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PubMedDate not supplied

Thoracic magnetic dust content, occupational exposure, and respiratory status of shipyard welders.

The net thoracic magnetic moment of 58 highly exposed nonsmoking shipyard welders and 13 unexposed nonsmoking electricians was measured with an alternating current susceptibility bridge. The welding cohort exhibits a thorax magnetic moment, which on the average is less diamagnetic than that of the controls. This shift is consistent with a median lung burden of 110 mg Fe3O4, or 220 mg of the welding fumes characteristic for shipyard exposures. Among welders with 5+ yr of exposure, there is a slight but statistically significant correlation (r = 0.49) (p less than .0001) between inferred lung burden and lifetime occupational exposure. Although chronic bronchitis incidence and average lung function parameter values of the welders are different from those of the nonexposed cohort, respiratory status does not correlate further with either self-reported exposure or measured lung retention.

Adult↗
PubMed2002

Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage.

Current methods to identify recombination between subtypes of human immunodeficiency virus 1 (HIV-1) fall into a sequential testing trap, in which significance is assessed conditional on parental representative sequences and crossover points (COPs) that maximize the same test statistic. We overcame this shortfall by testing for recombination while inferring parental heritage and COPs using an extended Bayesian multiple change-point model. The model assumes that aligned molecular sequence data consist of an unknown number of contiguous segments that may support alternative topologies or varying evolutionary pressures. We allowed for heterogeneity in the substitution process and specifically tested for intersubtype recombination using Bayes factors. We also developed a new class of priors to assess significance across a wide range of support for recombination in the data. We applied our method to three putative gag gene recombinants. HIV-1 isolate RW024 decisively supported recombination with an inferred parental heritage of AD and a COP 95% Bayesian credible interval of (1,152, 1,178) using the HXB2 numbering scheme. HIV-1 isolate VI557 barely supported recombination. HIV-1 isolate RF decisively rejected recombination as expected, given that the sequence is commonly used as a reference sequence for subtype B. We employed scaled regeneration quantile plots to assess convergence and found this approach convenient to use even for our variable dimensional model parameter space.

Algorithms↗
PubMed2005

TileMap: create chromosomal map of tiling array hybridizations.

MOTIVATION: Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is to develop effective statistical tools to identify genomic loci that show transcriptional or protein binding patterns of interest. RESULTS: A two-step approach is proposed and is implemented in TileMap. In the first step, a test-statistic is computed for each probe based on a hierarchical empirical Bayes model. In the second step, the test-statistics of probes within a genomic region are used to infer whether the region is of interest or not. Hierarchical empirical Bayes model shrinks variance estimates and increases sensitivity of the analysis. It allows complex multiple sample comparisons that are essential for the study of temporal and spatial patterns of hybridization across different experimental conditions. Neighboring probes are combined through a moving average method (MA) or a hidden Markov model (HMM). Unbalanced mixture subtraction is proposed to provide approximate estimates of false discovery rate for MA and model parameters for HMM. AVAILABILITY: TileMap is freely available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm. SUPPLEMENTARY INFORMATION: http://biogibbs.stanford.edu/~jihk/TileMap/index.htm (includes coloured versions of all figures).

Algorithms↗
PubMed2005

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.

MOTIVATION: Protein sequence comparison methods are routinely used to infer the intricate network of evolutionary relationships found within the rapidly growing library of protein sequences, and thereby to predict the structure and function of uncharacterized proteins. In the present study, we detail an improved statistical benchmark of pairwise protein sequence comparison algorithms. We use bootstrap resampling techniques to determine standard statistical errors and to estimate the confidence of our conclusions. We show that the underlying structure within benchmark databases causes Efron's standard, non-parametric bootstrap to be biased. Consequently, the standard bootstrap underpredicts average performance when used in the context of evaluating sequence comparison methods. We have developed, as an alternative, an unbiased statistical evaluation based on the Bayesian bootstrap, a resampling method operationally similar to the standard bootstrap. RESULTS: We apply our analysis to the comparative study of amino acid substitution matrix families and find that using modern matrices results in a small, but statistically significant improvement in remote homology detection compared with the classic PAM and BLOSUM matrices. AVAILABILITY: The sequence sets and code for performing these analyses are available from http://compbio.berkeley.edu/. CONTACT: brenner@compbio.berkeley.edu.

Algorithms↗
PubMed2005

A comparison study: applying segmentation to array CGH data for downstream analyses.

MOTIVATION: Array comparative genomic hybridization (CGH) allows detection and mapping of copy number of DNA segments. A challenge is to make inferences about the copy number structure of the genome. Several statistical methods have been proposed to determine genomic segments with different copy number levels. However, to date, no comprehensive comparison of various characteristics of these methods exists. Moreover, the segmentation results have not been utilized in downstream analyses. RESULTS: We describe a comparison of three popular and publicly available methods for the analysis of array CGH data and we demonstrate how segmentation results may be utilized in the downstream analyses such as testing and classification, yielding higher power and prediction accuracy. Since the methods operate on individual chromosomes, we also propose a novel procedure for merging segments across the genome, which results in an interpretable set of copy number levels, and thus facilitate identification of copy number alterations in each genome. AVAILABILITY: http://www.bioconductor.org

Algorithms↗
PubMed1999

Introgression through rare hybridization: A genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll, Scotland.

In this article we describe the structure of a hybrid zone in Argyll, Scotland, between native red deer (Cervus elaphus) and introduced Japanese sika deer (Cervus nippon), on the basis of a genetic analysis using 11 microsatellite markers and mitochondrial DNA. In contrast to the findings of a previous study of the same population, we conclude that the deer fall into two distinct genetic classes, corresponding to either a sika-like or red-like phenotype. Introgression is rare at any one locus, but where the taxa overlap up to 40% of deer carry apparently introgressed alleles. While most putative hybrids are heterozygous at only one locus, there are rare multiple heterozygotes, reflecting significant linkage disequilibrium within both sika- and red-like populations. The rate of backcrossing into the sika population is estimated as H = 0.002 per generation and into red, H = 0.001 per generation. On the basis of historical evidence that red deer entered Kintyre only recently, a diffusion model evaluated by maximum likelihood shows that sika have increased at approximately 9.2% yr-1 from low frequency and disperse at a rate of approximately 3.7 km yr-1. Introgression into the red-like population is greater in the south, while introgression into sika varies little along the transect. For both sika- and red-like populations, the degree of introgression is 30-40% of that predicted from the rates of current hybridization inferred from linkage disequilibria; however, in neither case is this statistically significant evidence for selection against introgression.

Alleles↗
PubMed2000

Cadaveric versus living donor kidney transplantation: a Medicare payment analysis.

BACKGROUND: We found previously that the clinical advantages of living donor (LD) renal transplantation lead to financial cost savings compared to either cadaveric donation (CAD) or dialysis. Here, we analyze the sources of the cost savings of LD versus CAD kidney transplantation. METHODS: We used United States Renal Data System data to merge United Network for Organ Sharing registry information with Medicare claims data for 1991-1996. Information was available for 42,868 CAD and 13,754 LD transplants. More than 5 million Medicare payment records were analyzed. We calculated the difference in average payments made by Medicare for CAD and LD for services provided during the first posttransplant year. RESULTS: Average total payments were $39,534 and $24,652 for CAD and LD, respectively (P<0.0001) during the first posttransplant year. The largest source of the difference in payments was in inpatient hospitals, representing $10,653.67 (P<0.0001). For patients who had Medicare as the primary payer, average transplant charges were significantly higher for CAD donation ($79,730 vs. $69,547, P<0.0001); average transplant payments demonstrated no statistical differences ($28,483 vs. $28,447, P = 0.858). Therefore, inferred profitability was significantly higher for LD. CONCLUSIONS: Medicare payments are remarkably lower for LD compared to CAD in every category. The single largest cost saving comes from inpatient hospital services. A portion of the savings from LD could be invested in programs to expand living kidney donation.

Cadaver↗
PubMed2025

Tractor Workflow Pipeline: A Scalable Nextflow Framework for Local Ancestry-Aware Genome-Wide Association Studies.

The routine exclusion of admixed individuals from traditional Genome-Wide Association Studies (GWAS) due to concerns about spurious associations has hindered genetic analyses involving multiple ancestries. Tractor GWAS addresses this issue by incorporating local ancestry into its analysis, empowering identification of ancestry-enriched hits and generating ancestry-specific summary statistics. However, Tractor requires accurate genomic phasing and local ancestry inference as prerequisite steps, which requires additional bioinformatics expertise and decision points regarding reference panel setup. To streamline, harmonize, and automate this process, we present a scalable Nextflow workflow that integrates all necessary steps, minimizing the need for manual intervention while remaining modular and customizable. The workflow supports multiple commonly used tools and offers flexibility in how Tractor is implemented. To demonstrate its utility, we applied this pipeline to analyze 32 blood biomarkers in 6,245 two-way AFR-EUR admixed individuals from the UK Biobank. This pipeline ran efficiently at scale, replicated known associations, and identified novel ancestry-specific loci. These novel associations were largely driven by variants present on African ancestral tracts but absent from European tracts, underscoring the value of local ancestry-aware methods in uncovering previously missed genetic signals. By enabling the efficient analysis of admixed individuals, our workflow facilitates Tractor use, paving the way for more broader genetic discovery.

Journal Article↗
PubMed2006

40Ca(alpha, gamma)44Ti reaction in the energy regime of supernova nucleosynthesis.

The 44Ti(t1/2=59 yr) nuclide, an important signature of supernova nucleosynthesis, has recently been observed as live radioactivity by gamma-ray astronomy from the Cas A remnant. We investigate in the laboratory the major 44Ti production reaction 40Ca(alpha, gamma)44Ti (Ec.m. approximately 0.6-1.2 MeV/u by direct off-line counting of 44Ti nuclei. The yield, significantly higher than inferred from previous experiments, is analyzed in terms of a statistical model using microscopic nuclear inputs. The associated stellar rate has important astrophysical consequences, increasing the calculated supernova 44Ti yield by a factor approximately 2 over previous estimates and bringing it closer to Cas A observations.

Journal Article↗
PubMed1985

Quantitative EEG and neuropsychological effects of piracetam and of the association piracetam-lecithin in healthy volunteers.

The electroencephalographic (EEG) and neuropsychological effects of single, oral doses or piracetam (800-6,400 mg) and of its association with lecithin (4,800 mg and 25 g, respectively) were investigated in two groups of healthy volunteers in placebo-controlled studies. The EEG was quantified by power spectral analysis; both parametric and nonparametric procedures were applied to process the EEG and neuropsychological data statistically. The drug plasma concentration was assessed (gas chromatography) in concomitance with the EEG and neuropsychological measurements. Piracetam was found to elicit systematic EEG effects, namely a decrease in the low-frequency components and an increase in the power of the 8.5- to 12.0-Hz and of the fast-frequency components. The EEG modifications were restricted to the anterior scalp areas; its detection by means of parametric statistics was conditioned by the relevant individual variability and was inferred resting upon a number of criteria (indication at nonparametric tests, topography, consistency across subjects, replicability, etc). The correlation between EEG changes and drug plasma concentration was ambiguous, and the compound was not found to be effective on any of the neuropsychological variables considered. The study exemplifies some of the methodological problems in quantitative pharmaco-EEG and emphasizes the relevance of topography and replication.

Brain↗
PubMed2004

D1S80 single-locus discrimination among African populations.

The highly polymorphic D1S80 locus has no known genetic function. However, this variable number of tandem repeats (VNTR) locus has been highly valuable in forensic identification. In this study we report the allele and genotype frequencies of five African populations (Benin, Cameroon, Egypt, Kenya, and Rwanda), which can be used as databases to help characterize populations and identify individuals. The allele frequencies were used to infer genetic associations through phylogenetic, principal component, and G test statistical analyses. Compliance with Hardy-Weinberg equilibrium expectations was determined as were F(ST) estimates, theta p values, and power of discrimination assessment for each population. Our analyses of 28 additional populations demonstrate that the D1S80 locus alone can be used to discriminate geographic and ethnic groups. We have generated databases useful for human identification and phylogenetic studies.

Africa↗
PubMed2002

Excessive daytime sleepiness in Campo Grande general population, Brazil.

The prevalence of excessive daytime sleepiness (EDS) in general population was determined by means of 408 home interviews of adults, in a representative sample of Campo Grande city, Brazil. The random sample was stratified by sex, age and economic social status. EDS was considered in those with indexes 11 or more in the Epworth Sleepiness Scale. Statistics used chi-square, Fisher and Pearson tests; and inferences based on binomial distribution parameters; the significance level was 5% and confidence interval (CI) was 95%. The prevalence of EDS was 18.9% of the general population ( SD=1.9%; CI 15.1% to 22.7%). No significant association was found between EDS and the use of hypnotics, nor with insomnia, body mass index, sex, age, years of schooling, economic social status, marital status, occupation and the use of alternative means to improve sleep. When the sample was separated according to sex, only the male group showed significant association between EDS and actual insomnia (p=0.005).

Adolescent↗
PubMed1998

Congenital eye malformations: clinical-epidemiological analysis of 1,124,654 consecutive births in Spain.

We analyzed Spanish Collaborative Study of Congenital Malformations (ECEMC) data on a series of 1,124,654 consecutive births to study congenital eye malformations from an epidemiological standpoint. We studied their frequencies as well as some causal and clinical aspects. Four hundred fourteen infants had eye malformations, for an overall prevalence of 3.68/10,000 newborns. Most frequent were: anophthalmia/microphthalmia (21.34/100,000), congenital cataract (6.31), coloboma (4.89), corneal opacity (3.11), and congenital glaucoma (2.85). In our data, the tendency of eye malformations to be associated with other congenital abnormalities is evident (only 21.01% of cases were isolated). Eye defects are heterogeneous, since we have observed them in clinical patterns with all modes of inheritance or caused by different environmental agents. Chromosomal syndromes represent 60% of total syndromes, followed by syndromes of autosomal-recessive inheritance (15%), environmental syndromes (10%), autosomal-dominant syndromes (5.83%), and other types which have a lower frequency. Regarding defects associated with eye malformations, most frequent are limb anomalies (affecting 59.3% of multiply malformed cases), auricular/facial (47.1%), central nervous system (42.5%), osteomuscular excluding limbs (42.2%), genital defects (30.6%), oral clefts (29.4%), and the rest of the body systems, which are less frequent. Using the method outlined by Prieto and Martínez-Frías [1996: Am J Med Genet 62:61-67], it was demonstrated that the association of coloboma and anophthalmia/microphthalmia was specific, as was the combination of cataract and anophthalmia/microphthalmia, and that of anophthalmia/microphthalmia with holoprosencephaly. From these statistical associations some pathogenetic relationships in human embryos can be inferred, supporting several previously proposed mechanisms.

Anophthalmos↗
PubMed2004

Model-based assignment and inference of protein backbone Nuclear Magnetic Resonances.

Nuclear Magnetic Resonance (NMR) spectroscopy is a key experimental technique used to study protein structure, dynamics, and interactions. NMR methods face the bottleneck of spectral analysis, in particular determining the resonance assignments, which help define the mapping between atoms in the protein and peaks in the spectra. A substantial amount of noise in spectral data, along with ambiguities in interpretation, make this analysis a daunting task, and there exists no generally accepted measure of uncertainty associated with the resulting solutions. This paper develops a model-based inference approach that addresses the problem of characterizing uncertainty in backbone resonance assignment. We argue that NMR spectra are subject to random variation, and ignoring this stochasticity can lead to false optimism and erroneous conclusions. We propose a Bayesian statistical model that accounts for various sources of uncertainty and provides an automatable framework for inference. While assignment has previously been viewed as a deterministic optimization problem, we demonstrate the importance of considering all solutions consistent with the data, and develop an algorithm to search this space within our statistical framework. Our approach is able to characterize the uncertainty associated with backbone resonance assignment in several ways: 1) it quantifies of uncertainty in the individually assigned resonances in terms of their posterior standard deviations; 2) it assesses the information content in the data with a posterior distribution of plausible assignments; and 3) it provides a measure of the overall plausibility of assignments. We demonstrate the value of our approach in a study of experimental data from two proteins, Human Ubiquitin and Cold-shock protein A from E. coli. In addition, we provide simulations showing the impact of experimental conditions on uncertainty in the assignments.

Journal Article↗
PubMed1996

Analysis of paired ordered categorical data in a factorial design.

In clinical trials and behavioral sciences, there exist situations where paired responses are obtained from each subject on an ordinal scale. Existing methods for analyzing such data in a factorial design are reviewed and new methods are developed with a special emphasis on pre- and post-treatment responses. The distribution of a square table is decomposed into successively independent pairs of discordant vectors, and assuming a logistic model, a statistics is computed to measure the shift in the marginal distributions. The approach is similar to McCullagh's approach (1). Two other criteria are proposed, one based on a Lehmann alternative used for comparing two distribution functions and the other based on a proportional odds model. These criteria are applied to the marginal distributions of a square table. For each case, a statistic measuring lack of marginal homogeneity and its variance are computed for each independent square table of a factorial design. Given such statistics, one can estimate a set of linear contrasts and compute its dispersion matrix for making inference. A numerical example is given.

Double-Blind Method↗
PubMed2004

Evaluation of fracture toughness of a fiber containing dental composite after flexural fatigue.

OBJECTIVE: The purpose of this study was to examine the effect of cyclic loading in four different environments on the fracture toughness of a fiber reinforced resin composite. METHODS: The specimens were 3 x 3 x 25 mm3 bars polished with 320 grit SiC paper. A 60 degrees v-notch was machined 1 mm deep at the midspan of each bar. The specimens were loaded in air, artificial saliva, water, and a 50/50 by volume mixture of ethanol and water at a frequency of 5 Hz with sinusoidal loads cycling between 10 and 20 N for 1, 1000, 10,000 and 100,000 cycles. Specimens were also aged for 4 months in each respective media. Following cyclic loading, the specimens were tested in three-point loading. Statistical analysis consisted of four 2-way ANOVAs followed by Tukey's HSD inference, and two 3-way ANOVAs followed by two-sample t-tests. RESULTS: The ANOVAs indicated no difference in the means of fracture toughness for the set numbers of cycles, but a significant difference for the aging solutions and the aging times. SIGNIFICANCE: Statistical analysis showed a significant decrease of fracture toughness from unaged to aged specimens when aged in air, saliva, and 50/50 ethanol/water. The latter showed the most pronounced decrease. The effect of the 50/50 by volume mixture of ethanol and water would appear to attack the resin matrix and/or the bond between the resin matrix and the filler, which resulted in the observed decrease in fracture toughness. In addition, the significant decrease in fracture toughness following aging is attributed to residual matrix stress around the large fiber filler particles resulting in separation of the fiber filler from the resin matrix.

Air↗
PubMed2003

Robustness of inference of haplotype block structure.

In this report, we examine the validity of the haplotype block concept by comparing block decompositions derived from public data sets by variants of several leading methods of block detection. We first develop a statistical method for assessing the concordance of two block decompositions. We then assess the robustness of inferred haplotype blocks to the specific detection method chosen, to arbitrary choices made in the block-detection algorithms, and to the sample analyzed. Although the block decompositions show levels of concordance that are very unlikely by chance, the absolute magnitude of the concordance may be low enough to limit the utility of the inference. For purposes of SNP selection, it seems likely that methods that do not arbitrarily impose block boundaries among correlated SNPs might perform better than block-based methods.

Algorithms↗
PubMed1990

Conditions for versatile learning, Helmholtz's unconscious inference, and the task of perception.

It is a mistake to consider perception and learning separately because what one learns is strongly constrained by what one perceives, and what one perceives depends on what one has experienced. I shall propose the hypothesis that perception is the computation of a representation that enables us to make reliable and versatile inferences about associations occurring in the world around us--that is, perception prepares the ground for learning. The statistical problem in learning is to determine whether a compound event such as "C followed by U" is a random co-occurrence or a significant association, for if it is the former it would be a mistake to pay any particular attention to C, whereas if it is the latter C is a conditional stimulus for U and a useful predictor for it. Now you cannot decide whether the association is random or not without knowledge of the prior probabilities of C and U: hence on my hypothesis when you perceive an object or event the representation must not only signal "it's there" or "it's happened", but must also make evident (or rapidly accessible) the prior probability of what has been signalled. Furthermore it must do this for all the objects or events that can act as conditional stimuli, and this implies that the representative elements should be statistically independent (or approximately so) in the normal environment. Forms of coding that would do this, and the relationship with Helmholtz's unconscious inference, will be discussed. These considerations imply that the task performed in perception has been overlooked both by learning theorists and by connectionists working on associative and adaptive networks. Coding for independence may be particularly important in understanding the developmental processes during the sensitive period: it may be the operation that leads ontogenetically-timed, activity-dependent, connections to imprint appropriate codes if the animal has experience, but inappropriate codes without experience.

Adaptation, Physiological↗