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At least 1,477 records · Page 82Linked to original sources
PubMed1993

Effects of host plant development and genetic determinants on the long-distance movement of cauliflower mosaic virus in Arabidopsis.

During systemic infections, viruses move long distances through the plant vascular system. The long-distance movement of cauliflower mosaic virus (CaMV) in Arabidopsis has been examined using a whole plant in situ hybridization technique called plant skeleton hybridization. CaMV moves long distance through the phloem largely following the flow of photoassimilates from source to sink leaves. During the course of plant development, sink-source relationships change and the region of the plant that CaMV can invade is progressively reduced. In Arabidopsis, we have found that conditions that influence the rate of plant development dramatically impact the long-distance movement of CaMV, because under normal conditions the rate of plant development is closely matched to the kinetics of virus movement. Ecotypes and mutants of Arabidopsis that flower early show a form of resistance to systemic CaMV infection, which we call "developmental resistance." Developmental resistance results from the fact that the rosette leaves mature early in the life of an early flowering plant and become inaccessible to virus. On the other hand, if the development of early flowering plants is retarded by suboptimal growth conditions, inoculated plants appear more susceptible to the virus and systemic infections become more widespread. We have found that other Arabidopsis ecotypes, such as Enkheim-2 (En-2), show another form of resistance to virus movement that is not based on developmental or growth conditions. The virus resistance in ecotype En-2 is largely conditioned by a dominant trait at a single locus.

Arabidopsis↗
PubMed2002

Hg(3)AlF(6)O(2)H, a structure with a short interpolyhedral O...O distance.

The crystal structure of Hg(3)AlF(6)O(2)H, trimercury(II) aluminium hydrogen hexafluoride dioxide, can be derived from a slightly distorted cubic close-packed (ccp) arrangement of the metal atoms, where three quarters of the positions are occupied by Hg atoms and one quarter by Al atoms. The F and O atoms are considerably dislocated from the tetrahedral voids of this arrangement, thus forming [HgO(2)F(6)] polyhedra, with two short Hg-O distances, two intermediate Hg-F distances and four longer Hg-F distances, and nearly ideal [AlF(6)] octahedra. The H atoms are presumably located close to the inversion centre. Their positions were derived from crystal chemical arguments, and they take part in the formation of O-H.O hydrogen bonds between two O atoms, with an O.O distance of 2.562 (9) A.

Journal Article↗
PubMed2000

A new relation between bond valence and bond distance.

A new empirical relationship s = s0(R0 - lambda)3/(R - lambda)3 between bond distances and bond valences is proposed, where s is the bond valence for the bond distance R, s0 is the reference bond valence for the reference system with the reference bond distance R0 and lambda is the sum of the cation radii of bonding atoms defined by Pauling. Since lambda is the size of the inner electron region, R - lambda represents the valence electron region between bonding atoms. The new relationship was derived based on the following three hypotheses. (i) The number of electrons (p) in the volumes of (R - lambda)3 in a coordination polyhedron are equal, even if the bond distances are not equal to each other. (ii) The average electron density p/(R - lambda)3 is a measure of covalent bond strength. (iii) The sum of the average electron densities around the central atom is conserved, even if the coordination number changes. The new relationship is applicable not only to polyhedra with one type of ligand atom, but also to polyhedra with two or more types of ligand atoms and explains why the Brown-Shannon formula [Brown & Shannon (1973). Acta Cryst. A29, 266-282] and the Brown-Altermatt formula [Brown & Altermatt (1985). Acta Cryst. B41, 244-247] work well. The new relationship was applied to a penta-coordinated silicon compound, strong hydrogen-bond systems and some organic compounds with carbon-carbon bonds.

Journal Article↗
PubMed1996

The rate of water equilibration in vapor-diffusion crystallizations: dependence on the distance from the droplet to the reservoir.

The rate of water equilibration in hanging-drop vapor-diffusion experiments was studied as a function of the distance separating the hanging drop from the surface of the reservoir solution. Hanging drops of 1.00 M NaCl were allowed to partially equilibrate with reservoirs of 2.00 M NaCl at room temperature. Over the range of droplet-reservoir distances examined, 7.6-119.4 mm, the larger the distance that separated the droplet and reservoir, the slower the droplet equilibrated with the reservoir. The variation of the rate of equilibration with droplet-reservoir distance was non-linear; the rate was most sensitive to variations in the droplet-reservoir separation at short separations. A mathematical model of the equilibration kinetics was developed that fits the experimental data. The model is based on the assumption that the rate-limiting step in vapor-diffusion equilibration is transit of water across the vapor space. A simple device to vary the rate of water equilibration, and thereby optimize macromolecular crystal growth conditions, is described.

Journal Article↗
PubMed2001

Determination of metal-metal distances: significance and accuracy.

Nature utilises a variety of metal clusters as catalytic centers. Some of them make use of two or more metals in the catalytic site. The variation of metal-metal distances plays an important role in several processes like charge transfer and weakening of bonds. X-ray absorption spectroscopy can determine these metal-metal distances in several states (crystal, solution or amorphous). However sometimes backscattering from light elements hides the metal-metal contribution to the fine structure. Here we point out significance and accuracy of metal-metal distances in a model system. Therefore a number of different refinement protocols are applied to the data. These protocols will be discussed focusing on the significance and accuracy of the metal-metal distances extracted from the data.

Journal Article↗
PubMed2005

On optimizing distance-based similarity search for biological databases.

Similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. We consider distance-based indexing for three important biological data types, protein k-mers with the metric PAM model, DNA k-mers with Hamming distance and peptide fragmentation spectra with a pseudo-metric derived from cosine distance. To date, the primary driver of this research has been multimedia applications, where similarity functions are often Euclidean norms on high dimensional feature vectors. We develop results showing that the character of these biological workloads is different from multimedia workloads. In particular, they are not intrinsically very high dimensional, and deserving different optimization heuristics. Based on MVP-trees, we develop a pivot selection heuristic seeking centers and show it outperforms the most widely used corner seeking heuristic. Similarly, we develop a data partitioning approach sensitive to the actual data distribution in lieu of median splits.

Algorithms↗
PubMed2004

Characterization of event related potentials using information theoretic distance measures.

Analysis of event-related potentials (ERPs) using signal processing tools has become extremely widespread in recent years. Nonstationary signal processing tools such as wavelets and time-frequency distributions have proven to be especially effective in characterizing the transient phenomena encountered in event-related potentials. In this paper, we focus on the analysis of event-related potentials collected during a psychological experiment where two groups of subjects, spider phobics and snake phobics, are shown the same set of stimulus: A blank stimulus, a neutral stimulus and a spider stimulus. We introduce a new approach, based on time-frequency distributions, for analyzing the ERPs. The difference in brain activity before and after a stimulus is presented is quantified using distance measures as adapted to the time-frequency plane. Three different distance measures, including a new information theoretic distance measure, are applied on the time-frequency plane to discriminate between the responses of the two groups of subjects. The results illustrate the effectiveness of using distance measures combined with time-frequency distributions in differentiating between the two classes of subjects and the different regions of the brain.

Algorithms↗
PubMed2006

Super-resolution registration using tissue-classified distance fields.

We present a method for registering the position and orientation of bones across multiple computed-tomography (CT) volumes of the same subject. The method is subvoxel accurate, can operate on multiple bones within a set of volumes, and registers bones that have features commensurate in size to the voxel dimension. First, a geometric object model is extracted from a reference volume image. We use then unsupervised tissue classification to generate from each volume to be registered a super-resolution distance field--a scalar field that specifies, at each point, the signed distance from the point to a material boundary. The distance fields and the geometric bone model are finally used to register an object through the sequence of CT images. In the case of multiobject structures, we infer a motion-directed hierarchy from the distance-field information that allows us to register objects that are not within each other's capture region. We describe a validation framework and evaluate the new technique in contrast with grey-value registration. Results on human wrist data show average accuracy improvements of 74% over grey-value registration. The method is of interest to any intrasubject, same-modality registration applications where subvoxel accuracy is desired.

Algorithms↗
PubMed2006

A binary linear programming formulation of the graph edit distance.

A binary linear programming formulation of the graph edit distance for unweighted, undirected graphs with vertex attributes is derived and applied to a graph recognition problem. A general formulation for editing graphs is used to derive a graph edit distance that is proven to be a metric, provided the cost function for individual edit operations is a metric. Then, a binary linear program is developed for computing this graph edit distance, and polynomial time methods for determining upper and lower bounds on the solution of the binary program are derived by applying solution methods for standard linear programming and the assignment problem. A recognition problem of comparing a sample input graph to a database of known prototype graphs in the context of a chemical information system is presented as an application of the new method. The costs associated with various edit operations are chosen by using a minimum normalized variance criterion applied to pairwise distances between nearest neighbors in the database of prototypes. The new metric is shown to perform quite well in comparison to existing metrics when applied to a database of chemical graphs.

Algorithms↗
PubMed2004

Optimal bundling of transmembrane helices using sparse distance constraints.

We present a two-step approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only sparse distance constraints, such as those derived from chemical cross-linking, dipolar EPR and FRET experiments. In Step 1, using an algorithm, we developed, the conformational space of membrane protein folds matching a set of distance constraints is explored to provide initial structures for local conformational searches. In Step 2, these structures refined against a custom penalty function that incorporates both measures derived from statistical analysis of solved membrane protein structures and distance constraints obtained from experiments. We begin by describing the statistical analysis of the solved membrane protein structures from which the theoretical portion of the penalty function was derived. We then describe the penalty function, and, using a set of six test cases, demonstrate that it is capable of distinguishing helical bundles that are close to the native bundle from those that are far from the native bundle. Finally, using a set of only 27 distance constraints extracted from the literature, we show that our method successfully recovers the structure of dark-adapted rhodopsin to within 3.2 A of the crystal structure.

Animals↗
PubMed2002

Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein.

Histidine pK(a) values were measured in charge-reversal (K78E, K97E, K127E, and K97E/K127E) and charge-neutralization (E10A, E101A, and R35A) mutants of staphylococcal nuclease (SNase) by (1)H-NMR spectroscopy. Energies of interaction between pairs of charges (DeltaG(ij)) were obtained from the shifts in pK(a) values relative to wild-type values. The data describe the distance dependence and salt sensitivity of pairwise coulombic interactions. Calculations with a continuum electrostatics method captured the experimental DeltaG(ij) when static structures were used and when the protein interior was treated empirically with a dielectric constant of 20. The DeltaG(ij) when r(ij) < or = 10 A were exaggerated slightly in the calculations. Coulomb's law with a dielectric constant near 80 and a Debye-Hückel term to account for screening by the ionic strength reproduced the salt sensitivity and distance dependence of DeltaG(ij) as well as the structure-based method. In their interactions with each other, surface charges behave as if immersed in water; the Debye length describes realistically the distance where interactions become negligible at a given ionic strength. On average, charges separated by distances (r(ij)) approximately 5 A interacted with DeltaG(ij) approximately 0.6 kcal/mole in 0.01 M KCl, but DeltaG(ij) decayed to < or =0.10 kcal/mole when r(ij) = 20 A. In 0.10 M KCl, DeltaG(ij) approximately 0.10 kcal/mole when r(ij) = 10 A. In 1.5 M KCl, only short-range interactions with r(ij) < or = 5 A persisted. Although at physiological ionic strengths the interactions between charges separated by more than 10 A are extremely weak, in situations where charge imbalance exists many weak interactions can cumulatively produce substantial effects.

Histidine↗
PubMed2001

Measurement errors in line transect surveys where detectability varies with distance and size.

When using bivariate line transect methods to estimate the biomass density of a tightly clustered biological population, it is generally assumed that both the perpendicular distance from the trackline to the cluster and the cluster size, or biomass, are measured without error. This is unlikely to be the case in practice. In this article, assuming additive mean zero errors in distance and multiplicative errors in size, we develop an estimator of density that corrects for these errors. We use the method of moments for the case of gamma cluster size, randomly placed transect lines, and the generalized exponential detection function. We derive results that show that it may not be necessary to correct for errors in distance or size when the distance and size estimates are not biased. When the size estimates are biased, the biomass density estimate has approximately the same bias as the size estimates. The work is illustrated in the context of annual aerial surveys for juvenile southern bluefin tuna in the Great Australian Bight.

Animals↗
PubMed2000

Isolation by distance in equilibrium and nonequilibrium populations of four talitrid species in the Mediterranean Sea.

Allozymic variation at 21-23 loci was studied in 28 populations of Talitrus saltator, 23 populations of Orchestia montagui, 13 populations of O. stephenseni, and five populations of Platorchestia platensis from the Mediterranean Basin. Different levels of gene flow (Nmtheta) were detected within each species at the scale of the whole Mediterranean: O. montagui and P. platensis had low population structure, with levels of Nmtheta > or = 1, whereas the T. saltator and 0. stephenseni populations have values of Nmtheta < 1. The relationship between Nmtheta and geographic distance was analyzed to test for the presence of an isolation by distance pattern in the spatial genetic variation within each species. A model of isolation by distance is useful to describe the pattern of genetic structuring of study species at the scale of the whole Mediterranean: geographic distance explained from 28% to 70% of the variation in gene flow. In the Aegean area all species showed an island model of genetic structuring regardless of the levels of gene flow.

Animals↗
PubMed1995

Skin-epidural distance in children.

The skin-epidural distance was measured in 274 children to assess the usefulness of 1 mm.kg-1 as a guideline. Children aged between 2 days and 16 years, weighing between 2 and 43 kg were investigated. Lumbar epidurals were performed under general anaesthesia using a midline approach in the L3-4 interspace with the patient in the lateral position. Good correlation between skin-epidural distance and age and weight was demonstrated. No statistical difference was shown when plotting the best fit regression line: skin-epidural distance (mm) = 0.8 weight (kg) + 3.93 (R2 = 0.74) and its 95% confidence limits and skin-epidural distance (mm) = weight (kg) for children between 6 months and 10 years. Poor correlation was noted below 6 months (n = 22) and over 10 years (n = 19). No dural puncture or bloody tap occurred. One mm.kg-1 body weight was shown to be a useful guideline for children between 6 months and 10 years of age.

Adolescent↗
PubMed1990

Genetic variation and distances of five Italian native sheep breeds.

Genetic distances among five of the most important Italian native sheep breeds were estimated by using gene frequencies of four blood group and seven blood protein loci and by three different computing methods. The values of the three distance matrices were highly correlated. Genetic distances were found within the range values reported in the literature for local breeds. Shorter distances fitted the historical evidence of migrations.

Animals↗
PubMed1979

Dermatoglyphic distances and position of 21 trisomy mosaics.

The position of 21 trisomy mosaics with an average proportion of trisomic cells approximating 0.5 in relation to normal subjects and those with complete 21 trisomy has been evaluated by means of dermatoglyphic distances, using samples of 142 mosaics, 302 normal controls and 225 complete 21 trisomics for males and females separately and combined. Distances were calculated by means of the simplified D2k method. Penrose's "size and shape" analysis of variance has been applied for comparison to obtain distance coefficients, C2H, based on pattern intensities. Results indicate that mosaics are not intermediate but much closer to 21 trisomics in spite of the fact that the average proportion of trisomic cells in blood approximates 0.5; secondly, that the degree of deviation from the intermediate position of the mosaic sample is roughly proportional to the degree of cytological mosaicism. The position of mosaics is appreciably more intermediate in respect of finger-tip patterns than in respect of palmar and sole loops and triradii. The results obtained here have thus given evidence for the usefulness of dermatoglyphic distances, which enable all the differences in frequencies or means of the respective characters to be conveniently represented by a single number, in studies of the abnormal development of phenotypic characteristics in cases of incomplete trisomy.

Dermatoglyphics↗
PubMed2005

Surface EMG of jaw elevator muscles: effect of electrode location and inter-electrode distance.

This study addresses methodological issues on surface electromyographic (EMG) signal recording from jaw elevator muscles. The aims were (i) to investigate the sensitivity to electrode displacements of amplitude and spectral surface EMG variables, (ii) to analyse if this sensitivity is affected by the inter-electrode distance of the bipolar recording, and (iii) to investigate the effect of inter-electrode distance on the estimated amplitude and spectral EMG variables. The superficial masseter and anterior temporalis muscles of 13 subjects were investigated by means of a linear electrode array. The percentage difference in EMG variable estimates from signals detected at different locations over the muscle was larger than 100% of the estimated value. Increasing the inter-electrode distance resulted in a significant reduction of the estimation variability because of electrode displacement. A criterion for electrode placement selection is suggested, with which the sensitivity of EMG variables to small electrode displacements was of the order of 2% for spectral and 6% for amplitude variables. Finally, spectral and, in particular, amplitude EMG variables were very sensitive to inter-electrode distance, which thus should be fixed when subjects or muscles are compared in the same or different experimental conditions.

Adult↗
PubMed1984

Hemagglutination and the closest distance of approach of normal, neuraminidase- and papain-treated erythrocytes.

By means of potential energy versus distance diagrams, derived from electrophoretic and surface tension data, the minimum distances of approach of normal (NOR) and of neuraminidase-treated (NEU) and papain-treated (PAP) human erythrocytes could be determined. The minimum distances between the actual cell membranes of two opposing red cells are: 184 A (NOR), 111 A (NEU), and 113 A (PAP), which agrees well with the fact that anti-D (Rho) antibodies of the IgG-class (which have a maximum distance of approximately 120 A between the two antibody-active sites) can hemagglutinate NEU and PAP cells, but are incapable of hemagglutinating normal D (Rho)-positive erythrocytes.

Antigen-Antibody Reactions↗