SEARCH · PubMed Health

Results for “variational inference”

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 541 records · Page 30Linked to original sources

PubMed2003

Population variation in opsin expression in the bluefin killifish, Lucania goodei: a real-time PCR study.

Quantitative genetics have not been used in vision studies because of the difficulty of objectively measuring large numbers of individuals. Here, we examine the effectiveness of a molecular technique, real-time PCR, as an inference of visual components in the bluefin killifish, Lucania goodei, to determine whether there is population variation in opsin expression. Previous work has shown that spring animals possess a higher frequency of UV and violet cones and a lower frequency of yellow and red cones than swamp animals. Here, we found a good qualitative match between the population differences in opsin expression and those found previously in cone frequency. Spring animals expressed higher amounts of SWS1 and SWS2B opsins (which correspond to UV and violet photopigments) and lower amounts of RH2 and LWS opsins (which correspond to yellow and red photopigments) than swamp animals. The counterintuitive pattern between color pattern, lighting environment, and vision remains. Males with blue anal fins are more abundant in swamps where animals express fewer SWS1 and SWS2B opsins and where transmission of UV/blue wavelengths is low. Understanding this system requires quantitative genetic studies. Real-time PCR is an effective tool for studies requiring inferences of visual physiology in large numbers of individuals.

Animals↗

PubMed2005

Genetic variation at the human alpha2B-adrenergic receptor locus: role in blood pressure variation and yohimbine response.

Exaggerated response to alpha2-adrenergic receptor (alpha2-AR) blockade by yohimbine in normotensive subjects is an intermediate phenotype that predicts increased risk for development of hypertension. Here, we assessed the 3 alpha2-AR loci (alpha2A, alpha2B, alpha2C) as candidate genes for their influence on baseline and yohimbine-mediated increase in mean arterial pressure. Because initial results with 173 individuals implicated a possible association of yohimbine response with genetic variation at a site in the alpha2B-AR gene, but not at sites in the other 2 alpha2-AR, we sequenced the alpha2B-AR gene (4.4 kb, including 1.2 kb upstream and 1.9 kb distal to the coding sequence) in those subjects and an additional 81 individuals to search for other alpha2B-AR variants. We identified 25 polymorphisms, of which 14 are previously unreported, and 2 major haplotypes that differ by the presence/absence of a 9-bp in-frame deletion that encodes Glu301 to Glu303. Frequency differences in haplotypes were observed between blacks and whites but did not predict response to yohimbine. Genotyping of 2 additional white cohorts, including 1269 individuals with extremes in blood pressure selected from >50,000 subjects, also failed to reveal an association of the 2 major alpha2B-AR haplotypes with differences in blood pressure. Thus, despite considerable polymorphism in alpha2-AR genes, such variation is not a major determinant of variability in yohimbine response and by inference, in susceptibility to essential hypertension.

Adrenergic alpha-Antagonists↗

PubMed2004

Reconstruction of ancestral protein sequences and its applications.

BACKGROUND: Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. RESULTS: We developed ANCESCON, a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families. To improve the accuracy of evolutionary distance estimation and ancestral sequence reconstruction, two approaches are proposed to estimate position-specific evolutionary rates. Comparisons show that at large evolutionary distances our method gives more accurate ancestral sequence reconstruction than PAML, PHYLIP and PAUP*. We apply the reconstructed ancestral sequences to homology inference and functional site prediction. We show that the usage of hypothetical ancestors together with the present day sequences improves profile-based sequence similarity searches; and that ancestral sequence reconstruction methods can be used to predict positions with functional specificity. CONCLUSIONS: As a computational tool to reconstruct ancestral protein sequences from a given multiple sequence alignment, ANCESCON shows high accuracy in tests and helps detection of remote homologs and prediction of functional sites. ANCESCON is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/ANCESCON/.

Amino Acid Sequence↗

PubMed2001

Neuronal contact guidance in magnetically aligned fibrin gels: effect of variation in gel mechano-structural properties.

Neurite outgrowth from chick dorsal root ganglia entrapped in isotropic and magnetically aligned fibrin gels was studied, and the dependence on the diameter of the fibrin fibrils was characterized. The fibrin fibril diameter was varied, as inferred from turbidity measurements, by using different Ca2+ concentrations in the fibrin-forming solution, but this variation was accomplished without affecting the degree of magnetic-induced alignment, as directly visualized in fluorescently spiked gels. Magnetically aligned fibrin gels possessing different fibril diameters but similar alignment resulted in drastic changes in the contact guidance response of neurites, with no response in gels formed in 1.2 mM Ca2+ (having smaller fibril diameter, ca. 150 nm), but a strong response in gels formed in 12 and 30 mM Ca2+ (having larger fibril diameter, ca. 510 nm) with an attendant two-fold increase in neurite length. These changes are attributed to variation of the mechano-structural properties of the network of aligned fibrils as the fibril diameter is varied.

Animals↗

PubMed2004

Genetic variation, disequilibrium and natural selection on reproductive traits in Allium vineale.

Bulbils and seeds collected from Allium vineale plants from natural populations were grown under uniform conditions. The bulbil-derived offspring represented the parental generation, whereas the seed-derived offspring represented the sexually produced offspring generation. Molecular markers were used to identify maternal genets. Variation in traits determining the allocation to sexual and asexual reproduction was partitioned among genets and ramet families in the parental and offspring generations. From observations of a release of genetic variation and slippage in the mean phenotype in the offspring generation, we inferred that there exists extensive genetic disequilibrium for reproductive traits in A. vineale populations, that most of the genetic variance is because of dominance effects, and that natural selection favours a reduced allocation to sexual reproduction. No genetic correlation between sexual and asexual allocation traits was found. We discuss the implications of these results with respect to the evolution of a mixed reproductive system in A. vineale.

Allium↗

PubMed1998

Limitations of metazoan 18S rRNA sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion.

We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.

Animals↗

PubMed2006

Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas.

Three distinct mitochondrial maternal lineages (haplotype Groups A, B, and C) have been found in the domestic sheep. Group B has been observed primarily in European domestic sheep. The European mouflon carries this haplotype group. This could suggest that European mouflon was independently domesticated in Europe, although archaeological evidence supports sheep domestication in the central part of the Fertile Crescent. To investigate this question, we sequenced a highly variable segment of mitochondrial DNA (mtDNA) in 406 unrelated animals from 48 breeds or local varieties. They originated from a wide area spanning northern Europe and the Balkans to the Altay Mountains in south Siberia. The sample included a representative cross-section of sheep breeds from areas close to the postulated Near Eastern domestication center and breeds from more distant northern areas. Four (A, B, C, and D) highly diverged sheep lineages were observed in Caucasus, 3 (A, B and C) in Central Asia, and 2 (A and B) in the eastern fringe of Europe, which included the area north and west of the Black Sea and the Ural Mountains. Only one example of Group D was detected. The other haplotype groups demonstrated signs of population expansion. Sequence variation within the lineages implied Group A to have expanded first. This group was the most frequent type only in Caucasian and Central Asian breeds. Expansion of Group C appeared most recently. The expansion of Group B involving Caucasian sheep took place at nearly the same time as the expansion of Group A. Group B expansion for the eastern European area started approximately 3,000 years after the earliest inferred expansion. An independent European domestication of sheep is unlikely. The distribution of Group A variation as well as other results are compatible with the Near East being the domestication site. Groups C and D may have been introgressed later into a domestic stock, but larger samples are needed to infer their geographical origin. The results suggest that some mitochondrial lineages arrived in northern Europe from the Near East across Russia.

Animals↗

PubMed2005

Attributional inference across cultures: similar automatic attributions and different controlled corrections.

Five studies examined the automatic and controlled components of attributional inference in U.S. and East Asian (EA) samples. Studies 1 through 3 used variations of the "anxious woman" paradigm, manipulating the inferential goal (dispositional or situational) and the normative impact of situational constraint information (discounting or augmenting). In each study, U.S. and EA participants under cognitive load produced strong automatic attributions to the focus of their inferential goal (dispositional or situational). Compared with the U.S. cognitive load participants, U.S. no load participants corrected their attributions according to the normative rules of inference. In contrast, EA no load participants corrected in the direction of situational causality, even when the specific content of the situational information provided should have promoted stronger dispositional inferences. Studies 4 and 5 examined and ruled out alternative accounts. Results are discussed in terms of a situational causality heuristic present in EA individuals.

Adult↗

PubMed2004

Modeling cellular processes with variational Bayesian cooperative vector quantizer.

Gene expression of a cell is controlled by sophisticated cellular processes. The capability of inferring the states of these cellular processes would provide insight into the mechanism of gene expression control system. In this paper, we propose and investigate the cooperative vector quantizer (CVQ) model for analysis of microarray data. The CVQ model could be capable of decomposing observed microarray data into many different regulatory subprocesses. To make the CVQ analysis tractable we develop and apply variational approximations. Bayesian model selection is employed in the model, so that the optimal number processes is determined purely from observed micro-array data. We test the model and algorithms on two datasets: (1) simulated gene-expression data and (2) real-world yeast cell-cycle microarray data. The results illustrate the ability of the CVQ approach to recover and characterize regulatory gene expression subprocesses, indicating a potential for advanced gene expression data analysis.

Algorithms↗

PubMed1986

Breast cancer 1985. What have we learned?

A popular misconception infers that all breast cancers are systemic from their inception, that variations of primary therapy will not affect prognosis, and that an effective systemic therapy is already available. This is not so. Moderate improvement in long-term survival of breast cancer patients has occurred during the last three decades, and particularly more recently, due to increased detection of "early" disease. More patients are being encountered with early Stage I lesions that are confined to the breast or with minimal axillary involvement. These patients have a minimal risk of occult systemic spread, and the majority can anticipate long-term disease-free survival through adequate primary therapy that achieves total local control. The great majority of our patients who are free of disease 15 years following aggressive primary therapy remain so thereafter. Although adjuvant multichemotherapy has prolonged disease-free survival, its effect on long-term patient survival has been marginal. Optimum control of breast cancer is achieved through early detection (most important) and aggressive primary therapy that aims to achieve total local control, plus the use of the best available systemic therapy for patients with high risk of occult systemic disease.

Antineoplastic Combined Chemotherapy Protocols↗

PubMed2003

Multivariate group effect analysis in functional Magnetic Resonance Imaging.

In functional MRI (fMRI), analysis of multisubject data typically involves spatially normalizing (i.e. co-registering in a common standard space) all data sets and summarizing results in a single group activation map. This widely used approach does not explicitely account for between-subject anatomo-functional variability. Therefore, we propose a group effect analysis method which makes use of a multivariate model to select the main signal variations that are common to all subjects, while allowing final statistical inference on the individual scale. The normalization step is thus avoided and individual anatomo-functional features are preserved. The approach is evaluated by using simulated data and it is shown that sensitivity is drastically improved compared to more conventional individual analysis.

Algorithms↗

PubMed1979

Limitations of the Eadie-Hofstee plot to estimate kinetic parameters of intestinal transport in the presence of an unstirred water layer.

In the presence of an intestinal unstirred water layer, the relationship between substrate concentration (C1) and unidirectional flux (Jd) is not described by the equation for a rectangular hyperbole. Accordingly, transformations of the Michaelis-Menten equation may not necessarily be linear and may lead to serious errors in the estimation of the affinity constant (Km) and maximal transport rate (Jdm) of carrier-mediated processes. An equation has previously been derived which described Jd under conditions of varying effective thickness or surface area of the unstirred water layer, the free diffusion coefficient of the probe molecule, and the distribution of transport sites along the villus. These theoretical curves have been analyzed by using the Eadie-Hofstee transformation (Jd vs. Jd/C1) of the Michaelis-Menten equation. Use of this plot leads to serious discrepancies between the true and apparent affinity constants and between true and apparent maximal transport rates. These differences are further magnified by failure to correct for the contribution of passive permeation. The Eadie-Hofstee plot is of use, however, to infer certain qualitative characteristics of active transport processes, such as the variation in affinity constants and overlying resistance of the unstirred water layer at different sites along the villus and to predict the adequacy of the correction for the contribution of passive permeation.

Animals↗

PubMed2001

Linkage disequilibrium and haplotype analysis among eight novel single-nucleotide polymorphisms in the human tissue-type plasminogen activator (t-PA) gene.

Tissue-type plasminogen activator (t-PA), a serine protease, activates the conversion of plasminogen to the fibrinolytic protein, plasmin. The t-PA gene, mapped to chromosome 8p12-p11.2, contains 14 exons. An Alu insertion/deletion (I/D) polymorphism in this gene has been associated with an increased risk for myocardial infarction. In the work reported here we sequenced 11 kilobases (kb) of genomic DNA from 50 normal Japanese volunteers (100 alleles), to include all 14 exons of the t-PA gene, flanking intronic sequences, and 6kb of the 5' sequence. These experiments identified eight novel single-nucleotide polymorphisms (SNPs), in addition to the known Alu I/D polymorphism, from which genotypic data we constructed 12 haplotypes in the tested population. Two-way comparisons of SNPs and the Alu polymorphism revealed strong linkage disequilibrium between the Alu site and SNPs at positions 20,209 (chi2 = 92.263) and 27,555 (chi2 = 47.53), and between SNPs at positions 27,849 and 28,902 chi2 = 66.331). A phylogenic tree was constructed to infer a process of genome construction that would reflect the sequence variations we observed. Our results help to explain the lack of agreement among results of various disease-association studies in which a contribution of the human t-PA gene has been suspected but not always confirmed.

Alleles↗

PubMed2005

Influence of trivalent electrolytes on the humic colloid-borne transport of contaminant metals: competition and flocculation effects.

With the objective to assess the relevance of competitive effects in respect of the humic colloid-borne migration of actinides in case of release, the influence of Al(III) on humate complexation of La(III) as an analogue of trivalent actinides was investigated for various humic materials by using 140La as a radioactive tracer, allowing measurements in very dilute systems to simulate realistic settings. Generally, competition by aluminium is not detectable unless the metal-loading capacity of the humic colloids is nearly exhausted. For average contents of organic carbon, a threshold value of 10(-6) M Al(III) can be specified. The metal exchange turned out to be kinetically hindered. Effects on co-adsorption of La(III) and humic acid were found to be less important. Immobilization by the concomitantly induced flocculation process outweighs the role of displacement effects. Comparative studies on complexation and flocculation of humic acid with Al(III), Ga(III), In(III), Sc(III), Y(III), and La(III) were undertaken in order to evaluate the influence of specific properties apart from ion charge and to characterize the mechanism of flocculation. In spite of considerable variations in the binding affinities among these metals, it can be inferred that the possibility of significant competitive effects in natural aquatic systems is confined to Al(III). Complex stabilities and flocculation efficiencies proved to be interrelated. Precipitation is thus attributed to homocoagulation of humic colloids induced by charge compensation, which is further supported by flocculation experiments with Al(III) depending on pH, ionic strength, and humic acid concentration.

Adsorption↗

PubMed2004

Body proportions of Homo habilis reviewed.

The ratio of fore- to hindlimb size plays an important role in our understanding of human evolution. Although Homo habilis was relatively modern craniodentally, its body proportions are commonly believed to have been more apelike than in the earlier Australopithecus afarensis. The evidence for this, however, rests, on two fragmentary skeletons, OH 62 and KNM-ER 3735. The upper limb of the better-preserved OH 62 from Olduvai Gorge is long and slender, but its hindlimb is represented mainly by the proximal portion of a thin femur of uncertain length. The present analysis shows that upper-to-lower limb shaft proportions of both OH 62 and AL 288-1 (A. afarensis) fall in the modern human range of variation, although OH 62 also falls inside that of chimpanzees due to their overlap in small individuals. Despite being more fragmentary, the larger-bodied KNM-ER 3735 lies outside the chimpanzee range and close to the human mean. Because the differences between any of the three individuals are compatible with the range of variation seen in extant hominoid groups, it is not legitimate to infer more primitive upper-to-lower limb shaft proportions for either H. habilis or A. afarensis. Femur length of OH 62 can only be estimated by comparison. Its closest match in size and morphology is with the gracile OH 34 specimen, which therefore provides a better analogue for the reconstruction of OH 62 than the stocky AL 288-1 femur that is traditionally used. OH 34's slender proportions are hardly due to abrasion, but match those of a modern human of that body-size, suggesting that the relative length of OH 62's leg may have been human-like. Brachial proportions, however, remained primitive. Long legs may imply long distance terrestrial travel. Perhaps this adaptation evolved early in the genus Homo, with H. habilis providing an early representative of this important change.

Adaptation, Physiological↗

PubMed2006

Phylogeny, historical biogeography, and taxonomic ranking of Parnassiinae (Lepidoptera, Papilionidae) based on morphology and seven genes.

We tested the taxonomic utility of morphology and seven mitochondrial or nuclear genes in a phylogenetic reconstruction of swallowtail butterflies in the subfamily Parnassiinae. Our data included 236 morphological characters and DNA sequences for seven genes that are commonly used to infer lepidopteran relationships (COI+COII, ND5, ND1, 16S, EF-1alpha, and wg; total 5775 bp). Nuclear genes performed best for inferring phylogenies, particularly at higher taxonomic levels, while there was substantial variation in performance among mitochondrial genes. Multiple analyses of molecular data (MP, ML and Bayesian) consistently produced a tree topology different from that obtained by morphology alone. Based on molecular evidence, sister-group relationships were confirmed between the genera Hypermnestra and Parnassius, as well as between Archon and Luehdorfia, while the monophyly of the subfamily was weakly supported. We recognize three tribes within Parnassiinae, with Archon and Luehdorfia forming the tribe Luehdorfiini Tutt, 1896 [stat. rev.]. Three fossil taxa were incorporated into a molecular clock analysis with biogeographic time constraints. Based on dispersal-vicariance (DIVA) analysis, the most recent common ancestor of Parnassiinae occurred in the Iranian Plateau and Central Asia to China. Early diversification of Parnassiinae took place at the same time that India collided into Eurasia, 65-42 million years ago.

Animals↗

PubMed2000

Monomer composition of polysaccharides of seed cell walls and the taxonomy of the Vochysiaceae.

The distribution of polysaccharides from the seed cell walls of 57 samples of Vochysiaceae native to Brazil were studied, comprising 16 species distributed among the genera Callisthene, Qualea, Salvertia and Vochysia. The polysaccharides were extracted with hot water, then hydrolyzed with the resulting monomers analyzed by HPLC. All samples yielded arabinose, galactose, glucose. mannose and rhamnose, the relative amounts of each monomer, however, varying from one sample to another. Arabinose was always the predominant component, which implies that it might possibly be used as a marker of the Vochysiaceae. The quantitative distribution of monosaccharides was similar between the species of Qualea and Callisthene, characterized by the predominance of arabinose and mannose, and between the species of Salvertia and Vochysia, which contained higher amounts of arabinose and galactose. Such results are consistent with affinities inferred from floral morphology, wood anatomy and molecular data. Substantial intraspecific variation was observed for some species. UPGMA analysis based on the distribution of the monosaccharides reveals two main clusters, according to the links commented above. The resultant phenogram is not coherent with the current sectional classification of the Vochysiaceae, but the differences in the monosaccharides distribution between the two clusters are strongly supported by ANOVA.

Cell Wall↗

PubMedDate not supplied

Some neural network applications in environmental sciences. Part I: forward and inverse problems in geophysical remote measurements.

A broad class of neural network (NN) applications dealing with the remote measurements of geophysical (physical, chemical, and biological) parameters of the oceans, atmosphere, and land surface is presented. In order to infer these parameters from remote sensing (RS) measurements, standard retrieval and variational techniques are applied. Both techniques require a data converter (transfer function or forward model) to convert satellite measurements into geophysical parameters or vice versa. In many cases, the transfer function and the forward model can be represented as a continuous nonlinear mapping. Because the NN technique is a generic technique for nonlinear mapping, it can be used beneficially for modeling transfer functions and forward models. These applications are introduced in a broader framework of solving forward and inverse problems in RS. In this broader context, we show that NN is an appropriate and efficient tool for solving forward and inverse problems in RS and for developing fast and accurate forward models and accurate and robust retrieval algorithms. Theoretical considerations are illustrated by several real-life examples-operational NN applications developed by the authors for SSM/I and medium resolution imaging spectrometer sensors.

Environment↗