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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

Hydrological variability and long-term floristic-structural modifications in different habitats of a tropical semi-deciduous forest

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Journal of Forestry Research 2022年第3期33卷 801-811页

作者： Alisson Borges Miranda santos Vinicius Andrade Maia Cléber Rodrigo de Souza Natália de Aguiar-Campos Aurélio de jesus Rodrigues Pais Wilder Bento da Silva Nathalle Cristine Alencar Fagundes Jean Daniel Morel Rubens Manoel dos santos department of Forestry Sciences Federal University of LavrasCampus UniversitárioC.P.3037LavrasBrazil Faculty of Environmental Engineering and Natural Resources Zambeze UniversityChimoioC.P.2400Mozambique Biological Sciences Universidade do Estado de Minas GeraisUnidade ItuiutabaAv.Antônio Carlos 6627Ituiutaba31270-901Brazil department of Biology Federal University of LavrasUniversity campusC.P.3037Lavras37200-000Brazil

Shifts in hydrological regimes alter river flow rates and flood pulses, decrease environmental heterogeneity and the floristic-structural complexity of associated plant communities. We tested the hypothesis that drought events affect plant community composition and structure at a small-scale within a riparian fragment towards a reduction in floristic-structural complexity. The tree community was sampled in three habitats (wet, transitional and dry) and monitored in seven inventories carried out between 1991 and 2018. Hydrological variations were evaluated through annual rainfalls, river flow rates and water level data. The species richness and the detrended correspondence analysis axes were used to characterise the temporal modifications in floristic composition. Community structure was described in terms of biomass: accumulated, growth of survivors, mortality and recruitment. Generalised linear mixed models were fitted to evaluate the effects of time and environment in community. It was concluded that the climate has become drier in recent years due to declining precipitation that has affected flow rates and water levels. The floristic-structural complexity of the study fragment was maintained during the monitoring period. However, prolonged and extreme drought events displayed the potential to impact floristic-structural patterns.

关键词： Forest dynamics Climate changes Semi-deciduous seasonal forest Temporal change Functioning communities

Metabolic and nutritional triggers associated with increased risk of liver complications in SARS-CoV-2

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World Journal of Hepatology 2022年第1期14卷 80-97页

作者： Rosangela Passos de jesus Jozélio Freire de Carvalho Lucivalda Pereira Magalhães de Oliveira Carla de Magalhães Cunha Thaisy Cristina Honorato santos Alves Sandra Tavares Brito Vieira Virginia Maria Figueiredo Allain Amador Bueno Postgraduate Program in Food Nutrition and Health at the School of Nutrition of the Federal University of BahiaSalvador 40.110-150BahiaBrazil Institute of Health Sciences Federal University of BahiaSalvador 40231-300BahiaBrazil Institute of Life Sciences State University of BahiaSalvador 41.150-000BahiaBrazil department of Gastroenterology IPEMEDIpemed Faculty of Medical SciencesSalvador 40170-110BahiaBrazil College of Health Life and Environmental SciencesUniversity of WorcesterWorcester WR26AJUnited Kingdom

Obesity,diabetes,cardiovascular and respiratory diseases,cancer and smoking are risk factors for negative outcomes in severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),which can quickly induce severe respiratory failure in 5%of *** disease-associated liver injury may occur during progression of SARS-CoV-2 in patients with or without pre-existing liver disease,and damage to the liver parenchyma can be caused by infection of *** patients may be particularly vulnerable to SARS-CoV-2 if suffering with cirrhosis-associated immune ***,pharmacotherapies including macrolide or quinolone antibiotics and steroids can also induce liver *** this review we addressed nutritional status and nutritional interventions in severe SARS-CoV-2 liver *** guidelines for SARS-CoV-2 in intensive care(IC)specifically are not yet available,strategies for management of sepsis and SARS are suggested in *** enteral nutrition(EN)should be started soon after IC admission,preferably employing iso-osmolar polymeric formula with initial protein content at 0.8 g/kg per day progressively increasing up to 1.3 g/kg per day and enriched with fish oil at 0.1 g/kg per day to 0.2 g/kg per *** is necessary to identify signs of intolerance,hemodynamic instability and metabolic disorders,and transition to parenteral nutrition should not be delayed when energy and protein targets cannot be met via *** including vitamins A,C,D,E,B6,B12,folic acid,zinc,selenium andω-3 fatty acids have in isolation or in combination shown beneficial effects upon immune function and inflammation *** and monitored supplementation up to upper limits may be beneficial in management strategies for SARS-CoV-2 liver patients.

关键词： COVID-19 SARS-CoV-2 Enteral nutrition Parenteral nutrition Hepatic failure

Injection of bone marrow mesenchymal stem cells by intravenous or intraperitoneal routes is a viable alternative to spinal cord injury treatment in mice

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Neural Regeneration Research 2018年第6期13卷 1046-1053页

作者： bruna dos santos Ramalho FernANDa Martins de Almeida Conrado Mendonca Sales Silmara de Lima Ana Maria Blanco Martinez Laboratorio de Neurodegeneracao e Reparo Departamento de Patologia - Faculdade de Medicina HUCFF Universidade Federal do Rio de Janeiro Rio de laneiro Brazil

In spite of advances in surgical care and rehabilitation, the consequences of spinal cord injury （SCI） are still challenging. Several experimental therapeutic strategies have been studied in the SCI field, and recent advances have led to the development of therapies that may act on the inhibitory microenvironment. Assorted lineages of stem cells are considered a good treatment for SCI. This study investigated the effect of systemic transplantation of mesenchymal stem cells （MSCs） in a compressive SCI model. Here we present results of the intraperitoneal route, which has not been used previously for MSC administration after compressive SCI. We used adult female C57BL/6 mice that underwent laminectomy at the T9 level, followed by spinal cord compression for 1 minute with a 30-g vascular clip. The animals were divided into five groups： sham （anesthesia and laminectomy but without compression injury induction）, MSC i.p. （intraperitoneal injection of 8×10^5 MSCs in 500 μL of DMEM at 7 days after SCI）, MSC i.v. （intravenous injection of 8 × 10^5 MSCs in 500μL of DMEM at 7 days after SCI）, DMEM i.p. （intraperitoneal injection of 500μL of DMEM at 7 days after SCI）, DMEM i.v. （intravenous injection of 500 μL of DMEM at 7 days after SCI）. The effects of MSCs transplantation in white matter sparing were analyzed by luxol fast blue staining. The number of preserved fibers was counted in semithin sections stained with toluidine blue and the presence of trophic factors was analyzed by immunohistochemistry. In addition, we analyzed the locomotor performance with Basso Mouse Scale and Global Mobility Test. Our results showed white matter preservation and a larger number of preserved fibers in the MSC groups than in the DMEM groups. Furthermore, the MSC groups had higher levels of trophic factors （brain-derived neurotrophic factor, nerve growth factor, neurotrophin-3 and neurotrophin-4） in the spinal cord and improved locomotor performance. Our results indicate that injection of MSC

关键词： spinal cord injury mesenchymal stem cells intravenous route intraperitoneal route functional recovery systemic transplantation neural regeneration

Prediction of hospital mortality in intensive care unit patients from clinical and laboratory data: A machine learning approach

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World Journal of Critical Care Medicine 2022年第5期11卷 317-329页

作者： Elena Caires Silveira Soraya Mattos Pretti bruna Almeida santos Caio Fellipe santos Correa Leonardo Madureira Silva Fabricio Freire de Melo Multidisciplinary Institute of Health Federal University of BahiaVitória da Conquista 45-029094Brazil

BACKGROUND Intensive care unit(ICU)patients demand continuous monitoring of several clinical and laboratory parameters that directly influence their medical progress and the staff’s *** data are vital in the assistance of these patients,being already used by several scoring *** this context,machine learning approaches have been used for medical predictions based on clinical data,which includes patient *** To develop a binary classifier for the outcome of death in ICU patients based on clinical and laboratory parameters,a set formed by 1087 instances and 50 variables from ICU patients admitted to the emergency department was obtained in the“WiDS(Women in Data Science)Datathon 2020:ICU Mortality Prediction”*** For categorical variables,frequencies and risk ratios were *** variables were computed as means and standard deviations and Mann-Whitney U tests were *** then divided the data into a training(80%)and test(20%)*** training set was used to train a predictive model based on the Random Forest algorithm and the test set was used to evaluate the predictive effectiveness of the *** A statistically significant association was identified between need for intubation,as well predominant systemic cardiovascular involvement,and hospital death.A number of the numerical variables analyzed(for instance Glasgow Coma Score punctuations,mean arterial pressure,temperature,pH,and lactate,creatinine,albumin and bilirubin values)were also significantly associated with death *** proposed binary Random Forest classifier obtained on the test set(n=218)had an accuracy of 80.28%,sensitivity of 81.82%,specificity of 79.43%,positive predictive value of 73.26%,negative predictive value of 84.85%,F1 score of 0.74,and area under the curve score of *** predictive variables of the greatest importance were the maximum and minimum lactate values,adding up to a predictive importance of 15.54%.CONCLUSIO

关键词： Hospital mortality Machine learning Patient outcome assessment Routinely collected health data Intensive care units Critical care outcomes

Recognition of esophagitis in endoscopic images using transfer learning

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World Journal of Gastrointestinal Endoscopy 2022年第5期14卷 311-319页

作者： Elena Caires Silveira Caio Fellipe santos Corrêa Leonardo Madureira Silva bruna Almeida santos Soraya Mattos Pretti Fabrício Freire de Melo Multidisciplinary Institute of Health Federal University of BahiaVitória da Conquista 45029-094BahiaBrazil

BACKGROUND Esophagitis is an inflammatory and damaging process of the esophageal mucosa,which is confirmed by endoscopic visualization and may,in extreme cases,result in stenosis,fistulization and esophageal *** use of deep learning(a field of artificial intelligence)techniques can be considered to determine the presence of esophageal lesions compatible with *** To develop,using transfer learning,a deep neural network model to recognize the presence of esophagitis in endoscopic *** Endoscopic images of 1932 patients with a diagnosis of esophagitis and 1663 patients without any pathological diagnosis provenient from the KSAVIR and HyperKSAVIR datasets were splitted in training(80%)and test(20%)and used to develop and evaluate a binary deep learning classifier built using the denseNet-201 architecture,a densely connected convolutional network,with weights pretrained on the ImageNet image set and fine-tuned during *** classifier model performance was evaluated in the test set according to accuracy,sensitivity,specificity and area under the receiver operating characteristic curve(AUC).RESULTS The model was trained using Adam optimizer with a learning rate of 0.0001 and applying binary cross entropy loss *** the test set(n=719),the classifier achieved 93.32%accuracy,93.18%sensitivity,93.46%specificity and a 0.96 *** for spatial predictive relevance in esophagitis endoscopic images from the test set were also *** face of the obtained results,the use of dense convolutional neural networks with pretrained and fine-tuned weights proves to be a good strategy for predictive modeling for esophagitis recognition in endoscopic *** addition,adopting the classification approach combined with the subsequent plotting of heat maps associated with the classificatory decision gives greater explainability to the *** It is opportune to raise new studies involving transfer learning for the analysis of en

关键词： Esophagitis Endoscopy Artificial intelligence deep learning Transfer learning

Optimizing the evolution of strength for lime-stabilized rammed soil

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Journal of Rock Mechanics and Geotechnical Engineering 2019年第4期11卷 882-891页

作者： Jair de jesus Arrieta Baldovino Ronaldo Luis dos santos Izzo Eclesielter Batista Moreira Juliana Lundgren Rose department of Civil Construction Federal University of Technology-Parana

In the present study,unconfined compressive strength(qu)values of two lime-treated soils(soil 1 and 2)with curing times of 28 d,90 d and 360 d were *** influence of void/lime ratio was represented by the porosity/volumetric lime content ratio(η/Liv)as the main parameter.η/Liv represents the volume of void influenced by compaction effort and lime *** evolution of qu was analyzed for each soil using the coefficient of determination as the optimization *** at providing adjustments to the mechanical resistance values,the η/Liv parameter was modified to η/LivC using the adjustment exponent C(to make qu-η/Liv variation rates compatible).The results show that with the decrease of η/*** increases potentially and the optimized values of C were *** mechanical resistance data show similar trends between qu and η/LivC for the studied silty soil-ground lime mixtures,which were cured at ambient temperature(23±2)℃ with different curing times of 28-360 ***,optimized equations were presented using the normalized strengths and the proposed optimization model,which show 6% error and 95% acceptability on average.

关键词： Lime-treated soil Void/lime ratio Ground improvement

Real drive cycles analysis by ordered power methodology applied to fuel consumption,C0_(2),NO_(x) and PM emissions estimation

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Frontiers of Environmental Science & Engineering 2021年第1期15卷 77-90页

作者： Pol Masclans Abello Vicente Medina Iglesias M.Antonia de los santos Lopez jesus Alvarez-Florez Center for Engines and Heat Installation Research(CREMIT-UPC).Universitat Politecnica de Catalunya-BarcelonaTech.Av.Diagonal 547(ETSEIB)08028 Barcelona Spain department of Thermal Machinery of Universitat Politecnica de Catalunya-BarcelonaTech and CREMIT-UPC.-BarcelonaTech.Av.Diagonal 547(ETSEIB)08028 Barcelona Spain 3 department of Mechanical Engineering of Universitat Politecnica de Catalunya-BarcelonaTech and CREMIT-UPC.-BarcelonaTech.Av.Diagonal 547(ETSEIB)08028 Barcelona Spain

In this work three fuel consumption and exhaust emission models,ADVISOR,VT-MICRO and the European Environmental Agency Emission factors,have been used to obtain fuel consumption(FC)and exhaust *** models have been used at micro-scale,using the two signal treatment methods *** manuscript presents:1)a methodology to collect data in real urban driving cycles,2)an estimation of FC and tailpipe emissions using some available models in literature,and 3)a novel analysis of the results based on delivered wheel *** results include Fuel Consumption(FC),CO_(2),NO_(x) and PM_(10) emissions,which are derived from the three *** the first part of the paper we present a new procedure for incomplete drive cycle data treatment,which is necessary for real drive cycle acquisition in high density *** the models are used to obtain second by second FC and exhaust ***,a new methodology named Cycle Analysis by Ordered Power(CAbOP)is presented and used to compare the *** method consists in the re-ordering of time dependant data,considering the wheel mechanical power domain instead of the standard time *** new strategy allows the 5 situations in drive cycles to be clearly visualized:hard breaking zone,slowdowns,idle or stop zone,sustained speed zone and acceleration *** complete methodology is applied in two real drive cycles surveyed in Barcelona(Spain)and the results are compared with a standardized WLTC urban cycle.

关键词： Cycle Analysis by Ordered Power(CAbOP) Micro and macro models Real drive cycle NO_(x)/PM_(10)/CO_(2)emissions Wheel mechanical power domain Worldwide Harmonized Light-Duty Vehicles Test Cycle(WLTC)

COVID-19 neuropsychiatric repercussions:Current evidence on the subject

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World Journal of Methodology 2022年第5期12卷 365-380页

作者： Ronaldo Teixeira da Silva Júnior Jonathan santos Apolonio Beatriz Rocha Cuzzuol bruna Teixeira da Costa Camilo Santana Silva Glauber Rocha Lima Araújo Marcel Silva Luz Hanna santos Marques Luana Kauany de Sásantos Samuel Luca Rocha Pinheiro Vinícius Lima de Souza Gonçalves Mariana santos Calmon Fabrício Freire de Melo Instituto Multidisciplinar em Saúde Universidade Federal da BahiaVitória da Conquista 45029094Brazil Universidade Estadual do Sudoeste da Bahia Universidade Estadual do Sudoeste da BahiaVitória da Conquista 45083900Brazil

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection has affected the entire world,causing the coronavirus disease 2019(COVID-19)pandemic since it was first discovered in Wuhan,China in december *** the clinical presentation of the disease,in addition to fever,fatigue,cough,dyspnea,diarrhea,nausea,vomiting,and abdominal pain,infected patients may also experience neurological and psychiatric repercussions during the course of the disease and as a post-COVID-19 ***,headache,dizziness,olfactory and gustatory dysfunction,cerebrovascular disorders,neuromuscular abnormalities,anxiety,depression,and post-traumatic stress disorder can occur both from the infection itself and from social distancing and *** to current evidence about this infection,the virus has the ability to infect the central nervous system(CNS)via angiotensin-converting enzyme 2(ACE2)receptors on host *** studies have shown the presence of ACE2 in nerve cells and nasal mucosa,as well as transmembrane serine protease 2,key points for interaction with the viral Spike glycoprotein and entry into the CNS,being olfactory tract and blood-brain barrier,through hematogenous dissemination,potential ***,the presence of SARS-CoV-2 in the CNS supports the development of neuropsychiatric *** management of these manifestations seems more complex,given that the dense parenchyma and impermeability of brain tissue,despite protecting the brain from the infectious process,may hinder virus ***,some alternatives used in non-COVID-19 situations may lead to worse prognosis of acute respiratory syndrome,requiring ***,the aim of this review is to bring more current points related to this infection in the CNS,as well as the repercussions of the isolation involved by the pandemic and to present perspectives on interventions in this scenario.

关键词： SARS-CoV-2 COVID-19 Central nervous system Quarantine Neurologic disorders Mental disorders