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At least 19 recordsLinked to original sources
PubMed2005

A study of fitness distance correlation as a difficulty measure in genetic programming.

We present an approach to genetic programming difficulty based on a statistical study of program fitness landscapes. The fitness distance correlation is used as an indicator of problem hardness and we empirically show that such a statistic is adequate in nearly all cases studied here. However, fitness distance correlation has some known problems and these are investigated by constructing an artificial landscape for which the correlation gives contradictory indications. Although our results confirm the usefulness of fitness distance correlation, we point out its shortcomings and give some hints for improvement in assessing problem hardness in genetic programming.

Algorithms↗
PubMedDate not supplied

Risk of injury during alpine and telemark skiing and snowboarding. The equipment-specific distance-correlated injury index.

Estimation of injury risk in alpine sports is difficult. We present a new method of calculating an injury index related to the distance traveled on ski or snowboard. The distance-correlated injury index equals the number of injuries per 100,000 km traveled distance. This injury index can also be correlated to the type of equipment used. The equipment-specific distance-correlated injury index is the same as the distance-correlated injury index, but it is sport-specific. We found the distance-correlated injury index for alpine skiing to be 3.9 (95% Cl = 2.8 to 5.4); for snowboarding, 13.5 (95% Cl = 8.3 to 22.0); and for telemark skiing, 3.0 (95% Cl = 1.0 to 9.4), suggesting a three- to four-times higher incidence of injuries requiring hospital treatment among snowboarders than among alpine and telemark skiers.

Athletic Injuries↗
PubMed2026

Testing for Genetic Interactions in Complex Disease With Distance Correlation.

Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an association measure that characterizes general statistical independence between random variables, not only the linear one. Here, we propose distance correlation as a novel tool for the detection of epistasis from case-control data of single-nucleotide polymorphisms. On the methodological side, we highlight the derivation of the explicit asymptotic null distribution of the test statistic. We show that this is the only way to obtain enough computational speed for the method to be used in practice, in a scenario where the resampling techniques found in the literature are impractical. Our simulations show satisfactory calibration of significance, as well as comparable or better power than existing methodology. We conclude with the application of our technique to a schizophrenia genetics dataset, obtaining biologically sound insights.

Epistasis, Genetic↗
PubMed2005

Fluorophore-quencher distance correlation functions from single-molecule photon arrival trajectories.

We generalize and simplify the method of Yang and Xie (J. Chem. Phys. 2002, 117, 10965) to obtain distance correlation functions from photon arrival trajectories of single fluorophores whose lifetime, [k(r)](-1), depends on the distance to a quencher. It is assumed that this distance does not change during the fluorescence lifetime. The experimental trajectory is first transformed by replacing the delay time (i.e., the interval between the photon arrival and the nearest laser pulse) by a certain function of this delay time. This function is the inverse Laplace transform of r(k), which is the solution of k(r) = 1. The correlation function of the transformed data then directly gives the distance correlation function. Illustrative examples include Förster energy transfer and quenching due to electron transfer.

Diffusion↗
PubMed1995

Correlation distance measurements of the female breast.

Ultrasonic waves propagating through soft tissue experience wavefront distortion. Adaptive wavefront compensation algorithms attempt to correct such distortion. A valuable design parameter is the isoplanatic patch size of the imaging medium. Its lateral extent is the FWHM of the correlation function. The range extent is defined similarly. The significance of the isoplanatic patch is that a new wavefront correction vector must be obtained whenever the ultrasound beam is moved a patch length. This paper reports measurements of wavefront correlation functions as well as statistics of the lateral correlation distance rho d (half the FWHM) within the female breast obtained from a population of 22 women (44 breasts) and measured at 3 and 4 MHz with a large acoustic aperture (9.6 cm). A set of complex wavefronts radiated from single pointlike sources was measured from the opposing side of the breast. The propagation distance was 12 cm. rho d is the distance between two sources at which the correlation between their wavefronts drops to 0.5. The mean value at 3 MHz was found to be less than 1.5 mm for the premenopausal dense breast, 2.5 mm for the premenopausal fatty breast, and 2.0 mm for the postmenopausal breast. The mean value dropped by a factor of 2 at 4 MHz for a group consisting of premenopausal fatty and postmenopausal breasts.

Adult↗
PubMed2003

Short-distance correlation properties of the Lieb-Liniger system and momentum distributions of trapped one-dimensional atomic gases.

We derive exact closed-form expressions for the first few terms of the short-distance Taylor expansion of the one-body correlation function of the Lieb-Liniger gas. As an intermediate result, we obtain the high-p asymptotics of the momentum distribution of both free and harmonically trapped atoms and show that it obeys a universal 1/p(4) law for all values of the interaction strength. We discuss the ways to observe the predicted momentum distributions experimentally, regarding them as a sensitive identifier for the Tonks-Girardeau regime of strong correlations.

Journal Article↗
PubMed1990

Isolation by distance and correlation analysis of distance measures in the study of population structure: example from the Island of Hvar.

Assessment of the population structure on the island of Hvar is based on the analysis of Malécot's isolation by distance model. We have tested the fit of the model by regression analysis of different measures of similarity (genetic kinship) and distance [Hamming's HSM distance for linguistic data; Mahalanobis's D2 distances for anthropometric head and body dimensions, radiogrammetric dimensions of metacarpal bones, physiological (cardiorespiratory) traits, and quantitative dermatoglyphic properties of the digitopalmar complex; and Edwards's E2 for frequencies of erythrocyte antigens]. Good fit of the model for linguistic and anthropometric data, which was demonstrated in previous studies on other eastern Adriatic populations, is confirmed. We compared parameters of the model with those already published for various populations in the eastern Adriatic and other parts of the world. We also evaluated the pattern of correlations between different measures of geographic, biological, and sociocultural distances through principal components analysis and interpreted the results within the context of microevolutionary theory and the population's ethnohistorical background.

Adult↗
PubMed2006

Metric for measuring the effectiveness of clustering of DNA microarray expression.

BACKGROUND: The recent advancement of microarray technology with lower noise and better affordability makes it possible to determine expression of several thousand genes simultaneously. The differentially expressed genes are filtered first and then clustered based on the expression profiles of the genes. A large number of clustering algorithms and distance measuring matrices are proposed in the literature. The popular ones among them include hierarchal clustering and k-means clustering. These algorithms have often used the Euclidian distance or Pearson correlation distance. The biologists or the practitioners are often confused as to which algorithm to use since there is no clear winner among algorithms or among distance measuring metrics. Several validation indices have been proposed in the literature and these are based directly or indirectly on distances; hence a method that uses any of these indices does not relate to any biological features such as biological processes or molecular functions. RESULTS: In this paper we have proposed a metric to measure the effectiveness of clustering algorithms of genes by computing inter-cluster cohesiveness and as well as the intra-cluster separation with respect to biological features such as biological processes or molecular functions. We have applied this metric to the clusters on the data set that we have created as part of a larger study to determine the cancer suppressive mechanism of a class of chemicals called retinoids.We have considered hierarchal and k-means clustering with Euclidian and Pearson correlation distances. Our results show that genes of similar expression profiles are more likely to be closely related to biological processes than they are to molecular functions. The findings have been supported by many works in the area of gene clustering. CONCLUSION: The best clustering algorithm of genes must achieve cohesiveness within a cluster with respect to some biological features, and as well as maximum separation between clusters in terms of the distribution of genes of a behavioral group across clusters. We claim that our proposed metric is novel in this respect and that it provides a measure of both inter and intra cluster cohesiveness. Best of all, computation of the proposed metric is easy and it provides a single quantitative value, which makes comparison of different algorithms easier. The maximum cluster cohesiveness and the maximum intra-cluster separation are indicated by the metric when its value is 0.We have demonstrated the metric by applying it to a data set with gene behavioral groupings such as biological process and molecular functions. The metric can be easily extended to other features of a gene such as DNA binding sites and protein-protein interactions of the gene product, special features of the intron-exon structure, promoter characteristics, etc. The metric can also be used in other domains that use two different parametric spaces; one for clustering and the other one for measuring the effectiveness.

Algorithms↗
PubMed2002

Two class minimax distance transform correlation filter.

A new correlation filter formulation (that we refer to as the minimax distance transform correlation filter (MDTCF) is presented that minimizes the average squared distance from the filtered desired (or true-) class training images to a filtered reference image while maximizing the mean squared distance of the filtered undesired (or false-) class training images to this filtered reference image. This approach increases the separation between the false-class correlation outputs and the true-class correlation outputs. Classification can be performned using the squared distance of a filtered test image to the chosen filtered reference image. We show that the previously introduced distance classifier correlation filter (DCCF) is similar to a special case of MDTCF. We also examine the differences between the DCCF and the MDTCF, and show that MDTCF can offer increased discrimination performance. Also, MDTCF performance is evaluated on two different face databases.

Journal Article↗
PubMed2003

Polynomial distance classifier correlation filter for pattern recognition.

We introduce what is to our knowledge a new nonlinear shift-invariant classifier called the polynomial distance classifier correlation filter (PDCCF). The underlying theory extends the original linear distance classifier correlation filter [Appl. Opt. 35, 3127 (1996)] to include nonlinear functions of the input pattern. This new filter provides a framework (for combining different classification filters) that takes advantage of the individual filter strengths. In this new filter design, all filters are optimized jointly. We demonstrate the advantage of the new PDCCF method using simulated and real multi-class synthetic aperture radar images.

Journal Article↗
PubMed1979

Light scattering of normal human lens I. Application of random density and orientation fluctuation theory.

Light-scattering intensities in the I parallel and I+ mode were obtained on thin sections of three human lenses. Random density and orientation fluctuation theory, without cross correlation, was employed to evaluate light-scattering parameters. Both the density correlation distances, as well as the orientation correlation distances, were related to structural elements in the lens fiber cell that have been observed by other investigators with different techniques. The magnitude of these fluctuations were evaluated, and it was demonstrated that the density fluctuations are the main contributors to light scattering in normal human lenses. Changes in the light-scattering parameters were evaluated as a function of position within the lens. The changes observed agree with the biochemical data in the literature that reflects that an aging process occurs when one proceeds from the periphery of the lens toward the center.

Adult↗
PubMed2004

Rivers influence the population genetic structure of bonobos (Pan paniscus).

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

Africa↗
PubMed2006

Y-chromosome analysis confirms highly sex-biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus).

Dispersal is a rare event that is difficult to observe in slowly maturing, long-lived wild animal species such as the bonobo. In this study we used sex-linked (mitochondrial DNA sequence and Y-chromosome microsatellite) markers from the same set of individuals to estimate the magnitude of difference in effective dispersal between the sexes and to investigate the long-term demographic history of bonobos. We sampled 34 males from four distinct geographical areas across the bonobo distribution range. As predicted for a female-dispersing species, we found much higher levels of differentiation among local bonobo populations based upon Y-chromosomal than mtDNA genetic variation. Specifically, almost all of the Y-chromosomal variation distinguished populations, while nearly all of the mtDNA variation was shared between populations. Furthermore, genetic distance correlated with geographical distance for mtDNA but not for the Y chromosome. Female bonobos have a much higher migration rate and/or effective population size as compared to males, and the estimate for the mitochondrial TMRCA (time to most recent common ancestor) was approximately 10 times greater than the estimate for the Y chromosome (410,000 vs. 40,000-45,000). For humans the difference is merely a factor of two, suggesting a more stable demographic history in bonobos in comparison to humans.

Analysis of Variance↗
PubMed1998

The clinical utility of a six-minute walk test in peripheral arterial occlusive disease patients.

OBJECTIVES: To determine the test-retest reliability of the distance covered and the steps taken to complete a 6-minute walk test by peripheral arterial occlusive disease (PAOD) patients with intermittent claudication. To determine the relationship between the total distance and steps covered during the 6-minute walk test and clinical measures of PAOD severity. DESIGN: Cross-sectional design. SETTING: The Claude Pepper Older Americans Independence Center at the University of Maryland at Baltimore. PARTICIPANTS: Sixty-four PAOD patients between the ages of 45 and 88 years (age = 68 +/- 7 years, ankle/brachial index (ABI) = .61 +/- .19) were recruited from the Vascular Clinic at the Baltimore Veterans Affairs Medical Center and from radio and newspaper advertisements. MEASUREMENTS: Patients were assessed on a 6-minute walk test and a treadmill graded exercise test. A second 6-minute walk test was administered approximately 1 week later. Patients also were characterized in regard to blood pressure in the arms and legs, ABI, anthropometry, body composition, and physical activity. RESULTS: The distances walked during the two 6-minute walk tests were similar (350 +/- 78 m vs 360 +/- 73 m), resulting in a high reliability coefficient (R = .94) and a low coefficient of variation (10.4%). The total steps taken during the 6-minute walk test also were similar (562 +/- 113 steps vs 587 +/- 107 steps), resulting in a high reliability coefficient (R = .90) and a low coefficient of variation (11.7%). Furthermore, the 6-minute walking distance correlated with the distances to onset (r = .346, P = .007) and with maximal claudication pain (r = .525, P < .001) during the treadmill test as well as with ABI (r = .552, P < .001). CONCLUSION: The 6-minute walk test yields highly reliable measurements, which are related to the functional and hemodynamic severity of PAOD, in patients with intermittent claudication.

Aged↗
PubMed1988

Reproducibility of walking test results in chronic obstructive airways disease.

Thirty six patients with chronic airflow obstruction were studied to examine (1) the reproducibility and order effect of repeated walking tests when performed over consecutive days or consecutive weeks; (2) the correlation between walking distance and spirometric measurements; and (3) the effect of static visual clues on performance. In study 1, where 12 patients performed 12 walks over three consecutive days, five minute walking distance increased by 33% between walks 1 and 12, half of the increase occurring after the first three walks. In study 2, where 24 patients performed 12 walks over four consecutive weeks, five minute walking distance increased by 8.5% between walks 1 and 12. A learning effect was seen over the first nine walks. Static visual clues to performance did not affect the distance walked. Spirometric measurements showed no order effect in either study. Although walking distance correlated significantly with FEV1, forced vital capacity, and peak expiratory flow, these measurements were poor predictors of exercise performance. The learning effects seen on repeated performance of walking tests over short intervals should be considered when an individual's response to treatment is being interpreted. When walking tests are used in clinical trials a placebo group or randomised crossover design is essential.

Aged↗