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integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression

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Journal of Genetics and Genomics 2020年第2期47卷 69-83页

作者： Raoxu Wang Bowen Li Sin Man Lam Guanghou Shui State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology.Chinese Acadmy of SciencesBeijing.100101China University of Chinese Academy of Sciences Beijing100101China Lipidall Technologies Company Limited Changzhou213000China

Mass spectrometry(MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular metabolic phenotypes.The metabolomes of cells,tissues,and organisms comprise a variety of molecules including lipids,amino acids,sugars,organic acids,and so on.Metabolomics mainly focus on the hydrophilic classes,while lipidomics has emerged as an independent omics owing to the complexities of the organismal lipidomes.The potential roles of lipids and small metabolites in disease pathogenesis have been widely investigated in various human diseases,but system-level understanding is largely lacking,which could be partly attributed to the insufficiency in terms of metabolite coverage and quantitation accuracy in current analytical technologies.While scientists are continuously striving to develop high-coverage omics approaches,integration of metabolomics and lipidomics is becoming an emerging approach to mechanistic investigation.integration of metabolome and lipidome offers a complete atlas of the metabolic landscape,enabling comprehensive network analysis to identify critical metabolic drivers in disease pathology,facilitating the study of interconnection between lipids and other metabolites in disease progression.In this review,we summarize omics-based findings on the roles of lipids and metabolites in the pathogenesis of selected major diseases threatening public health.We also discuss the advantages of integrating lipidomics and metabolomics for in-depth understanding of molecular mechanism in disease pathogenesis.

关键词： Metabolomics Lipidomics integration Disease progression

The global integrative network:integration of signaling and metabolic pathways

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aBIOTECH 2022年第4期3卷 281-291页

作者： Yuying Lin Shen Yan Xiao Chang Xiaoquan Qi Xu Chi Department of Dermatology Xuan Wu HospitalBeijing100053China Agricultural Information Institute Chinese Academy of Agricultural ScienceBeijing100081China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing100093China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes.The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis.However,current databases use distinct structures to present signaling and metabolic pathways,which leads to the chaos in the integrated networks.Moreover,for the metabolic pathways,the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes,which hinders the topological analysis of the integrated networks.Here,we propose a novel“meta-pathway”structure,which uses the uniformed structure to display the signaling and metabolic pathways,and resolves the difficulty in linking the metabolic enzymes to the reactions topologically.We compiled a comprehensive collection of global integrative networks(GINs)by merging the meta-pathways of 7077 species.We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human,mouse,Arabidopsis,and rice.Almost all of the nodes were assembled into one major network for each of the four species,which provided opportunities for robust crosstalk and topological analysis,and knowledge graph construction.

关键词： Signaling pathways Metabolic pathways integration Crosstalk of pathways

integration, Quality Assurance, and Usage of Global Aircraft Observations in CRA

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Journal of Meteorological Research 2021年第1期35卷 1-16页

作者： Jie LIAO Huiying WANG Zijiang ZHOU Zhiquan LIU Lipeng JIANG Fang YUAN National Meteorological Information Center China Meteorological AdministrationBeijing 100081China National Center for Atmospheric Research CO 80301USA

This paper presents a detailed description of integration, quality assurance procedure, and usage of global aircraft observations for China's first generation global atmospheric reanalysis(CRA) product(1979–2018). An integration method named "classified integration" is developed. Aircraft observations from nine different sources are integrated into the Integrated Global Meteorological Observation Archive from Aircraft(IGMOAA), a new dataset from the National Meteorological Information Center(NMIC) of the China Meteorological Administration(CMA). IGMOAA consists of global aircraft temperature, wind, and humidity data from the surface to 100 h Pa, extending from 1973 to the present. Compared with observations assimilated in the Climate Forecast System Reanalysis(CFSR) of NCEP,the observation number of IGMOAA increased by 12.9% between 2010 and 2014, mainly as a result of adding more Chinese Aircraft Meteorological Data Relay(AMDAR) data. Complex quality control procedures for aircraft observations of NCEP are applied to detect data errors. Observations are compared with ERA-Interim reanalysis from 1979 to 2018 to investigate data quality of different types and aircraft, and subsequently to develop the blacklists for CRA. IGMOAA data have been assimilated in CRA in 2018 and are real-time updated at the CMA Data-as-a-Service(CMADaa S) platform. For CRA, the fits to observations improve over time. From 1994 to 2018, root-meansquare error(RMSE) of observations relative to CRA background decreases from 1.8 to 1.0℃ for temperature above 300 h Pa, and from 4.5 to 3 m s^(-1) for zonal wind. The RMSE for humidity appears to exhibit an apparent seasonal variation with larger errors in summer and smaller ones in winter.

关键词： aircraft observation integration quality assurance blacklist China's global atmospheric reanalysis(CRA)product

Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy

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Science China(Life Sciences) 2023年第5期66卷 1183-1195页

作者： Shaoqi Chen Bin Duan Chenyu Zhu Chen Tang Shuguang Wang Yicheng Gao Shaliu Fu Lixin Fan Qiang Yang Qi Liu Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic Department of Tongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Department of AI WeBankShenzhen 518055China Translational Medical Center for Stem Cell Therapy and Institution for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China

The rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses.However,the privacy issue has existed but being ignored,since we are limited to access and utilize all the reference datasets distributed in different institutions globally due to the prohibited data transmission across institutions by data regulation laws.To this end,we present scPrivacy,which is the first and generalized automatically single-cell type identification prototype to facilitate single cell annotations in a data privacy-preserving collaboration manner.We evaluated scPrivacy on a comprehensive set of publicly available benchmark datasets for single-cell type identification to stimulate the scenario that the reference datasets are rapidly generated and distributed in multiple institutions,while they are prohibited to be integrated directly or exposed to each other due to the data privacy regulations,demonstrating its effectiveness,time efficiency and robustness for privacy-preserving integration of multiple institutional datasets in single cell annotations.

关键词： preserving integration utilize

Computational Methods for Single-cell Multi-omics integration and Alignment

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 836-849页

作者： Stefan Stanojevic Yijun Li Aleksandar Ristivojevic Lana X.Garmire Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48109USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Amherst College AmherstMA 01002USA

Recently developed technologies to generate single-cell genomic data have made a revolutionary impact in the field of biology.Multi-omics assays offer even greater opportunities to understand cellular states and biological processes.The problem of integrating different omics data with very different dimensionality and statistical properties remains,however,quite challenging.A growing body of computational tools is being developed for this task,leveraging ideas ranging from machine translation to the theory of networks,and represents another frontier on the interface of biology and data science.Our goal in this review is to provide a comprehensive,up-to-date survey of computational techniques for the integration of single-cell multi-omics data,while making the concepts behind each algorithm approachable to a non-expert audience.

关键词： Single-cell Multi-omics Machine learning Unsupervised learning integration

Frequently Used Allopathic and Traditional Medicine for COVID-19 Treatment and Feasibility of Their integration

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Chinese Journal of Integrative Medicine 2022年第11期28卷 1040-1047页

作者： Aditya Upadhayay Gopal Patel Dharm Pal Awanish Kumar Department of Biotechnology National Institute of TechnologyRaipurCG(492010)India Laboratory of Medicinal Plant Biotechnology College of PharmacyZhejiang Chinese Medical UniversityHangzhou(310053)China Department of Chemical Engineering National Institute of TechnologyRaipurCG(492010)India

To date,no satisfactory treatment for COVID-19 is available.This review reported few recent updates regarding the drugs(allopathy/traditional medicines)used for the treatment of COVID-19 concerning clinical studies.Content of the article spotlight the contribution of allopathic and Ayurvedic drugs to the scientific basis for utilization as a potential therapy against COVID-19 infection and provide new insights on the integration of allopathy and traditional medicine.It advocated the combination of these two systems of treatment will ascertain their integrations,and there would be a good possibility and scope for developing a model of integration in the management of COVID-19.Provided discussion may help researchers,physicians,and healthcare policymakers to encourage for effective and integrated use of allopathic and Ayurvedic medicines to control the COVID-19 pandemic more effectively.

关键词： COVID-19 allopathy traditional medicine integration promising therapy

integration of AYUSH and allopathy—pros and cons

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Journal of Integrative Medicine 2019年第1期17卷 1-2页

作者： Preethi Mohan Department of Agada Tantra and Vyavahara Ayurveda(Toxicology Jurisprudence and Forensic Medicine) Amrita School of Ayurveda

1.Introduction These comments are in reference to the article "Awareness, practice and views about integrating AYUSH in allopathic curricu- lum of allopathic doctors and interns in a tertiary care teaching hospital in... 详细信息

关键词： integration AYUSH allopathy--pros and cons

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电子显示纺织品的设计与集成

中国科学:材料科学(英文版) 2023年第10期66卷 3782-3794页

作者：季东晓梁雯宇滕飞李欣欣覃小红 Key Laboratory of Textile Science&Technology Ministry of EducationCollege of TextilesDonghua UniversityShanghai 201620China

显示器是现代电子产品中人与机器交互的重要媒介.将显示器与纺织品相结合,已成为下一代智能可穿戴设备领域备受瞩目的方向之一.然而,从传统的刚性显示器向基于纺织品的柔性显示器过渡面临着诸多挑战,比如对显示器的纺织柔性化设计与精... 详细信息

显示器是现代电子产品中人与机器交互的重要媒介.将显示器与纺织品相结合,已成为下一代智能可穿戴设备领域备受瞩目的方向之一.然而,从传统的刚性显示器向基于纺织品的柔性显示器过渡面临着诸多挑战,比如对显示器的纺织柔性化设计与精确集成技术的要求不断提高.这篇综述将重点概述这一领域最前沿的研究成果,主要涉及发光原理、典型材料以及结构设计的相互关联,其中纺织品和电子显示系统的无缝集成是本文的重点.此外,我们还将探索纺织品电子显示器的预期发展轨迹,并强调纱线发光器件的重要作用,以及微电子工程的集成方法和技术所带来的主要挑战.

关键词： display textiles integration wearable electronics smart yarns electroluminescence

integration of energy recovery network including recycling residual pressure energy with pinch technology

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Chinese Journal of Chemical Engineering 2017年第4期25卷 453-462页

作者： Jianqiang Deng Zheng Cao Dongbo Zhang Xiao Feng School of Chemical Engineering and Technology Xi'an Jiaotong University Shaanxi Coal and Chemical Technology Institute Co. Ltd

Work exchange is a promising innovative technology in recovering residual pressure energy. However, at the systematic level, the comprehensive utilization of different energy resources in an energy system has become an issue of concern. In this work, a systematic approach is proposed, one that successively integrates heat, work and adjusts operation parameters. A detailed procedure for building a heat-work coupling transfer network is provided. The synthesis mainly consists of constructing a work exchange sub-network with pinch analysis based on positive displacement type work exchangers. Simultaneously, another kind of sub-network based on turbine-type work exchangers is built as a schematic comparison. The influence of applying a positive displacement work exchanger on the system is investigated. Finally, as a case study, a renovation design of a typical rectisol process in the coal-water slurry gasification section of an ammonia plant is presented. The results show that the added work exchanger has little impact on the existing heat exchange sub-network. Moreover,extra pressure energy is recovered by coupling the transfer network. It is concluded that the heat-work systematic design is a promising and powerful method to use energy more efficiently.

关键词： integration Process systems Heat exchanger network Work exchange network Pinch technology Optimization