Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Distance”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources
PubMed1988

Merging of distance matrices and classification by dynamic clustering.

The graphical representation of distance matrices in a Euclidean space allows the merging of two distance matrices since the two matrices have shared elements. The graphical representation of the merging of the two distance matrices is associated with a robust method of classification that allows one to distinguish species for which membership to a cluster cannot be established with certainty. These possibilities are exploited to test the consistency of phylogenetic trees, and to establish exact relations between species for which one possesses different independent distance measurements (distance matrices established from several types of sequences for instance). The whole set of programs is written in BASIC and runs on microcomputers.

Classification↗
PubMed2006

Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data.

MOTIVATION: Because co-expressed genes are likely to share the same biological function, cluster analysis of gene expression profiles has been applied for gene function discovery. Most existing clustering methods ignore known gene functions in the process of clustering. RESULTS: To take advantage of accumulating gene functional annotations, we propose incorporating known gene functions into a new distance metric, which shrinks a gene expression-based distance towards 0 if and only if the two genes share a common gene function. A two-step procedure is used. First, the shrinkage distance metric is used in any distance-based clustering method, e.g. K-medoids or hierarchical clustering, to cluster the genes with known functions. Second, while keeping the clustering results from the first step for the genes with known functions, the expression-based distance metric is used to cluster the remaining genes of unknown function, assigning each of them to either one of the clusters obtained in the first step or some new clusters. A simulation study and an application to gene function prediction for the yeast demonstrate the advantage of our proposal over the standard method.

Algorithms↗
PubMed2005

In vivo evidence for radial migration of neurons by long-distance somal translocation in the developing ferret visual cortex.

During the development of the cerebral cortex, neurons generated in the cortical ventricular zone migrate radially toward the marginal zone. Radially migrating neurons are thought to display 1 of 2 morphologies: cells with a long, pia-contacting, apical process utilized for somal translocation early in development, when the cortex is still relatively thin; or cells with a short leading process, abundant at late stages of corticogenesis when neurons need to travel for longer distances. In large convoluted brains, like those of many primates and carnivores, radially migrating neurons must travel distances up to several millimeters before reaching their final destination, often following curvilinear trajectories. Here we analyze modes and morphologies of radially migrating neurons in convoluted brains by studying the visual cortex of developing ferrets. We provide in vivo and in vitro evidence for the existence of late-born cortical neurons that migrate radially by long-distance somal translocation within a long apical process extended to the cortical plate, in contrast to the early somal translocation observed in rodents. Long-distance translocating neurons in the ferret show a discontinuous rhythm of migration, alternating periods of advance with periods of stall. Furthermore, by combining different labeling methods we find the simultaneous presence in the developing ferret cortex of long-distance translocating neurons and neurons migrating within a short leading process.

Adenoviridae↗
PubMed2002

Recombination at his-3 in Neurospora declines exponentially with distance from the initiator, cog.

By deletion of 1.8 kb of sequence between cog(L) and his-3 and replacement with sequences of different lengths, we have generated a set of Neurospora strains in which the distance between cog(L) and the site at which recombination is selected varies from 1.7 to nearly 6 kb. Each of the manipulated strains includes cog(L), a highly active recombination hotspot, and rec-2, thus allowing high-frequency recombination. In addition, each is a his-3 mutant, either K26 or K480. The frequency of His(+) recombinants in progeny of these crosses is inversely proportional to the distance between his-3 and cog. Specifically, there is a linear relationship between log(10) (recombination frequency) and the distance in base pairs, indicating that as distance decreases, the rate of interallelic recombination increases exponentially. An exponential relationship between distance separating markers and the chance of co-conversion has been found in both Drosophila and fission yeast, indicating that the extension of recombination events may be a stochastic process in most organisms. On the basis of these and additional data presented in this article, we conclude that recombination is initiated at cog(L) in >17% of meioses, that most conversion tracts are very short, and that few extend >14 kb.

Hydro-Lyases↗
PubMed2006

Conserved distances between vertebrate highly conserved elements.

High numbers of sequence element with very high (>95%) sequence conservation between the human and other vertebrate genomes have been reported and ascribed putative cis-regulatory functions. We have investigated the structural relationships between such elements in mammalian genomes and find that not only their sequences, but also the distances between them are significantly (P<2.2x10(-16)) more conserved than corresponding distances between orthologous protein-coding genes or between exons within these genes. Regions of largely conserved distance between consecutive highly conserved elements (HCE) generally overlap previously identified HCE clusters, but may be far longer (up to 20 Mb) and possibly cover close to 25% of the human genome sequence. Similar conservation of distance is found between bird (chicken) and mammalian genomes and is also discernible in comparisons between fish and mammals. The data suggest either that a substantial amount of essential (functionally active) elements with lower sequence conservation occupy the space between the HCEs or that distance itself is an important factor in transcriptional regulation or chromatin modelling.

Animals↗
PubMed2003

Is patient travel distance associated with survival on phase II clinical trials in oncology?

BACKGROUND: Prior research has suggested that patients who travel out of their neighborhood for elective care from specialized medical centers may have better outcomes than local patients with the same illnesses who are treated at the same centers. We hypothesized that this phenomenon, often called "referral bias" or "distance bias," may also be evident in curative-intent cancer trials at specialized cancer centers. METHODS: We evaluated associations between overall survival and progression-free survival and the distance from the patient residence to the treating institution for 110 patients treated on one of four phase II curative-intent chemoradiotherapy protocols for locoregionally advanced squamous cell cancer of the head and neck conducted at the University of Chicago over 7 years. RESULTS: Using Cox regression that adjusted for standard patient-level disease and demographic factors and neighborhood-level economic factors, we found a positive association between the distance patients traveled from their residence to the treatment center and survival. Patients who lived more than 15 miles from the treating institution had only one-third the hazard of death of those living closer (hazard ratio [HR] = 0.32, 95% confidence interval [CI] = 0.12 to 0.84). Moreover, with every 10 miles that a patient traveled for care, the hazard of death decreased by 3.2% (HR = 0.97, 95% CI = 0.94 to 0.99). Similar results were obtained for progression-free survival. CONCLUSION: Results of phase II curative-intent clinical trials in oncology that are conducted at specialized cancer centers may be confounded by patient travel distance, which captures prognostic significance beyond cancer stage, performance status, and wealth. More work is needed to determine what unmeasured factors travel distance is mediating.

Adult↗
PubMed2004

Local homology recognition and distance measures in linear time using compressed amino acid alphabets.

Methods for discovery of local similarities and estimation of evolutionary distance by identifying k-mers (contiguous subsequences of length k) common to two sequences are described. Given unaligned sequences of length L, these methods have O(L) time complexity. The ability of compressed amino acid alphabets to extend these techniques to distantly related proteins was investigated. The performance of these algorithms was evaluated for different alphabets and choices of k using a test set of 1848 pairs of structurally alignable sequences selected from the FSSP database. Distance measures derived from k-mer counting were found to correlate well with percentage identity derived from sequence alignments. Compressed alphabets were seen to improve performance in local similarity discovery, but no evidence was found of improvements when applied to distance estimates. The performance of our local similarity discovery method was compared with the fast Fourier transform (FFT) used in MAFFT, which has O(L log L) time complexity. The method for achieving comparable coverage to FFT is revealed here, and is more than an order of magnitude faster. We suggest using k-mer distance for fast, approximate phylogenetic tree construction, and show that a speed improvement of more than three orders of magnitude can be achieved relative to standard distance methods, which require alignments.

Algorithms↗
PubMed1996

Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies.

The statistical properties of the paralinear and LogDet distances under nonstationary nucleotide frequencies were studied. First, we developed formulas for correcting the estimation biases of the paralinear and LogDet distances, i.e., the bias-corrected distance is estimated by dc = d - 2var(d), where d and var(d) are the estimated distance and sampling variance, respectively. The performances of these formulas and the formulas for sampling variances were examined by computer simulation. Second, we developed a method for estimating the variance-covariance matrix of paralinear distances, so that statistical tests of DNA phylogenies can be conducted in the nonstationary case. Third, a new LogDet-based method for testing the molecular clock hypothesis was developed under nonstationary nucleotide frequencies.

Analysis of Variance↗
PubMed1991

Molecular distance and divergence time in carnivores and primates.

Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the results of empirical studies conflict and are difficult to compare because they differ widely in their choice of taxa, genetic techniques, or methods for calibrating rates of molecular evolution. We use a single methodology to analyze the relationship of molecular distance and divergence time in 86 taxa (72 carnivores and 14 primates). These taxa have divergence times of 0.01-55 Myr and provide a graded series of phylogenetic divergences such that the shape of the curve relating genetic distance and divergence time is often well defined. The techniques used to obtain genetic distance estimates include one- and two-dimensional protein electrophoresis, DNA hybridization, and microcomplement fixation. Our results suggest that estimates of molecular distance and divergence time are highly correlated. However, rates of molecular evolution are not constant; rather, in general they decline with increasing divergence time in a linear fashion. The rate of decline may differ according to technique and taxa. Moreover, in some cases the variability in evolutionary rates changes with increasing divergence time such that the accuracy of nodes in a phylogenetic tree varies predictably with time.

Animals↗
PubMed1988

Functional ambulation velocity and distance requirements in rural and urban communities. A clinical report.

The purposes of this clinical report are 1) to document the distances and velocities that individuals must ambulate to function independently in their community and 2) to demonstrate the differences in travel distances and velocities among communities of various sizes. In seven communities of different sizes, we measured distances from a designated parking space to commonly frequented sites (eg, stores, post offices, banks, and medical buildings). We also measured street widths and the time allowed by crossing signals to cross streets safely. From these data, we calculated the velocities needed to safely cross streets in each community. The study results showed that ambulation distances and velocities vary depending on the size of the community and that for individuals to function independently within their community, they must ambulate at velocities and distances much greater than the ambulation objectives that may be set at most rehabilitation settings. Based on the results of this study, we suggest that they receive the majority of their patients to more accurately prepare patients for functional independence after rehabilitation discharge.

Activities of Daily Living↗
PubMed1987

Thermoluminescence dosimetry of gamma rays from the Hiroshima atomic bomb at distances of 1.27 to 1.46 kilometers from the hypocenter.

Sixteen ornamental tile samples were collected from 1982 to 1983 from the rooftops of two buildings at Hiroshima University, Hiroshima, Japan. Quartz grains 50-150 microns in size extracted from the samples were analyzed for their thermoluminescence (TL) intensities. Conversion of TL intensity to 60Co gamma exposure resulted in the following estimates: 40.5 to 27.6 mC kg-1 (157 to 107 R) for five samples (one each) collected from five sites at distances of 1.27 to 1.34 km from the hypocenter of the atomic bomb detonated in 1945; 23.7 +/- 1.4 mC kg-1 (92 +/- 5 R) for three samples from one site at a distance of 1.39 km; 21.4 to 17.0 mC kg-1 (83 to 66 R) for three samples (one sample per site) from three sites at distances of 1.40 to 1.43 km; 19.8 +/- 1.3 mC kg-1 (77 +/- 5 R) for four samples from one site at a distance of 1.45 km; and 13.2 mC kg-1 (51 R) for one sample at a distance of 1.46 km. At face value, these estimates are greater by a factor of about 2.5 than previous estimates based on the tentative 1965 radiation dose estimates for atomic bomb survivors (a tentative dosimetry model proposed in 1965), but agree within +32% to -13% (+15% on the average) with recent estimates using modern computational techniques using an improved model of the atomic bomb explosion.

Cobalt Radioisotopes↗
PubMed2002

Social distance in response to psychiatric labels.

Several factors contribute to the amount of social distance individuals desire from each other, including the presence of a psychiatric label. This study examines aspects of the relationship between four specific psychiatric labels and social distance. A social distance scale was developed for this purpose and used in a pilot study. Three-hundred-and-thirteen participants answered questions about their willingness to be involved in relationships of varying degrees of closeness with people who have psychiatric diagnoses. We found that individuals who have a close friend or family member with a mental illness, in contrast to those who have no such relationship, desire less social distance from people with mental illness. Those who were given some information about specific diagnoses desired greater social distance from people who have mental illness than participants who were given only diagnostic labels. These findings highlight the need to evaluate how people who are not in the helping professions learn about psychiatric conditions and how this knowledge impacts beliefs and behaviors.

Adult↗
PubMedDate not supplied

Observer Performance as a function of viewing distance.

The performance of observers in detecting solitary lung nodules of 1.0 and 1.5 cm diameter has been measured for viewing distances of 46, 91, 183, and 470 cm. The data indicate that observer accuracy for detection of 1.5-cm nodules as measured by the area under the ROC curves is essentially unchanged for the three closest viewing distances and falls of by about 30% at the largest viewing distance. Observer performance for detection of 1.0 cm nodules, however, improves as the viewing distance is increased from 46 to 91 cm and then decreases at larger viewing distances.

Humans↗
PubMed1991

The diagnostic value of interpediculate distance assessment on plain films in thoracic and lumbar spine injuries.

In a retrospective study of 107 fractured vertebrae in the thoracic and lumbar spine, the interpediculate distance could be accurately assessed on plain roentgenograms in 96%. When these findings were compared with those of conventional tomography, there were no false-positive or false-negative results concerning normal or increased interpediculate distance. In 22 injured vertebrae the increased interpediculate distance was measured. In all these cases there was a fracture of the pedicle or lamina in addition to an injury of the vertebral body. We conclude that interpediculate distance can almost always be assessed and that an increased interpediculate distance on plain films is 100% reliable as an indicator of damage to the vertebral body, the pedicle, or lamina.

Adolescent↗
PubMed1990

Determinants of rural travel distance for obstetrics care.

This study examines the distances traveled for inpatient obstetrics care by women residing in rural Alabama in 1983 and 1988. During that time 23 rural hospitals in the state stopped providing obstetrics services and mean travel distances increased by 6.8 miles. However, in 1988 50% of rural pregnant women bypassed the nearest rural hospital still providing obstetrics services. Multivariate techniques are used to examine the effects of distance and service offerings of rural hospitals and their substitutes on the actual distance traveled for care. Patient characteristics are also considered. The most important finding is that a 5% increase in per capita income in the woman's home county is associated with a 20% increase in actual travel distance, other things equal. Implications for rural health policy are discussed.

Alabama↗
PubMed1998

Predicting competition performance in long-distance running by means of a treadmill test.

PURPOSE: The purpose of this study was to examine the power of 16 parameters beside the individual anaerobic threshold (IAT) in predicting performance in various competition distances. METHODS: This study examined 427 competitive runners to test the prediction probability of the IAT and other parameters for various running distances. All runners (339 men, 88 women; ages, 32.5 +/- 10.14 yr; training, 7.1 +/- 5.53 yr; training distance, 77.9 +/- 35.63 km.wk-1) performed an increment test on the treadmill (starting speed, 6 or 8 km.h-1; increments, 2 km.h-1; increment duration, 3 min to exhaustion). The heart rate (HR) and the lactate concentrations in hemolyzed whole blood were measured at rest and at the end of each exercise level. The IAT was defined as the running speed at a net increase in lactate concentration 1.5 mmol.L-1 above the lactate concentration at LT. RESULTS: Significant correlations (r = 0.88-0.93) with the mean competition speed were found for the competition distances and could be increased using stepwise multiple regression (r = 0.953-0.968) with a set of additional parameters from the training history, anthropometric data, or the performance diagnostics. CONCLUSIONS: The running speed at a defined net lactate increase thus produces an increasing prediction accuracy with increasing distance. A parallel curve of the identity straight lines with the straight lines of regression indicates the independence of at least a second independent performance determining factor.

Adult↗
PubMed2001

Blood lipids in young distance runners.

PURPOSE: The purpose of this study was to examine the age-and sex-associated variation in blood lipids among young athletes. METHODS: A mixed-longitudinal design was used to examine the development of blood lipids in competitive young distance runners followed from 1982 to 1985. Serial data included 99 annual measurements for 27 male subjects and 84 annual measurements for 27 female subjects aged 9-18 yr. Total cholesterol (TC), high-density lipoprotein (HDL-C), low-density lipoprotein (LDL-C), and triglycerides (TG) were determined by standard procedures. RESULTS: In general, cross-sectional age group means showed that TC and LDL-C remained stable and HDL-C declined with age, especially in male subjects. TG increased with age. Age-related trends were statistically significant for HDL-C and TG in boys only (P < 0.05). TC and LDL-C were slightly greater in boys at all ages except 11, 15, and 17 yr (P > 0.05). HDL-C was similar between the sexes until 13 yr when values became greater in girls (3.2-13.8 mg.dL(-1)) (P < 0.05 in 17+ yr). No clear pattern of sex differences emerged for TG. Compared with the general population, blood lipids of young distance runners showed the following trends: 1) TC was above reference medians, 2) LDL-C tended to approximate or to be slightly above reference medians, 3) TG fluctuated about the reference medians, and 4) HDL-C was higher in distance runners compared to the reference medians before age 14 yr, but in the older age groups, especially male subjects, HDL-C either approximated or fell slightly below the reference medians. There was considerable variability in blood lipid levels among the runners. In 21 male and 18 female subjects with serial data for 3-5 yr, HDL-C declined 22.4 and 18.3 mg.dL(-1) (P < 0.05), whereas TG increased 18.0 and 14.0 mg.dL(-1)(P < 0.05 in female subjects only) in male and female subjects, respectively. Tracking coefficients over intervals of 3-5 yr were moderate to high (0.48-0.90), except for TG in male subjects (0.08). CONCLUSIONS: The results indicate that the development of blood lipids in young distance runners is similar to youth in the general population. In contrast to observations in adult endurance athletes, young distance runners did not possess a superior blood lipid profile except for HDL-C in the younger age groups.

Adolescent↗
PubMed2001

Stroke volume does not plateau during graded exercise in elite male distance runners.

UNLABELLED: Stroke volume (SV) responses during graded treadmill exercise were studied in 1) elite male distance runners (N = 5), 2) male university distance runners (N = 10), and 3) male untrained university students (N = 10). METHODS: Cardiac output (Q) and SV were determined by a modified acetylene rebreathing procedure. RESULTS: There were no differences in SV responses among the three groups during the transition from rest to light exercise (P > 0.05). However, the rates of change of SV during light to maximal exercise in untrained subjects (slope = -0.1544 mL x beat(-1)) and university distance runners (slope = 0.1041) did not change, whereas it dramatically increased (P < 0.001) in elite distant runners (slope = 0.6734). Moreover, the elite distance runners showed a further slope increase in SV when heart rate was above 160 bpm, which resulted in an average maximal SV of 187 +/- 14 mL x beat(-1) compared with 145 +/- 8 and 128 +/- 14 mL x beat(-1) in the university runners and untrained students, respectively (P < 0.001). Similarly, max Q reached 33.8 +/- 2.3, 26.3 +/- 1.7, and 21.3 +/- 1.5 L x min(-1) in the three groups, respectively (P < 0.001). On the other hand, there was a nonsignificant tendency for maximal arteriovenous oxygen content difference to be lower in the elite athletes compared with the other groups. CONCLUSION: Results from university distance runners and untrained university students support the classic observation that SV plateaus at about 40% of maximal oxygen consumption despite increasing intensity of exercise. In contrast, stroke volume in the elite athletes does not plateau but increases continuously with increasing intensity of exercise over the full range of the incremental exercise test.

Adult↗