33 resultados para python django bootstrap


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A range of organohalogen compounds (10 polychlorinated biphenyl [PCB] congeners, DDT and metabolites, chlordane-related compounds, the potential natural organochlorine compound Q1, toxaphene, hexachlorobenzene, hexachlorocyclohexanes, dieldrin, and several yet unidentified brominated compounds) were detected in the blubber of four bottlenose dolphins (Tursiops truncatus), one common dolphin (Delphinus delphis), and seven dugongs (Dugong dugon), as well as in adipose tissue of a green turtle (Chelonia mydas) and a python (Morelia spilota) from northeast Queensland (Australia). The green turtle and dugongs accumulated lower organohalogen levels than the dolphins. Lower levels in dugongs were expected because this species is exclusively herbivorous. Highest PCB and DDT levels recorded in dugongs were 209 and 173 mug/kg lipids, respectively. Levels of the nonanthropogenic heptachlorinated compound Q1 (highest level in dugongs was 160 mug/kg lipids) were estimated using the ECD response factor of trans-nonachlor. Highest organohalogen levels were found in blubber of dolphins for sumDDT (575-52,500 mug/kg) and PCBs (600-25,500 mug/kg lipids). Furthermore, Q1 was a major organohalogen detected in all samples analyzed, ranging from 450 -9,100 mug/kg lipids. The highest concentration of Q1 determined in this study represents the highest concentration reported to date in an environmental sample. Levels of chlordane-related compounds were also high (280-7,700 mug/kg, mainly derived from trans-nonachlor), but concentrations of hexachlorobenzene, hexachlorocyclohexanes, dieldrin, and toxaphene were relatively low and contributed little to the overall organohalogen contamination. Furthermore, a series of three major (BC-1, BC-2, and BC-3) and six minor (BC-4 through BC-9) unknown brominated compounds were observable by extracting m/z 79 and m/z 81 from the GC/ECNI-MS full scan run. Structural proposals were made for the two major recalcitrant compounds (referred to as BC-1 and BC-2). BC-2 appears to be a tetrabromo-methoxy-diphenylether (512 u) and BC-1 has 14 u (corresponding with an additional CH2 group) more relative to BC-1. In general the organohalogen pattern observed in blubber of dolphins was different compared to similar samples from other locations in the world, which is apparent from the fact that the four major abundant signals in the GC/ECD chromatogram. of D. delphis originated from the four unknown compounds Q1, BC-1, BC-2, and BC-3.

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Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

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Most of the modem developments with classification trees are aimed at improving their predictive capacity. This article considers a curiously neglected aspect of classification trees, namely the reliability of predictions that come from a given classification tree. In the sense that a node of a tree represents a point in the predictor space in the limit, the aim of this article is the development of localized assessment of the reliability of prediction rules. A classification tree may be used either to provide a probability forecast, where for each node the membership probabilities for each class constitutes the prediction, or a true classification where each new observation is predictively assigned to a unique class. Correspondingly, two types of reliability measure will be derived-namely, prediction reliability and classification reliability. We use bootstrapping methods as the main tool to construct these measures. We also provide a suite of graphical displays by which they may be easily appreciated. In addition to providing some estimate of the reliability of specific forecasts of each type, these measures can also be used to guide future data collection to improve the effectiveness of the tree model. The motivating example we give has a binary response, namely the presence or absence of a species of Eucalypt, Eucalyptus cloeziana, at a given sampling location in response to a suite of environmental covariates, (although the methods are not restricted to binary response data).

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Background: Reliability or validity studies are important for the evaluation of measurement error in dietary assessment methods. An approach to validation known as the method of triads uses triangulation techniques to calculate the validity coefficient of a food-frequency questionnaire (FFQ). Objective: To assess the validity of an FFQ estimates of carotenoid and vitamin E intake against serum biomarker measurements and weighed food records (WFRs), by applying the method of triads. Design: The study population was a sub-sample of adult participants in a randomised controlled trial of beta-carotene and sunscreen in the prevention of skin cancer. Dietary intake was assessed by a self-administered FFQ and a WFR. Nonfasting blood samples were collected and plasma analysed for five carotenoids (alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein, lycopene) and vitamin E. Correlation coefficients were calculated between each of the dietary methods and the validity coefficient was calculated using the method of triads. The 95% confidence intervals for the validity coefficients were estimated using bootstrap sampling. Results: The validity coefficients of the FFQ were highest for alpha-carotene (0.85) and lycopene (0.62), followed by beta- carotene (0.55) and total carotenoids (0.55), while the lowest validity coefficient was for lutein (0.19). The method of triads could not be used for b- cryptoxanthin and vitamin E, as one of the three underlying correlations was negative. Conclusions: Results were similar to other studies of validity using biomarkers and the method of triads. For many dietary factors, the upper limit of the validity coefficients was less than 0.5 and therefore only strong relationships between dietary exposure and disease will be detected.

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An investigation was conducted to evaluate the impact of experimental designs and spatial analyses (single-trial models) of the response to selection for grain yield in the northern grains region of Australia (Queensland and northern New South Wales). Two sets of multi-environment experiments were considered. One set, based on 33 trials conducted from 1994 to 1996, was used to represent the testing system of the wheat breeding program and is referred to as the multi-environment trial (MET). The second set, based on 47 trials conducted from 1986 to 1993, sampled a more diverse set of years and management regimes and was used to represent the target population of environments (TPE). There were 18 genotypes in common between the MET and TPE sets of trials. From indirect selection theory, the phenotypic correlation coefficient between the MET and TPE single-trial adjusted genotype means [r(p(MT))] was used to determine the effect of the single-trial model on the expected indirect response to selection for grain yield in the TPE based on selection in the MET. Five single-trial models were considered: randomised complete block (RCB), incomplete block (IB), spatial analysis (SS), spatial analysis with a measurement error (SSM) and a combination of spatial analysis and experimental design information to identify the preferred (PF) model. Bootstrap-resampling methodology was used to construct multiple MET data sets, ranging in size from 2 to 20 environments per MET sample. The size and environmental composition of the MET and the single-trial model influenced the r(p(MT)). On average, the PF model resulted in a higher r(p(MT)) than the IB, SS and SSM models, which were in turn superior to the RCB model for MET sizes based on fewer than ten environments. For METs based on ten or more environments, the r(p(MT)) was similar for all single-trial models.

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The bispectrum and third-order moment can be viewed as equivalent tools for testing for the presence of nonlinearity in stationary time series. This is because the bispectrum is the Fourier transform of the third-order moment. An advantage of the bispectrum is that its estimator comprises terms that are asymptotically independent at distinct bifrequencies under the null hypothesis of linearity. An advantage of the third-order moment is that its values in any subset of joint lags can be used in the test, whereas when using the bispectrum the entire (or truncated) third-order moment is required to construct the Fourier transform. In this paper, we propose a test for nonlinearity based upon the estimated third-order moment. We use the phase scrambling bootstrap method to give a nonparametric estimate of the variance of our test statistic under the null hypothesis. Using a simulation study, we demonstrate that the test obtains its target significance level, with large power, when compared to an existing standard parametric test that uses the bispectrum. Further we show how the proposed test can be used to identify the source of nonlinearity due to interactions at specific frequencies. We also investigate implications for heuristic diagnosis of nonstationarity.

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The 40 life history, myological, and osteological characters that Tibbetts (1992) used in his study of the hemiramphids are evaluated for both saury genera (Cololabis and Scomberesox) to determine if the Scomberesocidae are more closely related to the Zenarchopteridae, to the needlefishes (Belonidae), or to the halfbeaks (Hemiramphidae) and flyingfishes (Exocoetidae). Data were analyzed using PAUP*, and eight equally parsimonious trees were found (70 steps, CI 0.814, RI 0.938). This analysis indicates that sauries are most closely related to needlefishes, supporting the historical concept of the superfamily Scomberesocoidea as a monophyletic assemblage. A caudal displacement of the origin of the retractor dorsalis muscle is a tentative additional synapomorphy for all four saury species. Zenarchopteridae is strongly supported as a valid family sister to the Scomberesocoidea (decay index = 19, bootstrap = 100). Resolution of the internal structure of the Belonidae and the Hemiramphidae requires the identification of additional characters and examination of a greater number of taxa.

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The nuclectide sequence for pituitary prolactin cDNA from the marsupial bandicoot (Isoodon macrourus) was determined by reverse transcription-polymerase chain reaction and 5'/3' rapid amplification of cDNA ends. The deduced amino acid sequence showed high sequence identity with brushtail possum prolactin (95%) and all of the expected structural features of a quadruped prolactin. A prolactin gene tree was constructed and rates of evolution calculated for bandicoot, possum, opossum and several mammalian and non-mammalian prolactins. Bootstrap analysis provided strong support for marsupials as a sister group with eutherian mammals and weak support for opossum and bandicoot as an independent grouping from the brushtail possum. The rates of molecular evolution for marsupial prolactins were comparable to the slow rate seen in the majority of quadruped prolactins that have been sequenced. (c) 2005 Elsevier Inc. All rights reserved.

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Determining the dimensionality of G provides an important perspective on the genetic basis of a multivariate suite of traits. Since the introduction of Fisher's geometric model, the number of genetically independent traits underlying a set of functionally related phenotypic traits has been recognized as an important factor influencing the response to selection. Here, we show how the effective dimensionality of G can be established, using a method for the determination of the dimensionality of the effect space from a multivariate general linear model introduced by AMEMIYA (1985). We compare this approach with two other available methods, factor-analytic modeling and bootstrapping, using a half-sib experiment that estimated G for eight cuticular hydrocarbons of Drosophila serrata. In our example, eight pheromone traits were shown to be adequately represented by only two underlying genetic dimensions by Amemiya's approach and factor-analytic modeling of the covariance structure at the sire level. In, contrast, bootstrapping identified four dimensions with significant genetic variance. A simulation study indicated that while the performance of Amemiya's method was more sensitive to power constraints, it performed as well or better than factor-analytic modeling in correctly identifying the original genetic dimensions at moderate to high levels of heritability. The bootstrap approach consistently overestimated the number of dimensions in all cases and performed less well than Amemiya's method at subspace recovery.

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Objective: To devise more-effective physical activity interventions, the mediating mechanisms yielding behavioral change need to be identified. The Baron-Kenny method is most commonly used. but has low statistical power and May not identify mechanisms of behavioral change in small-to-medium size Studies. More powerful statistical tests are available, Study Design and Setting: Inactive adults (N = 52) were randomized to either a print or a print-plus-telephone intervention. Walking and exercise-related social support Were assessed at baseline, after file intervention, and 4 weeks later. The Baron-Kenny and three alternative methods of mediational analysis (Freedman-Schatzkin; MacKinnon et al.: bootstrap method) were used to examine the effects of social support on initial behavior change and maintenance. Results: A significant mediational effect of social support on initial behavior change was indicated by the MacKinnon et al., bootstrap. and. marginally. Freedman-Schatzkin methods, but not by the Baron-Kenny method. No significant mediational effecl of social support on maintenance of walking was found. Conclusions: Methodologically rigorous intervention studies to identify mediators of change in physical activity are costly and labor intensive, and may not be feasible with large samples. The Use of statistically powerful tests of mediational effects in small-scale studies can inform the development of more effective interventions. (C) 2006 Elsevier Inc. All rights reserved.

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The thelastomatoid fauna of Macropanesthia rhinoceros was examined from 13 localities across its range in Queensland, Australia. Nine species of thelastomatoids, including two representing new genera, Geoscaphenema megaovum n. g., n. sp. and Jaidenema rhinoceratum n. g., n. sp., were found. Macropanesthia rhinoceros is reported as a new host for seven species previously recorded from Panesthia cribrata (Blaberidae: Panesthiinae) and P. tryoni tryoni, viz, Blattophila sphaerolaima, Leidynemella fusiformis, Cordonicola gibsoni, Travassosinema jaidenae, Coronostoma australiae, Hammerschmidtiella hochi and Desmicola ornata. Overall estimated richness for the system ranged from 10.1-13.5 species. The high degree of parasite faunal overlap between M. rhinoceros and the two Panesthia species is surprising given the disparate ecological niches that they occupy; P. cribrata and P. tryoni tryoni burrow in, and feed upon, moist decaying wood and require a climate that is moist all year round, whereas M. rhinoceros burrows in loose soil, feeds on fallen leaf litter and is tolerant of much drier environments.

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This paper elaborates the notion of balanced'' financial development that is contingent on a country's general level of development. We develop an empirical framework to address this point, referring to threshold regressions and a bootstrap test for structural shift in a growth equation. We find that countries gain less from financial activity, if the latter fails to keep up with or exceeds what would follow from a balanced expansion path. These analyses contribute to the finance and growth literature in providing empirical support for the balanced'' financial development hypothesis.

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Background and Objective: To describe the diagnostic accuracy and practical application of the Peter James Centre Falls Risk Assessment Tool (PJC-FRAT), a multidisciplinary falls risk screening and intervention deployment instrument. Methods: In phase 1, the accuracy of the PJC-FRAT was prospectively compared to a gold standard (the STRATIFY) on a cohort of subacute hospital patients (n = 122). In phase 2, the PJC-FRAT was temporally reassessed using a subsequent cohort (n = 316), with results compared to those of phase 1. Primary outcomes were falls (events), fallers (patients who fell), and hospital completion rates of the PJC-FRAT. Results: In phase 1, PJC-FRAT accuracy of identifying falters showed sensitivity of 73% (bootstrap 95% confidence interval CI = 55, 90) and specificity of 75% (95% CI = 66, 83), compared with the STRATIFY (cutoff >= 2/5) sensitivity of 77% (95% CI = 59, 92) and specificity of 51% (95% CI = 41, 61). This difference was not significant. In phase 2, accuracy of nursing staff using the PJC-FRAT was lower. PJC-FRAT completion rates varied among disciplines over both phases: nurses and physiotherapists, >= 90%; occupational therapists, >= 82%; and medical officers, >= 57%. Conclusion: The PJC-FRAT was practical and relatively accurate as a predictor of falls and a deployment instrument for falls prevention interventions, although continued staff education may be necessary to maintain its accuracy. (c) 2006 Elsevier Inc. All rights reserved.

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We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.