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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 c.mara 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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Exponential continuous Non-Parametric Neural Identifier With Predefined convergence Velocity

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IEEE/cAA Journal of Automatica Sinica 2022年第6期9卷 1049-1060页

作者： Mariana ballesteros Rita Q.Fuentes-Aguilar Isaac chairez Instituto Politécnico Nacional Centro de Innovación y Desarrollo Tecnológico en Cómputo Unidad Profesional Interdisciplinaria de Biotecnología 07340Mexico CityMexico Tecnológico de Monterrey School of Engineering and SciencesZapopanJalisco 45138Mexico Department of Bioprocesses UPIBIInstituto Politécnico Nacional07340Mexico City

This paper addresses the design of an exponential function-based learning law for artificial neural networks(ANNs)with continuous *** ANN structure is used to obtain a non-parametric model of systems with uncertainties,which are described by a set of nonlinear ordinary differential *** novel adaptive algorithms with predefined exponential convergence rate adjust the weights of the *** first algorithm includes an adaptive gain depending on the identification error which accelerated the convergence of the weights and promotes a faster convergence between the states of the uncertain system and the trajectories of the neural *** second approach uses a time-dependent sigmoidal gain that forces the convergence of the identification error to an invariant set characterized by an *** generalized volume of this ellipsoid depends on the upper bounds of uncertainties,perturbations and modeling *** application of the invariant ellipsoid method yields to obtain an algorithm to reduce the volume of the convergence region for the identification *** adaptive algorithms are derived from the application of a non-standard exponential dependent function and an associated controlled Lyapunov *** examples demonstrate the improvements enforced by the algorithms introduced in this study by comparing the convergence settings concerning classical schemes with non-exponential continuous learning *** proposed identifiers overcome the results of the classical identifier achieving a faster convergence to an invariant set of smaller dimensions.

关键词： Exponential Lyapunov functions learning laws non-parametric identifier predefined convergence rate

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Determination of particulate polycyclic aromatic hydrocarbons in ambient air by gas chromatography-mass spectrometry after molecularly imprinted polymer extraction

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Journal of Environmental Sciences 2023年第2期124卷 644-654页

作者： Maria chiara Pietrogrande Giorgia Demaria mara Russo Department of chemical Pharmaceutical and Agraricultural SciencesUniversity of FerraraVia Fossato di Mortara 17/1944121 FerraraItaly

A solid phase extraction procedure(SPE)is described for the quantitative analysis of polycyclic aromatic hydrocarbons(PAHs)in atmospheric particulate matter(PM),as ubiquitous environmental pollutants routinely measured in air qualitymonitoring.A SPE cartridge was used based on a molecular imprinted polymer(MIP-SPE)properly tailored for selective retention of PAHs with 4 and more benzene fused *** performance of the clean-up procedure was evaluated with the specific concern of selective purification towards saturated hydrocarbons,which are the PM components mostly interfering Gc analysis of target *** optimized operative conditions,the MIP-SPE provided analyte recovery close to 95%for heavier PAHs,from benzo(α)pyrene to benzo(ghi)perylene,and close to 90%for four benzene rings PAHs,with good reproducibility(RSDs:2.5%-5.9%).Otherwise,c_(17)-c_(32) n-alkanes were nearly completely *** proposed method was critically compared with Solid Phase Micro Extraction(SPME)using a polyacrylate *** methods were successfully applied to the analysis of ambient PM2.5 samples collected at an urban polluted *** the two procedures,the MIP-SPE provided the highest recovery(R%≥93%)for PAHs with 5 and more benzene rings,but lower for lighter *** contrast,SPME showed a mean acceptable R%value(∼80%)for all the investigated PAHs,except for the heaviest PAHs in the most polluted samples(R%:110%-138%),suggesting an incomplete purification from the interfering n-hydrocarbons.

关键词： Polycyclic aromatic hydrocarbons Atmospheric particle matter Molecularly imprinted polymers-solid-phase extraction Solid phase micro extraction Gc/MS analysis

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Long-term reconstruction of flash floods in the Qilian Mountains,china,based on dendrogeomorphic methods

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Journal of Mountain Science 2022年第11期19卷 3163-3177页

作者： QIE Jia-zhi ZHANG Yong TRAPPMANN Daniel ZHONG Yi-hua ballesteros-cÁNOVAS Juan Antonio FAVILLIER Adrien STOFFEL Markus Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China climate change Impacts and Risks in the Anthropocene(c-cIA) Institute for Environmental SciencesUniversity of GenevaGeneva CH-1205Switzerland Dendrolab.ch Department of Earth SciencesUniversity of GenevaGeneva CH-1205Switzerland National Museum of Natural Sciences MNCN-CSICC/Serrano 115bis28006MadridSpain Department F.-A.Forel for Environmental and Aquatic Sciences University of GenevaGeneva CH-1205Switzerland

In china,flash floods are one of the main natural disasters causing loss of life and damage to *** threat of flash floods is exacerbated with climate change and increased human activities,such that the number of disasters has shown a clear upward trend in recent ***,due to the scarcity of instrumental data or overly short timeseries,we are still lacking critical data to understand spatio-temporal patterns and driving factors of extreme flash *** missing knowledge is however crucial for a proper management of these hazards,especially in remote mountain *** forested catchments,dendrogeomorphology allows the reconstruction of past process activity based on growth disturbances(GDs)in trees that have been affected by past flash ***,in our study,for the first time,we reconstruct past flash floods in the Qilian Mountains,northeast Tibetan Plateau,over past *** this end,we sampled 99 Qinghai spruce(Picea crassifolia)trees affected by flash floods,with a total of 194increment cores,and identified 302 GDs induced by past flash *** GDs have been caused by at least 21 flash floods that we are able to reconstruct over the last 170 *** position of GDs within tree rings and the intra-seasonal dating of past events also allowed discussion of the likely synoptic situations that may have led to the triggering of flash floods in the *** regression analysis confirms that significant correlation exists between cumulative maximum 5-day August-September precipitation and reconstructed flash floods,which is corresponding to the majority of scars and related tangential rows of traumatic resin ducts(TRDs)found in the latewood portion of growth *** results support the idea that abundant precipitation occurring at the end of the summer season and early fall is the key factor driving flash floods in our study *** research not only fills the gaps regarding historical flash flood histories in

关键词： Tree ring Dendrogeomorphology Flash floods Qinghai spruce Qilian Mountains

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Philippine retinoblastoma initiative multi-eye center study 2010-2020

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International Journal of Ophthalmology(English edition) 2024年第1期17卷 144-156页

作者： Roland Joseph D.Tan Gary John V.Mercado Patricia E.cabrera Paulita Pamela P.Astudillo Rolando Enrique D.Domingo Josept Mari S.Poblete charmaine Grace M.cabebe Adriel Vincent R.Te Melissa Anne S.Gonzales Jocelyn G.Sy Beltran Alexis A.Aclan Jayson T.So Fatima G.Regala Kimberley Amanda K.comia Josemaria M.castro mara Augustine S.Galang Aldous Dominic c.cabanlas Benedicto Juan E.Aguilar Gabrielle S.Evangelista Jo Michael Maniwan Andrei P.Martin calvin Y.Martinez John Alfred H.Lim Rena Ivy Bascuna Rachel M.Ng Kevin B.Agsaoay Kris Zanna A.Acluba-Arao Ellaine Rose V.Apostol Beatriz M.Prieto Department of Ophthalmology and Visual Sciences Philippine General HospitalManila 1000Philippines Department of Ophthalmology Baguio General Hospital and Medical CenterBaguio City 2600Philippines Department of Ophthalmology Manila Doctors HospitalManila 1000Philippines Department of Ophthalmology Rizal Medical CenterPasig City 1600Philippines Department of Ophthalmology Jose B.Lingad Memorial Regional HospitalPampanga 2000Philippines Department of Ophthalmology Southern Philippines Medical CenterDavao City 8000Philippines Department of Ophthalmology East Avenue Medical CenterQuezon City 1100Philippines Department of Ophthalmology Northern Mindanao Medical CenterCagayan de Oro City 9000Philippines Department of Ophthalmology Cebu Velez General HospitalCebu City 6000Philippines Legazpi Eye center Legazpi City 4500Philippines Department of Ophthalmology Cagayan Valley Medical CenterTuguegarao City 3500Philippines

AIM:To provide a comprehensive and more representative national data on the disease,especially on treatment options and outcomes,and to determine access of retinoblastoma patients from Luzon,Visayas and Mindanao to eye care,and determine if access is associated with delay in consultation,staging and ***:cohort study of retinoblastoma patients seen in eleven institutions located in the three major areas of the Philippines namely Luzon,Vizayas and Mindanao from ***:Totally 636 patients,involving 821 eyes,were ***(57%)were from Luzon and were seen in institutions in Luzon(72%).Annually,58±10 new cases were seen with 71%having unilateral *** delay of consultation remained long at 9(3,17)mo,longest in patients with unilateral disease(Pcular *** was the most common treatment received by 484 patients while intravenous chemotherapy was received by *** were 250(39%)patients alive,195(31%)dead,85(13%)abandoned,17(3%)refused and 89(14%)with no ***:This study presents the largest cohort of retinoblastoma patients in the Philippines in terms of patients’and participating institutions’number and geographical location and type of institution(private and public).It also presents more comprehensive data on the treatments used and outcomes(survival,globe salvage,and vision retention rates).Delay in consultation was still long among patients leading to advanced disease stage and lower survival *** increasing capacity to diagnose and manage retinoblastoma in the country,the delay of consultation remains long primarily due to accessibility issues to eye care institutions especially in the Visayas and financial *** delay was still significant that overall survival rate remain low.

关键词： retinoblastoma Philippines clinical profile

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Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity

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Microsystems & Nanoengineering 2022年第6期8卷 97-112页

作者： Kenza Samlali chiara Leal Alves mara Jezernik Steve c.c.Shih Department of Electrical and computer Engineering Concordia UniversityMontréalQCCanada centre for Applied Synthetic Biology Concordia UniversityMontréalQCCanada Department of chemical Engineering and Applied chemistry University of TorontoTorontoONCanada Department of Biology Concordia UniversityMontréalQCCanada

Fungal cell-wall-degrading enzymes have great utility in the agricultural and food *** cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic *** existing methods used to discover these enzymes are not well adapted to fungi culture and morphology,which prevents the proper evaluation of these *** report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized *** new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days(2–4 days)and could be sorted without droplet *** long-term culture,we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based *** also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes,such as chitinases,β-glucanases,and β-Nacetylgalactosaminidases,from a filamentous fungi droplet library that had been incubated for>4 *** new system is portable,affordable for any laboratory,and user-friendly compared to classical droplet-based microfluidic *** propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.

关键词： system fluid culture

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Sand wave migration near the southeastern corner of Martha's Vineyard, Massachusetts, USA

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International Journal of Sediment Research 2023年第5期38卷 629-642页

作者： Vinícius Santos Pessanha Peter cheng chu Matthew Kenneth Gough Peter Traykovski mara Morgenstern Orescanin Department of Oceanography Naval Postgraduate School Department of Applied Ocean Physics and Engineering Woods Hole Oceanographic Institution

Sand waves of approximately 2 m in height were observed to migrate nearly 40 m with counterclockwise rotation between two bathymetric surveys performed three months apart near the southeastern corner of Martha’s Vineyard, Massachusetts. The region is characterized by strong tidal currents, intermittent energetic surface wave events, and shallow water with local depth ranging from 2 to 7 m. This study uses the process-based model, Delft3D, with a three-dimensional approach to examine the sand wave dynamics by incorporating surface waves, winds, currents, and bathymetric observations. The model successfully simulates sand wave migration in comparisons to observations. Model sensitivity analyses show that the sand wave migration reduces by 65% with the absence of the surface waves. The modeled sand wave migration speed is correlated with the tidal current Shields parameter, and sharp increases in migration speed occur when the wave-driven Shields parameter increases in response to energetic surface wave events. The combined effect of tides, surface waves, and bathymetry is the origin of the rotational aspect of the sand wave, using the Shields parameter as an indicator of tidal currents and surface wave influence on sand wave dynamics.

关键词： Sand wave migration Numerical morphological modeling Delft3D Sandy seafloor Martha's Vineyard

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Hepatocellular carcinoma and food contamination: Ochratoxin A as a great prompter

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World Journal of Gastroenterology 2013年第24期19卷 3723-3725页

作者： Raphael JF Felizardo Niels OS c.mara Division of Nephrology Department of Medicine Federal University of Sao PauloSao Paulo CEP 05508-900 Brazil Department of Immunology Institute of Biomedical Sciences University of S o PauloSao Paulo CEP 05508-900 Brazil

Ochratoxin A (OTA) is a secondary metabolite of Asper-gillus and Penicillium, microorganisms that can be haz-ardous to health when present as food contaminants. OTA is a potent member of a group of mycotoxins. Prolonged exposure to mycotoxins in the diet is related to cancer, among other diseases. Hepatocellular car-cinoma (Hcc) accounts for 70%-90% of primary liver cancers and is the third leading cause of cancer-related deaths worldwide. In a recent study, Ibrahim et al proposed a correlation between the incidence of Hcc and contamination with OTA. Analysis of OTA in serum samples showed that Hcc patients had the highest incidence of OTA of the subjects examined (5-fold higher than that of the control group). OTA levels were significantly increased in Hcc patients. This study demonstrates that chronic exposure to high levels of OTA may be associated with a high risk of liver cancer development. Future epidemiologic studies of Hcc should focus on good practices in food preparation, food storage and the consumption of OTA-containing foods.

关键词： Ochratoxin A Mycotoxin Food contamination Hepatocellular carcinoma Liver cancer Egypt

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corrigendum to“3cpro of FMDV inhibits type II interferon-stimulated JAK-STAT signaling pathway by blocking STAT1 nuclear translocation”[Virol Sin 38(2023)387–397]

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Virologica Sinica 2024年第2期39卷 351-354页

作者： Xiangju Wu Lei chen chao Sui Yue Hu Dandan Jiang Fan Yang Laura c.Miller Juntong Li Xiaoyan cong Nataliia Hrabchenko changhee Lee Yijun Du Jing Qi Shandong Key Laboratory of Animal Disease control and Breeding Key Laboratory of Livestock and Poultry Multi-omics of MARAInstitute of Animal Science and Veterinary MedicineInstitute of Crop Germplasm ResourcesShandong Academy of Agricultural SciencesJinan250100China college of Life Science Shandong Normal UniversityJinan250358China State Key Laboratory of Veterinary Etiological Biology National Foot and Mouth Disease Reference LaboratoryKey Laboratory of Animal Virology of Ministry of AgricultureLanzhou Veterinary Research InstituteChinese Academy of Agricultural SciencesLanzhou730050China Department of Diagnostic Medicine and Pathobiology College of Veterinary MedicineKansas State UniversityManhattanKS66506USA college of Veterinary Medicine and Virus Vaccine Research center Gyeongsang National UniversityJinju52828Republic of Korea

Due to our negligence,the original version of this article,published online on Mar 14,2023,contained some mistakes in several *** Fig.2D,the positions of the bands for protein 3A and 3B were incorrectly *** has been m... 详细信息

关键词： STAT1 FMDV bands

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State of the Art on Micromilling of Materials,a Review

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Journal of Materials Science & Technology 2012年第8期28卷 673-685页

作者： M.A.c.mara J.c. campos Rubio A.M. Abro J.P. Davim Department of Mechanical Engineering Universidade Federal de Minas GeraisAv.Ant onio Carlos6627-Pampulha Belo Horizonte MGCEP:31.270-901Brazil Department of Mechanical Engineering University of AveiroCampus Universitrio de Santiago3810-193AveiroPortugal

The trend towards miniaturization has increased dramatically over the last decade, especially within the fields concerned with bioengineering, microelectronics, and aerospace. Micromillin8 is among the principal manu- facturing processes which have allowed the development of components possessing micrometric dimensions, being used to the manufacture of both forming tools and the final product. The aim of this work is to present the principal aspects related to this technology, with emphasis on the work material requirements, tool ma- terials and geometry, cutting forces and temperature, quality of the finished product, process modelling and monitoring and machine tool requirements. It can be noticed that size effect possesses a relevant role with regard to the selection of both work material （grain size） and tooling （edge radius）. Low forces and temper- ature are recorded during micromillin8, however, the specific cutting force may reach high values because of the ploughing effect observed as the uncut chip thickness is reduced. Finally, burr formation is the principal concern with regard to the quality of the finished part.

关键词： Micro-milling Micromachining Size effect Miniaturization

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