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PubMed2005

Barriers and distances as determinants for the evolution of bird migration links: the arctic shorebird system.

We analysed migratory connectivity between different winter quarters and breeding sectors in the circumpolar tundra region for arctic shorebirds, in relation to migratory distances and ecological barriers. Total distances and barriers were calculated and measured for all potential migratory orthodrome links between 10 selected winter regions and 12 breeding sectors. The migratory segment between the northernmost stopover site and the breeding area, associated with the entry to and exit from the tundra during spring and autumn migration, respectively, was also identified and measured for each potential link. The analysis indicated that the evolution of migratory links among arctic shorebirds is constrained not by distance as such but by distance across ecological barriers, possibly because of the complex adaptations required for barrier crossing and extensive detour migration (and in a few cases because barrier distances exceed the birds' theoretical flight range capacity). A particularly pronounced barrier effect of the Arctic Ocean, as apparent from a sharp decline in migratory connectivity between the opposite sides of the Arctic Ocean, may reflect a crucial importance of favourable entry and exit conditions for successfully occupying different sectors of the tundra breeding area by shorebirds from winter regions situated at widely different total distances in both the southern and northern hemispheres.

Animal Migration↗

PubMed2004

Indel-based evolutionary distance and mouse-human divergence.

We propose a method for estimating the evolutionary distance between DNA sequences in terms of insertions and deletions (indels), defined as the per site number of indels accumulated in the course of divergence of the two sequences. We derive a maximal likelihood estimate of this distance from differences between lengths of orthologous introns or other segments of sequences delimited by conservative markers. When indels accumulate, lengths of orthologous introns diverge only slightly slower than linearly, because long indels occur with substantial frequencies. Thus, saturation is not a major obstacle for estimating indel-based evolutionary distance. For introns of medium lengths, our method recovers the known evolutionary distance between rat and mouse, 0.014 indels per site, with good precision. We estimate that mouse-human divergence exceeds rat-mouse divergence by a factor of 4, so that mouse-human evolutionary distance in terms of selectively neutral indels is 0.056. Because in mammals, indels are approximately 14 times less frequent than nucleotide substitutions, mouse-human evolutionary distance in terms of selectively neutral substitutions is approximately 0.8.

Animals↗

PubMed1995

Long-distance movement factor: a transport function of the potyvirus helper component proteinase.

Transport of viruses from cell to cell in plants typically involves one or more viral proteins that supply dedicated movement functions. Transport from leaf to leaf through phloem, or long-distance transport, is a poorly understood process with requirements differing from those of cell-to-cell movement. Through genetic analysis of tobacco etch virus (TEV; potyvirus group), a novel long-distance movement factor was identified that facilitates vascular-associated movement in tobacco. A mutation in the central region of the helper component proteinase (HC-Pro), a TEV-encoded protein with previously described activities in aphid-mediated transmission and polyprotein processing, inactivated long-distance movement. This mutant virus exhibited only minor defects in genome amplification and cell-to-cell movement functions. In situ histochemical analysis revealed that the mutant was capable of infecting mesophyll, bundle sheath, and phloem cells within inoculated leaves, suggesting that the long-distance movement block was associated with entry into or exit from sieve elements. The long-distance movement defect was specifically complemented by HC-Pro supplied in trans by a transgenic host. The data indicate that HC-Pro functions in one or more steps unique to long-distance transport.

Biological Transport↗

PubMed2005

Enhanced perceptual distance functions and indexing for image replica recognition.

The proliferation of digital images and the widespread distribution of digital data that has been made possible by the Internet has increased problems associated with copyright infringement on digital images. Watermarking schemes have been proposed to safeguard copyrighted images, but watermarks are vulnerable to image processing and geometric distortions and may not be very effective. Thus, the content-based detection of pirated images has become an important application. In this paper, we discuss two important aspects of such a replica detection system: distance functions for similarity measurement and scalability. We extend our previous work on perceptual distance functions, which proposed the Dynamic Partial Function (DPF), and present enhanced techniques that overcome the limitations of DPF. These techniques include the Thresholding, Sampling, and Weighting schemes. Experimental evaluations show superior performance compared to DPF and other distance functions. We then address the issue of using these perceptual distance functions to efficiently detect replicas in large image data sets. The problem of indexing is made challenging by the high-dimensionality and the nonmetric nature of the distance functions. We propose using Locality Sensitive Hashing (LSH) to index images while using the above perceptual distance functions and demonstrate good performance through empirical studies on a very large database of diverse images.

Algorithms↗

PubMed2003

Linear habitats and the nested clade analysis: an empirical evaluation of geographic versus river distances using an Ozark crayfish (Decapoda: Cambaridae).

The nested clade analysis can be extremely useful in testing for an association between genetic variation and geography and in explaining these observed patterns in terms of historical or contemporary population processes. The strength of this method lies in its ability to test a variety of processes simultaneously under a rigorous statistical framework. Indeed, many recent studies have used the nested analysis in a wide range of terrestrial and aquatic taxa. However, it has been suggested that riverine, riparian, or coastal species may be better examined using river (or coastal) distances rather than the standard geographic (great circle) distances among populations. It is thought that the standard geographic distances may not adequately describe the actual distances involved between populations of species inhabiting these one-dimensional (riverine) habitats. Therefore, we analyzed population data from an Ozark crayfish, Orconectes lutetus, to examine the effects on the results of a nested clade analysis using river distances. In most cases, the haplotypes detected in this crayfish were unique to a particular drainage or a group of neighboring drainages, indicating very little movement of individuals among drainages. Five major population groups were detected, corresponding to many of the major river drainages sampled in this study. The two types of distance analyses obtain similar results for higher-level (older) clades, but differ in many of the inferences made for lower-level (younger) clades. However, we suggest that the comparison of both types of analyses for riverine species may enhance the process of elucidating historical and contemporary population processes, especially in cases where the transfer of individuals among different drainages are involved.

Animals↗

PubMed2004

Individual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance.

In many species genes move over limited distances, such that genetic differences among populations or individuals are expected to increase as a function of geographical distance. In other species, however, genes may move any distance over a single generation time, such that no increase of genetic differences is expected to occur with distance. Patterns of gene dispersal have been assessed typically using this theoretical property. In this study, this classical approach based on a Mantel test was compared to a new method using individual assignment to reveal contrasts in dispersal patterns between 15 populations of brook charr Salvelinus fontinalis and 10 populations of Atlantic salmon Salmo salar sampled in eastern Canada, where both species co-occur naturally. Based on the Mantel test, we found evidence for neither an increase of genetic differences with distance in either species nor a significant contrast between them. The individual-based method, in contrast, revealed that individual assignment in both species was non random, being significantly biased toward geographically proximate locations. Furthermore, brook charr were on average assigned to a closer river than were salmon, according to a priori expectations based on the dispersal behaviour of the two species. We thus propose that individual assignment methods might be a promising and more powerful alternative to Mantel tests when isolation by distance cannot be postulated a priori.

Animals↗

PubMed1983

Family distances can reveal hidden consanguinity.

Family distances, defined as summary measures of all possible geographic distances between birthplaces of paternal ancestors and birthplaces of maternal ancestors in a given generation, were compared in patients with autosomal recessive disorders and patients with Down's syndrome. In general, family distances in Down's syndrome patients were twice the family distances in patients with autosomal recessive disorders, even after the exclusion of rare disorders or cases with overt consanguinity. In modern, Western European societies grandparental and great-grandparental family distances may be more appropriate measures of the effect of population structure than parental distance or parental consanguinity.

Consanguinity↗

PubMed1987

Stroke and minute distance in pregnancy: a longitudinal study using Doppler ultrasound.

Using Doppler ultrasound directed at the aortic arch, stroke and minute distance were measured in 45 normal singleton pregnancies and compared with 42 controls. In the non-pregnant controls, stroke distance was 5% more in the supine than in the left lateral position (P less than 0.01) and during pregnancy this relativity was maintained until 36 weeks gestation. In the supine and left lateral positions respectively, stroke distance was increased by 8% (both) at 4 weeks (P less than 0.05 and NS), by 14 and 11% at 8 weeks (P less than 0.001 and P less than 0.01) and showed a maximum increase of 21 and 20% at 16 weeks gestation (both P less than 0.001). At 40 weeks, supine stroke distance was 14% less than the non-pregnant control value (P less than 0.001), and 6% less than the value in the left lateral position (P less than 0.05), which was itself not significantly different from that in the non-pregnant controls. The maximum increase of heart rate was at 32 weeks, by 24% in the supine and by 19% in the left lateral position (both P less than 0.001). Minute distance was maximally increased by 37% in the supine at 16 weeks (P less than 0.001) and by 30% in the left lateral position at 24 weeks (P less than 0.001). Thereafter, minute distance, measured in both positions, declined until at 40 weeks it was not significantly different from the non-pregnant control value.

Adult↗

PubMed1996

The effect of the impeller-driver magnetic coupling distance on hemolysis in a compact centrifugal pump.

Blood trauma is one of the important performance parameters of centrifugal pumps. To investigate the blood trauma induced by these pumps, in vitro hemolysis tests have become an important procedure and are increasingly used for pump development and comparisons. The Baylor compact eccentric inlet port (CIE) centrifugal blood pump was developed as a long-term centrifugal ventricular assist device (VAD) as well as a cardiopulmonary bypass pump (CPB). The Baylor CIE pump incorporates a seal-less design with a blood stagnation-free structure. This pump can provide flows of 5 L/min against 350 mm Hg of total pressure head at 2,600 revolutions per minute. The pump impeller is magnetically coupled to the driver magnet in a seal-less manner. The latest hemolysis study revealed that hemolysis may be affected by the gap distance between the driver and the impeller magnet. The purpose of this study was to verify the effect of the magnetic coupling distance on the normalized index of hemolysis (NIH) with the CIE model and to obtain an optimal gap distance. The NIH value was clearly decreased by alteration of the magnetic coupling distance from 7.7 to 9.7 mm in CPB and left ventricular assist device (LVAD) conditions. The NIH, when using the pump as an LVAD condition, was reduced to a level of 0.0056 from 0.095 when the magnetic coupling distance was extended. The same results were also obtained when the pumps were used in a CPB condition. The magnetic coupling distance is an important factor for the CIE model in terms of hemolysis. Different coupling forces effect the bearings and impeller stability. These results suggest that an optimal driving condition with a proper magnetic coupling and an optimal force between the impeller and driver is necessary to develop an atraumatic centrifugal pump.

Blood Flow Velocity↗

PubMedDate not supplied

Predicting the distance for nasojejunal tube insertion in children.

ISSUES AND PURPOSE: As no consistent predictor of insertion tube distance has been determined for intestinal feeding tubes and fluoroscopic placement is very expensive, this study sought a reliable method of blind placement. DESIGN AND METHODS: This cross-sectional study measured the internal distance from the lip to the pylorus in 387 children undergoing upper gastrointestinal endoscopy and compared those measurements to the external distances measured from the nose around the ear to the 10th rib and lip around the ear to the 10th rib. RESULTS: Regression equations using height fitted in four age groups were the best predictors of the internal pyloric distances. PRACTICE IMPLICATIONS: Predicting this distance with height may help healthcare providers be more successful in blind placement of intestinal feeding tubes. A table of predicted nasointestinal tube insertion distances is included.

Adolescent↗

PubMedDate not supplied

Change of collision efficiency with distance in bacterial transport experiments.

Understanding the mechanisms of bacterial transport in aquifers is important in developing bioremediation strategies. Collision efficiency (alpha) is one important parameter used in modeling bacterial transport. This study was undertaken to measure change in alpha with distance by performing a bacterial transport experiment in Oyster, Virginia. Following injection of a bacterium, Comamonas sp., into a well, water samples were collected at various distances along the flowpath and injected into columns packed with homogenized South Oyster focus area sediment. Zeta potentials of the bacteria in the samples were measured. Values of alpha were determined at various locations in the field in two ways: based on field breakthrough concentrations at the sampling points and based on column breakthrough concentrations. The alpha values estimated from field breakthrough decreased with distance, whereas those estimated from column breakthrough increased with distance. Bacterial cell surface charge became progressively more negative with distance in the field. We hypothesize that the apparent contradiction between field and column alpha values was caused by differences in the flow of the two systems. Flow in the columns was forced to occur through fine-grained zones of iron and aluminum hydroxide coatings that selectively removed the most negatively charged bacteria. In contrast, in the field, the injected cells did not come into contact with the positively charged coatings because the bulk solution bypassed them due to heterogeneous hydraulic properties. These results suggest that laboratory-based models may underestimate bacterial transport distance in the field. A more realistic approach may be necessary to capture the degree of heterogeneity.

Colony Count, Microbial↗

PubMed2004

Estimation of distance between a unipolar recording electrode and a myocardial bundle based on signal characteristics.

The aim of the present paper, is the estimation of the distance between an electrode used as a recording site of the extracellular potential field and a surviving myocardial bundle. The importance of the reliable solution of this problem lies among others in controlling ablation. For our purposes one-dimensional propagation is considered and current sources are activated along a cable simulating the propagating waves with constant velocity. Different models of current sources are explored. By use of these models, the corresponding functions expressing extracellular potentials are calculated, using the volume conductor equation. This way, extracellular potentials are modeled as parametric functions of longitudinal distance, while perpendicular distance, current source strength, and other factors related to the propagated wave are parameters of the functions. Simulated annealing is applied for model parameter estimation and appropriate Time Domain and Wavelet Domain cost functions are investigated. Different combinations of model and cost function are evaluated regarding the accuracy of distance estimation. A continuous source model function with a wavelet cost function was found to be the most accurate combination. The accuracy of distance estimation is related to the selected source model and to the actual distance of recording in a nonmonotonic way.

Action Potentials↗

PubMed2003

Improving the resolution of dynamic intensity modulated radiation therapy delivery by reducing the multileaf collimator sampling distance.

The conformality of a dose distribution delivered by a multileaf collimator (MLC) for intensity modulated radiation therapy (IMRT) is limited in the direction perpendicular to leaf motion by the finite leaf width. Two methods of improving the resolution of IMRT intensity maps in this direction were investigated. In the first, the desired fluence distribution is considered to be sampled by the MLC, with the sampling distance being the center-to-center distance between the MLC leaves. The sampling distance is reduced below the leaf width by combining separate irradiations with a couch shift between them. This has been applied to static field therapy [Galvin et al., Int. J. Radiat. Oncol., Biol., Phys. 35, 89-94 (1996)], and was proposed for IMRT by Bortfeld et al. [Med. Phys. 27, 2494-2502 (2000)]. In the second method, two MLC component fluences, with leaf width L = 2deltay and offset by deltay, are combined to reproduce desired intensity bins with deltay width. The effect of MLC leaf sampling distance on dose resolution was quantified for both 1.0 and 0.5 cm MLC leaf widths, utilizing a high resolution bar-pattern fluence, an annular shaped fluence, and an intensity step-edge. Improvement in resolution was found for the 1.0 cm leaf width at a sampling distance of 0.5 cm, with only a small benefit for further reduction. For the 0.5 cm leaf width, a sampling distance of 0.25 cm resulted in a dose resolution that was nearly independent of direction.

Algorithms↗

PubMed2002

The effects of spatial separation in distance on the informational and energetic masking of a nearby speech signal.

Although many studies have shown that intelligibility improves when a speech signal and an interfering sound source are spatially separated in azimuth, little is known about the effect that spatial separation in distance has on the perception of competing sound sources near the head. In this experiment, head-related transfer functions (HRTFs) were used to process stimuli in order to simulate a target talker and a masking sound located at different distances along the listener's interaural axis. One of the signals was always presented at a distance of 1 m, and the other signal was presented 1 m, 25 cm, or 12 cm from the center of the listener's head. The results show that distance separation has very different effects on speech segregation for different types of maskers. When speech-shaped noise was used as the masker, most of the intelligibility advantages of spatial separation could be accounted for by spectral differences in the target and masking signals at the ear with the higher signal-to-noise ratio (SNR). When a same-sex talker was used as the masker, the intelligibility advantages of spatial separation in distance were dominated by binaural effects that produced the same performance improvements as a 4-5-dB increase in the SNR of a diotic stimulus. These results suggest that distance-dependent changes in the interaural difference cues of nearby sources play a much larger role in the reduction of the informational masking produced by an interfering speech signal than in the reduction of the energetic masking produced by an interfering noise source.

Adult↗

PubMed1984

Discrimination of relative distance in the auditory modality: the success and failure of the loudness discrimination hypothesis.

Difference limens for auditory distance discrimination were determined using the method of limits. Eight untrained subjects were tested across a wide range of distances (49 to 4876 cm) using broadband noise sources. For sources in excess of 304 cm, the Weber ratios observed approximated the function predicted by the inverse first power loss equation. At the longer distances, the subjects appear to be judging distance on the basis of the loudness difference cue. At the shorter distances (49 to 304 cm), the Weber ratios were considerably larger than would be predicted from the inverse first power loss equation. In this range, distance discrimination becomes increasingly degraded as the referent source approaches the subject.

Adult↗

PubMed1992

Use of sound-pressure level in auditory distance discrimination by 6-month-old infants and adults.

Six-month-old infants have been found to respond differentially to sounding objects placed within reach and beyond reach when no visual cues were available. The goal of the present study was to investigate whether sound-pressure level (SPL) serves as an auditory cue in distance discrimination. Thirty-two 6-month-olds were presented with recordings of sounding objects first in the light at midline position, then in the dark at 45 degrees to the right and left. On half of the dark trials the object was near (15 cm), and on half it was far (100 cm). For the control group the near sound was naturally 7 dB louder than the far. The experimental group had SPL counterbalanced across near and far locations to provide an inconsistent cue. Measures of infant reaching were scored from videotape. Two groups of adults were run under similar conditions; adults were tested on reaching as well as verbal reports of distance judgment. All infants reached more for the near object, regardless of the sound's SPL, suggesting that infants did not rely on this as a major distance cue. In contrast, adults' verbal judgments of distance were based heavily on SPL, a strategy that produced higher error rates in the group with SPL counterbalanced across distance. A followup study in which adults were instructed to move their heads before judging the sound's distance did not support the hypothesis that infants' head movements were responsible for their overcoming the misleading SPL information.

Adult↗

PubMed1995

Role of cucumovirus capsid protein in long-distance movement within the infected plant.

Direct evidence is presented for a host-specific role of the cucumovirus capsid protein in long-distance movement within infected plants. Cucumber (Cucumis sativus L.) is a systemic host for cucumber mosaic cucumovirus (CMV). Tomato aspermy cucumovirus, strain 1 (1-TAV), multiplied to the levels of CMV (i.e., replicated, moved from cell to cell, and formed infectious particles) in the inoculated leaves of cucumbers but was completely unable to spread systemically. The defective long-distance systemic movement of 1-TAV was complemented by CMV in mixed infections. Coinfection of cucumbers with 1-TAV RNA with various combinations of transcripts from full-length cDNA clones of CMV genomic RNA 1, RNA2, and RNA3 showed that CMV RNA3 alone complemented 1-TAV long-distance movement. We obtained mutants containing mutations in the two open reading frames in CMV RNA3 encoding the 3a protein and the capsid protein (CP), both of which are necessary for cell-to-cell movement of CMV. Complementation experiments with mutant CMV RNA3 showed that only 3a protein mutants, i.e., those with an intact CP, complemented the long-distance movement of 1-TAV in cucumbers. Since CMV and TAV have common systemic host plants, the results presented here are strong evidence for an active, host-specific function of the CPs of these two cucumoviruses for long-distance spread in the phloem. The results also suggest that the plasmodesmata in the vascular system and/or at the boundary between the mesophyll and the vascular system, involved in long-distance movement through the phloem, and those in the mesophyll, involved in cell-to-cell movement, differ functionally.

Capsid↗

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↗