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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 2016.By intention,the 15 FAIR guiding principles do not dictate specific technological implementations,but provide guidance for improving Findability,Accessibility,Interoperability and Reusability of digital resources.This has likely contributed to the broad adoption of the FAIR principles,because individual stakeholder communities can implement their own FAIR solutions.However,it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible implementations.Thus,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)-usable.We introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible,robust,widespread and consistent FAIR implementations.Any 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 future.Here,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

The efficacy of vitamin E in preventing arthrofibrosis after joint replacement

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Animal Models and Experimental Medicine 2024年第2期7卷 145-155页

作者： Yingfang Fan Jean Yuh Sashank Lekkala Mehmet d.Asik Andrew Thomson Madeline McCanne mark A.Randolph Antonia F.Chen Ebru Oral Harris Orthopaedic Laboratory Department of Orthopaedic SurgeryMassachusetts General HospitalBostonMassachusettsUSA department of Orthopaedic Surgery Harvard Medical SchoolBostonMassachusettsUSA department of Surgery Harvard Medical SchoolBostonMassachusettsUSA department of Orthopaedic Surgery Brigham and Women's HospitalBostonMassachusettsUSA

Background:Arthrofibrosis is a joint disorder characterized by excessive scar formation in the joint tissues.Vitamin E is an antioxidant with potential anti-fibroblastic effect.The aim of this study was to establish an arthrofibrosis rat model after joint replacement and assess the effects of vitamin E supplementation on joint fibrosis.Methods:We simulated knee replacement in 16 male Sprague–dawley rats.We immobilized the surgical leg with a suture in full flexion.The control groups were killed at 2 and 12 weeks(n=5 per group),and the test group was supplemented daily with vitamin E(0.2 mg/mL)in their drinking water for 12 weeks(n=6).We performed histological staining to investigate the presence and severity of arthrofibrosis.Immunofluorescent staining andα2-macroglobulin(α2M)enzyme-linked immunosorbent assay(ELISA)were used to assess local and systemic inflammation.Static weight bearing(total internal reflection)and range of motion(ROM)were collected for functional assessment.Results:The ROM and weight-bearing symmetry decreased after the procedure and recovered slowly with still significant deficit at the end of the study for both groups.Histological analysis confirmed fibrosis in both lateral and posterior periarticular tissue.Vitamin E supplementation showed a moderate anti-inflammatory effect on the local and systemic levels.The vitamin E group exhibited significant improvement in ROM and weight-bearing symmetry at day 84 compared to the control group.Conclusions:This model is viable for simulating arthrofibrosis after joint replacement.Vitamin E may benefit postsurgical arthrofibrosis,and further studies are needed for dosing requirements.

关键词： arthrofibrosis range of motion total knee arthroplasty vitamin E

A three-dimensional feature extraction-based method for coal cleat characterization using X-ray μCT and its application to a Bowen Basin coal specimen

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第1期16卷 153-166页

作者： Yulai Zhang Matthew Tsang mark Knackstedt Michael Turner Shane Latham Euan Macaulay Rhys Pitchers ARC Training Centre for M3d Innovation Research School of PhysicsAustralian National UniversityCanberraACT2601Australia department of Materials Physics Research School of PhysicsAustralian National UniversityCanberraACT2601Australia Anglo American Steelmaking Coal BrisbaneQLD4000Australia SCT Operations Pty Ltd. WollongongNSW2500Australia

Cleats are the dominant micro-fracture network controlling the macro-mechanical behavior of coal.Improved understanding of the spatial characteristics of cleat networks is therefore important to the coal mining industry.discrete fracture networks(dFNs)are increasingly used in engineering analyses to spatially model fractures at various scales.The reliability of coal dFNs largely depends on the confidence in the input cleat statistics.Estimates of these parameters can be made from image-based three-dimensional(3d)characterization of coal cleats using X-ray micro-computed tomography(m CT).One key step in this process,after cleat extraction,is the separation of individual cleats,without which the cleats are a connected network and statistics for different cleat sets cannot be measured.In this paper,a feature extraction-based image processing method is introduced to identify and separate distinct cleat groups from 3d X-ray m CT images.Kernels(filters)representing explicit cleat features of coal are built and cleat separation is successfully achieved by convolutional operations on 3d coal images.The new method is applied to a coal specimen with 80 mm in diameter and 100 mm in length acquired from an Anglo American Steelmaking Coal mine in the Bowen Basin,Queensland,Australia.It is demonstrated that the new method produces reliable cleat separation capable of defining individual cleats and preserving 3d topology after separation.Bedding-parallel fractures are also identified and separated,which has his-torically been challenging to delineate and rarely reported.A variety of cleat/fracture statistics is measured which not only can quantitatively characterize the cleat/fracture system but also can be used for dFN modeling.Finally,variability and heterogeneity with respect to the core axis are investigated.Significant heterogeneity is observed and suggests that the representative elementary volume(REV)of the cleat groups for engineering purposes may be a complex problem requiring careful consideration.

关键词： Cleat separation Cleat statistics Feature extraction discrete fracture network(dFN)modeling

Treatment and prevention of epilepsy in onchocerciasis-endemic areas is urgently needed

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Infectious diseases of Poverty 2024年第1期13卷 85-89页

作者： Robert Colebunders Joseph Nelson Siewe Fodjo Olivia Kamoen Luis-Jorge Amaral Amber Hadermann Chiara Trevisan mark J.Taylor Julia Gauglitz Achim Hoerauf Yasuaki Sato Katja Polman Maria-Gloria Basanez dan Bhwana Thomson Lakwo Gasim Abd-Elfarag Sebastien d.Pion Global Health Institute University of AntwerpAntwerpBelgium department of Neurology Heilig Hart ZiekenhuisLierBelgium department of Public Health Institute of Tropical MedicineAntwerpBelgium Liverpool School of Tropical Medicine LiverpoolUK department of Computer Science University of AntwerpAntwerpBelgium Institute of Medical Microbiology Immunology and ParasitologyUniversity Hospital BonnBonnGermany German Center for Infection Research(dZIF) Partner Site Bonn-CologneBonnGermany School of Global Humanities and Social Sciences Nagasaki UniversityNagasakiJapan MRC Centre for Global Infectious disease Analysis and London Centre for Neglected Tropicaldisease Research Department of Infectious Disease EpidemiologySchool of Public HealthImperial College LondonLondonUK National Institute for Medical Research TangaTanzania Vector Control division Ministry of HealthKampalaUganda School of Public Health University of JubaJubaSouth Sudan Access for Humanity JubaSouth Sudan French National Research Institute for Sustainable development MontpellierFrance

Background There is increasing epidemiological evidence supporting the association between onchocerciasis and seizures,reinforcing the concept of onchocerciasis-associated epilepsy(OAE).The aim of this paper is to provide an update on the new knowledge about OAE and to propose recommendations to the World Health Organization how to address this public health problem.Main text during the 2nd International Workshop on OAE held on 19-21 September,2023,in Antwerp,Belgium,participants recognised OAE as a substantial yet neglected public health problem,particularly in areas of sub-Saharan Africa where onchocerciasis remains hyperendemic.Evidence from prospective population-based studies suggest that strengthening onchocerciasis elimination efforts leads to a significant reduction of OAE incidence.There is a need to validate an OAE case definition to estimate the burden of disease and identify onchocerciasis-endemic areas requiring intensification of onchocerciasis elimination programmes and integration of epilepsy care t is expected that raising awareness about OAE will boost the population uptake of ivermectin.The implementation of a commu-nity-based epilepsy treatment programme offering free anti-seizure medications(ASMs)has shown high effectiveness in reducing the frequency of seizures and improving the overall quality of life of people with epilepsy.Conclusions To reduce OAE burden,enhanced collaboration between onchocerciasis and mental health pro-grammes at community,national,and international levels is required.Urgent efforts are needed to ensure the uninter-rupted provision of free ASMs in onchocerciasis-endemic areas.Furthermore,OAE should be included in the quantif-cation of the onchocerciasis disease burden.

关键词： Onchocerciasis Morbidity Burden of disease Prevention Ivermectin Epilepsy Nodding syndrome Treatment Children Policy

Measuring Pedestrian Stress Response (MPSR) Using Wearable Technologies

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Journal of Transportation Technologies 2024年第2期14卷 224-235页

作者： Ishita dash Rachael Anne Muscatello mark d. Abkowitz Ella R. Mostoller Mike Sewell department of Civil and Environmental Engineering Vanderbilt University 2301 Vanderbilt Place Nashville USA department of Psychiatry and Behavioral Sciences SENSE Lab Vanderbilt University Medical Center 1211 Medical Center Drive Nashville USA Gresham Smith 111 West Main Street Suite 201 Louisville USA

Walkability is an essential aspect of urban transportation systems. Properly designed walking paths can enhance transportation safety, encourage pedestrian activity, and improve community quality of life. This, in turn, can help achieve sustainable development goals in urban areas. This pilot study uses wearable technology data to present a new method for measuring pedestrian stress in urban environments and the results were presented as an interactive geographic information system map to support risk-informed decision-making. The approach involves analyzing data from wearable devices using heart rate variability (RMSSd and slope analysis) to identify high-stress locations. This data-driven approach can help urban planners and safety experts identify and address pedestrian stressors, ultimately creating safer, more walkable cities. The study addresses a significant challenge in pedestrian safety by providing insights into factors and locations that trigger stress in pedestrians. during the pilot study, high-stress pedestrian experiences were identified due to issues like pedestrian-scooter interaction on pedestrian paths, pedestrian behavior around high foot traffic areas, and poor visibility at pedestrian crossings due to inadequate lighting.

关键词： Wearable Technology Walkability Built Environment Pedestrian Safety

A network-based cognitive training induces cognitive improvements and neuroplastic changes in patients with relapsing-remitting multiple sclerosis:an exploratory case-control study

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Neural Regeneration Research 2021年第6期16卷 1111-1120页

作者： Riccardo Manca Micaela Mitolo Iain d.wilkinson david Paling Basil Sharrack Annalena Venneri department of Neuroscience University of SheffieldSheffieldUK Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna Diagnostica Funzionale NeuroradiologicaBolognaItaly Academic Unit of Radiology University of SheffieldSheffieldUK Academic department of Neuroscience Sheffield Teaching HospitalNational Health Service Foundation TrustSheffieldUK

Cognitive impairments are commonly observed in patients with multiple sclerosis and are associated with lower levels of quality of life.No consensus has been reached on how to tackle effectively cognitive decline in this clinical population non-pharmacologically.This exploratory case-control study aims to investigate the effectiveness of a hypothesis-based cognitive training designed to target multiple domains by promoting the synchronous co-activation of different brain areas and thereby improve cognition and induce changes in functional connectivity in patients with relapsing-remitting multiple sclerosis.Forty-five patients(36 females and 9 males,mean age 44.62±8.80 years)with clinically stable relapsing-remitting multiple sclerosis were assigned to either a standard cognitive training or to control groups(sham training and nonactive control).The standard training included twenty sessions of computerized exercises involving various cognitive functions supported by distinct brain networks.The sham training was a modified version of the standard training that comprised the same exercises and number of sessions but with increased processing speed load.The non-active control group received no cognitive training.All patients underwent comprehensive neuropsychological and magnetic resonance imaging assessments at baseline and after 5 weeks.Cognitive and resting-state magnetic resonance imaging data were analyzed using repeated measures models.At reassessment,the standard training group showed significant cognitive improvements compared to both control groups in memory tasks not specifically targeted by the training:the Buschke Selective Reminding Test and the Semantic Fluency test.The standard training group showed reductions in functional connectivity of the salience network,in the anterior cingulate cortex,associated with improvements on the Buschke Selective Reminding Test.No changes were observed in the sham training group.These findings suggest that multi-domain training that stimulates multiple brain areas sync

关键词： cognitive training magnetic resonance imaging multiple sclerosis neuroplasticity neuropsychology rehabilitation salience network

Modulating p-type doping of two-dimensional material palladium diselenide

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Nano Research 2024年第4期17卷 3232-3244页

作者： Jiali Yang Yu Liu En-Yang Wang Jinbo Pang Shirong Huang Thomas Gemming Jinshun Bi Alicja Bachmatiuk Hao Jia Shu-Xian Hu Chongyun Jiang Hong Liu Gianaurelio Cuniberti Weijia Zhou mark H Rümmeli Institute for Advanced Interdisciplinary Research(iAIR) University of JinanJinan 250022China Institute for Materials Chemistry Leibniz Institute for Solid State and Materials Research Dresden(IFW Dresden)20 Helmholtz StrasseDresden 01069Germany State Key Lab of Transducer Technology Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghai 200050China College of Energy Soochow Institute for Energy and Materials Innovations Soochow UniversitySuzhou 215006China Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu Province Soochow UniversitySuzhou 215006China School of Integrated Circuits University of Chinese Academy of SciencesBeijing 101408China Institute of Microelectronics of Tianjin Binhai New Area Tianjin 300451China Institute of Microelectronics Chinese Academy of SciencesBeijing 100029China Lukasiewicz Research Network PORT Polish Center for Technology DevelopmentStablowicka 147Wroclaw 54-066Poland School of Mathematics and Physics University of Science and Technology BeijingBeijing 100083China College of electronic information and optical engineering Nankai UniversityTianjin 300350China Centre of Polymer and Carbon Materials Polish Academy of SciencesM.Curie Sklodowskiej 34Zabrze 41-819Poland Center for Energy and Environmental Technologies VŠB-Technical University of Ostrava17.Listopadu 15Ostrava 70833Czech Republic State Key Laboratory of Crystal Materials Center of Bio&Micro/Nano Functional MaterialsShandong UniversityJinan 250100China dresden Center for Computational Materials Science Technische Universität DresdenDresden 01062Germany dresden Center for Intelligent Materials(GCL dCIM) Technische Universität DresdenDresden 01062Germany Institute for Materials Science and Max Bergmann Center of Biomaterials Technische Universität DresdenDresden 01069Germany Center for Advancing Electronics dresden Technische Universität DresdenDresden 01069Germany

The van der Waals heterostructures have evolved as novel materials for complementing the Si-based semiconductor technologies.Group-10 noble metal dichalcogenides(e.g.,PtS_(2),PtSe_(2),PdS_(2),and PdSe_(2))have been listed into two-dimensional(2d)materials toolkit to assemble van der Waals heterostructures.Among them,PdSe_(2) demonstrates advantages of high stability in air,high mobility,and wide tunable bandgap.However,the regulation of p-type doping of PdSe_(2) remains unsolved problem prior to fabricating p–n junction as a fundamental platform of semiconductor physics.Besides,a quantitative method for the controllable doping of PdSe_(2) is yet to be reported.In this study,the doping level of PdSe_(2) was correlated with the concentration of Lewis acids,for example,SnCl_(4),used for soaking.Considering the transfer characteristics,the threshold voltage(the gate voltage corresponding to the minimum drain current)increased after SnCl_(4) soaking treatment.PdSe_(2) transistors were soaked in SnCl_(4) solutions with five different concentrations.The threshold voltages from the as-obtained transfer curves were extracted for linear fitting to the threshold voltage versus doping concentration correlation equation.This study provides in-depth insights into the controllable p-type doping of PdSe_(2).It may also push forward the research of the regulation of conductivity behaviors of 2d materials.

关键词： two-dimensional(2d)materials Lewis acid treatment p-type doping field-effect transistors transfer characteristic

Causes of Cretaceous subduction termination below South China and Borneo:Was the Proto-South China Sea underlain by an oceanic plateau?

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Geoscience Frontiers 2024年第2期15卷 100-124页

作者： Suzanna H.A.van de Lagemaat Licheng Cao Junaidi Asis Eldert L.Advokaat Paul R.d.Mason mark J.dekkers douwe J.J.van Hinsbergen department of Earth Sciences Utrecht UniversityUtrechtthe Netherlands College of Marine Science and Technology China University of GeosciencesWuhanChina Faculty of Science and Natural Resources Universiti Malaysia SabahKota KinabaluMalaysia

The South China,Indochina,and Borneo margins surrounding the South China Sea contain long-lived arcs that became inactive at approximately 85 Ma,even though an embayment of oceanic crust(the‘Proto-South China Sea’)remained in the intervening region.This oceanic crust eventually subducted in the Cenozoic below Borneo and the Cagayan arc,while the modern South China Sea opened in its wake.To investigate the enigmatic cessation of Mesozoic subduction below South China and Borneo,we studied a fragment of oceanic crust and overlying trench-fill sediments that accreted to NW Borneo during the final stages of Paleo-Pacific subduction.Based on radiolarian biostratigraphy of cherts overlying the pillow basalts and detrital zircon geochronology of the trench-fill,we constrained the minimum age of the oceanic crust during accretion to 40 Ma.This shows that subduction cessation was not related to ridge subduction.Geochemical analysis of pillow basalts revealed an enriched mid-ocean ridge basalt signature comparable to oceanic plateaus.Using paleomagnetism,we show that this fragment of oceanic crust was not part of the Izanagi Plate but was part of a plate(the‘Pontus’Plate)separated from the Izanagi Plate by a subduction zone.Based on the minimum 40 Ma age of the oceanic crust and its geochemistry,we suggest that Mesozoic subduction below South China and Borneo stopped when an oceanic plateau entered the trench,while the eastern plate margin with the Izanagi Plate remained active.We show how our findings offer opportunities to restore plate configurations of the Panthalassa-Tethys junction region.

关键词： Proto-South China Sea Paleomagnetism Geochemistry Borneo Paleo-Pacific Izanagi Plate

LKB1 depletion-mediated epithelial-mesenchymal transition induces fibroblast activation in lung fibrosis

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Genes & diseases 2024年第3期11卷 417-426页

作者： Zijian Xu Elizabeth R.davies Liudi Yao Yilu Zhou Juanjuan Li Aiman Alzetani Ben G.Marshall david Hancock Tim Wallis Julian downward Rob M.Ewing donna E.davies mark G.Jones Yihua Wang Biological Sciences Faculty of Environmental and Life SciencesUniversity of SouthamptonSouthampton SO171BJUK clinical and Experimental Sciences Faculty of MedicineUniversity of SouthamptonSouthampton SO166YDUK Institute for Life Sciences University of SouthamptonSouthampton SO171BJUK NIHR Southampton Biomedical Research Centre University Hospital SouthamptonSouthampton SO166YDUK University Hospital Southampton Southampton SO166YDUK Oncogene Biology The Francis Crick InstituteLondon NW11ATUK

The factors that determine fibrosis progression or normal tissue repair are largely unknown.We previously demonstrated that autophagy inhibition-mediated epithelial-mesenchymal transition(EMT)in human alveolar epithelial type Il(ATIl)cells augments local myofibroblast differentiation in pulmonary fibrosis by paracrine signaling.Here,we report that liver kinase B1(LKB1)inactivation in ATIl cells inhibits autophagy and induces EMT as a conse-quence.In IPF lungs,this is caused by the down-regulation of CAB39L,a key subunit within the LKB1 complex.3d co-cultures of ATIl cells and MRC5 lung fibroblasts coupled with RNA sequencing(RNA-seq)confirmed that paracrine signaling between LKB1-depleted ATIl cells and fibroblasts augmented myofibroblast differentiation.Together,these data suggest that reduced autophagy caused by LKB1 inhibition can induce EMT in ATIl cells and contribute to fibrosis via aberrant epithelial-fibroblast crosstalk.

关键词： CAB39L Crosstalk EMT LKB1 Pulmonary fibrosis