SEARCH · PubMed Health

Results for “bootstrap”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources

PubMed2000

What is the phylogenetic position of Cryptosporidium?

The phylogenetic position of Cryptosporidium is elusive. Although previous studies based solely upon small-subunit (SSU) rRNA sequences suggested that the genus was an early emerging lineage among the Apicomplexa, bootstrap support for this placement was low. Here, the phylogenetic position of Cryptosporidium has been re-evaluated for SSU rRNA, fused SSU/large-subunit (LSU) rRNA and six protein sequences using traditional distance-based neighbour-joining, maximum-parsimony and maximum-likelihood methods of phylogenetic reconstruction as well as the new Slow-Fast analysis, which focuses upon the slowly evolving positions within sequences and is especially useful if a long-branch attraction (LBA) artefact is suspected. All the methods of reconstruction indicated a trend for the early emergence of Cryptosporidium at the base of the Apicomplexa and showed that an LBA artefact plays no role in this placement. Although the inclusion of additional numbers of neither species nor genes has significantly enhanced the bootstrap support for this phylogenetic position, recent biochemical, molecular and ultrastructural data are congruent with it. Therefore, we favour a working hypothesis that this genus constitutes an early emerging branch of the Apicomplexa.

Animals↗

PubMed2001

Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila.

The genera Anaplasma, Ehrlichia, Cowdria, Neorickettsia and Wolbachia encompass a group of obligate intracellular bacteria that reside in vacuoles of eukaryotic cells and were previously placed in taxa based upon morphological, ecological, epidemiological and clinical characteristics. Recent genetic analyses of 16S rRNA genes, groESL and surface protein genes have indicated that the existing taxa designations are flawed. All 16S rRNA gene and groESL sequences deposited in GenBank prior to 2000 and selected sequences deposited thereafter were aligned and phylogenetic trees and bootstrap values were calculated using the neighbour-joining method and compared with trees generated with maximum-probability, maximum-likelihood, majority-rule consensus and parsimony methods. Supported by bootstrap probabilities of at least 54%, 16S rRNA gene comparisons consistently clustered to yield four distinct clades characterized roughly as Anaplasma (including the Ehrlichia phagocytophila group, Ehrlichia platys and Ehrlichia bovis) with a minimum of 96.1% similarity, Ehrlichia (including Cowdria ruminantium) with a minimum of 97.7% similarity, Wolbachia with a minimum of 95.6% similarity and Neorickettsia (including Ehrlichia sennetsu and Ehrlichia risticii) with a minimum of 94.9% similarity. Maximum similarity between clades ranged from 87.1 to 94.9%. Insufficient differences existed among E. phagocytophila, Ehrlichia equi and the human granulocytic ehrlichiosis (HGE) agent to support separate species designations, and this group was at least 98.2% similar to any Anaplasma species. These 16S rRNA gene analyses are strongly supported by similar groESL clades, as well as biological and antigenic characteristics. It is proposed that all members of the tribes Ehrlichieae and Wolbachieae be transferred to the family Anaplasmataceae and that the tribe structure of the family Rickettsiaceae be eliminated. The genus Anaplasma should be emended to include Anaplasma (Ehrlichia) phagocytophila comb. nov. (which also encompasses the former E. equi and the HGE agent), Anaplasma (Ehrlichia) bovis comb. nov. and Anaplasma (Ehrlichia) platys comb. nov., the genus Ehrlichia should be emended to include Ehrlichia (Cowdria) ruminantium comb. nov. and the genus Neorickettsia should be emended to include Neorickettsia (Ehrlichia) risticii comb. nov. and Neorickettsia (Ehrlichia) sennetsu comb. nov.

Anaplasma↗

PubMed2001

New insights into the phylogenetic position of diplonemids: G+C content bias, differences of evolutionary rate and a new environmental sequence.

The phylum Euglenozoa consists of three distinct groups: the euglenoids, diplonemids and kinetoplastids. The phylogenetic position of the diplonemids within this phylum remains unsettled, since both morphological and molecular data produce weak and contradictory results. It is shown here that taxonomic sampling, G+C content bias, mutational saturation and differences of evolutionary rate among lineages are major factors affecting the topology of the small-subunit rRNA euglenozoan tree. When these problems are minimized by using a larger diplonemid sampling (including a sequence of environmental origin) and correcting for G+C bias (by using both paralinear distances or an unbiased dataset), a diplonemids+euglenoids sisterhood is retrieved. Bootstrap support for this relationship is still moderate, but it is retrieved by all analysis methods, overcoming previously reported disagreements. In addition, the inclusion of a large number of euglenoid sequences in the analysis improves some phylogenetic relationships within this group. Some problematic taxa, such as the species Khawkinea quartana, are now placed with high bootstrap support and monophyly is found for two interesting groups (the photosynthetic genera Eutreptia+Eutreptiella and the loricate genera Strombomonas+Trachelomonas), although with weak statistical support.

Animals↗

PubMed2002

A mathematical method for determining genome divergence and species delineation using AFLP.

The delineation of bacterial species is presently achieved using direct DNA-DNA relatedness studies of whole genomes. It would be helpful to obtain the same genomically based delineation by indirect methods, provided that descriptions of individual genome composition of bacterial genomes are obtained and included in species descriptions. The amplified fragment length polymorphism (AFLP) technique could provide the necessary data if the nucleotides involved in restriction and amplification are fundamental to the description of genomic divergences. Firstly, in order to verify that AFLP analysis permits a realistic exploration of bacterial genome composition, the strong correspondence between predicted and experimental AFLP data was demonstrated using Agrobacterium strain C58 as a model system. Secondly, a method is proposed for determining current genome mispairing and evolutionary genome divergences between pairs of bacteria, based on arbitrary sampling of genomes by using AFLP. The measure of current genome mispairing was validated by comparison with DNA-DNA relatedness data, which itself correlates with base mispairing. The evolutionary genome divergence is the estimated rate of nucleotide substitution that has occurred since the strains diverged from a common ancestor. Current genome mispairing and evolutionary genome divergence were used to compare members of Agrobacterium, used as a model of closely related genomic species. A strong and highly significant correlation was found between calculated genome mispairing and DNA-DNA relatedness values within genomic species. The canonical 70% DNA-DNA hybridization value used to delineate genomic species was found to correspond to a range of current genome mispairing of 13-13.6%. These limits correspond to 0.097 and 0.104 nucleotide substitutions per site, respectively. In addition, experimental data showed that the large Ti and cryptic plasmids of Agrobacterium had little effect on the estimation of genome divergence. Evolutionary genome divergence was used for phylogenetic inferences. Data showed that members of the same genomic species clustered consistently, as supported by bootstrap resampling. On the basis of these results, it is proposed that the genomic delineation of bacterial species could be based, in future, on phylogenetic groups supported by bootstraps and genome descriptions of individual strains, obtained by AFLP analysis, recorded in accessible databases; this approach might eventually replace DNA-DNA hybridization studies.

Biological Evolution↗

PubMed1996

The phylogenetic position and ultrastructure of the uncultured bacterium Achromatium oxaliferum.

Achromatium oxaliferum is a large, morphologically conspicuous, sediment-dwelling bacterium. Nothing is known concerning its phylogeny and it has eluded all attempts at laboratory cultivation. The limited physiological description of A. oxaliferum has been based on morphological features of the bacterium such as the presence of intracellular sulphur inclusions. A. oxaliferum cells were purified from a wetland region close to Rydal Water (Cumbria, UK). Scanning and transmission electron microscopy revealed that a number of morphologically distinct A. oxaliferum cell-types, based on cell surface features and the size and abundance of calcite and sulphur inclusions within the cells, were present in a single sample of purified cells. PCR was used to amplify almost full-length 16S rRNA gene sequences from DNA extracted from A. oxaliferum cells directly purified from sediments. The PCR products were cloned and partial sequences (approx. 400 bp) were determined for seven of the clones. Three different sequence clusters were recovered from the clone libraries. A near full-length (1489 bp) 16S rRNA gene sequence was determined for a representative clone of the most dominant sequence-type (52% of the sequences). Comparative sequence analysis showed A. oxaliferum to form a deep branching lineage within the gamma-subdivision of the Proteobacteria. A. oxaliferum was related most closely to the Chromatium assemblage that includes sulphur-oxidizing symbiotic bacteria, purple sulphur bacteria, and sulphur- and iron-oxidizing thiobacilli. Phylogenetic inferences made using distance, parsimony and maximum likelihood methods all placed A. oxaliferum with this group of bacteria. Bootstrap support for a relationship with any particular lineage within the assemblage was weak. The seven clone sequences recovered from the A. oxaliferum cells however formed a monophyletic group well supported by bootstrap analysis (85-100% support depending on the analysis done). It was concluded that A. oxaliferum was related to organisms of the Chromatium assemblage but constituted a novel lineage within this group of bacteria. A. oxaliferum cells were confirmed as the source of the 16S rRNA sequence obtained, by the use of a fluorescently-labelled 16S rRNA-targeted oligonucleotide specific for the A. oxaliferum rRNA sequence.

Base Sequence↗

PubMed2002

High-beta equilibria of drift-optimized compact stellarators.

Compact stellarator configurations have been obtained with good neoclassical confinement that are stable to both pressure- and current-driven modes for high values of beta. These configurations are drift-optimized tokamak-stellarator hybrids with a high-shear tokamak-like rotational transform profile and /B/ that is approximately poloidally symmetric. The bootstrap current is consistent with the required equilibrium current and, while larger than that in existing stellarators, is typically only a small fraction (1/3-1/5) of that in an equivalent tokamak. These configurations have strong magnetic wells and consequently high interchange stability beta limits up to beta=23%. Because of the reduced bootstrap current, these configurations are stable to low-n ideal MHD kink modes with no wall stabilization for values of beta ( approximately 7%-11%) significantly larger than in an equivalent advanced tokamak.

Journal Article↗

PubMed2005

Ensembling local learners through multimodal perturbation.

Ensemble learning algorithms train multiple component learners and then combine their predictions. In order to generate a strong ensemble, the component learners should be with high accuracy as well as high diversity. A popularly used scheme in generating accurate but diverse component learners is to perturb the training data with resampling methods, such as the bootstrap sampling used in bagging. However, such a scheme is not very effective on local learners such as nearest-neighbor classifiers because a slight change in training data can hardly result in local learners with big differences. In this paper, a new ensemble algorithm named Filtered Attribute Subspace based Bagging with Injected Randomness (FASBIR) is proposed for building ensembles of local learners, which utilizes multimodal perturbation to help generate accurate but diverse component learners. In detail, FASBIR employs the perturbation on the training data with bootstrap sampling, the perturbation on the input attributes with attribute filtering and attribute subspace selection, and the perturbation on the learning parameters with randomly configured distance metrics. A large empirical study shows that FASBIR is effective in building ensembles of nearest-neighbor classifiers, whose performance is better than that of many other ensemble algorithms.

Algorithms↗

PubMedDate not supplied

Genetic evidence for bidirectional effects of early lexical and grammatical development.

This article addresses the autonomy hypothesis of vocabulary and grammar and bootstrapping mechanisms in early language development. Two birth cohorts of 1,505 and 1,049 same-sex twin pairs from the UK were assessed at 2 and 3 years on grammar and vocabulary, using adapted versions of the MacArthur Communicative Development Inventory. Vocabulary and grammar correlate strongly at both 2 and 3 years in both cohorts. Multivariate genetic modeling reveals a consistently high genetic correlation between vocabulary and grammar at 2 and 3 years. This finding suggests the same genetic influences operate for both vocabulary and grammar, a finding incompatible with traditional autonomy hypothesis, at least in early acquisition. Crosslagged longitudinal genetic models indicate both lexical and syntactical bootstrapping operate from 2 to 3 years.

Child Language↗

PubMed2000

Mixture models, robustness, and the weighted likelihood methodology.

Problems associated with the analysis of data from a mixture of distributions include the presence of outliers in the sample, the fact that a component may not be well represented in the data, and the problem of biases that occur when the model is slightly misspecified. We study the performance of weighted likelihood in this context. The method produces estimates with low bias and mean squared error, and it is useful in that it unearths data substructures in the form of multiple roots. This in turn indicates multiple potential mixture model fits due to the presence of more components than originally specified in the model. To compute the weighted likelihood estimates, we use as starting values the method of moment estimates computed on bootstrap subsamples drawn from the data. We address a number of important practical issues involving bootstrap sample size selection, the role of starting values, and the behavior of the roots. The algorithm used to compute the weighted likelihood estimates is competitive with EM, and it is similar to EM when the components are not well separated. Moreover, we propose a new statistical stopping rule for the termination of the algorithm. An example and a small simulation study illustrate the above points.

Animals↗

PubMed2000

Statistical comparison of axon-scaled neurochemical production.

Treatments designed to increase neurochemical levels may also result in increases in the numbers of axons that produce the neurochemicals of interest. A natural research question is how does one compare the average neurochemical production per axon between two (or more) experimental groups. Two statistical methods are proposed for this problem. The first method utilizes a delta-method approximation to the variance of a function of random variables while the second method is based on the bootstrap. These methods are illustrated with data obtained from perivascular norepinephrine following intracerebroventricular infusion of neurotrophin nerve growth factor in adult rats and are studied in a small simulation experiment. The delta-method confidence intervals exhibited better coverage properties than the bootstrap alternative.

Animals↗

PubMed2001

Estimating the frequency distribution of crossovers during meiosis from recombination data.

Estimation of tetrad crossover frequency distributions from genetic recombination data is a classic problem dating back to Weinstein (1936, Genetics 21, 155-199). But a number of important issues, such as how to specify the maximum number of crossovers, how to construct confidence intervals for crossover probabilities, and how to obtain correct p-values for hypothesis tests, have never been adequately addressed. In this article, we obtain some properties of the maximum likelihood estimate (MLE) for crossover probabilities that imply guidelines for choosing the maximum number of crossovers. We give these results for both normal meiosis and meiosis with nondisjunction. We also develop an accelerated EM algorithm to find the MLE more efficiently. We propose bootstrap-based methods to find confidence intervals and p-values and conduct simulation studies to check the validity of the bootstrap approach.

Algorithms↗

PubMed2003

Estimation of false discovery rates in multiple testing: application to gene microarray data.

Testing for significance with gene expression data from DNA microarray experiments involves simultaneous comparisons of hundreds or thousands of genes. If R denotes the number of rejections (declared significant genes) and V denotes the number of false rejections, then V/R, if R > 0, is the proportion of false rejected hypotheses. This paper proposes a model for the distribution of the number of rejections and the conditional distribution of V given R, V / R. Under the independence assumption, the distribution of R is a convolution of two binomials and the distribution of V / R has a noncentral hypergeometric distribution. Under an equicorrelated model, the distributions are more complex and are also derived. Five false discovery rate probability error measures are considered: FDR = E(V/R), pFDR = E(V/R / R > 0) (positive FDR), cFDR = E(V/R / R = r) (conditional FDR), mFDR = E(V)/E(R) (marginal FDR), and eFDR = E(V)/r (empirical FDR). The pFDR, cFDR, and mFDR are shown to be equivalent under the Bayesian framework, in which the number of true null hypotheses is modeled as a random variable. We present a parametric and a bootstrap procedure to estimate the FDRs. Monte Carlo simulations were conducted to evaluate the performance of these two methods. The bootstrap procedure appears to perform reasonably well, even when the alternative hypotheses are correlated (rho = .25). An example from a toxicogenomic microarray experiment is presented for illustration.

Bayes Theorem↗

PubMed2004

Testing for marginal independence between two categorical variables with multiple responses.

Questions that ask respondents to "choose all that apply" from a set of items occur frequently in surveys. Categorical variables that summarize this type of survey data are called both pick any/c variables and multiple-response categorical variables. It is often of interest to test for independence between two categorical variables. When both categorical variables can have multiple responses, traditional Pearson chi-square tests for independence should not be used because of the within-subject dependence among responses. An intuitively constructed version of the Pearson statistic is proposed to perform the test using bootstrap procedures to approximate its sampling distribution. First- and second-order adjustments to the proposed statistic are given in order to use a chi-square distribution approximation. A Bonferroni adjustment is proposed to perform the test when the joint set of responses for individual subjects is unavailable. Simulations show that the bootstrap procedures hold the correct size more consistently than the other procedures.

Algorithms↗

PubMed2005

Genetic susceptibility to prostate, breast, and colorectal cancer among Nordic twins.

To investigate the role of genetics in the development of cancer, we developed a new approach to analyze data on prostate, breast, and colorectal cancer from the Swedish, Danish, and Finnish twin registries on monozygotic (MZ) and same-sex dizygotic (DZ) twins. In the spirit of a sensitivity analysis, we modeled genetic inheritance as either an autosomal recessive or dominant cancer susceptibility (CS) genotype that involves either a single gene, many genes with equal allele frequencies, or three genes with a ninefold range of allele frequencies. We also modeled the joint probability of cancer incidence among five age categories, conditional on the presence or absence of the CS genotype. The main assumptions are: (1) The joint distribution of unobserved environmental effects in a twin pair conditional on the presence or absence of the CS genotype is the same for MZ and DZ twins, (2) the probability of cancer conditional on the presence or absence of the CS genotype and the unobserved environmental effects (i.e., the gene-environment interaction) is the same for MZ and DZ twins, and (3) the probability of cancer is independent between twins with the CS genotype. Estimation was maximum likelihood via a search over allele frequency and two levels of EM algorithms. Models had acceptable or good fits. Variability was estimated using a bootstrap approach, but only 50 replications were feasible. The 94th percentile of bootstrap replications for the estimated fraction of cancers with the CS genotype ranged, over the various genetic models, from 0.16 to 0.45 for prostate cancer, 0.12 to 0.30 for breast cancer, and 0.08 to 0.27 for colorectal cancer. We conclude that genetic susceptibility makes only a small to moderate contribution to the incidence of prostate, breast, and colorectal cancer.

Algorithms↗

PubMed2004

A likelihood-based approach to estimating and testing for isolation by distance.

Simple regression of genetic similarities between pairs of populations on their corresponding geographic distances is frequently used to detect the presence of isolation by distance (IBD). However, these pairwise values are obviously not independent and there is no parametric procedure for estimating and testing for the IBD intercepts and slopes based on standard regression theory. Nonparametric tests, such as the Mantel test, and resampling techniques, such as bootstrapping, have been exploited with limited success. Here, I describe a likelihood-based analysis to allow for simultaneously detecting patterns of correlated residuals and estimating and testing for the presence of IBD. It is shown, through the analysis of two molecular datasets in pine species, that different covariance structures of the residuals exist. More over, the likelihood ratio tests under these covariance structures are less sensitive to the presence of IBD than the Mantel test and the simple regression analysis but more sensitive than the bootstrap and jackknife samples over independent populations or population pairs. Because the likelihood analysis directly models and accounts for nonindependence of residuals, it should legitimately detect the presence of IBD, thereby allowing for accurate inferences about evolutionary and demographic processes influencing the extent and patterns of IBD.

Analysis of Variance↗

PubMed2004

Population structure of Salmonella investigated by amplified fragment length polymorphism.

AIMS: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. METHODS AND RESULTS: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal whereas others are highly divergent. CONCLUSIONS: AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme electrophoresis (MLEE) and sequence-based studies of the population structure in Salmonella. SIGNIFICANCE AND IMPACT OF THE STUDY: AFLP with the enzyme combination BglII and BspDI allows discrimination of individual strains and provides evidence for the usefulness of AFLP in studies of population structure in Salmonella.

Base Sequence↗

PubMed2006

A comparison of multivariable regression models to analyse cost data.

RATIONALE, AIMS AND OBJECTIVES: Analysis of cost data is important in providing reliable information to aid budgeting decisions. Certain features of cost data, such as its typically highly skewed distribution and the need to estimate arithmetic mean costs in order to allow inferences to be made on total costs, make it difficult to analyse. Multivariable regression analysis is useful for estimating the influence of explanatory variables on cost in order to predict costs of future patients and allows for the control of variables which influence cost but whose distributions differ between comparison groups. This is especially important in the case of observational studies, where there may be no control over the balance of characteristics between the comparison groups. METHOD: This paper compares the appropriateness of various multivariable models of cost data by examining regression diagnostics, using as an example data collected on costs incurred in the treatment of inflammatory bowel disease. The models compared are normal and bootstrapped multiple linear regression, median regression, gamma model with the log link and normal linear regression (NLR) of log costs. RESULTS: Gamma modelling with the log link was found to be the most suitable model. CONCLUSIONS: Bootstrapping was found to make very little difference to conclusions from the NLR model.

Health Care Costs↗

PubMed2005

Investigation of Japanese quail (Coturnix japonica) as a pharmacokinetic model for cockatiels (Nymphicus hollandicus) and Poicephalus parrots via comparison of the pharmacokinetics of a single intravenous injection of oxytetracycline hydrochloride.

The purpose of this study was to determine whether Japanese quail (Coturnix japonica) would serve as a pharmacokinetic animal model for two small companion parrots: cockatiels (Nymphicus hollandicus) and Poicephalus parrots. Oxytetracycline (OTC) was the pharmacologic agent chosen for this study as it is eliminated primarily by renal glomerular filtration and undergoes minimal metabolism. A single intravenous injection of 20 mg/kg oxytetracycline hydrochloride was administered to the three study groups and blood samples were obtained at 5, 10, 15, and 30 min post-OTC injection as well as 1, 2, 4, 8, 12 and 24 h post-OTC injection. Quantification of plasma OTC was accomplished using a standardized microbial inhibition assay. Naïve-pooled data (NPD) analysis of the plasma concentration-time profile of OTC best fit a two-compartment open model for all three avian species. Noncompartmental analysis of the mean data yielded the following parameters for quail, cockatiels and Poicephalus parrots respectively: lambda(z) = 3.14, 4.57, 3.71 h; AUC = 38.9, 42.7, 49.6 microg x h/mL; and Cl = 514, 468, 403 mL/h/kg. Based on the similarity of these pharmacokinetic parameters, it appears that quail could be used as a model species to predict the appropriate OTC dosing regimen for small psittacine birds. A bootstrap procedure was also applied to these sparse data sets for both compartmental and noncompartmental analysis. The bootstrap procedure allowed for the calculation of variability of parameters; however, the estimates of the parameters were very similar to those calculated using the NPD and the data mean values.

Animals↗