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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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FAIR data Point:A FAIR-Oriented Approach for Metadata Publication

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data Intelligence 2023年第1期5卷 163-183页

作者： Luiz Olavo Bonino da Silva Santos Kees Burger Rajaram Kaliyaperumal mark d.wilkinson Services and Cybersecurity group Faculty of Electrical EngineeringMathematics and Computer ScienceUniversity of Twente-Enschede7513GBthe Netherlands Biosemantics group Department of Human GeneticsLeiden University Medical Center-LeidenNL 2333 ZCthe Netherlands Escuela Técnica Superior de Ingenieria Agronomica Alimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain

Metadata,data about other digital objects,play an important role in FAIR with a direct relation to all FAIR *** this paper we present and discuss the FAIR data Point(FdP),a software architecture aiming to define a common approach to publish semantically-rich and machine-actionable metadata according to the FAIR *** present the core components and features of the FdP,its approach to metadata provision,the criteria to evaluate whether an application adheres to the FdP specifications and the service to register,index and allow users to search for metadata content of available FdPs.

关键词： FAIR FAIR data point FAIR principles Metadata Interoperability Linked data Semantic interoperability

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

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

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design Improvements and Validation of a Novel Fully 3d Printed Analogue Lumbar Spine Motion Segment

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Journal of Bionic Engineering 2024年第3期21卷 1388-1396页

作者： Siril Teja dukkipati mark driscoll Musculoskeletal Biomechanics Research Lab Department of Mechanical EngineeringMcGill University845 Sherbrooke St.W(163)MontréalQCH3A 0C3Canada Orthopaedic Research Lab Montreal General Hospital1650 Cedar Ave(LS1.409)MontréalQCH3G 1A4Canada

Spine biomechanical testing methods in the past few decades have not evolved beyond employing either cadaveric studies or finite element modeling ***,both these approaches may have inherent cost and time *** studies are the present gold standard for spinal implant design and regulatory approval,but they introduce significant variability in measurements across patients,often requiring large sample *** element modeling demands considerable expertise and can be computationally expensive when complex geometry and material nonlinearity are *** analogue spine models could complement these traditional methods as a low-cost and high-fidelity alternative.A fully 3d printable L-S1 analogue spine model with ligaments is developed and validated in this *** stiffness of the model under pure bending loading in flexion-extension,Lateral Bending(LB)and Axial Rotation(AR)is evaluated and compared against historical ex vivo and in silico ***,the effect of interspinous,intertransverse ligaments and the Thoracolumbar Fascia(TLF)on spinal stiffness is evaluated by systematic construction of the *** flexion,model Range of Motion(ROM)was 12.92±0.11°(ex vivo:16.58°,in silico:12.96°)at *** LB,average ROM was 13.67±0.12°at 7.5 Nm(ex vivo:15.21±1.89°,in silico:15.49±0.23°).Similarly,in AR,average ROM was 17.69±2.12°at 7.5Nm(ex vivo:14.12±0.31°,in silico:15.91±0.28°).The addition of interspinous and intertransverse ligaments increased both flexion and LB stiffnesses by approximately 5%.Addition of TLF showed increase in flexion and AR stiffnesses by 29%and 24%,*** novel model can reproduce physiological ROMs with high repeatability and could be a useful open-source tool in spine biomechanics.

关键词： Lumbar spine 3d printing Intervertebral disc Biomechanical testing Spine mechanics

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Analysis of the inflection points of height-diameter models

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Forest Ecosystems 2024年第4期11卷 414-422页

作者： Tzeng Yih Lam mark J.ducey department of Forest Resources Management Faculty of ForestryThe University of British Columbia2045-2424 Main MallVancouverBCV6T 1Z4 Canada department of Natural Resources and the Environment University of New Hampshire114 James HallDurhamNH 03824USA

The inflection point is an important feature of sigmoidal height-diameter(H-d)*** is often cited as one of the properties favoring sigmoidal model ***,there are very few studies analyzing the inflection points of H-d *** goals of this study were to theoretically and empirically examine the behaviors of inflection points of six common H-d models with a regional *** six models were the Wykoff(WYK),Schumacher(SCH),Curtis(CUR),HossfeldⅣ(HOS),von Bertalanffy-Richards(VBR),and Gompertz(GPZ)*** models were first fitted in their base forms with tree species as random effects and were then expanded to include functional traits and spatial *** distributions of the estimated inflection points were similar between the two-parameter models WYK,SCH,and CUR,but were different between the threeparameter models HOS,VBR,and *** produced some of the largest inflection *** and VBR produced concave H-d curves without inflection points for 12.7%and 39.7%of the tree *** species or decreasing shade tolerance resulted in larger inflection *** trends in the estimated inflection points of HOS and VBR were entirely opposite across the ***,HOS could produce concave H-d curves for portions of the *** on the studied behaviors,the choice between two-parameter models may not *** recommend comparing seve ral three-parameter model forms for consistency in estimated inflection points before deciding on *** sigmoidal models to have inflection points does not necessarily mean that they will produce fitted curves with *** study highlights the need to integrate analysis of inflection points into modeling H-d relationships.

关键词： Concavity Forest inventory and analysis Generalized height-diameter models Growth functions Height-diameter functions Mixed-effects modeling Points of inflection Species-specific models

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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 *** consensus has been reached on how to tackle effectively cognitive decline in this clinical population *** 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 ***-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 *** sham training was a modified version of the standard training that comprised the same exercises and number of sessions but with increased processing speed *** non-active control group received no cognitive *** patients underwent comprehensive neuropsychological and magnetic resonance imaging assessments at baseline and after 5 *** and resting-state magnetic resonance imaging data were analyzed using repeated measures *** 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 *** 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 *** changes were observed in the sham training *** findings suggest that multi-domain tr

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

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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 *** E is an antioxidant with potential anti-fibroblastic *** aim of this study was to establish an arthrofibrosis rat model after joint replacement and assess the effects of vitamin E supplementation on joint ***:We simulated knee replacement in 16 male Sprague–dawley *** immobilized the surgical leg with a suture in full *** 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 *** staining andα2-macroglobulin(α2M)enzyme-linked immunosorbent assay(ELISA)were used to assess local and systemic *** weight bearing(total internal reflection)and range of motion(ROM)were collected for functional ***: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 *** analysis confirmed fibrosis in both lateral and posterior periarticular *** E supplementation showed a moderate anti-inflammatory effect on the local and systemic *** vitamin E group exhibited significant improvement in ROM and weight-bearing symmetry at day 84 compared to the control ***:This model is viable for simulating arthrofibrosis after joint *** 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

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Biopolymer stabilization of clayey soil

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第7期16卷 2801-2812页

作者： Mahdieh Azimi Amin Soltani Mehdi Mirzababaei mark B.Jaksa Nanjappa Ashwath College of Engineering and Aviation School of Engineering and TechnologyCQUniversityMelbourneVIC 3000Australia Institute of Innovation Science and Sustainabilityand Future Regions Research CenterFederation UniversityChurchillVIC 3842Australia department of Infrastructure Engineering Faculty of Engineering and Information TechnologyThe University of MelbourneParkvilleVIC 3010Australia School of Architecture and Civil Engineering The University of AdelaideAdelaideSA 5005Australia School of Health Medical and Applied SciencesCQUniversityRockhamptonQLD 4701Australia

This study investigates the efficacy of sodium alginate(SA),xanthan gum(XG),guar gum(GG)and chitosan(CS)d each applied at five different solid biopolymer-to-water mass ratios(or dosages)and cured for 7 d and 28 d d on the unconfined compressive strength(UCS)performance of a high plasticity clayey ***,on identifying the optimum biopolymer-treatment scenarios,their performance was compared against conventional stabilization using hydrated *** a given curing time,the UCS for all biopolymers followed a riseefall trend with increasing biopolymer dosage,peaking at an optimum dosage and then subsequently decreasing,such that all biopolymer-stabilized samples mobilized higher UCS values compared to the unamended *** optimum dosage was found to be 1.5%for SA,XG and CS,while a notably lower dosage of 0.5%was deemed optimum for ***,for a given biopolymer type and dosage,increasing the curing time from 7 d to 28 d further enhanced the UCS,with the achieved improvements being generally more pronounced for XG-and CS-treated *** of the investigated biopolymers was able to produce UCS improvements equivalent to those obtained by the 28-d soilelime samples;however,the optimum XG,GG and CS dosages,particularly after 28 d of curing,were easily able to replicate 7-d lime stabilization outcomes achieved with as high as twice the soil’s lime ***,the fundamental principles of clay chemistry,in conjunction with the soil mechanics framework,were employed to identify and discuss the clayebiopolymer stabilization mechanisms.

关键词： Soil stabilization High plasticity clay Biopolymer dosage Hydrated lime Curing time Unconfined compressive strength(UCS)

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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 *** understanding of the spatial characteristics of cleat networks is therefore important to the coal mining *** fracture networks(dFNs)are increasingly used in engineering analyses to spatially model fractures at various *** reliability of coal dFNs largely depends on the confidence in the input cleat *** 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 *** this paper,a feature extraction-based image processing method is introduced to identify and separate distinct cleat groups from 3d X-ray m CT ***(filters)representing explicit cleat features of coal are built and cleat separation is successfully achieved by convolutional operations on 3d coal *** 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,*** is demonstrated that the new method produces reliable cleat separation capable of defining individual cleats and preserving 3d topology after ***-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 ***,variability and heterogeneity with respect to the core axis are *** heterogeneity is observed and suggests that the representative elementary volume(REV)of the cleat groups for engineering purposes may be a complex problem requ

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

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does a large prostate size,small lesion volume,or long needle distance from the probe to the lesion reduce magnetic resonance imaging–targeted cancer detection?

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Current Urology 2024年第2期18卷 144-147页

作者： mark d.Bevill Justin N.drobish Kevin J.Flynn Maheen Rajput Catherine Metz Chad R.Tracy Paul T.Gellhaus department of Urology University of Iowa Carver College of MedicineIowa CityIAUSA department of Radiology University of Iowa Carver College of MedicineIowa CityIAUSA

Background:We aimed to evaluate whether large prostate size,small lesion volume,or long lesion distance from the ultrasound probe tip would decrease cancer detection in transrectal magnetic resonance imaging(MRI)–targeted *** and methods:Patients who underwent MRI-targeted biopsy at our institution between May 2017 and August 2019 were enrolled in a prospective *** to 5 cores were obtained from≥2 prostate imaging reporting and data system v2 lesions.A multivariable model was created that included needle distance to the lesion,prostate specific antigen,prostate imaging reporting and data system,lesion volume,and prostate ***:A total of 377 patients with 533 lesions underwent a biopsy during the study period.A total of 233(44%)lesions were positive for prostate cancer,and 173(32%)lesions had clinically significant prostate *** mean needle distance to the lesion was 11.7mm(interquartile range,7.6–15.5mm).The likelihood of obtaining a positive core on biopsy decreased as the distance fromthe ultrasound probe increased for all prostate cancers and clinically significant prostate cancer(p=0.018 and p=0.004,respectively).Every 10mmfrom the rectum,there was an 8%–10%decrease in the rate of cancer ***,as the prostate volume increased,the odds of obtaining a positive core also decreased(p=0.039).There was no significant association between the lesion size and amount of cancer obtained on ***:Our data showed that transrectal MRI-targeted biopsy cancer detection modestly decreased the lesion from the ultrasound probe and with a large prostate volume but could not prove that lesion volume was a significant predictor of the amount of cancer detected.

关键词： Prostate cancer Biopsy Magnetic resonance imaging

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