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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

Climatic and tectonic controls on the fluvial morphology of the Northeastern Tibetan Plateau （China）

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Journal of Geographical Sciences 2017年第11期27卷 1325-1340页

作者： WANG Xianyan Jef vanDENBERGHE LU Huayu ronald van BALEN School of Geographic and Oceanographic Sciences Nanjing University Nanjing 210023 China Department of Earth Sciences VU University Amsterdam De Boelelaan 1085 1081 HV Amsterdam The Netherlands

The geomorphological evolution of the Northeastern Tibetan Plateau （NETP） could provide valuable information for reconstructing the tectonic movements of the region. And the considerable uplift and climatic changes at here, provide an opportunity for studying the im- pact of tectonic and monsoon climate on fluvial morphological development and sedimentary architecture of fluvial deposits. The development of peneplain-like surface and related land- scape transition from basin filling to incision indicate an intense uplift event with morphologi- cal significance at around 10-17 Ma in the NETP. After that, incision into the peneplain was not continuous but a staircase of terraces, developed as a result of climatic influences. In spite of the generally persisting uplift of the whole region, the neighbouring tectonic blocks had different uplift rates, leading to a complicated fluvial response with accumulation terraces alternating with erosion terraces at a small spatial and temporal scale. The change in fluvial activity as a response to climatic impact is reflected in the general sedimentary sequence on the terraces from high-energy （braided） channel deposits （at full glacial） to lower-energy de- posits of small channels （towards the end of the glacial）, mostly separated by a rather sharp boundary from overlying flood-Ioams （at the glacial-interglacial transition） and overall soil formation （interglacial）. Pronounced incision took place at the subsequent warm-cold transi- tions. In addition, it is hypothesized that in some strongly uplifted blocks energy thresholds could be crossed to allow terrace formation as a response to small climatic fluctuations （10^3-10^4 year timescale）. Although studies of morpho-tectonic and geomorphological evolu- tion of the NETP, improve understanding on the impacts of tectonic motions and monsoonal climate on fluvial processes, a number of aspects, such as the distribution and correlation of peneplain and the related morphological feature

关键词： peneplain Miocene uplift fluvial terraces fluvial deposit climatic impact tectonic impact Northeastern Tibetan Plateau

Direct Retrieval of NO_(2)Vertical Columns from UV-Vis(390-495nm)Spectral Radiances Using a Neural Network

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Journal of Remote Sensing 2022年第1期2022卷 200-216页

作者： Chi Li Xiaoguang Xu Xiong Liu Jun Wang Kang Sun Jos van Geffen Qindan Zhu Jianzhong Ma Junli Jin Kai Qin Qin He Pinhua Xie Bo Ren ronald C.Cohen Department of Chemistry University of CaliforniaBerkeleyBerkeleyCAUSA Joint Center for Earth Systems Technology University of MarylandBaltimore CountyBaltimoreMAUSA Department of Chemical and Biochemical Engineering Center for Global and Regional Environmental ResearchAnd Informatics InitiativeThe University of IowaIowa CityIAUSA Harvard-Smithsonian Center for Astrophysics CambridgeMAUSA Department of Civil Structural and Environmental EngineeringUniversity at BuffaloBuffaloNYUSA Research and Education in Energy Environment and Water InstituteUniversity at BuffaloBuffaloNYUSA Satellite Observations Department Royal Netherlands Meteorological Institute(KNMI)De BiltNetherlands Department of Earth and Planetary Science University of CaliforniaBerkeleyBerkeleyCAUSA Chinese Academy of Meteorology Science China Meteorological AdministrationBeijingChina Meteorological Observation Center China Meteorological AdministrationBeijingChina School of Environment and Spatial Informatics China University of Mining and TechnologyXuzhouChina Key Laboratory of Environmental Optics and Technology Anhui Institute of Optics and Fine MechanicsHefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina

Satellite retrievals of columnar nitrogen dioxide(NO_(2))are essential for the characterization of nitrogen oxides(NO_(x))processes and *** requirements of modeled a priori profiles present an outstanding bottleneck in operational satellite NO_(2)*** this work,we instead use neural network(NN)models trained from over 360,000 radiative transfer(RT)simulations to translate satellite radiances across 390-495nm to total NO_(2)vertical column(NO_(2)C).Despite the wide variability of the many input parameters in the RT simulations,only a small number of key variables were found essential to the accurate prediction of NO_(2)C,including observing angles,surface reflectivity and altitude,and several key principal component scores of the *** addition to the NO_(2)C,the NN training and cross-validation experiments show that the wider retrieval window allows some information about the vertical distribution to be retrieved(e.g.,extending the rightmost wavelength from 465 to 495 nm decreases the root-mean-square-error by 0.75%)under high-NO_(2)C *** to four months of TROPOMI data,the trained NN model shows strong ability to reproduce the NO_(2)C observed by the ground-based Pandonia Global *** coefficient of determination(R2,0.75)and normalized mean bias(NMB,-33%)are competitive with the level 2 operational TROPOMI product(R^(2)=0:77,NMB=−29%)over clear(geometric cloud fraction<0:2)and polluted(NO_(2)C≥7:5×10^(15)molecules/cm2)*** NN retrieval approach is~12 times faster than predictions using high spatial resolution(~3 km)a priori profiles from chemical transport modeling,which is especially attractive to the handling of large volume satellite data.

关键词： Vertical attractive faster

Avian introgression in the genomic era

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Avian Research 2017年第4期8卷 181-191页

作者： Jente Ottenburghs Robert H.S.Kraus Pim van Hooft Sipke E.van Wieren ronald C.Ydenberg Herbert H.T.Prins Resource Ecology Group Wageningen UniversityDroevendaalsesteeg 3a6708 PB WageningenThe Netherlands Department of Biology University of Konstanz78457 ConstanceGermany Department of Migration and Immuno-Ecology Max Planck Institute for OrnithologyAm Obstberg 178315 RadolfzellGermany Centre of Wildlife Ecology Simon Fraser UniversityBurnabyBC V5A 1S6Canada

Introgression,the incorporation of genetic material from one(sub)species into the gene pool of another by means of hybridization and backcrossing,is a common phenomenon in birds and can provide important insights into the speciation *** the last decade,the toolkit for studying introgression has expanded together with the development of molecular *** this review,we explore how genomic data,the most recent step in this methodological progress,impacts different aspects in the study of avian ***,the detection of hybrids and backcrosses has improved *** most widely used software package is *** discordance(*** loci resulting in discordant gene trees) is another means for the detection of introgression,although it should be regarded as a starting point for further analyses,not as a definitive proof of ***,disentangling introgression from other biological processes,such as incomplete lineage sorting,remains a challenging endeavour,although new techniques,such as the D-statistic,are being *** addition,phylogenetics might require a shift from trees to ***,the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and ***,because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction,hybrid zones should be studied across different temporal and/or spatial scales.A third powerful tool is the genome *** debate on which evolutionary processes underlie the genomic landscape is still ongoing,as is the question whether loci involved in reproductive isolation cluster together in ‘islands of speciation' or whether they are scattered throughout the *** genomic landscapes across the avian tree of life will be an exciting field for further ***,the findings from these different methods shoul

关键词： Admixture Cline theory D-statictic Genomic landscape Hybridization Phylogenetic discordance

Phylogeny of the industrial relevant,thermophilic genera Myceliophthora and Corynascus

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Fungal Diversity 2012年第1期52卷 197-207页

作者： Joost van den Brink Robert A.Samson Ferry Hagen Teun Boekhout ronald P.de Vries CBS-KNAW Fungal Biodiversity Centre P.O.Box 851673508 AD UtrechtThe Netherlands

Species of the genus Myceliophthora and its teleomorph Corynascus have attracted increasing interest due to their potential to produce thermostable *** study re-assessed the phylogenetic relationship of 49 isolates of nine species belonging to Myceliophthora and *** species,***,was shown not to belong to the genus Myceliophthora and should be placed in the genus *** other species belonged to two phylogenetic clusters:mesophilic fungi with the type species *** and ***,and thermophilic fungi with ***,*** and *** phylogenetic data provides no clear separation of the two genera Corynascus and *** avoid confusion in future taxonomic studies,it is proposed that all existing Corynascus species be renamed to Myceliophthora,which is the old name and the one more frequently ***,this study identified two groups within the isolates listed as *** and assigned one group(five isolates)to *** based on AFLP analysis and mating *** study provides new insights into the genetic differences within the genus Myceliophthora and will therefore be essential for the interpretation of future genomic and physiological studies of these species.

关键词： Myceliophthora Corynascus Thermophiles M.heterothallica M.thermophila.Thermophilic fungi Multigene phylogeny AFLP analysis Mating behavior

Soil conservation and sustainable development goals(SDGs)achievement in Europe and central Asia:Which role for the European soil partnership?

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International Soil and Water Conservation Research 2021年第3期9卷 360-369页

作者： Hakki Emrah Erdogan Elena Havlicek Carmelo Dazzi Luca Montanarella Marc van Liedekerke Borut Vrscaj Pavel Krasilnikov Gulchekhra Khasankhanova ronald Vargas Republic of Turkey Ministry of Agriculture and Forestry AnkaraTurkey Federal Office for the Environment FOEN Soil and Biotechnology Division3003BemeSwitzerland University of Palermo Italy European Commission Joint Research Centre1-21027IspraVAItaly Department for Agro-ecology and Natural Resources Centre for Soil and EnvironmentAgricultural Institute of SloveniaLjubljanaSlovenia Environmental Protection College VelenjeSlovenia Lomonosov Moscow State University Eurasian Centre for Food SecurityMoscowRussian Federation UZGIP Institute Ministry of Water ResourcesTashkentUzbekistan Food and Agriculture Organization of the United Nations RomeItaly

Voluntary soil protection measures are not sufficient to achieve sustainable soil management at a global ***,binding soil protection legislation at national and international levels has also proved to be insufficient for the effective protection of this almost non-renewable natural *** European Soil Partnership(ESP)and its sub-regional partnerships(Eurasian Sub-Regional Soil Partnership,Alpine Soil Partnership)were established in the context of FAO's Global Soil Partnership(GSP)with the mission to facilitate and contribute to the exchange of knowledge and technologies related to soils,to develop dialogue and to raise awareness for the need to establish a binding global agreement for sustainable soil management The ESP has taken a role of an umbrella network covering countries in Europe and Central *** aims to improve the dialogue in the whole region and has encouraged establishing goals that would promote sustainable soil management taking into account various national and local approaches and priorities,as well as cultural *** ESP first regional implementation plan for the 2017—2020 period was adopted and implemented along the five GSP pillars of *** on the experience of the last four years,this study demonstrates that establishing sub-regional and national partnerships is an additional step in a concrete sustainable soil management implementation *** also suggests that a complementary approach between legal instruments and voluntary initiatives linked to the development of efficient communication and strong commitment is the key to success.

关键词： Sustainable soil management Soil partnership Soil policy Voluntary versus 52 mandatory approaches Multilevel coordination Communication and cooperation

Ex-vivo evaluation of gene therapy vectors in human pancreatic (cancer) tissue slices

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World Journal of Gastroenterology 2009年第11期15卷 1359-1366页

作者： Michael A van Geer Koert FD Kuhlmann Conny T Bakker Fibo JW ten Kate ronald PJ Oude Elferink Piter J Bosma Liver Center Academic Medical Center of the University of AmsterdamMeibergdreef 69/711105 BK AmsterdamThe Netherlands Department of Surgery Academic Medical Center of the University of AmsterdamMeibergdreef 91105BK AmsterdamThe Netherlands Department of Pathology Academic Medical Center of the University of AmsterdamMeibergdreef 91105 BK AmsterdamThe Netherlands

AIM:To culture human pancreatic tissue obtained from small resection specimens as a pre-clinical model for examining virus-host interactions. METHODS:Human pancreatic tissue samples (malignant and normal)were obtained from surgical specimens and processed immediately to tissue slices. Tissue slices were cultured ex vivo for 1-6 d in an incubator using 95%*** were subsequently analyzed for viability and *** addition the slices were incubated with different viral vectors expressing the reporter genes GFP or DsRed. Expression of these reporter genes was measured at 72 h after ***:With the Krumdieck tissue slicer,uniform slices could be generated from pancreatic tissue but only upon embedding the tissue in 3%low melting *** examination showed the presence of all pancreatic cell *** normal and cancer tissue slices could be cultured for up to 6 d,while retaining viability and a moderate to good *** gene expression indicated that the slices could be infected and transduced efficiently by adenoviral vectors and by adeno associated viral vectors,whereas transduction with lentiviral vectors was *** the adenoviral vector,the transduction seemed limited to the peripheral layers of the explants. CONCLUSION:The presented system allows reproducible processing of minimal amounts of pancreatic tissue into slices uniform in size,suitable for pre-clinical evaluation of gene therapy vectors.

关键词：基因治疗载体组织切片人胰腺癌体外评价癌症腺相关病毒载体免疫组织化学检查腺病毒载体

Ephrin A2 receptor targeting does not increase adenoviral pancreatic cancer transduction in vivo

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World Journal of Gastroenterology 2009年第22期15卷 2754-2762页

作者： Michael A van Geer Conny T Bakker Naoya Koizumi Hiroyuki Mizuguchi John G Wesseling ronald PJ Oude Elferink Piter J Bosma Liver Center of the Academic Medical Center of the University of Amsterdam Laboratory of Gene Transfer and Regulation National Institute of Biomedical Innovation

AIM:To generate an adenoviral vector specifically targeting the EphA2 receptor(EphA2R) highly expressed on pancreatic cancer cells in ***:YSA,a small peptide ligand that binds the EphA2R with high affinity,was inserted into the HI loop of the adenovirus serotype 5 fiber *** further increase the specificity of this vector,binding sites for native adenoviral receptors,the coxsackie and adenovirus receptor(CAR) and integrin,were ablated from the viral *** ablated retargeted adenoviral vector was produced on 293T *** c targeting of this novel adenoviral vector to pancreatic cancer was investigated on established human pancreatic cancer cell *** demonstrating specifi c in vitro targeting,in vivo targeting to subcutaneous growing human pancreatic cancer was tested by intravenous and intraperitoneal administration of the ablated adenoviral ***:Ablation of native cellular binding sites reduced adenoviral transduction at least *** of the YSA peptide in the HI loop restored adenoviral transduction of EphA2R-expressing cells but not of cells lacking this ***-mediated transduction was inhibited by addition of synthetic YSA *** transduction specificity of the ablated retargeted vector towards human pancreatic cancer cells was enhanced almost 10-fold in *** a subsequent in vivo study in a nude(nu/nu) mouse model however,no increased adenoviral targeting to subcutaneously growing human pancreas cancer nodules was seen upon injection into the tail vein,nor upon injection into the ***:Targeting the EphA2 receptor increases specificity of adenoviral transduction of human pancreatic cancer cells in vitro but fails to enhance pancreatic cancer transduction in vivo.

关键词：腺病毒胰腺癌体内转导定位受体 n素

Anaphylaxis and generalized urticaria from eating Chinese bayberry fruit

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2012年第10期13卷 851-854页

作者： Hui-ying WANG Zhong-shan GAO Zhao-wei YANG Jing-xin SHAO Xiu-zhen ZHAO Yu DAI ronald van REE Department of Allergy and Clinical Immunology the Second Affili-ated HospitalSchool of MedicineZhejiang UniversityHangzhou310013China Allergy Research Center Department of HorticultureCollege ofAgriculture and BiotechnologyZhejiang UniversityHangzhou310058China Department of Clinic Laboratory the Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou 310013China Department of Experimental Immunology and Department ofOtorhinolaryngology Academic Medical CenterUniversity of Am-sterdamMeibergdreef 91105 AZAmsterdamthe Netherlands

Chinese bayberry Myrica rubra is a very popular fruit in southeastern *** spite of its wide consumption,no allergies to this fruit have been reported *** we report on a 40-year-old woman suffering from anaphylaxis to Chinese bayberry ***-prick skin tests revealed strong reactions to fresh Chinese bayberry fruits as well as to peach,and weaker reactions to some other fruits including apple,melon,and *** analysis revealed identical titers of specific IgE(4.3 kU A /L) to peach extract and its lipid transfer protein(LTP,rPru p 3),which was confirmed by detection of a 9 kD band following *** analysis with Chinese bayberry extract gave bands of 22,45,and 90 kD,but no 9 kD band was *** was also no evidence of LTP recognition for loquat(36 kD) or melon(24 kD).This first report of a severe allergic reaction to Chinese bayberry fruit in a patient with LTP-mediated peach allergy indicates that other as yet unidentified non-pollen related fruit allergens are involved in this new severe fruit allergy.

关键词： Chinese bayberry Fruit allergy Anaphylaxis