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Highly parallel and efficient single cell mRNA sequencing with paired picoliter chambers

Nature Communications 2020年第1期11卷 2118-2118页

作者： Zhang, Mingxia Zou, Yuan Xu, Xing Zhang, Xuebing Gao, Mingxuan Song, Jia Huang, Peifeng Chen, Qin Zhu, Zhi Lin, Wei Zare, Richard N. Yang, Chaoyong State Key Laboratory of Physical Chemistry of Solid Surfaces The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation Key Laboratory for Chemical Biology of Fujian Province Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China Department of Chemistry Stanford University Stanford 94305 CA United States Hangzhou Weizhu Biological Technology Co. Ltd Hangzhou China Institute of Molecular Medicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China Translational Genomics Research Institute Molecular Medicine Division Phoenix AZ United States Hunan Provincial Key Lab of Emergency and Critical Care Hunan People’s Hospital Changsha China

ScRNA-seq has the ability to reveal accurate and precise cell types and states. Existing scRNA-seq platforms utilize bead-based technologies uniquely barcoding individual cells, facing practical challenges for precious samples with limited cell number. Here, we present a scRNA-seq platform, named Paired-seq, with high cells/beads utilization efficiency, cell-free RNAs removal capability, high gene detection ability and low cost. We utilize the differential flow resistance principle to achieve single cell/barcoded bead pairing with high cell utilization efficiency (95%). The integration of valves and pumps enables the complete removal of cell-free RNAs, efficient cell lysis and mRNA capture, achieving highest mRNA detection accuracy (R = 0.955) and comparable sensitivity. Lower reaction volume and higher mRNA capture and barcoding efficiency significantly reduce the cost of reagents and sequencing. The single-cell expression profile of mES and drug treated cells reveal cell heterogeneity, demonstrating the enormous potential of Paired-seq for cell biology, developmental biology and precision medicine. © 2020, The Author(s).

关键词： Lab-on-a-chip Sequencing RNA sequencing Stem-cell differentiation

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Deep learning based high-resolution incoherent X-ray imaging with a single-pixel detector

arXiv

引用

arXiv 2019年

作者： He, Yu-Hang Zhang, Ai-Xin Li, Ming-Fei Huang, Yi-Yi Quan, Bao-Gang Li, Da-Zhang Wu, Ling-An Chen, Li-Ming Institute of Physics Chinese Academy of Sciences Beijing100191 China University of Chinese Academy of Sciences Beijing100049 China Beijing Institute of Aerospace Control Devices Beijing100039 China Songshan Lake Material Laboratory Guangdong523808 China Institute of High Energy Physics Chinese Academy of Sciences Beijing100049 China IFSA Collaborative Innovation Center Shanghai Jiao Tong University Shanghai200240 China Quantum Engineering Research Center China Aerospace Science and Technology Corporation Beijing100094 China

X-ray "ghost" imaging has drawn great attention for its potential to lower radiation dose in medical diagnosis. For practical implementation, however, the efficiency and image quality have to be greatly improved. Here we demonstrate a computational ghost imaging scheme where a bucket detector and specially designed modulation masks are used, together with a new robust deep learning algorithm in which a compressed set of Hadamard matrices is incorporated into a multi-level wavelet convolutional neural network. By this means we have obtained an image of a real object from only 18.75% of the Nyquist sampling rate, using a portable tabletop incoherent X-ray source of ~37 μ m diameter. A high imaging resolution of ~10 μ m is achieved, which represents a concrete step towards the realization of a practical low cost X-ray ghost imaging camera for applications in biomedicine, archeology, material science, and so forth. Copyright © 2019, The Authors. All rights reserved.

关键词： Deep learning

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Tunable Topological energy Bands in 2D Dialkali-Metal Monoxides

arXiv

引用

arXiv 2019年

作者： Hua, Chenqiang Li, Si Xu, Zhu-An Zheng, Yi Yang, Shengyuan A. Lu, Yunhao Zhejiang Province Key Laboratory of Quantum Technology and Device Department of Physics in Zhejiang University State Key Lab of Silicon Materials School of Materials Science and Engineering in Zhejiang University Hangzhou310027 China School of Physics and Electronics Hunan Normal University ChangshaHunan410081 China Research Laboratory for Quantum Materials in Singapore University of Technology and Design Singapore487372 Singapore Center for Quantum Transport and Thermal Energy Science School of Physics and Technology Nanjing Normal University Nanjing210023 China Zhejiang Province Key Laboratory of Quantum Technology and Device Department of Physics in Zhejiang University Hangzhou310027 China Collaborative Innovation Centre of Advanced Microstructures in Nanjing University Nanjing210093 China

2D materials with nontrivial energy bands are highly desirable for exploring various topological phases of matter, as low dimensionality opens unprecedented opportunities for manipulating the quantum states. Here, it is reported that monolayer (ML) dialkali-metal monoxides, in the well-known 2H-MoS2 type lattice, host multiple symmetry-protected topological phases with emergent fermions, which can be effectively tuned by strain engineering. Based on first-principles calculations, it is found that in the equilibrium state, ML Na2O is a 2D double Weyl semimetal, while ML K2O is a 2D pseudospin-1 metal. These exotic topological states exhibit a range of fascinating effects, including universal optical absorbance, super Klein tunneling, and super collimation effect. By introducing biaxial or uniaxial strain, a series of quantum phase transitions between 2D double Weyl semimetal, 2D Dirac semimetal, 2D pseudospin-1 metal, and semiconductor phases can be realized. The results suggest monolayer dialkali-metal monoxides as a promising platform to explore fascinating physical phenomena associated with novel 2D emergent fermions. Copyright © 2019, The Authors. All rights reserved.

关键词： Phase transitions

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Frontispiece: Bifunctional Catalysts for Reversible Oxygen Evolution Reaction and Oxygen Reduction Reaction

引用

Chemistry – A European Journal 2020年第18期26卷

作者： Xing Wu Prof. Chongjian Tang Prof. Yi Cheng Prof. Xiaobo Min Prof. San Ping Jiang Prof. Shuangyin Wang School of Metallurgy and Environment Central South University Changsha 410083 P. R. China National Engineering Technology Research Center for Control and Treatment of Heavy-metal Pollution Changsha 410083 P. R. China Fuels and Energy Technology Institute & Western Australia School of Mines: Minerals Energy and Chemical Engineering Curtin University Perth WA 6102 Australia Laboratory for Graphene Materials and Devices College of Chemistry and Chemical Engineering Hunan University Changsha 410082 P. R. China

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Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis

iMetaOmics

引用

iMetaOmics 2024年第2期1卷

作者： Salsabeel Yousuf Hao Luo Meiyin Zeng Lei Chen Tengfei Ma Xiaofang Li Maosheng Zheng Xin Zhou Liang Chen Jiao Xi Hongye Lu Huiluo Cao Xiaoya Ma Bian Bian Pengfan Zhang Jiqiu Wu Renyou Gan Baolei Jia Linyang Sun Zhicheng Ju Yunyun Gao Waqar Afzal Malik Chuang Ma Hujie Lyu Yahui Li Huiyu Hou Yuanping Zhou Defeng Bai Yao Wang Haifei Yang Jiani Xun Shengda Du Tianyuan Zhang Xiulin Wan Kai Peng Shanshan Xu Tao Wen Tong Chen Yong-Xin Liu Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China Department of Vascular Surgery Fu Xing Hospital Capital Medical University Beijing China State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems Centre for Grassland Microbiome College of Pastoral Agriculture Science and Technology Lanzhou University Lanzhou Gansu China Centre for Agricultural Resources Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences Shijiazhuang Hebei China College of Environmental Science and Engineering North China Electric Power University Beijing China State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing China Biomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines Beijing Shijitan Hospital Capital Medical University Beijing China College of Natural Resources and Environment Northwest A&F University Yangling Shaanxi China Stomatology Hospital School of Stomatology Zhejiang University School of Medicine Zhejiang Provincial Clinical Research Center for Oral Diseases Key Laboratory of Oral Biomedical Research of Zhejiang Province Cancer Center of Zhejiang University Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province Hangzhou Zhejiang China Department of Microbiology University of Hong Kong Pok Fu Lam Hong Kong China Center for Energy Metabolism and Reproduction Institute of Biomedicine and Biotechnology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen Guangdong China Department of Cardiology Shenzhen Guangming District People's Hospital Shenzhen Guangdong China Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Chiba Japan Innovative Genomics Institute University of California Berkeley C

The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub ( https://***/YongxinLiu/EasyAmplicon ). EasyAmplicon offers a fully automated, user-friendly pipeline for comprehensive amplicon sequencing analysis, seamlessly integrating various bioinformatics tools. The pipeline supports efficient data preprocessing, diversity analysis, and advanced visualization, making high-throughput data analysis accessible to a broader range of researchers. Each step is documented, along with troubleshooting tips and solutions, for users' convenience.

关键词： computational biology EasyAmplicon metagenome microbiome

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State-space model of an inverter-based micro-grid

State-space model of an inverter-based micro-grid

引用

International Conference on Intelligent Green Building and Smart Grid (IGBSG)

作者： Changbin Hu Yang Wang Shanna Luo Fudong Zhang College of Electrical and Control Engineering North China University of Technology Beijing China Collaborative Innovation Center of Key Energy Saving Technologies in Beijing Beijing China State Grid Hebei Electric Power Research Institute Registration Hebei China

In order to describe the micro-grid and its dynamic performance more accurately, the state space models for the micro-grid components and systems have been developed in this paper. Considering about the interaction between inverters and effectiveness of dynamic networks, the state-space model of micro-grid including parallel voltage-controlled inverters has been proposed. Droop control has been adopted in micro-grid to automatically share power and regulate output voltage of parallel voltage-controlled inverters (VCIs) in micro-grids. The dynamic characteristics of the sources, distribution lines and control have been integrated in the developed state space model. The model focus on the detail of the control loops of the inverter but not the switching actions. The state-space model of micro-grid has been verified using Matlab/Simulink simulations.

关键词： Inverters Voltage control State-space methods Current control Mathematical model Load modeling Active filters

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A Novel energy Benchmarking Methodology Based on an Agent-Based Modeling Method

引用

Procedia engineering 2017年 205卷 1725-1732页

作者： Yujian Huang Zhun (Jerry) Yu Jun Li Yaping Zhou Jin Zhou Guoqiang Zhang College of Civil Engineering Hunan University National Center for International Research Collaboration in Building Safety and Environment Hunan University Hunan Collaborative Innovation Center of Building Energy Conservation & Environmental Control Changsha Hunan 410082 China

Occupant behavior has an important impact on building energy use while it was seldom taken into consideration in existing building energy benchmarking studies. This may result in an inaccurate benchmarking value and cause a poor building energy performance evaluation. To overcome the limitation, this paper proposes a novel methodology based on the Agent-based modeling method that was able to mimic real occupant behavior in buildings. To demonstrate its applicability, an Agent-based model was developed for a typical household, in which occupant behavior associated with different appliances has been considered. The simulated energy use was utilized as the benchmarking value to further evaluate the building’s energy-saving potential. The results show that, compared with existing methods, the proposed methodology can provide a more practical and reliable building energy benchmarking value, thereby improving the accuracy of identified energy-saving potential. It is suggested that future research should put more effort into developing a more systematic method with different factors being considered such as socioeconomic factors.

关键词： energy benchmarking Agent-based modeling Occupant behavior energy-saving potential

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The Effect of Temporal Resolution on the Accuracy of Predicting Building Occupant Behaviour based on Markov Chain Models

引用

Procedia engineering 2017年 205卷 1698-1704页

作者： Yaping Zhou Zhun (Jerry) Yu Jun Li Yujian Huang Guoqiang Zhang College of Civil Engineering Hunan University National Center for International Research Collaboration in Building Safety and Environment Hunan University Hunan Collaborative Innovation Center of Building Energy Conservation & Environmental Control Changsha Hunan 410082 China

A key issue associated with the development and application of Markov chain models in building occupancy prediction is how to select temporal resolutions in terms of its effect on prediction accuracy. Here temporal resolutions include both time steps and ChangeTransitionMatrix (i.e., during how many minutes a different transition matrix is used). However, so far few studies have focused on this issue. The primary objective of this paper is to assess the effect of temporal resolutions on the prediction accuracy of Markov chain models. To achieve this objective, we developed Markov chain models based on the UK Time-Use Survey database. Then, the model accuracy based on four commonly-used time steps (10 mins, 20mins, 30mins, 1h) and four different ChangeTransitionMatrix (10 min, 30 min, 1h, 2h) was compared. The results show that temporal resolutions play a crucial role in model performance improvement and should be carefully and reasonably selected. Moreover, it is suggested that future research should put more effort into developing a reliable and systematic method for identifying the optimal temporal resolutions.

关键词： Occupant behaviour Occupancy Markov chain model Temporal resolution Accuracy

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Graphene induced growth of Sb 2 WO 6 nanosheets for high-performance pseudocapacitive lithium-ion storage

引用

Journal of Alloys and Compounds 2020年 839卷

作者： Fei Wang Yong Liu Huijie Wei Guangxin Wang Fengzhang Ren Xianming Liu Min Chen Alex A. Volinsky Shizhong Wei Yan-Bing He Provincial and Ministerial Co-construction of Collaborative Innovation Center for Non-ferrous Metal new Materials and Advanced Processing Technology National Joint Engineering Research Center for Abrasion Control and Molding of Metal Materials Henan Key Laboratory of Non-Ferrous Materials Science & Processing Technology School of Materials Science and Engineering Henan University of Science and Technology Luoyang 471023 PR China Key Laboratory of Function-oriented Porous Materials College of Chemistry and Chemical Engineering Luoyang Normal University Luoyang 471934 PR China School of Materials Science and Energy Engineering Foshan University Foshan 528000 PR China Department of Mechanical Engineering University of South Florida Tampa FL 33620 USA Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen 518055 PR China

Transition metal oxides with the Aurivillius structure have been studied as electrode materials in lithium-ion batteries (LIBs) owing to their high capacity and proper redox voltage. With the opened Aurivillius structure, the antimony tungstate (Sb 2 WO 6 , SWO) constituted of {Sb 2 O 2 } 2n+ and {WO 4 } 2n− is rarely used as negative electrode material for lithium-ion batteries. Herein, the SWO nanosheets/reduced graphene oxide (rGO) hybrid clusters were synthesized, and their electrochemical performances, kinetics and lithium storage mechanism were systematically studied as negative electrode materials for LIBs. Results show that the graphene oxide (GO) not only restricts the growth of layered-structure SWO, but also induces SWO growth along (002) lattice plane and changes SWO particles to SWO nanosheets. The strong interaction between SWO nanosheets and rGO greatly improve conductivity and structure stability of SWO nanosheets/rGO hybrid clusters, which also can efficiently alleviate agglomeration and volume change of SWO nanosheets during cycling. Meanwhile, the dominating pseudocapacitive contribution (78.2% at 0.8 mV s −1 ) effectively enhanced the electrochemical performance. As an anode material for LIBs, the SWO nanosheets/rGO hybrids deliver a high specific capacity of 1141 mAh g −1 at a current density of 0.2 A g −1 , and their specific discharge capacity is 595 mAh g −1 after 130 cycles at 0.2 A g −1 . This work demonstrates that the SWO nanosheets/rGO hybrid clusters are a promising negative electrode material for high-energy-density LIBs.

关键词： Sb 2 WO 6 nanosheets Graphene induced growth Hybrid clusters Pseudocapacitive Anode Lithium-ion batteries

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Near-real-time monitoring of global CO2 emissions reveals the effects of the COVID-19 pandemic (vol 11, 5172, 2020)

引用

NATURE COMMUNICATIONS 2020年第1期11卷 5172页

作者： Liu, Zhu Ciais, Philippe Deng, Zhu Lei, Ruixue Davis, Steven J. Feng, Sha Zheng, Bo Cui, Duo Dou, Xinyu Zhu, Biqing Guo, Rui Ke, Piyu Sun, Taochun Lu, Chenxi He, Pan Wang, Yuan Yue, Xu Wang, Yilong Lei, Yadong Zhou, Hao Cai, Zhaonan Wu, Yuhui Guo, Runtao Han, Tingxuan Xue, Jinjun Boucher, Olivier Boucher, Eulalie Chevallier, Frederic Tanaka, Katsumasa Wei, Yiming Zhong, Haiwang Kang, Chongqing Zhang, Ning Chen, Bin Xi, Fengming Liu, Miaomiao Breon, Francois-Marie Lu, Yonglong Zhang, Qiang Guan, Dabo Gong, Peng Kammen, Daniel M. He, Kebin Schellnhuber, Hans Joachim Department of Earth System Science Tsinghua University Beijing China. zhuliu@***. Laboratoire des Sciences du Climat et de l'Environnement LSCE CEA CNRS UVSQ Centre d'Etudes Orme de Merisiers Gif-sur-Yvette France. Department of Earth System Science Tsinghua University Beijing China. Department of Meteorology and Atmospheric Science The Pennsylvania State University University Park PA USA. Department of Earth System Science University of California Irvine 3232 Croul Hall Irvine CA USA. Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA. Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control Collaborative Innovation Center of Atmospheric Environment and Equipment Technology School of Environmental Science and Engineering Nanjing University of Information Science & Technology Nanjing China. Key Laboratory of Land Surface Pattern and Simulation Institute of Geographical Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China. Climate Change Research Center Institute of Atmospheric Physics Chinese Academy of Sciences Beijing China. Key Laboratory of Middle Atmosphere and Global Environment Observation Institute of Atmospheric Physics Chinese Academy of Sciences Beijing China. School of Environment Tsinghua University Beijing China. School of Mathematical School Tsinghua University Beijing China. Department of Mathematical Sciences Tsinghua University Beijing China. Center of Hubei Cooperative Innovation for Emissions Trading System Wuhan China. Institut Pierre-Simon Laplace Sorbonne Université / CNRS Paris France. Université Paris Dauphine Place du Maréchal de Lattre de Tassigny 75016 Paris France. Center for Energy and Environmental Policy Research Beijing Institute of Technology Beijing China. Department of Electrical Engineering the State Key Lab of Control and Simulation of Power Systems and Generation Equipment Institute for National Governance and G

A Correction to this paper has been published: https://***/10.1038/s41467-020-20254-5

关键词： Climate sciences Atmospheric science Environmental sciences Environmental social sciences

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