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PubMedDate not supplied

Statistical analysis for dependent dichotomous data.

The analysis of means for attributes data (ANOMAD) is used--when normal approximation applies to binomial distribution--by extending the analysis of means (ANOM) introduced by Ott and Schilling. ANOMAD compares the individual proportions or dependent percentages or set of frequencies of subjects responding to different stimuli, with the grand average of the proportions. It is interesting to see if all temporal values of some risk factors in cardiovascular diseases (CD)--acting as "stimuli"--can provide the same effect on a group of subjects by emphasizing the most important ones.

Aged↗
PubMed1997

Prediction of gene expression specificity by promoter sequence patterns.

We present here a heuristic method toward predicting the expression specificity in the transcriptional process, which is known to be regulated in large part by promoter sequences, by observing the appearance of conserved sequence patterns in a group of known promoters, such as for housekeeping or tissue-specific genes. Statistically conserved patterns were automatically extracted from a set of unaligned sequences up to 200 bp upstream of the transcription initiation site, by a standard procedure using the Markov chain and binomial distribution models. Furthermore, to obtain signal sequences of optimal lengths we devised a method that combines the multiple alignment and the analysis of the information content (or relative entropy). Groups of related promoters were compiled from the EPD eukaryotic promoter database and the EMBL nucleic acid sequence database. Each promoter was examined for its specificity by linear discriminant analysis to test the validity of the extracted patterns. Our method could correctly discriminate 77.6% of the housekeeping gene promoters and 62.9% of the liver promoters.

Algorithms↗
PubMed1999

Maximum-Likelihood-Binomial method for genetic model-free linkage analysis of quantitative traits in sibships.

Sib-pair linkage studies are widely used to investigate the genetic factors implicated in complex quantitative traits. To analyze these data, we propose a Maximum-Likelihood-Binomial (MLB) approach, which considers the sibship as a whole and relies on the idea of binomial distributions of parental alleles among offsprings. The method is based on the introduction of a latent binary variable capturing the linkage information between the observed quantitative trait and the marker, and the final likelihood can be expressed assuming a parametric distribution for the studied trait but also without any assumption on this distribution. The test for linkage is a simple likelihood ratio test involving a single parameter. The performances of the MLB method are assessed by a simulation study in different kinds of family samples. In the case of families with various sibship sizes, both MLB approaches (assuming or not a parametric distribution for the quantitative trait) provide very consistent results in terms of type I errors and yield power levels generally higher than those of the classical Haseman-Elston method. In the case of extremely discordant sib pairs, we analytically show that, for a common asymptotic type I error, the distribution-free MLB statistic is expected to be more powerful than the test proposed by Risch and Zhang [(1995) Science 268:1584-1589]. In samples including both extremely concordant and discordant sib-pairs, simulation studies show that the MLB approach is at least as powerful as the EDAC method [Gu et al. (1996) Genet Epidemiol 13:513-533]. This MLB method, which can be easily extended to perform multipoint analysis and to account for genetic heterogeneity, appears to be quite an interesting alternative for mapping quantitative trait loci in humans.

Alleles↗
PubMed2005

Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations.

A statistical modeling framework is described for estimating the abundances of spatially distinct subpopulations of animals surveyed using removal sampling. To illustrate this framework, hierarchical models are developed using the Poisson and negative-binomial distributions to model variation in abundance among subpopulations and using the beta distribution to model variation in capture probabilities. These models are fitted to the removal counts observed in a survey of a federally endangered fish species. The resulting estimates of abundance have similar or better precision than those computed using the conventional approach of analyzing the removal counts of each subpopulation separately. Extension of the hierarchical models to include spatial covariates of abundance is straightforward and may be used to identify important features of an animal's habitat or to predict the abundance of animals at unsampled locations.

Animals↗
PubMed1997

Metazoan parasites of sika deer from east Hokkaido, Japan and ecological analyses of their abomasal nematodes.

Metazoan parasites of 50 sika deer (Cervus nippon yezoensis) collected in March 1991 in the Ashoro District in east Hokkaido, Japan, were evaluated. Ten species of helminths and three species of ectoparasites were obtained. Estimated abundance of males of two species of abomasal nematodes, Spiculopteragia houdemeri and Rinadia andreevae, were positively correlated with each other, and were overdispersed; S. houdemeri followed Poisson's and R. andreevae followed a negative binomial distribution. No significant relationship was detected between the estimated abundance of males of these two nematode species and nutritional condition of the hosts. Using a general linear model, the fourth-root transformed estimated abundance of male S. houndemeri was influenced by the main effects of host sex and age. This phenomenon was attributable to the ecological and behavioral features of the deer. The low diversity of the abomasal nematode community was regarded as the result of the extinction of some species of nematodes on Hokkaido Island.

Abomasum↗
PubMed1991

Magnetic resonance imaging in minor head injury.

STUDY OBJECTIVES: To investigate the role of cranial magnetic resonance (MR) imaging in evaluating patients discharged from the emergency department after minor head injury. DESIGN: A prospective blinded cohort study. SETTING: University hospital ED. TYPE OF PARTICIPANTS: Fifty-eight patients with minor head injury who were discharged from the ED with written head injury instructions. Patients admitted to the hospital were excluded. INTERVENTIONS: Ultra-low-field cranial MR scans were performed on patients within 24 hours of discharge. Scans were read blindly by two radiologists. MEASUREMENTS AND MAIN RESULTS: Fisher's exact test was used to compare symptoms in patients with abnormal and normal MR scans. There was no significant difference in symptoms between patients with abnormal and those with normal scans (P greater than .10). The proportion of abnormal MR scans was analyzed using the binomial distribution. Six of the 58 patients (10.3%) had traumatic intracranial abnormalities (proportion, 0.103; SD, 0.04; 95% CI, 0.04-0.21). Three had cortical contusions, and three had small subdural hematomas. Two of the six patients with abnormal MR scans, both with small subdural hematomas, had normal computed tomography scans. CONCLUSION: Ten percent of patients discharged from the ED after minor head injury had abnormal ultra-low-field cranial MR scans. Additional research is needed to establish the clinical importance of this unexpected observation.

Adolescent↗
PubMed1990

Bacteremia following laser and conventional surgery in hamsters.

The CO2 laser prevents bleeding by sealing blood and lymph vessels as it vaporizes tissue. Bacteremia following oral surgery might not occur under these conditions. To test this hypothesis, a 0.2-mm-deep incision 1 cm long was made in the right buccal cheek pouch of hamsters using either laser, electrosurgery, or a scalpel. Twenty minutes later, 1 mL of blood was taken from each animal by cardiac puncture, inoculated on a blood agar medium, and incubated anaerobically for 4 days; then the colonies were counted. Using an operational definition of bacteremia as five colonies or more per plate, there were no positive results out of 18 trials (0/18) for laser surgery, 7/8 for electrosurgery, and 8/12 for scalpel surgery. Based on the Student t test using the binomial distribution, the laser produced statistically less bacteremia than the other two methods (P less than .01). Because the five-colony cutoff was arbitrary, the nonparametric Wilcoxon Rank test was also used. Colony formation from blood from the laser group was significantly less than from the electrosurgery group (P less than .01) and the scalpel group (P less than .05). The laser surgery group was not statistically different from the control (nonsurgerized) group. These results suggest that there is a considerable bacteremia following scalpel and electrosurgery, but that laser surgery produces no bacteremia.

Animals↗
PubMed2004

A mathematical model of the population dynamics of Heterakis gallinarum in turkeys (Meleagridis gallopavo).

Heterakis gallinarum is a relatively nonpathogenic organism, but it is important as the transport host for the pathogenic protozoan Histomonas meleagridis. A mathematical model was developed to describe the population dynamics of Heterakis gallinarum in a turkey flock to study its kinetics in a number of hosts. The model includes quantitative (parasite burden) and qualitative (number of hosts without mature parasite) descriptions of these dynamics. To understand the role of Heterakis as a transport host, the various elements that delay the beginning of development of the parasite population (e.g., necessary delay of larval stage, the probability of having a male and female in the same host) were taken into account. From published data, the negative binomial distribution parameter k = 0.24, which described the aggregated distribution of the Heterakis among the hosts, was calculated. The sensibility study showed that when the k parameter decreased (i.e., when the population was more aggregated), infestation increased quantitatively (mean parasite burden increased) but not qualitatively (the number of host without mature parasite increased). The model demonstrated that the population dynamics of Heterakis takes time; for instance, with an aggregated population of Heterakis at d 90, the host is mainly free of adult parasite. These results may be used in the future to test the role of Heterakis in the spread of Histomonas.

Animals↗
PubMedDate not supplied

Planning and revising the sample size for a trial.

The sample size for a trial depends on the type I and type II error rates and on the minimum relevant clinical difference, all of which are known, and on the anticipated, but unknown, value of a measure of variation for the key response. This measure is the overall response rate when the key response is binomially distributed, or the residual variance in each treatment group when the key response is continuous and normally distributed. Since the true value of the measure is unknown, it must be guessed or estimated from previous trials. We describe approaches to determine an appropriate value for it, both before the trial begins and after it has begun, for use in calculating the final sample size. These approaches differ from previously described 'internal pilot' methods in not requiring unblinding of the treatment assignments in the trial. They preserve the power and do not affect the type I error rate materially. The approaches can be applied to longitudinal studies where the rate of change over time is the response of interest, and to group sequential trials.

Algorithms↗
PubMed1990

Honey bee mortality due to tracheal mite parasitism.

We demonstrate, by truncating the expected negative binomial distribution, that the tracheal mite parasite, Acarapis woodi, causes mortality in the European honey bee, Apis mellifera, but, that this mortality can be documented only during periods of low mite densities (mites per bee). At high mite densities, this technique no longer reveals mite-induced mortality. We suggest that this paradox results from a reduction in the mortality threshold at high mite densities, concealing mortality from our truncation procedures. Longitudinal comparisons of hive and forager bee cohorts, nevertheless, suggests mortality at all levels of infestation. We propose that persistent parasitism overcomes a colony's ability to compensate for losses, leading to its sudden decline and death.

Animals↗
PubMed1996

Estimation of the number of hematopoietic precursor cells during fetal mouse development by covariance analysis.

Differentiation of hematopoietic precursor cells results in the formation of clonally related descendent cells. Using the mosaic expression of beta-galactosidase in female mouse fetuses heterozygous for an X-linked lacZ transgene, we analyzed the clonal relationship of the hematopoietic progeny. The proportion of beta-galactosidase positive cells for different T- and B-lymphoid and myeloid cell populations was determined at different stages of fetal development. We found excellent correlations of the proportion of beta-galactosidase expressing cells for all hematopoietic lineages confirming that they share a common ancestry. Therefore, it was possible to estimate the number of common precursor cells (PC) based on binomial distribution and covariance analysis of pairs of different hematopoietic cell populations. Our results obtained from hematopoietic cells at 15.5 to 18.5 days of gestation indicated the presence of 15 to 18 lymphoid and 18 to 22 myeloid/lymphoid specific precursor cells. Statistical analysis of the precursor cell numbers showed a trend of increasing numbers that was highly significant. The precursor cell number was inversely related to maturity of the cell populations analyzed; ie, the lowest number of lymphoid and lymphoid/myeloid precursors was calculated when the most mature CD3+ T-cell population was used for comparison. Determination of PC numbers can therefore be used to assess the relative maturity and developmental potential of individual cell populations.

Analysis of Variance↗
PubMed2003

Modelling the transmission dynamics of Echinococcus granulosus in sheep and cattle in Kazakhstan.

Cystic echinococcosis, caused by Echinococcus granulosus, is an emerging disease in many parts of the world and, in particular, in eastern Europe and the former Soviet Union. This paper examines the abundance and prevalence of infection of E. granulosus in cattle and sheep in Kazakhstan. Observed data are fitted to a mathematical model in order to determine if the parasite population is partly regulated by intermediate host immunity and to define parameters in the model. Such data would be useful to develop simulation models for the control of this disease. Maximum likelihood techniques were used to define the parameters and their confidence limits in the model and the negative binomial distribution was used to define the error variance in the observed data. The results indicated that there are significant variations in the infection pressure to sheep depending on their location. In particular sheep from Almaty Oblast and from central and northern Kazakhstan appeared to have a greater exposure than sheep from Jambyl or South Kazakhstan Oblasts. The infection pressure to cattle was somewhat lower in comparison. In common with other similar studies, there was no evidence of parasite-induced immunity in sheep or cattle in Kazakhstan due to natural infection. The highest abundance and prevalence were seen in the oldest age classes of animals.

Age Factors↗
PubMed2002

Zero-inflated models for regression analysis of count data: a study of growth and development.

Poisson regression is widely used in medical studies, and can be extended to negative binomial regression to allow for heterogeneity. When there is an excess number of zero counts, a useful approach is to used a mixture model with a proportion P of subjects not at risk, and a proportion of 1--P at-risk subjects who take on outcome values following a Poisson or negative binomial distribution. Covariate effects can be incorporated into both components of the models. In child assessment, fine motor development is often measured by test items that involve a process of imitation and a process of fine motor exercise. One such developmental milestone is 'building a tower of cubes'. This study analyses the impact of foetal growth and postnatal somatic growth on this milestone, operationalized as the number of cubes and measured around the age of 22 months. It is shown that the two aspects of early growth may have different implications for imitation and fine motor dexterity. The usual approach of recording and analysing the milestone as a binary outcome, such as whether the child can build a tower of three cubes, may leave out important information.

Binomial Distribution↗
PubMed2003

Unilateral temporomandibular disorder and asymmetry of occlusal contacts.

STATEMENT OF PROBLEM: The relationship between temporomandibular disorders and occlusal tooth contacts is unclear and controversial. PURPOSE: This study assessed whether unilateral temporomandibular disorders were associated with the absence of bilateral symmetry in the number of occlusal contacts. MATERIAL AND METHODS: Fifteen university dental students who had complete natural dentition and normal occlusion and exhibited unilateral signs and symptoms of temporomandibular disorders were compared to 15 age- and sex-matched healthy control subjects. All participants met specific inclusion and exclusion criteria. Occlusal contacts were recorded in the intercuspal position with wax registrations. Dental impressions were made and poured in type I stone. Contacts were classified according to location and intensity. Four experienced dentists using an established protocol made all measurements. Assessment of the reliability of the occlusal registration procedure showed a small (<4%) within-subject variability. Statistical analysis was based on the binomial distribution and nonparametric tests (P < .05). RESULTS: Subjects with unilateral temporomandibular disorders had greater bilateral difference in the number of contacts than controls. The median (95% confidence interval) difference was 3 (2 to 4) and 2 (1 to 2), respectively. In unilateral temporomandibular disorder subjects, the number of occlusal contacts was greater on the side with, rather than without, disorder (median number 20 vs. 16). The median (95% confidence interval) difference between sides with and without unilateral temporomandibular disorders was 3 (2 to 4) for all contacts and 2 (1 to 3) for contacts on the posterior teeth. CONCLUSION: Within the population of this study, a weak association was found between unilateral temporomandibular disorders and asymmetry in the number of occlusal contacts.

Adult↗
PubMed1995

Estimation of a common odds ratio under binary cluster sampling.

We present results from a simulation study for the estimation of a common odds ratio in multiple 2 x 2 tables when the data are correlated within clusters. We model the correlation of the data by the beta-binomial distribution. Through a simulation study, we compare the Mantel-Haenszel estimator with Rao and Scott's estimator in terms of their biases, observed variances, relative efficiencies of their variances and 95 per cent coverage proportions. We limit the simulation study to the case where there are the same number of subjects in each cluster and the same number of observations in each row of each stratum. When rho = 0, we recommend use of the Mantel-Haenszel estimator gamma MH with an unadjusted variance and Rao and Scott's estimator gamma RSP with a pooled design effect. In general, when rho > 0, we recommend the Mantel-Haenszel estimator gamma MH with an adjusted variance and Rao and Scott's estimator gamma RSP with a pooled design effect.

Bias↗
PubMed1992

The western fence lizard Sceloporus occidentalis: evidence of field exposure to Borrelia burgdorferi in relation to infestation by Ixodes pacificus (Acari: Ixodidae).

The role of the Western fence lizard Sceloporus occidentalis in the enzootiology of the Lyme disease spirochete Borrelia burgdorferi was evaluated in the Hopland and Ukiah areas of Mendocino County, California. In 1989, half of 74 lizards collected monthly from April to October at Hopland were infested by the immature western black-legged tick Ixodes pacificus at a mean intensity of 6.0 ticks per lizard. The prevalence of infestation of lizards by immature I. pacificus (36 of 73) at Ukiah was similar, but the mean intensity (12.9) was approximately twice as great. Overall, zero of 223 larvae and 2 (0.6%) of 330 nymphs from both sites were found to contain spirochetes by direct immunofluorescence. Larval and nymphal I. pacificus fit the negative binomial distribution in spring, and the prevalence and abundance of these stages were significantly greater in spring than in summer at both sites. Spirochetes were not visualized in thick blood films prepared from 133 lizards from both localities. Plasma antibodies against B. burgdorferi were detected in seven of 10 experimentally inoculated lizards, in five (8%) of 63 lizards from Hopland, and in 10 (14%) of 70 lizards from Ukiah. Adult lizards had a significantly greater tick burden and seropositivity rate than juvenile lizards only at Ukiah. In 1991, efforts to detect and culture spirochetes from the blood of 21 wild-caught lizards and from the tissues of 189 associated ticks that fed xenodiagnostically on them were unsuccessful.(ABSTRACT TRUNCATED AT 250 WORDS)

Age Factors↗
PubMed1997

Conserved clusters of functionally related genes in two bacterial genomes.

An approach for genome comparison, combining function classification of gene products and sequence comparison, is presented. The genomes of Haemophilus influenzae and Escherichia coli are analyzed, and all genes are classified into nine major functional classes, corresponding to important cellular processes. To study gene order relationships and genome organization in the two bacteria, we performed statistics on neighboring pairs of genes. To estimate the significance of the observations, a statistical model based on binomial distributions has been developed. Significant patterns of gene order are observed within, as well as between, the two bacterial genomes: Functionally related genes tend to be neighbors more often than do unrelated genes. Some of these groups represent well-known operons, but additional gene clusters are identified. These clusters correspond to genomic elements that have been conserved during bacterial evolution. In addition to nearest-neighbor relationships, the method is also useful to study the relative direction of transcription in genomes, which is also highly conserved between homologous gene pairs. This new approach combines the high-level description of molecular function with pair statistics that express genome organization. It is expected to complement traditional methods of sequence analysis in the study of genomic structure, function, and evolution.

Binomial Distribution↗
PubMed2005

A comparison of two approaches to assessment of speech recognition ability in single cases.

Single-case design with the randomization test (RT) has been proposed as an alternative to the binomial distribution (BD) tables of Thornton and Raffin (1978) to assess changes in speech recognition performance in individual subjects. The present study investigated whether data analyzed using both approaches would result in similar outcomes. Sixty-two adults with normal hearing were evaluated using phoneme scoring and a restricted alternating treatments design under two signal-to-noise conditions. Results revealed a significant correlation between the RT and a BD analysis using at least 50-word lists, although the BD analysis was a more sensitive measure. The absence of correlation between the RT with a BD analysis using 25-word lists challenges the common clinical practice of using reduced list size, and supports the use of phoneme scoring and other attempts to find clinically acceptable yet evidence-based solutions to overcome the conflict between time and accuracy.

Acoustic Stimulation↗