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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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Neuron-to-astrocyte proteostatic stress signaling in response to tau pathology

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Neural Regeneration Research 2024年第3期19卷 505-506页

作者： Kevin Llewelyn Batenburg Wiep Scheper Amsterdam UMC location Vrije Universiteit Amsterdam Department of Human GeneticsAmsterdam Neuroscience-NeurodegenerationAmsterdamThe Netherlands Department of Functional Genomics Center for Neurogenomics and Cognitive ResearchVrije Universiteit AmsterdamAmsterdam Neuroscience-NeurodegenerationAmsterdamThe Netherlands

Maintenance of protein homeostasis or“proteostasis”is essential for the functioning and viability of *** is in particular the case for cells like neurons that cannot self-renew and acquire unique functional properties during their *** proteostatic stress responses are in place to protect cells from damage in case of proteostatic *** integrated stress response(ISR)is one of the key proteostatic stress responses in the cell(Costa-Mattioli and Walter,2020).The ISR is the downstream convergence point for the four stress-induced eIF2αkinases(EIF2AK1-4)that control stress-regulated protein translation via phosphorylation of the translation factor eIF2α.ISR activation results in a transient reduction of global translation while it concomitantly enhances the translation of specific mRNAs,including that encoding the activating transcription factor 4(ATF4).Together,the translational control mediated by the ISR results in a temporary reduction of the overall protein load and the selectively increased expression of proteins that contribute to restoration of the proteostatic balance.

关键词： translation stress Together

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Consumer transparency in the production chain for plant varieties produced using new genomic techniques

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aBIOTECH 2024年第2期5卷 239-246页

作者： J.M.Lukasiewicz C.C.M.van de Wiel L.A.P.Lotz M.J.M.Smulders Wageningen University&Research P.O.Box 386NL-6700 AJ WageningenThe Netherlands

Plants edited with new genomic techniques(NGTs)currently fall under the Genetically Modified Organisms Directive(2001/18/EC)in the European *** the proposal of the European Commission,NGT plants are partially exempted from the regulations of this *** proposal makes a distinction between two categories of NGT plants:NGT-1 and ***-1 category plants are considered equal to plants obtained through conventional breeding *** plants will not be labelled for the consumer,although they will be labelled as ***-2 category plants may be labelled with additional information as a positive *** of seeds of varieties made with gene editing,but not the products,would mean that most steps in the production chain are transparent,but not the last step towards ***“right to know”and increasing knowledge of gene-edited food is a common theme in food labelling towards ***,we describe current labelling regimes and registers and how these may be applied to provide transparency on gene-edited products to ***,we also look into consumer studies,which indicate a greater acceptance of gene-edited food among consumers,especially when additional benefits such as sustainability are mentioned.

关键词： Labelling New genomic techniques Consumer transparency Plant products

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Mid-term survival of the Optimys short stem: A prospective case series of 500 patients

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World Journal of Orthopedics 2024年第3期15卷 257-265页

作者： Bryan Hamans Sheryl de Waard Sjoerd Kaarsemaker Esther R C Janssen Inger N Sierevelt Gino M M J Kerkhoffs Daniël Haverkamp Department of Orthopaedic Surgery Xpert ClinicAmsterdam 1101EANetherlands Department of Orthopedic Surgery Amsterdam University Medical CenterAmsterdam 1105 AZNetherlands Esther R C Janssen Department of Orthopaedic SurgeryViecuri Medisch CentrumVenlo 5912 BLNetherlands Centre for Orthopaedic Research Spaarne ZiekenhuisHoofddorp 2134 TMNetherlands Department of Orthopaedic Surgery and Sports Medicine Amsterdam UMC-Location AMCAmsterdam 1105 AZNetherlands Department of Orthopedic Surgery Xpert Orthopedic Surgery ClinicAmsterdam 1101 EANetherlands

BACKGROUND In recent years,there has been an increase in the number of total hip arthroplasty procedures in the younger patient *** active group has higher expectations of their prosthesis in comparison to the older population,and there is a greater physical demand for the *** femoral stems were in-troduced to retain proximal bone stock and joint biomechanics and became more common to implant in this specific ***,the long-term survival and functional outcomes of various short stems are still being investigated in different *** To determine the 5-year survival of the Optimys hip *** This was a prospective multicenter cohort study of 500 patients conducted in two hospitals in the *** patients received the Optimys short stem(Mathys Ltd,Bettlach,Switzerland).The primary outcome measure was survival of the hip stem,with revision as the *** secondary outcome measurements included patient-reported outcome measures(PROMs).Kaplan-Meier analysis was used to calculate the 5-year survival ***-minus-log transformation was performed to calculate the 95%confidence interval(95%CI).Mixed model analyses were performed to assess the course of the PROMs during the 1st 2 years after *** were modeled separately for the 1st and 2nd years to calculate the yearly change in PROMs during both follow-up periods with accompanying 95%*** The mean age of the total 500 patients was 62.3 years(standard deviation:10.6)and 202 were male(40%).At a median follow-up of 5.5 years(interquartile range:4.5-6.7),7 patients were deceased and 6 revisions were registered,for infection(n=3),subsidence(n=2)and malposition(n=1).This resulted in an overall 5-year survival of 98.8%(95%CI:97.3-99.5).If infection was left out as reason for revision,a stem survival of 99.4%(95%CI:98.1-99.8)was *** questionnaires were completed by 471 patients(94%),317 patients(63%)completed the 1-year follow-up questionna

关键词： Total hip arthroplasty Femoral stem Short stem Optimys Survival 5-year survival Revision PROMs

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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Parametric investigation of railway fastenings into the formation and mitigation of short pitch corrugation

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Railway Engineering Science 2024年第3期32卷 286-306页

作者： Pan Zhang Shaoguang Li Rolf Dollevoet Zili Li Section of Railway Engineering Delft University of TechnologyStevinweg 12628 CN Delftthe Netherlands

Short pitch corrugation has been a problem for railways worldwide over one *** this paper,a parametric investigation of fastenings is conducted to understand the corrugation formation mechanism and gain insights into corrugation mitigation.A three-dimensional finite element vehicle-track dynamic interaction model is employed,which considers the coupling between the structural dynamics and the contact mechanics,while the damage mechanism is assumed to be differential *** fastening models with different configurations,boundary conditions,and parameters of stiffness and damping are built up and *** models may represent different service stages of fastenings in the ***,the effect of train speeds on corrugation features is *** results indicate:(1)Fastening parameters and modelling play an important role in corrugation formation.(2)The fastening longitudinal constraint to the rail is the major factor that determines the corrugation *** fastening vertical and lateral constraints influence corrugation features in terms of spatial distribution and wavelength components.(3)The strengthening of fastening constraints in the longitudinal dimension helps to mitigate ***,the inner fastening constraint in the lateral direction is necessary for corrugation alleviation.(4)The increase in fastening longitudinal stiffness and damping can reduce the vibration amplitudes of longitudinal compression modes and thus reduce the track corrugation *** simulation in this work can well explain the field corrugation in terms of the occurrence possibility and major wavelength *** can also explain the field data with respect to the small variation between the corrugation wavelength and train speed,which is caused by frequency selection and jump between rail longitudinal compression modes.

关键词： Short pitch corrugation Fastening modelling and parameters Corrugation formation and mitigation Rail longitudinal compression modes Finite element vehicle-track interaction model

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Operando NMR methods for studying electrocatalysis

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Magnetic Resonance Letters 2024年第2期4卷 54-64页

作者： Zhiyu Zhu Ruipeng Luo Evan Wenbo Zhao Magnetic Resonance Research Center Institute for Molecules and MaterialsRadboud University6525 AJ Nijmegenthe Netherlands

The combination of electrochemical measurements with spectroscopic characterizations provides valuable insights into reaction *** magnetic resonance(NMR)spectroscopy,as a powerful technique due to its atomic specificity and versatility in studying gas,liquid,and solid,allows the study of electrolyte solution,catalyst and catalyst-adsorbate *** applied in operando,NMR can offer molecular-level insights into various electrochemical *** NMR has been applied extensively in battery research,but relatively underexplored for electrocatalysis in the past two *** this mini review,we first introduce the operando electrochemical NMR setups,categorized by different probe *** we review the applications of operando NMR for monitoring the electrolyte solution and the catalyst-adsorbate *** the high environmental impact of electrochemical conversion of CO_(2)into value-added products,we zoom in to the use of operando NMR in studying electrochemical CO_(2)***,we provide our perspective on further developing and applying operando NMR methods for understanding the complex reaction network of Cu-catalyzed electrochemical CO_(2)reduction.

关键词： Operando NMR In situ NMR EC-NMR Electrocatalysis Electrochemical CO_(2)reduction

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Epidemiology of insertional and midportion Achilles tendinopathy in runners:A prospective cohort study

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Journal of Sport and Health Science 2024年第2期13卷 256-263页

作者： Wenbo Chen Kyra L.A.Cloosterman Sita M.A.Bierma-Zeinstra Marienke van Middelkoop Robert-Jan de Vos Department of Orthopaedic Surgery and Sports Medicine Erasmus MC University Medical CenterRotterdam 3015GDthe Netherlands Department of General Practice Erasmus MC University Medical CenterRotterdam 3015GDthe Netherlands Department of Sports Medicine Huashan HospitalFudan UniversityShanghai 200040China

Background:Achilles tendinopathy(AT)is a common problem among *** is only limited evidence for risk factors for AT,and most studies have not defined the AT *** study has compared the incidence and risk factors between insertional AT and midportion AT,though they are considered *** study aimed to assess incidence and risk factors of AT based on data from a large prospective *** secondary aim was to explore differences in risk factors between insertional and midportion ***:Participants were recruited from among registered runners at registration for running *** were completed at baseline,1 month before the event,1 week before the event,and 1 month after the *** concerning demographics,training load,registered events,and running-related injuries were collected at *** follow-up questionnaires collected information about new injuries.A pain map was used to diagnose midportion and insertional *** primary outcome was the incidence of *** logistic regression analysis was applied to identify risk factors for the ***:We included 3379 participants with a mean follow-up of 20.4 *** incidence of AT was 4.2%.The proportion of insertional AT was 27.7%and of midportion AT was 63.8%;the remaining proportion was a combined type of insertional and midportion *** had a significantly higher incidence(5%,95%confidence interval(95%CI):4.1%-6.0%)than women(2.8%,95%CI:2.0%-3.8%).AT in the past12 months was the most predominant risk factor for new-onset AT(odds ratio(OR)=6.47,95%CI:4.27-9.81).This was similar for both subcategories of AT(insertional:OR=5.45,95%CI:2.51-11.81;midportion:OR=6.96,95%CI:4.24-11.40).Participants registering for an event with a distance of 10/10.55 km were less likely to develop a new-onset AT(OR=0.59,95%CI:0.36-0.97)or midportion AT(OR=0.47,95%CI:0.23-0.93).Higher age had a significant negative association with insertional AT(OR=0.97,95%CI:0.9

关键词： Achilles tendon injury Incidence Risk factor Running-related injury

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Deciding on life-saving treatment after a violent suicide attempt:an ethical case report

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General Psychiatry 2024年第2期37卷 289-291页

作者： Robert Wichers Hanna M Heller Sisco van Veen Department of Child and Adolescent Psychiatry&Psychosocial Care Amsterdam University Medical CenterLocation AMCAmsterdamThe Netherlands Amsterdam Public Health Mental Health programAmsterdamThe Netherlands Department of Hospital Psychiatry Amsterdam University Medical CenterLocation VUmcAmsterdamThe Netherlands Research Department 113 Suicide PreventionAmsterdamThe Netherlands Department of Psychiatry&Department of Ethics Law and HumanitiesAmsterdam University Medical CenterAmsterdamThe Netherlands GGZ inGeest Mental Health Care AmsterdamThe Netherlands

To the editor:In the USA alone,there were 1.7 million suicide attempts in 2021.1 Although the majority of suicide attempts are not fatal,immediate medical attention is often necessary,especially when violent methods are used.2 These methods include jumping from heights,using a firearm,crashing a motor vehicle,and lying down or jumping in front of a moving object.

关键词： treatment editor alone

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Liquid injectivity in a SAG foam process:Effect of permeability

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Petroleum Science 2024年第1期21卷 302-314页

作者： Jia-Kun Gong Yuan Wang Ridhwan-Zhafri B.Kamarul Bahrim Raj-Deo Tewari Mohammad-Iqbal Mahamad Amir Rouhi Farajzadeh William Rossen College of Mechanics and Materials Hohai UniversityNanjing210098JiangsuChina College of Water Conservancy&Hydropower Engineering Hohai UniversityNanjing210098JiangsuChina PETRONAS Kuala Lumpur50088Malaysia Department of Geoscience and Engineering Delft University of Technology2628 CNDelftthe Netherlands Shell Global Solutions International B.V. 1031 HWAmsterdamthe Netherlands

Foam is utilized in enhanced oil recovery and CO_(2) ***-alternating-gas(SAG)is a preferred approach for placing foam into reservoirs,due to it enhances gas injection and minimizes corrosion in *** previous studies with similar permeability cores show that during SAG injection,several banks occupy the area near the well where fluid exhibits distinct ***,underground reservoirs are heterogeneous,often *** is crucial to understand the effect of permeability on fluid behaviour and injectivity in a SAG *** this work,coreflood experiments are conducted in cores with permeabilities ranging from 16 to 2300 *** observe the same sequence of banks in cores with different ***,the speed at which banks propagate and their overall mobility can vary depending on *** higher permeabilities,the gas-dissolution bank and the forced-imbibition bank progress more rapidly during liquid *** total mobilities of both banks decrease with *** utilizing a bank-propagation model,we scale up our experimental findings and compare them to results obtained using the Peaceman *** findings reveal that the liquid injectivity in a SAG foam process is misestimated by conventional simulators based on the Peaceman *** lower the formation permeability,the greater the error.

关键词： Foam Enhanced oil recovery Surfactant-alternating-gas Injectivity Permeability

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