Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data resolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed2003

Chemometric resolution of ATR-IR spectra data for polycondensation reaction of bis(hydroxyethylterephthalate) with a combination of self-modeling curve resolution (SMCR) and local rank analysis.

Self-modeling curve resolution (SMCR) methods, simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) and alternating least squares (ALS) were used to calculate pure concentration profiles and pure spectra for the two-way spectral data collected during the on-line polycondensation reaction of bis(hydroxyethylterephthalate) with an ATR-FT-IR spectrometer. In order to improve the resolution results, SIMPLISMA was combined with local rank analysis method, fixed size moving window evolving factor analysis (FSMWEFA) to search for selective regions of various components and then look for the purest wavenumber variables in the selective regions. Such combination allows more accurate determination of the number of chemical components in the reaction system and the calculations of more accurate concentration profiles and spectra.

Journal Article↗
PubMed2006

Assessing the reliability of standardized performance indicators.

OBJECTIVE: . To investigate the reliability of self-reported standardized performance indicators introduced by the Joint Commission on Accreditation of Healthcare Organizations in July 2002 and implemented in approximately 3400 accredited US hospitals. The study sought to identify the most common data quality problems and determine causes and possible strategies for resolution. DESIGN: Data were independently reabstracted from a random sample of 30 hospitals. Reabstracted data were compared with data originally abstracted, and discrepancies were adjudicated with hospital staff. Structured interviews were used to probe possible reasons for abstraction discrepancies. RESULTS: The mean data element agreement rate for the 61 data elements evaluated was 91.9%, and the mean kappa statistic for binary data elements was 0.68. The rate of agreement for individual data elements ranged from 100 to 62.4%. The mean difference between calculated indicator rates was 4.88% (absolute value) and the range of differences was 0.0-13.3%. Symmetry of disagreement among original abstractors and reabstractors identified eight indicators whose differences in calculated rates were statistically unlikely to have occurred through random chance (P < 0.05). CONCLUSION: Although improvement in the accuracy and completeness of the self-reported data is possible and desirable, the baseline level of data reliability appears to be acceptable for indicators used to assess and improve hospital performance on selected clinical topics.

Hospitals↗
PubMed2005

Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.

Panicum mosaic virus (PMV), a spherical virus of diameter about 300 A, has been crystallized in a form suitable for high-resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be flash-frozen directly from their mother liquor. The crystals diffracted to beyond 2.7 A resolution. A data set was collected at 100 K to an effective resolution of 3.2 A [Weiss (2001), J. Appl. Cryst. 34, 130-135]. The crystals belonged to space group P2(1), with unit-cell parameters a=411.7, b=403.9, c=412.5 A, beta=89.7 degrees . Self-rotation functions and molecular replacement with tobacco necrosis virus as the probe model yielded tentative positions and orientations for the two entire virus particles comprising the asymmetric unit and implied a pseudo-face-centered cubic packing arrangement. Investigation of lightly glutaraldehyde-fixed crystals in water using atomic force microscopy confirms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite virus to PMV, known as satellite panicum mosaic virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice. This is the first observation of such a phenomenon in macromolecular crystals.

Crystallography, X-Ray↗
PubMed2005

Molecular modelling of drug targets: the past, the present and the future.

Most currently used therapeutic drugs have an enzyme or a membrane-bound receptor as site of action. The sequencing of the human and other genomes has provided a potential to identify many hitherto unknown proteins that might serve as new drug targets. To achieve this, knowledge about three-dimensional protein structures is crucial for the understanding of their functional mechanisms, and for a rational drug design. Over the last decade atomic resolution crystal structures of soluble proteins have been reported in a rapidly increasing number, but the detailed three-dimensional structures are still unknown for the majority of membrane proteins since their membrane association makes experimental structure determinations complicated. Computerized modelling of protein structures, based on experimentally determined structures of homologue proteins, may be a useful methodological alternative, especially for membrane proteins. In the past, molecular modelling of transporters and G-protein-coupled receptors was based on low-resolution structural data obtained by cryo-electron microscopy. Recent high-resolution crystal structure determinations of a G-protein-coupled receptor, rhodopsin, and several different transporter proteins and ion channels have enabled construction of more accurate receptor and transporter models. For the future, collaborative structural genomics initiatives aim at determining the three-dimensional structure of all known proteins, based on a combination of experimental structure determination and molecular modelling. Development of still more powerful computer hardware and software will enable extensive studies of the protein structure and dynamics of new potential drug targets, but raises a new challenge in the validation and calibration of computerized methods of biosimulations.

Carrier Proteins↗
PubMed1995

Structure of human diferric lactoferrin refined at 2.2 A resolution.

The three-dimensional structure of the diferric form of human lactoferrin has been refined at 2.2 A resolution, using synchrotron data combined with a lower resolution (3.2 A) diffractometer data set. Following restrained least-squares refinement and model rebuilding the final model comprises 5330 protein atoms (691 residues), 2Fe(3+) and 2CO(3)(2-) ions, 469 solvent molecules and 98 carbohydrate atoms (eight sugar residues). Root-mean-square deviations from standard geometry are 0.015 A for bond lengths and 0.038 A for angle (1-3) distances, and the final crystallographic R-factor is 0.179 for all 39 113 reflections in the resolution range 8.0-2.2 A. A close structural similarity is seen between the two lobes of the molecule, with differences mainly in loops and turns. The two binding sites are extremely similar, the only apparent differences being a slightly more asymmetric bidentate binding of the carbonate ion to the metal, and a slightly longer Fe-O bond to one of the Tyr ligands, in the N-lobe site relative to the C-lobe site. Distinct differences are seen in the interactions made by two cationic groups, Arg210 and Lys546, behind the iron site, and these may influence the stability of the two metal sites. Analysis of interdomain and interlobe interactions shows that these are few in number which is consistent with the known flexibility of the molecule with respect to domain and lobe movements. Internal water molecules are found in discrete sites and in two large clusters (in the two interdomain clefts) and one tightly bound water molecule is present 3.8 A from the Fe atom in each lobe. The carbohydrate is weakly defined and has been modelled to a limited extent; two sugar residues of the N-lobe glycan and six of the C-lobe glycan. Only one direct protein-carbohydrate contact can be found.

Journal Article↗
PubMed1999

On 'globbicity' of low-resolution protein structures.

Using Harker's [Harker (1953). Acta Cryst. 6, 731-736] idea of spherically averaged polyatomic groups or 'globs' as the units of structure suitable for analyzing low-resolution diffraction data from protein crystals, 'globbic' scattering factors have been calculated for main-chain peptide units and amino-acid side-chain groups to 3 A resolution via Debye's [Debye (1915). Ann. Phys. (Leipzig), 46, 809-823] scattering formula. It is shown that the scattering factors are insensitive to intra-globbic conformational variation and can be approximated fairly well by a single-Gaussian formula, i.e. fg(s) = Zg exp(-1.7Zgs2), where s = (sin theta)/lambda and Zg is the total electron count for the atoms of the glob. Phase errors due to the globbic approximation and their effect on electron-density maps at 3.5 A resolution have been assessed via calculations for the crambin structure; this analysis indicates that the globbic scattering factors will be useful in efforts to develop procedures for direct-methods phasing of diffraction data to approximately 3.5 A resolution from protein crystals.

Crystallography, X-Ray↗
PubMed2006

Spatially encoded pulse sequences for the acquisition of high resolution NMR spectra in inhomogeneous fields.

We have recently proposed a protocol for retrieving nuclear magnetic resonance (NMR) spectra based on a spatially-dependent encoding of the MR interactions. It has also been shown that the spatial selectivity with which spins are manipulated during such encoding opens up new avenues towards the removal of magnetic field inhomogeneities; not by demanding extreme Bo field uniformities, but rather by compensating for the dephasing effects introduced by the field distribution at a radiofrequency excitation and/or refocusing level. The present study discusses in further detail a number of strategies deriving from this principle, geared at acquiring both uni- as well as multi-dimensional spectroscopic data at high resolution conditions. Different variants are presented, tailored according to the relative sensitivity and chemical nature of the spin system being explored. In particular a simple multi-scan experiment is discussed capable of affording substantial improvements in the spectral resolution, at nearly no sensitivity or scaling penalties. This new compensation scheme is therefore well-suited for the collection of high-resolution data in low-field systems possessing limited signal-to-noise ratios, where magnetic field heterogeneities might present a serious obstacle. Potential areas of applications of these techniques include high-field in vivo NMR studies in regions near tissue/air interfaces, clinical low field MR spectroscopy on relatively large off-center volumes difficult to shim, and ex situ NMR. The principles of the different compensation methods are reviewed and experimentally demonstrated for one-dimensional inhomogeneities; further improvements and extensions are briefly discussed.

Butanes↗
PubMed2006

Real-time rigid body motion correction and shimming using cloverleaf navigators.

Subject motion during scanning can greatly reduce MRI image quality and is a major reason for discarding data in both clinical and research scanning. The quality of the high-resolution structural data used for morphometric analysis is especially compromised by subject movement because high-resolution scans are of longer duration. A method is presented that measures and corrects rigid body motion and associated first-order shim changes in real time, using a pulse sequence with embedded cloverleaf navigators and a feedback control mechanism. The procedure requires a 12-s preliminary mapping scan. A single-path, 4.2-ms cloverleaf navigator is inserted every repetition time (TR) after the readout of a 3D fast low-angle shot (FLASH) sequence, requiring no additional RF pulses and minimally impacting scan duration. Every TR, a rigid body motion estimate is made and a correction is fed back to adjust the gradients and shim offsets. Images are corrected and reconstructed on the scanner computer for immediate access. Correction for between-scan motion can be accomplished by using the same reference map for each scan repetition. Human and phantom tests demonstrated a consistent improvement in image quality if motion occurred during the acquisition.

Algorithms↗
PubMed2002

Crystal structure of the inclusion complex of beta-cyclodextrin with mefenamic acid from high-resolution synchrotron powder-diffraction data in combination with molecular-mechanics calculations.

The crystal structure of the inclusion complex of beta-cyclo-dextrin with mefenamic acid has been determined from a combination of high-resolution synchrotron powder-diffraction data and molecular-mechanics calculations. A grid search indicates two possible solutions, which are corroborated by molecular-mechanics calculations, while Rietveld-refinement results suggest the crystal structure that is more likely to be formed in the solid state. Mefenamic acid is partially included in beta-cyclodextrin with either the xylyl or the benzoic-acid moiety being inside its cavity. In both solutions mefenamic acid and beta-cyclodextrin form a monomeric complex in a herringbone packing scheme.

Journal Article↗
PubMed1999

Electron density distribution and Madelung potential in alpha-spodumene, LiAl(SiO3)2, from two-wavelength high-resolution X-ray diffraction data.

The electron density distribution in alpha-spodumene, LiAl(SiO(3))(2), was derived from high-resolution X-ray diffraction experiments. The results obtained from both Mo Kalpha- and Ag Kalpha-wavelength data sets are reported. The features of the Si-O and Al-O bonds are related to the geometrical parameters of the Si-O-Al and Si-O-Si bridges on the one hand and to the O.Li(+) interaction on the other. Kappa refinements against the two data sets yielded almost the same net charges for the Si (+1.8 e) and O (-1.0 e) atoms in spodumene. However, the Al net charge obtained from the Ag Kalpha data (+1.9 e) is larger than the net charge derived from the Mo Kalpha data (+1.5 e). This difference correlates with a more contracted Al valence shell revealed by the shorter X-ray wavelength (kappa = 1.4 for the Ag Kalpha data set). The derived net charges were used to calculate the Madelung potential at the spodumene atomic sites. The electrostatic energy for the chemical formula LiAl(SiO(3))(2) was -8.60 e(2) Å(-1) (-123.84 eV) from the net charges derived from the Ag Kalpha data and -6.97 e(2) Å(-1) (-100.37 eV) from the net charges derived from the Mo Kalpha data.

Journal Article↗
PubMed1994

Low-resolution X-ray diffraction data obtained from hexagonal crystals of methylamine-treated alpha2-macroglobulin.

Two hexagonal crystal forms of tetrameric human methylamine-treated alpha(2)-macroglobulin have been grown by vapour diffusion. One of the crystal forms diffracts X-rays beyond 9 A resolution. The space group of this form is P6(2)22 or P6(4)22 with a = b = 327, c = 219 A and with one dimer of alpha(2)-macroglobulin in the asymmetric unit. Several data sets have been collected by the use of synchrotron radiation at cryogenic temperature. A native data set extending to 10 A resolution has been obtained. The merging R factor of these data is 10.3%.

Journal Article↗
PubMed2004

Fourier components of inhomogeneously broadened water resonances in breast: a new source of MRI contrast.

High spectral and spatial resolution (HiSS) MR data were acquired at 1.5 T using echo-planar spectroscopic imaging from patients with suspicious breast lesions. The water resonances in small voxels are inhomogenously broadened and often have distinct components. Images were calculated with intensity proportional to the Fourier components of the water resonance in each voxel at different offsets from the peak frequency. The results demonstrate that in breast the off-peak Fourier component images of water are qualitatively different from those derived from the peak height of the water resonance. These differences most likely reflect underlying anatomy or physiology. In conventional images, the superposition of the various Fourier components of the water signal may cause loss of detail. The synthesis of water Fourier component images from high spectral and spatial resolution data may provide a new form of contrast, and increase sensitivity to subvoxel physiology and anatomy.

Body Water↗
PubMed1996

Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions.

Biomolecular interactions can be defined by combining thermodynamic data on the energetic properties of the interaction with high-resolution structural data. The development of high sensitivity isothermal titration calorimetric equipment provides a dramatic advance in the gathering of thermodynamic data, and the interactions between biological macromolecules can now be described with unprecedented accuracy.

Calorimetry↗
PubMed2003

Subtleties in crystal structure solution from powder diffraction data using simulated annealing: ranitidine hydrochloride.

Recent advances in crystallographic computing and availability of high-resolution diffraction data have made it relatively easy to solve crystal structures from powders that would have traditionally required single crystal samples. The success of direct space methods depends heavily on starting with an accurate molecular model. In this paper we address the applicability of using these methods in finding subtleties such as disorder in the molecular conformation that might not be known a priori. We use ranitidine HCl as our test sample as it is known to have a conformational disorder from single crystal structural work. We redetermine the structure from powder data using simulated annealing and show that the conformational disorder is clearly revealed by this method.

Algorithms↗
PubMedDate not supplied

Interactive fitting augmented by force-feedback and virtual reality.

The synthesis of low-resolution electron microscopy data with high-resolution molecular structures has become a common routine in the modeling of biomolecular assemblies. In contrast to algorithmic "black box" solutions, the interactive "fitting by eye" takes advantage of an expert's structural or biochemical knowledge and can be used with very noisy experimental data. In the solution proposed in this paper, we support the expert user in an interactive fitting session by haptic rendering and virtual reality. The quantitative and tactile feedback facilitates and objectifies the otherwise unrestrained modeling. We introduce a highly accurate reduced representation of the gradient of the cross-correlation coefficient that sustains force updates for haptic rendering at sufficiently high refresh rates.

Algorithms↗
PubMed1995

Multichannel PC-based data-acquisition system for high-resolution EEG.

This paper describes a complete, high-performance data-acquisition system for high-resolution EEG. The system includes preamplified EEG electrodes, rigid helmets, differential instrumentation and software-controlled gain amplifiers, digitizing and control circuitry, and optical coupling to a 486 PC. Miniaturized preamplifiers mounted on individual electrodes reduce coupling to external electromagnetic fields and minimize signal distortion caused by increased and/or imbalanced electrode impedances. Electrodes are applied quickly and with minimal skin preparation, yet with high packing densities and repositioning consistent to about 1-3 mm in repeated applications. Extensive testing under realistic conditions demonstrates that the system provides superior electrical performance compared to currently available commercial systems.

Analog-Digital Conversion↗
PubMed2005

The accuracy of human population maps for public health application.

OBJECTIVES: Human population totals are used for generating burden of disease estimates at global, continental and national scales to help guide priority setting in international health financing. These exercises should be aware of the accuracy of the demographic information used. METHODS: The analysis presented in this paper tests the accuracy of five large-area, public-domain human population distribution data maps against high spatial resolution population census data enumerated in Kenya in 1999. We illustrate the epidemiological significance, by assessing the impact of using these different human population surfaces in determining populations at risk of various levels of climate suitability for malaria transmission. We also describe how areal weighting, pycnophylactic interpolation and accessibility potential interpolation techniques can be used to generate novel human population distribution surfaces from local census information and evaluate to what accuracy this can be achieved. RESULTS: We demonstrate which human population distribution surface performed best and which population interpolation techniques generated the most accurate bespoke distributions. Despite various levels of modelling complexity, the accuracy achieved by the different surfaces was primarily determined by the spatial resolution of the input population data. The simplest technique of areal weighting performed best. CONCLUSIONS: Differences in estimates of populations at risk of malaria in Kenya of over 1 million persons can be generated by the choice of surface, highlighting the importance of these considerations in deriving per capita health metrics in public health. Despite focussing on Kenya the results of these analyses have general application and are discussed in this wider context.

Climate↗
PubMed2000

High-resolution geoacoustic inversion in shallow water: a joint time- and frequency-domain technique

High-resolution geoacoustic data are required for accurate predictions of acoustic propagation and scattering in shallow water. Since direct measurement of geoacoustic data is difficult, time-consuming, and expensive, inversion of acoustic data is a promising alternative. However, the main problem encountered in geoacoustic inversion is the problem of uniqueness, i.e., many diverse geoacoustic models can be made to fit the same data set. A key, and perhaps unique, aspect of this approach is the combination of data analysis in both the space-time and the space-frequency domains. This combination attempts to ameliorate the uniqueness problem by exploiting as much independent data as possible. In order to meet the stringent requirements of high spatial resolution and uniqueness, an entire method has been developed including a new measurement technique, processing/analysis technique, and inversion strategy. These techniques are described and then illustrated with a shallow-water data set. Sound-speed gradients in the upper few meters of the sub-bottom appear to be much higher (one order of magnitude) than generally assumed. And, although often ignored, a large density gradient was observed in the top layer that played an acoustically significant role.

Journal Article↗