SEARCH · PubMed Health

Results for “Likelihood Functions”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources

PubMed1994

Reliability of percutaneous intramuscular electrodes for upper extremity functional neuromuscular stimulation in adolescents with C5 tetraplegia.

Chronically indwelling percutaneous intramuscular electrodes were implanted in the upper extremity muscles of five adolescents with C5 or C5-6 tetraplegia in an effort to provide lateral and palmar prehension using the neuroprosthetic system designed by Case Western Reserve University. The responses from 177 electrodes were evaluated at 3-month intervals and included measurements of electrical impedance and an assessment of recruitment properties. Electrode failures were categorized as breakage, an altered stimulated response or adverse sensation during stimulation. Survival probabilities were generated for all electrodes, each muscle group, the volar and dorsal exit sites, intrinsic and extrinsic muscles, and according to the subjects' time postinjury. The overall probability of an electrode surviving to 6 months was 0.75 and the 1 year survival probability was 0.56. Among muscle groups, the finger extensor and thumb adductor electrodes had the highest proportion of failures and the poorest survival likelihoods within the first year after implant. According to the Breslow test, significantly smaller survival chances were predicted for electrodes exiting dorsally and for the newly-injured adolescents (< 1 year postinjury). The cumulative survival likelihoods of this study are smaller than those reported in adult applications using the same electrode design. Factors that may account for the disparate results are discussed.

Adolescent↗

PubMed1998

Young-onset Parkinson's disease revisited--clinical features, natural history, and mortality.

The authors report on clinical features and mortality rates in a group of 149 patients with apparent idiopathic parkinsonism starting before the age of 40 years. Ten had juvenile parkinsonism (JP; onset before age 21 years) and 139 had young-onset Parkinson's disease (YOPD; onset at age 21 to 40 years). Included were 60 patients originally reported 10 years ago. Fifty percent of the JP group had a positive family history of parkinsonism in a first-degree relative, and clinical presentation was heterogeneous. Mortality risk was threefold that of the normal population. In the YOPD group, the mortality risk was double that of the normal population. Poor initial response to L-dopa was a risk factor for early death. In two previously reported patients, the diagnosis had been changed to multiple system atrophy and Machado-Joseph disease. After a median disease duration of 18 years, cognitive impairment was found in only 19% of YOPD patients (13% of those younger than 60 years and 43% of those 60 years or older). Age was the most important factor for development of dementia, but female sex and positive family history of parkinsonism also had more modest predictive value. After a disease duration of 10 years or less, only 5% of patients were experiencing falls and 30% freezing, but all patients had developed L-dopa-related fluctuations and dyskinesias. The authors conclude that the mortality rate in parkinsonism starting before the age of 40 is increased in comparison to the normal population and is similar to the general Parkinson's disease population. Intellectual function and postural reflexes are usually well preserved for many years despite a long history of parkinsonism and the early and frequent occurrence of treatment complications, provided the patients remain biologically and chronologically young.

Adolescent↗

PubMed2002

Increased taxon sampling greatly reduces phylogenetic error.

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.

Likelihood Functions↗

PubMed1999

A gene for X-linked idiopathic congenital nystagmus (NYS1) maps to chromosome Xp11.4-p11.3.

Congenital nystagmus (CN) is a common oculomotor disorder (frequency of 1/1,500 live births) characterized by bilateral uncontrollable ocular oscillations, with onset typically at birth or within the first few months of life. This condition is regarded as idiopathic, after exclusion of nervous and ocular diseases. X-linked, autosomal dominant, and autosomal recessive modes of inheritance have been reported, but X-linked inheritance is probably the most common. In this article, we report the mapping of a gene for X-linked dominant CN (NYS1) to the short arm of chromosome X, by showing close linkage of NYS1 to polymorphic markers on chromosome Xp11.4-p11.3 (maximum LOD score of 3.20, over locus DXS993). Because no candidate gene, by virtue of its function, has been found in this region of chromosome Xp, further studies are required, to reduce the genetic interval encompassing the NYS1 gene. It is hoped that the complete gene characterization will address the complex pathophysiology of CN.

Child↗

PubMed2000

Local estimation of age-dependent variance components from longitudinal twin data.

In the study of longitudinal twin and family data, interest is often in the covariance structure of the data and the decomposition of this covariance structure into genetic and environmental components rather than in estimating the mean function. Various parametric models for covariance structures have been proposed but, e.g., in studies of children where growth spurts occur at various ages, it is difficult to a priori determine an appropriate parametric model for the covariance structure. In particular, there is a general lack of the visualization procedures, such as lowess, that are invaluable in the initial stages of constructing a parametric model for a mean function. Here we use kernel smoothing to modify a cross-sectional approach based on the sample covariance matrices to obtain smoothed estimates of the genetic and environmental variances and correlations for longitudinal twin data. The methods are proposed to be exploratory as an aid to parametric modeling rather than inferential, although approximate asymptotic standard errors are derived in the Appendix.

Age Factors↗

PubMed2000

Adaptive growth restriction as a pattern of birth weight discordance in twin gestations.

OBJECTIVE: To challenge the hypothesis that discordant growth is a normal variation by relating birth weight discordance to total twin birth weight. METHODS Among 12,565 Israeli live-born twin pairs (1993-98), we compared total twin birth weight decile, the frequencies of three levels of discordance in the general population, over 25% discordance between like- versus unlike-sex pairs, and over 25% discordance between pairs delivered by primiparas versus multiparas. RESULTS: We found a marked change in the best-fit correlation function with increased discordance: level 15-24.9% was inversely linear whereas levels 25-34.9% and over 34.9% were inversely logarithmic (R(2) =.47,.88, and.9, respectively). The best-fit correlation of frequencies of more than 25% discordance was inversely logarithmic and similar in like- and unlike-sexed twins across deciles functions (P =.7, odds ratio [OR] 1.0, 95% confidence interval [CI] 0.9, 1.2). The overall frequencies of discordance were also similar (9.3% versus 10.2%, P =.11, OR 0.9, 95% CI 0.8, 1.0). The frequencies of primiparas decreased linearly (R(2) =.98) and the frequencies of more than 25% discordant pairs in multiparas and primiparas across the deciles had similar inversely logarithmic patterns (P =.55, OR 1.0, 95% CI 0.9, 1.2). Discordance over 25% was significantly more frequent among primiparas (P <.001, OR 1.45, 95% CI 1.3, 1.6). CONCLUSION: The observed patterns of birth weight discordance did not substantiate normal variation but an adaptive growth restriction that might explain why the likelihood of discordant growth decreases as total twin birth weight increases.

Adaptation, Physiological↗

PubMed2000

Functions of oral candidiasis episodes that are highly prognostic for AIDS.

Although oral candidiasis lesions are widely recognized as markers for AIDS, the relative prognostic significance of functions of these episodes has not been examined. We compare the associations with time to AIDS of one fixed and six time-dependent metrics of oral candidiasis lesions, including proximity of a lesion to seroconversion, any candidiasis history, and recency of a lesion. We show in Cox regression models that two metrics are clinically and statistically far more significant than the others, alone or in combination: any history of candidiasis since HIV seroconversion, and recency of a candidiasis episode. The latter metric indicates that the risk of an AIDS diagnosis is high during a candidiasis episode. The results hold for two cohorts of male seroconverters, 627 haemophiliacs and 196 men who have sex with men. Identification of highly prognostic functions of a patient's oral candidiasis history allows clinicians and researchers to focus on these aspects of the history and to omit extraneous information from data collection. Our method extends well beyond candidiasis and AIDS, and may shed light on associations of covariates with outcomes in a variety of settings.

Acquired Immunodeficiency Syndrome↗

PubMed1998

A comparison of two algorithms for electron-density map improvement by introduction of atomicity: skeletonization, and map sorting followed by refinement.

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148-157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347-351]. Tests carried out using the 3.0 A resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762-10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3 degrees is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4 degrees is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

Algorithms↗

PubMed1992

Estimation, reference ranges and goodness of fit for the three-parameter log-normal distribution.

The three-parameter log-normal distribution (3PL) is an appropriate model for many of the continuous variables encountered in medicine. It is shown how to obtain different types of estimate and approximate (sometimes conservative) confidence intervals for the parameters of the 3PL and for certain functions of them, particularly in the calculation of reference ranges of clinical measurements. A simple non-iterative estimate of the shift parameter is described. The Shapiro-Wilk test of non-normality is modified to allow it to be used for testing for departure from the 3PL. Its power is compared with that of other well-known tests. The methods are illustrated using several data sets.

Algorithms↗

PubMed2005

Evolutionary origin of cAMP-based chemoattraction in the social amoebae.

Phenotypic novelties can arise if integrated developmental pathways are expressed at new developmental stages and then recruited to serve new functions. We analyze the origin of a novel developmental trait of Dictyostelid amoebae: the evolution of cAMP as a developmental chemoattractant. We show that cAMP's role of attracting starving amoebae arose through recruitment of a pathway that originally evolved to coordinate fruiting body morphogenesis. Orthologues of the high-affinity cAMP receptor (cAR), cAR1, were identified in a selection of species that span the Dictyostelid phylogeny. The cAR1 orthologue from the basal species Dictyostelium minutum restored aggregation and development when expressed in an aggregation-defective mutant of the derived species Dictyostelium discoideum that lacks high-affinity cARs, thus demonstrating that the D. minutum cAR is a fully functional cAR. cAR1 orthologues from basal species are expressed during fruiting body formation, and only this process, and not aggregation, was disrupted by abrogation of cAR1 function. This is in contrast to derived species, where cAR1 is also expressed during aggregation and critically regulates this process. Our data show that coordination of fruiting body formation is the ancestral function of extracellular cAMP signaling, whereas its derived role in aggregation evolved by recruitment of a preexisting pathway to an earlier stage of development. This most likely occurred by addition of distal cis-regulatory regions to existing cAMP signaling genes.

Amino Acid Sequence↗

PubMed2006

Gene cooption without duplication during the evolution of a male-pregnancy gene in pipefish.

Comparative studies of developmental processes suggest that novel traits usually evolve through the cooption of preexisting genes and proteins, mainly via gene duplication and functional specialization of paralogs. However, an alternative hypothesis is that novel protein function can evolve without gene duplication, through changes in the spatiotemporal patterns of gene expression (e.g., via cis-regulatory elements), or functional modifications (e.g., addition of functional domains) of the proteins they encode, or both. Here we present an astacin metalloprotease, dubbed patristacin, which has been coopted without duplication, via alteration in the expression of a preexisting gene from the kidney and liver of bony fishes, for a novel role in the brood pouch of pregnant male pipefish. We examined the molecular evolution of patristacin and found conservation of astacin-specific motifs but also several positively selected amino acids that may represent functional modifications for male pregnancy. Overall, our results pinpoint a clear case in which gene cooption occurred without gene duplication during the genesis of an evolutionarily significant novel structure, the male brood pouch. These findings contribute to a growing understanding of morphological innovation, a critically important but poorly understood process in evolutionary biology.

Amino Acid Sequence↗

PubMed2005

The effects of artificial selection on the maize genome.

Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modern maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial selection. The remaining genes retain evidence of a population bottleneck associated with domestication. Candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte. If we assume that our sample of genes is representative, approximately 1200 genes throughout the maize genome have been affected by artificial selection.

Amino Acids↗

PubMed2004

Evolution of DMY, a newly emergent male sex-determination gene of medaka fish.

The Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (d(N)) to that of synonymous substitution (d(S)) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the d(N)/d(S) ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.

Amino Acid Sequence↗

PubMed1996

Quasilikelihood estimation in measurement error models with correlated replicates.

We consider quasilikelihood models when some of the predictors are measured with error. In many cases, the true but fallible predictor is impossible to measure, and the best one can do is to obtain replicates of the fallible predictor. We consider the case that the replicates are not independent. If one assumes that replicates are independent and they are not, one typically underestimates the extent of the measurement error, leading to an inconsistent errors in variables correction. We devise techniques for estimating the measurement error covariance matrix. In addition, we discuss how one might perform a quasilikelihood analysis by computing the mean and variance functions of the observed data, both using approximations and also exactly through a Monte Carlo method. The methods are illustrated on a data set involving systolic blood pressure and urinary sodium chloride, where the measurement errors appear to be approximately normally distributed but highly correlated, and the distribution of the true predictor is reasonably modeled as a mixture of normals.

Analysis of Variance↗

PubMed1990

A mathematical model for recurrent twinning.

In an attempt to improve our understanding of the factors that affect human twinning, we further developed the models given by Hellin (1895) and Peller (1946). The connection between these models and our own model ("Fellman's law") were studied. These attempts have resulted in a more general model, which was then applied to data from Aland Islands (1750-1939), Nmes (1790-1875), Stuttgart (about 1790-1900) and Utah (1850-1900). The product of the mean sibship size and the total twinning rate can be considered as a crude estimate of the expected number of sets of twins in a sibship. The same can be said about the twinning parameter in our model. These estimates are in good agreement. If we consider twinning data only, we obtain the geometric distribution, and log (Nk), where Nk is the number of mothers with k twin maternities, is a linear function of the number of recurrences. Graphically, this property can easily be checked. For sibships containing three or more sets of twins, all four populations show higher values than expected, particularly the populations from Stuttgart and Utah, which data also show poor agreement according to a chi 2-test. A more exact model would demand more detailed demographic information, such as distribution of sibship sizes, age-specific twinning rates and temporal variations in twinning. The observed number of mothers in Aland with several recurrences of multiple maternities shows a considerable excess over the expected number as predicted by Peller's rule. The parameters in our model can be estimated by the maximum likelihood method and the obtained model fits the data better then Peller's model.

Female↗

PubMed2001

Modeling age x major gene interaction by a variance component approach.

The variance component method has become popular for linkage analysis due to its computational simplicity and generally high power. In this paper we model phenotypic variability of an individual as a mixed effects model in which both the major gene as well as the polygene effects interact with age. We applied the proposed model to the simulated data of Genetic Analysis Workshop 12. We considered the quantitative trait, Q4, in the outbred population. Two major genes influence this trait, each interacting with age independently. Consequently, trait variability is a function of age and also there is interaction of major gene effects with age. By using our model we were able to detect interaction between the major gene effects and age for this trait.

Adolescent↗

PubMed1997

Gallstones in a community free of obesity but prone to slow intestinal transit.

OBJECTIVES: To verify anecdotal reports that gallstones were frequent in a remote community where obesity is rare and to look for possible explanations of their occurrence, including slow intestinal transit. DESIGN: Population survey of gallbladder status and stool form. SETTING: Two villages in Ladakh, a mountainous region of northern India; for comparison, a stratified random sample from general practitioners' lists in East Bristol. SUBJECTS: Women aged 25-59 years, 437 in Ladakh and 974 in Bristol. MAIN OUTCOME MEASURES: Presence of gallstones on ultrasonography and response to questionnaires about parity, the intake of dried legume seeds (pulses) and bowel function including the form or appearance of the stools on a seven-point, transit-sensitive scale. Weight, height and waist circumference were also recorded. RESULTS: Gallstone disease was at least as frequent in Ladakh as in Bristol although Ladakhi women were uniformly slim and their weight, waist size and body mass index failed to rise with age. After adjustment for age, gallstone disease was associated with higher body mass index and waist size in Bristol but not in Ladakh. It was associated with increased parity in Bristol, but not significantly so after adjusting for age and not at all in Ladakh. Gallstone disease was not directly associated with bowel function but Ladakhis often reported their stools to be lumpy (42.4 vs. 26.5% of Bristol women) and seldom as soft or loose (6.4 vs. 42.5%), implying that their intestinal transit tends to be slow. CONCLUSION: Gallstones can be common in a population free of obesity but prone to intestinal stasis.

Adult↗

PubMed2004

Modeling and decoding motor cortical activity using a switching Kalman filter.

We present a switching Kalman filter model for the real-time inference of hand kinematics from a population of motor cortical neurons. Firing rates are modeled as a Gaussian mixture where the mean of each Gaussian component is a linear function of hand kinematics. A "hidden state" models the probability of each mixture component and evolves over time in a Markov chain. The model generalizes previous encoding and decoding methods, addresses the non-Gaussian nature of firing rates, and can cope with crudely sorted neural data common in on-line prosthetic applications.

Action Potentials↗