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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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Urban forest loss using a GIS-based approach and instruments for integrated urban planning:A case study of Jo?o Pessoa,Brazil

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Journal of Geographical Sciences 2021年第10期31卷 1529-1552页

作者： Leandro Ismael de Azevedo LACERDA Joséaugusto Ribeiro da SILVEIRA Celso augusto Guimarães santos Richarde Marques da silva Alexandro Medeiros silva Thiago Victor Medeiros do NASCIMENTO Edson Leite RIBEIRO Paulo Vitor Nascimento de FREITAS Federal University of Paraíba Laboratory of Urban and Built Environment-LAURBE58051-900 João PessoaParaíbaBrazil Federal University of Paraíba Department of Architecture and Urbanism58051-900 João PessoaPBBrazil Federal University of Paraíba Department of Civil and Environmental Engineering58051-900 João PessoaPBBrazil Federal University of Paraíba Department of Geosciences58051-900 João PessoaPBBrazil Ministry of Cities Setor de Autarquias SulQuadra 01Lote 01/06Bloco HEd.Telemundi II70070-010 BrasíliaDFBrazil

Urban forests play an important role in the thermal comfort and overall life of local populations in large-and medium-sized *** study analyzes urban forest loss and maps land use and land cover(LULC)changes between 1991 and 2018 by evaluating the use of urban planning instruments for the mitigation of urban forest loss in Jo?o Pessoa,*** this purpose,satellite-derived LULC images from 1991,2006,2010 and 2018 and data on urban forest loss areas obtained using the Google Earth Engine were *** addition,this paper also discusses the instruments used for integrated urban planning,which are(a)the legal sector,responsibility and nature;(b)the urban expansion process;and(c)the elements of urban *** results show a clear shift in land use in the study *** major changes in LULC classes occurred in urban areas and herbaceous vegetation,while the greatest loss was in arboreal/shrub ***,an increase in the pressure to occupy zones intended for environmental preservation could be *** results showed similar accuracies with other studies and more spatial *** characteristics of the patterns,traces,and hotspots of urban expansion and forest cover loss were *** highlighted the potential use of this proposed framework to be applied and validated in other parts of the world to help better understand and quantify various aspects of urban-related problems such as urban forest loss mapping using instruments for integrated urban planning and low-cost approaches.

关键词： integrated planning mapping thematic synthesis urban afforestation urban planning

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Renin-angiotensin system in the pathogenesis of liver fibrosis

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World Journal of Gastroenterology 2009年第21期15卷 2579-2586页

作者： Regina Maria Pereira Robson augusto Souza dos santos Filipi Leles da Costa Dias Mauro Martins Teixeira Ana Cristina Simoes e silva Department of Pediatrics Faculty of MedicineFederal University of Minas Gerais Laboratory of Hypertension Department of Physiology and BiophysicsInstitute of Biological SciencesFederal University of Minas Gerais Laboratory of Immunopharmacology Department of Biochemistry and ImmunologyInstitute of Biological SciencesFederal University of Minas Gerais

Hepatic fibrosis is considered a common response to many chronic hepatic injuries. It is a multifunctional process that involves several cell types, cytokines, chemokines and growth factors leading to a disruption of homeostatic mechanisms that maintain the liver ecosystem. In spite of many studies regarding the development of fibrosis, the understanding of the pathogenesis remains obscure. The hepatic tissue remodeling process is highly complex, resulting from the balance between collagen degradation and synthesis. Among the many mediators that take part in this process, the components of the Renin angiotensin system （RAS） have progressively assumed an important role. Angiotensin （Ang） II acts as a profibrotic mediator and Ang-（1-7）, the newly recognized RAS component, appears to exert a counter-regulatory role in liver tissue. We briefly review the liver fibrosis process and current aspects of the RAS. This review also aims to discuss some experimental evidence regarding the participation of RAS mediators in the pathogenesis of liver fibrosis, focusing on the putative role of the ACE2-Ang-（1-7）- Mas receptor axis.

关键词： Hepatic fibrosis Renin angiotensin system Angiotensin II Angiotensin-(1-7) Receptor Mas Angiotensin converting enzyme 2

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The effect of drying of Piper hispidinervium bydifferent methods and its influence on the yield ofessential oil and safrole

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Information Processing in Agriculture 2023年第1期10卷 28-39页

作者： Helder Kiyoshi Miyagawa Alberdan silva santos Systematic Investigation in Biotechnology and Molecular Biodiversity Laboratory Federal University of Para´Bele´m 66075-110PABrazil

The Piper hispidinervium leaves and thin stems were dried under laboratory and field *** drying was performed using a shade dryer operating with and without forced convection and an oven dryer operating at 30 and 40*** experiments were conducted using solar dryers with three different covers,i.e.,transparent,black plastic,and palm straw *** essential oil extraction was performed by steam distillation,and the safrole content was analyzed by gas *** mathematical models(Page,logarithmic,Henderson and Pabis,fractional,and diffusion)were fitted with the experimental data and compared based on the coefficient of determination(R2),root mean square error(RMSE)and *** suggest that the best model was the logarithmic model(R2>0.99,RMSE<0.0005,and v2<0.005).With sufficient drying,the safrole content increased up to 95%of the extracted oil;however,when the drying time was prolonged,both the oil yield and safrole content of the extracted oil decreased.

关键词： Modeling Drying kinetics Essential oil extraction Safrole extraction Piperaceae

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Adipose-derived stromal/stem cells from different adipose depots in obesity development

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World Journal of Stem Cells 2019年第3期11卷 147-166页

作者： Karina Ribeiro silva Leandra santos Baptista Laboratory of Tissue Bioengineering Directory of Metrology Applied to Life Sciences National Institute of Metrology Quality and Technology Post-Graduation Program of Biotechnology National Institute of Metrology Quality and Technology Multidisciplinary Center for Biological Research (Numpex-Bio) Federal University of Rio de Janeiro Campus Duque de Caxias

The increasing prevalence of obesity is alarming because it is a risk factor for cardiovascular and metabolic diseases(such as type 2 diabetes). The occurrence of these comorbidities in obese patients can arise from white adipose tissue(WAT) dysfunctions, which affect metabolism, insulin sensitivity and promote local and systemic inflammation. In mammals, WAT depots at different anatomical locations(subcutaneous, preperitoneal and visceral) are highly heterogeneous in their morpho-phenotypic profiles and contribute differently to homeostasis and obesity development, depending on their ability to trigger and modulate WAT inflammation. This heterogeneity is likely due to the differential behavior of cells from each depot. Numerous studies suggest that adiposederived stem/stromal cells(ASC; referred to as adipose progenitor cells, in vivo)with depot-specific gene expression profiles and adipogenic and immunomodulatory potentials are keys for the establishment of the morphofunctional heterogeneity between WAT depots, as well as for the development of depot-specific responses to metabolic challenges. In this review, we discuss depot-specific ASC properties and how they can contribute to the pathophysiology of obesity and metabolic disorders, to provide guidance for researchers and clinicians in the development of ASC-based therapeutic approaches.

关键词： White adipose tissue Metabolic diseases Obesity Adipose-derived stromal/stem cells Adipose depot Inflammation

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The Use of Triancinolone for the Treatment of Keloid Scars

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Journal of Cosmetics, Dermatological Sciences and Applications 2024年第3期14卷 270-275页

作者： José Humberto Cardoso Resende Luís Otávio Torres Anderson Alves Brandão Delma dos santos Assis Mercadante Jessyka Oliveira Barbosa Batista William Felix de Oliveira Pacheco Elisangelo Aparecido Costa Da silva Douglas Henrique Farias de Oliveira Nébia Maria Almeida de Figueiredo UNIFAN-Centro Universitrio Alfredo Nasser Aparecida de Goinia Brazil UNIRIO Rio de Janeiro Brazil

Scars, when in good evolution, result in a smooth, thin and discreet tissue. Keloid scars, however, are a type of abnormal and exacerbated repair response to tissue injury, whether in surgical interventions or in various injuries, which present in a prominent and gross way. In this context, there is an excess of collagen deposition in the tissue repair process, which can lead to the formation of keloids. The diagnosis of the condition presented is made by the medical professional or by the patient himself after the surgical intervention or skin injury. Under this analysis, protruding, rough and bad-looking scars are identified. In addition, we highlight the existence of keloids similar to large tumors, described as Jorge Lobo disease. The treatment encompasses massages, compressions, corticosteroids, chemotherapy, collagenase and cryotherapy. At first, we used corticosteroid-based massages, and then we started using compressive dressings until we started intrakeloid infiltrations with injectable triamcinolone. Triamcinolone 10 mg injectable—1/10—in 0.9% saline, with syringe and fixed needle 0.3 mm × 8 mm, intralesional infiltrate, in this context, proved to be effective for its treatment when applied sequentially and linearly. In cases where the medication was applied, there was an improvement after 21 days of application and a definitive improvement 2 months after the injury. In comparison, on the other hand, patients who were not subjected to the application of the medication may improve after 4 months of the injury or worsen compared to the initial case. We have come to the conclusion that this procedure may be one of the chosen ones for the treatment of keloid scars, being one of the most recommended for cases of keloid already installed.

关键词： Keloid Scar Hypertrophy Collagen Affection

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Effects of Yerba Mate Consumption (Ilex paraguariensis) on Cardiac Remodeling in Rats

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Food and Nutrition Sciences 2024年第8期15卷 827-845页

作者： Carlos Eduardo Brochini de Paiva Thaíssa Baptista Brochini de Paiva Isabelle Tiburcio Pecin Ferreira Sandra Cristina Genaro Danilo silva Martins santos Thaoan Bruno Mariano Robson Chacon Castoldi Rafael Stuani Floriano Julia Amanda Rodrigues Fracasso Lucas Pires Guarnier Marina Politi Okoshi Francis Lopes Pacagnelli Postgraduate Program in Health Sciences Unoeste Presidente Prudente Brazil Faculty of Medicine Unoeste Presidente Prudente Brazil Department of Physiotherapy Unoeste Presidente Prudente Brazil Department of Nutrition Unoeste Presidente Prudente Brazil Postgraduate Program in Science and Movement Unesp Rio Claro Brazil Postgraduate Program in Health Promotion University of Northern Paran (UNOPAR) Londrina Brazil School of Dentistry So Paulo State University (UNESP) Araatuba Brazil Department of Genetics Ribeiro Preto Medical School University of So Paulo USP Ribeiro Preto Brazil Internal Medicine Department Botucatu Medical School So Paulo State University (UNESP) Botucatu Brazil

This study investigated the effects of yerba mate consumption, a South American beverage, on cardiac remodeling in rats. For this purpose, 24 male Wistar rats were divided into Control Group (CG) which received filtered water and a standard diet, and Yerba Mate Group (YM), 6 g of Ilex paraguariensis in 100 ml water and the same diet, for 30 days. The YM group showed a reduction in final body weight and food consumption without altering weight gain. Regarding cardiac remodeling, the YM group exhibited a decrease in the right ventricle weight/final body weight ratio, suggesting cardiac atrophy, without affecting the atria and left ventricle. There was no change in cardiomyocyte area or nuclear fractal dimension in both groups. However, animals that consumed yerba mate showed increased collagen deposition and a smaller fractal dimension in the left ventricle. The consumption of yerba mate at room temperature for 30 days induced changes in cardiac remodeling, as evidenced by increased collagen deposition and alterations in fractal dimension in the left ventricle.

关键词： Tereré Ilex paraguariensis Yerba Mate Cardiac Remodeling Fractal Dimension Hypertrophy

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Effects of Physical Activity Levels on Fatigue Perception in Patients with Parkinson’s Disease and Neurologically Healthy Individuals

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Health 2014年第21期6卷 2927-2933页

作者： Paulo Cezar Rocha dos santos Fabio augusto Barbieri diego Orcioli-silva Lucas Simieli Lilian Teresa Bucken Gobbi UNESP Univ Estadual Paulista at Rio Claro Rio Claro/SP Brazil UNESP Univ Estadual Paulista at Bauru Bauru/SP Brazil

Background: Recent researches involving fatigue and Parkinson’s disease (PD) sought to verify its incidence and the impacts of fatigue on quality life of patients with PD. Despite the importance of regular physical activity practice, there are only few studies that verified the influence of the levels of physical activity on fatigue in patients with PD. Objective: The aim of this study was to compare perception of fatigue between individuals with PD and neurologically healthy individuals (control group), considering the physical activity levels;and to verify the relation between physical activity levels and fatigue dimensions for individuals with PD and control group. Methods: Eighty individuals (40 patients with PD and 40 control individuals) participated in this study. Physical activity levels were evaluated through Modified Baecke Questionnaire for Older Adults. Multidimensional Fatigue Inventory (MFI) was used in order to evaluate fatigue dimensions (general, physical and mental fatigue, reduced motivation and activity). MANOVA two-way and Pearson linear correlation test were performed to analyze the data. Results: Patients with PD presented higher levels of fatigue, in all dimensions evaluated by MFI, comparing to control individuals. There was no association between physical activity levels and perception of fatigue for patients with PD and control individuals. Conclusion: Patients with PD showed increased perception of fatigue when compared to control individuals, due to PD characteristics. In addition, the perception of fatigue’s symptom was not influenced and had no relation by the level of physical activity.

关键词： Parkinson’s Disease Symptom of Fatigue Physical Activity Levels Non-Motor Symptom

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Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines

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Genomics, Proteomics & Bioinformatics 2021年第1期19卷 25-43页

作者： José Alexandre Ferreira Marta Relvas-santos Andreia Peixoto AndréM.N.silva Lúcio Lara santos Experimental Pathology and Therapeutics Group Portuguese Institute of OncologyPorto 4200-072Portugal Institute of Biomedical Sciences Abel Salazar University of PortoPorto 4050-313Portugal Porto Comprehensive Cancer Center(P.ccc) Porto 4200-072Portugal REQUIMTE-LAQV Department of Chemistry and BiochemistryFaculty of Sciences of the University of PortoPorto 4169-007Portugal

Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing(NGS),supported by robust *** quest for genomicsbased cancer medicine set the foundations for improved patient stratification,while unveiling a wide array of neoantigens for *** pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target ***,the low mutational burden presented by many lesions challenges the generalization of these solutions,requiring the diversification of neoantigen *** utilizing customized databases for protein annotation by mass spectrometry(MS)is a powerful tool toward this *** the concept toward exploring proteoforms originated from post-translational modifications(PTMs)will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer *** through the path of systems biology,we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted ***,we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics *** envisage that such rationale may flag a rather neglected research field,generating novel paradigms for precision oncology and immunotherapy.

关键词： Glycoproteogenomics Oncoproteogenomics Cancer neoantigens Glycosylation Precision oncology

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Technical Evaluation of Hybrid Clones of Corymbia spp. to Produce Market Pulp

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Paper And Biomaterials 2022年第3期7卷 1-6页

作者： Marcelo Moreira da Costa Ricardo de Carvalho Bittencourt Thales augusto Pinto Coelho Nogueira Larissa Soares silva Weslley Henrique Martins da silva Sebastião Renato Valverde Gleison augusto Dos santos Daniel Alexander Fernandes Coelho Claudilene Aparecida Alves Pena Department of Forest Sciences Federal University of VicosaVicosaMinas Gerais36570900Brazil Aperam BioEnergia Co. CapelinhaMinas Gerais39680000Brazil

This study presents hybrid clones of Corymbia *** by Aperam BioEnergia as potential substitutes for Eucalyptus wood in the pulp *** biomass of Eucalyptus *** compared with that of Corymbia *** performing modified kraft pulping and basic density *** were made by analyzing their respective mean annual increments of cellulose(MAI_(cel))and specific wood consumption(SWC),estimated using a kappa number of(19±1).The results showed that one of the hybrid clones(Corymbia citriodora×Corymbia torelliana,ID 4)had higher basic wood density,higher screened yield,better MAI_(cel#k19),and lower SWC than the other samples,reaching values of 0.608 t/m^(3),54.1%,24.6 ADt/ha/year(i.e.,air dry ton/hectare/year),and 2.74 m^(3)/ADt,***,clone ID 4 had the highest MAI_(cel)/SWC ratio score(8.98).Given its high forest productivity and low industrial cost compared with other samples,as well as its advantages over Eucalyptus ***,we concluded that clone ID 4 has great potential as an alternative biomass for pulp production.

关键词： Corymbia hybrids modified kraft pulping mean annual increments of cellulose(MAIcel) specific wood consumption(SWC)

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