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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.
이재규(Jae-Kyu Lee),이기은(Gi-Eun Lee),Renan Benigno Saraiva(Renan Benigno Saraiva ),Robert A. Nash(Robert A. Nash ),Lorraine Hope(Lorraine Hope ),이장한(Jang-Han Lee) 한국자료분석학회 2024 Journal of the Korean Data Analysis Society Vol.26 No.2
본 연구는 목격자 식별의 신빙성을 객관적이고 정량적으로 평가할 수 있는 목격자 식별 맥락에 특화된 메타기억 측정 도구인 목격자 메타기억 척도(Eyewitness Metamemory Scale)를 국내 실정에 맞게 타당화하였다. 이를 위해 만 19세 이상 60세 미만 362명을 대상으로 응답을 수집하여 원판의 개발 이전 초기 35개 문항에 대한 문항 분석, 요인분석, 수렴 및 변별타당도 분석, 신뢰도 분석을 실시하였다. 문항분석 및 요인적재량을 기준으로 원판의 개발 이전 초기 35개 문항 중 10개 문항을 제거한 25개 문항을 추출하였으며, 최종적으로 25개의 문항을 사용하여 확인적 요인분석을 실시한 결과 한국형 목격자 메타기억척도가 원판과 동일한 3개 요인 구조를 가지고 있음을 확인하였다. 또한 적절한 수렴 및 변별 타당도와 내적합치도를 보여 한국형 목격자 메타기억척도가 타당한 도구임이 확인되었다. 이러한 결과는 본 연구에서 타당화한 한국형 목격자 메타기억척도가 국내 범인식별절차 간 법적 의사결정을 보조할 수 있는 수단으로서 역할을 할 수 있음을 지지하며, 목격자 식별 맥락에서 메타기억의 문화적인 비교를 바탕으로 연구를 수행할 수 있는 기초 정보로써 제공될 수 있을 것이다. This study validated the Eyewitness Metamemory Scale, developed for the specific context of eyewitness identification, under Korean conditions. Data from 362 participants between the ages of 19 and 60 were subjected to item analysis, factor analysis, convergent and discriminant validity and reliability using the original 35 items. After extraction, 25 items were retained, 10 items were removed and 3 new items were added. Factor analysis confirmed the three-factor structure of the Korean version, which reflected the original scale and achieved a reasonable model fit. Adequate convergent and discriminant validity, as well as internal consistency, supported the reliability and validity of the Korean Eyewitness Metamemory Scale. These findings confirm the utility of the Korean Eyewitness Metamemory Scale as a tool to aid legal decision-making in the Korean criminal identification process and provide a basis for cross-cultural metamemory research in the context of eyewitness identification.
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.