temperature.

关键词： anaerobic fermentation hydrogen production sewage sludge thermally pretreated temperature

Weakening of the anisotropy of surface roughness in ultra-precision turning of single-crystal silicon

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Chinese j.urnal of Aeronautics 2015年第4期28卷 1273-1280页

作者： Wang Minghai Wang ben Zheng Yaohui Key Laboratory of Fundamental Science for National Defense of Aeronautical Digital Manufacturing Process Shenyang Aerospace University School of Mechanical Engineering & Automation Beijing University of Aeronautics & Astronautics

Ultra-precision machining causes materials to undergo a greatly strained deformation process in a short period of *** effect of shear strain rates on machining quality, in particular on surface anisotropy, is a topic deserving of research that has thus far been *** study analyzes the impact of the strain rate during the ultra-precision turning of single-crystal silicon on the anisotropy of surface *** on the establishment of cutting models considering the tool rake angle and the edge radius, this is the first research that takes into account the strain rate dislocation emission criteria in studying the effects of the edge radius, the cutting speed, and the cutting thickness on the plastic deformation of single-crystal *** results of this study show that the uses of a smaller edge radius, faster cutting speeds, and a reduced cutting thickness can result in optimally uniform surface roughness, while the use of a very sharp cutting tool is essential when operating with smaller cutting thicknesses.A further finding is that insufficient plastic deformation is the maj.r cause of increased surface roughness in the ultra-precision turning of brittle *** this basis, we propose that the capacity of single-crystal silicon to emit dislocations be improved as much as possible before brittle fracture occurs, thereby promoting plastic deformation and minimizing the anisotropy of surface roughness in the machined workpiece.

关键词： Anisotropy of surface roughness Cutting speed Edge radius Single-crystal silicon Strain rate Ultra-precision turning Weakening

Particulate matter(PM(2.5)) exposure season-dependently induces neuronal apoptosis and synaptic inj.ries

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j.urnal of Environmental Sciences 2017年第4期29卷 336-345页

作者： Minj.n Chen ben Li Nan Sang College of Environment and Resource Research Center of Environment and HealthShanxi University

Epidemiological studies have shown that particulate matter 2.5（PM（2.5）） not only increases the incidence of cardiopulmonary illnesses but also relates to the development of neurodegenerative diseases. Considering that PM（2.5）is highly heterogeneous with regional disparity and seasonal variation, we investigated whether PM（2.5）exposure induced neuronal apoptosis and synaptic inj.ries in a season-dependent manner. The results indicated that PM（2.5）altered the expression of apoptosis-related proteins（mainly bax and bcl-2）, activated caspase-3 and caused neuronal apoptosis. Additionally, PM（2.5）decreased the levels of synaptic structural protein postsynaptic density（PSD-95） and synaptic functional protein N-methyl-D-aspartate（NMDA） receptor subunit（NR2B） expression. These effects occurred in a season-dependent manner, and PM（2.5）collected from the winter showed the strongest changes. Furthermore, the effect was coupled with the inhibition of phosphorylated extracellular signal-regulated kinase 1/2（p-ERK1/2） and phosphorylated c AMP-response element binding protein（p-CREB）. Based on the findings, we analyzed the correlations between the chemical composition of PM（2.5）samples and the biological effects, and confirmed that winter PM（2.5）played a maj.r role in causing neuronal apoptosis and synaptic inj.ries among different season samples.

关键词： Particulate matter(PM(2.5)) Season-dependent effect Neuronal apoptosis Synaptic inj.ry

A review of the current state of biofuels production from lignocellulosic biomass using thermochemical conversion routes

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Chinese j.urnal of Chemical Engineering 2019年第7期27卷 1523-1535页

作者： Paola Ibarra-Gonzalez ben-guang Rong Department of Chemical Engineering Biotechnology and Environmental Technology University of Southern Denmark

The rapid increase in energy demand,the extensive use of fossil fuels and the urgent need to reduce the carbon dioxide emissions have raised concerns in the transportation *** renewable and sustainable sources have become the ultimate solution to overcome the expected depletion of fossil *** conversion of lignocellulosic biomass to liquid(BtL)transportation fuels seems to be a promising path and presents advantages over first generation biofuels and fossil ***,development of BtL systems is critical to increase the potential of this resource in a sustainable and economic *** of lignocellulosic BtL transportation fuels,such as,gasoline,diesel and j.t fuel can be accomplished through various thermochemical processes and processing *** maj.r steps for the production of BtL fuels involve feedstock selection,physical pretreatment,production of bio-oil,upgrading of bio-oil to transportation fuels and recovery of value-added *** present work is aiming to give a comprehensive review of the current process technologies following these maj.r steps and the current scenarios of biomass to liquid facilities for the production of biofuels.

关键词： Biofuels Lignocellulosic biomass Process route Thermochemical conversion Upgrading Separation

Numerical analysis for impacts of nozzle end-clearances on aerodynamic performance and forced response in a VNT turbine

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Chinese j.urnal of Aeronautics 2018年第5期31卷 1030-1040页

作者： ben ZHAO Leilei WANG Hongj.n HOU Michigan State University East Lansing 48824 USA Hebei University of Engineering Handan 056038 China

It has been well known that nozzle end-clearances in a Variable Nozzle Turbine（VNT）are unfavorable for aerodynamic performance, especially at small openings, and efforts to further decrease size of the clearances are very hard due to thermal expansion. In this paper, both the different sizes of nozzle end-clearances and the various ratios of their distribution at the hub and shroud sides were modelled and investigated by performing 3D Computational Fluid Dynamics（CFD） and Finite Element Analysis（FEA） simulations with a code of transferring the aerodynamic pressure from the CFD results to the FEA calculations. It was found that increasing the size of the nozzle end-clearances divided equally at the hub and shroud sides deteriorates turbine efficiency and turbine wheel reliability, yet increases turbine flow capacity. And, when the total nozzle endclearances remain the same, varying nozzle end-clearances＇ distribution at the hub and shroud sides not only shifts operation point of a VNT turbine, but also affects the turbine wheel vibration *** with nozzle hub clearance, the shroud clearance is more sensitive to both aerodynamic performance and reliability of a VNT turbine. Consequently, a possibility is put forward to improve VNT turbine efficiency meanwhile decrease vibration stress by optimizing nozzle end-clearances＇ distribution.

关键词： Clearance Forced response Mode analysis Performance Reliability Variable Nozzle Turbine(VNT)

Impacts of household living consumption on energy use and carbon emissions in China based on the input–output model

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Advances in Climate Change Research 2020年第2期11卷 118-130页

作者： ZHOU Xiao-Yu gu A-Lun Institute of Energy Environment and EconomyTsinghua UniversityBeijing100084China

China must urgently accelerate its decrease of energy use,optimize its energy structure,reduce CO2 emissions,and promote the early realization of an ecological ***,meeting the growing consumer demand is one of the reasons for the increase in energy *** study investigates the impacts of household consumption on energy use and CO2 emissions from the perspective of the lifestyle of Chinese *** the basis of the input–output model of 30 provinces,we analyze the current situation of energy use and CO2 emissions in different regions(spatial scale)with economic development and income improvement(time scale),investigate the pulling effect of household consumption in different provinces on industrial sectors,examine the influencing factors of indirect CO2 emissions from food,clothing,housing,and transportation in key regions,and explore the policy implications of the transition to a low-carbon lifestyle in different *** show that the fuel structure of Chinese residents should be optimized *** household energy consumption and total CO2 emissions considerably *** 2012,total household energy consumption accounted for nearly 30%of total energy consumption,while indirect CO2 emissions accounted for 66.3%of total household *** regard to the structures of indirect household energy consumption,the housing sector accounted for the largest proportion,reaching 23.4%in indirect energy consumption in *** pulling effect of the housing sector on industrial sectors was also *** decomposition analysis showed that the rapid increase in indirect household CO2 emissions was primarily due to the increase in per capita living *** consumption structures in different provinces produced various impacts,and the energy intensity effect was identified as an important factor for reducing indirect household CO2 emissions.

关键词： Household living consumption CO2 emissions Input–output model Logarithmic mean divisia index(LMDI)decomposition Regional differences