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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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V型胶原导致的硬皮病样重塑

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世界核心医学期刊文摘（皮肤病学分册） 2006年第8期2卷 27-27页

作者： bezerra M.C. Teodoro W.R. De Oliveira C.C. V.L. Capelozzi 王琼 Department of Pathology from Faculty of Medicine University of So Paulo Av. Dr. Arnaldo 455 01246- 903 So Paulo Brazil

Recently, we discovered that New Zealand rabbits immunized with human type V collagen plus Freund’ s adjuvant present fibrosis and vasculitis of organs usually affected by systemic sclerosis. In this way, we studied the fibrillogenesis process to identify possible factors involved in altered remodeling observed in this scleroderma-like model. Additionally, we have done a very preliminary comparison with human skins obtained from scleroderma patients (n = 3). Female New Zealand rabbits (n = 10) were immunized subcutaneously with two doses of 1 mg collagen V (COL V) plus complete Freund’ s adjuvant for a 30-day interval, followed by two additional intramuscular booster immunizations in incomplete Freund’ s adjuvant for a 15-day interval. Animals from control group (n = 10), were only inoculated with complete and incomplete Freund’ s adjuvant given at same conditions of COL V. Histological analysis of skins from animals and patients were done by Masson’ s trichrome staining, and immunofluorescence method to detect collagen fibers and interactions of types I, III and V collagen in the remodeling process. The analysis of animal skins showed collagen fibril deposits in the dermis after 7 days of sensibilization and an increase in these deposits after 75 and 120 days, respectively. skin thickness and atrophy of sebaceous and sweat glands were progressively more intense in late sacrificed animals and correlated with increased amount of collagen deposition. surprisingly, type V collagen was overexpressed both in animals and patients, forming dense and atypical collagen fibers in the dermis. We suggest that this anomalous expression of morphologically different type V collagen could justify the remodeling observed in scleroderma plaque.

关键词： V型胶原硬皮病样 Masson三色染色法完全弗氏佐剂系统性硬化病新西兰兔皮下免疫硬皮病患者组织学分析免疫荧光法

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日籍巴西人群中幽门螺杆菌血清阳性与Lewis和secretor基因多态性的联系

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世界核心医学期刊文摘（胃肠病学分册） 2005年第3期1卷 50-51页

作者： Oba-hinjo s.M. Uno M. Ito L.s. 王志宇 Laboratory of Molecular Biology Department of Neurology University of So Paulo Av. Dr. Arnaldo 455 01246-903 So Paulo SP Brazil

Background. secretor (se) and Lewis (Le) genes are involved in the synthesis of Lewis b (Leb) and type I antigens throughout the body, especially in the epithelial cells of gastric mucosa. Helicobacter pylori can attach to the gastric epithelial cells with the blood group antigen binding adhesin, which binds to Leb or H type I carbohydrate structures. In a previous study, a marked association between H. pylori seropositivity and polymorphism of the se and Le genes was observed among Japanese outpatients of a gastroenterology clinic. The present work aims to investigate the associations between se and Le gene polymorphisms and H. pylori infection among Japanese Brazilians. Methods. The subjects consisted of 942 healthy volunteer Japanese Brazilians, who were tested for the presence of anti H. pylori IgG antibodies and genotyped for se and Le polymorphisms. Results. The sex age adjusted odds ratios (aORs) for H. pylori seropositivity were 0.99 for the sese genotype relative to the sese genotype (95%confidence interval , 0.73-1.33), and 1.03 for sese relative to sese (95%CI, 0.71-1.48). On the other hand, the aOR for the subjects with the le allele (Lele or lele) relative to the LeLe genotype was 1.48 (95%CI, 1.07-1.79). When the se and Le genotypes were analyzed in combination according to risk group, no statistically significant association was observed. Conclusions. These results are inconsistent with previous work and may have been modulated by an external factor or some other unidentified factor. Japanese Brazilians are geno typically the same as Japanese, but their lifestyle is adapted to that of Brazil. Further investigations are necessary to clarify this influence on susceptibility to H. pylori infection.

关键词： Lewis secretor 基因多态性血清阳性胃上皮细胞血型抗原胃黏膜上皮巴西人黏附素胃肠病

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Methylprednisolone Pulse Therapy in COVID-19 as the First Choice for Public Health: When Right Timing Breaks Controversies—Emergency Guide

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Open Journal of Emergency Medicine 2021年第3期9卷 84-114页

作者： Luiz Gonzaga Francisco de Assis Barros D’Elia Zanella Daniela Kallíope de sá Paraskevopoulos Luciana de Lima Galvã o Augusto Yamaguti Infectious Disease Department—Hospital do servidor Público do Estado de sã o Paulo—HsPE (MI-HsPE) Pedro de Toledo Avenue Vila Clementino S&atilde o Paulo Brazil school of Medicine—University of sã o Paulo—PhD Program in Allergy and Immunopathology Dr. Arnaldo Avenue S&atilde o Paulo Brazil

Based on Russian and the Middle East corticosteroids trials in MERs-CoV, we performed methylprednisolone pulse therapy (MPT), resulting in a clinical trial still without result. Our previous cohort (not compared n = 1... 详细信息

Based on Russian and the Middle East corticosteroids trials in MERS-CoV, we performed methylprednisolone pulse therapy (MPT), resulting in a clinical trial still without result. Our previous cohort (not compared n = 18) showed 76% of MPT patients did not progress to orotracheal intubation as MTP blocked the cytokine storm, a lower result compared to Tehran’s study explained by performing MPT in any lung phase. The Middle East study had been carried out during the initial lung phase. We are in an international emergency. Considering previous protocols and clinical practice, we understand that MPT must be used in COVID-19, and the indication to avoid going to the hospital when the first symptoms appear should be changed urgently for the population with inflammatory comorbidities. This article aims to: 1) show the Iranian protocol to reduce deaths and intubations bspan style="font-family:Verdana;">y COVID-19;2) present a possible approach to the patient COVID-19 with methylprednisolone pulse and strict criteria for orotracheal intubation to avoid hypoxemia;3) highlight that there is already a protocol that can be an international guideline-based on the Iranian work for the treatment of COVID-19;and 4) argue that corticosteroids are not controversial, but their use in a period outside the best timing period makes it controversial;and 5) emphasise the urgency of modifying the current protocol that postpones the visit of patients to the hospital in case of symptoms, since late hospital evaluation has been catastrophic for a world population.

关键词： Methylprednisolone COVID-19 Pulse-Therapy Hypoxemia

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对高危人群进行活检研究证实DCs液基系统对宫颈病变的诊断比传统巴氏涂片法更有效

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世界核心医学期刊文摘（妇产科学分册） 2005年第9期1卷 29-30页

作者： Longatto Filho A. Miranda Pereira s.M. Di Loreto C. 张丽娟 Adolfo Lutz Institute Pathology Division Dr. Arnaldo Avenue 355 01246-902 Sao Paulo SP Brazil

Objective. To compare the performances of Papanicolaou test (Pap Test) and of a new liquid-based cytology method, DNA-Citoliq. system (DCs), in a high-ri sk population, with histology confirmation. Methods. Paired specimens of exfolia ted cervical cells were collected under split-sample protocol. All patients wer e submitted to colposcopy and a biopsy taken when any atypical transformation zo ne was seen. sensitivity, specificity, positive and negative predictive values, and overall accuracy of both conventional and DCs methods were computed in relat ion to histology. Results. A total of 1,095 patients were analyzed by two cytol ogy methods and, in 425 (38.8%), histologically. There were significantly more adequate samples with DCs (98.63%) than with conventional (89.6%) smears (P sCUs was diagnosed significantly more with DCs than with conventional P ap (P sclassified as normal 55.4%(158/285) of case s with either LsIL or HsIL or cancer at histology, whereas DCs misclassified 31. 2%(89/285) of cases (P s had a significantly higher sensitivity (70 %and 91.3%) than the conventional Pap (49.8%and 72.8%) to detect both LsIL+ and HsIL+at histology, respectively. On the other hand, specificity of conventi onal smear (88.2%and 85.2%) was significantly higher than DCs (75.4%and 70.9 %) considering both LsIL+and HsIL+at histology, respectively. Conclusions. Th is study confirms the superiority of the liquid-based cytology system DCs to de tect cervical lesions. The rate of adequate DsC slides was significantly higher than with conventional cytology.

关键词：传统巴氏涂片法 DCs 高危人群基系巴氏法组织学病理阴道镜检查组织学活检巴氏涂片阴性预测值

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