J. A. D. Costa, Carolina Azevedo, M. Nascimento, F. F. Silva, M. Resende, A. C. Nascimento
. The quality of fit of a multiple linear regression model often encounters multicollinearity and high dimensionality problems, making it impossible to obtain stable estimates through the traditional method of estimation based on ordinary least squares. To overcome such challenges, dimensionality reduction methods have been proposed, because of their simple theory and easy application. We compared three dimensionality reduction methods: Principal Components Regression (PCR), Partial Least Squares (PLS), and Independent Components Regression (ICR). An important step for dimensionality reduction and prediction is selecting the number of components, as it affects the linear combinations of the explanatory variables. The linear combinations are inserted into the model to predict the response based on a reduced number of parameters. We examined the criteria for the selection of the number of components. The dimensionality reduction methods were applied to genomic and phenotype data. We evaluated 370 accessions of Asian rice, Oryza sativa , which were genotyped for 36,901 SNPs markers considered to predict the genomic values for the number of panicles per plant trait. This data set presented multicollinearity and high dimensionality. The computational time for each method was also recorded. Among the methods, PCR and ICR gave the highest accuracy values, with ICR standing out for presenting estimates of the least biased genomic values. However, ICR required more computational time than the other methodologies.
{"title":"Research Article A comparison of regression methods based on dimensional reduction for genomic prediction","authors":"J. A. D. Costa, Carolina Azevedo, M. Nascimento, F. F. Silva, M. Resende, A. C. Nascimento","doi":"10.4238/GMR18877","DOIUrl":"https://doi.org/10.4238/GMR18877","url":null,"abstract":". The quality of fit of a multiple linear regression model often encounters multicollinearity and high dimensionality problems, making it impossible to obtain stable estimates through the traditional method of estimation based on ordinary least squares. To overcome such challenges, dimensionality reduction methods have been proposed, because of their simple theory and easy application. We compared three dimensionality reduction methods: Principal Components Regression (PCR), Partial Least Squares (PLS), and Independent Components Regression (ICR). An important step for dimensionality reduction and prediction is selecting the number of components, as it affects the linear combinations of the explanatory variables. The linear combinations are inserted into the model to predict the response based on a reduced number of parameters. We examined the criteria for the selection of the number of components. The dimensionality reduction methods were applied to genomic and phenotype data. We evaluated 370 accessions of Asian rice, Oryza sativa , which were genotyped for 36,901 SNPs markers considered to predict the genomic values for the number of panicles per plant trait. This data set presented multicollinearity and high dimensionality. The computational time for each method was also recorded. Among the methods, PCR and ICR gave the highest accuracy values, with ICR standing out for presenting estimates of the least biased genomic values. However, ICR required more computational time than the other methodologies.","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"56 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70933271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. Alessi, J. Da Silva, V. Pansera, J.A. da Rosa, I. Carvalho, F. Lautenchleger, M. S. Jung, de F. Colet, C. Teixeira, N. Basso, J. V. Tisott, C. M. Babeski
{"title":"Research Article Simulation of wheat yield by nitrogen and ear components in harvest prediction analysis","authors":"O. Alessi, J. Da Silva, V. Pansera, J.A. da Rosa, I. Carvalho, F. Lautenchleger, M. S. Jung, de F. Colet, C. Teixeira, N. Basso, J. V. Tisott, C. M. Babeski","doi":"10.4238/gmr18943","DOIUrl":"https://doi.org/10.4238/gmr18943","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"1 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70934272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Pacheco, P. P. Orellana, C. Andrade, J.E. Torracchi
Staphylococcus aureus is one of the main pathogens of importance in health care. Distributed worldwide, it has considerable impact on community and nosocomial infections. This bacteria has the tst and lukS-F PV genes that code for the TSST-1 toxin and leucocidin. These pathogenic microorganisms have the ability to survive for long periods on inert surfaces such as mobile phone screens. Senior dentistry students work in clinics and use their cell phones often, which could potentially spread this pathogen. We looked for the tst and lukS-F PV genes in S. aureus isolated from mobile phone screens of final year dentistry students. This was a descriptive cross-sectional observational study using 92 samples from the mobile phone screens of dental students, among which 16 were positive for S. aureus. They were identified by means of culture methods and detection of the nuc, nucA and femB genes. The DNA was extracted using the alkaline lysis method; PCR was used in the molecular identification of the tst and lukS-F PV genes. Nine of the 16 S. aureus isolates had the tst gene, and 1/16 the lukS-F PV gene. This study shows the high frequency of virulent S. aureus on the
{"title":"Research Article Virulence genes in Staphylococcus aureus isolated from cell phone screens of dentistry students in Cuenca-Ecuador","authors":"M. Pacheco, P. P. Orellana, C. Andrade, J.E. Torracchi","doi":"10.4238/gmr18928","DOIUrl":"https://doi.org/10.4238/gmr18928","url":null,"abstract":"Staphylococcus aureus is one of the main pathogens of importance in health care. Distributed worldwide, it has considerable impact on community and nosocomial infections. This bacteria has the tst and lukS-F PV genes that code for the TSST-1 toxin and leucocidin. These pathogenic microorganisms have the ability to survive for long periods on inert surfaces such as mobile phone screens. Senior dentistry students work in clinics and use their cell phones often, which could potentially spread this pathogen. We looked for the tst and lukS-F PV genes in S. aureus isolated from mobile phone screens of final year dentistry students. This was a descriptive cross-sectional observational study using 92 samples from the mobile phone screens of dental students, among which 16 were positive for S. aureus. They were identified by means of culture methods and detection of the nuc, nucA and femB genes. The DNA was extracted using the alkaline lysis method; PCR was used in the molecular identification of the tst and lukS-F PV genes. Nine of the 16 S. aureus isolates had the tst gene, and 1/16 the lukS-F PV gene. This study shows the high frequency of virulent S. aureus on the","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"1 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70934277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Reis, C. Araujo, E. Silva, Thales Biffe Alves, Y.M.F. Ternes, R. Santos
{"title":"Research Article Strategies for cervical cancer screening in the scope of the Brazilian Unified National Health System","authors":"A. Reis, C. Araujo, E. Silva, Thales Biffe Alves, Y.M.F. Ternes, R. Santos","doi":"10.4238/GMR18719","DOIUrl":"https://doi.org/10.4238/GMR18719","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"20 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70930750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. D. Phúc, L. Ky, N. Binh, N. T. Tuan, N. Van, T. X. Hai, V. Thuc
{"title":"Research Article Standard and immunohistochemical staining methods for diagnosis of cervical lymph node metastasis in nasopharyngeal carcinoma","authors":"N. D. Phúc, L. Ky, N. Binh, N. T. Tuan, N. Van, T. X. Hai, V. Thuc","doi":"10.4238/GMR18735","DOIUrl":"https://doi.org/10.4238/GMR18735","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"20 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70930935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Research Article Thrombolysis and thrombectomy as an effective treatment for ischemic cerebral circulation disorders","authors":"N. H. Ngoc, N. V. Thống, N. An","doi":"10.4238/GMR18740","DOIUrl":"https://doi.org/10.4238/GMR18740","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"20 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70931261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Research Article Anticancer and antimicrobial activities of diosmin","authors":"A. Kilit, O. Köse, Gülmen Imi, E. Aydemir","doi":"10.4238/GMR18752","DOIUrl":"https://doi.org/10.4238/GMR18752","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"20 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70932154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adriza Silva, A. T. Machado, P. P. Torga, C. Silva-Neto, P. G. Bustamante, P. Bianchini, R. P. Soratto, J. P. Oliveira
{"title":"Research Article Common bean (Phaseolus vulgaris) mulatinho type accessions conserved ex situ in Brazil","authors":"Adriza Silva, A. T. Machado, P. P. Torga, C. Silva-Neto, P. G. Bustamante, P. Bianchini, R. P. Soratto, J. P. Oliveira","doi":"10.4238/GMR18770","DOIUrl":"https://doi.org/10.4238/GMR18770","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"268 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70932358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. D. Barbosa, P. Fernandes, A. Marcelino, F. A. Silva, M. S. Dias, C.R.C. Silva, R. C. Santos
Water stress triggers various cellular responses in plants, altering normal metabolic flow. Pyruvate, an important component of the glycolysis pathway, is directly involved in cell processes, triggering genes that influence drought tolerance. Research with Arabidopsis has shown that synthetic pyruvate relieves drought damage. We evaluated the effects of exogenous pyruvate at 100 and 50,000 μM on mitigation of drought stress in two peanut cultivars submitted to water restriction. The evaluations were based on growth, gas exchange, and photosynthesis rate analyses. In addition, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) enzymes, and free proline were also assayed. In general, exogenous application of pyruvate contributed to mitigate the effects of water stress in the cultivar IAC Caiapó (sensitive to drought), based on gas exchange and instantaneous efficiency of water use. Exogenous pyruvate contributed to restore the action of antioxidative enzymes in BR 1 (tolerant to drought), based on measures of SOD (45%), CAT (129%) and APX (60%) in stressed plants, and full recovery at 50,000 μM. When treated with proline, stress attenuation was found only at 100 μM in both cultivars; the excess seemed to have a negative effect on stressed plants, probably affecting the cell
{"title":"Research Article Exogenous pyruvate mitigates the detrimental effects of water stress in contrasting peanut genotypes","authors":"D. D. Barbosa, P. Fernandes, A. Marcelino, F. A. Silva, M. S. Dias, C.R.C. Silva, R. C. Santos","doi":"10.4238/gmr18907","DOIUrl":"https://doi.org/10.4238/gmr18907","url":null,"abstract":"Water stress triggers various cellular responses in plants, altering normal metabolic flow. Pyruvate, an important component of the glycolysis pathway, is directly involved in cell processes, triggering genes that influence drought tolerance. Research with Arabidopsis has shown that synthetic pyruvate relieves drought damage. We evaluated the effects of exogenous pyruvate at 100 and 50,000 μM on mitigation of drought stress in two peanut cultivars submitted to water restriction. The evaluations were based on growth, gas exchange, and photosynthesis rate analyses. In addition, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) enzymes, and free proline were also assayed. In general, exogenous application of pyruvate contributed to mitigate the effects of water stress in the cultivar IAC Caiapó (sensitive to drought), based on gas exchange and instantaneous efficiency of water use. Exogenous pyruvate contributed to restore the action of antioxidative enzymes in BR 1 (tolerant to drought), based on measures of SOD (45%), CAT (129%) and APX (60%) in stressed plants, and full recovery at 50,000 μM. When treated with proline, stress attenuation was found only at 100 μM in both cultivars; the excess seemed to have a negative effect on stressed plants, probably affecting the cell","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"1 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70933603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
I. S. Jesus, A. C. Cruz, C. Santos, Elem Cristina Macedo Barra, J. H. Costa, T. Monteiro, Camila de Cássia dos Santos, Keila Feitosa Valente, Barbara Wilka Leal Silva, É. D. L. Rodrigues, J. C. F. Almeida, E. S. Filho, M. Figueiredo, Sinerey Karla Salim Aragão de Sousa, S. P. Silva, L. M. Casseb, A. Negrão, A. Casseb
{"title":"Research Article Molecular diagnosis and clinicopathological characteristics of canine distemper neurologic disease","authors":"I. S. Jesus, A. C. Cruz, C. Santos, Elem Cristina Macedo Barra, J. H. Costa, T. Monteiro, Camila de Cássia dos Santos, Keila Feitosa Valente, Barbara Wilka Leal Silva, É. D. L. Rodrigues, J. C. F. Almeida, E. S. Filho, M. Figueiredo, Sinerey Karla Salim Aragão de Sousa, S. P. Silva, L. M. Casseb, A. Negrão, A. Casseb","doi":"10.4238/gmr18884","DOIUrl":"https://doi.org/10.4238/gmr18884","url":null,"abstract":"","PeriodicalId":12518,"journal":{"name":"Genetics and Molecular Research","volume":"1 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70933693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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