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Results for “distance correlation”

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At least 55 records · Page 3Linked to original sources

PubMed2004

Dynamic light scattering microscopy. A novel optical technique to image submicroscopic motions. I: theory.

The theoretical basis of an optical microscope technique to image dynamically scattered light fluctuation decay rates (dynamic light scattering microscopy) is developed. It is shown that relative motions between scattering centers even smaller than the optical resolution of the microscope are sufficient to produce significant phase variations resulting in interference intensity fluctuations in the image plane. The timescale and time dependence for the temporal autocorrelation function of these intensity fluctuations is derived. The spatial correlation distance, which reports the average distance between constructive and destructive interference in the image plane, is calculated and compared with the pixel size, and the distance dependence of the spatial correlation function is derived. The accompanying article in this issue describes an experimental implementation of dynamic light scattering microscopy.

Cell Movement↗

PubMed2005

Explicit treatment of spin labels in modeling of distance constraints from dipolar EPR and DEER.

Current SDSL-EPR methods allow measurement of dipolar distances in the 8-70 A range; however, the use of extrinsic probes complicates the interpretation of these distances in modeling macromolecular structure and conformational changes. The data presented here show that interprobe distances correlate only weakly with Cbeta-Cbeta distances, especially for distances that are on the order of the spin label tether lengths. Explicitly incorporating the spin label into the modeling process increases the experiment/model correlation 4-fold and reduces the distance error from 6 A to 3 A.

Carbon↗

PubMed1993

Investigation of solution structure of d(GAATTTAAATTC)2 by 1H NMR, molecular dynamics, mechanics, refinement by back-calculation of the NOESY spectrum and analysis of this structure using X-ray data.

1H NMR spectroscopy, restrained molecular mechanics and dynamics and refinements after back-calculation of the NOESY spectrum have been performed to study the structure of the d(GAATTTAAATTC)2 duplex and to determine whether it is bent or not. It is found that the duplex adopts a B-type conformation; all sugar conformations belong to the C2' endo region and purines have a larger pseudorotation angle as compared to pyrimidines. The cross-strand AH2(n)-AH1' (m + 1) distance (where (n) and (m) are complementary residues), crucial for an anomalous A/T tract structure, is large on the TA step and gradually decreases at the 3' and 5' ends of the TTTAAA tract and follows the rules proposed previously [Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Yu, Kim, S.G., Kintanar, A., and Reid, B.R., Proc. Natl. Acad. Sci. U.S.A. 88, 9087 (1991)]. The changes in this distance correlate with those in the T1 value for AH2 protons which we measured for several oligonucleotide sequences. A total number of about 250 interproton distance constraints were determined from NOESY spectra and were used for structure determination by molecular mechanics, dynamics and refinement by back-calculations. It is shown that these data are not enough to determine whether the duplex is bent or not. The whole family of B-type conformations including bent and straight structures fit well with the available NMR data. In principle, additional non-NMR data could be used in order to reduce the number of the allowable structures. The refinement of the structures with additional different non-NMR constraints (used as a driving force) on P-P or H1'-H1' minor groove width distances in the TA region shows a very good correlation between these distances and the angle of bending of the dodecamer. The more the minor groove width increases in the TA region the more the duplex is bent at the major groove of this region. On the other hand, there is also a very good correlation between P-P, H1'-H1' and AH2-H1' cross-strand distances as follows from analysis of X-ray B-type structures. These two correlations, together with the increased AH2-H1' cross-strand NMR distance in the TA region of the dodecamer indicate that the duplex should be characterized by a wider minor groove in the TA region and be bent in the major groove in this region.

Base Sequence↗

PubMed1998

Effect of pressure on individual hydrogen bonds in proteins. Basic pancreatic trypsin inhibitor.

By performing two-dimensional 1H NMR measurements at 750 MHz at varying hydrostatic pressure (1-2000 bar) in an aqueous environment (90% 1H2O/10% 2H2O), we found that the signals of the peptide NH protons of basic pancreatic trypsin inhibitor (BPTI) in the folded state shift their positions linearly and reversibly with pressure. The strong tendency for low-field shifts of these protons indicates that most of the amide groups form hydrogen bonds either with carbonyls or with water and that these hydrogen bonds are shortened by pressure. The NH protons interacting favorably with solvent water tend to exhibit larger pressure-induced shifts than others, showing that the shift can be used as a diagnostic probe for the hydrogen bonding state of an NH group with water. Furthermore, we estimated shortening of individual H...O distances of the NH...O=C hydrogen bonds at 2000 bar on the basis of the empirical shift-distance correlation for BPTI. The estimated shortened distances varied considerably from site to site in the range of 0-0.11 A, larger in the turn but smaller in the interiors of secondary structures. These variations suggest that the volume fluctuation is heterogeneous within BPTI and that high-pressure NMR at high field can offer a unique opportunity for detecting microscopic structural fluctuation in proteins.

Aprotinin↗

PubMed1995

Phylogeny inferred from codon usage pattern in 31 organisms.

We employed the Codonusage database to analyze the codon usage pattern in 31 organisms from all the main biological taxa. We tested the similarity in codon usage pattern between each organism and all the others by the Pearson linear correlation coefficient. The 465 values obtained were located in a 31 x 31 triangular matrix from which a correlation distance matrix was calculated. An evolutionary dendrogram was then constructed from these distances. The results showed a fair correlation between codon usage patterns and phylogenetic relationships, at least for organisms which diverged in rather recent times (end of Jurassic--beginning of Cretaceous).

Animals↗

PubMed1978

Perimetry of contrast detection thresholds of moving spatial sine wave patterns. III. The target extent as a sensitivity controlling parameter.

Contrast detection thresholds for moving sine wave gratings were obtained at the fovea and at eccentricities of 6 degrees, 21 degrees, and 50 degrees on the nasal horizontal meridian. The targets subtended from 30 X 30 minutes of arc up to 16 degrees X 16 degrees. We have found that the contrast detection thresholds depend critically on the extent of the target field. If this extent is large enough peripheral detection thresholds are on a par with those measured at the fovea, only the sensitivity range is shifted to lower spatial frequencies. We show that if the just resolvable distance at any eccentricity is taken as a yardstick, and field width and spatial frequency are scaled accordingly, then the spatio-temporal contrast detection thresholds become identical over the whole visual field. It is shown that a smaller area, measuring several just resolvable distances across, has to be stimulated before successive or simultaneous contrast detection is possible at all. Detection performance improves if the stimulated area is enlarged up to diameters of at least 10(2) just resolvable distances. The just resolvable distance correlates well with mean interganglion cell distance, and with the cortical magnification factor.

Adult↗

PubMed1992

[Measurements and variations in the region of the optic canal. CT and anatomy].

This investigation of the optic canal is based on measurements of 60 macerated adult European skulls from the Alexander-Ecker Collection at the Anatomy Department of the University of Freiburg. An indian skull is also described, in which the cranial end of the left optic canal is closed by a bony plate. Computer tomographical and anatomical measurements were compared in order to assess the correlation of the two methods of investigation and the accuracy of the CT representation of osseous structures. The coronal projection of the optic canal proved to be optimal for CT examination--the sections meet the optic canal at an angle of 85.5 degrees. The measurements of transverse diameters correlate poorly, whereas vertical diameters and distances correlate well. The extent to which anatomical variations can be assessed by CT was also investigated. All anatomical variants could be observed in coronal sections, except the bony lamina in the Indian skull, which could not be seen until a contrast medium was used. The so-called "keyhole anomaly" appeared in 3.3% in our material, the "figure-of-eight" variant in 2.5%, and a carotid clinoid canal in 13.3%.

Adult↗

PubMed2000

Actin dynamics at the living cell submembrane imaged by total internal reflection fluorescence photobleaching.

Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about relevant chemical kinetic rates in vivo. Total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP), an established technique previously demonstrated to measure reversible biomolecular kinetic rates at surfaces in vitro, is extended here to measure reversible biomolecular kinetic rates of actin at the cytofacial (subplasma membrane) surface of living cells. For the first time, spatial imaging (with a charge-coupled device camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging produces both spatial maps of kinetic parameters (off-rates and mobile fractions) and estimates of kinetic correlation distances, cell-wide kinetic gradients, and dependences of kinetic parameters on initial fluorescence intensity. For microinjected rhodamine actin in living cultured smooth muscle (BC3H1) cells, the unbinding rate at or near the cytofacial surface of the plasma membrane (averaged over the entire cell) is measured at 0.032 +/- 0.007 s(-1). The corresponding rate for actin marked by microinjected rhodamine phalloidin is very similar, 0.033 +/- 0.013 s(-1), suggesting that TIR/FRAP is reporting the dynamics of entire filaments or protofilaments. For submembrane fluorescence-marked actin, the intensity, off-rate, and mobile fraction show a positive correlation over a characteristic distance of 1-3 microm and a negative correlation over larger distances greater than approximately 7-14 microm. Furthermore, the kinetic parameters display a statistically significant cell-wide gradient, with the cell having a "fast" and "slow" end with respect to actin kinetics.

Actins↗

PubMed1978

An HLA map of Europe.

HLA--A and B antigen frequencies from 65 different population samples (61 European and 4 non-European) have been tabulated. Pairwise genetic distances were calculated between some of the populations using HLA--A and B data. The distances obtained with these two series were very strongly correlated. Distances obtained with ABO blood groups (in part of the material) showed weaker but still highly significant correlation with those obtained from combined HLA--A and B data. In general, neighbouring countries had low distances, and of the populations studied, Essen would represent the 'middle' population in Europe. The supposedly inbred population of Sardinia showed the highest distances. The data may be useful for comparison in new HLA studies and can be used for further phylogenic studies.

ABO Blood-Group System↗

PubMed2003

Spatial patterns of cystic fibrosis mutation spectra in European populations.

Cystic fibrosis (CF) is the most frequent severe recessive disorder in European populations. We have analyzed its mutation frequency spectrum in 94 European, North African and SW Asian populations taken from the literature. Most major mutations as well as the incidence of CF mutations showed clinals patterns as demonstrated by autocorrelogram analysis. More importantly, measures of mutation diversity did also show clinal patterns, with mutation spectra being more diverse in southern than in northern Europe. This increased diversity would imply roughly a three-fold long-term effective population size in southern than in northern Europe. Distances were computed among populations based on their CF mutation frequencies and compared with distances based on other genic regions. CF-based distances correlated with mtDNA but not with Y-chromosome-based distances, which may be a consequence of the relatively homogeneous CF mutation frequencies in European populations.

Cystic Fibrosis↗

PubMed2003

The spectral input to honeybee visual odometry.

Bees returning from a feeder placed in a narrow tunnel that is lined with a chequered pattern will strongly overestimate travel distance. This finding supports the view that their distance estimation is based on integrating optic flow experienced during flight. Here, we use chequered tunnels with various colour combinations as a tool to identify the spectral channel used by bees to gauge travel distance. The probability of bees performing waggle dances after a short travel distance correlates only with the low range of the green contrast of the pattern in the tunnel. But it does not correlate with the pattern's chromatic contrast or brightness contrast. Distance estimation is therefore colour blind. We also evaluated the waggle runs as a function of colour pattern. Their duration is the code for the food source distance. Waggle run duration is entirely independent of the colour pattern used, implying that once green contrast is above detection threshold, distance estimation depends solely on the angular motion of the landscape passed in flight.

Animal Communication↗

PubMed1975

[Proceedings: Determination of the severity of aortic insufficiency with pulsed Doppler-ultrasound in the common carotid artery].

The severity of aortic incompetence can be assessed by quantifying the alteration of blood flow in the common carotid artery. The use of a pulsed multichannel ultrasonic Doppler device in 41 patients with aortic valve disease yielded a satisfactory correlation between the ultrasonic parameters and the maximal aortic regurgitation distance. Correlations between Doppler parameters and regurgitation (thermodilution) were less strict.

Adult↗

PubMed2006

Limitations of the New York Heart Association functional classification system and self-reported walking distances in chronic heart failure.

BACKGROUND: Two ways to evaluate the symptoms of heart failure are the New York Heart Association (NYHA) classification and asking patients how far they can walk (walk distance). The NYHA system is commonly used, although it is not clear how individual clinicians apply it. AIM: To investigate how useful these measures are to assess heart failure and whether other questions might be more helpful. METHODS: 30 cardiologists were asked what questions they used when assessing patients with heart failure. To assess interoperator variability, two cardiologists assessed a series of 50 patients in classes II and III using the NYHA classification. 45 patients who had undergone cardiopulmonary testing were interviewed using a specially formulated questionnaire. They were also asked how far they could walk before being stopped by symptoms, and then tested on their ability to estimate distance. RESULTS: The survey of cardiologists showed no consistent method for assessing NYHA class and a literature survey showed that 99% of research papers do not reference or describe their methods for assigning NYHA classes. The interoperator variability study showed only 54% concordance between the two cardiologists. 70% of cardiologists asked patients for their walk distance; however, this walk distance correlated poorly with actual exercise capacity measured by cardiopulmonary testing (rho = 0.04, p = 0.82). CONCLUSION: No consistent method of assessing NYHA class is in use and the interoperator study on class II and class III patients gave a result little better than chance. Some potential questions are offered for use in assessment. Walking distance, although frequently asked, does not correlate with formally measured exercise capacity, even after correction for patient perception of distance, and has never been found to have prognostic relevance. Its value is therefore doubtful.

Activities of Daily Living↗

PubMed1994

Covariation of optic disc measurements and ocular parameters in the healthy eye.

To understand the variations in optic disc topography that may affect the local susceptibility of nerve fibers to glaucomatous damage, we evaluated the correlations between optic disc topography and selected ocular parameters in 210 normal eyes of healthy Japanese. In the total study group, eyes with a longer axial length had a longer distance between the disc and foveola, a larger index of ovalness and a larger disc (P < 0.01). A longer disc-foveola distance correlated with a larger index of ovalness (P < 0.01). The optic discs of severely myopic eyes had a considerably different structure from other eyes. Eyes with a tilted optic disc were unique in that the area of the optic disc was not large despite a positive correlation with long axial length (P < 0.01) a long disc-foveola distance (P < 0.01), and a large index of ovalness (P < 0.01). Eyes with a rotated optic disc were another special case. This eye type correlated in a contradictory fashion with two parameters: a large axial length (P < 0.01) and a short disc-foveola distance (P < 0.01). These findings suggest that changes in optic disc topography or susceptibility to glaucomatous damage correlate with selected ocular parameters but are not completely parallel.

Anthropometry↗

PubMed1988

Genetic variation within a linguistic group: Apalai-Wayana and other Carib tribes.

A total of 136 individuals were studied in relation to 31 genetic systems, and the results were compared with South American Indian averages and previous surveys on the Wayana of French Guiana and Surinam. The information was afterwards integrated with data from other Carib groups, and two types of genetic distances (Nei's and Edwards') were calculated a) between five groups, considering ten systems; and b) between nine groups, using five systems. The two measures of genetic distances correlated well (Spearman's correlation coefficient around 0.70), and there was good agreement between the geographical and genetic distances. All analyses indicated a peripheral position for the Apalai-Wayana and their distinctiveness from the Wayana of French Guiana and Surinam, suggesting that intertribal fusions may play an important role in the genetic differentiation of these populations.

Anthropology, Physical↗

PubMedDate not supplied

[Peculiarities of thoracic and abdominal combs of fleas (Siphonaptera)].

The structure of pseudosetae, spinelets, and spines of combs (ctenidia) was studied by means of light and SE microscopy in 80% of genera and subgenera of the World fauna. It is found out that peculiarities of ctenidiae in the prothorax and in tergites of the abdomen are characteristics of families and infraorders of fleas. Some characters of ctenidiae found in certain flea genera are reductions and apparently caused by habitation in some extremal conditions. An absence of ctenidiae in the unfraorder Pulicomorpha is compensated by more developed posterior margin of prothorax and general abbreviation of all thoracal segments. Reasons of ctenidiae absence, which is observed in certain genera of the infraorders Ceratophyllomorpha, Pygiopsyllomorpha and Hystricopsillomorpha associated with the same hosts, is not clear. It is confirmed, that distance between ctenidiae in different flea species associated with the same species host species, however it is recovered, that this distance correlates with the diameter of most thin hair of host. In some flea species the distance between ctenidia spices in females is larger, than in males. It is found, that sexual dimorphism by this character may not be expressed in certain species of closely related species group of fleas. It is suggested that ctenidiae were present even in the common ancestor of fleas. The hypothesis on origin of spines and pseudosetae from setae of the posterior walls of toracal and abdominal segments in the common ancestor of fleas is proposed.

Animals↗

PubMed1986

Quantitation of facial affection in scleroderma.

The interincisor distance, the vertical lip distance, and the horizontal oral distance were measured in 68 patients with generalized scleroderma and in 66 healthy individuals. Interincisor distance and vertical lip distance were decreased in scleroderma (p less than 0.001 and p less than 0.001). Vertical lip distance and horizontal oral distance provided clinically a clear differentiation between minor and major affection (p less than 0.001 and p less than 0.001), while the interincisor distance provided a weaker differentiation (p less than 0.05). The horizontal oral distance correlated with the duration of scleroderma (r = -0.289, p less than 0.05), and the vertical lip distances tended to do so (r = -0.208, n.s.). In healthy individuals interincisor and vertical lip distances decreased significantly with age (in males only), while the horizontal oral distance showed no significant decrease. In conclusion, interincisor and vertical lip distances are preferable for diagnosis and the horizontal oral distance for follow-up of facial scleroderma. If only one vertical parameter is wanted, the authors prefer the vertical lip distance to the interincisor distance.

Adult↗

PubMed1992

Evaluation of the metabolic compensation after treadmill test in patients with peripheral occlusive arterial disease.

Patterns of release of lactate, hypoxanthine, and arginine into the bloodstream after a standardized treadmill test (twelve minutes, 1.6-2.8 mph, inclination 0,5,10,15%) were recorded in 21 consecutive patients with stage II peripheral arterial occlusive disease. Heart rate, systolic blood pressure, ankle blood pressure, and ankle/brachial systolic blood pressure ratio (A/B ratio), as well as plasma lactate, plasma hypoxanthine and serum arginine were recorded before and at fifteen to thirty-minute intervals for up to two hours after the treadmill test. Immediately after the treadmill test, lactate levels (36.6 +/- 3.7 mg/L) and hypoxanthine levels (2.73 +/- 0.19 mmol/L) were significantly (p less than 0.001) increased but returned to preexercise levels after thirty and sixty minutes, respectively. Arginine levels did not change significantly. Ankle blood pressure (57 +/- 5 mm Hg) and A/B ratio (0.40 +/- 0.04) were significantly (p less than 0.001) decreased after exercise, while heart rate and systolic blood pressure were increased. These parameters returned to normal as well within a half hour after exercise. Absolute walking distance correlated significantly (p less than 0.01) with the postexercise systolic blood pressure (r = -0.62), ankle pressure (r = 0.63) and A/B ratio (r = 0.72). Induced hypoxanthine and lactate production intercorrelated significantly positively (r = 0.57, p = 0.007) but were independent of the absolute walking distance. In contrast with lactate, hypoxanthine production correlated significantly with postexercise ankle pressure (r = 0.49, p = 0.02) and exercise-induced fall in A/B ratio (r = 0.66, p = 0.001).(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗