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Identifying differentially expressed genes using the Polya urn scheme
Saraiva, Erlandson Ferreira,Suzuki, Adriano Kamimura,Milan, Luis Aparecido The Korean Statistical Society 2017 Communications for statistical applications and me Vol.24 No.6
A common interest in gene expression data analysis is to identify genes that present significant changes in expression levels among biological experimental conditions. In this paper, we develop a Bayesian approach to make a gene-by-gene comparison in the case with a control and more than one treatment experimental condition. The proposed approach is within a Bayesian framework with a Dirichlet process prior. The comparison procedure is based on a model selection procedure developed using the discreteness of the Dirichlet process and its representation via Polya urn scheme. The posterior probabilities for models considered are calculated using a Gibbs sampling algorithm. A numerical simulation study is conducted to understand and compare the performance of the proposed method in relation to usual methods based on analysis of variance (ANOVA) followed by a Tukey test. The comparison among methods is made in terms of a true positive rate and false discovery rate. We find that proposed method outperforms the other methods based on ANOVA followed by a Tukey test. We also apply the methodologies to a publicly available data set on Plasmodium falciparum protein.
Saraiva, Erlandson F.,Suzuki, Adriano K.,Filho, Ciro A.O.,Louzada, Francisco The Korean Statistical Society 2016 Communications for statistical applications and me Vol.23 No.4
Football match predictions are of great interest to fans and sports press. In the last few years it has been the focus of several studies. In this paper, we propose the Poisson regression model in order to football match outcomes. We applied the proposed methodology to two national competitions: the 2012-2013 English Premier League and the 2015 Brazilian Football League. The number of goals scored by each team in a match is assumed to follow Poisson distribution, whose average reflects the strength of the attack, defense and the home team advantage. Inferences about all unknown quantities involved are made using a Bayesian approach. We calculate the probabilities of win, draw and loss for each match using a simulation procedure. Besides, also using simulation, the probability of a team qualifying for continental tournaments, being crowned champion or relegated to the second division is obtained.
Torres Tatiana Saraiva,Sena Luciano Silva,Santos Gleyson Vieira dos,Figueiredo Filho Luiz Antonio Silva,Barbosa Bruna Lima,Júnior Antônio de Sousa,Britto Fábio Barros,Sarmento José Lindenberg Rocha 아세아·태평양축산학회 2021 Animal Bioscience Vol.34 No.4
Objective: The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the efficiency of including genomic information in the analyses. Methods: There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses. Results: The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from –0.65±0.31 to 0.59±0.19, using A, and from –0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses. Conclusion: The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses. Objective: The genetic evaluation of Santa Inês sheep was performed for resistance to gastrointestinal nematode infection (RGNI) and body size using different relationship matrices to assess the efficiency of including genomic information in the analyses.Methods: There were 1,637 animals in the pedigree and 500, 980, and 980 records of RGNI, thoracic depth (TD), and rump height (RH), respectively. The genomic data consisted of 42,748 SNPs and 388 samples genotyped with the OvineSNP50 BeadChip. The (co)variance components were estimated in single- and multi-trait analyses using the numerator relationship matrix (A) and the hybrid matrix H, which blends A with the genomic relationship matrix (G). The BLUP and single-step genomic BLUP methods were used. The accuracies of estimated breeding values and Spearman rank correlation were also used to assess the feasibility of incorporating genomic information in the analyses.Results: The heritability estimates ranged from 0.11±0.07, for TD (in single-trait analysis using the A matrix), to 0.38±0.08, for RH (using the H matrix in multi-trait analysis). The estimates of genetic correlation ranged from –0.65±0.31 to 0.59±0.19, using A, and from –0.42±0.30 to 0.57±0.16 using H. The gains in accuracy of estimated breeding values ranged from 2.22% to 75.00% with the inclusion of genomic information in the analyses.Conclusion: The inclusion of genomic information will benefit the direct selection for the traits in this study, especially RGNI and TD. More information is necessary to improve the understanding on the genetic relationship between resistance to nematode infection and body size in Santa Inês sheep. The genetic evaluation for the evaluated traits was more efficient when genomic information was included in the analyses.
Ako Muto,Rui Saraiva 서울대학교 통일평화연구원 2020 Asian Journal of Peacebuilding Vol.8 No.2
As contemporary armed conflicts become increasingly complex, peacebuilding actors have been unable to prevent or respond effectively to related crises. Considering the policy trends evoked by the United Nations sustaining peace agenda and context- specific peacebuilding theories, this article examines peacebuilding initiatives amid complex contexts in Syria and Mozambique. It argues that the adaptive approaches of the National Agenda for the Future of Syria and the architecture of the negotiations surrounding the new peace process in Mozambique represent examples of context- specific, innovative, and non-linear peacebuilding methods that foster the self- organization capabilities of the respective conflict-affected societies. It concludes by asserting that through pragmatism, local and national ownership, and process facilitation, there is an increased potential for the effectiveness of peacebuilding interventions in complex conflict-affect situations.
Organoids as host models for infection biology – a review of methods
Aguilar Carmen,Alves da Silva Marta,Saraiva Margarida,Neyazi Mastura,Olsson I. Anna S.,Bartfeld Sina 생화학분자생물학회 2021 Experimental and molecular medicine Vol.53 No.-
Infectious diseases are a major threat worldwide. With the alarming rise of antimicrobial resistance and emergence of new potential pathogens, a better understanding of the infection process is urgently needed. Over the last century, the development of in vitro and in vivo models has led to remarkable contributions to the current knowledge in the field of infection biology. However, applying recent advances in organoid culture technology to research infectious diseases is now taking the field to a higher level of complexity. Here, we describe the current methods available for the study of infectious diseases using organoid cultures.