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Articles by M. Alam
Total Records ( 3 ) for M. Alam
  Kai Man Kam , Cindy K. Y. Luey , Michele B. Parsons , Kara L. F. Cooper , G. B. Nair , M. Alam , M. Atiqul Islam , Danny T. L. Cheung , Y. W. Chu , T. Ramamurthy , G. P. Pazhani , S. K. Bhattacharya , H. Watanabe , J. Terajima , E. Arakawa , O.-A. Ratchtrachenchai , S. Huttayananont , Efrain M. Ribot , Peter Gerner-Smidt and Bala Swaminathan
  The pandemic spread of Vibrio parahaemolyticus is an international public health issue. Because of the outbreak potential of the organism, it is critical to establish an internationally recognized molecular subtyping protocol for V. parahaemolyticus that is both rapid and robust as a means to monitor its further spread and to guide control measures in combination with epidemiologic data. Here we describe the results of a multicenter, multicountry validation of a new PulseNet International standardized V. parahaemolyticus pulsed-field gel electrophoresis (PFGE) protocol. The results are from a composite analysis of 36 well-characterized V. parahaemolyticus isolates from six participating laboratories, and the isolates represent predominant serotypes and various genotypes isolated from different geographic regions and time periods. The discriminatory power is very high, as 34 out of 36 sporadic V. parahaemolyticus strains tested fell into 34 distinguishable PFGE groups when the data obtained with two restriction enzymes (SfiI and NotI) were combined. PFGE was further able to cluster members of known pandemic serogroups. The study also identified quality measures which may affect the performance of the protocol. Nonadherence to the recommended procedure may lead to high background in the PFGE gel patterns, partial digestion, and poor fragment resolution. When these quality measures were implemented, the PulseNet V. parahaemolyticus protocol was found to be both robust and reproducible among the collaborating laboratories.
  C.I. Cho , M. Alam , T.J. Choi and K.H. Cho
  The purpose of this study, was to determine the accuracy of imputation for non-genotyped sires using their progenies genotypes and to compare the accuracy of genomic breeding values from imputed sires with respect to their true genomic data. A total of 1,800 were simulated to construct phenotypic data and pedigree data. A genotype panel for all animals was prepared as well. Among them, 20 sires were selected randomly and imputed assuming that their genotypes were missing. The average accuracy of imputation for sires through 100 simulation repeats was 88.7% and the obtained range of accuracies was 87-90.4%. The accuracy of Genomic Breeding Values (GEBV) of whole population was slightly higher than for pedigree based Breeding Values (EBV) 0.639 and 0.611, respectively. The accuracy for GEBV from 20 selected sires using true or imputed genotypes were 0.673 and 0.669, respectively. These results indicated that imputation of missing sire genotypes can obtain an accuracy which is almost close to the accuracy of estimates from their true genotypes. Therefore, it can be concluded that there is a possibility in genomic selection for using imputed sires which have no genotypes but yet have their progenies genotypes available. These results deemed more applicable in Korean dairy genomic evaluation, i.e., for Holstein where most sire genotypes are difficult to obtain due to an extensive use of imported semen.
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