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Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization

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npj Computational Materials 2022年第1期8卷 467-479页

作者： andrép.Carvalho Sérgio M.Santos Germán pérez-Sánchez JoséD.Gouveia JoséR.B.gomes Miguel Jorge CICECO-Aveiro Institute of Materials Department of ChemistryUniversity of AveiroCampus Universitário de Santiago3810-193AveiroPortugal Department of Chemical and process Engineering University of Strathclyde75 Montrose StreetGlasgowG11XJUK

We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis–*** close to ambient temperatures and over a wide range of *** key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky *** simplicity of the model,its applicability in standard parallelized molecular dynamics codes,and its compatibility with the widely used MARTINI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time *** model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point,and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle.

关键词： silica polymerization dynamics

Changes on Anuran Tadpole Functional Diversity along an Environmental Gradient at the Southernmost Atlantic Rainforest Remnant

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Asian Herpetological Research 2020年第1期11卷 63-70页

作者： Victor Mendes LIpINSKI andre passaglia SCHUCH Tiago gomes dos SANTOS post Graduation program of Animal Biodiversity Federal University of Santa MariaLaboratory of HerpetologyDepartment of BiologyAv.Roraima no 1000 building 17room 1140Camobi97105-900Santa MariaRSBrazil Universidade Federal do pampa Av.Antonio Trilha1847Centro973000000 Sao GabrielRSBrasil Southern Regional Space Research Center CRS/INPE-MCTIP.O.Box 5021room 104197110-970Santa MariaRSBrazil

For decades the ecologists are using the same methods in order to determine the environmental health of a community,however,the crescent need on defining how these processes act,triggered the development of new methods that could classify the organisms and their function at the *** we used the anuran larvae to understand the effects of an environmental gradient on the structure and organization of the anuran assemblages along it,and to access in a realistic form,the actual state of preservation of the la rgest remnant of Atlantic Rainforest on the Southernmost portion of *** found that despite the higher diversity of species and the conservation unit status of the place,the ecosystem itself is still in danger,given the low number of functional groups and thus a higher number of ecosystem services that can be lost.

关键词： Anuran ecosystem function conservation unities tadpoles

Targeting the premetastatic niche:epigenetic therapies in the spotlight

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Signal Transduction and Targeted Therapy 2020年第1期5卷 1871-1872页

作者： Vivien Low John Blenis Ana p.gomes Meyer Cancer Center Weill Cornell MedicineNew YorkNYUSA Department of pharmacology Weill Cornell MedicineNew YorkNYUSA

The treatment of metastatic cancers remains a challenge in the clinic,with recurrences persisting at high rates even after surgical resection of primary *** the perseverance of circulating tumor cells after resection,this phenomenon is abetted by the formation of the premetastatic niche(pMN),a distant environment ripe for the colonization of new metastases,which is conditioned by factors and extracellular vesicles secreted by the primary *** their recent paper,Lu et *** how such pMNs in the lung can be disrupted by low-dose adjuvant epigenetic therapy,and propose a novel therapeutic avenue to supplement tumor resection.

关键词： metastatic epigenetic al

Extraintestinal manifestations of inflammatory bowel disease, nitroxidative stress and dysbiosis: What is the link between them?

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BIOCELL 2021年第3期45卷 461-481页

作者： AMYLLY SANUELLY DA pAZ MARTINS SAMARA BOMFIM gomes CAMpOS MARÍLia OLIVEIRA FONSECA GOULART FABiaNA andrÉA MOURA programa de pós-Graduação da Rede Nordeste de Biotecnologia(RENORBIO) Universidade Federal de Alagoas(UFAL)MaceióAL 57072-970Brazil programa de pós-Graduação em Ciências da Saúde(ppGCS) Universidade Federal de Alagoas(UFAL)MaceióAL 57072-970Brazil programa de pós-Graduação em Química e Biotecnologia(ppGQB/UFAL) Campus A.C.SimõesAvenida Lourival Melo Motas/nTabuleiro dos MartinsMaceióAL 57072-970Brazil programa de pós-Graduação em Nutrição(ppGNU/UFAL) Programa de Pós-Graduação em Ciências Médicas(PPGCM/UFAL)Universidade Federal de Alagoas(UFAL)MaceióAL 57072-970Brazil

Inflammatory bowel disease(IBD),which includes Crohn’s disease and ulcerative colitis,has a not yet completely defined aetiology and is characterized by a progressive chronic inflammation that involves nitroxidative stress and *** manifestations can occur and affect several organs,including the liver and bile ducts,joints,skin,eyes,and less frequently,the heart,brain,and kidneys,increasing the risk of morbidity and *** repercussions may be associated with the activity or severity of *** present review proposes to report and analyse the participation of dysbiosis and nitroxidative stress in the genesis of extraintestinal manifestations,aiming to contribute to a better understanding of the disease and to focus on the development of individualized preventive and therapeutic strategies.

关键词： Oxidative stress Microbiota Bacterial translocation Ulcerative colitis Crohn disease

Ultrastructural and enzymatic alterations in the ovary of Rhodnius prolixus infected with Trypanosoma rangeli

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Asian pacific Journal of Tropical Medicine 2022年第2期15卷 71-78页

作者： Guilherme S.Machado Rosane L.Lopes Simone S.C.Oliveira Simone p.C.Freitas Jacenir R.Santos-Mallet andréL.S.Santos Denise Feder Suzete A.O.gomes programa de pós-Graduação em Ciências e Biotecnologia Instituto de BiologiaUniversidade Federal FluminenseNiteróiRJBrazil Laboratório de Biodiversidade de Insetos e patógenos Departamento de Biologia GeralInstituto de BiologiaUniversidade Federal FluminenseNiteróiRJBrazil Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes Departamento de Microbiologia GeralInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRJBrazil Fundação Oswaldo Cruz piauí TeresinaPIBrazil Laboratório Interdisciplinar de Vigilância Entomológica em Díptera e Hemíptera Instituto Oswaldo CruzFundação Oswaldo CruzRio de JaneiroRJBrazil Universidade Iguaçu Nova IguaçuRJBrazil Laboratório de Biologia de Insetos Departamento de Biologia GeralInstituto de BiologiaUniversidade Federal FluminenseNiteróiRJBrazil

Objective:To investigate the morphological structure of ovarian follicular cells and biochemical parameters of both ovaries and fat bodies(sites of vitellogenesis)from Rhodnius(R.)prolixus infected with Trypanosoma(T.)***:Adult virgin females of *** were fed upon a membrane apparatus containing heat-inactivated citrated rabbit blood and a suspension of *** epimastigotes(Macias strain).Females from the control group and all the males received parasite-free *** electron microscopy was used to reveal the morphological aspects of ovarian follicle cells in both control and parasite-infected *** profile,proteolytic activities and Western blotting analyses were performed in either ovary or fat body samples of control and parasite-infected ***:According to the ultrastructural data,*** infection elicited a degeneration process in the ovarian follicular cells of *** assays indicated a reduction in the activity of aspartic peptidases in the ovary and fat body from parasite-infected group,while a significant increase in the cysteine peptidase activity was measured in both insect ***,immunoblotting revealed that vitellogenin was overexpressed in the ovary of parasite-infected ***:*** infection seems to elicit an early programmed cell death in the ovarian follicle cells as well as induces the modulation on the activities of different peptidase classes in either ovaries or fat bodies and the overexpression of the vitellogenin in the ovary of ***.

关键词： Trypanosoma rangeli Rhodnius prolixus Ovarian follicle Vitellogenin Aspartic protease Cysteine protease

The role of surface functionalization of silica nanoparticles for bioimaging

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Journal of Innovative Optical Health Sciences 2016年第4期9卷 11-26页

作者： Maria C.gomes Angela Cunha Tito Trindade João p.C.Tome QOpNA University of Aveiro 3810-193 AveiroPortugal CICECO and Department of Chemistry University of Aveiro 3810-193 AveiroPortugal CESAM and Department of Biology University of Aveiro 3810-193 AveiroPortugal Centro de Quimica Estrutural Instituto Superior Tecnico Universidade de LisboaAv.Rovisco Pais1049-001 LisboaPortugal Department of Organic and Macromolecular Chemistry Ghent University B-9000 Gent Belgium

Among the several types of inorganic nanoparticles available,silica nanoparticles(SNp)have earned their relevance in biological applications namely,as bioimaging *** fact,uorescent SNp(FSNp)have been explored in this-eld as protective nanocarriers,overcoming some limitations presented by conventional organic dyes such as high photobleaching rates.A crucial aspect on the use of uorescent SNp relates to their surface properties,since it determines the extent of interaction between nanoparticles and biological systems,namely in terms of colloidal stability in water,cellular recognition and internalization,tracking,biodistribution and speci-city,among ***,it is imperative to understand the mechanisms underlying the interaction between biosystems and the SNp surfaces,making surface functionalization a relevant step in order to take full advantage of particle *** versatility of the surface chemistry on silica platforms,together with the intrinsic hydrophilicity and biocompatibility,make these systems suitable for bioimaging applications,such as those mentioned in this review.

关键词： Fluorescent silica nanoparticles bioimaging surface functionalization nanoparticlecell interactions.

Species diversity,population structure and regeneration of woody species in fallows and mature stands of tropical woodlands of southeast Angola

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Journal of Forestry Research 2018年第6期29卷 1569-1579页

作者： Francisco M.p.Goncalves Rasmus Revermann Manuel J.Cachissapa Amandio L.gomes Marcos p.M.Aidar Herbarium of Lubango ISCED HuilaSarmento Rodrigues Str.230 LubangoAngola Biocentre Klein Flottbek University of HamburgOhnhorststr.1822609 HamburgGermany Department of Biology Faculty of SciencesAgostinho Neto UniversityAv.4 de Fevereiro 714th FloorLuandaAngola plant physiology and Biochemistry Institute of BotanyCP 3005Sao PauloSP CEP:01061-970Brazil

This study in the dry tropical woodlands of SE Angola in Cuando-Cubango province assessed the diversity and composition of woody species in fallows compared to those in mature woodlands. We assessed the population structure of the most harvested woody species by calculating size class distribution and evaluated their regeneration potential based on the density of saplings. The vegetation was surveyed in 20 plots of 20 × 50 m(1000 m2). In each plot, we measured the diameter at breast height(DBH) of all woody species with DBH ≥ 5 cm. The saplings were counted, identified and recorded; 718 individuals, corresponding to 34 species in 32 genera and 15 families were recorded. The size class distribution of target woody species showed three different patterns in fallows and mature woodlands. In general,most of the smaller diameter classes had more individuals than the larger ones did, showing that the regeneration may take place. However, in some diameter classes, the absence of larger stems indicated selective logging of larger trees. Few saplings were recorded in the fallows or mature woodlands; fire frequency and intensity is probably the main obstacle for seed germination and seedling survival rates in the studied area.

关键词： Baikiaea woodlands Fallows Mature woodlands Regeneration Woody species

A Cell-Based Smoothed Finite Element Method for Modal Analysis of Non-Woven Fabrics

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Computers, Materials & Continua 2021年第6期67卷 2765-2795页

作者： Nguyen T.Quyen N.Dourado A.J.p.gomes F.B.N.Ferreira C2T—Centro de Ciência e Tecnologia Têxtil Departamento de Engenharia TêxtilUniversidade do MinhoCampus de AzurémGuimarães4804-533Portugal CMEMS-UMinho Departamento de Engenharia MecânicaUniversidade do MinhoCampus de AzurémGuimarães4804-533Portugal Department of Computer Science Universidade da Beira InteriorConvento de Sto.AntónioCovilhã6201-001Portugal Instituto de Telecomunicações R.Marquês deÁvila e BolamaCovilhã6201-001Portugal

The combination of a 4-node quadrilateral mixed interpolation of tensorial components element(MITC4)and the cell-based smoothed finite element method(CSFEM)was formulated and implemented in this work for the analysis of free vibration and unidirectional buckling of shell *** formulation was applied to numerous numerical examples of non-woven *** CSFEM schemes do not require coordinate transformation,spurious modes and numerical instabilities are prevented using bilinear quadrilateral element subdivided into two,three and four smoothing *** improvement of the original CSFEM formulation was made regarding the calculation of outward unit normal vectors,which allowed to remove the integral operator in the strain smoothing *** procedure conducted both to the simplification of the developed formulation and the reduction of computational cost.A wide range of values for the thickness-to-length ratio and edge boundary conditions were *** developed numerical model proved to overcome the shear locking phenomenon with success,revealing both reduced implementation effort and computational cost in comparison to the conventional FEM *** cell-based strain smoothing technique used in this work yields accurate results and generally attains higher convergence rate in energy at low computational cost.

关键词： Mindlin-Reissner theory of plates shear-locking gradient/strain smoothing technique non-woven fabric

Integrating vegetation indices and geo-environmental factors in GIS-based landslide-susceptibility mapping:using logistic regression

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Journal of Mountain Science 2022年第2期19卷 477-492页

作者： Himasha D.ABEYSIRIWARDANA pattiyage I.A.gomes Department of Civil Engineering Faculty of EngineeringSri Lanka Institute of Information TechnologyMalabe 101115Sri Lanka

This study aimed to assess the potential of in-situ measured soil and vegetation characteristics in landslide susceptibility ***,data for eight independent variables,i.e.,soil moisture content,soil organic content,compaction of soil(soil toughness),plant root strength,crop biomass,tree diameter at knee height,Shannon Wiener Index(SWI)for trees and herbs was assembled from field tests at two historic landslide locations:Aranayaka and Kurukudegama,Sri *** economical,finer resolution database was obtained as the field tests were not *** logistic regression(LR)analysis showed that soil moisture content,compaction of soil,SWI for trees and herbs were statistically significant at piance inflation factors(VIFs)were computed to test for *** values(pendent variables in the LR *** Operating Characteristics(ROC)curve and Confusion Metrix(CM)methods were used to validate the *** ROC analysis,areas under the curve of Success Rate Curve and prediction Rate Curve were 84.5% and 96.6%,respectively,demonstrating the model’s excellent compatibility and *** to the CM,the model demonstrated a 79.6% accuracy,63.6% precision,100% recall,and a F-measure of 77.8%.The model coefficients revealed that the vegetation cover has a more significant contribution to landslide susceptibility than soil ***,the susceptibility map,which was then classified as low,medium,and highly susceptible areas based on the natural breaks(Jenks)method,was generated using geographical information systems(GIS)*** the historic landslide locations fell into the high susceptibility ***,validation of the model and inspection of the susceptibility map indicated that the in-situ soil and vegetation characteristics used in the model could be employed to demarcate historical landslide patches and identify landslide susceptibl

关键词： Landslide Susceptibility Slope stability GIS Logistic regression Area under the curve Confusion Metrix