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PubMed2000

Interpreting colonization of the Calathus (Coleoptera: Carabidae) on the Canary Islands and Madeira through the application of the parametric bootstrap.

The Canary Islands have proven to be an interesting archipelago for the phylogeographic study of colonization and diversification with a number of recent studies reporting evolutionary patterns and processes across a diversity of floral and faunal groups. The Canary Islands differ from the Hawaiian and Galapagos Islands by their close proximity to a continental land mass, being 110 km from the northwestern coast of Africa. This close proximity to a continent obviously increases the potential for colonization, and it can be expected that at the level of the genus some groups will be the result of more than one colonization. In this study we investigate the phylogeography of a group of carabid beetles from the genus Calathus on the Canary Islands and Madeira, located 450 km to the north of the Canaries and 650 km from the continent. The Calathus are well represented on these islands with a total of 29 species, and on the continent there are many more. Mitochondrial cytochrome oxidase I and II sequence data has been used to identify the phylogenetic relationships among the island species and a selection of continental species. Specific hypotheses of monophyly for the island fauna are tested with parametric bootstrap analysis. Data suggest that the Canary Islands have been colonized three times and Madeira twice. Four of these colonizations are of continental origin, but it is possible that one Madeiran clade may be monophyletic with a Canarian clade. The Calathus faunas of Tenerife and Madeira are recent in origin, similar to patterns previously reported for La Gomera, El Hierro, and Gran Canaria.

Animals↗

PubMed1994

Cell genealogies in a plant meristem deduced with the aid of a 'bootstrap' L-system.

The primary root meristem of maize (Zea mays L.) contains longitudinal files of cells arranged in groups of familial descent (sisters, cousins, etc.). These groups, or packets, show ordered sequences of cell division which are transverse with respect to the apico-basal axis of the root. The sequences have been analysed in three zones of the meristem during the course of the first four cell generations following germination. In this period, the number of cells in the packets increases from one to 16. Theoretically, there are 48 possible division pathways that lead to the eight-cell stage, and nearly 2 x 10(6) that lead to the 16-cell stage. However, analysis shows that only a few of all the possible pathways are used in any particular zone of the root. This restriction of pathways results from inherited sequences of asymmetric cell divisions which lead to sister cells of unequal length. All possible division pathways can be generated by deterministic 'bootstrap' L-systems which assign different lifespans to sister cells of successive generations and hence specify their subsequent sequence of divisions. These systems simulate propagating patterns of cell divisions which agree with those actually found within the growing packets that comprise the root meristem. The patterns of division are specific to cells originating in various regions of the meristem of the germinating root. The importance of such systems is that they simulate patterns of cellular proliferation where there is ancestral dependency. They can therefore be applied in other growing and proliferating systems where this is suspected.

Algorithms↗

PubMed1994

Bootstrapping in human genetic linkage.

Linkage analysis of discrete Mendelian traits has made a major contribution to the mapping of the human genome. However, in more complex situations, particularly Mendelian disorders showing locus heterogeneity, linkage results have sometimes been misleading. The bootstrap confidence interval provides an assessment of the goodness of fit of the data to the genetic model and the presence of heterogeneity can inflate the confidence interval indicating that the fit is poor. The loss in statistical power and the potential unreliability of linkage analyses based on small samples or subsamples of pedigree material is explored and illustrated by using simulated data and also real data on 37 families affected by the heterogeneous disorder, tuberous sclerosis.

Chromosome Mapping↗

PubMedDate not supplied

Bootstrap sensitometry for nuclear medicine.

A full radioscintigraphic monitor/film system sensitometric curve has been obtained utilizing a bootstrap technique in which individual characteristic curve segments, obtained from stepwedge-graded exposures, are tied together at the point of overlap. Curve segments were first smoothed by employing the linearized form of the logistic distribution function. This function allows calculation of gradient-exposure and gradient-density relations for the full characteristic curve.

Humans↗

PubMed1994

Do infants perceive word boundaries? An empirical study of the bootstrapping of lexical acquisition.

Babies, like adults, hear mostly continuous speech. Unlike adults, however, they are not acquainted with the words that constitute the utterances; yet in order to construct representations for words, they have to retrieve them from the speech wave. Given the apparent lack of obvious cues to word boundaries (such as pauses between words), this is not a trivial problem. Among the several mechanisms that could be explored to solve this bootstrapping problem for lexical acquisition, a tentative but reasonable one posits the existence of some cues (other than silence) that signal word boundaries. In order to test this hypothesis, infants were used as informants in our experiments. It was hypothesized that if word boundary cues exist, and if infants are to use them in the course of language acquisition, then they should at least perceive these cues. As a consequence, infants should be able to discriminate sequences that contain a word boundary from those that do not. A number of bisyllabic stimuli were extracted either from within French words (e.g., mati in mathématicien), or from between words (e.g., mati in panorama typique). Three-day-old infants were tested with a non-nutritive sucking paradigm, and the results of two experiments suggest that infants can discriminate between items that contain a word boundary and items that do not. It is therefore conceivable that newborns are already sensitive to cues that correlate with word boundaries. This result lends plausibility to the hypothesis that infants might use word boundary cues during lexical acquisition.

Arousal↗

PubMed2001

Bootstrap statistics of ECASS II data: just another post hoc analysis of a negative stroke trial?

UNLABELLED: The results of the Second European-Australasian Acute Stroke Study (ECASS II) were negative with respect to the primary endpoint. This post hoc analysis of ECASS II data was designed to make the least number of a priori assumptions. This is accomplished by a bootstrap-based hypothesis test on a non-parametric test statistic. No assumptions are made on shape or variance of population distributions and the method does not suffer from the disadvantages of dichotomization. By reducing the number of a priori assumptions, the possibilities to modify the test result by adjusting the test procedure are minimized. RESULTS: If rt-PA does not improve the outcome (null hypothesis), the probability of observing a difference of modified ranking scale equal or larger than the one observed in ECASS II is 0.047. We therefore rejected the null hypothesis.

Controlled Clinical Trials as Topic↗

PubMed2000

Bootstrapping neural networks.

Knowledge about the distribution of a statistical estimator is important for various purposes, such as the construction of confidence intervals for model parameters or the determination of critical values of tests. A widely used method to estimate this distribution is the so-called boot-strap, which is based on an imitation of the probabilistic structure of the data-generating process on the basis of the information provided by a given set of random observations. In this article we investigate this classical method in the context of artificial neural networks used for estimating a mapping from input to output space. We establish consistency results for bootstrap estimates of the distribution of parameter estimates.

Artifacts↗

PubMedDate not supplied

Learning from and about others: towards using imitation to bootstrap the social understanding of others by robots.

We want to build robots capable of rich social interactions with humans, including natural communication and cooperation. This work explores how imitation as a social learning and teaching process may be applied to building socially intelligent robots, and summarizes our progress toward building a robot capable of learning how to imitate facial expressions from simple imitative games played with a human, using biologically inspired mechanisms. It is possible for the robot to bootstrap from this imitative ability to infer the affective reaction of the human with whom it interacts and then use this affective assessment to guide its subsequent behavior. Our approach is heavily influenced by the ways human infants learn to communicate with their caregivers and come to understand the actions and expressive behavior of others in intentional and motivational terms. Specifically, our approach is guided by the hypothesis that imitative interactions between infant and caregiver, starting with facial mimicry, are a significant stepping-stone to developing appropriate social behavior, to predicting others' actions, and ultimately to understanding people as social beings.

Comprehension↗

PubMed2003

Bootstrapped learning of novel objects.

Recognition of familiar objects in cluttered backgrounds is a challenging computational problem. Camouflage provides a particularly striking case, where an object is difficult to detect, recognize, and segment even when in "plain view." Current computational approaches combine low-level features with high-level models to recognize objects. But what if the object is unfamiliar? A novel camouflaged object poses a paradox: A visual system would seem to require a model of an object's shape in order to detect, recognize, and segment it when camouflaged. But, how is the visual system to build such a model of the object without easily segmentable samples? One possibility is that learning to identify and segment is opportunistic in the sense that learning of novel objects takes place only when distinctive clues permit object segmentation from background, such as when target color or motion enables segmentation on single presentations. We tested this idea and discovered that, on the contrary, human observers can learn to identify and segment a novel target shape, even when for any given training image the target object is camouflaged. Further, perfect recognition can be achieved without accurate segmentation. We call the ability to build a shape model from high-ambiguity presentations bootstrapped learning.

Animals↗

PubMedDate not supplied

The use of bootstrap resampling to assess the variability of Draize tissue scores.

The acute dermal and ocular effects of chemicals are generally assessed by performing the Draize skin and eye tests, respectively. Because the animal data obtained in these tests are also used for the development and validation of alternative methods for skin and eye irritation, it is important to assess the inherent variability of the animal data, since this variability places an upper limit on the predictive performance that can be expected of any alternative model. The statistical method of bootstrap resampling was used to estimate the variability arising from the use of different animals and time-points, and the estimates of variability were used to determine the maximal extent to which Draize test tissue scores can be predicted.

Animal Testing Alternatives↗

PubMed2006

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach.

BACKGROUND: Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. RESULTS: Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions and transpositions. We found that adjacent chloroplast genes in C. reinhardtii were located on the same strand much more frequently than in simulated genomes that were generated under a random rearrangement processes (increased sidedness; p < 0.0001). In addition, functionally related genes were found to be more clustered than those evolved under random rearrangements (p < 0.0001). We report evidence of co-transcription of neighboring genes, which may be responsible for the observed gene clusters in C. reinhardtii cpDNA. CONCLUSION: Simulations and experimental evidence suggest that both selective maintenance and directional selection for gene clusters are determinants of chloroplast gene order.

Adaptation, Physiological↗

PubMed2003

Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data.

Informative missingness of parental genotype data occurs when the genotype of a parent influences the probability of the parent's genotype data being observed. Informative missingness can occur in a number of plausible ways and can affect both the validity and power of procedures that assume the data are missing at random (MAR). We propose a bootstrap calibration of MAR procedures to account for informative missingness and apply our methodology to refine the approach implemented in the TRANSMIT program. We illustrate this approach by applying it to data on hypertensive probands and their parents who participated in the Framingham Heart Study.

Adult Children↗

PubMed2002

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

BACKGROUND: Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes. RESULTS: We adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group. CONCLUSIONS: In some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny. Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.

Journal Article↗

PubMed2005

Stability of response characteristics of a Delphi panel: application of bootstrap data expansion.

BACKGROUND: Delphi surveys with panels of experts in a particular area of interest have been widely utilized in the fields of clinical medicine, nursing practice, medical education and healthcare services. Despite this wide applicability of the Delphi methodology, there is no clear identification of what constitutes a sufficient number of Delphi survey participants to ensure stability of results. METHODS: The study analyzed the response characteristics from the first round of a Delphi survey conducted with 23 experts in healthcare quality and patient safety. The panel members had similar training and subject matter understanding of the Malcolm Baldrige Criteria for Performance Excellence in Healthcare. The raw data from the first round sampling, which usually contains the largest diversity of responses, were augmented via bootstrap sampling to obtain computer-generated results for two larger samples obtained by sampling with replacement. Response characteristics (mean, trimmed mean, standard deviation and 95% confidence intervals) for 54 survey items were compared for the responses of the 23 actual study participants and two computer-generated samples of 1000 and 2000 resampling iterations. RESULTS: The results from this study indicate that the response characteristics of a small expert panel in a well-defined knowledge area are stable in light of augmented sampling. CONCLUSION: Panels of similarly trained experts (who possess a general understanding in the field of interest) provide effective and reliable utilization of a small sample from a limited number of experts in a field of study to develop reliable criteria that inform judgment and support effective decision-making.

Consensus Statements as Topic↗

PubMed2003

Latent mixed Markov modelling of smoking transitions using Monte Carlo bootstrapping.

It has been established that measures and reports of smoking behaviours are subject to substantial measurement errors. Thus, the manifest Markov model which does not consider measurement error in observed responses may not be adequate to mathematically model changes in adolescent smoking behaviour over time. For this purpose we fit several Mixed Markov Latent Class (MMLC) models using data sets from two longitudinal panel studies--the third Waterloo Smoking Prevention study and the UWO smoking study, which have varying numbers of measurements on adolescent smoking behaviour. However, the conventional statistics used for testing goodness of fit of these models do not follow the theoretical chi-square distribution when there is data sparsity. The two data sets analysed had varying degrees of sparsity. This problem can be solved by estimating the proper distribution of fit measures using Monte Carlo bootstrap simulation. In this study, we showed that incorporating response uncertainty in smoking behaviour significantly improved the fit of a single Markov chain model. However, the single chain latent Markov model did not adequately fit the two data sets indicating that the smoking process was heterogeneous with regard to latent Markov chains. It was found that a higher percentage of students (except for never smokers) changed their smoking behaviours over time at the manifest level compared to the latent or true level. The smoking process generally accelerated with time. The students had a tendency to underreport their smoking behaviours while response uncertainty was estimated to be considerably less for the Waterloo smoking study which adopted the 'bogus pipeline' method for reducing measurement error while the UWO study did not. For the two-chain latent mixed Markov models, incorporating a 'stayer' chain to an unrestricted Markov chain led to a significant improvement in model fit for the UWO study only. For both data sets, the assumption for the existence of an independence chain did not lead to significant improvement in model fit. The unrestricted two-chain latent mixed Markov model led to a significant improvement of model fit compared to a simple latent Markov model, but this model was overparameterized when the latent transition probabilities and/or response probabilities were assumed nonstationary. For the other models, the manifest/latent transition probabilities and response probabilities (for the four-wave Waterloo study only) were tested to be nonstationary for both data sets.

Adolescent↗

PubMed2003

Tape-assisted reciprocal teaching: cognitive bootstrapping for poor decoders.

BACKGROUND: Students who have limited skills in decoding and comprehension and who lack motivation to read present difficulties for practitioners. Difficulties may be compounded when these students lack access to age-appropriate and interesting text and have lost the notion of reading as a process of obtaining meaning from print. AIMS: This research examined the effects of a modified reciprocal teaching intervention for readers with poor decoding skills and poor comprehension. Tape-assisted reciprocal teaching was used to help students with poor decoding skills develop cognitive and metacognitive strategies and improve their comprehension of high interest expository texts. METHODS: Two single-subject research design studies involving four groups of students were conducted. Study I involved one experimental group and Study II was a multiple baseline design involving three experimental groups. SAMPLE: Each experimental group comprised a heterogeneous mix of six students, three with poor decoding skills and three with adequate decoding skills, all of whom showed poor comprehension. RESULTS: As a result of the tape-assisted reciprocal teaching, the poor decoders demonstrated improved application of cognitive and metacognitive strategies and improved comprehension. These improvements were shown on both researcher-developed and standardised tests as well as on maintenance and transfer measures. The students with adequate decoding skills also showed improvements in comprehension. CONCLUSIONS: The success of the intervention for poor decoders suggests that tape assisted reciprocal teaching may be seen as a form of 'cognitive bootstrapping' to enable poor readers to escape the cycle of reading failure and engage more meaningfully in the process of reading.

Child↗

PubMed1999

Gender differences in the reliability of the EPQ? A bootstrapping approach.

Reliability indicates the degree of stability or homogeneity of a measurement, but also places an upper limit on the degree of association with other variables. Various methods are available to estimate the reliability of a measurement scale. However, an issue that has rarely been examined is that the reliability of a measurement, as estimated by coefficient alpha, may differ between groups. If a measurement has a different reliability for groups within a sample, spurious moderator effects may occur. The present study examines the reliability of the four subscales of a widely used psychological measurement instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R), across gender. A bootstrapping methodology is employed which allows empirically derived standard errors to be calculated, and therefore tests of significance of difference to be computed. No significant differences were found in the reliability of the EPQ-R across sexes.

Adult↗

PubMed2005

Estimation of the limit of detection with a bootstrap-derived standard error by a partly non-parametric approach. Application to HPLC drug assays.

A recently proposed procedure for estimating the limit of detection (LoD) of an assay using a partly non-parametric approach is applied to five HPLC drug assays. The non-parametrically determined 95th percentile of the blank measurements (LoB) is obtained as the value of the N (95/100) + 0.5 ordered observations. The LoD is the lowest level of analyte that is likely to yield a measured result exceeding the LoB. The LoD equals LoB + c(beta) x SD(S), where SD S is the analytical SD at low concentrations, and c(beta) = z(1-beta)/(1-1/(4 x f )) (f = degrees of freedom). c(beta) approximately 1.65 for a type II error of 5%. The blank distributions deviated significantly from normality for four of the five assays because of skewness to the right. The estimated LoB ranged from 3.3 to 10.2 nmol/L. The LoDs were in the interval from 7.8 to 17.2 nmol/L. A new procedure for estimation of the standard error (SE) of the estimated LoD that is partly based on the bootstrap principle showed good performance in simulation studies. In conclusion, the partly non-parametric procedure for estimation of the LoD of typical HPLC drug assays was found to be a suitable approach.

Antidepressive Agents↗