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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

Mitigating adjacent channel interference in vehicular communication systems

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Digital Communications and Networks 2016年第2期2卷 57-64页

作者： Joao Almeida Muhammad Alam Joacluim Ferreira arnaldo s.R. Oliveira lnstituto de Telecomunicar/ses Campus Universitdirio de Santiago 3810-193 Aveiro Portugal DETI - Universidade de Aveiro Campus Universitdrio de Santiago 3810-193 Aveiro Portugal EsTGA - Universidade de Aveiro 3754-909 gueda Portugal

In the last few decades, dedicated wireless channels were specifically allocated to enable the development and implementation of vehicular communication systems. The two main protocol stacks, the WAVE standards proposed by the IEEE in the United states and the ETsI ITs-G5 in Europe, reserved 10 MHz wide channels in the 5.9 GHz spectrum band. Despite the exclusive use of these frequencies for vehicular communication purposes, there are still cross channel interference problems that have been widely reported in the literature. In order to mitigate these issues, this paper presents the design of a two-stage FIR low-pass filter, targeting the integration with a digital baseband receiver chain of a custom vehicular communications platform. The filter was tested, evaluated and optimized, with the simulation results proving the effectiveness of the proposed method and the low delay introduced in the overall operation of the receiver chain.

关键词： Intelligent transportation systems Vehicular communications Adjacent Channel Interference Filter design Multi-rate systems Digital Hardware Design

Photonic smart bandage for wound healing assessment

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Photonics Research 2021年第3期9卷 272-280页

作者： arnaldo Leal-Junior Jingjing Guo Rui Min Antonio Jose Fernandes Anselmo Frizera Carlos Marques Telecommunications Laboratory(LABTEL) Graduate Program in Electrical EngineeringFederal University of Espi’rito SantoVitoria-ES 29075-910Brazil school of Instrumentation and Optoelectronic Engineering Beihang UniversityBeijing 100191China Center for Cognition and Neuroergonomics State Key Laboratory of Cognitive Neuroscience and LearningBeijing Normal UniversityZhuhai 519087China Physics Department&I3N Universidade de AveiroCampus Universitario de SantiagoAveiro 3810-193Portugal

Chronic wounds affect around 2% of the world population with an annual multi-billion dollar cost to the healthcare system. This background pushes the development of new therapies and procedures for wound healing and its assessment. Among them, the potential of hydrogen(pH) assessment is an important indicator of the wound healing stage and condition. This paper presents the development of the first optical fiber-embedded smart wound dressing for pH assessment. An intrinsically pH-sensitive optical fiber is fabricated using a polydimethylsiloxane(PDMs) precursor doped with rhodamine B dye. Raman and Fourier transform infrared(FTIR) spectroscopies are performed in order to verify the presence of rhodamine B and PDMs in the fiber samples. Then, the fiber is embedded in gauze fabric and hydrocolloid wound dressing. In addition, such low Young’s modulus of PDMs fiber enables its use as a highly sensitive pressure sensor, where the results show that the fiber-embedded bandage can measure pressures as low as 0.1 kPa with a high linearity in the range of 0 to 0.3 kPa. The smart bandage is subjected to different pH, which resulted in a wavelength shift of 0.67 nm/pH when the absorption peak at 515 nm was analyzed. Furthermore, pH increase leads to linear decrease of the transmitted optical power(R2 of 0.998), with rise and fall times below 20 s and 30 s, respectively. Therefore, the proposed optical fiber-embedded smart bandage enables the simultaneous assessment of pressure and pH on the wound region.

关键词： fiber smart healing

Bioactive extracts of red seaweeds Pterocladiella capillacea and Osmundaria obtusiloba(Floridophyceae:Rhodophyta) with antioxidant and bacterial agglutination potential

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Asian Pacific Journal of Tropical Medicine 2016年第4期9卷 363-370页

作者： Daniel Barroso de Alencar Fátima Cristiane Teles de Carvalho Rosa Helena Rebouas Daniel Rodrigues dos santos Kelma Maria dos santos Pires-Cavalcante Rebeca Larangeira de Lima Bárbara Mendes Baracho Rayssa Mendes.bezerra Francisco arnaldo Viana Regine Helena silva dos Fernandes Vieira Alexandre Holanda sampaio Oscarina Viana de sousa silvana saker-sampaio Laboratrio de Produtos Naturais Marinhos.Departamento de Engenharia de Pesca Universidade Federal do Ceará.Campus do Pici.Ar.Mister Hull.s/nCaixa Postal 6043 Laboratrio de Microbiologia Ambiental e do Pescado.Instituto de Ciências do Mar.Universidade Federal do Ceará.Av.da Abolicao 3207 Laboratrio de Microbiologia Ambiental e do Pescado.Instituto de Ciências do Mar.Universidade Federal do Ceará Laboratrio de Produtos Naturais Marinhos.Departamento de Engenharia de Pesca Universidade Federal do Ceará Laboratrio de Cromatografia Departamento de QuimicaUniversidade do Estado do Rio Grande do NorteCampus Universitário Central

Objective:To evaluate the antioxidant,antibacterial and bacterial cell agglutination activities of the hexane(Hex) and 70%ethanol(70%EtOH) extracts of two species of red seaweeds Pterocladiella capillacea(***) and Osmundaria ***:In vitro antioxidant activity was determined by DPPH radical scavenging assay,ferric-reducing antioxidant power assay,ferrous ion chelating assay,β-carotene bleaching assay and total phenolic content *** activity was tested using the method of disc diffusion on Mueller-Hinton *** ability of algal extracts to agglutinate bacterial cells was also ***:The 70%EtOH extract of the two algae showed the highest values of total phenolic content compared to the Hex *** results of DPPH for both extracts(Hex,70%EtOH) of Osmundaria obtusiloba(43.46%and 99.47%) were higher than those of ***(33.04%and 40.81%) at a concentration of 1 000 μg/*** for the ferrous ion chelating,there was an opposite behavior,extracts of *** had a higher *** extracts showed a low ferric-reducing antioxidant power,with optical density ranging from0.054 to *** activities of all extracts evaluated for β-carotene bleaching were above 40%.There was no antibacterial activity against bacterial strains ***,the extracts of both species were able to agglutinate bacterial Gram positive cells of staphylococcus aureus and Gram negative cells of Escherichia coli,multidrug-resistant salmonella and Vibrio *** This is the first report of the interaction between these algal extracts,rich in natural compounds with antioxidant potential,and Gram positive and Gram negative bacterial cells.

关键词： Bioactive compounds Antioxidant Bacterial agglutination Rhodophyta

Endoscopic ultrasonography findings in autoimmune pancreatitis

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World Journal of Gastroenterology 2011年第16期17卷 2080-2085页

作者： Elisabetta Buscarini stefania De Lisi Paolo Giorgio Arcidiacono Maria Chiara Petrone arnaldo Fuini Rita Conigliaro Guido Manfredi Raffaele Manta Dario Reggio Claudio De Angelis Department of Gastroenterology Maggiore Hospital Department of Gastroenterology Di.Bi.M.I.S.University of Palermo Department of Gastroenterology I.R.C.C.S San RaffaeleUniversità Vita e Salute San Raffaele Department of Gastroenterology and Digestive Endoscopy Ospedale Civile Maggiore Department of Gastroenterology and Digestive Endoscopy New Civil Hospital S.Agostino Estense Chirurgia Trapianti di Fegato San Giovanni Battista Hospital Department of Gastroenterology San Giovanni Battista Hospital

Endoscopic ultrasonography is an established diagnostic tool for pancreatic masses and chronic *** recent years there has been a growing interest in the worldwide medical community in autoimmune pancreatitis (AIP),a form of chronic pancreatitis caused by an autoimmune *** paper reviews the current available literature about the endoscopic ultrasonographic findings of AIP and the role of this imaging technique in the management of this protean disease.

关键词：自身免疫性检查结果胰腺炎超声内镜诊断工具成像技术疾病管理

Determination of Hypoxanthine in the Presence of Copper by Adsorptive stripping Voltammetry

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American Journal of Analytical Chemistry 2014年第5期5卷 291-300页

作者： Percio Augusto Mardini Farias arnaldo Aguiar Castro Department of Chemistry Pontifícia Universidade Católica Rua Marquês de S&atilde o Vicente Rio de Janeiro Brazil Facultad Quimica Quimica Analitica Universidad de La Habana Havana Cuba

A stripping method for the determination of hypoxanthine in the presence of copper at the submicromolar concentration levels is described. The method is based on controlled adsorptive accumulation of hypoxanthine-copper at the thin-film mercury electrode followed by a fast linear scan voltammetric measurement of the surface species. Optimum experimental conditions were found to be the use of 1.0 × 10﹣3 mol·L﹣1 NaOH solution as electrolyte supporting, an accumulation potential of ﹣0.50 V and a linear scan rate of 200 mV·s﹣1. The response of hypoxanthine-copper is linear over the concentration ranges of 10 - 60 ppb. For an accumulation time of 30 minutes, the detection limit was found to be 250 ppt (1.8 × 10﹣9 mol·L﹣1). Adequate conditions for measuring the hypoxanthine in the presence of metal ions, xanthine, uric acid and other nitrogenated bases were also investigated. The utility of the method is demonstrated by the presence of hypoxanthine associated in ATP or ssDNA.

关键词： Hypoxanthine Determination Xanthine Uric Acid Copper Ion ATP ssDNA Thin-Film Mercury Electrode Fast Linear scan stripping Voltammetry

Litterfall dynamics and soil carbon and nitrogen stocks in the Brazilian palm swamp ecosystems

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Forest Ecosystems 2020年第3期7卷 499-510页

作者： Gracielle de Brito sales Taynan Aquilles Marinho Lessa Daniela Aparecida Freitas Maria das Dores Magalhães Veloso Maria Ligia de souza silva Luiz arnaldo Fernandes Leidivan Almeida Frazão Instituto de Ciências Agrárias Universidade Federal de Minas GeraisAvenida Universitária1000Montes ClarosMG39404-547Brazil Universidade Estadual de Montes Claros Avenida Professor Rui Braga S/NMontes ClarosMG39401-089Brazil Universidade Federal de Lavras Campus UniversitárioCP 3037LavrasMG37299-000Brazil

Background: This study aimed to determine the litterfall production, accumulation, decomposition rate and nutrient stocks, and to estimate the soil carbon(C) and nitrogen(N) stocks in three palm swamp ecosystems with different land use intensities in the southeast of ***: Three palm swamp ecosystems with different land use intensities were evaluated: Agua Doce(AD),conserved area;Capivara(CV), area with small agricultural practices;and Buriti Grosso(BG), area with an intensive land use. Produced and accumulated litterfall from the Cerrado areas surrounding the palm swamps were collected from October 2014 to september 2015, and the Ca, Mg, K, and P concentrations were determined in the dry and rainy seasons. soil samples were collected in the surrounding Cerrado and within the palm swamps until 100 cm soil depth to determine bulk density and soil C and N contents and ***: Annual litterfall production in the Cerrado surrounding palm swamps was similar in AD(3.58 Mg·ha^-1·year^-1) and CV(3.79 Mg·ha^-1·year^-1), and was lower in BG(2.84 Mg·ha^-1·year^-1), and was more intense during the dry season. Furthermore, litterfall accumulation was higher in CV(7.12 Mg·ha^-1·year^-1) and BG(6.75 Mg·ha^-1·year^-1), culminating in lower decomposition rates. AD showed the highest decomposition rate(0.60) due to its vegetation structure and conservation. The macronutrient contents from the production and accumulated litterfall had a low influence of the land use, decreasing in the following order: Ca > K > Mg > P. soils in CV and BG palm swamp areas showed higher values of C and N contents, due to the use of land for agricultural crops and cattle raising in an extensive(rangeland) system. The BG palm swamp, showed the highest C(124.03 Mg·ha^-1) and N(10.54 Mg·ha^-1) stocks due to the land use history with different agricultural practices over ***: The litterfall dynamics in the Cerrado surrounding palm swamps was more affected by climatic variables t

关键词： Nutrient cycling soil fertility soil organic matter Decomposition rate

Diversity of the endophytic filamentous fungal leaf community at different development stages of eucalyptus

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Journal of Forestry Research 2019年第3期30卷 1093-1103页

作者： Paulo sergio Balbino Miguel Fabio Balbino Miguel Bruno Coutinho Moreira Marcelo Nagem Valerio de Oliveira Julio Cesar Delvaux Fernanda de souza Freitas arnaldo Chaer Borges Maurcio Dutra Costa Departamento de Medicina e Enfermagem Universidade Federal de VicosaVicosaMinas Gerais 36570-000Brazil Departamento de Quimica Universidade Federal de Juiz de ForaJuiz de ForaMinas Gerais 36036-300Brazil Colegiado de Engenharia Agronomica Universidade Federal do Vale do Sao FranciscoPetrolinaPernambuco 56300-990 Brazil Departamento de Ciencias Basicas da Vida Campus Governador Valadares Universidade Federal de Juiz de Fora Governador ValadaresMinas Gerais 35012-140Brazil Coordenacao Geral de Ensino Pesquisa e Extensao Instituto Federal do Triangulo MineiroItuiutabaMinas Gerais 38035-200Brazil Departamento de Microbiologia Instituto de Biotecnologia Aplicada aAgropecuariaUniversidade Federal de Vicosa VicosaMinas Gerais 36570-000Brazil

Fungal endophytic species inhabiting the leaves of eucalypts are capable of utilising leaf sugars and can influence both plant growth and health. Endophytic fungal symbionts can use simple soluble sugars in leaves as their main carbon source. This study set out to determine the diversity and distribution of the endophytic filamentous fungal leaf community in the hybrid Eucalyptus urograndis due to its economic importance. The fungal leaf community was characterised using denaturing gradient electrophoresis (DGGE) and correlated with levels of leaf nutrients and sugars throughout plant development. sequencing of DGGE bands revealed the presence of Basidiomycota and Ascomycota phyla. Fourteen species and three genera of filamentous fungi were identified, and the population structure was affected by the plant developmental stage. Levels of K, Cu, N and Mn influenced communities from the clonal garden, whereas leaves in the field had higher glucose, fructose and sucrose. Many fungi were found to be specific to a certain development stages: Diplomitoporus crustulinus, Podosphaera tridactyla and Aspergillus restrictus to the clonal garden stage;Chaetomella acutiseta and Ascotricha chartarum to the shading stage;Erratomyces patelii and saxomyces sp. to the shading output stage;Lepidostroma sp. and saxomyces sp. to the dispatch stage;and Mycosphaerella populicola to the field stage. Teratosphaeria toledana and Teratosphaeria acidotherma were found at more than one developmental stage. Cladosporium sp. and Rhodosporidium fluviale colonized and persisted in plants at the dispatch and field stages. This is the first report of P. tridactyla, A. restrictus, E. patelii, saxomyces and Lepidostroma sp. as endophytes in eucalipt.

关键词： Diversity 18s rRNA Denaturing gradient electrophoresis(DGGE) sequencing

sUMOylation Inhibition Mediated by Disruption of sUMO El-E2 Interactions Confers Plant susceptibility to Necrotrophic Fungal Pathogens

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Molecular Plant 2017年第5期10卷 709-720页

作者： Laura Castano-Miquel Abraham Mas Ines Teixeira Josep segui Anna Perearnau Bhagyasree N. Thampi arnaldo L. schapire Natalia Rodrigo Gaelle La Verde silvia Manrique Maria Coca L. Maria Lois Center for Research in Agricultural Genomics - CRAG Edifici CRAG-Campus UAB Bellaterra (Cerdanyola del Vall~s) 08193 Barcelona Spain

Protein modification by sUMO modulates essential biological processes in eukaryotes. sUMOylation is facilitated by sequential action of the El-activating, E2-conjugating, and E3-1igase enzymes. In plants, sUMO regulates plant development and stress responses, which are key determinants in agricultural productivity. To generate additional tools for advancing our knowledge about the sUMO biology, we have developed a strategy for inhibiting in vivo sUMO conjugation based on disruption of sUMO El-E2 interactions through expression of E1 sAE2uFDct domain. Targeted mutagenesis and phylogenetic analyses revealed that this inhibition involves a short motif in sAE2uFDct highly divergent across kingdoms. Transgenic plants expressing the sAE2UFDCt domain displayed dose-dependent inhibition of sUMO conjugation, and have revealed the existence of a post-transcriptional mechanism that regulates sUMO E2 conjugating enzyme levels. Interestingly, these transgenic plants displayed increased suscep- tibility to necrotrophic fungal infections by Botrytis cinerea and Plectosphaerella cucumerina. Early after fungal inoculation, host sUMO conjugation was post-transcriptionally downregulated, suggesting that targeting sUMOylation machinery could constitute a novel mechanism for fungal pathogenicity. These findings support the role of sUMOylation as a mechanism involved in plant protection from environmental stresses. In addition, the strategy for inhibiting sUMO conjugation in vivo described in this study might be applicable in important crop plants and other non-plant organisms regardless of their genetic complexity.

关键词： sUMQ inhibition development flowering necrotrophic fungi El-activating enzyme El-E2interaction disruption