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PubMed1989

Characterizing life events as risk factors for depression: the role of fateful loss events.

Empirical associations between life events and health are often weak, in part because event exposure measures may group together very different kinds of experiences within a single event category. Attempts to refine the measures (by using respondents' subjective appraisals of event stressfulness or by taking into consideration situational and personal factors that influence the contextual threat of the events) may strengthen the association, but they cloud the clarity of any causal inference by confounding the measure with extraneous variation. Instead, the use of descriptive information about what actually happened before, during, and after each event is recommended to define exposure to potent, fateful life events. In a comparison of 96 patients with major depression and 404 community residents with no apparent depression, the odds that a person would have experienced one or more events meeting criteria for fatefulness and disruptiveness was 2.5 times greater in the depressed group.

Adult↗
PubMed2004

Assessing interactive causal influence.

The discovery of conjunctive causes--factors that act in concert to produce or prevent an effect--has been explained by purely covariational theories. Such theories assume that concomitant variations in observable events directly license causal inferences, without postulating the existence of unobservable causal relations. This article discusses problems with these theories, proposes a causal-power theory that overcomes the problems, and reports empirical evidence favoring the new theory. Unlike earlier models, the new theory derives (a). the conditions under which covariation implies conjunctive causation and (b). functions relating observable events to unobservable conjunctive causal strength. This psychological theory, which concerns simple cases involving 2 binary candidate causes and a binary effect, raises questions about normative statistics for testing causal hypotheses regarding categorical data resulting from discrete variables.

Humans↗
PubMed2006

Spectral characteristics of longitudinal corneal apex velocities and their relation to the cardiopulmonary system.

PURPOSE: To study the naturally occurring kinetic characteristics of corneal surface. METHODS: The right eyes of three subjects (young, early presbyope, and presbyope) were examined. Cardiac signal and longitudinal corneal apex movements were simultaneously measured with electrocardiography (ECG) and a high-speed videokeratoscope, respectively. Time, frequency, and combined time-frequency representations of the acquired signals were derived to establish their temporal and spectral contents. Coherence analysis was used to assess the correlation between the corneal apex velocities and the cardiopulmonary system. RESULTS: In all measurements, longitudinal corneal apex velocity signals showed close correlation with the corresponding ECG signals. The signatures of the pulse frequency, which was inferred from the ECG spectra and their variations in time, were clearly visible in the spectral content of corneal apex velocities. For the young subject, the correlation was the strongest and all of the spectral content of the pulse signal including the harmonics was propagating to the corneal apex velocities. For the other two subjects, there was a clear propagation of the pulse signal itself but not of all pulse harmonics. CONCLUSIONS: Longitudinal movements of the corneal apex are closely related to the cardiopulmonary system. The differences in propagation of pulse harmonics to the corneal apex velocities for different subjects suggest that the frequency characteristics of apex velocity could be related to pulsative variations in the intraocular pressure and biomechanical properties of the eye. These findings could potentially be used in noninvasive assessment of the hemodynamic status of the eye with high-speed videokeratoscopy.

Adult↗
PubMed2004

Estimating genome conservation between crop and model legume species.

Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion/deletion of individual genes or groups of genes and lineage-specific expansion/contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.

Crops, Agricultural↗
PubMed1989

Y chromosome evolution in the subgenus Mus (genus Mus).

A 305 base pair DNA sequence isolated from the Y chromosome of the inbred mouse strain C57BL/10 was used to investigate the pattern and tempo of evolution of Y chromosome DNA sequences for five species in the subgenus Mus, including Mus spretus, Mus hortulanus, Mus abbotti, Mus musculus and Mus domesticus. Variation in hybridization patterns between species was characterized by differences in fragment lengths of both intensely and faintly hybridizing fragments, whereas variation in hybridization patterns within species was characterized primarily by differences in fragment lengths of faintly hybridizing fragments. Phylogenetic analyses were conducted based on fragment size variation within and among species. Phylogenetic relationships inferred from these analyses partly agree with the phylogenetic relationships obtained from biochemical and mitochondrial DNA data. We conclude that a set of DNA sequences common to the Y chromosomes of a closely related group of species in the subgenus Mus has evolved rapidly as reflected by sequence divergence and sequence amplification.

Animals↗
PubMed2000

Hitchhiking under positive Darwinian selection.

Positive selection can be inferred from its effect on linked neutral variation. In the restrictive case when there is no recombination, all linked variation is removed. If recombination is present but rare, both deterministic and stochastic models of positive selection show that linked variation hitchhikes to either low or high frequencies. While the frequency distribution of variation can be influenced by a number of evolutionary processes, an excess of derived variants at high frequency is a unique pattern produced by hitchhiking (derived refers to the nonancestral state as determined from an outgroup). We adopt a statistic, H, to measure an excess of high compared to intermediate frequency variants. Only a few high-frequency variants are needed to detect hitchhiking since not many are expected under neutrality. This is of particular utility in regions of low recombination where there is not much variation and in regions of normal or high recombination, where the hitchhiking effect can be limited to a small (<1 kb) region. Application of the H test to published surveys of Drosophila variation reveals an excess of high frequency variants that are likely to have been influenced by positive selection.

Animals↗
PubMed2001

An analysis of anemia and child mortality.

The relationship of anemia as a risk factor for child mortality was analyzed by using cross-sectional, longitudinal and case-control studies, and randomized trials. Five methods of estimation were adopted: 1) the proportion of child deaths attributable to anemia; 2) the proportion of anemic children who die in hospital studies; 3) the population-attributable risk of child mortality due to anemia; 4) survival analyses of mortality in anemic children; and 5) cause-specific anemia-related child mortality. Most of the data available were hospital based. For children aged 0-5 y the percentage of deaths due to anemia was comparable for reports from highly malarious areas in Africa (Sierra Leone 11.2%, Zaire 12.2%, Kenya 14.3%). Ten values available for hemoglobin values <50 g/L showed a variation in case fatality from 2 to 29.3%. The data suggested little if any dose-response relating increasing hemoglobin level (whether by mean value or selected cut-off values) with decreasing mortality. Although mortality was increased in anemic children with hemoglobin <50 g/L, the evidence for increased risk with less severe anemia was inconclusive. The wide variation for mortality with hemoglobin <50 g/L is related to methodological variation and places severe limits on causal inference; in view of this, it is premature to generate projections on population-attributable risk. A preliminary survival analysis of an infant cohort from Malawi indicated that if the hemoglobin decreases by 10 g/L at age 6 mo, the risk of dying becomes 1.72 times higher. Evidence from a number of studies suggests that mortality due to malarial severe anemia is greater than that due to iron-deficiency anemia. Data are scarce on anemia and child mortality from non-malarious regions. Primary prevention of iron-deficiency anemia and malaria in young children could have substantive effects on reducing child mortality from severe anemia in children living in malarious areas.

Adolescent↗
PubMed2001

Variation in Bordetella bronchiseptica flaA does not correlate with typing by macro-restriction analysis by pulsed-field gel electrophoresis.

A genotyping method based on PCR-RFLP analysis of the flagellin gene (flaA) was applied to 30 mainly feline isolates of Bordetella bronchiseptica. These isolates were separated into three PCR-RFLP groups with the restriction endonucleases HaeIII, MspI, MboI and RsaI. flaA nucleotide sequences representing each of the three groups differed from each other by 11-13%. One of the groups exhibited far greater flaA sequence identity with the cryptic flagellin gene sequence of B. pertussis (>97%) than with flaA sequences from representatives of the other B. bronchiseptica PCR-RFLP groups. Amongst the 30 isolates were at least 10 representing each of the two major genotypes (A and B) identified in a previous study by macro-restriction analysis and pulsed-field gel electrophoresis (PFGE), as well as representatives of other less common genotypes. Each of the major PFGE genotypes contained strains representing more than one flagellin genotype. Indeed, there was no correlation between the two molecular typing methods. PFGE analysis may identify differences due to genomic re-arrangements rather than genuine variations in gene content. If so, relationships inferred on the basis of PFGE or other molecular methods for whole genome comparison should be treated with caution.

Bacterial Typing Techniques↗
PubMed2006

Quantifying the influence of sociality on population structure in bottlenose dolphins.

1. The social structure of a population plays a key role in many aspects of its ecology and biology. It influences its genetic make-up, the way diseases spread through it and the way animals exploit their environment. However, the description of social structure in nonprimate animals is receiving little attention because of the difficulty in abstracting social structure from the description of association patterns between individuals. 2. Here we focus on recently developed analytical techniques that facilitate inference about social structure from association patterns. We apply them to the population of bottlenose dolphins residing along the Scottish east coast, to detect the presence of communities within this population and infer its social structure from the temporal variation in association patterns between individuals. 3. Using network analytical techniques, we show that the population is composed of two social units with restricted interactions. These two units seem to be related to known differences in the ranging pattern of individuals. By examining social structuring at different spatial scales, we confirm that the identification of these two units is the result of genuine social affiliation and is not an artefact of their spatial distribution. 4. We also show that the structure of this fission-fusion society relies principally on short-term casual acquaintances lasting a few days with a smaller proportion of associations lasting several years. These findings highlight how network analyses can be used to detect and understand the forces driving social organization of bottlenose dolphins and other social species.

Animals↗
PubMed2002

Ecological statistics of Gestalt laws for the perceptual organization of contours.

Although numerous studies have measured the strength of visual grouping cues for controlled psychophysical stimuli, little is known about the statistical utility of these various cues for natural images. In this study, we conducted experiments in which human participants trace perceived contours in natural images. These contours are automatically mapped to sequences of discrete tangent elements detected in the image. By examining relational properties between pairs of successive tangents on these traced curves, and between randomly selected pairs of tangents, we are able to estimate the likelihood distributions required to construct an optimal Bayesian model for contour grouping. We employed this novel methodology to investigate the inferential power of three classical Gestalt cues for contour grouping: proximity, good continuation, and luminance similarity. The study yielded a number of important results: (1) these cues, when appropriately defined, are approximately uncorrelated, suggesting a simple factorial model for statistical inference; (2) moderate image-to-image variation of the statistics indicates the utility of general probabilistic models for perceptual organization; (3) these cues differ greatly in their inferential power, proximity being by far the most powerful; and (4) statistical modeling of the proximity cue indicates a scale-invariant power law in close agreement with prior psychophysics.

Form Perception↗
PubMed2005

Quantifying and addressing parameter indeterminacy in the classical twin design.

The classical twin design (CTD) is the most common method used to infer genetic and environmental causes of phenotypic variation. As has long been acknowledged, different combinations of the common environment/assortative mating, and additive, dominant, and epistatic genetic effects can lead to the same observed covariation between twin pairs, meaning that there is an inherent indeterminacy in parameter estimates arising from the CTD. The CTD circumvents this indeterminacy by assuming that higher-order epistasis is negligible and that the effects of either dominant genetic variation or the common environment are nonexistent. These assumptions, however, lead to consistent biases in parameter estimation. The current paper quantifies these biases and discusses alternative strategies for dealing with parameter indeterminacy in twin designs. One strategy is to model the similarity among other relatives in addition to twins (extended twin-family designs), which reduces but does not eliminate indeterminacy in parameter estimates. A more general strategy, applicable to all twin designs, is to present the parameter indeterminacy explicitly, as in a graph. Presenting the space of mathematically equally likely parameter values is important, not only because it aids the proper interpretation of twin design findings, but also because it keeps behavioral geneticists themselves mindful of methodological assumptions that can easily go unexamined.

Humans↗
PubMed2007

Transferring critically ill patients out of hospital improves the standardized mortality ratio: a simulation study.

BACKGROUND: Transferring critically ill patients to other acute care hospitals may artificially impact benchmarking measures. We sought to quantify the effect of out-of-hospital transfers on the standardized mortality ratio (SMR), an outcome-based measure of ICU performance. METHODS: We performed a cohort study and Monte Carlo simulation using data from 85 ICUs participating in the acute physiology and chronic health evaluation (APACHE) clinical information system from 2002 to 2003. The SMR (observed divided by expected hospital mortality) was calculated for each ICU using APACHE IV risk adjustment. A set number of patients was randomly assigned to be transferred out alive rather than experience their original outcome. The SMR was recalculated, and the mean simulated SMR was compared to the original. RESULTS: The mean (+/- SD) baseline SMR was 1.06 +/- 0.19. In the simulation, increasing the number of transfers by 2% and 6% over baseline decreased the SMR by 0.10 +/- 0.03 and 0.14 +/- 0.03, respectively. At a 2% increase, 27 ICUs had a decrease in SMR of > 0.10, and two ICUs had a decrease in SMR of > 0.20. Transferring only one additional patient per month was enough to create a bias of > 0.1 in 27 ICUs. CONCLUSIONS: Increasing the number of acute care transfers by a small amount can significantly bias the SMR, leading to incorrect inference about ICU quality. Sensitivity to the variation in hospital discharge practices greatly limits the use of the SMR as a quality measure.

APACHE↗
PubMed2006

Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes.

We present a Bayesian framework for inferring spatial preferences of recombination from multiple putative recombinant nucleotide sequences. Phylogenetic recombination detection has been an active area of research for the last 15 years. However, only recently attempts to summarize information from several instances of recombination have been made. We propose a hierarchical model that allows for simultaneous inference of recombination breakpoint locations and spatial variation in recombination frequency. The dual multiple change-point model for phylogenetic recombination detection resides at the lowest level of our hierarchy under the umbrella of a common prior on breakpoint locations. The hierarchical prior allows for information about spatial preferences of recombination to be shared among individual data sets. To overcome the sparseness of breakpoint data, dictated by the modest number of available recombinant sequences, we a priori impose a biologically relevant correlation structure on recombination location log odds via a Gaussian Markov random field hyperprior. To examine the capabilities of our model to recover spatial variation in recombination frequency, we simulate recombination from a predefined distribution of breakpoint locations. We then proceed with the analysis of 42 human immunodeficiency virus (HIV) intersubtype gag recombinants and identify a putative recombination hotspot.

Animals↗
PubMed2006

Maxillary sinus septa: prevalence, height, location, and morphology. A reformatted computed tomography scan analysis.

BACKGROUND: The sinus lift technique may be difficult to perform if an aberrant sinus anatomy is encountered during surgical exposure, such as when a septum is present on the sinus floor. The objective of this study was to determine the prevalence, size, location, and morphology of maxillary sinus septa in the atrophic/edentulous and non-atrophic/dentate maxillary segments. METHODS: The sample population consisted of 100 patients (41 women and 59 men, with a mean age of 50 years, ranging between 19 and 87 years) for whom treatment was being planned for implant-supported restorations. Reformatted computerized tomograms (CT) from 200 sinuses were analyzed using imaging software. RESULTS: The prevalence of one or more septa per sinus was found to be 26.5% (53/200), 31.76% (27/85), and 22.61% (26/115) in the overall study population and the atrophic/edentulous and the non-atrophic/dentate maxillary segments, respectively. In the analysis of the anatomic location of the septa within the sinus, it was revealed that 15 (25.4%) were located in the anterior region, 30 (50.8%) in the middle region, and 14 (23.7%) in the posterior region. The measured heights of the septa varied among the different areas. The mean heights of the septa were 1.63 +/- 2.44, 3.55 +/- 2.58, and 5.46 +/- 3.09 mm in the lateral, middle, and medial areas, respectively. CONCLUSIONS: It can be inferred that there is a wide anatomical variation in the prevalence, size, location, and morphology of maxillary sinus septa, irrespective of the degree of atrophy. Therefore, to prevent the likelihood of complications arising during sinus augmentation procedures, a thorough and extensive understanding of the anatomic structures inherent to the maxillary sinus is indispensable.

Adolescent↗
PubMed2004

A morphological study on the human obturator externus muscle with reference to anomalous muscle and anomalous fasciculus originating from the obturator externus muscle.

To elucidate the essential nature of the human obturator externus muscle (OE), the gross anatomy of the anomalous muscle and anomalous fasciculus originating from this muscle as well as the posterior division of the obturator nerve (P) were examined in 73 thighs of 45 Japanese adult cadavers. The investigation of anomalous muscle and anomalous fasciculus was effected by observation of the supernumerary muscular branch and supernumerary muscular twig from the P. The anomalous muscle occurring between the adductor brevis muscle (AB) and adductor minimus muscle (AMi) (37/73 thighs; 50.7%) and the anomalous fasciculus fused to the posterior surface of the AMi (18/73 thighs; 24.7%) were detected. It was demonstrated by the course of the P and the suppling nerve, that the OE was divided into its superior fasciculus (or fasciculi) (SF) and main belly by the P, moreover the anomalous muscle originated from the former and the anomalous fasciculus from the latter. Presumably, in the process of ontogeny, the SF of the original OE retained its original morphology (23/73 thighs; 31.5%), a part of the SF was converted to anomalous muscle (27/73 thighs; 37.0%), the entire SF was converted to anomalous muscle (10/73 thighs; 13.7%), and the entire SF underwent retrogression and disappeared (13/73 thighs; 17.8%). The presence (50/73 thighs; 68.5%) or absence (23/73 thighs; 31.5%) of piercing of the OE by the P seemed to depend upon the circumstances surrounding the morphological change in the SF. The original OE was considered to occur as an OE pierced by the P not possessing any supernumerary muscular branch or twig. Actually, the original OE was confirmed to occur with a low frequency (15/73 thighs; 20.5%). It was inferred that the original OE readily underwent variation in the process of ontogeny due to the influence of the obturator nerve. The segmental composition of the obturator nerve was considered not to be involved in the morphological change in the OE.

Adult↗
PubMed2004

Genetic parameters for stillbirth in Danish Holstein cows using a Bayesian threshold model.

The objective of this study was to make an inference about the direct and maternal genetic variation of stillbirth for first-calving Holstein cows and to estimate the effect of breed and heterosis for original Danish black and white and Holstein-Friesian. A Bayesian threshold model, which included correlated genetic effects of sires and maternal grandsires was used. Marginal posterior distributions of effects were obtained using Gibbs sampling. Point estimates were compared with results from a linear model using REML. Data with and without twins were analyzed and models with and without effects of breed and heterosis were fitted, but estimates of genetic parameters were almost identical. In all the analyses with threshold models, the marginal posterior mean (and standard deviation) was 0.10 (0.014) for the direct heritability, 0.13 (0.015) for the maternal heritability, and 0.05 (0.10) for the genetic correlation between direct and maternal effects. The stillbirth rate tended to increase with a higher proportion of Holstein-Friesian in the calf and in the dam, but no effects of breed and heterosis were significant. Joint sampling of all location parameters was found superior to univariate sampling in terms of much better mixing properties of the fixed effects. Based on the results showing genetic variation for stillbirth at first calving, both the direct and the maternal effect could be included in the breeding program.

Animals↗
PubMed2026

POISE: Spectral Inference of Parent-of-Origin Effects in Unlabeled Genomic Data.

MOTIVATION: Parent of Origin Effects (POEs), where the effect of an an allele on a phenotype differs based on maternal or paternal inheritance implicated in growth, metabolism, and neurodevelopment. Traditional tests for POEs require family data to determine parental origins of transmitted alleles. Given that such studies are expensive and time consuming compared to genome-wide association studies (GWAS), tests that function absent inheritance information are highly desirable. We develop a method, based on community detection from machine learning, that infers POEs via a spectral decomposition, obtains confidence intervals via a non-parametric bootstrap, and safeguards against confounding by non POE sources of variation. We refer to our method as Parent of Origin Inference via Spectral Estimation (POISE). RESULTS: We demonstrate that POISE is well-calibrated under both Gaussian and heavy-tailed noise in simulation studies, with improved robustness to true POEs compared to existing covariance-based tests. POISE provides per-trait effect estimates with bias-corrected bootstrap confidence intervals and incorporates an information-theoretic minimum detectable effect size that filters unreliable estimates, conferring robustness to covariance-deflating variance QTL. We then apply POISE to GWAS data from the UK Biobank using BMI, LDL cholesterol, and HDL cholesterol. POISE recovers established POE loci and identifies 134 additional variants at genes implicated in lipid metabolism, immune regulation, and growth. AVAILABILITY AND IMPLEMENTATION: The code for this method in Python is available at https://github.com/bystrogenomics/POISE.

Community Detection↗
PubMed2001

Chromosomal effects of rapid gene evolution in Drosophila melanogaster.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.

Alleles↗