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Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane

The Crop Journal 2023年第6期11卷 1805-1815页

作者： Ricardo JoséGonzaga Pimenta Alexandre Hild Aono Roberto Carlos Villavicencio Burbano marcel Fernando da silva Ivan Antônio dos Anjos marcos Guimarães de Andrade Landell marcos Cesar Gonçalves Luciana Rossini Pinto Anete pereira de Souza Centre for Molecular Biology and Genetic Engineering University of CampinasCampinasBrazil Gustavo Galindo Velasco Campus Littoral Polytechnic Superior SchoolGuayaquilEcuador Advanced Centre for Technological Research in Sugarcane Agribusiness Agronomic Institute of CampinasRibeirão PretoBrazil Plant Protection Research Centre Biological InstituteSão PauloBrazil Department of Plant Biology Institute of BiologyUniversity of CampinasCampinasBrazil

Sugarcane mosaic virus(SCMV)is the main etiological agent of sugarcane mosaic disease,which affects sugarcane and other grass *** the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize,the genetic basis of this trait in sugarcane is largely ***,a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane *** single-nucleotide polymorphisms(SNPs)explained up to 29.9%of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy,precision,recall,and F1 scores(the harmonic mean of precision and recall).Both marker sets were validated in additional sugarcane genotypes,in which the SNPs explained up to 23.6%of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%.Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane,explaining why this major resistance source has not been identified in this ***,using sugarcane RNA-Seq data,markers associated with resistance to SCMV were annotated,and a gene coexpression network was constructed to identify the predicted biological processes involved in *** network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses,photosynthesis,and the regulation of transcription and translation in resistance to *** results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance.

关键词： Saccharum SCMV GWAS machine learning RNA-Seq

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Tandem running by foraging Pachycondyla striata workers in field conditions vary in response to food type,food distance,and environmental conditions

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Current Zoology 2021年第5期67卷 541-549页

作者： Janiele pereira silva Lohan VALADARES maria Eduarda Lima VIEIRA Serafino TESEO Nicolas CHALINE LEEEIS Departamento de Psicologia ExperimentalInstituto de Psicologia ExperimentalUniversidade de Sao PauloSao PauloSPCEP 05508-030Brazil Programa de pos-graduacao em Psicologia Experimental USPSao PauloSPCEP 05508-030Brazil Evolution GenomesBehavior and EcologyCNRS1 Avenue de la TerrasseGifsur-Yvette 91987France LBC Departamento de Fisiologia e ComportamentoCentro de BiocienciasUniversidade Federal do Rio Grande do NorteNatalRNCEP 59078-970Brazil School of Biological Sciences Nanyang Technological University60 Nanyang DriveSingapore 637551Singapore

Ants show collective and individual behavioral flexibility in their response to immediate context,choosing for example between different foraging *** Pachycondyla striata,workers can forage solitarily or recruit and guide nestmates to larger food sources through tandem *** considered more ancestral and less efficient than pheromone trail-laying,this strategy is common especially in species with small colony *** is not known is how the decision to recruit or follow varies according to the immediate *** is,how fine adjustments in information transfer affect immediate foraging decisions at the colony ***,we studied individually marked workers and evaluated their foraging decisions when food items varied in nature(protein versus carbohydrate),size,and distance from the nest at different temperatures and humidity *** results show that tandem run leaders and potential followers adjust their behavior according to a combination of external *** 84.2%of trips were solitary,most ants(81%)performed at least 1 tandem ***,tandem runs were more frequent for nearby resources and at higher relative ***,when food items were located far away,tandem runs were more successful when heading to protein sources(75%)compared with carbohydrate sources(42%).Our results suggest that the social information transfer between leaders and followers conveys more information than previously thought,and also relies on their experience and motivation.

关键词： collective behavior decision-making emotional states flexibility Ponerinae social learning

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Appropriateness of the study of iron deficiency anemia prior to referral for small bowel evaluation at a tertiary center

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World Journal of Gastroenterology 2017年第24期23卷 4444-4453页

作者： Jaime pereira Rodrigues Rolando Pinho Joana silva Ana Ponte mafalda Sousa Joao Carlos silva Joao Carvalho Department of Gastroenterology Centro Hospitalar Vila Nova de Gaia/EspinhoRua Conceicao FernandesVila Nova de Gaia

AIM To evaluate the adequacy of the study of iron deficiency anemia(IDA)in real life practice prior to referral to a gastroenterology department for small bowel *** All consecutive patients referred to a gastroenterology department for small bowel investigation due to iron deficiency anemia,between January 2013 and December2015 were *** patients referred from general practitioners or directly from different hospital departments were *** clinical information regarding prior anemia workup was retrospectively collected from medical *** appropriate pre-referral study was considered the execution of esophagogastroduodenoscopy(EGD)with Helicobacter pylori(***)investigation,colonoscopy with quality standards(recent,total and with adequate preparation)and celiac disease(CD)screening(through serologic testing and/or histopathological investigation).RESULTS A total of 77 patients(58.4% female,mean age 67.1±16.7 years)were ***(53.2%)patients were referred from general practitioners,41.6% from other hospital specialties and 5.2% directly from the emergency *** mean pre-referral hemoglobin concentration was 8.8±2.0 g/d L and the majority of anemias had microcytic(71.4%)and hypochromic(72.7%)characteristics.77.9%of patients presented with an incomplete pre-referral study:EGD in 97.4%,with *** investigation in 58.3%,colonoscopy with quality criteria in 63.6%,and CD screening in 24.7%.Patients with an appropriate study at the time of referral were younger(48.7±17.7 vs 72.3±12.3 years,Pmall bowel evaluation was ultimately undertaken in 72.7%of patients,with a more frequent evaluation in patients with a quality colonoscopy at referral(78.6%vs 23.8%);Pmall bowel angioectasia(18.2%)but additional causes were also found in the upper and lower gastrointestinal tracts of near 20% of *** bowel stud

关键词： Iron deficiency anemia Colonoscopy Celiac disease Esophagogastroduodenoscopy Helicobacter pylori Small bowel

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Respiratory muscle training with electronic devices in the postoperative period of hepatectomy:A randomized study

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World Journal of Hepatology 2023年第5期15卷 688-698页

作者： marcelo Gustavo pereira Aurea maria Oliveira silva Fernanda Diório masi Galhardo Beatriz Dellamutta Miranda Almeida Railaine Lais Lopes Ilka de Fatima Santana Ferreira Boin Hospital de Clínicas Universidade Estadual de CampinasCampinas 13076-4151São PauloBrazil Faculdade de Ciências Médicas Universidade Estadual de CampinasCampinas 13083-887São PauloBrazil Hospital de Clínicas da Unicamp Universidade Estadual de CampinasCampinas 13083-888São PauloBrazil

BACKGROUND many studies have been developed with a focus on surgical techniques and drugs,but few that address the importance of rehabilitation in the pre and postoperative period,and the specific benefits for each surgical procedure or type of neoplasm,aiming to minimize respiratory complications in the postoperative *** To compare the strength of the respiratory muscles in the pre and postoperative periods of hepatectomy by laparotomy and to verify the incidence of postoperative pulmonary complications among the groups *** Prospective,randomized,clinical trial study that compared the inspiratory muscle training group(GTMI)with the control group(CG).After the collection of sociodemographic and clinical data,in both groups,preoperatively,on the first and fifth postoperative days,vital signs and pulmonary mechanics were evaluated and *** and bilirubin values were recorded for the albumin-bilirubin(ALBI)*** randomization and allocation of participants,those in the CG underwent conventional physical therapy and those in the GTMI underwent conventional physical therapy plus inspiratory muscle,in both groups for five postoperative *** Of 76 subjects met eligibility *** collection of 41 participants was completed:20 in the CG and 21 in the *** most frequent diagnosis was 41.5%with liver metastasis,followed by 26.8%with hepatocellular *** for respiratory complications in the GTMI,there was no *** the CG,there were three respiratory *** in the CG classified as ALBI score 3 presented,statistically,a higher energy value compared to patients classified as ALBI score 1 and 2(P=0.0187).Respiratory variables,measured preoperatively and on the first postoperative day,had a significant drop in both groups from the preoperative to the first postoperative day(P≤0.0001).When comparing the preoperative period and the fifth postoperative day between the GTMI and the CG,the maximal inspira

关键词： postoperative shorter fifth

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Case report of a criminal dismemberment in Northeast Brazil

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Forensic Sciences Research 2022年第4期7卷 637-642页

作者： Evelyne Pessoa Soriano maria do Socorro Dantas de Araújo Francisca de Assis Nascimento pereira Francisca Divina Silveira de Melo Cristiane Helena da silva Barbosa Freire marcus Vitor Diniz de Carvalho Medico-legal Institute of João Pessoa ParaíbaBrazil Faculty of Dentistry(FOP) Center for Studies in Forensic Anthropology(CEAF)University of Pernambuco(UPE)RecifeBrazil

Several decomposed body parts were received for examination by the Forensic Anthropology section of the Medico-legal Institute of João Pessoa,Paraíba,*** portions of the lower and upper limbs,ribs,vertebrae,and a skull were thoroughly *** biological profile indicated a male individual with an estimated age range between 23 and 57 years and a mean age of 35.2 years(SD=9.4;phase IV,Suchey-Brooks).The skeleton showed injuries caused by sharp force and sharp-blunt force trauma that affected all body ***,the lesions are mainly in the diaphyseal segments of the long bones,sacrum,pelvis,mandible,maxilla,scapulae,sternum,vertebrae,the distal epiphysis of the left fibula,and the distal epiphysis of the left tibia displayed characteristics compatible with injuries produced *** was not possible to determine the cause of *** resulted in a positive *** of common difficulties faced in forensic practice,it is often not possible for forensic anthropologists to go to the crime scene,X-ray or body scanners are frequently unavailable,and the victim’s medical and/or dental records are sometimes *** difficulties make identification ultimately depend on genetic analysis,which is more time-consuming than other identification *** this,bone fragment examination in dismemberment cases is a complex *** Anthropology can shed light on cases involving the identification of dismembered remains,which are challenging because of the number of traumatic injuries,as well as different injury patterns,on bones.

关键词： Forensic sciences forensic anthropology dismemberment human identification

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Perspective on the use of synthetic biology in rudimentary food fermentations

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Systems Microbiology and Biomanufacturing 2023年第1期3卷 150-165页

作者： Alexander da silva Vale Gilberto Vinícius de Melo pereira Leonardo martins Santana Dão Pedro de Carvalho Neto Brigitte Sthepani Orozco Colonia Vanete Thomaz Soccol Bruna Leal maske Carlos Ricardo Soccol Department of Bioprocess Engineering and Biotechnology Federal University of Paraná(UFPR)CuritibaPRBrazil Department of Genetics University of São Paulo(USP)Ribeirão PretoSPBrazil Federal Institute of Education Science and Technology of Paraná(IFPR)LondrinaPRBrazil

Rudimentary food fermentation can be defined as a spontaneous process of conversion of food components through enzy-matic action.A great variety of fermented foods are produced using spontaneous approaches;however,cocoa and coffee represent the most important agricultural commodities on international *** a manner to increase the efficiency of these processes,starter cultures have been developed and applied under field *** selection process begins with the recovery of microbial strains from spontaneous fermentation through phenotypic and metabolic ***,mutation-based breeding is used to develop and improve well-adapted starter *** advances in synthetic biology,especially in the last decade,the development of robust cellular fabrications with high fermentative capacity has become easier-largely due to the development of genomic approaches,such as next-generation sequencing techniques,CRISPR-Cas system and bioinformatics *** review brings prospects on the use of synthetic biology to design new robust strains for use in cocoa and coffee fermentations,but which can be extended to other rudimentary *** addition,metabolic traits and target genes(e.g.,UvrA,RecA,GPD1,and GPP2)are proposed as a starting point for the improvement of cocoa and coffee ***,the regulatory and safety requirements for these food crops are *** review aims to stimulate research on the process of fermentation and the associated synthetic biology tools to produce fermented food efficiently and sustainably.

关键词： Coffee fermentation Cocoa fermentation Starter cultures CRISPR-Cas Synthetic promoters

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Pulp and Paper from Sugarcane:Properties of Rind and Core Fractions

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Journal of Renewable materials 2018年第2期6卷 160-168页

作者： Lísias pereira Novo Julien Bras Mohamed Naceur Belgacem Antonio Aprigio da silva Curvelo Department of materials Engineering Sao Carlos School of EngineeringUniversity of Sao PauloAv.Joao Dagnone 110013563-120Sao CarlosSao PauloBrazil Department of Physical Chemistry Sao Carlos Institute of ChemistryUniversity of Sao PauloAv.Trabalhador Sao Carlense 40013560-970Sao CarlosSao PauloBrazil Grenoble Alpes University LGP2F-38000 GrenobleFrance CNRS LGP2F-38000 GrenobleFrance

Two distinct lignocellulosic fractions(rind and core)can be obtained through a physical separation of sugarcane *** presenting differences in morphology,both fractions can be employed to produce pulps and *** pulps and paper sheets produced from the core and rind fractions were characterized by their chemical composition,physical properties and mechanical *** pulps obtained from the core presented a higher amount of fines,lower drainage ability and rendered denser and stiffer *** pulps from the rind,which have a higher content of fibers and higher degree of polymerization,produced sheets with higher air permeability and water *** paper sheets presented mechanical and physical properties comparable to commercial papers and papers from different cellulosic *** different properties exhibited by the papers produced from each fraction allow their use for distinct purposes,and expands the opportunities in the context of sugarcane biorefinery.

关键词： Sugarcane core and rind fractions papermaking pulp and paper

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In vitro antileishmanial effects of Physalis angulata root extract on Leishmania infantum

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Journal of Integrative Medicine 2018年第6期16卷 404-410页

作者： Bruno Jose martins Da silva Sandro Wilson Gomes pereira Ana Paula Drummond Rodrigues Jose Luiz martins Do Nascimento Edilene Oliveira silva Laboratory of Structural Biology Institute of Biological SciencesFederal University of PardBelemPard 66075-110Brazil National Institute of Science and Technology in Structural Biology and Bioimaging(INCT-INBEB) Rio de Janeiro 21941-901Brazil Laboratory of Electron Microscopy Department of Health SurveillanceMinistry of HealthEvandro Chagas InstituteBelemPard 66087-082Brazil Laboratory of Molecular and Cellular Neurochemistry Institute of Biological SciencesFederal University of PardBelemPard 66075-110Brazil National Institute of Science and Technology in Neuroimmunomodulation(INCT-NIM) Rio de Janeiro 21040-360Brazil

Objective： In the present study, we evaluated the effects of the aqueous extract of Physalis angulata root （AEPa） on Leishmania infanturn proliferation, morphology, and the driving mechanism in leishmanicidal activity and modulatory action on macrophages. Methods： I., infantum promastigotes were treated with 50 and 100 μg/mL AEPa for 72 h and then antipro- mastigote assay was performed by counts in a Newbauer chamber, morphological changes were analyzed by transmission electron microscopy and the mechanism of the leishmanicidal activity was detected. In addition, macrophages were infected with L. infantum and were used to evaluate anti-amastigote activity of AEPa and effects of AEPa on cytokine secretion after 72-hour treatment. Results： Treatment with AEPa reduced the numbers ofL infantum promastigotes （50% inhibitory concen- tration （ICso） = 65.9μg/mL; selectivity index （SI）= 22.1） and amastigotes （ICso = 37.9 μg/mL; SI = 38.5） compared with the untreated control. Amphotericin B reduced 100% of the promastigote numbers after 72 h of treatment （IC50 = 0.2μg/mL）. AEPa induced several morphological changes and increased the production of reactive oxygen species and apoptotic death in promastigotes after treating for 72 h. AEPa （100 μg/mL） promoted tumor necrosis factor-α secretion in macrophages infected with L. infantum after 72 h of treatment, but did not induce an increase in this cytokine in noninfected macrophages. In addition, AEPa showed no cytotoxic effect on J774-A1 cells （50% cytotoxic concentration 〉1000μg/mL）. Conclusion： AEPa presented antileishmanial activity against the promastigotes and amastigotes of I.. infantum without macrophage cytotoxicity; these results show that natural products such as P. angulata have leishmanicidal potential and in the future may be an alternative treatment for leishmaniasis.

关键词： Leishmanicidal activity Leishmania infantum Reactive oxygen species Apoptosis Physalis angulata

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High Order of Accuracy for Poisson Equation Obtained by Grouping of Repeated Richardson Extrapolation with Fourth Order Schemes

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Computer Modeling in Engineering & Sciences 2021年第8期128卷 699-715页

作者： Luciano pereira da silva Bruno Benato Rutyna Aline Roberta Santos Righi marcio Augusto Villela Pinto Graduate Program in Numerical Methods in Engineering Federal University of ParanaCuritiba81531-980Brazil Graduate Program in Space Sciences and Technologies Aeronautics Institute of TechnologySao Jose dos Campos12228-900Brazil Department of Mechanical Engineering Federal University of ParanaCuritiba81531-980Brazil

In this article,we improve the order of precision of the two-dimensional Poisson equation by combining extrapolation techniques with high order *** high order solutions obtained traditionally generate non-sparse matrices and the calculation time is very *** can obtain sparse matrices by applying compact *** this article,we compare compact and exponential finite difference schemes of fourth *** numerical solutions are calculated in quadruple precision(Real*16 or extended precision)in FORTRAN language,and iteratively obtained until reaching the round-off error magnitude around 1.0E−*** procedure is performed to ensure that there is no iteration *** Repeated Richardson Extrapolation(RRE)method combines numerical solutions in different grids,determining higher orders of *** main contribution of this work is based on a process that initializes with fourth order solutions combining with RRE in order to find solutions of sixth,eighth,and tenth order of *** multigrid Full Approximation Scheme(FAS)is also applied to accelerate the convergence and obtain the numerical solutions on the fine grids.

关键词： Tenth order accuracy RRE compact scheme exponential scheme multigrid finite difference

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Indirect printing of hierarchical patient-specific scaffolds for meniscus tissue engineering

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Bio-Design and manufacturing 2019年第4期2卷 225-241页

作者： Joao BCosta Joana silva-Correia Sandra Pina Alain da silva Morais Sílvia Vieira Hélder pereira Joao Espregueira-Mendes Rui LReis Joaquim M.Oliveira B′s Research Group I3Bs-Research Institute on BiomaterialsBiodegradables and BiomimeticsUniversity of MinhoHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineAveParkZona Industrial da Gandra4805-017 Barco GmrPortugal ICVS/3B’s-PT Government Associate Laboratory Braga/GuimaraesPortugal The Discoveries Centre for Regenerative and Precision Medicine Headquarters at University of MinhoAvepark4805-017 BarcoGuimar'sPortugal Ripoll y De Prado Sports Clinic:Murcia-madrid FIFA Medical Centre of Excellence MurciaSpain Orthopedic Department Centro Hospitalar Póvoa de Varzim Vila do CondePortugal Clínica do Dragao Espregueira-Mendes Sports CentreFIFA Medical Centre of ExcellencePortoPortugal Dom Henrique Research Centre PortoPortugal Orthopedic Department University of MinhoBragaPortugal

The complex meniscus tissue plays a critical role in the knee. The high susceptibility to injury has led to an intense pursuit for better tissue engineering regenerative strategies, where scaffolds play a major role. In this study, indirect printed hierarchical multilayered sca ffolds composed by a silk fibroin (SF) upper layer and an 80/20 (w/w) ratio of SF/ionic-doped β-tricalcium phosphate (TCP) bottom layer were developed. Furthermore, a comparative analysis between two types of sca ffolds pro- duced using di fferent SF concentrations, i.e., 8% (w/v) (Hi8) and 16% (w/v) (Hi16) was performed. In terms of architecture and morphology, the produced sca ffolds presented homogeneous porosity in both layers and no di fferences were observed when comparing both sca ffolds. A decrease in terms of mechanical performance of the sca ffolds was observed when SF concentration decreased from 16 to 8% (w/v). Hi16 revealed a static compressive modulus of 0.66 ± 0.05 MPa and dynamical mechanical properties ranging from 2.17 ± 0.25 to 3.19 ± 0.38 MPa. By its turn, Hi8 presented a compressive modulus of 0.27 ± 0.08 MPa and dynamical mechanical properties ranging from 1.03 ± 0.08 MPa to 1.56 ± 0.13 MPa. In vitro bioactivity studies showed formation of apatite crystals onto the surface of Hi8 and Hi16 bottom layers. Human meniscus cells (hMCs) and human primary osteoblasts were cultured separately onto the top layer (SF8 and SF16) and bottom layer (SF8/TCP and SF16/TCP) of the hierarchical sca ffolds Hi8 and Hi16, respectively. Both cell types showed good adhesion and proliferation as denoted by the live/dead staining, Alamar Blue assay and DNA quanti fication analysis. Subcutaneous implantation in mice revealed weak in flammation and sca ffold’s integrity. The hierarchical indirect printed SF sca ffolds can be promising candidate for meniscus TE sca ffolding applications due their suitable mechanical properties, good biological performance and possibility of being applied in a patie

关键词： Patient-specific Indirect printing Hierarchical Silk fibroin Enzymatic-cross-linking Meniscus

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