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Data Analysis of Multiplex Sequencing at SOLiD Platform:A Probabilistic Approach to Characterization and Reliability Increase

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American Journal of Molecular Biology 2018年第1期8卷 26-38页

作者： fábio manoel franca Lobato Carlos Diego Damasceno Daniela Soares Leite Andrea Kelly Ribeiro-dos-Santos Sylvain Darnet Carlos Renato francês Nandamudi Lankalapalli Vijaykumar Adamo Lima de Santana Engineering and Geoscience Institute Federal University of Western Pará (UFOPa) Santarém Brazil Technological Institute Federal University of Pará (UFPa) Belém Brazil Institute of Mathematical and Computer Sciences University of Sao Paulo (USP) Sao Carlos Brazil Department of Morphology and Physiological Sciences State University of Pará Marabá Brazil Biological Science Institute Federal University of Pará (UFPa) Belém Brazil Laboratory of Computing and Applied Mathematics National Institute for Space Research (INPE) Sao José Dos Campos Brazil

New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.

关键词： Probabilistic Modeling Health Informatics SOLiD Barcoding System Statistical Analysis Multiplex Sequencing

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Enterobacteria and Vibrio from Macrobrachium amazonicum prawn farming in fortaleza,Ceará,Brazil

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Asian Pacific Journal of Tropical Medicine 2016年第1期9卷 24-28页

作者： Débora de Souza Collares Maia Castelo-Branco Jamille Alencar Sales Raimunda Samia Nogueira Brilhante Glaucia Morgana de Melo Guedes Yago Brito de Ponte Celia Maria de Souza Sampaio Tereza de Jesus Pinheiro Gomes Bandeira José Luciano Bezerra Moreira Lucas Pereira de Alencar manoel de Araújo Neto Paiva Rossana de Aguiar Cordeiro André Jalles Monteiro Waldemiro de Aquino Pereira-Neto José Júlio Costa Sidrim Marcos fábio Gadelha Rocha Department of Pathology and Legal Medicine Postgraduate Program in Medical MicrobiologySpecialized Medical Mycology CenterFederal University of Ceará School of Veterinary Medicine Postgraduate Program in Veterinary SciencesState University of Ceará Department of Statistics and Applied Mathematics Federal University of Ceará

Objective:To investigate the isolation of enterobacteria associated with Macrobrachium amazonicum(***) farming and evaluate the in vitro antimicrobial susceptibility of Vibrio ***:Strains were isolated from female *** prawns and environmental and hatchery *** assays were used to identify bacterial genera and those belonging to the genus Vibrio were submitted to further analyses for species identification,through Vitek 2 automated system and *** test was performed according to Clinical Laboratory Standards ***:The following genera of enlerobacteria were recovered:Enterobacter(n=11),Citrobacter(n=10),Proteus(n=2),Serratia(n=2),Kluyvera(n=2),Providencia(n=2),Cedecea(n=1),Escherichia(n=1).Edwardsiella(n=1) and BulliauxeUa(n=1).As for Vibrio,three species were identified:Vibrio cholerae non-O1/non-O139(n=4).Vibrio vulnificus(***)(n=1) and Vibrio mimicus(n=1).Vibrio *** minimum inhibitory concentrations values within the susceptibility range established by Clinical Laboratory Standards Institute for almost all antibiotics,except for ***,which presented intermediate profile to ***:Enterobacteria do not seem to be the most important pathogens associated with *** farming,whereas the recovery of Vibrio *** larviculture,with emphasis on Vibrio cholerae and ***,deserves special attention due to their role as potentially zoonotic aquaculture-associated ***,the intermediate susceptibility of *** to ampicillin reflects the importance of monitoring drug use in prawn farming.

关键词： Prawn Water Enterobacteria Vibrio Antibiotics

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Inheritance of AfLP markers and genetic linkage analysis in two full-sib families of the marine shrimp Litopenaeus vannamei(Crustacea,Decapoda)

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Advances in Bioscience and Biotechnology 2014年第3期5卷 273-281页

作者： Michele Mantovani Goncalves Luciana Correia de Almeida Regitano Cosme Damiao Cruz Caio Cesio Salgado Patricia Domingues de freitas Joao Luis Rocha Ana Karina Guerrelhas Teixeira Pedro manoel Galetti-Junior Departamento de Genetica e Evolucao Universidade Federal de Sao CarlosSao CarlosBrasil Embrapa Pecuaria Sudeste Sao CarlosSPBrasil Departamento de Biologia Geral Universidade Federal de VicosaVicosaBrasil Genearch Aquacultura Ltda Rua Pedro Zuca s/nPraia de PititingaRio do FogoRNBrasil

The cultivation of the marine species of shrimp Litopenaeus vannamei has emerged as one of the segments that best develop in the Brazilian aquaculture, representing the agribusiness that grew the most in recent years. Regarding the economic importance of the farming of this species in Brazil, further studies on genetic improvement were conducted. A f2 segregating population consisting of 192 samples for each G1 and G2 families, from crossing inbred lines was used for the studies performed in the present work. The genetic linkage analysis was based on polymorphic markers derived from nine AfLP (Amplified fragment Length Polymorphism) primers. fourteen genetic linkage groups including 103 segregating polymorphic markers were constructed covering350 cMfor G1 and four genetic linkage groups including 59 markers were constructed covering300 cMfor G2. Simple marker analyses were performed among individuals evaluated phenotypically, finding markers linked to genes that may be potentially important and useful to assess characteristics of economic importance for traits related to weight and the disease IMN (idiopathic muscle necrosis). The statistical model including markers explained major proportion of phenotypic characteristic weight in relation to disease incidence IMN.

关键词： Shrimp Litopenaeus vannamei AfLP Genetic Linkage Groups

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Oxidation of Amino Acids by Chlorpromazine Cation Radical and Co-Catalysis by Chlorpromazine

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Pharmacology & Pharmacy（药理与制药） 2012年第1期

作者： Valdecir f. Ximenes Giovana B. Quaggio fernanda S. Graciani manoel L. de Menezes

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Biotechnological Potential of Endophytic Bacteria to Improve the Micropropagated Seedling of Variety RB92579 Sugarcane(Saccharum officinarum L.)

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Advances in Microbiology 2018年第11期8卷 859-873页

作者： Maria do Carmo Silva Barreto Márcia do Vale Barreto figueiredo Márcia Vanusa da Silva Arnóbio Gon?alves de Andrade José de Paula de Oliveira Clébia Maria Alves Almeida Livia Caroline Alexandre de Araújo Odemar Vicente dos Reis Junior manoel Urbano ferreira Junior Antonio félix da Costa Vera Lucia de Menezes Lima Departamento de Bioquímica Centro de Biociências Universidade Federal de Pernambuco Recife Brazil Laboratório de Biologia do Solo Instituto Agron&#244 mico de Pernambuco Recife Brazil Departamento de Química Universidade Federal Rural de Pernambuco Recife Brazil Centro de Tecnologias Estratégicas do Nordeste Recife Brazil

Endophytic bacteria may influence agricultural production in several ways, including promoting plant growth. Two experiments were conducted in order to evaluate the combination of endophytic bacteria from the Brazilian Northeast region aims at the commercial introduction of the inoculation of these bacteria in micropropagated sugarcane plants using a temporary immersion bioreactor. One experiment was done in tubes with sterile commercial substrate, and the other was done in pots with soil;both were installed in a greenhouse. A mixed inoculation was performed in six inoculated endophytic diazotrophic bacteria in micropropagated sugarcane plants, variety RB92579. In the experiment with soil, the mixed inoculation significantly increased the shoot dry matter of plants without the addition of nitrogen fertilizer. However, the accumulation of total-N in the tissues showed no significant differences between treatments with and without nitrogen fertilization. The evaluation of micropropagated seedlings showed no increases in the parameters tested. The results showed that the response of inoculation in temporary immersion bioreactor micropropagation is possible, and that the application of homologous strains may have contributed to a better response by the interaction of endophytic bacteria with sugarcane RB92579. further studies should be conducted to improve the methodology, which indicates a great potential to optimize this process on a commercial scale.

关键词： Biological Nitrogen fixation Meristem Culture Diazotrophic Bacteria Endophytes Micropropagation

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Carbon Burial in Young Tropical Reservoirs Is Higher at Lower Latitudes*

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Journal of Geoscience and Environment Protection 2021年第12期9卷 84-99页

作者： Elizabeth Sikar Marco Aurelio dos Santos Ana Carolina Moterani Isabella Matvienko Ana Carla Martins Veras Juliana Pinto Pereira Dias Orleno Marques da Silva Junior Claudio Pavani Marcelo Amorim Teodosio das Neves Milisse Nzualo Ayr manoel Portilho Bentes Junior Rogerio Duarte Construmaq Sã o Carlos S&#227 o Carlos SP Brazil Programa de Planejamento Energético da Universidade federal do Rio de Janeiro Brazil Laboratório de Energias Renováveis e Estudos Ambientais da Universidade federal do Rio de Janeiro Brazil Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá Brazil Programa de Pós-Graduaç ã o em Geografia da Universidade federal do Amapá Brazil

Man-made environments such as tropical hydroelectric reservoirs alter the preexisting carbon (C) cycle and remove C from circulation through burial in sediments. Carbon burial (CB) was measured using the silica-tracer method during four field surveys in the less than six-year-old Belo Monte tropical reservoir. fresh C sedimentation was also measured. Belo Monte’s CB median rate 276 (n = 84;min 0;max 352,625 mg C·m-2·d-1) is within the range (230 to 436 mg C·m-2·d-1) of CB rates measured further downstream at the Xingu Ria and higher than the averaged over 50 years oceanic rate 244 mg C·m-2·df4f4f;font-family:-apple-system, "font-si

关键词： Carbon Burial Sediments Hydroelectric Reservoirs

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Physicians and Conflicts of Interest

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International Journal of Clinical Medicine（临床医学国际期刊） 2014年第16期

作者： Deborah Pimentel Maria-Jésia Vieira Jo？o Pedro Declerc f. S. Neves manoel Juvenal da Costa-Neto Laís Costa Souza Oliveira

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Qualitative evaluation and character heritability of leaf blade and stem from Pennisetum ***

Qualitative evaluation and character heritability of leaf bl...

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ⅩⅪ International Grassland Congress and the Ⅷ International Rangeland Congress

作者： M.V.f.dos Santos M.A.da Silva M.de A.Lira J.C.B Dubeux,Jr. G.G.L.de Araujo E.V.de freitas UfRPE Depto.de ZootecniaRua Dom Manoel de MedeirosS/NDois Irmaos52171-900 IPA-Av.Gal.San Martin BongiRecifePEBrazil EMBRAPA SEMI-aRIDO PetrolinaPEBrazil

＜正＞Introduction Pennisetum purpureum *** a tropical grass known by its adaptability to a wide range of environments and its productivity potential and forage *** nutritive value has a direct influence on animal *** is a very important parameter to predict characters that may influence genetically forage chemical *** objective of this *** was to determine the nutritive value and heritability on five Pennisetum clones under cut in the dry forest zone of Pernambuco State,Brazil.

关键词： chemical composition genetic parameter Pennisetum purpureum

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