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Building Expertise on FAIR Through Evolving Bring Your Own Data(BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé Lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis Luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel Lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de Ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.Wilkinson Egon L.Willighagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly Department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands Department of Medical imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands Department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands Department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands Department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The Leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring Your Own Data"workshops(BYODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The BYOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these BYODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring Your Own Data Workshop BYOD

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Liver natural killer cells： subsets and roles in liver immunity

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Cellular & molecular Immunology 2016年第3期13卷 328-336页

作者： Hui Peng Eddie Wisse Zhigang Tian institute of Immunology and The CAS Key Laboratory of Innate Immunity and Chronic Disease School of Life Sciences and Medical Center University of Science and Technology of China Hefei Anhui China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases State Key Laboratory for Diagnosis and Treatment of Infectious Diseases First Affiliated Hospital College of Medicine Zhejiang University Hangzhou Zhejiang China maastricht multimodal molecular imaging institute Division of Nanoscopy Universiteitssingel 50 Maastricht The Netherlands

The liver represents a frontline immune organ that is constantly exposed to a variety of gut-derived antigens as a result of its unique location and blood supply, With a predominant role in innate immunity, the liver is enriched with various innate immune cells, among which natural killer （NK） cells play important roles in host defense and in maintaining immune balance, Hepatic NK cells were first described as ＇pit cells＇ in the rat liver in the 1970s, Recent studies of NK cells in mouse and human livers have shown that two distinct NK cell subsets, liver-resident NK cells and conventional NK （cNK） cells, are present in this organ, Here, we review liver NK cell subsets in different species, revisiting rat hepatic pit ceils and highlighting recent progress related to resident NK cells in mouse and human livers, and also discuss the dual roles of NK cells in liver immunity,

关键词： conventional NK cell liver liver-resident NK cell pit cell tolerance.

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Recent methodology advances in fluorescence molecular tomography

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Visual Computing for Industry,Biomedicine,and Art 2018年第1期1卷 1-11页

作者： Yu An Kun Wang Jie Tian Key Laboratory of molecular imaging Institute of AutomationChinese Academy of SciencesBeijingChina

molecular imaging(MI)is a novel imaging discipline that has been continuously developed in recent *** combines biochemistry,multimodal imaging,biomathematics,bioinformatics,cell&molecular physiology,biophysics,and pharmacology,and it provides a new technology platform for the early diagnosis and quantitative analysis of diseases,treatment monitoring and evaluation,and the development of comprehensive *** molecular Tomography(FMT)is a type of optical imaging modality in MI that captures the three-dimensional distribution of fluorescence within a biological tissue generated by a specific molecule of fluorescent material within a biological *** with other optical molecular imaging methods,FMT has the characteristics of high sensitivity,low cost,and safety and *** has become the research frontier and research hotspot of optical molecular imaging *** paper took an overview of the recent methodology advances in FMT,mainly focused on the photon propagation model of FMT based on the radiative transfer equation(RTE),and the reconstruction problem solution consist of forward problem and inverse *** introduce the detailed technologies utilized in reconstruction of ***,the challenges in FMT were *** survey aims at summarizing current research hotspots in methodology of FMT,fromwhich future research may benefit.

关键词： Fluorescence molecular tomography Image reconstruction Photon propagation model Forward problem Inverse problem

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Acceptor-engineering tailored type-Ⅰ photosensitizer with aggregation-induced NIR-II emission for cancer multimodal phototheranostics

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Science China Chemistry 2024年第8期67卷 2647-2660页

作者： Jiangao Li Niu Niu Deliang Wang Xue Liu Yi Qin Lei Wang Ben Zhong Tang Dong Wang Center for AIE Research Shenzhen Key Laboratory of Polymer Science and TechnologyGuangdong Research Center for Interfacial Engineering of Functional MaterialsCollege of Materials Science and EngineeringShenzhen UniversityShenzhen 518060China Guangzhou Municipal and Guangdong Provincial Key Laboratory of molecular Target Clinical Pharmacologythe State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences and the Fifth Affiliated HospitalGuangzhou Medical UniversityGuangzhou 511436China School of Science and Engineering Shenzhen Institute of Aggregate Science and TechnologyThe Chinese University of Hong KongShenzhen(CUHK-Shenzhen)Shenzhen 518172China

Exploration of single molecular species synchronously featured by long excitation/emission wavelength, accurate diagnosis, and effective therapy, remains supremely appealing to implement high-performance cancer phototheranostics. However, those previously established phototheranostic agents are undiversified and stereotyped in terms of structural skeleton, and generally exhibit insufficient phototheranostic outcomes. Herein, we innovatively utilized indanone-condensed thiadiazolo[3,4-g]quinoxaline(ITQ) as electron acceptor to construct novel photosensitizer with second near-infrared(NIR-II) emission. Experimental study and theoretical calculation demonstrated that comparing with the counterparts constituting by widely employed NIR-II building block benzobisthiadiazole(BBTD) and 6,7-diphenylthiadiazoloquinoxaline(DPTQ), ITQ-based photosensitizer(TITQ) showed superior aggregation-induced emission(AIE) characteristics, much stronger type-I reactive oxygen species(ROS) production, and prominent photothermal conversion capacity. Furthermore, TITQ nanoparticles with excellent biocompatibility were capable of effectively accumulating in the tumor site and visualizing tumor through fluorescence-photoacoustic-photothermal trimodal imaging with highly spatiotemporal resolution, and completely eliminating tumor by type-I photodynamic-photothermal therapy.

关键词： phototheranostics aggregation-induced emission NIR-Ⅱfluorescence acceptor engineering photodynamic-photothermal therapy

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Application and prospects of AI-based radiomics in ultrasound diagnosis

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Visual Computing for Industry,Biomedicine,and Art 2023年第1期6卷 288-303页

作者： Haoyan Zhang Zheling Meng Jinyu Ru Yaqing Meng Kun Wang CAS Key Laboratory of molecular imaging Institute of AutomationChinese Academy of SciencesBeijing 100190China School of Artificial Intelligence University of Chinese Academy of SciencesBeijing 100190China

Artificial intelligence (AI)-based radiomics has attracted considerable research attention in the field of medical imaging, including ultrasound diagnosis. Ultrasound imaging has unique advantages such as high temporal resolution, low cost, and no radiation exposure. This renders it a preferred imaging modality for several clinical scenarios. This review includes a detailed introduction to imaging modalities, including Brightness-mode ultrasound, color Doppler flow imaging, ultrasound elastography, contrast-enhanced ultrasound, and multi-modal fusion analysis. It provides an overview of the current status and prospects of AI-based radiomics in ultrasound diagnosis, highlighting the application of AI-based radiomics to static ultrasound images, dynamic ultrasound videos, and multi-modal ultrasound fusion analysis.

关键词： Radiomics Ultrasound imaging Artificial intelligence Deep learning B-mode ultrasound Color Doppler flow imaging Ultrasound elastography Contrast-enhanced ultrasound multimodal ultrasound

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Aggregation-induced emission luminogens for in vivo molecular imaging and theranostics in cancer

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Aggregate 2023年第5期4卷 34-62页

作者： Peili Cen Jiani Huang Chentao Jin Jing Wang Yen Wei Hong Zhang Mei Tian Department of Nuclear Medicine and PET Center The Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiangChina institute of Nuclear Medicine and molecular imaging of Zhejiang University HangzhouZhejiangChina Key Laboratory of Medical molecular imaging of Zhejiang Province HangzhouZhejiangChina Department of Chemistry and the Tsinghua Center for Frontier Polymer Research Tsinghua UniversityBeijingChina College of Biomedical Engineering&Instrument Science Zhejiang UniversityHangzhouZhejiangChina Key Laboratory for Biomedical Engineering of Ministry of Education Zhejiang UniversityHangzhouZhejiangChina Human Phenome institute Fudan UniversityShanghaiChina

Cancer is one of the most fatal diseases for ***-induced emission luminogens(AIEgens)have been recently used as molecular imaging or therapeutic agents in cancers,due to the advantages of large Stokes shift,high quantum yield,great biocompatibility,and strong *** can specifically target different types of cancer via diverse targeting ***-based fluorescence imaging,especially near-infrared imaging,demonstrated deep penetration and suitable signal-to-noise ratio,which allows reliable in vivo cancer *** with other imaging modalities,AIEgen-based multimodal imaging could provide multidimensional cancer hallmarks from different *** addition,AIEgenbased phototherapy can be used for photodynamic therapy and photothermal therapy,which facilitate ablation of cancer cells with good biosafety and high therapeutic effects in *** nanoparticles fabricated with some specific chemicals,drugs,or siRNA,could display synergistic therapeutic effects for *** paper comprehensively describes the current status and future perspectives of AIEgens,which have showed a great potential for the future preclinical and clinical translation on in vivo molecular imaging and theranostics in cancer.

关键词： aggregation-induced emission cancer near-infrared imaging phototherapy targeting strategy theranostics

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Highly doped NaErF_(4)-based nanocrystals for multi-tasking application

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Journal of Rare Earths 2021年第12期39卷 1467-1476,I0001页

作者： Yulin Xie Qing Chen Man Wang Weilin Chen Zewei Quan Chunxia Li institute of molecular Sciences and Engineering Institute of Frontier and Interdisciplinarity ScienceShandong UniversityQingdao 266237China Department of Chemistry Southern University of Science and TechnologyShenzhen 518055China

How to engineer single nanocrystal to achieve multiple functions is still a huge *** this work,a novel highly doped rare earth nanocrystal NaErF_(4)@NaGdF_(4)@NaDyF_(4)(Er@Gd@Dy)was designed and fabricated,which exhibits various performances by itself,including the longitudinal(T1)and transverse relaxation time(T2)double-mode magnetic resonance imaging(MRI),upconversion luminescence and down-shifting *** irradiation of 808 nm near-infrared(NIR)light,the upconverted red light can indirectly activate the photo sensitizer Ce6 conjugated on the surface of nanocrystals for photodynamic therapy(PDT).In vivo experiments demonstrate that the nano materials can eradicate notably primary tumors without obvious systematic *** addition,the longitudinal and transverse relaxation rates of Er@Gd@Dy are 24.83 and 319.86(mmol/L)^(-1)/s,respectively,which are superior to those of the nanocrystals reported ***,the nanocrystals have the ability to generate NIR-Ⅱlight located at 1530 nm,favorable in bioimaging in deeper *** a consequence,this new nanoplatform will advance the improvement of multimodal imaging guided tumor diagnosis and treatment.

关键词： Rare earth nanocrystals MRI Upconversion NIR-Ⅱwindow Photodynamic therapy

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Porous hollow palladium nanoplafform for imaging-guided trimodal chemo-, photothermal-, and radiotherapy

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Nano Research 2018年第5期11卷 2796-2808页

作者： Menglin Song Nian Liu Le He Gang Liu Daishun Ling Xinhui Su Xiaolian Sun State Key Laboratory of molecular Vaccinology and molecular Diagnostics & Center for molecular imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361005 China Department of Pharmaceutical Analysis China Pharmaceutical University Nanjing 210009 China institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices Soochow University Suzhou 215123 China Zhejiang Province Key Laboratory of Anti-Cancer Drug Research College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 China Department of Nuclear Medicine Zhongshan Hospital Xiamen University Xiamen 361004 China

Cancer is one of the major causes of human death. There are many types of cancer treatment including surgery, chemotherapy, radiotherapy, and photothermal therapy. Combining different therapies can synergistically enhance the therapeutic effect. We developed porous hollow palladium nanoparticles （PHPdNPs） to co-deliver ^131I （a radioisotope that is commonly used in radiotherapy） and doxorubicin （DOX; a chemotherapy drug）. Compared with other mesoporous nanocarriers, our PHPdNPs exhibited impressive photothermal conversion efficiency and stability. Drug loading is high and drug release is controllable by repeated laser irradiation and acidic pH in tumor microenvironments. Owing to the specific interaction between palladium and iodine, the PHPdNPs serve as effective ^131I delivery vehicles with excellent radiochemical stability. A single dose of [^131I]PHPdNPs-DOX has superior antitumor efficacy because it enables a combination of chemo-, photothermal-, and radio-therapy. Moreover, the nanocomplex has no obvious side-effects in mice. Therefore, we believe that PHPdNPs are excellent candidates for multimodal imaging-guided therapy.

关键词： porous hollo wnanopartides radiotherapy phototherrnal therapy chemotherapy

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Advances in magnetic resonance imaging contrast agents for glioblastoma-targeting theranostics

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Regenerative Biomaterials 2021年第6期8卷 273-296页

作者： Zijun Wu Lixiong Dai Ke Tang Yiqi Ma Bin Song Yanrong Zhang Jinxing Li Su Lui Qiyong Gong Min Wu Huaxi MR Research Center(HMRRC) Department of RadiologyFunctional and Molecular Imaging Key Laboratory of Sichuan ProvinceWest China HospitalSichuan UniversityChengdu 610041China Wenzhou institute University of Chinese Academy of SciencesWenzhouZhejiang 325000China Department of Radiology School of MedicineStanford UniversityStanfordCA 94305USA

Glioblastoma(GBM)is the most aggressive malignant brain tumour,with a median survival of 3 months without treatment and 15 months with *** GBM diagnosis can significantly improve patient survival due to early treatment and management *** resonance imaging(MRI)using contrast agents is the preferred method for the preoperative detection of GBM ***,commercially available clinical contrast agents do not accurately distinguish between GBM,surrounding normal tissue and other cancer types due to their limited ability to cross the blood-brain barrier,their low relaxivity and their potential *** GBM-specific contrast agents are urgently needed to overcome the limitations of current contrast *** advances in nanotechnology have produced alternative GBM-targeting contrast *** surfaces of nanoparticles(NPs)can be modified with multimodal contrast imaging agents and ligands that can specifically enhance the accumulation of NPs at GBM *** advanced imaging technology,multimodal NP-based contrast agents have been used to obtain accurate GBM diagnoses in addition to an increased amount of clinical diagnostic *** can also serve as drug delivery systems for GBM *** review focuses on the research progress for GBMtargeting MRI contrast agents as well as MRI-guided GBM therapy.

关键词： glioblastoma MRI targeted contrast agents therapy drug delivery

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Structural,Functional,and molecular imaging of Autism Spectrum Disorder

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Neuroscience Bulletin 2021年第7期37卷 1051-1071页

作者： Xiaoyi Li Kai Zhang Xiao He Jinyun Zhou Chentao Jin Lesang Shen Yuanxue Gao Mei Tian Hong Zhang Department of Nuclear Medicine and Medical PET Center The Second Hospital of Zhejiang University School of MedicineHangzhou 310009China Key Laboratory of Medical molecular imaging of Zhejiang Province Hangzhou 310009China Key Laboratory for Biomedical Engineering of Ministry of Education Zhejiang UniversityHangzhou 310027China Laboratory for Pathophysiological and Health Science RIKEN Center for Biosystems Dynamics ResearchHyogo 650-0047Japan Department of Surgical Oncology The Second Hospital of Zhejiang University School of MedicineHangzhou 310009China institute of Nuclear Medicine and molecular imaging Zhejiang UniversityHangzhou 310009China The College of Biomedical Engineering and Instrument Science of Zhejiang University Hangzhou 310027China

Autism spectrum disorder(ASD)is a heterogeneous neurodevelopmental disorder associated with both genetic and environmental *** approaches have been widely employed to parse the neurophysiological mechanisms underlying ASD,and provide critical insights into the anatomical,functional,and neurochemical *** reviewed recent advances in neuroimaging studies that focused on ASD by using magnetic resonance imaging(MRI),positron emission tomography(PET),or single-positron emission tomography(SPECT).Longitudinal structural MRI has delineated an abnormal developmental trajectory of ASD that is associated with cascading neurobiological processes,and functional MRI has pointed to disrupted functional neural ***,PET and SPECT imaging have revealed that metabolic and neurotransmitter abnormalities may contribute to shaping the aberrant neural circuits of *** large-scale,multi-center,multimodal investigations are essential to elucidate the neurophysiological underpinnings of ASD,and facilitate the development of novel diagnostic biomarkers and better-targeted therapy.

关键词： Autism spectrum disorder Positron emission tomography Magnetic resonance imaging molecular imaging Functional connectivity Serotonin Oxytocin

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