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At least 631 records · Page 35Linked to original sources
PubMed1996

Fast dynamic imaging using two reference images.

This paper presents a fast dynamic imaging method which is characterized by the acquisition of two high-resolution reference images and a sequence of low-resolution dynamic data sets. Image reconstruction is accomplished using a generalized series based algorithm. Experimental results demonstrate that dynamic images with high temporal resolution can be obtained while maintaining excellent spatial resolution. This method will be useful for a variety of dynamic imaging applications including contrast-enhanced dynamic imaging and functional brain studies.

Algorithms↗
PubMed2005

Dynamic autocalibrated parallel imaging using temporal GRAPPA (TGRAPPA).

Current parallel imaging techniques for accelerated imaging require a fully encoded reference data set to estimate the spatial coil sensitivity information needed for reconstruction. In dynamic parallel imaging a time-interleaved acquisition scheme can be used, which eliminates the need for separately acquiring additional reference data, since the signal from directly adjacent time frames can be merged to build a set of fully encoded full-resolution reference data for coil calibration. In this work, we demonstrate that a time-interleaved sampling scheme, in combination with autocalibrated GRAPPA (referred to as TGRAPPA), allows one to easily update the coil weights for the GRAPPA algorithm dynamically, thereby improving the acquisition efficiency. This method may update coil sensitivity estimates frame by frame, thereby tracking changes in relative coil sensitivities that may occur during the data acquisition.

Algorithms↗
PubMed2005

Application of satellite infrared data for mapping of thermal plume contamination in coastal ecosystem of Korea.

The 5900 MW Younggwang nuclear power station on the west coast of Korea discharges warm water affecting coastal ecology [KORDI report (2003). Wide area observation of the impact of the operation of Younggwang nuclear power plant 5 and 6, No. BSPI 319-00-1426-3, KORDI, Seoul, Korea]. Here the spatial and temporal characteristics of the thermal plume signature of warm water are reported from a time series (1985-2003) of space-borne, thermal infrared data from Landsat and National Oceanic and Atmospheric Administration (NOAA) satellites. Sea surface temperature (SST) were characterized using advanced very high resolution radiometer data from the NOAA satellites. These data demonstrated the general pattern and extension of the thermal plume signature in the Younggwang coastal areas. In contrast, the analysis of SST from thematic mapper data using the Landsat-5 and 7 satellites provided enhanced information about the plume shape, dimension and direction of dispersion in these waters. The thermal plume signature was detected from 70 to 100 km to the south of the discharge during the summer monsoon and 50 to 70 km to the northwest during the winter monsoon. The mean detected plume temperature was 28 degrees C in summer and 12 degrees C in winter. The DeltaT varied from 2 to 4 degrees C in winter and 2 degrees C in summer. These values are lower than the re-circulating water temperature (6-9 degrees C). In addition the temperature difference between tidal flats and offshore (SSTtidal flats - SSToffsore) was found to vary from 5.4 to 8.5 degrees C during the flood tides and 3.5 degrees C during the ebb tide. The data also suggest that water heated by direct solar radiation on the tidal flats during the flood tides might have been transported offshore during the ebb tide. Based on these results we suggest that there is an urgent need to protect the health of Younggwang coastal marine ecosystem from the severe thermal impact by the large quantity of warm water discharged from the Younggwang nuclear power plant.

Ecosystem↗
PubMed1999

Crystallization and preliminary X-ray analysis of tryparedoxin I from Crithidia fasciculata.

The thioredoxin-related protein tryparedoxin I from Crithidia fasciculata has been crystallized using PEG 4000 as a precipitant. The enzyme forms long needle-shaped crystals which diffract to at least 1.7 A. A native data set has been collected at the DESY synchrotron from a flash-frozen crystal at 90 K to 1.7 A resolution. The data set shows that the crystals belong to the orthorhombic space group P212121 and have unit-cell parameters a = 37.94, b = 51. 39, c = 71.46 A. Tryparedoxin I is involved in a trypanothione-dependent peroxide metabolic pathway specific for trypanosomatids and may therefore be a suitable candidate for the design of drugs for the specific treatment of a variety of important tropical diseases caused by these parasites.

Animals↗
PubMed1977

Method for obtaining a high resolution protein map starting from a low resolution map.

A method is described for estimating the phases of high resolution single-crystal diffraction data from proteins, by using as a starting point a set of low resolution phases (about 3 A) derived by multiple isomorphous replacement (or other) methods. The method consists in refining by least-squares the positions and thermal parameters of a set of dummy atoms placed in the initial low resolution electron density map, so as to minimize the discrepancy between the calculated scattering intensities and the scattering intensities observed in the high resolution data set. Phases calculated from these refined atomic positions are used to extend the resolution and to improve the quality of the electron density map. The success of the method depends on a new least-squares algorithm that has a radius of convergence of about 0.75 A. This large radius of convergence, together with the severe restrictions placed on the initial positions of the dummy atoms by the requirement that they lie within limited regions of the isomorphous electron density map, and the constraint imposed by the polymeric nature of a polypeptide chain account for the success of the method. The method has been successfully used to phase the structure factors of 2-zinc insulin at a resolution of 2 A and 1.5 A, starting from a set of isomorphous phases at 3-A resolution.

Insulin↗
PubMed2004

Shadowing and absorption corrections of high-pressure powder diffraction data: toward accurate electron-density determinations.

The shadowing of the primary beam and of reflections from a powder crystal sample enclosed in a diamond-anvil high-pressure cell (DAC) is described for unrestricted data-collection procedures. The corrections account for the shadowing of the data measured with point- or area-detector diffractometers and can be applied for any containers of environment devices enclosing a powdered sample. The general procedure for correcting the powder diffraction data can be applied for analysing and optimizing diffractometric procedures of data collection and provides facilities for collecting high-pressure powder diffraction data with the DAC positioned optimally and rotated to counteract the preferred-orientation and particle-size effects, and to increase the resolution of data. The quadrature effects of numerical integration for the accuracy of computed corrections have been analysed.

Journal Article↗
PubMedDate not supplied

Spatial interpolation methods for nonstationary plume data.

Plume interpolation consists of estimating contaminant concentrations at unsampled locations using the available contaminant data surrounding those locations. The goal of ground water plume interpolation is to maximize the accuracy in estimating the spatial distribution of the contaminant plume given the data limitations associated with sparse monitoring networks with irregular geometries. Beyond data limitations, contaminant plume interpolation is a difficult task because contaminant concentration fields are highly heterogeneous, anisotropic, and nonstationary phenomena. This study provides a comprehensive performance analysis of six interpolation methods for scatter-point concentration data, ranging in complexity from intrinsic kriging based on intrinsic random function theory to a traditional implementation of inverse-distance weighting. High resolution simulation data of perchloroethylene (PCE) contamination in a highly heterogeneous alluvial aquifer were used to generate three test cases, which vary in the size and complexity of their contaminant plumes as well as the number of data available to support interpolation. Overall, the variability of PCE samples and preferential sampling controlled how well each of the interpolation schemes performed. Quantile kriging was the most robust of the interpolation methods, showing the least bias from both of these factors. This study provides guidance to practitioners balancing opposing theoretical perspectives, ease-of-implementation, and effectiveness when choosing a plume interpolation method.

Forecasting↗
PubMed2001

A hierarchical storage management (HSM) scheme for cost-effective on-line archival using lossy compression.

A hierarchical storage management (HSM) scheme for cost-effective on-line archival of image data using lossy compression is described. This HSM scheme also provides an off-site tape backup mechanism and disaster recovery. The full-resolution image data are viewed originally for primary diagnosis, then losslessly compressed and sent off site to a tape backup archive. In addition, the original data are wavelet lossy compressed (at approximately 25:1 for computed radiography, 10:1 for computed tomography, and 5:1 for magnetic resonance) and stored on a large RAID device for maximum cost-effective, on-line storage and immediate retrieval of images for review and comparison. This HSM scheme provides a solution to 4 problems in image archiving, namely cost-effective on-line storage, disaster recovery of data, off-site tape backup for the legal record, and maximum intermediate storage and retrieval through the use of on-site lossy compression.

Algorithms↗
PubMed2006

Diving behaviour of whale sharks in relation to a predictable food pulse.

We present diving data for four whale sharks in relation to a predictable food pulse (reef fish spawn) and an analysis of the longest continuous fine-resolution diving record for a planktivorous shark. Fine-resolution pressure data from a recovered pop-up archival satellite tag deployed for 206 days on a whale shark were analysed using the fast Fourier Transform method for frequency domain analysis of time-series. The results demonstrated that a free-ranging whale shark displays ultradian, diel and circa-lunar rhythmicity of diving behaviour. Whale sharks dive to over 979.5 m and can tolerate a temperature range of 26.4 degrees C. The whale sharks made primarily diurnal deep dives and remained in relatively shallow waters at night. Whale shark diving patterns are influenced by a seasonally predictable food source, with shallower dives made during fish spawning periods.

Animals↗
PubMed2005

Opportunities for using spatial property assessment data in air pollution exposure assessments.

BACKGROUND: Many epidemiological studies examining the relationships between adverse health outcomes and exposure to air pollutants use ambient air pollution measurements as a proxy for personal exposure levels. When pollution levels vary at neighbourhood levels, using ambient pollution data from sparsely located fixed monitors may inadequately capture the spatial variation in ambient pollution. A major constraint to moving toward exposure assessments and epidemiological studies of air pollution at a neighbourhood level is the lack of readily available data at appropriate spatial resolutions. Spatial property assessment data are widely available in North America and may provide an opportunity for developing neighbourhood level air pollution exposure assessments. RESULTS: This paper provides a detailed description of spatial property assessment data available in the Pacific Northwest of Canada and the United States, and provides examples of potential applications of spatial property assessment data for improving air pollution exposure assessment at the neighbourhood scale, including: (1) creating variables for use in land use regression modelling of neighbourhood levels of ambient air pollution; (2) enhancing wood smoke exposure estimates by mapping fireplace locations; and (3) using data available on individual building characteristics to produce a regional air pollution infiltration model. CONCLUSION: Spatial property assessment data are an extremely detailed data source at a fine spatial resolution, and therefore a source of information that could improve the quality and spatial resolution of current air pollution exposure assessments.

Journal Article↗
PubMed1995

Direct-space methods in phase extension and phase determination. III. Phase refinement using Sayre's equation.

An algorithm is described for refining a set of phases to agree with the Sayre equation. All operations are carried out using Fourier transforms with modest computer-store requirements even for very large systems. The procedure is tested with two moderate-sized proteins, one containing heavy atoms, and is found to give good refinement with data at more than atomic resolution (1.17 A) and useful, if less good, refinement when the data resolution is lower (1.5 A). It is concluded that at atomic resolution, or slightly below, the Sayre equation still has something to offer both for phase refinement and phase extension, especially if used cautiously with weighted multiple isomorphous replacement phases acting as a constraint on the phase changes. Even when the Sayre equation on its own refines phases badly, or not at all, it may still make an important contribution in conjunction with other real-space refinement procedures.

Journal Article↗
PubMed2002

Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution.

From the first days of protein neutron structure determination sperm whale myoglobin was an object under investigation [Nature 224 (1969) 143, J. Mol. Biol. 220 (1991) 381]. Nevertheless myoglobin is still of interest [Proc. Natl. Acad. Sci. USA 97 (2000) 3872]. The feasibility of the monochromatic neutron diffractometer BIX-3 at the JRR-3M reactor at the JAERI [J. Phys. Chem. Solids 60 (1999) 1623], to collect high-resolution diffraction data in a relatively short time stimulated us to repeat the structural determination of myoglobin. The structure of metmyoglobin has been determined up to a resolution of 1.5 A. The hydrogen atoms were replaced in part, by deuterium soaking the crystals for more than 10 years in D(2)O. A refinement of all atoms has been performed including the refinement of individual mean square displacements and occupancies of the exchangeable protons in backbone hydrogen bonds. A method is described to show clear negative scattering densities of the H atoms. Water molecules within the protein and on the molecule surface are shown. The exchangeability of H atoms is correlated with structural distribution and flexibility.

Animals↗
PubMed1999

X-ray crystallographic determination of the structure of the influenza C virus haemagglutinin-esterase-fusion glycoprotein.

The structure of the haemagglutinin-esterase-fusion (HEF) glycoprotein from influenza C virus has been determined to 3.2 A resolution by X-ray crystallography. A synthetic mercury-containing esterase inhibitor and receptor analogue, 9-acetamidosialic acid alpha-thiomethylmercuryglycoside, was designed as the single isomorphous heavy-atom derivative. The asymmetric unit of one crystal form (form I; P4322, a = b = 155.4, c = 414.4 A) contained an HEF trimer. Six mercury sites identifying the three haemagglutination and three esterase sites were located by difference Patterson map analysis of a 6.5 A resolution derivative data set. These positions defined the molecular threefold-symmetry axis of the HEF trimer. A molecular envelope was defined by averaging a 7.0 A resolution electron-density map, phased by single isomorphous replacement (SIR), about the non-crystallographic threefold-symmetry axis. Iterative non-crystallographic symmetry averaging in real space, solvent flattening and histogram matching were used to extend the phases to 3.5 A resolution. Molecular replacement of the model into a second crystal form (form II; P43212, a = b = 217.4, c = 421.4 A) containing two HEF trimers per asymmetric unit permitted iterative ninefold averaging of the electron density. The 3.5 A electron-density map allowed an unambiguous tracing of the polypeptide chain and identification of N-linked carbohydrates. The model has been refined by least squares to 3.2 A resolution (Rfree = 26.7%).

Acetylesterase↗
PubMed1995

High-resolution structure of a DNA helix forming (C.G)*G base triplets.

Triple helices result from interaction between single- and double-stranded nucleic acids. Their formation is a possible mechanism for recombination of homologous gene sequences in nature and provides, inter alia, a basis for artificial control of gene activity. Triple-helix motifs have been extensively studied by a variety of techniques, but few high-resolution structural data are available. The only triplet structures characterized so far by X-ray diffraction were in protein-DNA complexes studied at about 3 A resolution. We report here the X-ray analysis of a DNA nonamer, d(GCGAATTCG), to a resolution of 2.05 A, in which the extended crystal structure contains (C.G)*G triplets as a fragment of triple helix. The guanosine-containing chains are in a parallel orientation. This arrangement is a necessary feature of models for homologous recombination which results ultimately in replacement of one length of DNA by another of similar sequence. The present-structure agrees with many published predictions of triplex organization, and provides an accurate representation of an element that allows sequence-specific association between single- and double-stranded nucleic acids.

Base Sequence↗
PubMed1989

Analysis of relaxation time data from a low-resolution 1H-NMR-pulse-spectrometer.

Systematic investigations have been undertaken in order to evaluate the potential of low resolution NMR for characterization of biological tissue (in vitro) during early post mortem period. Test measurements from corn-oil samples are compared with computer simulated data. Furthermore, time-after-excision dependence of mouse-liver tissue is presented using the in vitro protocol developed in our laboratory. Quantitative data from biexponential model fit are shown and results are discussed in terms of the "best guess" model.

Animals↗
PubMed1999

Partial 28S rDNA sequences and the antiquity of hydrothermal vent endemic gastropods.

A molecular phylogenetic investigation of the hypothesized antiquity of the hydrothermal vent endemic Neomphalina (Mollusca; Gastropoda) is reported. Sequences of two domains of the gene encoding for 28S ribosomal RNA were acquired for 3 outgroup and 32 gastropod genera. Use of the likelihood ratio test indicated complex substitution patterns for these domains and taxa, corresponding to a general time-reversible model with among-site rate variation. Phylogenetic analyses were performed using this model under maximum likelihood criteria. The data lacked resolution of gastropod radiations of the Paleozoic and all three of the outgroup sequences were randomized relative to the ingroup. Acceleration of evolutionary rates had additionally randomized the sequences of the Patellogastropoda relative to the other Gastropoda. The data resolved radiations of the Mesozoic and supported monophyly of the sampled Neritopsina, Vetigastropoda, Neomphalina, Caenogastropoda (including Campanile and the Architaenioglossa), and Heterobranchia (Valvata + Euthyneura), although several results were not significantly different from nonmonophyletic alternatives. Mesozoic origins of the hydrothermal vent endemic Neomphalina are preliminarily supported and implications for the hydrothermal vent refugia hypothesis discussed. Issues related to phylogenetic resolution of the Gastropoda are additionally discussed.

Animals↗
PubMed2003

Structure of viscotoxin A3: disulfide location from weak SAD data.

The crystal structure of viscotoxin A3 (VT A3) extracted from European mistletoe (Viscum album L.) has been solved using the anomalous diffraction of the native S atoms measured in-house with Cu Kalpha radiation to a resolution of 2.2 A and truncated to 2.5 A. A 1.75 A resolution synchrotron data set was used for phase expansion and refinement. An innovation in the dual-space substructure-solution program SHELXD enabled the individual S atoms of the disulfide bonds to be located using the Cu Kalpha data; this resulted in a marked improvement in the phasing compared with the use of super-S atoms. The VT A3 monomer consists of 46 amino acids with three disulfide bridges and has an overall fold resembling the canonical architecture of the alpha- and beta-thionins, a capital letter L. The asymmetric unit consists of two monomers related by a local twofold axis and held together by hydrophobic interactions between the monomer units. One phosphate anion (confirmed by 31P-NMR and MS) is associated with each monomer.

Binding Sites↗
PubMed1992

Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution.

The structure of the tri-N-acetylchitotriose inhibitor complex of hen egg-white lysozyme has been refined at 1.75 A resolution, using data collected from a complex crystal with ligand bound at less than full occupancy. To determine the exact value of the inhibitor occupancy, a model comprising unliganded and sugar-bound protein molecules was generated and refined against the 1.75 A data, using a modified version of the Hendrickson & Konnert least-squares procedure. The crystallographic R-factor for the model was found to fall to a minimum at 55% bound sugar. Conventional refinement assuming unit occupancy was found to yield incorrect thermal and positional parameters. Application of the same refinement procedures to an earlier 2.0 A data set, collected independently on different complex crystals by Blake et al. gave less consistent results than the 1.75 A refinement. From an analysis of the high resolution structure a detailed picture of the protein-carbohydrate interactions in the non-productive complex has emerged, together with the conformation and mobility changes that accompany ligand binding. The specificity of interaction between the protein and inhibitor, bound in subsites A to C of the active site, is seen to be generated primarily by an extensive network of hydrogen bonds, both to the protein itself and to bound solvent molecules. The latter also play an important role in maintaining the structural integrity of the active site cleft in the apo-protein.

Binding Sites↗