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Results for “Likelihood Functions”

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PubMed1993

The value of the forced expiratory time in the physical diagnosis of obstructive airways disease.

OBJECTIVE: To evaluate the test characteristics of the forced expiratory time (FET) in the diagnosis of obstructive airways disease. DESIGN: A cross-sectional diagnostic test study. The FET of 400 subjects was measured by a physician examiner and was compared with the criterion standard of spirometry. In a second sample of 100 subjects, the FET was measured by pairs of physician examiners to evaluate interexaminer agreement. SETTING: A pulmonary function test laboratory at a tertiary care hospital that receives referrals for preoperative evaluations, acute and chronic pulmonary disease, and occupational lung disease. SUBJECTS: A consecutive sample of patients who were referred to the pulmonary function laboratory from primary care internists, pulmonary physicians, and surgeons. INTERVENTIONS: None. MAIN OUTCOME MEASURES: The sensitivity and specificity of the FET in the diagnosis of obstructive airways disease at cutoff values ranging from 2 to 14 seconds. A receiver operating characteristic curve was used to evaluate the diagnostic performance of the FET. Likelihood ratio lines were determined using a logistic regression model adjusting for the subjects age. Interexaminer agreement was evaluated with a kappa statistic. RESULTS: Using the FET maneuver with a cutoff value of 6 seconds will correctly diagnose the greatest number of subjects with obstructive airways disease. The FET maneuver is more discriminating for subjects 60 years or older compared with younger subjects. The positive likelihood ratio for a subject aged 60 years or older with an FET of 4 to 6 seconds is 0.42 (95% confidence interval [CI], 0.24 to 0.73); of 6 to 8 seconds, 2.19 (95% CI, 1.02 to 4.80); and of greater than 8 seconds, 4.08 (95% CI, 2.54 to 6.79). The kappa statistic for interexaminer agreement is 0.70. CONCLUSIONS: The FET demonstrates moderately good performance as a diagnostic test for obstructive airways disease. The value of the test will depend on the pretest probability of disease and the clinical circumstances in which it is used.

Adult↗

PubMedDate not supplied

Assessment of the Gould-Shih procedure for sample size re-estimation.

The power of a clinical trial is partly dependent upon its sample size. With continuous data, the sample size needed to attain a desired power is a function of the within-group standard deviation. An estimate of this standard deviation can be obtained during the trial itself based upon interim data; the estimate is then used to re-estimate the sample size. Gould and Shih proposed a method, based on the EM algorithm, which they claim produces a maximum likelihood estimate of the within-group standard deviation while preserving the blind, and that the estimate is quite satisfactory. However, others have claimed that the method can produce non-unique and/or severe underestimates of the true within-group standard deviation. Here the method is thoroughly examined to resolve the conflicting claims and, via simulation, to assess its validity and the properties of its estimates. The results show that the apparent non-uniqueness of the method's estimate is due to an apparently innocuous alteration that Gould and Shih made to the EM algorithm. When this alteration is removed, the method is valid in that it produces the maximum likelihood estimate of the within-group standard deviation (and also of the within-group means). However, the estimate is negatively biased and has a large standard deviation. The simulations show that with a standardized difference of 1 or less, which is typical in most clinical trials, the standard deviation from the combined samples ignoring the groups is a better estimator, despite its obvious positive bias.

Algorithms↗

PubMed1995

A QALY-based societal health statistic for Canada, 1985.

This paper assesses the appropriateness of QALYs (quality adjusted life years) as a foundation for an index of societal health, and the feasibility of using such an index to guide health care policy. Results of this paper suggest that the standard aggregate QALY index imposes an ethical position on policy makers which may promote inequality in well-being associated with health. It is possible to rectify this problem in theory, but current data are insufficient to estimate such corrected indices. A QALY-based index, constructed using the best available data, indicates morbidity has a significant effect on Canadian health status (e.g. life expectancy figures alone overstate community health by about 10%), that the impact of morbidity is unequal across regions and gender, and that role (the ability to fulfil social functions) and mobility dysfunction are important determinants of ill-health in this population.

Adolescent↗

PubMed2004

Combining phylogenetic and hidden Markov models in biosequence analysis.

A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models of molecular evolution, which apply to individual sites, and hidden Markov models, which allow for changes from site to site. Besides improving the realism of ordinary phylogenetic models, they are potentially very powerful tools for inference and prediction--for example, for gene finding or prediction of secondary structure. In this paper, we review progress on combined phylogenetic and hidden Markov models and present some extensions to previous work. Our main result is a simple and efficient method for accommodating higher-order states in the HMM, which allows for context-dependent models of substitution--that is, models that consider the effects of neighboring bases on the pattern of substitution. We present experimental results indicating that higher-order states, autocorrelated rates, and multiple functional categories all lead to significant improvements in the fit of a combined phylogenetic and hidden Markov model, with the effect of higher-order states being particularly pronounced.

Computational Biology↗

PubMed2003

Three neuropeptide Y receptor genes in the spiny dogfish, Squalus acanthias, support en bloc duplications in early vertebrate evolution.

It has been debated whether the increase in gene number during early vertebrate evolution was due to multiple independent gene duplications or synchronous duplications of many genes. We describe here the cloning of three neuropeptide Y (NPY) receptor genes belonging to the Y1 subfamily in the spiny dogfish, Squalus acanthias, a cartilaginous fish. The three genes are orthologs of the mammalian subtypes Y1, Y4, and Y6, which are located in paralogous gene regions on different chromosomes in mammals. Thus, these genes arose by duplications of a chromosome region before the radiation of gnathostomes (jawed vertebrates). Estimates of duplication times from linearized trees together with evidence from other gene families supports two rounds of chromosome duplications or tetraploidizations early in vertebrate evolution. The anatomical distribution of mRNA was determined by reverse-transcriptase PCR and was found to differ from mammals, suggesting differential functional diversification of the new gene copies during the radiation of the vertebrate classes.

Amino Acid Sequence↗

PubMed2006

Identification of measurement differences between English and Spanish language versions of the Mini-Mental State Examination. Detecting differential item functioning using MIMIC modeling.

BACKGROUND: Knowledge of the extent to which measurement of adult cognitive functioning differs between Spanish and English language administrations of the Mini-Mental State Examination (MMSE) is critical for inclusive, representative, and valid research of older adults in the United States. OBJECTIVES: We sought to demonstrate the use of an item response theory (IRT) based structural equation model, that is, the MIMIC model (multiple indicators, multiple causes), to evaluate MMSE responses for evidence of differential item functioning (DIF) attributable to language of administration. SUBJECTS: We studied participants in a dementia case registry study (n = 1546), 42% of whom were examined with the Spanish language MMSE. RESULTS: Twelve of 21 items were identified as having significant uniform DIF. The 4 most discrepant included orientation to season, orientation to state, repeat phrase, and follow command. DIF accounted for two-thirds of the observed difference in underlying level of cognitive functioning between Spanish- and English-language administration groups. CONCLUSIONS: Failing to account for measurement differences may lead to spurious inferences regarding language group differences in level of underlying level of cognitive functioning. The MIMIC model can be used to detect and adjust for such measurement differences in substantive research.

Aged↗

PubMed2004

Improved Poisson intensity estimation: denoising application using Poisson data.

Recently, Timmermann and Nowak developed algorithms for estimating the means of independent Poisson random variables. The algorithms are based on a multiscale model where certain random variables are assumed to obey a beta-mixture density function. Timmermann and Nowak simplify the density estimation problem by assuming the beta parameters are known and only one mixture parameter is unknown. They use the observed data and the method of moments to estimate the unknown mixture parameter. Taking a different approach, we generate training data from the observed data and compute maximum likelihood estimates of all of the beta-mixture parameters. To assess the improved performance obtained by the proposed modification, we consider a denoising application using Poisson data.

Algorithms↗

PubMed2002

Test-retest reliability estimation of functional MRI data.

Functional magnetic resonance imaging (fMRI) data are commonly used to construct activation maps for the human brain. It is important to quantify the reliability of such maps. We have developed statistical models to provide precise estimates for reliability from several runs of the same paradigm over time. Specifically, our method extends the premise of maximum likelihood (ML) developed by Genovese et al. (Magn Reson Med 1997;38:497-507) by incorporating spatial context into the estimation process. Experiments indicate that our methodology provides more conservative estimates of true positives compared to those obtained by Genovese et al. The reliability estimates can be used to obtain voxel-specific reliability measures for activated as well as inactivated regions in future experiments. We derive statistical methodology to determine optimal thresholds for region- and context-specific activations. Empirical guidelines are also provided on the number of repeat scans to acquire in order to arrive at accurate reliability estimates. We report the results from experiments involving a motor paradigm performed on a single subject several times over a period of 2 months.

Brain↗

PubMed2001

Genetic linkage methods for quantitative traits.

We discuss methods for detecting genetic linkage for quantitative data. The usual LOD score method uses a pseudolikelihood formulation and has optimal power provided all parameters are correctly specified, but can lead to erroneous estimates of the location for the locus influencing a trait under misspecification of parameters describing the variance of the trait. Alternative methods, in which attention focuses upon modelling covariation among relatives as a function of genetic marker, similarity lead to unbiased estimates of the location and major gene heritability of the trait influencing locus. The Haseman-Elston approach uses a regression method to perform linkage analysis and its properties have been widely studied. This method is generally less powerful than variance components procedures, but the maximum likelihood-based variance components procedures require normality of the trait to ensure robustness of the genetic linkage tests (i.e. a correct false positive rate). When samples are non-randomly selected an ascertainment correction is generally required in order to obtain unbiased parameter estimates when applying variance components methods. For quantitative traits, ascertainment corrections usually condition either on the proband exceeding a threshold, or on the trait value of the proband. We summarize simulations that show that both approaches lead to similar efficiencies for estimating genetic effects. Finally, we discuss methods for analysing diseases that include time-to-onset information. A variety of methods are available for the linkage analysis of quantitative traits. Here, we have reviewed the most commonly used methods.

Biometry↗

PubMed1996

Testing of hypotheses about altitude decompression sickness by statistical analyses.

This communication extends a statistical analysis of forced-descent decompression sickness at altitude in exercising subjects (J Appl Physiol 1994; 76:2726-2734) with a data subset having an additional explanatory variable, rate of ascent. The original explanatory variables for risk-function analysis were environmental pressure of the altitude, duration of exposure, and duration of pure-O2 breathing before exposure; the best fit was consistent with the idea that instantaneous risk increases linearly as altitude exposure continues. Use of the new explanatory variable improved the fit of the smaller data subset, as indicated by log likelihood. Also, with ascent rate accounted for, replacement of the term for linear accrual of instantaneous risk by a term for rise and then decay made a highly significant improvement upon the original model (log likelihood increased by 37 log units). The authors conclude that a more representative data set and removal of the variability attributable to ascent rate allowed the rise-and-decay mechanism, which is expected from theory and observations, to become manifest.

Altitude↗

PubMed1993

A bivariate survival model with modified gamma frailty for assessing the impact of interventions.

Bivariate survival analysis models that incorporate random effects or 'frailty' provide a useful framework for determining the effectiveness of interventions. These models are based on the notion that two paired survival times are correlated because they share a common unobserved value of a random variate from a frailty distribution. In some applications, however, investigators may have some information that characterizes pairs and thus provides information about their frailty. Alternatively, there may be an interest in assessing whether the correlation within certain types of pairs is different from the correlation within other types of pairs. In this paper, we present a method to incorporate 'pair-wise' covariate information into the dependence parameter of the bivariate survival function. We provide an example using data from the Framingham Heart Study to investigate the times until the occurrence of two events within an individual: the first detection of hypertension and the first cardiovascular disease event. We model the dependence between these two events as a function of the age of the individual at the time of enrollment into the Framingham Study.

Adult↗

PubMed2002

Gene duplication and gene conversion shape the evolution of archaeal chaperonins.

Chaperonins are multi-subunit double-ring complexes that mediate the folding of nascent or denatured proteins. Gene duplication has been a potent force in the evolution of chaperonins in Archaea. Here we show that gene conversion has also been an important factor. We utilized a novel maximum likehood-based phylogenetic method for scanning DNA sequence alignments for regions of anomalous phylogenetic signal, such as those affected by gene conversion. Our results suggest that in crenarchaeotes, where an ancient gene duplication producing alpha and beta subunits took place in the common ancestor of the Pyrodictium, Aeropyrum, Pyrobaculum and Sulfolobus lineages, multiple independent gene conversions have occurred between the alpha and beta genes independently in each of these groups. Significantly, the conversions have repeatedly homogenized the region of the gene encoding the substrate-binding domain. This suggests that while the alpha and beta subunits in crenarchaeotes share only 50-60% overall amino acid sequence identity, they do not possess distinct roles in the binding of substrate. Cryptic gene conversion between distantly related paralogs may be more common than is currently appreciated, and could be a significant factor in slowing the functional differentiation of proteins encoded by duplicate genes long after their duplication.

Amino Acid Sequence↗

PubMed1999

Generalizable patterns in neuroimaging: how many principal components?

Generalization can be defined quantitatively and can be used to assess the performance of principal component analysis (PCA). The generalizability of PCA depends on the number of principal components retained in the analysis. We provide analytic and test set estimates of generalization. We show how the generalization error can be used to select the number of principal components in two analyses of functional magnetic resonance imaging activation sets.

Algorithms↗

PubMed2006

Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae.

In a set of 190 duplicate gene pairs in yeast Saccharomyces cerevisiae, the sharing of transcription factors tended to decrease with increased divergence in coding sequence, at both synonymous and nonsynonymous sites. Our results showed a significantly higher sharing of transcription factors by duplicated gene pairs falling within duplicated genomic blocks than in other duplicated gene pairs; and genes in duplicated blocks also showed significantly greater conservation at the coding sequence level. In spite of the overall trends, there were certain gene pairs, both in duplicated blocks and in other genomic regions, which were highly divergent in coding sequence and yet had identical patterns of transcription factor binding. These results suggest that functional differentiation of genes after duplication is a multi-dimensional process, with different duplicate pairs differentiating in different ways.

Base Sequence↗

PubMed2005

Predictors of successful extubation of preterm low-birth-weight infants with respiratory distress syndrome.

OBJECTIVE: The aim of the study was to measure pulmonary mechanics in infants with respiratory distress syndrome before extubation and to correlate pulmonary function values with successful extubation. DESIGN: Clinical study. SETTING: Neonatal intensive care unit. PATIENTS: Fifty-one infants (birth weight, 1158.6 +/- 150.6 g; gestational age, 29.1 +/- 2.0 wks). INTERVENTIONS: Ventilation and daily ventilatory management. MEASUREMENTS AND MAIN RESULTS: Of the 51 infants studied, 35 (60.8%) were successfully extubated, whereas 16 (39.2%) required reintubation and mechanical ventilation within 72 hrs after extubation. All patients met the clinical and biochemical criteria for extubation. Variables of artificial ventilation before extubation were minimal in all the studied cases (Fio(2) </=0.4, inspiratory pressure </=20 cm H(2)O, ventilatory rate, </=10/min). Pulmonary mechanics were measured before extubation using a noninvasive, mobile VenTrak measuring station. RESULTS: Significant differences in pulmonary function values between the groups were found. Lower resistance of airways and work of breathing and higher dynamic compliance, tidal volume, and minute ventilation before extubation were associated with successful extubation. CONCLUSION: On the average, tidal volume values of >6 mL/kg, minute ventilation of >309 mL/kg/min, work of breathing of <0.172 J/L, dynamic compliance of >/=1 mL/cm H(2)O/kg, and resistance of airways of </=176 cm H(2)O/L/sec predicted successful extubation. We recommend measurement of pulmonary function as an assessment tool in determining readiness for extubation.

Aminophylline↗

PubMed2005

Selfing and resource allocation in Schiedea salicaria (Caryophyllaceae), a gynodioecious species.

Abstract Levels of selfing and resource allocation patterns were investigated in Schiedea salicaria (Caryophyllaceae), a gynodioecious species with high levels of inbreeding depression and nuclear control of male sterility. Selfing levels were higher in hermaphrodites than females, especially when adjusted for early acting inbreeding depression. The sexes of S. salicaria were similar in most allocation patterns including number of flowers and capsules per inflorescence, seeds per flower, and seed mass. Seeds produced by females had higher levels of germination than seeds of hermaphrodites, a likely result of high selfing levels and the expression of inbreeding depression in the progeny of hermaphrodites. Invasion of females in populations of S. salicaria is probably related to the expression of inbreeding depression at germination and in later life history stages. Comparisons with related species of Schiedea that also have nuclear control of male sterility suggest that reallocation of resources in hermaphrodites to male function occurs as females increase in frequency, but that resource reallocation is not important for the success of females when they first invade populations.

Caryophyllaceae↗

PubMed2005

Quantitating effector and regulatory T lymphocytes in immune responses by limiting dilution analysis modeling.

Although there is currently no doubt that regulatory lymphocytes represent a master player in the immune system, a major unresolved problem is the accurate quantitation of these cells among unfractionated cell populations. This difficulty mainly arises because there are no specific immunophenotypic markers that can reliably discriminate between effector and regulatory lymphocytes. To face this problem, we have developed computational models of limiting dilution analyses addressing the question of the accurate estimation of the frequencies of effector and regulatory cells functionally engaged in an immune response. A set of generic equations were provided to form a framework for modeling limiting dilution data, enabling discrimination between qualitatively different models of suppression. These models include either one or two subpopulations of regulatory cells, featured by either low or potent regulatory activity. The potential of this modeling approach was illustrated by the accurate determination of the frequencies of effector and regulatory T lymphocytes in one real limiting dilution experiment of CD4+ CD25+ T lymphocytes performed in the context of an allogeneic response in the human system. The crucial advantage of the limiting dilution method over the "static, phenotype-based" method is the dynamic evaluation of effector and regulatory T cell biology through their actual functional activity.

Animals↗

PubMed2004

Flexible modelling of discrete failure time including time-varying smooth effects.

Discrete survival models have been extended in several ways. More flexible models are obtained by including time-varying coefficients and covariates which determine the hazard rate in an additive but not further specified form. In this paper, a general model is considered which comprises both types of covariate effects. An additional extension is the incorporation of smooth interaction between time and covariates. Thus, in the linear predictor smooth effects of covariates which may vary across time are allowed. It is shown how simple duration models produce artefacts which may be avoided by flexible models. For the general model which includes parametric terms, time-varying coefficients in parametric terms and time-varying smooth effects estimation procedures are derived which are based on the regularized expansion of smooth effects in basis functions. The approach is used to model the sojourn time in a psychiatric hospital. It is demonstrated how initial conditions which have non-linear influence are damped over time.

Germany↗