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Single-cell technologies:From research to application

The Innovation 2022年第6期3卷 92-108页

作者： Lu Wen Guoqiang Li Tao Huang Wei Geng Hao Pei Jialiang Yang Miao Zhu Pengfei Zhang Rui Hou Geng Tian Wentao Su Jian Chen Dake Zhang Pingan Zhu Wei Zhang Xiuxin Zhang Ning Zhang Yunlong Zhao Xin Cao Guangdun Peng Xianwen Ren Nan Jiang Caihuan Tian Zi-Jiang Chen Biomedical Pioneering Innovation Centre(BIOPIC) Peking UniversityBeijing 100871China Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China School of Chemical Engineering and Technology Sun Yat-Sen UniversityZhuhai 519082China Mozhuo Biotech(Zhejiang)Co. Ltd.TongxiangJiaxing 314500China Geneis(Beijing)Co. Ltd.Beijing 100102China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Department of Medical Oncology Zhongshan HospitalFudan UniversityShanghai 200032China School of Food Science and Technology Dalian Polytechnic UniversityDalian 116034China State Key Laboratory of Transducer Technology Aerospace Information Research InstituteChinese Academy of SciencesBeijing 100190China Key Laboratory of Biomechanics and Mechanobiology Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing 100083China Department of Mechanical Engineering City University of Hong KongHong Kong 999077China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China Center of Peony Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Flower Crops(North China)Key Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsBeijing 100081China Department of Hepatic Surgery Fudan University Shanghai Cancer CenterShanghai 200032China Advanced Technology Institute University of SurreyGuildfordSurreyGU27XHUK National Physical Laboratory TeddingtonMiddlesex TW110LWUK Institute of Clinical Science Zhongshan HospitalFudan UniversityShanghai 200032China West China School of Basic Medical Sciences&Forensic Medicine Sichuan UniversityChengdu 610041China Jinfeng Laboratory Chongqing 401329China Center for Reproduc

In recent years,more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects,such as the Human Cell Atlas,the Mouse Cell Atlas,the Mouse RNA Atlas,the Mouse ATAC Atlas,and the Plant Cell *** on these single-cell big data,thousands of bioinformatics algorithms for quality control,clustering,cell-type annotation,developmental inference,cell-cell transition,cell-cell interaction,and spatial analysis are *** powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence,the molecular landscape at the single-cell level can be revealed.

关键词： Atlas landscape application

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互操作性本体:智能精准医学的基础

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中国医学伦理学 2021年第3期34卷 265-279页

作者：何勇群谢江安万灵杨啸林朱彦周伟李元放陆伟胜吴健民刘开永王海河刘清平余红 University of Michigan Medical School Ann ArborMI 48109 重庆邮电大学生物信息学院重庆400065 南京昂吉网智网络技术有限公司江苏南京211199 中国医学科学院基础医学研究所北京100005 中国中医科学院中医药信息研究所北京100700 国家人口健康科学数据中心北京100700 Faculty of information Technology Monash UniversityClaytonVic 3800 北京大学肿瘤医院癌症生物信息学中心北京100142 安徽医科大学公共卫生学院安徽合肥230032 哈尔滨医科大学大庆分校黑龙江大庆163319 广州中医药大学广东广州510006 贵州大学医学院/贵州省人民医院/国家卫生健康委员会肺脏免疫性疾病诊治重点实验室贵州贵阳550002

近年来,互联网与物联网等技术的快速发展为探寻精准医学与人工智能之间的关联应用提供了战略机遇。然而,如何组织、集成和共享复杂异构的生物医学数据业已成为阻碍该领域发展的严重技术挑战。本体因其能够提供知识与元数据层面的语义基... 详细信息

近年来,互联网与物联网等技术的快速发展为探寻精准医学与人工智能之间的关联应用提供了战略机遇。然而,如何组织、集成和共享复杂异构的生物医学数据业已成为阻碍该领域发展的严重技术挑战。本体因其能够提供知识与元数据层面的语义基础而推动了生物医学人工智能的发展,而基于互操作性的本体对异构知识与数据的整合和分析发挥着关键性的作用。将人工智能与精准医疗的有机集合称之为智能精准医疗,并提出一个“河马假设”,用以阐明互操作性本体与智能精准医疗之间的正相关关系及如何发挥协同增效作用;同时,提出和展示了使用可扩展本体开发的原理和工具来实现本体的互操作性,进而支持智能精准医疗的应用与发展。此外,还对国内外互操作性本体的研究现状、本体中国的成立与发展以及医学伦理在智能精准医疗中的重要性等进行了综述和深入探讨。

关键词：本体互操作性本体生物医学大数据精准医学人工智能本体中国

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Fungal diversity notes 1–110:taxonomic and phylogenetic contributions to fungal species

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Fungal Diversity 2015年第3期72卷 1-197页

作者： Jian Kui Liu Kevin D.Hyde E.B.Gareth Jones Hiran A.Ariyawansa Darbhe J.Bhat Saranyaphat Boonmee Sajeewa S.N.Maharachchikumbura Eric H.C.McKenzie Rungtiwa Phookamsak Chayanard Phukhamsakda Belle Damodara Shenoy Mohamed A,Abdel-Wahab Bart Buyck Jie Chen K.W.Thilini Chethana Chonticha Singtripop Dong Qin Dai Yu Cheng Dai Dinushani ADaranagama Asha J.Dissanayake Mingkwan Doilom Melvina J.D’souza Xin Lei Fan Ishani DGoonasekara Kazuyuki Hirayama Sinang Hongsanan Subashini C.Jayasiri Ruvishika S.Jayawardena Samantha C.Karunarathna Wen Jing Li Ausana Mapook Chada Norphanphoun Ka Lai Pang Rekhani H.Perera Derek Peršoh Umpava Pinruan Indunil CSenanayake Sayanh Somrithipol Satinee Suetrong Kazuaki Tanaka Kasun M.Thambugala Qing Tian Saowaluck Tibpromma Danushka Udayanga Nalin N.Wijayawardene Dhanuska Wanasinghe Komsit Wisitrassameewong Xiang Yu Zeng Faten AAbdel-Aziz Slavomir Adamčík Ali H.Bahkali Nattawut Boonyuen Timur Bulgakov Philippe Callac Putarak Chomnunti Katrin Greiner Akira Hashimoto Valerie Hofstetter Ji Chuan Kang David Lewis Xing Hong Li Xing Zhong Liu Zuo Yi Liu Misato Matsumura Peter E.Mortimer Gerhard Rambold Emile Randrianjohany Genki Sato Veera Sri-Indrasutdhi Cheng Ming Tian Annemieke Verbeken Wolfgang von Brackel Yong Wang Ting Chi Wen Jian Chu Xu Ji Ye Yan Rui Lin Zhao Erio Camporesi Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouChina Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina Institute of Excellence in Fungal Research and School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand Formerly Department of Botany Goa UniversityGoaIndia No.128/1–J Azad Housing SocietyCurcaGoa VelhaIndia Muséum national d’histoire naturelle Dépt.Systématique etévolutionUMR 720575005 ParisFrance Institute of Microbiology&Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityPO Box 61Beijing 100083China Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesNo.9 of Shu Guang Hua Yuan Zhong LuHaidian DistrictBeijing 10097China The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing 100083China Mycology University of BayreuthUniversitätsstraße 3095440 BayreuthGermany The United Graduate School of Agricultural Sciences Iwate University18-8 Ueda 3 chomeMorioka 020-8550Japan Apple Experiment Station Aomori Prefectural Agriculture and Forestry Research Center24 FukutamiBotandairaKuroishiAomori 036-0332Japan Department of Plant Protection Agroscope Changins-Wadenswil Research Station ACWRte de Duiller1260 NyonSwitzerland Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia Department of Botany Faculty of ScienceSohag UniversitySohagEgypt Institute of Botany Slovak Academy of SciencesDúbravskácesta 984523 BratislavaSlovakia Hirosaki University Bleakwood262 CR 3062NewtonTexas 75966USA Faculty of Agriculture and Life Sciences Hirosaki University3 Bunkyo-choHirosakiAomori

This paper is a compilation of notes on 110 fungal taxa,including one new family,10 new genera,and 76 new species,representing a wide taxonomic and geographic *** new family,Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique *** family is sister to Biatriosporaceae and *** new genera are Allophaeosphaeria(Phaeosphaeriaceae),Amphibambusa(Amphisphaeriaceae),Brunneomycosphaerella(Capnodiales genera incertae cedis),Chaetocapnodium(Capnodiaceae),Flammeascoma(Anteagloniaceae),Multiseptospora(Pleosporales genera incertae cedis),Neogaeumannomyces(Magnaporthaceae),Palmiascoma(Bambusicolaceae),Paralecia(Squamarinaceae)and Sarimanas(Melanommataceae).The newly described species are the Ascomycota Aliquandostipite manochii,Allophaeosphaeria dactylidis,***,Alternaria cesenica,Amphibambusa bambusicola,Amphisphaeria sorbi,Annulohypoxylon thailandicum,Atrotorquata spartii,Brunneomycosphaerella laburni,Byssosphaeria musae,Camarosporium aborescentis,***,***,Chaetocapnodium siamensis,Chaetothyrium agathis,Colletotrichum sedi,Conicomyces pseudotransvaalensis,Cytospora berberidis,***,Diaporthe thunbergiicola,Diatrype palmicola,Dictyosporium aquaticum,***,***,Didymella cirsii,Dinemasporium nelloi,Flammeascoma bambusae,Kalmusia italica,***,Keissleriella sparticola,Lauriomyces synnematicus,Leptosphaeria ebuli,Lophiostoma pseudodictyosporium,***,Lophiotrema eburnoides,Montagnula graminicola,Multiseptospora thailandica,Myrothecium macrosporum,Natantispora unipolaris,Neogaeumannomyces bambusicola,Neosetophoma clematidis,***,Oxydothis atypica,Palmiascoma gregariascomum,Paraconiothyrium nelloi,***,Paradictyoarthrinium tectonicola,Paralecia pratorum,Paraphaeosphaeria spartii,Pestalotiopsis digitalis,***,***,Phaeoisaria pseudoclematidis,Phragmocapnias philippinensis,Pseudocamarosporium cotinae,Pseudocercospora tam

关键词： Ascomycota Basidiomycota Global Taxonomy Initiative Phylogeny Taxonomy

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Clinical epidemiology of chronic viral hepatitis B:A Tuscany real-world large-scale cohort study

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World Journal of Hepatology 2018年第5期10卷 409-416页

作者： Cristina Stasi Caterina Silvestri Roberto Berni Maurizia Rossana Brunetto Anna Linda Zignego Cristina Orsini Stefano Milani Liana Ricciardi Andrea De Luca Pierluigi Blanc Cesira Nencioni Donatella Aquilini Alessandro Bartoloni Giampaolo Bresci Santino Marchi Franco Filipponi Piero Colombatto Paolo Forte Andrea Galli Sauro Luchi Silvia Chigiotti Alessandro Nerli Giampaolo Corti Rodolfo Sacco Paola Carrai Angelo Ricchiuti Massimo Giusti Paolo Almi Andrea Cozzi Silvia Carloppi Giacomo Laffi Fabio Voller Francesco Cipriani Observatory of Epidemiology Regional Health Agency of TuscanyFlorence 50141Italy Center for Systemic Manifestations of Hepatitis Viruses(MaSVE) Internal Medicine and Liver UnitDepartment of Experimental and Clinical MedicineCareggi University HospitalFlorence 50134Italy Web Solutions Data Visualization and Scientific DocumentationRegional Health Agency of TuscanyFlorence 50141Italy Hepatology Unit Department of Clinical and Experimental MedicineUniversity Hospital of PisaPisa 56100Italy Gastroenterology Research Unit Department of Experimental and Clinical Biomedical Sciences“Mario Serio”Careggi University HospitalFlorence 50134Italy Infectious Disease Unit Hospital of LuccaLucca 55100Italy Infectious Diseases Unit Department of Medical BiotechnologiesSiena University HospitalSiena 53100Italy Infectious Disease Unit “S.Maria Annunziata”HospitalPonte a Niccheri 50012Italy Infectious Disease Unit Hospital of GrossetoGrosseto 58100Italy Infectious Disease Unit Hospital of PratoPrato 59100Italy Infectious and Tropical Diseases Unit Department of Experimental and Clinical MedicineCareggi University HospitalFlorence 50134Italy Gastroenterology and Metabolic Disorders Department of SurgeryCisanello University HospitalPisa 56100Italy Gastroenterology Unit Department of Translational Research and New Technologies in Medicine and SurgeryCisanello University Hospital of PisaPisa 56100Italy Liver Surgery and Transplantation Unit Department of Surgical PathologyMedicineMolecular and Critical AreaCisanello University HospitalPisa 56100Italy Internal Medicine Unit “San Jacopo”HospitalPistoia 51100Italy Infectious Diseases and Hepatology Unit Department of Internal and Specialized MedicineUniversity Hospital of SienaSiena 53100Italy Gastroenterology Unit San Giuseppe HospitalEmpoli 50053Italy Internal Medicine and Liver Unit Department of Experimental and Clinical MedicineCareggi University HospitalFlorence 50135Italy Department of Prevention Central Tuscany Local UnitFlorence 5

AIM To build a regional database of chronic patients to define the clinical epidemiology of hepatitis B virus(HBV)-infected patients in the Tuscan public health care *** This study used a cross-sectional cohort design. We evaluated chronic viral hepatitis patients with HBV referred to the outpatient services of 16 hospital units. information in the case report forms included main demographic data, blood chemistry data, viral hepatitis markers, instrumental evaluations, and eligibility for treatment or ongoing therapy and liver transplantation. RESULTS Of 4015 chronic viral hepatitis patients, 1096(27.3%) were HBV infected. The case report form was correctly completed for only 833 patients(64% males, 36% females; mean age 50.1 ± 15.4). Of these HBV-infected patients, 73% were Caucasian, 21% Asian, 4% Central African, 1% North African and 1% American. Stratifying patients by age and nationality, we found that 21.7% of HBV-infected patients were aged < 34 years(only 2.8% were Italian). The most represented routes of transmission were nosocomial/dental procedures(23%), mother-to-child(17%) and sexual transmission(12%). The most represented HBV genotypes were D(72%) and A(14%). Of the patients, 24.7% of patients were HBe Ag positive, and 75.3% were HBe Ag negative. Of the HBV patients 7% were anti-HDV positive. In the whole cohort, 26.9% were cirrhotic(35.8% aged < 45 years), and 47% were eligible for or currently undergoing treatment, of whom 41.9 % were cirrhotic. CONCLUSION Only 27.3% of chronic viral hepatitis patients were HBV infected. Our results provide evidence of HBV infection in people aged < 34 years, especially in the foreign population not protected by vaccination. In our cohort of patients, liver cirrhosis was also found in young adults.

关键词： Hepatitis B virus infection Liver fibrosis Cirrhosis Public health Epidemiology

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