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Open Journal of Biophysics 2023年第3期13卷 35-49页

作者： Yuri Alves de Oliveira Só Marcelo Lopes Pereira junior Wiliam Ferreira Giozza rafael timóteo de sousa junior Ricardo Gargano Luiz Antônio Ribeiro Júnior Institute of Physics University of Brasília Brasília Brazil department of Electrical Engineering University of Brasília Brasília Brazil

Virtual screening can be a helpful approach to propose treatments for COVID-19 by developing inhibitors for blocking the attachment of the virus to human cells. This study uses molecular docking, recovery time and dynamics to analyze if potential inhibitors of main protease (Mpro) of SARS-CoV-2 can interfere in the attachment of nanobodies, specifically Nb20, in the receptor binding domain (RBD) of SARS-CoV-2. The potential inhibitors are four compounds previously identified in a fluorescence resonance energy transfer (FRET)-based enzymatic assay for the SARS-CoV-2 Mpro: Boceprevir, Calpain Inhibitor II, Calpain Inhibitor XII, and GC376. The findings reveal that Boceprevir has the higher affinity with the RBD/Nb20 complex, followed by Calpain Inhibitor XII, GC376 and Calpain Inhibitor II. The recovery time indicates that the RBD/Nb20 complex needs a relatively short time to return to what it was before the presence of the ligands. For the RMSD the Boceprevir and Calpain Inhibitor II have the shortest interaction times, while Calpain Inhibitor XII shows slightly more interaction, but with significant pose fluctuations. On the other hand, GC376 remains stably bound for a longer duration compared to the other compounds, suggesting that they can potentially interfere with the neutralization process of Nb20.

关键词： SARS-CoV-2 Main protease Mpro Boceprevir Calpain Inhibitor II Calpain Inhibitor XII GC376 Nanobody Nb20 In Silico

Evaluation of Peppermint Leaf Flavonoids as SARS-CoV-2 Spike Receptor-Binding Domain Attachment Inhibitors to the Human ACE2 Receptor: A Molecular Docking Study

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Open Journal of Biophysics 2022年第2期12卷 132-152页

作者： Marcelo Lopes Pereira Júnior rafael timóteo de sousa junior Georges Daniel Amvame Nze William Ferreira Giozza Luiz Antônio Ribeiro Júnior department of Electrical Engineering University of Brasília Brasília Brazil Institute of Physics University of Brasília Brasília Brazil

Virtual screening is a computational technique widely used for identifying small molecules which are most likely to bind to a protein target. In the present work, a molecular docking study is carried out to propose potential candidates for preventing the RBD/ACE2 attachment. These candidates are sixteen different flavonoids present in the peppermint leaf. Results showed that Luteolin 7-O-neohesperidoside is the peppermint flavonoid with a higher binding affinity regarding the RBD/ACE2 complex (about -9.18 Kcal/mol). On the other hand, Sakuranetin presented the lowest affinity (about -6.38 Kcal/mol). Binding affinities of the other peppermint flavonoids ranged from -6.44 Kcal/mol up to -9.05 Kcal/mol. The binding site surface analysis showed pocket-like regions on the RBD/ACE2 complex that yield several interactions (mostly hydrogen bonds) between the flavonoid and the amino acid residues of the proteins. This study can open channels for the understanding of the roles of flavonoids against COVID-19 infection.

关键词： Coronavirus Sars-CoV-2 Peppermint Flavonoids RBD/ACE2 Inhibitors

Extrahepatic cholestasis associated with paracoccidioidomycosis:Challenges in the differential diagnosis of biliopancreatic neoplasia

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2531-2540页

作者： Jose Sebastiao dos Santos Vitor de Moura Arrais William Jose Rosseto Ferreira Ricardo Ribeiro Correa Filho Mariangela Ottoboni Brunaldi rafael Kemp Ajith Kumar Sankanrakutty Jorge Elias junior Fernando Bellissimo-Rodrigues Roberto Martinez Edson Zangiacomi Martinez Jose Celso Ardengh Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP) Departamento de Cirurgia e AnatomiaRibeirao Preto 14049-900Sao PauloBrazil Universidade de Sao Paulo Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP)Departamento de PatologiaRibeirao Preto 14048900Sao PauloBrazil Universidade de Sao Paulo Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP)Departamento de Imagens MédicasHematologia e Oncologia ClínicaRibeirao Preto 14048900Sao PauloBrazil Universidade de Sao Paulo Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP)Departamento de Medicina SocialRibeirao Preto 14015-010Sao PauloBrazil Universidade de Sao Paulo Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP)Departamento de Clínica MédicaRibeirao Preto 14015-010Sao PauloBrazil Universidade de Sao Paulo Faculdade de Medicina de Ribeirao Preto da Universidade de Sao Paulo(FMRP-USP)Departamento de Cirurgia e AnatomiaRibeirao Preto 14049-900Sao PauloBrazil and Hospital MoriahServico de Endoscopia DigestivaSao Paulo 04084-002Sao PauloBrazil

BACKGROUND Paracoccidioidomycosis(PCM)may involve the hepatic pedicle and peripan creatic lymph nodes,cause damage to the bile duct and manifest,exceptionally,in combination with extrahepatic cholestasis(EHC),making investigation and treatment *** To investigate the management of patients with visceral PCM admitted with *** All patients diagnosed with PCM treated in a public,tertiary teaching hospital between 1982 and 2020 were retrospectively *** also identified with EHC were allocated to two groups according to the treatment approach for the purpose of comparing clinical,laboratory,and imaging findings,resources used for etiological diagnosis,treatment results,and *** analyses were performed using the linear mixed-effects model(random and fixed effects),which was adjusted using the PROC MIXED procedure of the SAS®9.0 software,and Fisher’s exact *** Of 1645 patients diagnosed with PCM,40(2.4%)had *** these,20(50.0%)lived in the rural area and 29(72.5%)were men,with a mean age of 27.1 years(3-65 years).Jaundice as first symptom and weight loss of at least 10 kg were observed in 16 patients(40.0%),and a mass in the head of the pancreas was observed in 8(20.0%).The etiological diagnosis was made by tissue collection during surgery in 4 cases(10.0%)and by endoscopic methods in 3 cases(7.5%).Twenty-seven patients(67.5%)received drug treatment alone(Group 1),whereas 13(32.5%)underwent endoscopic and/or surgical procedures in combination with drug treatment(Group 2).EHC was significantly reduced in both groups(40.7% in Group 1,with a mean time of 3 months;and 38.4% in Group 2,with a mean time of 7.5 months),with no statistically significant difference between *** recurrence rates,associated mainly with treatment nonadherence,were similar in both groups:37% in Group 1 and 15.4% in Group *** mortality rate was 18.5% in Group 1 and 23% in Group 2,with survival estimates of 71.3% and 72.5%,respectively,with

关键词： Cholestasis Jaundice Obstructive Blastomycosis Paracoccidioides Diagnosis Treatment

Object-based image analysis supported by data mining to discriminate large areas of soybean

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International Journal of Digital Earth 2019年第3期12卷 270-292页

作者： Carlos Antonio da Silva junior Marcos rafael Nanni José Francisco de Oliveira-Júnior Everson Cezar Paulo Eduardo teodoro rafael Coll delgado Luciano Shozo Shiratsuchi Muhammad Shakir Marcelo Luiz Chicati Geotechnology Applied in Agriculture and Forest(GAAF) State University of Mato Grosso(UNEMAT)Alta FlorestaMato GrossoBrazil department of Agronomy(DAG/PGA) State University of Maringá(UEM)MaringáParanáBrazil Institute of Atmospheric Sciences(ICAT) Federal University of Alagoas(UFAL)MaceióAlagoasBrazil Federal University of Mato Grosso do Sul(UFMS) Chapadão do SulMato Grosso do SulBrazil department of Environmental Sciences(DCA) Forestry Institute(IF)Federal Rural University of Rio de Janeiro(UFRRJ)SeropédicaRio de JaneiroBrazil AgCenter Louisiana State University(LSU)Baton RougeLAUSA Institute of Space Technology Islamabad Pakistan IslamabadPakistan

This research aimed to analyze the possibility to estimate and automatically map large areas of soybean cultivation through the use of MODIS(Moderate-Resolution Imaging Spectroradiometer)*** major techniques were used:GEOgraphic-Object-Based Image Analysis(GEOBIA)and Data Mining(DM).In order to obtain the images,the segmentation algorithm implemented by definiens developer was used.A decision tree(DT)was created from a training set previously ***-series of images from the MODIS sensor aboard the Terra satellite were acquired in order to represent the wide variation of the vegetation pattern along the soybean crop *** time-series data were used only for the CEI ***,to compare the results obtained from GEOBIA,the slicing technique was used at the CEI *** the training,the DT was applied to the vegetation indices generating the thematic map of the spatial distribution of *** accordance with the error matrix and kappa parameter analysis,tests for statistical significance were *** indicate that the classification achieved by Kappa coefficients is *** short,the obtained results proved that combining vegetation indices and time-series data using GEOBIA return promising results for mapping soybean plantation on a regional scale.

关键词： GEOBIA time-series vegetation indices MODIS vegetation dynamics

Therapeutic and biological activities of Calotropis procera(Ait.) ***.

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Asian Pacific Journal of Tropical Medicine 2010年第4期3卷 332-336页

作者： Marcia Calheiros Chaves Silva Antonio Batista da Silva Fabiano Moura Teixeira Paulo Cesar Pereira de sousa Regina Maria Macedo Rondon Jose Eduardo Ribeiro Honorio junior Luiz rafael Leite Sampaio Samanda Lima Oliveira Angela Nadyla Martins Holonda Silvania Maria Mendes de Vasconcelos Enfermeira Mestre em Farmacologia/Universidade Federal do Ceara/UFC Farmaceutico Mestre em Patologia Tropical/Universidade Federal do Amazonas/UFAM Biologo Mestre em Bioquimica/Universidade Federal do Ceara/UFC Farmaceutico Mestre em Ciencias Farmaceutica/Universidade Federal do Ceara/UFC Biologa Mestre em Producao Animal/Universidade Estadual do Ceara/UECE Biologo Mestre em Fisiologia da Universidade Estadual do Ceara/UECE Enfermeiro Mestrando em Farmacologia da Universidade Federal do Ceara/UFC Aluna de Farmacia da Universidade Federal do Ceara/UFC Enfermeira Professora Adjunto do Depto.de Fisiologia e Farmacologia da Universidade Federal do Ceara/UFC

Medicinal plants have been used to treat various ailments of the poor population around the world;hence the interest among researchers to know the active ingredients of certain plants has being *** Calotropis procera(***) is a plant original from Africa,commonly found in northeastern *** is well known for their pharmacological properties,since it produces large amounts of *** important role that medicinal plants play in folk medicine has led us to develop this article in order to review the major pharmacological activities of C. procera.

关键词： Calotropis procera Pharmacological activity Medicinal plants

Extreme Events Assessment Methodology Coupling debris Flow,Flooding and Tidal Levels in the Coastal Floodplain of the Sao Paulo North Coast(Brazil)

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International Journal of Geosciences 2013年第5期4卷 30-38页

作者： rafael de Oliveira Sakai Diego Lourenco Cartacho Emilia Arasaki Paolo Alfredini Alessandro Pezzoli Wilson Cabral de sousa junior Maurizio Rosso Luca Magni Polytechnic School of Sao Paulo University Department of Hydraulic and Environmental EngineeringHarbour and Coastal Area of the Hydraulic LaboratoryAvenida Professor Luciano GualbertoTravessa 3n.380Cidade UniversitariaSao PauloBrazil National Institute of for Space Research Av.Dos Astronautas n.1758Sao Jose dos CamposSao PauloBrazil Polytechnic of Torino Engineering FacultyDepartment of EnvironmentLand and Infrastructure EngineeringCorso Duca degli Abruzzi n.24TorinoItaly Technological Institute of Aeronautics Infrastructure Engineering DivisionDepartment of Hydric Resources and Environmental SanitationPraca Marechal Eduardo Gomes n.50ITA-IEISao Jose dos CamposSao PauloBrazil Studio Rosso Ingegneri Associati s.r.l. Corso Principe OddoneTorinoItaly

The North Coastal Region of the State of S?o Paulo, which comprises the Municipalities of Caraguatatuba, S?o Sebasti?o, Ilhabela and Ubatuba, is one of the most prone to flooding and debris flow deposition Brazilian areas, owing to hydrological extreme rainfall events usually coupled with extreme tidal levels. This risk is also high due to human lives and material assets, with increasing population rates and the establishment of large companies such as the Oil industry, with reduced defense/prevention measures and *** catastrophic scenario of the city of Caraguatatuba, in March 1967, resulting from one of the most serious natural disasters in Brazil, fosters discussions about probabilities of heavy rainfall-caused events and rise in the sea level in coastal areas. Hence, this research is a consequence of this reality. The research is founded on an innovative methodology based on the analysis of past data of rainfall and tidal stations, complemented with debris flow registers in the region of the north coastal zone of the State of S?o Paulo (Brazil). The anaysis developed involved the meteorological, hydraulic, geotechnical and statistical knowledge *** results are intended to be used for urban planning, designs of macro-drainage, fluvial, maritime projects and debris flow retention structures. These practical applications will then associate the probability of occurrence of certain types of heavy rainfall-caused events such as flooding or debris flow coupled with a corresponding increase in tidal levels.

关键词： Meteorology Hydrology Maritime Hydraulics Rainfall Tidal Levels Extreme Events Natural Disasters Geomorphology debris-Flow Flooding

Root Growth, Nutrition and Yield of Maize with Applied Different Limestone Particle Size in the Cerrado Soil

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American Journal of Plant Sciences 2014年第4期5卷 463-472页

作者： rafael Felippe Ratke Hamilton Seron Pereira Joao de deus Gomes dos Santos junior Joaquim JoséFrazao Juliano Magalhaes Barbosa Bruno de Oliveira Dias departamento de Engenharias AgronomiaCampus Professora Cinobelina ElvasUniversidade Federal do PiauíBom JesusBrazil Instituto de Ciencias Agrárias Universidade Federal de UberlandiaUberlandiaBrazil Embrapa Centro Nacional de Pesquisa no CerradoPlanaltinaBrazil Programa de Pós-Graduacao em Agronomia Universidade Federal de GoiásGoianiaBrazil

The limestone with smaller particle size provides rapid correction of soil acidity. However, the limestone with large particles can promote bigger root growth, and may still have a residual effect on the soil. The aim of this study was to evaluate the residual effect of the application and incorporation of different limestone with a particle size bigger than 0.30 mm in root growth, nutrition and yield of maize in Cerrado soil. A randomized completed block utilized in this experiment, with five treatments and four replications. The grain sizes of dolomitic limestone incorporated into the Oxisol were: 0 (control, no-lime), 2.00-0.82 mm, 0.82-0.56 mm, 0.56-0.30 mm, 0.30-0.20 mm, in doses of 6.5 t·ha-1, 3.9 t·ha-1, 2.6 t·ha-1 and 1.3 t·ha-1 respectively. The limestone applied in introduction no-tillage. The maize were evaluated of root attributes, nutrition and grain yield in two years 2009 and 2010. The use of limestone particle size of 2.00-0.82 mm, and the quantity of 6.5 t·ha-1 applied to the soil and incorporated showed elongation and root growth of maize thin depth of 20-40 cm in the soil. In that, same proposed management of the limestone was the highest maize grain yield in the first year. The rooting characteristics evaluated correlated with leaf Ca and Cu and maizegrain yield.

关键词： Limestone No-Tillage Zea Mays

Root Growth, Nutrition and Yield of Maize with Applied Finely Limestone in Surface of Cerrado Soil

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American Journal of Plant Sciences 2014年第6期5卷 834-844页

作者： rafael Felippe Ratke Hamilton Seron Pereira Joao de deus Gomes dos Santos junior Joaquim JoséFrazao Juliano Magalhaes Barbosa Bruno de Oliveira Dias departamento de Engenharias AgronomiaCampus Professora Cinobelina ElvasUniversidade Federal do PiauíBom JesusBrazil Instituto de Ciencias Agrárias Universidade Federal de UberlandiaUberlândiaBrazil Embrapa Centro Nacional de Pesquisa no CerradoPlanaltinaBrazil Programa de Pós-graduacao em Agronomia Universidade Federal de GoiásGoianiaBrazil

The surface applies lime to correcting soil acidity in no-tillage and promotes root development and yield of maize. However, limestone with a particle size smaller than 0.30 mm cannot promote this effect. The aim of this study was to determine the root attributes, nutrition and productivity of maize with limestone ground in no-tillage. The experimental design was randomized blocks with five treatments and four replications. The treatments consisted of different particle sizes of limestone applying superficially to the soil under NT 0) control, without lime, 1) 0.30 mm to 0.20 mm 2) 0.20 mm to 0.10 mm, 3) 0, 10 mm to 0.05 mm 4) 0.05 mm to 0.01 mm. Attributes root, leaf nutrition and grain yield of maize were evaluated in two years 2009 and 2010. The elongation of roots in a 20-40 cm depth was greater when using limestone with particle size between 0.30 mm and 0.20 mm. The root length of maize plants correlated with the levels of Mn in maize leaves. The root development promoted by liming effect was not reflected in the productivity of maize.

关键词： Particle Size No-Tillage Limestone

Application of NURBS for Obtaining Free Form Curves and Surfaces in Spur and Helical Gears by Using CMM （Coordinate Measurement Machine）

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Journal of Mechanics Engineering and Automation 2014年第5期4卷 432-440页

作者： Luiz Henrique Melo Silva Nobrega Verilton Nunes da Silva Jose Carlos de Lima junior Joao Bosco de Aquino Silva Igor Lucena Peixoto Andrezza rafael Franklin Alves Silva department of Mechanical Engineering Federal University of Paraiba Jo6o Pessoa 58051-900 Brazil department of Mechanical Engineering Federal Institute of Bahia SimOes Filho 43700-000 Brazil Informatics Center Federal University of Paraiba Jo6o Pessoa 58051-900 Brazil department of Mechanical Engineering Federal Institute of Paraiba Jo6o Pessoa 58900-000 Brazil

Currently, engineering processes require reduced manufacturing time and low cost, in addition to the growing demand for workpieces with high accuracy. Workpieces with complex geometries and free forms has been a common practice in industries from different sectors such as： automotive, aeronautics, bioengineering among others. One way to satisfy the market requirements satisfactorily is making measurements more efficient to make the production process faster, in other words, it is necessary to make the inspection system more accurate and flexible. The coordinate measuring evolved over the past three decades and today it is the technology that best meets the requirements of modem manufacturing through CMMs （coordinate measurement machines）. The CMMs are important tool for design, fabrication and inspection of manufactured products, also used in the application of reverse engineering. These machines are also used by engineers in order to produce an accurate digital model in a virtual space for later use in CAD （computer-aided design）/CAM （computer-aided manufacturing）. It is worth mentioning that the accuracy of the modeling process of given piece depends on the number of control points that are captured on the workpiece surface. Consequently, the laser inspection systems are the best tools for use in reverse engineering, but more expensive when compared to contact measurement systems that use the TTP （touch trigger probe）, also used by CMMs. In this case, this paper aims to present an approach based on NURBS （non-uniform rational B-splines） to obtain free form curves and surfaces from a group of points obtained by using a contact sensor, the touch trigger probe. NURBS is an important mathematical tool and consists of generalizations of Bezier curves and surfaces and B-splines. The approach proposed in this paper can be applied for obtaining free form curves and surfaces in spur and helical gears. Experimental results obtained by measuring spur gears showed that the NU

关键词： Coordinate measurement machine touch trigger probe NURBS reverse engineering.

Visible Losses to the Mechanical Harvesting of Ratoon Sugarcane Using the Harvester John deere 3520

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American Journal of Analytical Chemistry 2018年第11期9卷 580-590页

作者： Carmen Maria Coimbra Manhaes Francisco Mauricio Alves Francelino rafael Alves de Araujo Danilo Gomes de Oliveira Helenilson de Oliveira Francelino Mirian Peixoto Soares da Silva Aline da Silva Santos Mauricio Donato de Moura junior Federal Institute of Education Science and Technology of Tocantins—FTOPalmasBrazil State University of North Fluminense Rio de JaneiroBrazil

The aim of this study was to evaluate the visible loss of sugar cane and the damage to the knuckles, using the John deere 3520 harvester on three different travel speeds (3.0;4.0 and 5.0 km·h-1), in DIC with five repetitions in Campos dos Goytacazes, Rio de Janeiro/Brazil. Each treatment was composed by six lines of harvested cane stumps, with a length of 290 m each. In these six lines, the remains of sugar cane left in the field were collected by placing the sampling frame in two central lines every 50 m, and separating 40 m of edge. The sampling area was surrounded by 2 m wide and 10 m long, totaling 20 m2. To calculate the damage to stumps, a visual methodology by [1], was used, which classifies the damage grade, ranging from 1 to 4. Fifty stumps were assessed randomly for each speed, in a sampling area of 1800 m2. The data were submitted to ANOVA and Tukey test at 5%, in order to compare the effect of different speeds on the losses and damages. There was no significant difference regarding the loss or damage by comparing the different speeds. Therefore, it is more advantageous to use the speed of 5.0 km·h-1, harvesting more in less time and causing the same level of damage.

关键词： Damages Saccharum spp. Travel Speed John deere 3520 Harvester