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A Generic Workflow for the Data FAIRification Process

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Data Intelligence 2020年第1期2卷 56-65页

作者： Annika Jacobsen Rajaram Kaliyaperumal Luiz Olavo Bonino da Silva Santos Barend Mons Erik Schultes marco roos Mark Thompson Leiden University Medical Center Leiden2333 ZAThe Netherlands GO FAIR International Support&Coordination Office(GFISCO) LeidenThe Netherlands

The FAIR guiding principles aim to enhance the Findability,Accessibility,Interoperability and Reusability of digital resources such as data,for both humans and *** process of making data FAIR(“FAIRification”)can be described in multiple *** this paper,we describe a generic step-by-step FAIRification workflow to be performed in a multidisciplinary team guided by FAIR data *** FAIRification workflow should be applicable to any type of data and has been developed and used for“Bring Your Own Data”(BYOD)workshops,as well as for the FAIRification of e.g.,rare diseases *** steps are:1)identify the FAIRification objective,2)analyze data,3)analyze metadata,4)define semantic model for data(4a)and metadata(4b),5)make data(5a)and metadata(5b)linkable,6)host FAIR data,and 7)assess FAIR *** each step we describe how the data are processed,what expertise is required,which procedures and tools can be used,and which FAIR principles they relate to.

关键词： FAIR data FAIRification workflow FAIR data stewardship Hands-on FAIRification FAIR dissemination

The“A”of FAIR-As Open as Possible,as Closed as Necessary

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Data Intelligence 2020年第1期2卷 47-55,303,304页

作者： Annalisa Landi Mark Thompson Viviana Giannuzzi Fedele Bonifazi Ignasi Labastida Luiz Olavo Bonino da Silva Santos marco roos Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus 30-70010 Valenzano(BA)Italy Leiden University Medical Center Leiden2333 ZAThe Netherlands Learning and Research Resources Centre(CRAI) Universitat de BarcelonaCatalunya 08007Spain GO FAIR International Support&Coordination Office(GFISCO) LeidenThe Netherlands

In order to provide responsible access to health data by reconciling benefits of data sharing with privacy rights and ethical and regulatory requirements,Findable,Accessible,Interoperable and Reusable(FAIR)metadata should be *** to the H2020 Program Guidelines on FAIR Data,data should be"as open as possible and as closed as necessary","open"in order to foster the reusability and to accelerate research,but at the same time they should be"closed"to safeguard the privacy of the *** provisions on the protection of natural persons with regard to the processing of personal data have been endorsed by the European General Data Protection Regulation(GDPR),Reg(EU)2016/679,that came into force in May *** work aims to solve accessibility problems related to the protection of personal data in the digital era and to achieve a responsible access to and responsible use of health *** strongly suggest associating each data set with FAIR metadata describing both the type of data collected and the accessibility conditions by considering data protection obligations and ethical and regulatory ***,an existing FAIR infrastructure component has been used as an example to explain how FAIR metadata could facilitate data sharing while ensuring protection of individuals.

关键词： Accessibility of health data FAIR metadata GDPR Data sharing ELSI

Role of copper chelating agents: between old applications and new perspectives in neuroscience

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Neural Regeneration Research 2025年第3期20卷 751-762页

作者： Rosalba Leuci Leonardo Brunetti Vincenzo Tufarelli marco Cerini marco Paparella Nikola Puvača Luca Piemontese Department of Pharmacy-Pharmaceutical Science University of Bari Aldo MoroBariItaly Department of Precision and Regenerative Medicine and Jonian Area(DiMePRe-J) Section of Veterinary Science and Animal ProductionUniversity of Bari Aldo MoroBariItaly Department of Engineering Management in Biotechnology Faculty of Economics and Engineering Management in Novi SadUniversity Business Academy in Novi SadNovi SadSerbia

The role of copper element has been an increasingly relevant topic in recent years in the fields of human and animal health, for both the study of new drugs and innovative food and feed supplements. This metal plays an important role in the central nervous system, where it is associated with glutamatergic signaling, and it is widely involved in inflammatory processes. Thus, diseases involving copper(Ⅱ) dyshomeostasis often have neurological symptoms, as exemplified by Alzheimer's and other diseases(such as Parkinson's and Wilson's diseases). Moreover, imbalanced copper ion concentrations have also been associated with diabetes and certain types of cancer, including glioma. In this paper, we propose a comprehensive overview of recent results that show the importance of these metal ions in several pathologies, mainly Alzheimer's disease, through the lens of the development and use of copper chelators as research compounds and potential therapeutics if included in multi-target hybrid drugs. Seeing how copper homeostasis is important for the well-being of animals as well as humans, we shortly describe the state of the art regarding the effects of copper and its chelators in agriculture, livestock rearing, and aquaculture, as ingredients for the formulation of feed supplements as well as to prevent the effects of pollution on animal productions.

关键词： agriculture Alzheimer's disease chelators copper feed supplements multi-target

From mice to humans:a need for comparable results in mammalian neuroplasticity

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Neural Regeneration Research 2025年第2期20卷 464-466页

作者： marco Ghibaudi Enrica Boda Luca Bonfanti Neuroscience Institute Cavalieri Ottolenghi OrbassanoItaly Department of Veterinary Sciences University of TurinTurinItaly Department of Neuroscience Rita Levi-Montalcini University of TurinTurinItaly

Brain plasticity-A universal tool with many variations:The study of brain plasticity has been gaining interest since almost a century and has now reached a huge amount of information(>80,000 results in PubMed).Overall,different types of plasticity,including stem cell-driven genesis of new neurons(adult neurogenesis),cells in arrested maturation(dormant neurons),neuro-glial and synaptic plasticity,can coexist and contribute to grant plastic changes in the brain,from a cellular to system level(Benedetti and Couillard-Despres,2022;Bonfanti et al.,2023).

关键词： plasticity al. arrest

Novel Methodologies for Preventing Crack Propagation in Steel Gas Pipelines Considering the Temperature Effect

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Structural Durability & Health Monitoring 2025年第1期19卷 1-23页

作者： Nurlan Zhangabay Ulzhan Ibraimova marco Bonopera Ulanbator Suleimenov Konstantin Avramov Maryna Chernobryvko Aigerim Yessengali Department of Architecture and Urban Planning Mukhtar Auezov South Kazakhstan UniversityShymkent160012Kazakhstan Department of Industrial Civil and Road Construction Mukhtar Auezov South Kazakhstan UniversityShymkent160012Kazakhstan Mechanics Sound&Vibration LaboratoryDepartment of Civil EngineeringCollege of EngineeringNational Taiwan UniversityTaipei10617Taiwan Department of Reability&Dynamic Strength A.Pidhornyi Institute of Mechanical Engineering Problems of National Academy of Sciences of UkraineKharkiv61046Ukraine

Using the software ANSYS-19.2/Explicit Dynamics,this study performedﬁnite-element modeling of the large-diameter steel pipeline cross-section for the Beineu-Bozoy-Shymkent gas pipeline with a non-through straight crack,strengthened by steel wire *** effects of the thread tensile force of the steel winding in the form of single rings at the crack edges and the wires with different winding diameters and pitches were also *** results showed that the strengthening was preferably executed at a minimum value of the thread tensile force,which was 6.4%more effective than that at its maximum *** analysis of the inﬂuence of the winding dia-meters showed that the equivalent stresses increased by 32%from the beginning of the crack growth until the wire *** increment in winding diameter decelerated the disclosure of the edge crack and reduced its length by 8.2%.The analysis of the inﬂuence of the winding pitch showed that decreasing the distance between the winding turns also led to a 33.6%reduction in the length of the straight crack and a 7.9%reduction in the maximum stres-ses on the strengthened pipeline *** analysis of the temperature effect on the pipeline material,within a range from-40℃ to+50℃,resulted in a crack length change of up to 5.8%.As the temperature dropped,the crack length *** such a temperature range,the maximum stresses were observed along the cen-tral area of the crack,which were equal to 413 MPa at+50℃ and 440 MPa at-40℃.The results also showed that the presence of the steel winding in the pipeline signiﬁcantly reduced the length of crack propagation up to 8.4 times,depending on the temperature effect and design parameters of *** work integrated the existing methods for crack localization along steel gas pipelines.

关键词： Crack propagation ﬁnite-element internal pressure prestressing steel gas pipeline temperature effect

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

FAIR Principles:Interpretations and Implementation Considerations

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Data Intelligence 2020年第1期2卷 10-29,293-302,322页

作者： Annika Jacobsen Ricardo de Miranda Azevedo Nick Juty Dominique Batista Simon Coles Ronald Cornet Melanie Courtot Merce Crosas Michel Dumontier Chris T.Evelo Carole Goble Giancarlo Guizzardi Karsten Kryger Hansen Ali Hasnain Kristina Hettne Jaap Heringa Rob W.W.Hooft Melanie Imming Keith G.Jeffery Rajaram Kaliyaperumal Martijn GKersloot Christine R.Kirkpatrick Tobias Kuhn Ignasi Labastida Barbara Magagna PeterMcQuilton Natalie Meyers Annalisa Montesanti Mirjam van Reisen Philippe Rocca-Serra Robert Pergl Susanna-Assunta Sansone Luiz Olavo Bonino da Silva Santos Juliane Schneider George Strawn Mark Thompson Andra Waagmeester Tobias Weigel Mark D.Wilkinson Egon L.Willighagen Peter Wittenburg marco roos Barend Mons Erik Schultes Leiden University Medical Center Leiden2333 ZAThe Netherlands Institute of Data Science Maastricht UniversityUniversiteitssingel 60Maastricht 6229 ERThe Netherlands Department of Computer Science The University of ManchesterOxford RoadManchester M139PLUK Oxford e-Research Centre Department of Engineering SciencesUniversity of OxfordOxford OX13PJUK School of Chemistry Faculty of Engineering and Physical SciencesUniversity of SouthamptonSO171BJUK Amsterdam UMC University of AmsterdamAmsterdam 1000 GGThe Netherlands European Bioinformatics Institute(EMBL-EBI) HinxtonCambridgeCB101SDUK Harvard University CambridgeMassachusetts 02138USA Department of Bioinformatics–BiGCaT NUTRIMMaastricht UniversityMaastricht 6229 ERThe Netherlands Conceptual and Cognitive Modeling Research Group(CORE) Free University of Bozen-BolzanoBolzano 39100Italy Aalborg University Aalborg DK-9220Denmark Insight Centre for Data Analytics National University of Ireland GalwayH91 TK33Ireland Centre for Digital Scholarship Leiden University LibrariesLeiden2333 ZAThe Netherlands Department of Computer Science Vrije Universiteit AmsterdamDe Boelelaan 11051081 HV AmsterdamThe Netherlands Dutch Techcentre for Life Sciences(DTL) UtrechtThe Netherlands SURF Utrecht 3511 EPThe Netherlands Keith G Jeffery Consultants FaringdonUK Castor EDC Paasheuvelweg 25Wing 5D1105 BPAmsterdamThe Netherlands San Diego Supercomputer Center University of California San DiegoLa JollaCalifornia 92093USA Learning and Research Resources Centre(CRAI) Universitat de Barcelona08007 BarcelonaSpain Environment Agency Austria A-1090 ViennaAustria University of Notre Dame 75004 ParisFrance Health Research Board(HRB) Dublin 2DO2 H638Ireland Liacs Institute of Advanced Computer Science Leiden University2311 GJ LeidenThe Netherlands Czech Technical University in Prague Faculty of Information Technology(FIT CTU)16000 Prague 6Czech Republic GO FAIR International Support&Coordination Office(GFISCO) LeidenThe Netherlands Harvard Catalys

The FAIR principles have been widely cited,endorsed and adopted by a broad range of stakeholders since their publication in *** intention,the 15 FAIR guiding principles do not dictate specific technological implementations,but provide guidance for improving Findability,Accessibility,Interoperability and Reusability of digital *** has likely contributed to the broad adoption of the FAIR principles,because individual stakeholder communities can implement their own FAIR ***,it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible ***,while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways,for true interoperability we need to support convergence in implementation choices that are widely accessible and(re)-*** introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible,robust,widespread and consistent FAIR *** self-identified stakeholder community may either choose to reuse solutions from existing implementations,or when they spot a gap,accept the challenge to create the needed solution,which,ideally,can be used again by other communities in the ***,we provide interpretations and implementation considerations(choices and challenges)for each FAIR principle.

关键词： FAIR guiding principles FAIR implementation FAIR convergence FAIR communities choices and challenges

Measurement of vibration frequencies of ties in masonry arches by means of a robotic total station

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Earthquake Engineering and Engineering Vibration 2022年第2期21卷 489-500页

作者： marco Gatti Dipartimento di Ingegneria University of Ferraravia Saragat 144123 FerraraItaly

Measurement of the vibration frequencies of eight ties set in masonry arches of a church by means of a robotic total station is *** instrument made continuous recordings(up to ten per second)of the three-dimensional positions of a reflector situated at 1/2 or 1/4 of the length of the tie during vertical oscillation induced by an impulsive *** recording slips,vibration amplitudes(and their accuracy),hourly diagram and experimental spectra of vibrations,and the corresponding frequencies were *** results were verified by comparing them with the vibration frequencies and indirectly the tension and fixed support constraint calculated from accelerometric *** study provides interesting information on the accuracies of the reflector′s three-dimensional coordinates,but highlighted certain limits in the application of robotized total stations for measuring vibration frequencies of ties in masonry arches.

关键词： RTS frequency vibrations ties arches

σ-Phase in Lean Duplex Stainless Steel Sheets

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Acta Metallurgica Sinica(English Letters) 2015年第3期28卷 331-337页

作者： marco Breda Massimo Pellizzari marco Frigo Industrial Engineering Department(DII) University of PadovaVia Marzolo 9Int.435131 PaduaItaly Industrial Engineering Department(DII) University of TrentoVia Mesiano 7738123 TrentoItaly Outokumpu S.p.A. Piazza Piccapietra 916121 GenoaItaly

The precipitation kinetics of secondary phases in two austeno-ferritic lean duplex stainless steels（lean DSS）were examined after aging the materials at 800 ℃.Owing to the instability of ferrite,all DSS are known to be sensitive to solid-state phase transformations in the critical temperature range 600-1,000 ℃ and different secondary phases may form,depending on composition and *** performed thermodynamic simulations revealed the proneness to the precipitation of such phases also have been done in lean DSS,but only information on the equilibrium microstructures were ***,the materials were aged at various times,in order to verify the simulations and determine the precipitation *** occurred structural modifications were observed and quantified by scanning electron microscope and X-ray diffraction measurements,determining phase type,composition and volumetric *** 800 ℃,grade 2101 was found to be only affected by Cr_2N nitrides precipitation,whereas a significant amount of σ-phase was found to form in LDX 2404 for treatment longer than 1 h,almost totally replacing ferrite after 50 *** to now,the intermetallic σ-phase has been observed only in the high alloyed DSS,and the unexpected precipitation in grade 2404 highlighted that the increased content of molybdenum in this steel might be considered as determinant for the formation.

关键词： Lean duplex stainless steels Isothermal heat treatments σ-Phase Chromium nitrides Precipitation kinetics