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Neotropical mustelids: fecal metabolome diversity and its potential for taxonomic discrimination

Integrative Zoology 2023年第3期18卷 518-529页

作者： Lana Resende de ALMEIDA Marina Amaral ALVES Ana Maria obino MASTELLA rafael GARRETT Maria João Ramos PEREIRA Bird and Mammal Evolution Systematics and Ecology LabPrograma de Pós-Graduação em Biologia AnimalUniversidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil Programa de Pós-Graduação em Biologia Animal Universidade Federal do Rio Grande do SulPorto AlegreRio Grande do SulBrazil Chemistry Institute Metabolomics Laboratory(LabMeta–LADETEC/IQ–UFRJ)Avenida Horácio MacedoFederal University of Rio de JaneiroRio de JaneiroRJBrazil Walter Mors Institute of Research on Natural Products Universidade Federal do Rio de JaneiroRio de JaneiroRJBrazil

Chemical proﬁles of non-invasive biological material,such as feces,have great potential to study elusive animals or those with low population ***,we use a metabolomic approach to evaluate Neotropical mustelids as a biological model to describe the diversity of the metabolites present in fecal samples,as well as to evaluate the potential of chemical proﬁles for taxonomic *** collected fecal samples from captive individuals of 5 species of mustelids occurring in Brazil and analyzed them by liquid chromatography coupled to high-resolution mass *** 200 compounds have been annotated;“bile acids,alcohols and derivatives”was the most expressive class in the metabolome of all the *** successfully discriminated 3 taxonomic groups:1—tayra(Eira barbara);2—otters(Lontra longicaudis and Pteronura brasiliensis;1);and 3—grisons(Galictis vittata and Galictis cuja).Several compounds seemed to be associated with food intake and the digestive process,while others were found for theﬁrst time in Neotropical *** concluded that mustelids show high metabolome diversity and that species-speciﬁc identiﬁcation through metabolomic proﬁles is possible,thus contributing to the development and implementation of additional non-invasive approaches in the study of mustelids.

关键词： chemical proﬁles ecology high-resolution mass spectrometry metabolomics Mustelidae

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A Simple and Efficient Structural Topology optimization Implementation Using open-Source Software for All Steps of the Algorithm:Modeling, Sensitivity Analysis and optimization

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Computer Modeling in Engineering & Sciences 2023年第8期136卷 1371-1397页

作者： rafael Marin Ferro Renato Pavanello Coordination of Mechanical Engineering Federal Institute of Science and Technology of ES-IFESAracruz-ES29192-733Brazil Department of Computational Mechanics Faculty of Mechanical EngineeringUnicampCampinas-SP13083-860Brazil

This work analyzes the implementation of a continuous method of structural topology optimization(STo)using open-source software for all stages of the topology optimization problem:modeling,sensitivity analysis and *** implementation involves three main components:numerical analysis using the Finite Element Method(FEM),sensitivity analysis using an Adjoint method and an optimization *** order to allow the automated numerical solution of Partial Differential Equations(PDEs)and perform a sensitivity analysis,FEniCS and Dolfin Adjoint software are used as tools,which are open-source *** the optimization process,Ipopt(Interior Point oPTimizer)is used,which is a software package for nonlinear optimization scale designed to find(local)solutions of mathematical optimization *** topological optimization method used is based on the SIMP-Solid IsotropicMaterial with Penalization *** considered problem is the minimization of compliance/maximization of stiffness,considering the examples of recurrent structures in the literature in 2D and 3D.A density filtering algorithm based on Helmholtz formulation is *** complete code involves 51 lines of programming and is presented and commented in detail in this article.

关键词： Structural topology optimization finite element method FEniCS Dolfin Adjoint

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Response to Commentary by Dr. Matthew J. Clarkson on

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Journal of Sport and Health Science 2024年第5期13卷 670-671页

作者： Hugo de Luca Corrêa Lysleine Alves Deus Dahan da Cunha Nascimento Nicholas Rolnick Rodrigo Vanerson Passos Neves Andrea Lucena Reis Thais Branquinho de Araújo Carmen Tzanno-Martins Fernanda Silveira Tavares Luiz Sinésio Silva Neto Cláudio Avelino Rodrigues Santos Paolo Lucas Rodrigues-Silva Fernando Honorato Souza Vitória Marra da Motta Vilalva Mestrinho rafael Lavarini dos Santos Rosangela Vieira Andrade Jonato Prestes Thiago dos Santos Rosa Post-graduate Program of Physical Education Catholic University of BrasıliaBrasılia 71966-700Brazil The Human Performance Mechanic Lehman CollegeNew YorkNY 10011USA Clinical Group Home Dialysis Center and RenalClass Sao Paulo 01239-040Brazil Department of Medicine Catholic University of BrasıliaBrasılia 71966-700Brazil Faculty of Medicine Federal University of TocantinsTocantins 77001-090Brazil Embrapa Genetic Resources and Biotechnology Brasılia 70770-917Brazil g Graduate Program of Genomic Sciences and Biotechnology Brasılia 71966-700Brazil

Dear editor:We sincerely thank Matthew *** for his insightful commentary1 on our recent publication in the Journal of Sport and Health Science.2 Clarkson's pioneering work in the development and application of blood flow restriction (BFR) exercise protocols has undeniably laid the groundwork for subsequent investigations in this field,including our own.(3-6)His commentary not only highlights the relevance and timeliness of our study but also offers valuable perspectives on refining safety considerations for intradialytic BFR exercise among hemodialysis patients.

关键词： patients application flow

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Free and open source software for geospatial applications(FoSS4G)to support Future Earth

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International Journal of Digital Earth 2017年第4期10卷 386-404页

作者： Maria Antonia Brovelli Marco Minghini rafael moreno-Sanchez Ricardo oliveira Department of Civil and Environmental Engineering Politecnico di MilanoComoItaly Department of Geography and Environmental Sciences University of Colorado DenverDenverCOUSA

The development,integration,and distribution of the information and spatial data infrastructure(*** Earth;DE)necessary to support the vision and goals of Future Earth(FE)will occur in a distributed fashion,in very diverse technological,institutional,socio-cultural,and economic contexts around the *** complex context and ambitious goals require bringing to bear not only the best minds,but also the best science and technologies *** and open Source Software for Geospatial Applications(FoSS4G)offers mature,capable and reliable software to contribute to the creation of this *** this paper we point to a selected set of some of the most mature and reliable FoSS4G solutions that can be used to develop the functionality required as part of DE and *** provide examples of large-scale,sophisticated,mission-critical applications of each software to illustrate their power and capabilities in systems where they perform roles or functionality similar to the ones they could perform as part of DE and *** provide information and resources to assist the readers in carrying out their own assessments to select the best FoSS4G solutions for their particular contexts and system development needs.

关键词： open source software geospatial software FoSS4G Future Earth Digital Earth

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National assessment of the evolution of forest fragmentation in Mexico

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Journal of Forestry Research 2011年第2期22卷 167-174页

作者： rafael moreno-Sanchez Francisco.moreno-Sanchez Juan Manuel Torres-Rojo University of Colorado Denver Department of Geography and Environmental SciencesCampus Box 172 P.O.Box 173364DenverCO 80217-3364USA Instituto Nacional de Investigaciones Forestales y Agropecuarias(INIFAP) Av Progreso #5CoyoacánMéxico D.F.04100México Centro de Investigación y Docencia Económicas(CIDE) Carretera México-Toluca 3655Col.Lomas de Santa FeMéxicoD.F.01210México

This paper presents assessments of the fragmentation of the temperate and tropical forests in Mexico at the national level for two dates 1993 and *** study was based on land use and vegetation cover data sets scale 1：250,*** broad forest types（Temperate Forests and Tropical Forests） and five more specific forest types（Broadleaf Forests,and Coniferous Forests;Tropical Dry Deciduous Forests,Tropical Sub-evergreen Forests,and Tropical Evergreen Forests） were defined to conduct the *** 3.3 was used to estimate nine metrics of the spatial pattern of the forests for each forest type and date *** results indicate that the land cover transitions that have occurred between 1993 and 2002 have resulted in more isolated forest patches with simpler shapes in both the Temperate and Tropical *** remaining Tropical Forest patches have become smaller and more *** contrast,the remaining Temperate Forest patches are fewer and on average *** the more specific forest types defined in this study,the Broadleaf Forests have the highest indicators of *** these forests are usually embedded or adjacent to Coniferous *** more concern for conservation purposes are the high values of fragmentation metrics found for the Tropical Evergreen Forests and Tropical Dry Deciduous Forests,because these forest types are usually surrounded by non-forest land covers or anthropogenic land uses.

关键词： forest fragmentation Mexico FragStats.

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Immersed Boundary Approach to Biofilm Spread on Surfaces

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Communications in Computational Physics 2022年第1期31卷 257-292页

作者： Ana Carpio rafael Gonzalez-Albaladejo Departamento de Matematica Aplicada Universidad Complutense28040 MadridSpain

We propose a computational model to study the growth and spread of bacterial biofilms on interfaces,as well as the action of antibiotics on *** membranes are represented by boundaries immersed in a fluid matrix and subject to interaction ***,division and death of bacterial cells follow dynamic energy budget rules,in response to variations in environmental concentrations of nutrients,toxicants and substances released by the *** this way,we create,destroy and enlarge boundaries,either spherical or *** forces represent details of the interaction between cells,and the interaction with the *** can investigate geometrical arrangements and the formation of porous *** simulations illustrate the evolution of top views and diametral slices of small biofilm seeds,as well as the action of *** show that cocktails of antibiotics targeting active and dormant cells can entirely eradicate a biofilm.

关键词： Hybrid multiscale models immersed boundary methods dynamic energy budget models bacterial biofilm antibiotic resistance

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Nylon 6-cellulose composite hosted in a hypodermic needle: Biofluid extraction and analysis by ambient mass spectrometry in a single device

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Journal of Pharmaceutical Analysis 2023年第11期13卷 1346-1352页

作者： Jaime Millan-Santiago rafael Lucena Soledad Cardenas Affordable and Sustainable Sample Preparation(AS2P)Research Group Analytical Chemistry DepartmentChemical Institute for Energy and Environment(IQUEMA)University of CordobaE-14071CordobaSpain

This study proposes a hypodermic needle(HN)as a sorbent holder and an electrospray(ESI)emitter,thus combining extraction and analysis in a single device.A novel nylon 6-cellulose(N6-Cel)composite sorbent is proposed to extract methadone from oral fluid *** cellulosic substrate provides the composite with high porosity,permitting the flow-through of the sample,while the polyamide contributes to the extraction of the *** low price of the devices(considering the holder and the sorbent)contributes to the affordability of the method,and their small size allows easy transportation,opening the door to on-site *** the optimum conditions,the analyte can be determined by high-resolution ambient ionization mass spectrometry at a limit of detection(LoD)as low as 0.3 mg/L and precision(expressed as relative standard deviation,RSD)better than 9.3%.The trueness,expressed as relative recovery(RR),ranged from 90%to 109%.As high-resolution mass spectrometers are not available in many laboratories,the method was also adapted to low-resolution *** this sense,the direct infusion of the eluates in a triple quadrupole-mass spectrometry provided an LoD of 2.2 mg/*** RSD was better than 5.3%,and the RR ranged from 96%to 121%.

关键词： ESI emitter Mass spectrometry Hypodermic needle Composite Methadone

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Sampling lattices in semi-grand canonical ensemble with autoregressive machine learning

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npj Computational Materials 2022年第1期8卷 588-597页

作者： James Damewood Daniel Schwalbe-Koda rafael Gómez-Bombarelli Department of Materials Science and Engineering Massachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02319USA

Calculating thermodynamic potentials and observables efficiently and accurately is key for the application of statistical mechanics simulations to materials ***,naive Monte Carlo approaches,on which such calculations are often dependent,struggle to scale to complex materials in many state-of-the-art disciplines such as the design of high entropy alloys or multi-component *** address this issue,we adapt sampling tools built upon machine learning-based generative modeling to the materials space by transforming them into the semi-grand canonical ***,we show that the resulting models are transferable across wide ranges of thermodynamic conditions and can be implemented with any internal energy model U,allowing integration into many existing materials *** demonstrate the applicability of this approach to the simulation of benchmark systems (AgPd,CuAu) that exhibit diverse thermodynamic behavior in their phase ***,we discuss remaining challenges in model development and promising research directions for future improvements.

关键词： canonical thermodynamic directions

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Ion dynamics into different pore size distributions in supercapacitors under compression

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Journal of Energy Chemistry 2023年第5期80卷 110-119,I0004页

作者： João Pedro Aguiar dos Santos Cesar J.B.Pagan rafael Vicentini Reinaldo F.Teófilo Renato Beraldo Leonardo M.Da Silva Hudson Zanin Brazilian Renewable Energies Center for Innovation on New EnergiesSchool of Electrical and Computer EngineeringUniversity of CampinasAv.Albert Einstein 40CampinasSP13083-852Brazil School of Electrical and Computer Engineering University of CampinasSP 13083-852Brazil Multivariate Chemical Data Analysis Laboratory Department of ChemistryUniversidade Federal de Viçosa36570-900 ViçosaMGBrazil Department of Chemistry Laboratory of Fundamental and Applied ElectrochemistryFederal University of Jequitinhonha and Mucuri's ValleyRodovia MGT 367km 5835000 Alto da Jacuba39100-000DiamantinaMGBrazil

Compressing supercapacitor(SCs)electrode is essential for improving the energy storage characteristics and minimizing ions’distance travel,faradaic reactions,and overall ohmic *** comprising the ion dynamics in SC electrodes under compression are still ***,the ionic dynamics of five aqueous electrolytes in electrodes under compression were studied in this work for tracking electrochemical and structural changes under mechanical stress.A superionic state is formed when the electrode is compressed until the micropores match the dimensions with the electrolyte’s hydrated ion sizes,which increases the *** excessive compression is applied,the accessible pore regions decrease,and the capacitance ***,as the studied hydrated ions have different dimensions,the match between ion/pore sizes *** the LioH and NaClo4electrolytes,increasing the pressure from 60 to 120 and 100 PSI raised the capacitance from 13.5 to 35.2 F g^(-1)and 30.9 to 39.0 F g^(-1),***,the KoH electrolyte with the lowest and LiCl with the biggest combination of hydrated ion size have their point of maximum capacitance(39.5 and 36.7F g^(-1))achieved at 140 and 80 PSI,*** LiCl and KCl electrolytes,overcompression causes a drop in capacitance higher than 23%.

关键词： Mechanic compression Pore size distribution lon dynamics Activated carbon Supercapacitors

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Analysing the quality of Swiss National Forest Inventory measurements of woody species richness

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Forest Ecosystems 2020年第3期7卷 478-488页

作者： Berthold Traub rafael o.Wüest Scientific Service NFI Swiss Federal Research Institute WSLZürcherstrasse 1118903BirmensdorfSwitzerland Spatial Evolutionary Ecology Swiss Federal Research Institute WSLZürcherstrasse 1118903BirmensdorfSwitzerland

Background: Under ongoing climate and land-use change, biodiversity is continuously decreasing and monitoring biodiversity is becoming increasingly important. National Forest Inventory(NFI) programmes provide valuable timeseries data on biodiversity and thus contribute to assessments of the state and trends in biodiversity, as well as ecosystem functioning. Data quality in this context is of paramount relevance, particularly for ensuring a meaningful interpretation of changes. The Swiss NFI revisits about 8%–10% of its sample plots regularly in repeat surveys to supervise the quality of ***: We analysed the relevance of observer bias with equivalence tests, examined data quality objectives defined by the Swiss NFI instructors, and calculated the pseudo-turnover(PT) of species composition, that is, the percentage of species not observed by both teams. Three attributes of woody species richness from the latest Swiss NFI cycles(3 and 4) were analysed: occurrence of small tree and shrub species(1) on the sample plot and(2) at the forest edge, and(3) main shrub and trees species in the upper ***: We found equivalent results between regular and repeat surveys for all attributes. Data quality, however,was significantly below expectations in all cases, that is, as much as 20%–30% below the expected data quality limit of 70%–80%(proportion of observations that should not deviate from a predefined threshold). PT values were about 10%–20%, and the PT of two out of three attributes decreased significantly in NFI4. This type of uncertainty –typically caused by a mixture of overlooking and misidentifying species – should be considered carefully when interpreting change figures on species richness estimates from NFI ***: our results provide important information on the data quality achieved in Swiss NFIs in terms of the reproducibility of the collected data. The three applied approaches proved to be effective for evaluating the quality of plot

关键词： Biodiversity Data quality Equivalence test Forest inventory Monitoring observer agreement Richness Pseudo-turnover

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