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PubMed1999

A distance to the galaxy NGC4258 from observations of Cepheid variable stars.

Cepheid variable stars pulsate in a way that is correlated with their intrinsic luminosity, making them useful as 'standard candles' for determining distances to galaxies; the potential systematic uncertainties in the resulting distances have been estimated to be only 8-10%. They have played a crucial role in establishing the extragalactic distance scale and hence the value of the Hubble constant. Here we report observations of Cepheids in the nearby galaxy NGC4258; the distance calculated from the Cepheids is 8.1 +/- 0.4 Mpc, where the uncertainty does not include possible systematic errors. There is an independently determined geometric distance to this galaxy of 7.2 +/- 0.5 Mpc, based on the observed proper motions of water masers orbiting the central black hole; the distances differ by 1.3sigma. If the maser-based distance is adopted and the Cepheid distance scale revised accordingly, the derived value of the Hubble constant would increase by 12 +/- 9%, while the expansion age of the Universe would decrease by the same amount.

Journal Article↗
PubMed2004

Isolation by language and distance in Belgium.

The isonymy structure of trilingual Belgium was studied using the surname distributions for 1,118,004 private telephone users. The users were distributed in 77 Flemish, 76 French, and 3 German speaking towns, selected on a geographic basis to form an approximately regular grid over Belgium. Lasker's distance was found to be considerably higher between languages than within languages. For the whole of Belgium, irrespective of language, it was highly correlated with linear geographic distance, with r = 0.721+/-0.014, which is the highest correlation observed in European countries to date. Within Belgium and within languages, the correlation was highest among the Flemish (r = 0.878 +/- 0.007), and lowest among the French (r = 0.631+/-0.020). Isolation by distance in Belgium is the highest we have found in Europe, and as high as in Switzerland where the different languages are separated by geographical barriers. This is not the case in Belgium, so that the considerable isolating power of languages emerges clearly from the present analysis. From the comparison of Lasker's distance between (9.48) and within (8.16) languages, and from its regression over geographic distance (b = 0.01206), it was possible to establish a quantitative relationship between the isolating power of languages and that of geographic distance as (9.48-8.16)/0.01206 = 109 kilometres. This transformation of language distance into an equivalent geographic distance, given here for Belgium, can be applied to any similar geo-linguistic situation.

Belgium↗
PubMed2002

Intraoperative measurements of the subacromial distance.

PURPOSE: The purpose of this study was 2-fold: to document the accuracy of a new measuring device and to intraoperatively compare the subacromial distance between controls and patients with impingement syndrome before and after arthroscopic subacromial decompression (ASD). TYPE OF STUDY: Clinical study. METHODS: When performing an ASD, it is important that bone resection is adequate. Today the correct subacromial distance after bone resection is only assessed by eye, directly or indirectly. The subacromial distance was measured between the anterolateral corner of the acromion and the supraspinatus tendon in the lateral decubitus position. The device was inserted 2 to 3 cm below the anterolateral acromion. There was no subacromial pathology among the controls (n = 15, mean age, 28 years). In 30 patients with impingement syndrome (average age, 53 years) an ASD was performed. The subacromial distance was measured after bursectomy and then after bone resection. Intraindividual and interindividual assessment was performed. RESULTS: The mean value of the subacromial distance in controls was 16 mm, the 95% confidence limits between 14 and 18 mm. The mean value in the group of patients with impingement syndrome was 8 mm before and 16 mm after the decompression. Due to the pressure within the subacromial space, the subacromial distance increased 1 mm. Intraindividual measurements never varied more than 1 mm (n = 5). The correlation coefficient between the measurements by both authors was 0.99. CONCLUSIONS: In this study, we assessed and described the use of a measuring device that enables the surgeon to quantify the subacromial distance before and after bone resection. After bone resection, the mean value of the subacromial distance was well within the control values. The amount of bone resected varied from 5 to 13 mm. This new device enables documentation in clinical work as well as in research.

Acromioclavicular Joint↗
PubMed1991

Explicit distance geometry: identification of all the degrees of freedom in a large RNA molecule.

An alternative approach to distance geometry ("explicit" distance geometry) is being developed for problems, such as the modeling of RNA folding in the ribosome, where relatively few distances are known. The approach explicitly identifies minimal sets of additional distances that can be added to a distance matrix in order to calculate structures that are consistent with all the known information without distorting the original input data. These additional distances are bounded to the extent possible by the known distances. These explicitly added distances can be treated as degrees of freedom and used to explore the full range of alternative foldings consistent with the original input in an organized way. The present paper establishes that it is practical to explicitly determine such degrees of freedom for even very large RNAs. To demonstrate the feasibility of the approach tRNA was represented as a simple undirected graph containing all relevant information represented in the usual cloverleaf secondary structure and nine base-base tertiary interactions. Using a three atom representation for each residue a total of 206 degrees of freedom are explicitly identified. To accomplish this a graph theoretic approach was used in which a minimal covering cycle basis was determined.

Algorithms↗
PubMed2006

SDM: a fast distance-based approach for (super) tree building in phylogenomics.

Phylogenomic studies aim to build phylogenies from large sets of homologous genes. Such "genome-sized" data require fast methods, because of the typically large numbers of taxa examined. In this framework, distance-based methods are useful for exploratory studies and building a starting tree to be refined by a more powerful maximum likelihood (ML) approach. However, estimating evolutionary distances directly from concatenated genes gives poor topological signal as genes evolve at different rates. We propose a novel method, named super distance matrix (SDM), which follows the same line as average consensus supertree (ACS; Lapointe and Cucumel, 1997) and combines the evolutionary distances obtained from each gene into a single distance supermatrix to be analyzed using a standard distance-based algorithm. SDM deforms the source matrices, without modifying their topological message, to bring them as close as possible to each other; these deformed matrices are then averaged to obtain the distance supermatrix. We show that this problem is equivalent to the minimization of a least-squares criterion subject to linear constraints. This problem has a unique solution which is obtained by resolving a linear system. As this system is sparse, its practical resolution requires O(naka) time, where n is the number of taxa, k the number of matrices, and a < 2, which allows the distance supermatrix to be quickly obtained. Several uses of SDM are proposed, from fast exploratory studies to more accurate approaches requiring heavier computing time. Using simulations, we show that SDM is a relevant alternative to the standard matrix representation with parsimony (MRP) method, notably when the taxa sets of the different genes have low overlap. We also show that SDM can be used to build an excellent starting tree for an ML approach, which both reduces the computing time and increases the topogical accuracy. We use SDM to analyze the data set of Gatesy et al. (2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions.

Algorithms↗
PubMed1996

Constraining volume by matching the moments of a distance distribution.

The problem of computing a molecular structure from a set of distances arises in the interpretation of NMR data as well as other experimental methods that yield distance information. Techniques for computing structures must find conformations consistent with the distance data. There are often other constraints on the structure that must be satisfied as well. One of the most problematic constraints is the constraint on the total volume occupied by the atoms. In this paper, we use the first two moments (mean and variance) of an estimated distance distribution to constrain the volume of a computed structure. We show that a probabilistic algorithm for matching the first two moments of the estimated distance distribution significantly improves the quality of the solution, especially when the distance information alone is not sufficient to define the structure precisely. We also show that our method is not sensitive to small errors in the estimates of mean and variance of the distance distribution. Finally, we demonstrate the use of this constraint in computing a low-resolution structure of the 30S prokaryotic ribosomal subunit. Quantitative analysis of our results allows us to assess the information content contained in constraints on volume, and to show that in some cases addition of a volume constraint adds information roughly equivalent to doubling the number of input distances. Our results also demonstrate the flexibility of probabilistic representations of structural constraints, and the importance of including volume information to constrain structural computations-especially in the case of sparse data.

Algorithms↗
PubMed2004

Approximate geodesic distances reveal biologically relevant structures in microarray data.

MOTIVATION: Genome-wide gene expression measurements, as currently determined by the microarray technology, can be represented mathematically as points in a high-dimensional gene expression space. Genes interact with each other in regulatory networks, restricting the cellular gene expression profiles to a certain manifold, or surface, in gene expression space. To obtain knowledge about this manifold, various dimensionality reduction methods and distance metrics are used. For data points distributed on curved manifolds, a sensible distance measure would be the geodesic distance along the manifold. In this work, we examine whether an approximate geodesic distance measure captures biological similarities better than the traditionally used Euclidean distance. RESULTS: We computed approximate geodesic distances, determined by the Isomap algorithm, for one set of lymphoma and one set of lung cancer microarray samples. Compared with the ordinary Euclidean distance metric, this distance measure produced more instructive, biologically relevant, visualizations when applying multidimensional scaling. This suggests the Isomap algorithm as a promising tool for the interpretation of microarray data. Furthermore, the results demonstrate the benefit and importance of taking nonlinearities in gene expression data into account.

Algorithms↗
PubMed1985

Genetic distances based on quantitative traits.

Morphological data showing continuous distributions, polygenically controlled, may be particularly useful in intergroup classification below the species level; an appropriate distance analysis based on these traits is an important tool in evolutionary biology and in plant and animal breeding.--The interpretation of morphological distances in genetic terms is not easy because simple phenotypic data may lead to biased estimates of genetic distances. Convenient estimates can be obtained whenever it is possible to breed populations according to a suitable crossing design and to derive information from genetic parameters.--A general method for determining genetic distances is proposed. The procedure of multivariate analysis of variance is extended to estimate appropriate genetic parameters (genetic effects). Not only are optimal statistical estimates of parameters obtained but also the procedure allows the measurement of genetic distances between populations as linear functions of the estimated parameters, providing an appropriate distance matrix that can be defined in terms of these parameters. The use of the T2 statistic, defined in terms of the vector of contrasts specifying the distance, permits the testing of the significance of any distance between any pair of populations that may be of interest from a genetic point of view.--A numerical example from maize diallel data is reported in order to illustrate the procedure. In particular, heterosis effects are used as the basis for estimates of genetic divergence between populations.

Analysis of Variance↗
PubMed1996

Distance distributions in proteins: a six-parameter representation.

We present a statistical analysis of protein structures based on interatomic C alpha distances. The overall distance distributions reflect in detail the contents of sequence-specific substructures maintained by local interactions (such as alpha-helixes) and longer range interactions (such as disulfide bridges and beta-sheets). We also show that a volume scaling of the distances makes distance distributions for protein chains of different length superimposable. Distance distributions were also calculated specifically for amino acids separated by a given number of residues. Specific features in these distributions are visible for sequence separations of up to 20 amino acid residues. A simple representation, which preserves most of the information in the distance distributions, was obtained using six parameters only. The parameters give rise to canonical distance intervals and when predicting coarse-grained distance constraints by methods such as data-driven artificial neural networks, these should preferably be selected from these intervals. We discuss the use of the six parameters for determining or reconstructing 3-D protein structures.

Amino Acid Sequence↗
PubMed2002

Radiologic localization of esophageal level: comparison with distance from incisor at endoscopy.

RATIONALE AND OBJECTIVES: The esophageal level on radiography was compared with that at endoscopy by establishing a relationship between the radiologic landmarks, i.e., the vertebral level and the distance from the carina, and the distance from the incisor at endoscopy. METHODS: Three hundred ninety spot films in 65 patients who underwent endoscopic retrograde cholangiopancreatography were analyzed. Six spot films were obtained for each patient, wherein the distances of the endoscopic tip were located at 20, 25, 30, 35, 40, and 45 cm from the incisors. On each radiogram, the vertebral level scores were measured as 1 to 12, for the location of the endoscopic tip at the levels of T1 through T12, respectively. When the endoscopic tip was located at the lower half of the vertebral body, 0.5 point was added to the vertebral level score and when the tip was noted at the upper half of it, no additional score was given. The distance between the endoscopic tip and the carina was also measured. Correlations of the distance of the endoscopic tip from the incisors on endoscopy with the vertebral body levels and the distance from the carina on radiography, accounting for patient height, were analyzed by multiple linear regression and equations were extracted. RESULTS: Equation 1 for the vertebral level score (VL) for a given distance of endoscopic tip from incisor (DI) at a given patient height (H) was VL = 0.432DI - 0.048H + 0.099 (r2 = 0.968). Equation 2 for the distance from the carina (DC) for a given DI at a given H was DC = 0.957DI - 0.137H - 5.841 (r2 = 0.983). Two tables denoting radiologic VLs and DCs for given endoscopic DIs and patients' heights were generated using these equations. CONCLUSIONS: Regressed equations and tables will enable radiologists to better localize the esophageal lesions that are seen at endoscopy, and vice versa.

Body Height↗
PubMed2004

Older patients with serious mental illness: sensitivity to distance barriers for outpatient care.

OBJECTIVES: To inform health services delivery and to demonstrate the appropriateness of understanding access at the individual's level, we evaluated how patient characteristics affect sensitivity to access barriers. We examined one dimension of access: geographic accessibility. We assessed age differences in sensitivity to distance barriers for outpatient psychiatric and nonpsychiatric care among active Department of Veterans Affairs (VA) patients with serious mental illness. METHODS: Among 142,055 VA patients with bipolar disorder, schizophrenia, or other psychoses in fiscal year 2000, separate random intercepts mixed models were estimated (cluster: nearest site) for outpatient psychiatric and nonpsychiatric visit day volume. In addition to distance and age group (<45, 45-65, or >65), covariates included gender, ethnicity, rural location, psychiatric diagnosis type, Charlson comorbidity level, initial treatment location, and psychiatric diagnosis X distance interactions. Differential distance effects by age were assessed using age X distance interaction terms. RESULTS: Among VA patients with serious mental illness, distance limits the volume of VA outpatient visits. For nonpsychiatric outpatient care, patients older than 65 were substantially more sensitive to distance barriers (P < 0.0001). For psychiatric outpatient care volume, patients aged 45-65 had slightly increased sensitivity; however, this difference did not have clinical significance. DISCUSSION: The impact of geographic accessibility barriers depended on personal characteristics of the individual and the outpatient service type. For nonpsychiatric outpatient care, older VA patients were most negatively affected by distance barriers. Results may inform efforts to reduce barriers to health care among patients with serious mental illness.

Age Distribution↗
PubMed1994

Distance stereopsis in orthophores, heterophores, and intermittent strabismics.

The purpose of this study was to investigate the value of clinical testing of distance stereopsis. Distance stereopsis was assessed with the Mentor Binocular Vision Testing System (B-VAT) system for 45 patients with ocular deviations of 6 delta or more at distance (heterophoria and intermittent strabismus) and for 36 patients with orthophoria. On the average, distance stereopsis was better for patients with the smaller ocular deviations than for those with the larger ocular deviations. The mean distance stereoacuities, both contour and global, for the orthophores were 53 and 81 sec arc, for the heterophores 93 and 100 sec arc, and for the intermittent strabismics 95 and 169 sec arc. Although the average size of the deviation at distance and near for the heterophoric and strabismic patients was nearly the same, distance stereopsis tended to be poorer than near stereopsis. There was a significant difference between the proportion of orthophores and the proportion of intermittent strabismics exhibiting distance stereopsis with both contour and global stereo targets (p < 0.05).

Adolescent↗
PubMed2006

Small revisions to predicted distances around metal sites in proteins.

A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution < or =1.25 A and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of 'target distances' previously given. As well as small changes in many distances and a large improvement for Mg-O(carboxylate), the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M-O(carboxylate) distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M-O(1) and M-O(2) distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation.

Binding Sites↗
PubMed2007

Shape classification using the inner-distance.

Part structure and articulation are of fundamental importance in computer and human vision. We propose using the inner-distance to build shape descriptors that are robust to articulation and capture part structure. The inner-distance is defined as the length of the shortest path between landmark points within the shape silhouette. We show that it is articulation insensitive and more effective at capturing part structures than the Euclidean distance. This suggests that the inner-distance can be used as a replacement for the Euclidean distance to build more accurate descriptors for complex shapes, especially for those with articulated parts. In addition, texture information along the shortest path can be used to further improve shape classification. With this idea, we propose three approaches to using the inner-distance. The first method combines the inner-distance and multidimensional scaling (MDS) to build articulation invariant signatures for articulated shapes. The second method uses the inner-distance to build a new shape descriptor based on shape contexts. The third one extends the second one by considering the texture information along shortest paths. The proposed approaches have been tested on a variety of shape databases, including an articulated shape data set, MPEG7 CE-Shape-1, Kimia silhouettes, the ETH-80 data set, two leaf data sets, and a human motion silhouette data set. In all the experiments, our methods demonstrate effective performance compared with other algorithms.

Algorithms↗
PubMedDate not supplied

3D distance fields: a survey of techniques and applications.

A distance field is a representation where, at each point within the field, we know the distance from that point to the closest point on any object within the domain. In addition to distance, other properties may be derived from the distance field, such as the direction to the surface, and when the distance field is signed, we may also determine if the point is internal or external to objects within the domain. The distance field has been found to be a useful construction within the areas of computer vision, physics, and computer graphics. This paper serves as an exposition of methods for the production of distance fields, and a review of alternative representations and applications of distance fields. In the course of this paper, we present various methods from all three of the above areas, and we answer pertinent questions such as How accurate are these methods compared to each other? How simple are they to implement?, and What is the complexity and runtime of such methods?

Algorithms↗
PubMed2001

Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales.

Genetic isolation by distance (IBD) has rarely been described in marine species with high potential for dispersal at both the larval and adult life-history stages. Here, we report significant relationships between inferred levels of gene flow and geographic distance in the Atlantic cod, Gadus morhua, at 10 nuclear restriction-fragment-length-polymorphism (RFLP) loci at small regional scales in the western north Atlantic region (< 1,600 km) that mirror those previously detected over its entire geographic range (up to 7,300 km). Highly significant allele frequency differences were observed among eight northwestern Atlantic populations, although the mean FST for all 10 loci was only 0.014. Despite this weak population structuring, the distance separating populations explained between 54% and 62% of the variation in gene flow depending on whether nine or 10 loci were used to estimate Nm. Across the species' entire geographic range, highly significant differences were observed among six regional populations at nine of the 10 loci (mean FST = 0.068) and seven loci exhibited significant negative relationships between gene flow and distance. At this large geographic scale, natural selection acting in the vicinity of one RFLP locus (GM798) had a significant effect on the correlation between gene flow and distance, and eliminating it from the analysis caused the coefficient of determination to increase from 17% to 62%. The role of vicariance was assessed by sequentially removing populations from the analysis and was found to play a minor role in contributing to the relationship between gene flow and distance at either geographic scale. The correlation between gene flow and distance detected in G. morhua at small and large spatial scales suggests that dispersal distances and effective population sizes are much smaller than predicted for the species and that the recent age of populations, rather than extensive gene flow, may be responsible for its weak population structure. Our results suggest that interpreting limited genetic differences among populations as reflecting high levels of ongoing gene flow should be made with caution.

Animals↗
PubMed2004

Lifetime fitness of short- and long-distance dispersing great reed warblers.

Dispersal is of prime importance for many evolutionary processes and has been studied for decades. The reproductive consequences of dispersal have proven difficult to study, simply because it is difficult to keep track of dispersing individuals. In most previous studies evaluating the fitness effects of dispersal, immigrants at a study locality have been lumped into one category and compared to philopatric individuals. This is unfortunate, because there are reasons to believe that immigrants with long and short dispersal distances may differ substantially in reproductive success. In the present study, we used a combination of capture-recapturing and multilocus microsatellite genotyping to categorize great reed warblers at our Swedish study site as philopatric individuals or short- or long-distance dispersing immigrants. We then performed novel comparisons of lifetime reproductive success (LRS) and survival rates of these three dispersal categories. The birds belonged to cohorts 1987-1996, and data for their LRS were gathered between 1988 and 2003. The analyses showed that philopatric males attracted more females, produced more fledglings and recruits throughout their lives, and survived better than immigrants. Among the immigrant males, those categorized as long-distance dispersers had lowest LRS and survival probability. Models that included covariates of potential importance showed that the difference in LRS between dispersal categories was partly caused by corresponding variation in number of breeding years at our study site. These results indicate that short- and, in particular, long-distance dispersers were of poor phenotypic quality, but it may also be proposed that immigrants attracted few females because they were poorly adapted to the local social environment. In females, the number of local recruits corrected for the number of breeding years (as well as for number of fledglings) differed between dispersal categories in a pattern that suggests an intermediate optimal dispersal distance. Short-distance dispersers recruited more offspring per year (and per fledgling) than both philopatric individuals and long-distance dispersers. Data suggest that the low LRS of philopatric females was related to costs of inbreeding. The low LRS of long-distance dispersing females may have resulted from their offspring being especially prone to disperse outside the study area, but also other potential explanations exist, such as local maladaptation. Our study highlights the importance of separating immigrant birds on the basis of their genetic similarity to the local study population when analyzing variation in LRS and inferring realized gene flow.

Animals↗
PubMed2005

Visual acuity in 5-7-year-old children: individual variability and dependence on observation distance.

Accurate measurements of uncorrected binocular and monocular visual acuity were performed in 65 children aged 5-7 years at five viewing distances in the range 0.5-5.0 m by means of the test charts containing widely spaced E stimuli in four orientations. It was found that, in most children of this age, visual acuity (V) changed with test distance, as had been reported previously with older subjects. Visual acuity could be considered as practically independent of observation distance (Vmax-Vmin<or=0.2 decimal units) in <50% of children. The remaining children demonstrated evident distance dependence of visual acuity but the shape of the acuity-distance curve varied. The acuity-distance curve of most children peaked at an intermediate distance (1-2 m), the typical difference Vmax-Vmin being 0.4 decimal units. To explain the existence of an optimal observation distance in the majority of children, a number of developmental and environmental factors could be proposed that adjust the parameters of the visual system to the parameters of operational visual space and prevailing activity.

Aging↗