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PubMed2000

A small sample confidence interval approach to assess individual bioequivalence.

The concept of interchangeable pharmaceutical products has been examined in great detail in the literature. Anderson and Hauck proposed a statistical random coefficient model to study 'switchability', and coined the phrase 'individual bioequivalence' which they defined with a probability-based inequality. Since that paper there has been considerable work and discussion. The Food and Drug Administration has recommended the introduction of individual bioequivalence (IBE) and population bioequivalence (PBE) methods in a draft guidance document. The proposal in the draft guidance includes criteria for IBE and PBE and recommends the use of non-parametric bootstrap 95 per cent upper confidence intervals for the conclusion of either IBE or PBE. However, this method requires intensive computations. We have developed an alternative confidence interval procedure to assess IBE by the FDA recommended criteria. This method utilizes Howe's approximation I to a Cornish-Fisher expansion. Our proposed method is applicable to balanced or unbalanced data in a broad class of extended cross-over designs, and can be easily programmed using readily available software.

Confidence Intervals↗

PubMed2000

Use of an angular transformation for ratio estimation in cost-effectiveness analysis.

Economic evaluations of medical technologies involve a consideration of both costs and clinical benefits, and an increasing number of clinical studies include a specific objective of assessing cost-effectiveness. These studies measure the trade-off between costs and benefits using the cost-effectiveness ratio (CE ratio), which is defined as the net incremental cost per unit of benefit provided by the candidate therapy. In this paper we review the statistical methods which have been proposed for estimating 95 per cent confidence intervals for cost-effectiveness ratios. We show that the use of an angular transformation of the standardized ratio stabilizes the variance of the estimated CE ratio, and provides a clearer interpretation of study results. An estimate of the 95 per cent confidence interval for the CE ratio in the transformed scale is easily made using the jack-knife or bootstrap. The available methods are compared using data from a long term study of mortality in patients with congestive heart failure.

Angiotensin-Converting Enzyme Inhibitors↗

PubMed2000

A multi-state model for evolution of intensive care unit patients: prediction of nosocomial infections and deaths.

Nosocomial (hospital-acquired) infections are very frequent in intensive care units (ICU). The risk of death after severe infection is high, but the precise rate of death in ICU attributable to nosocomial infection is not known. The goal of this project was to build a statistical model to predict the occurrence of nosocomial infections in ICU and the outcome of the patients. We collected data on 676 consecutive patients admitted to an ICU for more than 24 hours between 1993 and 1996. The following data were collected for each patient: history; clinical examination at entry; subsequent infections; outcome. A multi-state heterogeneous semi-Markov model was determined and then validated; the initial data set was randomly split into two groups: two-thirds (450 patients) to build the model and one-third (226 patients) to validate it. The model defined five states: ICU admission; first simple infection; first complicated infection; death, and discharge from the ICU. Transitions between these states determined nine different events. The global model of patient histories can be divided into nine survival models, each corresponding to one of these events. The possible events from a given state were considered to be competing. Since many risk factors induced non-proportional hazard functions, piecewise exponential models were used to model event occurrence. The effect of continuous covariates on hazard functions has been described with a non-parametric method that enables non-linear relations to be shown. Among other things, the model allows patients' post-admission histories to be predicted from data available at ICU admission. The bootstrap estimator of the attributable risk of death due to simple or complicated nosocomial infections is 44.2 percent (95 percent CI 26.0-61.6 percent). We were also able to characterize the most highly exposed patients, those who comprise the high-risk group on whom prevention efforts must be focused.

Cross Infection↗

PubMed2001

Non-parametric estimates of overlap.

Kernel densities provide accurate non-parametric estimates of the overlapping coefficient or the proportion of similar responses (PSR) in two populations. Non-parametric estimates avoid strong assumptions on the shape of the populations, such as normality or equal variance, and possess sampling variation approaching that of parametric estimates. We obtain accurate standard error estimates by bootstrap resampling. We illustrate the practical use of these methods in two examples and use simulations to explore the properties of the estimators under various sampling situations.

Acetates↗

PubMed2001

Regression splines for threshold selection in survival data analysis.

The Cox proportional hazards model restricts the hazard ratio to be linear in the covariates. A survival model based on data from a clinical trial is developed using spline functions with variable knots to estimate the log hazard function. Moreover, the main point of the method is that a knot, seen as free parameters for a piecewise linear spline, represents a break point in the log hazard function which may be interpreted as a threshold value. The likelihood ratio test is used to select the final model and to determine the threshold number for a covariate. Confidence intervals for these threshold values are computed by bootstrapping the data. Two examples illustrate the method.

Carcinoma, Small Cell↗

PubMed2000

Analysis of longitudinal data from twins.

Longitudinal data from twin pairs may be used to determine how the genetic effects influencing a quantitative trait change with age. Here a model for mixed longitudinal data of Huggins and Loesch [1998] on unrelated individuals is extended to twin studies. The model is fitted using robust statistical methods and a bootstrap procedure is proposed to estimate the percentiles. The method is applied to longitudinal twin data on body mass index in male and female twin pairs aged 5-18 years.

Adolescent↗

PubMed2000

Characterization and evolutionary relevance of the sperm nuclear basic proteins from stickleback fish.

We have characterized the sperm nuclear basic proteins (SNBPs) of the sticklebacks in the suborder Gasterosteoidei. The complete amino acid sequence of the protamines from Aulorhynchus flavidus, Pungitius pungitius, Gasterosteus aculeatus, (anadromous) and G. wheatlandi, as well as the sequences of the protamines of several species pairs of freshwater G. aculeatus, have been determined. Analysis of the primary structure of these proteins has shown that: a) despite the relatively low amino acid complexity and small molecular mass of these basic proteins, they are very good molecular markers at the generic level. The bootstrap parsimony analysis using their sequences provides a phylogenetic relationship for the old anadromous species of Gasterosteoidei which is identical to that obtained from morphological and behavioral analysis; b) the comparison of the sequences also suggests that protamines from the suborder Gasterosteoidei have most likely evolved from a common gene in the early Acanthopterygii by an extension of the carboxy terminal portion of the molecule; c) protamines are not good markers for recent postglacial freshwater isolates of G. aculeatus. However, in the unique case of Enos Lake (British Columbia), we have been able to detect an additional minor protamine component in the benthic forms of G. aculeatus that is not present in the limnetic forms. Thus, this new protamine must have appeared during the past 12,000 years concomitantly with the speciation of benthics and limnetics in this lake.

Amino Acid Sequence↗

PubMed2001

Traditional Framingham risk factors fail to fully account for accelerated atherosclerosis in systemic lupus erythematosus.

OBJECTIVE: The frequency of coronary heart disease (CHD) and stroke are increased in systemic lupus erythematosus (SLE), but the extent of the increase is uncertain. We sought to determine to what extent the increase could not be explained by common risk factors. METHODS: The participants at two SLE registries were assessed retrospectively for the baseline level of the Framingham study risk factors and for the presence of vascular outcomes: nonfatal myocardial infarction (MI), death due to CHD, overall CHD (nonfatal MI, death due to CHD, angina pectoris, and congestive heart failure due to CHD), and stroke. For each patient, the probability of the given outcome was estimated based on the individual's risk profile and the Framingham multiple logistic regression model, corrected for observed followup. Ninety-five percent confidence intervals (95% CIs) were estimated by bootstrap techniques. RESULTS: Of 296 SLE patients, 33 with a vascular event prior to baseline were excluded. Of the 263 remaining patients, 34 had CHD events (17 nonfatal MIs, 12 CHD deaths) and 16 had strokes over a mean followup period of 8.6 years. After controlling for common risk factors at baseline, the increase in relative risk for these outcomes was 10.1 for nonfatal MI (95% CI 5.8-15.6), 17.0 for death due to CHD (95% CI 8.1-29.7), 7.5 for overall CHD (95% CI 5.1-10.4), and 7.9 for stroke (95% CI 4.0-13.6). CONCLUSION: There is a substantial and statistically significant increase in CHD and stroke in SLE that cannot be fully explained by traditional Framingham risk factors alone.

Adolescent↗

PubMed2005

Diagnostic model for sensitization in workers exposed to occupational high molecular weight allergens.

BACKGROUND: Occupational allergy has great impact on workers exposed to high molecular weight (HMW) allergens. The present study is aimed to develop and validate a generic diagnostic model for sensitization to HMW allergens, defined as positive IgE. METHODS: The model was developed in pooled data from Dutch laboratory animal (LA) workers and bakers using logistic regression analysis. Validity was assessed internally by bootstrapping procedure, and externally in British LA workers. RESULTS: The model included working hours/week, work-related symptoms, total IgE, and IgE to common allergen. Significant interactions between the type of work and the predictors resulted in different scores for LA workers and bakers. Internal and external validation showed that the model was satisfactorily calibrated and discriminated between workers at high and low risk of being sensitized. CONCLUSIONS: It is possible to develop a generic model for sensitization to occupational HMW allergens. However, the weighing of predictors differs across specific work environments.

Adult↗

PubMed1994

Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequences.

A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 tree [Gyllensten and Erlich, Hum Immunol 36:1-10, 1989]. Thus 3' DQA1 intron 1 and exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource.

Algorithms↗

PubMed2007

Call diversity of wild male orangutans: a phylogenetic approach.

Over the past 20 years several studies have attempted to clarify orangutan systematics based on DNA sequences and karyological and morphological data; however, the systematic and phylogenetic relationships among orangutan taxa remain controversial. Surprisingly, few systematic studies have used data from wild-living orangutans of exactly known provenance. Furthermore, most of these studies pooled data from huge geographic areas in their analyses, thus ignoring possibly distinct subpopulations. This study represents a new approach to orangutan systematics that uses orangutan long calls. Long calls are species-specific vocalizations used by many nonhuman primates, and data on their acoustical and temporal structures have been used to assess the relationships among, and phylogenies of, several primate taxa. Altogether, 78 long calls from wild-living orangutans from five populations in Borneo and five in Sumatra were included in the analyses. Aside from the chiefly paraphyletic topology of cladistic results, which neither support nor reject a Borneo-Sumatra dichotomy, bootstrap values support three monophyletic clades (northwest Borneo, northeast-east Borneo, and Ketambe) that corroborate geographic groups. The shortest trees and multivariate analyses provide some support for a closer relationship between Sumatran and specific Bornean demes than between particular Bornean demes themselves, indicating that conservation management should be based on orangutans from different populations rather than on just the two island-specific groups.

Animals↗

PubMed2001

Testing the taxonomic integrity of Paranthropus boisei sensu stricto.

The craniodental hypodigm of Paranthropus boisei sensu stricto is morphologically distinctive, but it has been suggested that the substantial variation in mandibular and dental size in that hypodigm may exceed that which is reasonable to subsume within a single hominin species. In this study, Fligner and Killeen, coefficient of variation (CV)-based and average taxonomic distance (ATD)-based bootstrap tests, were used to compare variation in size and shape of the mandibular corpus remains attributed to P. boisei s.s. with the variation observed in samples of great apes and modern humans. The degree of size variation in the P. boisei s.s. mandibular hypodigm is never observed in human and chimpanzee samples, is rare in gorillas, but is not uncommon in orangutans. However, the shape variation in the fossil group is comparable to the variation in the extant reference groups. Although the size variation in P. boisei s.s. is substantial, it is exaggerated by the effects of taphonomy. The small mandibles are more often abraded, whereas the large mandibles are more likely to have been infiltrated with matrix. On the basis of the results of this investigation of the mandibular corpus, there are no grounds for rejecting the "single-species" hypothesis for P. boisei s.s. When Sokal and Braumann's adjusted CV values were used to predict the index of sexual dimorphism (ISD) for the P. boisei s.s., despite the substantial geological time embraced by the mandibular corpus hypodigm, the predicted value of lnISD, when corrected for taphonomic factors, is comparable to the sexual dimorphism observed within Gorilla.

Animals↗

PubMed1992

Effects of fronto-occipital artificial cranial vault modification on the cranial base and face.

Artificial reshaping of the cranial vault has been practiced by many human groups and provides a natural experiment in which the relationships of neurocranial, cranial base, and facial growth can be investigated. We test the hypothesis that fronto-occipital artificial reshaping of the neurocranial vault results in specific changes in the cranial base and face. Fronto-occipital reshaping results from the application of pads or a cradle board which constrains cranial vault growth, limiting growth between the frontal and occipital and allowing compensatory growth of the parietals in a mediolateral direction. Two skeletal series including both normal and artificially modified crania are analyzed, a prehistoric Peruvian Ancon sample (47 normal, 64 modified crania) and a Songish Indian sample from British Columbia (6 normal, 4 modified). Three-dimensional coordinates of 53 landmarks were measured with a diagraph and used to form 9 finite elements as a prelude to finite element scaling analysis. Finite element scaling was used to compare average normal and modified crania and the results were evaluated for statistical significance using a bootstrap test. Fronto-occipitally reshaped Ancon crania are significantly different from normal in the vault, cranial base, and face. The vault is compressed along an anterior-superior to posterior-inferior axis and expanded along a mediolateral axis in modified individuals. The cranial base is wider and shallower in the modified crania and the face is foreshortened and wider with the anterior orbital rim moving inferior and posterior towards the cranial base. The Songish crania display a different modification of the vault and face, indicating that important differences may exist in the morphological effects of fronto-occipital reshaping from one group to another.

British Columbia↗

PubMed1993

Effects of annular cranial vault modification on the cranial base and face.

Artificial modification of the cranial vault was practiced by a number of prehistoric and protohistoric populations, frequently during an infant's first year of life. We test the hypothesis that, in addition to its direct effects on the cranial vault, annular cranial vault modification has a significant indirect effect on cranial base and facial morphology. Two skeletal series from the Pacific Northwest Coast, which include both nonmodified and modified crania, were used: the Kwakiutl (62 nonmodified, 45 modified) and Nootka (28 nonmodified, 20 modified). Three-dimensional coordinates of 53 landmarks were obtained using a diagraph, and 36 landmarks were used to define nine finite elements in the cranial vault, cranial base, and face. Finite element scaling was used to compare average nonmodified and average modified crania, and the significance of the results were evaluated using a bootstrap test. Annular modification of the cranial vault produces significant effects on the morphology of the cranial base and face. Annular modification in the Kwakiutl resulted in restrictions of the cranial vault in the medial-lateral and superior-inferior dimensions and an increase in anterior-posterior growth. Similar dimensional changes are observed in the cranial base. The Kwakiutl face is increased anterior-posteriorly and reduced anterior-laterally to posterior-medially. Similar effects of modification are observed in the Nootka cranial vault and cranial base, though not in the face. These results demonstrate the developmental interdependence of the cranial vault, cranial base, and face.

Cephalometry↗

PubMed1995

Euclidean distance matrix analysis: confidence intervals for form and growth differences.

Analysis of biological forms using landmark data has received substantial attention recently. Much of the statistical work in this area has concentrated on the estimation of average form, average form difference, and average growth difference. From the statistical, as well as the scientific point of view, it is important that any estimate of a scientifically relevant quantity be accompanied by a statement regarding its accuracy. Such a statement is contained in a confidence interval. The purpose of this paper is to provide a method to obtain confidence intervals for form difference and growth difference estimators. The estimators are based on Euclidean distance matrix analysis. The confidence intervals are calculated using the model independent bootstrap method. We illustrate the method by using three examples: morphological differences between samples of craniofacial patients and normal controls using two dimensional data from head X-rays, sexual dimorphism of craniofacial morphology in Cebus apella, and sexual dimorphism of facial growth in Cebus apella using three-dimensional data.

Animals↗

PubMed1995

Asymmetric vault modification in Hopi crania.

Cradleboarding was practiced by numerous prehistoric and historic populations, including the Hopi. In this group, one result of cradleboarding was bilateral or asymmetric flattening of the posterior occipital. We test whether cradleboarding had significant effects on the morphology of the cranial vault, cranial base, and face. Additionally, we examine associations between direction of flattening and asymmetric craniofacial growth. A skeletal sample of Hopi from the Old Walpi site includes both nonmodified (N = 43) and modified individuals (N = 39). Three-dimensional coordinates of 53 landmarks were obtained using a diagraph. Thirty-six landmarks were used to define nine finite elements in the cranial vault, cranial base, and face. Finite element scaling was used to compare average nonmodified individuals, with averages of bilaterally, right, and left modified individuals. The significance of variation among "treatment" groups was evaluated using a bootstrap test. Pearson product-moment correlations test the association of asymmetry with direction of modification. Hopi cradleboarding has a significant effect on growth of the cranial vault, but does not affect morphology of the cranial base or face. Bilateral flattening of the cranial vault leads to decreased length and increased width of the cranial vault. Flattening of the right or left cranial vault results in ipsilaterally decreased length and width coupled with a corresponding increased length and width on the contralateral side of the cranial vault. There is a significant correlation of size asymmetry with direction of modification in the cranial vault, but not with size or shape change in the cranial base or face.

Adult↗

PubMed2005

Dispersion dimorphism in human populations.

The aim of this paper is to verify the existence of dispersion (or variability) dimorphism in several anthropometric traits, i.e., some skeletal, muscular, and adipose dimensions, and to provide an evaluation of this scarcely considered aspect of sex differences. This research focuses on two human samples from two different European regions, Sardinia (Italy) and the Basque Country (Spain). Twenty-three anthropometric measurements were taken. A first qualitative analysis was carried out comparing the profiles of the coefficients of variation of each variable in both sexes. Secondly, the equality of variability was verified with different tests. In the normal case, Student's t-test, as proposed by Sokal and Braumann ([1980] Syst. Zool. 29:50-63), was applied. In the more general case, it was necessary to resort to resampling techniques. A suitable bootstrap test was constructed and the results were compared, when possible, with those obtained by other methods. The measurements showed parallel trends in the two populations. In particular, subcutaneous skinfolds showed significant dispersion dimorphism, with the greatest coefficients of variation in men. We suggest that this result was linked to stronger canalization in female dimensions related to the reproductive function and influenced by sociocultural factors. We also suggest defining dispersion dimorphism, whose existence is confirmed by the results presented in this paper, as a descriptive pattern of phenotype variability in both sexes that can be specific of a given class of anthropometric traits.

Anthropometry↗

PubMed2005

Three-dimensional analysis of mandibular morphology in Otolemur.

Euclidean distance matrix analysis (EDMA) of three-dimensional data is used here to examine mandibular morphology between two species of galagos. Otolemur crassicaudatus consumes primarily exudates, while O. garnettii is more frugivorous. Acquisition of exudates involves either gouging or scraping tree bark, and may involve different forces at the mandible than incising fruits. Previous studies of mandibular morphology in exudate-feeding primates produced mixed results, some suggesting that morphological specializations reflect adaptations for greater force at the anterior dentition, while others suggest specializations for producing a large gape. This study addresses these controversies by testing predictions associated with O. crassicaudatus generating greater force at the anterior dentition or producing a larger gape relative to O. garnettii. In addition, this study tests predictions associated with specializations of the anterior dentition in O. crassicaudatus as related to exudate-feeding. Crania and mandibles from 28 O. crassicaudatus and 17 O. garnettii were digitized in three dimensions, using 18 landmarks that summarize the shape of the jaw. Two-dimensional measurements were taken to assess incisor robusticity. All three-dimensional data were analyzed using EDMA, and bootstrap tests were executed to identify specific interlandmark differences that were driving any significant (P < 0.05) overall shape differences. Two-dimensional data were analyzed using Student's t-test for independent measures. Results revealed that there was a significant shape difference in mandibles between species, and that mandibles of O. crassicaudatus showed higher condyles, longer mandibles, decreased incisor procumbency, and greater incisor robusticity relative to O. garnettii. It is suggested that the results of the present study reflect adaptations for scraping in O. crassicaudatus rather than gouging.

Animals↗