Bootstrap resampling was used to examine the sampling variations in the average of a population w... more Bootstrap resampling was used to examine the sampling variations in the average of a population with a known mean. Two thousand bootstrap estimates of the mean were generated from a sample of 50 observations drawn from a population of 10 independent and identically distributed observations with an underlying uniform distribution on the unit interval. Analyses were performed using Mathematica, SAS/IML, S-PLUS, and STATA. Bootstrap approximations to the cumulative distribution function of the mean from these three software packages were identical and consistent with Normal Theory. This study demonstrates that the sampling variations of the mean can be estimated from a population of only 10 observations. The source code can be easily modified for any population. B. INTRODUCTION In ordinary usage, the phrase "resampling methods" refers to methods in which the observed data are used repeatedly, in a computer-intensive analysis, to provide inferences. In simple terms, resampling...
Page 1. Review article Highlights of the annual meeting of the European Association of Nuclear Me... more Page 1. Review article Highlights of the annual meeting of the European Association of Nuclear Medicine: Glasgow 1997 The Flowering of Science and Art of Nuclear Medicine in Europe Ignasi Carrió Department of Nuclear Medicine, Hospital Sant Pau, Barcelona, Spain ...
Data were waiting times between eruptions of the Old Faithful geyser in Yellowstone NationalPark,... more Data were waiting times between eruptions of the Old Faithful geyser in Yellowstone NationalPark, Wyoming, USA. The sample histogram showed evidence of bimodality. Forthwith, a twocomponentnormal mixture model was fitted to the data. The Gauss-Newton algorithm was usedto obtain the maximum likelihood estimate of the nuisance parameters in the mixture model. Analternative method which uses the Gibbs Sampler to obtain
A cDNA microarray resource has been developed with the goal of providing integrated functional ge... more A cDNA microarray resource has been developed with the goal of providing integrated functional genomics resources for cattle. The National Bovine Functional Genomics Consortium's (NBFGC) expressed sequence tag (EST) collection was established in 2001 to develop resources for functional genomics research. The NBFGC EST collection and microarray contains 18,263 unique transcripts, derived from many different tissue types and various physiologically important states within these tissues. The NBFGC microarray has been tested for false-positive rates using self-self hybridizations and was shown to yield robust results in test microarray experiments. A web-accessible database has been established to provide pertinent data related to NBFGC clones, including sequence data, BLAST results, and ontology information. The NBFGC microarray represents the largest cDNA microarray for a livestock species prepared to date and should prove to be a valuable tool in studying genome-wide gene express...
A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis a... more A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis and early embryonic development. We have screened bovine cDNA microarrays (containing expressed sequence tags representing >15,000 unique genes) with Cy3- and Cy5-labeled cDNA derived from bovine oocyte samples collected at two different stages of meiotic maturation (germinal vesicle vs. metaphase II; n = 3 samples per group). Here, we present a novel data analysis approach that uses all available information from above experiments to obtain and index the transcriptome of bovine oocytes and changes in transcriptome composition in response to meiotic maturation. Signal intensities (Fg) for all housekeeping genes were omitted prior to analysis. A local threshold for gene expression was computed as background intensity (Bg) plus 2 times the standard deviation of background and foreground signals. Within each array, data were normalized by the LOWESS procedure. Subsequently, a two-stage mi...
Recent developments in microarray technologies permit scientists to analyze expression of thousan... more Recent developments in microarray technologies permit scientists to analyze expression of thousands of genes simultaneously in diverse biological systems. In an effort to provide integrated resources for application of microarray technologies to studies of skeletal muscle growth and development in swine, we have constructed a normalized cDNA library from porcine skeletal muscle. The effectiveness of normalization was evaluated by DNA sequencing of clones randomly picked from the library before and after normalization, and also by Southern blot hybridization using probes representing abundant transcripts. Our data suggests that the normalization procedure successfully reduced the highly abundant cDNA species in the normalized library. To date, a total of 782 EST (expressed sequence tag) sequences have been generated from this normalized library (687 ESTs) and the original library (95 ESTs). The sequence information of these ESTs plus their BLAST results has been made available through a web accessible database (http://nbfgc.msu.edu). Cluster analysis of the data indicates that a total of 742 unique sequences are present in this collection. BLASTN search of the 742 EST sequences against the public database (dbEST) revealed that 139 had no significant matches (E-value > 10(-15)) to porcine ESTs already entered in the database, suggesting the possibility of their specific expression in porcine skeletal muscle. Generation of non-redundant ESTs from this library will allow us to construct cDNA microarrays for identification of gene expression changes that regulate muscle growth and affect meat quality in swine.
Mycobacterium avium subspecies paratuberculosis (MAP) and Mycobacterium avium subspecies avium (M... more Mycobacterium avium subspecies paratuberculosis (MAP) and Mycobacterium avium subspecies avium (MAA) represent two closely related intracellular bacteria with vastly different associated pathologies. MAA can cause severe respiratory infections in immune compromised humans but is nonpathogenic in ruminants and is more readily controlled by the bovine immune system than MAP. MAP causes a fatal wasting syndrome in ruminants, typified by granulomatous enteritis localized in the small intestine. MAP has also been cited as a potential cause of human Crohn's disease. We used a bovine immune-specific microarray (BOTL-5) to compare the response of mature bovine monocyte-derived macrophages (MDM cells) to MAP and MAA. Statistical analysis of microarray data revealed 21 genes not appreciably expressed in resting MDM cells that were activated following infection with either MAA or MAP. Further analysis revealed 144 genes differentially expressed in MDM cells following infection with MAA and...
Bootstrap resampling was used to examine the sampling variations in the average of a population w... more Bootstrap resampling was used to examine the sampling variations in the average of a population with a known mean. Two thousand bootstrap estimates of the mean were generated from a sample of 50 observations drawn from a population of 10 independent and identically distributed observations with an underlying uniform distribution on the unit interval. Analyses were performed using Mathematica, SAS/IML, S-PLUS, and STATA. Bootstrap approximations to the cumulative distribution function of the mean from these three software packages were identical and consistent with Normal Theory. This study demonstrates that the sampling variations of the mean can be estimated from a population of only 10 observations. The source code can be easily modified for any population. B. INTRODUCTION In ordinary usage, the phrase "resampling methods" refers to methods in which the observed data are used repeatedly, in a computer-intensive analysis, to provide inferences. In simple terms, resampling...
Page 1. Review article Highlights of the annual meeting of the European Association of Nuclear Me... more Page 1. Review article Highlights of the annual meeting of the European Association of Nuclear Medicine: Glasgow 1997 The Flowering of Science and Art of Nuclear Medicine in Europe Ignasi Carrió Department of Nuclear Medicine, Hospital Sant Pau, Barcelona, Spain ...
Data were waiting times between eruptions of the Old Faithful geyser in Yellowstone NationalPark,... more Data were waiting times between eruptions of the Old Faithful geyser in Yellowstone NationalPark, Wyoming, USA. The sample histogram showed evidence of bimodality. Forthwith, a twocomponentnormal mixture model was fitted to the data. The Gauss-Newton algorithm was usedto obtain the maximum likelihood estimate of the nuisance parameters in the mixture model. Analternative method which uses the Gibbs Sampler to obtain
A cDNA microarray resource has been developed with the goal of providing integrated functional ge... more A cDNA microarray resource has been developed with the goal of providing integrated functional genomics resources for cattle. The National Bovine Functional Genomics Consortium's (NBFGC) expressed sequence tag (EST) collection was established in 2001 to develop resources for functional genomics research. The NBFGC EST collection and microarray contains 18,263 unique transcripts, derived from many different tissue types and various physiologically important states within these tissues. The NBFGC microarray has been tested for false-positive rates using self-self hybridizations and was shown to yield robust results in test microarray experiments. A web-accessible database has been established to provide pertinent data related to NBFGC clones, including sequence data, BLAST results, and ontology information. The NBFGC microarray represents the largest cDNA microarray for a livestock species prepared to date and should prove to be a valuable tool in studying genome-wide gene express...
A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis a... more A growing body of evidence implicates the oocyte as a key regulator of ovarian folliculogenesis and early embryonic development. We have screened bovine cDNA microarrays (containing expressed sequence tags representing >15,000 unique genes) with Cy3- and Cy5-labeled cDNA derived from bovine oocyte samples collected at two different stages of meiotic maturation (germinal vesicle vs. metaphase II; n = 3 samples per group). Here, we present a novel data analysis approach that uses all available information from above experiments to obtain and index the transcriptome of bovine oocytes and changes in transcriptome composition in response to meiotic maturation. Signal intensities (Fg) for all housekeeping genes were omitted prior to analysis. A local threshold for gene expression was computed as background intensity (Bg) plus 2 times the standard deviation of background and foreground signals. Within each array, data were normalized by the LOWESS procedure. Subsequently, a two-stage mi...
Recent developments in microarray technologies permit scientists to analyze expression of thousan... more Recent developments in microarray technologies permit scientists to analyze expression of thousands of genes simultaneously in diverse biological systems. In an effort to provide integrated resources for application of microarray technologies to studies of skeletal muscle growth and development in swine, we have constructed a normalized cDNA library from porcine skeletal muscle. The effectiveness of normalization was evaluated by DNA sequencing of clones randomly picked from the library before and after normalization, and also by Southern blot hybridization using probes representing abundant transcripts. Our data suggests that the normalization procedure successfully reduced the highly abundant cDNA species in the normalized library. To date, a total of 782 EST (expressed sequence tag) sequences have been generated from this normalized library (687 ESTs) and the original library (95 ESTs). The sequence information of these ESTs plus their BLAST results has been made available through a web accessible database (http://nbfgc.msu.edu). Cluster analysis of the data indicates that a total of 742 unique sequences are present in this collection. BLASTN search of the 742 EST sequences against the public database (dbEST) revealed that 139 had no significant matches (E-value > 10(-15)) to porcine ESTs already entered in the database, suggesting the possibility of their specific expression in porcine skeletal muscle. Generation of non-redundant ESTs from this library will allow us to construct cDNA microarrays for identification of gene expression changes that regulate muscle growth and affect meat quality in swine.
Mycobacterium avium subspecies paratuberculosis (MAP) and Mycobacterium avium subspecies avium (M... more Mycobacterium avium subspecies paratuberculosis (MAP) and Mycobacterium avium subspecies avium (MAA) represent two closely related intracellular bacteria with vastly different associated pathologies. MAA can cause severe respiratory infections in immune compromised humans but is nonpathogenic in ruminants and is more readily controlled by the bovine immune system than MAP. MAP causes a fatal wasting syndrome in ruminants, typified by granulomatous enteritis localized in the small intestine. MAP has also been cited as a potential cause of human Crohn's disease. We used a bovine immune-specific microarray (BOTL-5) to compare the response of mature bovine monocyte-derived macrophages (MDM cells) to MAP and MAA. Statistical analysis of microarray data revealed 21 genes not appreciably expressed in resting MDM cells that were activated following infection with either MAA or MAP. Further analysis revealed 144 genes differentially expressed in MDM cells following infection with MAA and...
Uploads
Papers by Peter Saama