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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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Are school uniforms associated with gender inequalities in physical activity? A pooled analysis of population-level data from 135 countries/regions

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Journal of Sport and Health Science 2024年第4期13卷 590-598页

作者： Mairead Ryan Luiza I.C.Ricardo Nicole Nathan Riikka Hofmann esther van Sluijs Medical Research Council Epidemiology Unit University of CambridgeCambridge CB20QQUK Faculty of Education University of CambridgeCambridge CB28PQUK Hunter New England Population Health WallsendNSW 2287Australia School of Medicine and Public Health College of HealthMedicine and WellbeingUniversity of NewcastleCallaghanNSW 2308Australia Hunter Medical Research Institute New Lambton HeightsNSW 2305Australia National Centre of Implementation Science University of NewcastleCallaghanNSW 2308Australia

Purpose:It is aimed to assess whether school uniforms are associated with population-level gender inequalities in physical activity,and whether associations differ by school level,country/region income,and assessment ***:An ecological study design was *** collected data about global uniform practices using an online *** searched for country/region-level estimates of school-aged youth meeting physical activity guidelines from international surveillance *** selection was conducted in duplicate using a systematic process,and a random sample of all data was checked to ensure extraction and pooling processes were *** calculated absolute and relative gender inequalities in physical activity for each *** regression examined associations between country/region-level uniform practices(binary yes/no exposure variable) and country/region-level gender inequalities in physical activity guideline compliance(absolute and relative inequalities).We investigated moderation by school level,stratified analyses by income group,and repeated primary analyses using device-measured ***:Pooling data from 135 countries/regions(n=1,089,852),we found no association between population-level uniform practices and gender inequalities in physical activity across all ages(absolute:β=-0.2;95% confidence interval(95%CI):-1.7 to 1.3,p=0.74;relative:β=0.1;95%CI:-0.1 to 0.2,p=0.51).Subgroup analysis suggested a positive association in primary school settings(absolute:β=4.3;95%CI:-0.0 to 8.6,p=0.05).Among high-income countries,absolute inequalities were significantly greater in countries/regions with uniform practices(N=37) compared to those without(N=48)(9.1(SD=3.6) vs.7.8 percentage points(SD=4.3)).Repeating analyses using device-measured data(n=32,130;N=24) did not alter our primary *** initial descriptive statistics,we found that in countries/regions where a maj ority of schools(>50%) reportedly use uniforms,there was lower compli

关键词： School policy Clothing Child Adolescent Accelerometer

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Blossom-end rot:a century-old problem in tomato(Solanum lycopersicum L.)and other vegetables

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Molecular Horticulture 2022年第1期2卷 1-10页

作者： Yasin Topcu Savithri U.Nambeesan esther van der Knaap Institute of Plant Breeding Genetics and GenomicsUniversity of GeorgiaAthensGA 30602USA 2Department of HorticultureUniversity of GeorgiaAthensGA 30602USA

Blossom-end rot(BER)is a devastating physiological disorder affecting vegetable production *** research into the physiological aspects of the disorder has demonstrated that the underlying causes of BER are associated with perturbed calcium(Ca^(2+))homeostasis and irregular watering conditions in predominantly cultivated ***,Reactive Oxygen Species(ROS)are critical players in BER development which,combined with unbalanced Ca^(2+)concentrations,greatly affect the severity of the *** availability of a high-quality reference tomato genome as well as the whole genome resequencing of many accessions has recently permitted the genetic dissection of BER in segregating populations derived from crosses between cultivated tomato *** has led to the identification of five loci contributing to BER from several *** eventual cloning of the genes contributing to BER would result in a deeper understanding of the molecular bases of the *** will undoubtedly create crop improvement strategies for tomato as well as many other vegetables that suffer from BER.

关键词： Blossom-end rot(BER) Reactive Oxygen Species(ROS) Ca^(2+)deficiency Abiotic stress Cell wall Tomato Antioxidants Plant growth regulators Fruit morphology

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Perspectives of CRISPR/Cas-mediated cisengineering in horticulture:unlocking the neglected potential for crop improvement

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Horticulture Research 2020年第1期7卷 2317-2327页

作者： Qiang Li Manoj Sapkota esther van der Knaap College of Horticultural Science and Engineering Shandong Agricultural UniversityTai’anChina Center for Applied Genetic Technologies University of GeorgiaAthensGAUSA Institute for Plant Breeding Genetics and GenomicsUniversity of GeorgiaAthensGAUSA Department of Horticulture University of GeorgiaAthensGAUSA

Directed breeding of horticultural crops is essential for increasing yield,nutritional content,and consumer-valued characteristics such as shape and color of the ***,limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding *** genetic changes in cisregulatory regions of genes play important roles in shaping phenotypic diversity by altering their *** of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted *** advent of CRISPR/Cas-mediated cis-regulatory region engineering(cis-engineering)provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop ***,we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural *** describe strategies and limitations for its use in crop improvement,including de novo cis-regulatory element(CRE)discovery,precise genome editing,and transgene-free genome *** addition,we discuss the challenges and prospects regarding current technologies and ***/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.

关键词： CRISPR/Cas breeding crops

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Understanding and managing the morphology of branches incising into sand-clay deposits in the Dutch Rhine Delta

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International Journal of Sediment Research 2013年第2期28卷 127-138页

作者： Kees SLOFF(C.J.) Ary van SPIJK esther STOUTHAMER Arjan SIEBEN Deltares and Delft University of Technology PO Box 1772600MH Delftthe Netherlands Assis.Prof. Water management Rijkswaterstaat Zuid HollandPO Box 5563000 AN Rotterdamthe Netherlands Senior Advisor Utrecht University Faculty of GeosciencesPO Box 801153508 TCUtrechtthe Netherlands AssisProf. Water management Rijkswaterstaat Center for Water ManagementPO Box 178200 AA Lelystadthe Netherlands Senior Advisor

In the Rhine-Meuse delta in the south-western part of the Netherlands,the morphology of the river branches is highly dependent on the erodibility of the *** processes that were initiated after closure of the Haringvliet estuary branch by a dam(in 1970),caused a strong incision of several connecting *** to the geological evolution of this area the lithology of the subsoil shows large variations in highly erodible sand and poorly erodible peat and clay *** study shows how the geological information can be used to create 3D maps of the erodibility of the sub-soil, and how this information can be used to schematize the sub-soil in computational models for morphological *** incisement of sand patches between areas with poorly erodible bed causes deep scour holes,hence increasing the risk on river-bank instability(flow slides) and damage to constructions such as groynes,quays,tunnels, and *** types of mathematical models,ranging from 1D(SOBEK) to quasi-3D(Delft3D) have been applied to study the future development of the river bed and possible management *** results of these approaches demonstrate that models require inclusion of a layer-bookkeeping approach for sub-soil schematization, non-uniform sediment fractions(sand-mud),tidal and river-discharge boundary conditions,and capacity-reduction transport *** risk-reducing river management it has been shown how the development of the river bed can be addressed on a large scale and small *** instance,the use of sediment feeding and fixation of bed can be proposed for large-scale management,while monitoring and interventions at initiation of erosion can be proposed as response to small-scale developments that exceed predefined intervention levels.

关键词： River morphological modeling River-bed erodibility River management Erosion Bed stratigraphy Bank and dike stability Mathematical model

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The Diagnostic and Therapeutic Challenges of Fabry Nephropathy—A Review of the Literature, Illustrated by a Clinical Case

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Open Journal of Nephrology 2023年第4期13卷 349-368页

作者： Stefan van Cauwelaert Caroline Geers Dominique vandervelde esther Scheirlynck Alexander Gheldof Karl-Martin Wissing Department of Nephrology and Arterial Hypertension Universitair Ziekenhuis Brussel (UZ Brussel) Vrije Universiteit Brussel (VUB) Brussels Belgium Department of Pathology Universitair Ziekenhuis Brussel (UZ Brussel) Vrije Universiteit Brussel (VUB) Brussels Belgium Department of Nephrology H&ocircpitaux Iris-Sud (HIS) Brussels Belgium Department of Cardiology Universitair Ziekenhuis Brussel (UZ Brussel) Vrije Universiteit Brussel (VUB) Brussels Belgium Department of Medical Genetics Universitair Ziekenhuis Brussel (UZ Brussel) Vrije Universiteit Brussel (VUB) Brussels Belgium

Fabry Disease (FD) is a rare lysosomal storage disorder characterized by α-galactosidase A (α-Gal A) enzyme deficiency, resulting in glycosphingolipid accumulation. Its clinical spectrum ranges from severe classical to milder nonclassical or late-onset phenotypes. Renal involvement, termed Fabry Nephropathy (FN), can vary from mild proteinuria to kidney failure. FN diagnosis, especially in nonclassical cases with a genetic Variant of Unknown Significance (VUS) in the GLA gene, poses challenges. Measurement of plasma lyso-Gb3 levels is gaining importance in FN diagnosis, while renal biopsy with electron microscopy remains the gold standard in equivocal cases. Treatment options include Enzyme Replacement Therapy (ERT) and chaperone therapy, demanding careful candidate selection due to high treatment costs. Research has predominantly focused on classical FD, revealing modest treatment benefits. However, evidence for treating patients, especially females, with milder nonclassical or late-onset phenotypes is scarce, emphasizing the necessity for placebo-controlled clinical trials in these subgroups. Meanwhile, participation in global FD registries can improve our understanding of disease management. Case Presentation: A woman in her late sixties presented with moderate chronic kidney disease, mild proteinuria, and microscopic hematuria. Her family history included a prevalence of renal, cardiac and cerebrovascular diseases. Kidney biopsy revealed characteristic myelin figures and zebra bodies in podocytes, strongly suggestive of FN. Genetic analysis identified a VUS in the GLA gene (c.655A > C, ***219Leu), introducing diagnostic uncertainty. Further investigations revealed severe cardiac involvement. Considering the recurring difficulty presented by the finding of a VUS in the GLA gene during FN assessments, along with the uncertainty regarding the need for treatment in nonclassical or late-onset FD phenotypes, especially in women, this case becomes a central focus for

关键词： Fabry Disease Fabry Nephropathy Variants of Unknown Significance Diagnosis Treatment Selection Lysosomal Storage Disorder α-Galactosidase A Glycosphingolipid Accumulation Enzyme Replacement Therapy Migalastat

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利用颜色的非刚性物体跟踪方法(英文)

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自动化学报 2003年第3期29卷 345-355页

作者： Katja Nummiaro esther Koller-Meier Luc van Gool Katholieke Universiteit Leuven Swiss Federal Institute of Technology (ETH)Katholieke Universiteit Leuven ESAT/PSI-VISICS Kasteelpark Arenberg 10 3001 Heverlee BelgiumD-ITET/BIWI Gloriastrasse 35 8092 Zurich SwitzerlandESAT/PSI-VISICS Kasteelpark Arenberg 10 3001 Heverlee Belgium Swiss Federal Institute of Technology (ETH) D-ITET/BIWI Gloriastrasse 35 8092 Zurich Switzerland

提出了一个利用颜色特征实时跟踪非刚性物体的方法 .首先 ,建立了一个颜色分布模型 ,该模型对部分遮挡具鲁棒性 ,对放缩和旋转具不变性 ,且计算简单 .对非刚体物体的实时鲁棒跟踪是一个非常有挑战性的课题 ,本文提出了利用颜色特征实时... 详细信息

提出了一个利用颜色特征实时跟踪非刚性物体的方法 .首先 ,建立了一个颜色分布模型 ,该模型对部分遮挡具鲁棒性 ,对放缩和旋转具不变性 ,且计算简单 .对非刚体物体的实时鲁棒跟踪是一个非常有挑战性的课题 ,本文提出了利用颜色特征实时跟踪非刚体物体的方法 .首先 ,建立了一个颜色分布模型 ,该模型对部分遮挡具有鲁棒性 ,对放缩具有不变性 ,而且计算简单 .然后 ,采用粒子滤波的方法将颜色分布模型集成到一个动态状态估计的概率框架中 .为了处理光照变化等引起的外貌变化 ,进一步引入自适应模型更新过程 .同时。

关键词：非刚性物体跟踪方法颜色颜色分布模型 Bhattacharyya系数鲁棒性

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Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice

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Horticulture Research 2023年第7期10卷 176-191页

作者： Qiang Li Shuangxia Luo Liying Zhang Qian Feng Lijun Song Manoj Sapkota Shuxin Xuan Yanhua Wang Jianjun Zhao esther van der Knaap Xueping Chen Shuxing Shen College of Horticulture State Key Laboratory of North China Crop Improvement and RegulationKey Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiHebei Agricultural UniversityBaodingHebei 071000China Center for Applied Genetic Technologies Institute for Plant BreedingGenetics and GenomicsDepartment of HorticultureUniversity of GeorgiaAthensGAUSA

Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer ***,modification of fruit shape has become one of the major objectives for crop ***,the underlying mechanisms of fruit shape regulation are poorly *** this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato,cucumber,and peach as *** analyses suggest that the OFP-TRM(OVATE Family Protein-TONNEAU1 Recruiting Motif)and IQD(IQ67 domain)pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit ***,cucumber homologs of FRUITFULL(FUL1),CRABS CLAW(CRC)and 1-aminocyclopropane-1-carboxylate synthase 2(ACS2)were found to regulate fruit *** also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice,and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones,including brassinosteroids,gibberellic acids,and auxin,and microtubule *** addition,functional redundancy and divergence of the members of each of the OFP,TRM,and IQD families are also *** review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.

关键词： Arabidopsis Molecular probably

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Exploiting the diversity of tomato:the development of a phenotypically and genetically detailed germplasm collection

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Horticulture Research 2020年第1期7卷 1941-1954页

作者： Estefanía Mata-Nicolás Javier Montero-Pau esther Gimeno-Paez Víctor Garcia-Carpintero Peio Ziarsolo Naama Menda Lukas A.Mueller JoséBlanca Joaquín Cañizares esther van der Knaap María JoséDíez Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana.COMAV.Universitat Politècnica de València ValenciaSpain Department of Biochemistry and Molecular Biology Universitat de ValènciaValenciaSpain Boyce Thompson Institute IthacaNYUSA Institute of Plant Breeding Genetics and GenomicsUniversity of GeorgiaGeorgiaGAUSA Department of Horticulture University of GeorgiaGeorgiaGAUSA

A collection of 163 accessions,including Solanum pimpinellifolium,Solanum lycopersicum *** and Solanum lycopersicum ***,was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication:Andean regions of Peru and Ecuador and *** collection is enriched with *** *** from the Amazonian region that has not been analyzed previously nor used *** collection has been morphologically characterized showing diversity for fruit,flower and vegetative *** genomes were sequenced in the Varitome project and are publicly available(***/projects/varitome).The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff *** has shown associations for different traits,demonstrating the potential of this collection for this kind of *** have not only identified known QTLs and genes,but also new regions associated with traits such as fruit color,number of flowers per inflorescence or inflorescence *** speed up and facilitate the use of this information,F2 populations were constructed by crossing the whole collection with three different *** F2 collection is useful for testing SNPs identified by GWAs,selection sweeps or any other candidate *** data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC *** these resources together make this collection a good candidate for genetic studies.

关键词： germplasm collection traits

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Studying Design and Use of Healthcare Technologies in Interaction: The Social Learning Perspective in a Dutch Quality Improvement Collaborative Program

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Health 2014年第15期6卷 1903-1918页

作者： esther van Loon Nelly Oudshoorn Roland Bal Erasmus University Rotterdam The Netherlands University of Twente Enschede The Netherlands

Designing technologies is a process that relies on multiple interactions between design and use contexts. These interactions are essential to the development and establishment of technologies. This article seeks to understand the attempts of healthcare organisations to integrate use contexts into the design of healthcare technologies following insights of the theoretical approaches of social learning and user representations. We present a multiple case study of three healthcare technologies involved in improving elderly care practice. These cases were part of a Dutch quality improvement collaborative program, which urged that development of these technologies was not “just” development, but should occur in close collaboration with other parts of the collaborative program, which were more focused on implementation. These cases illustrate different ways to develop technologies in interaction with use contexts and users. Despite the infrastructure of the collaborative program, interactions were not without problems. We conclude by arguing that interactions between design and use are not naturally occurring phenomena, but must be actively organised in order to create effects.

关键词： Quality Improvement Collaborative Program Social Learning User Representation Healthcare Technology Long-Term Healthcare

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