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PubMed2002

Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets.

We introduce a new approach to estimate the evolutionary distance between two sequences. This approach uses a tree with three leaves: two of them correspond to the studied sequences, whereas the third is chosen to handle long-distance estimation. The branch lengths of this tree are obtained by likelihood maximization and are then used to deduce the desired distance. This approach, called TripleML, improves the precision of evolutionary distance estimates, and thus the topological accuracy of distance-based methods. TripleML can be used with neighbor-joining-like (NJ-like) methods not only to compute the initial distance matrix but also to estimate new distances encountered during the agglomeration process. Computer simulations indicate that using TripleML significantly improves the topological accuracy of NJ, BioNJ, and Weighbor, while conserving a reasonable computation time. With randomly generated 24-taxon trees and realistic parameter values, combining NJ with TripleML reduces the number of wrongly inferred branches by about 11% (against 2.6% and 5.5% for BioNJ and Weighbor, respectively). Moreover, this combination requires only about 1.5 min to infer a phylogeny of 96 sequences composed of 1,200 nucleotides, as compared with 6.5 h for FastDNAml on the same machine (PC 466 MHz).

Computer Simulation↗

PubMed1998

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino acid frequencies. These frequencies determine the maximum dissimilarity expected for highly diverged but functionally and structurally conserved sequences, and hence are crucial for estimating long distances. We introduce a codon-level model of coding sequence evolution in which position-specific amino acid frequencies are free parameters. In our implementation, these are estimated from an alignment using methods described previously. We use simulations to demonstrate the importance and feasibility of modeling such behavior; our model produces linear distance estimates over a wide range of distances, while several alternative models underestimate long distances relative to short distances. Site-to-site differences in rates, as well as synonymous/nonsynonymous and first/second/third-codon-position differences, arise as a natural consequence of the site-to-site differences in amino acid frequencies.

Amino Acids↗

PubMed1998

Assessment of oropharyngeal distance in children using magnetic resonance imaging.

UNLABELLED: Rational determination of oral airway size in children must account for the oropharyngeal length. We used magnetic resonance imaging (MRI) to measure the distance from the teeth/gums to the prevertebral pharyngeal space and created algorithms to predict this distance based on age, weight, and gender. After institutional review board approval, we reviewed 200 MRI head scans of children 0-17 yr old. Patient information, including midline distance from teeth/gums to prevertebral space (L1) and distance along a perpendicular line from L1 to the epiglottis tip (L2), was recorded. Two groups (Group 1 (n = 100) training group, Group 2 (n = 100) validation group) were then randomly selected from this sample. Predictive models created using Group 1 were tested using Group 2 as the sample group. Oropharyngeal distance was related to age, weight, and gender. A prediction equation using all data was estimated to determine the final model: predicted L1 = 5.51 + 0.25 (age [years]) -0.01 (age2) + 0.02 (weight [kg]) + 0.12 (male). We report equations to predict the oropharyngeal distance based on age, weight, and gender in children. The oral airway size will be 1-2 cm longer than these measurements to position the tooth/lip guard outside the lip. Variability in the distance to the epiglottis must be considered when selecting proper oral airway size for any child. This information will provide the foundation for a more rational determination of the proper oral airway size for infants and children. IMPLICATIONS: Age, weight, and gender can be used to predict the length of the oropharynx in children as determined by midline sagittal magnetic resonance image of the airway. Prediction of this length will lead to a more rational determination of proper oral airway size for infants and children and, potentially, more effective airway management.

Adolescent↗

PubMed2002

Threshold, comfortable level and impedance changes as a function of electrode-modiolar distance.

OBJECTIVE: The study investigated the hypothesis that threshold and comfortable levels recorded from cochlear implant patients would reduce, and dynamic range increase, as distance of the electrode from the modiolar wall (radial distance) decreases. Two groups of cochlear implant patients participated; one group using the Nucleus' 24 Contour electrode array, and one group using the Nucleus standard straight (banded) array. The Nucleus 24 Contour array has been shown in temporal bone studies to lie closer to the modiolus than the banded array. The relationship of electrode impedance and radial distance is also investigated. DESIGN: The study, conducted at three centers, evaluated 21 patients using the Contour array, and 36 patients using the banded array. For each patient, threshold, comfortable levels and dynamic range were measured at four time points. Common ground electrode impedance was recorded clinically from each patient, at time intervals up to 12 wk. An estimate of the radial distance of the electrode from the modiolus was made by analysis of Cochlear view x-rays. RESULTS: Threshold and comfortable levels were significantly lower for the Nucleus 24 Contour array than for the banded array. However, dynamic range measurements did not show the predicted increase. In a majority of subjects, a significant correlation was found between the estimated radial distance of the electrode from the modiolus and the measured threshold and comfortable levels. This trend was not observed for dynamic range. The analysis indicates that other factors than radial distance are involved in the resultant psychophysical levels. Clinical impedance measures (common ground) were found to be significantly higher for the Contour array. However, the electrodes on the Contour array are half-rings, which are approximately only half the geometric size of the full rings as electrodes of the standard array. When the geometric electrode area in the two array designs are normalized, the trends in the electrode impedance behavior are similar. CONCLUSIONS: The results support the hypothesis that the relationship between the radial distance of the electrode and the psychophysical measures are influenced by patterns of fibrous tissue growth and individual patient differences, such as etiology and neural survival. Impedance measures for the Nucleus 24 Contour electrode array were higher than the banded electrode array, but this is primarily due to the reduction in electrode surface area. The different outcomes in impedance over time suggest differences in the relative contributions of the components of impedance with the two arrays.

Acoustic Impedance Tests↗

PubMed1998

The gender difference in distance running performance has plateaued: an analysis of world rankings from 1980 to 1996.

PURPOSE: Annual world rankings from 1980-1996 were used i) to determine if the gender difference in distance running events has stabilized, and ii) to examine whether the relative decline in pace as race distance increases is different between men and women. World best (WB) and 100th best times in the 1500 m and the marathon (42 km) for each of the 17 years were the indices used to represent overall trends in men's vis-à-vis women's distance running. METHODS: These data were analyzed using regression analyses to develop and compare gender-specific equations. In the 1500 m, the gender difference in WB times (11.1 +/- 1.1%) was consistent from 1980 to 1996, and the slight rate of improvement in event depth (i.e., 100th rankings) was similar for men and women. RESULTS: In the marathon, the gender difference in WB times (11.2 +/- 0.9%) was essentially the same as for the 1500 m. In 1980, the marathon was a fairly new event for the women, having only just been sanctioned by the International Amateur Athletics Federation (IAAF). As a consequence, the depth of the field increased quickly from 1980 to 1984. Since the mid-1980s, the rate of improvement for women in 100th-ranked times has leveled off to equal that of men. The average declines in relative pace for men and women from the 1500 m to the 10 km to the marathon were found to be remarkably similar with no diminishing of the gender difference as race distance increased. CONCLUSIONS: Based on worldwide indices of competitive distance running, the gender difference in distance running performance has plateaued in recent years. Concomitantly, over the past decade, opportunities for women to train and compete have approached parity with those of men. It is likely that the current gender difference in performance will remain fairly constant because of biological differences between men and women that give men an advantage in distance running.

Databases as Topic↗

PubMed2002

Association of swim distance and age with body composition in adult female swimmers.

PURPOSE: The purpose of this investigation was to examine the relationship between average weekly swimming distance and age with body composition in adult female endurance swimmers. METHODS: Thirty-five women, aged 21-73 yr, volunteered to participate. Weekly swimming distance was determined from a self-reported exercise log. Body composition was estimated by dual-energy x-ray absorptiometry (DXA), waist circumference, abdominal sagittal diameter, and skinfold thickness measures. Associations between swimming distance and age with body composition were examined using regression analysis. RESULTS: Swimming distance had shared variances as follows: 23% with percent body fat, 26% with waist circumference, 20% with abdominal sagittal diameter, and 20%, 24%, and 22% with subscapular, suprailiac, and triceps skinfolds, respectively. Abdominal sagittal diameter was the only adiposity measure demonstrating a stronger relationship with age (R2 = 0.29, P = 0.00) than with swimming distance (R2 = 0.20, P = 0.03). Bone mineral content was linearly related to swimming distance and age having a negative association with age (r2 = 0.18, P = 0.01) and a positive one with swimming distance (r2 = 0.12, P = 0.05). In addition, there was a negative linear association observed between swimmer age and bone mineral density (r2 = 0.12, P = 0.05). CONCLUSION: In these female adults, endurance swimming was mildly associated with body adiposity. Age was not associated with body fat mass independently from swimming activity except with that measure reflecting abdominal visceral fat deposits. These data suggest that greater fat mass in female swimmers is more strongly related to lower levels of exercise than to age but that there is an additional influence of age on fat accumulation in the intra-abdominal area of the body.

Adipose Tissue↗

PubMed2004

Determination of the length of anteromedial screw trajectory by measuring interforaminal distance in the first sacral vertebra.

STUDY DESIGN: Measurements of the length of pediculocorporeal screw trajectory were performed on bony sacra. Outer interforaminal distances of the first sacral vertebra were measured on bony sacra and anteroposterior sacral radiographs. OBJECTIVES: To demonstrate the correlation of the length of pediculocorporeal screw trajectory of the first sacral vertebra on bony specimens with outer interforaminal distances on their anteroposterior radiographs. SUMMARY OF BACKGROUND DATA: Posterior fixation of the lumbosacral vertebra has been used in the treatment of unstable lumbar spine disorders. To achieve the strongest biomechanical stability and to avoid injury to anterior sacral structures for anteromedial insertion of the posterior transpedicular screw to the first sacral vertebra (S1), it is crucial to determine the optimum screw length for both unicortical and bicortical screw placement. METHODS: Fifty-one dry bony adult sacra were measured and correlated with anteroposterior lumbosacral radiographs. The length of S1 screw trajectory, which was accepted as between inferolateral border of superior articular facet of S1 and sacral promontory, and the outer interforaminal distances of anterior S1 foramens were measured on bony specimens. The outer interforaminal distances of anterior S1 foramens were also measured on anteroposterior sacral radiographs. RESULTS: The outer interforaminal distances were not statistically different from the length of the S1 screw trajectory on bony specimens. Radiographs of the S1 vertebra have also shown that outer interforaminal distances were not statistically different from the length of the S1 screw trajectory. CONCLUSION: In this study, we described an easy and a reliable method to determine the length of anteromedial screw by measuring outer interforaminal distance of S1 vertebra on anteroposterior radiograph of the sacrum.

Adult↗

PubMed1989

Ocular vergence under natural conditions. I. Continuous changes of target distance along the median plane.

Horizontal binocular eye movements of four subjects were recorded with the scleral sensor coil--revolving magnetic field technique while they fixated a natural target, whose distance was varied in a normally illuminated room. The distance of the target relative to the head of the subject was changed in three ways: (a) the target was moved manually by the experimenter; (b) the target was moved manually by the subject; (c) the target remained stationary while the subject moved his upper torso towards and away from the target. The rate of change of target distance was varied systematically in four levels, ranging from 'slow' to 'very fast', corresponding to changes in target vergence from about 10 degrees s-1 to about 100 degrees s-1. The dynamics of ocular vergence with regard to delay and speed were, under all three conditions, considerably better than could be expected from the literature on ocular vergence induced by disparity and/or blur. When 'very fast' changes in the distance of the target were made, subjects achieved maximum vergence speeds of up to about 100 degrees s-1. Delays of these fast vergence responses were generally smaller than 125 ms. Negative delays, i.e. ocular vergence leading the change in target distance, were observed. The eyes led the target (i.e. predicted target motion) by about 90 ms on average, when the subject used his hand to move the target. Vergence tracking was almost perfect when changes in distance were produced by moving the upper torso. In this condition, the eye led the target by about 5 ms. In the 'slow' and 'medium' conditions (stimulus speeds about 10-40 degrees s-1) tracking was accurate to within 1-2 degrees, irrespective of the way in which the target was moved. In the 'fast' and 'very fast' conditions (stimulus speeds about 40-100 degrees s-1), the accuracy of vergence tracking was better for self-induced than for experimenter-induced target displacements, and accuracy was best during voluntary movements of the upper torso. In the last case, ocular vergence speed was within about 10% of the rate of change of the vergence angle formed by the eyes and the stationary target. The dynamics of convergent and divergent vergence responses varied considerably. These variations were idiosyncratic. They were consistent within, but not between, subjects. Ocular vergence associated with attempted fixation of an imagined target, changing distance in darkness, could only be made by two of the four subjects.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗

PubMed2005

Aposematism and crypsis combined as a result of distance dependence: functional versatility of the colour pattern in the swallowtail butterfly larva.

The idea that an aposematic prey combines crypsis at a distance with conspicuousness close up was tested in an experiment using human subjects. We estimated detectability of the aposematic larva of the swallowtail butterfly, Papilio machaon, in two habitats, by presenting, on a touch screen, photographs taken at four different distances and measuring the time elapsed to discovery. The detectability of larvae in these images was compared with images that were manipulated, using existing colours either to increase or decrease conspicuousness. Detection time increased with distance for all colourations. However, at the closest distance, detection time was longer for the larvae manipulated to be more cryptic than for the natural and more conspicuous forms. This indicates that the natural colouration is not maximally cryptic at a short distance. Further, smaller increments in distance were needed to increase detection time for the natural than for the conspicuous larva. This indicates that the natural colouration is not maximally conspicuous at longer distances. Taken together, we present the first empirical support for the idea that some colour patterns may combine warning colouration at a close range with crypsis at a longer range. The implications of this result for the evolution of aposematism are discussed.

Adaptation, Biological↗

PubMed1998

Estimation of distances and map construction using radiation hybrids.

A method of estimating distances between pairs of genetic markers is described that directly uses their observed joint frequency distribution in a panel of radiation hybrids (RHs). The distance measure is based on the strength of association between marker pairs, which is high for close markers and decays with distance. These distances are then submitted to a previous method that generates linear coordinates for the markers directly from the intermarker distance matrix. This method of map building from RH data is simpler than others, because it uses only the observed joint frequency distributions of markers in the panel, and does not attempt to model unobserved quantities such as the retention of different sized fragments that contain the markers. It also incorporates directly the observed variation in retention of different markers, without needing a model for differential fragment retention dependent on chromosomal location, which is generally not known. Only small, precise distances are used in map construction, thereby reducing any effects of different fragment retention frequencies and local variations in X-ray sensitivity. The method is tested by simulation, and known marker distances and locations are successfully recovered from RH raw data. The method is also applied to publicly available data sets related to the recent transcript map of the human genome.

Animals↗

PubMed2004

Euclidean distance between syntactically linked words.

We study the Euclidean distance between syntactically linked words in sentences. The average distance is significantly small and is a very slowly growing function of sentence length. We consider two nonexcluding hypotheses: (a) the average distance is minimized and (b) the average distance is constrained. Support for (a) comes from the significantly small average distance real sentences achieve. The strength of the minimization hypothesis decreases with the length of the sentence. Support for (b) comes from the very slow growth of the average distance versus sentence length. Furthermore, (b) predicts, under ideal conditions, an exponential distribution of the distance between linked words, a trend that can be identified in real sentences.

Artificial Intelligence↗

PubMed2003

Exploring the conformational space of membrane protein folds matching distance constraints.

Herein we present a computational technique for generating helix-membrane protein folds matching a predefined set of distance constraints, such as those obtained from NMR NOE, chemical cross-linking, dipolar EPR, and FRET experiments. The purpose of the technique is to provide initial structures for local conformational searches based on either energetic considerations or ad-hoc scoring criteria. In order to properly screen the conformational space, the technique generates an exhaustive list of conformations within a specified root-mean-square deviation (RMSD) where the helices are positioned in order to match the provided distances. Our results indicate that the number of structures decreases exponentially as the number of distances increases, and increases exponentially as the errors associated with the distances increases. We also found the number of solutions to be smaller when all the distances share one helix in common, compared to the case where the distances connect helices in a daisy-chain manner. We found that for 7 helices, at least 15 distances with errors up to 8 A are needed to produce a number of solutions that is not too large to be processed by local search refinement procedures. Finally, without energetic considerations, our enumeration technique retrieved the transmembrane domains of Bacteriorhodopsin (PDB entry1c3w), Halorhodopsin (1e12), Rhodopsin (1f88), Aquaporin-1 (1fqy), Glycerol uptake facilitator protein (1fx8), Sensory Rhodopsin (1jgj), and a subunit of Fumarate reductase flavoprotein (1qlaC) with Calpha level RMSDs of 3.0 A, 2.3 A, 3.2 A, 4.6 A, 6.0 A, 3.7 A, and 4.4 A, respectively.

Membrane Proteins↗

PubMed2006

Genetic evidence of frequent long-distance recruitment in a vertebrate-dispersed tree.

The importance of dispersal for the maintenance of biodiversity, while long-recognized, has remained unresolved. We used molecular markers to measure effective dispersal in a natural population of the vertebrate-dispersed Neotropical tree, Simarouba amara (Simaroubaceae) by comparing the distances between maternal parents and their offspring and comparing gene movement via seed and pollen in the 50 ha plot of the Barro Colorado Island forest, Central Panama. In all cases (parent-pair, mother-offspring, father-offspring, sib-sib) distances between related pairs were significantly greater than distances to nearest possible neighbours within each category. Long-distance seedling establishment was frequent: 74% of assigned seedlings established > 100 m from the maternal parent [mean = 392 +/- 234.6 m (SD), range = 9.3-1000.5 m] and pollen-mediated gene flow was comparable to that of seed [mean = 345.0 +/- 157.7 m (SD), range 57.6-739.7 m]. For S. amara we found approximately a 10-fold difference between distances estimated by inverse modelling and mean seedling recruitment distances (39 m vs. 392 m). Our findings have important implications for future studies in forest demography and regeneration, with most seedlings establishing at distances far exceeding those demonstrated by negative density-dependent effects.

Animals↗

PubMed1989

Isonymy and migration distance.

The distribution of surnames of the living immigrants in the population of the town of Ferrara was studied by sex of immigrants and by distance of their place of origin from Ferrara. It was found that isonymy decreases with distance from the place of origin and that there is sexual dimorphism in migration distance: females migrate preferentially at short distances and males at long and very long distances. As indicators of the abundance of surnames in a distribution, the common ecological indices derived from entropy were used, and compared between migration ranges. It was found that redundancy, like isonymy, decreases with migration distance, and that it may be useful in detecting very-long-distance migration.

Emigration and Immigration↗

PubMed1987

The effect of position and delay on stroke and minute distance in late pregnancy.

Stroke and minute distance were measured in 12 women in late pregnancy using Doppler ultrasound. In each patient two sets of measurements were made every 2 min for 20 min in the supine and left lateral positions, the sequence of positions being reversed on the second occasion. Within each of the four 20 min measurement periods there were no significant changes with time in stroke distance, heart rate, or minute distance, or in their coefficients of variation. From this evidence there is no justification for delaying the measurement of cardiac output until a 'steady state' is reached. The measurements were influenced both by the sequence and the position in which they were taken, the effects being additive. Overall, stroke distance was 5.1% greater in the left lateral than in the supine position, heart rate was 3.7% less and minute distance not significantly different. Independent of posture, stroke distance was 6.5% greater in the second period of measurement than in the first, heart rate was 3% less and minute distance 2.8% more. In late pregnancy the relative magnitude of cardiac output in the left lateral and supine positions has to be interpreted in the light of a stepwise increase of aortic blood flow with change of posture.

Adult↗

PubMed2004

Interimplant distance and crestal bone resorption: a histologic study in the canine mandible.

BACKGROUND: Crestal bone loss has been shown to occur around dental implants. This crestal bone resorption may determine a more apical position of the gingival margin. A clear trend of increased bone loss with increased interimplant distance has been reported. PURPOSE: The aim of the present study was to evaluate, in the canine mandible, the crestal bone behavior around dental implants inserted with different interimplant distances. MATERIALS AND METHODS: Sandblasted and acid-etched implants (Bone System, Milano, Italy) were placed in the mandibles of six beagle dogs. Each dog received 10 implants in the mandible (five in the right side and five in the left side). A total of 60 implants was used in this study. The implants were divided in four groups: group I, with a 2 mm interimplant distance; group II, with a 3 mm interimplant distance; group III, with a 4 mm interimplant distance; and group IV, with a 5 mm interimplant distance. The dogs were killed after 12 months. RESULTS: No statistically significant differences were found in regard to vertical bone loss whereas on the contrary, statistically significant differences were found in regard to lateral bone loss (p = .0001). Statistically significant differences also were found in regard to vertical crestal bone loss (p = .0001). In fact vertical crestal bone loss decreased, from 1.98 mm in group I to 0.23 mm in group IV. CONCLUSIONS: The clinical significance of these data lies in the fact that the increased crestal bone loss results in an increase in the distance between the base of the contact points of the neighboring implants and the crest of bone, and this fact could determine whether the papilla is present or absent between two implants.

Alveolar Bone Loss↗

PubMed1999

Distance-dose curve for a miniature x-ray tube for stereotactic radiosurgery using an optimized aperture with a parallel-plate ionization chamber.

A recently developed miniature x-ray tube operating at 40 kV has been used in a randomized trial for the treatment of small intracranial lesions. The diameter of these lesions ranges from 10 to 30 mm. A thin window parallel-plate ionization chamber was used to calibrate the output of the x-ray tube, modified by the addition of a thin platinum aperture to reduce the charge collecting area of the chamber. The effect of such an aperture on the measurement of dose versus distance from the x-ray tube in a phantom has been examined as a function of aperture diameter. Aperture diameters were varied between 0 and 5 mm and dose measurements were made for distances between the x-ray source and the front surface of the chamber of 5-30 mm in water. The ratio of doses measured with and without an aperture, when normalized to unity at a distance of 10 mm, differs significantly from unity, for distances between 7.5 and 15 mm, for aperture diameters <1.5 mm and differs from unity, but less significantly, for apertures > or =3 mm. For intermediate diameters, however, this dose dependence is minimized, indicating an aperture diameter that provides a similar distance-dose curve as the measurement taken without an aperture over this range of distances. This diameter was found to be between 2 and 2.5 mm with a dose variation of less than +/- 1%. For distances <7.5 mm, measurements made with a 1.5-mm-diam aperture agree better with those taken with a 1.7-mm-diam chamber compared with a 5.2-mm-diam chamber.

Dose-Response Relationship, Radiation↗

PubMed1994

Perception of vowel height: the role of F1-F0 distance.

Perceived vowel height has been reported to vary inversely with the distance (in Bark) between the first formant frequency (F1) and the fundamental frequency (F0) [H. Traunmüller, J. Acoust. Soc. Am. 69, 1465-1475 (1981)]. Syrdal and Gopal [J. Acoust. Soc. Am. 79, 1086-1100 (1986)] observed that naturally produced [+high] and [-high] vowels tend to divide at a critical F1-F0 distance of 3-3.5 Bark, corresponding to the bandwidth of the "center of gravity" effect [L. Chistovich and V. Lublinskaja, Hear. Res. 1, 185-195 (1979)]. In the present study, listeners identified three sets of synthetic vowels varying orthogonally in F1 and F0 and ranging from /i/-/I/, /I/-/epsilon/, and /epsilon/-/ae/. For the /I/-/epsilon/ set, which corresponds to the [+high]/[-high] distinction, there was a relatively sharp identification boundary located at an F1-F0 distance of 3-3.5 Bark. However, for the /epsilon/-/ae/ and /i/-/I/ sets, which occupied regions where the F1-F0 distance was always greater than or always less than 3 Bark, vowel labeling varied more gradually as a function of F1-F0 distance. Also, F1-F0 distance was a better predictor of labeling performance than F1 alone only for the /I/-/epsilon/ set. Possible sources of the F1-F0 distance cue for vowel height are discussed.

Humans↗