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PubMedDate not supplied

Accurate determination of metabolic rates from dynamic positron emission tomography data with very-low temporal resolution.

PURPOSE: The graphical approach is widely used for the pixelwise determination of local metabolic rate of glucose from dynamic positron emission tomography (PET) data. In its conventional implementation, measured integrals over time frames are used to approximate instantaneous tracer concentrations at midframe times ("midframe approach"). This is justified in case of high temporal resolution of the PET measurement; that is, if scan protocols with a large number of short frames are used. This requires fast data handling and large amounts of memory. Cardiac gating and three-dimensional (3D) acquisition of dynamic studies is hardly possible with this approach. Therefore, a new variant of the graphical method is proposed which can be used with a very low number of rather long frames. METHODS: An operational equation of the graphical method was derived which uses measured time integrals only and, thus, avoids the systematic errors of the midframe approximation. This "integral approach" was evaluated in computer simulations based on experimental data. RESULTS: The integral approach enables the use of protocols with 3 frames only without compromising accuracy of the derived metabolic rates whereas the midframe approach leads to bias of about 10% to 20% for these protocols. Furthermore, test-retest stability can significantly be improved when using the integral approach. CONCLUSION: The integral approach to the graphical evaluation of dynamic PET data yields accurate and precise results using scan protocols with down to only 3 frames. This can be relevant to gating and/or 3D acquisition of dynamic studies. The integral approach is applied most naturally whenever the input function is derived from the dynamic PET data.

Brain↗
PubMedDate not supplied

FEMME database: topologic and geometric information of macromolecules.

FEMME (Feature Extraction in a Multi-resolution Macromolecular Environment: http://www.biocomp.cnb.uam.es/FEMME/) database version 1.0 is a new bioinformatics data resource that collects topologic and geometric information obtained from macromolecular structures solved by three-dimensional electron microscopy (3D-EM). Although the FEMME database is focused on medium resolution data, the methodology employed (based on the so-called alpha-shape theory) is applicable to atomic resolution data as well. The alpha-shape representation allows the automatic extraction of structural features from 3D-EM volumes and their subsequent characterisation. FEMME is being populated with 3D-EM data stored in the electron microscopy database EMD-DB (http://www.ebi.ac.uk/msd/). However, and since the number of entries in EMD-DB is still relatively small, FEMME is also being populated in this initial phase with structural data from PDB and PQS databases (http://www.rcsb.org/pdb/ and pqs.ebi.ac.uk/, respectively) whose resolution has been lowered accordingly. Each FEMME entry contains macromolecular geometry and topology information with a detailed description of its structural features. Moreover, FEMME data have facilitated the study and development of a method to retrieve macromolecular structures by their structural content based on the combined use of spin images and neural networks with encouraging results. Therefore, the FEMME database constitutes a powerful tool that provides a uniform and automatic way of analysing volumes coming from 3D-EM that will hopefully help the scientific community to perform wide structural comparisons.

Computational Biology↗
PubMed2004

Improved DOSY NMR data processing by data enhancement and combination of multivariate curve resolution with non-linear least square fitting.

The quality of DOSY NMR data can be improved by careful pre-processing techniques. Baseline drift, peak shift, and phase shift commonly exist in real-world DOSY NMR data. These phenomena seriously hinder the data analysis and should be removed as much as possible. In this paper, a series of preprocessing operations are proposed so that the subsequent multivariate curve resolution can yield optimal results. First, the baseline is corrected according to a method by Golotvin and Williams. Next, frequency and phase shift are removed by a new combination of reference deconvolution (FIDDLE), and a method presented by Witjes et al. that can correct several spectra simultaneously. The corrected data are analysed by the combination of multivariate curve resolution with non-linear least square regression (MCR-NLR). The MCR-NLR method turns out to be more robust and leads to better resolution of the pure components than classic MCR.

Journal Article↗
PubMed2002

Aortic intimal injuries from blunt trauma: resolution profile in nonoperative management.

OBJECTIVE: To provide preliminary data on the resolution profile of aortic intimal injuries treated nonoperatively and on the safety of nonoperative management of these injuries. METHODS: Five blunt trauma patients diagnosed by transesophageal echocardiography (TEE) with traumatic intimal injury of the aorta were assigned to nonoperative management. This included beta-blockade to maintain systolic blood pressure between 80 and 90 mm Hg and heart rate between 60 and 80 beats/min, serial TEE studies, and invasive monitoring in the intensive care unit. The evolution of injury, the effectiveness of nonoperative treatment, and the potential need for an operative intervention were monitored. RESULTS: The patients had a mean Injury Severity Score of 32 and sustained multiple associated thoracic and extrathoracic injuries. Aortic injuries were located at the level of the ligamentum arteriosum and in the descending aorta adjacent to the diaphragm in three and two patients, respectively. The mean size of injury was 12.5 mm (range, 5-20 mm) and a thrombus attached to the endothelium was present in three of the five patients. Complete resolution of injury occurred within 9.4 +/- 6.6 days (range, 3-19 days). All patients remained hemodynamically stable and adequately perfused. All demonstrated progressive resolution of their aortic intimal injuries. No complications related to the aortic injuries were identified during a mean follow-up of 16.8 months. CONCLUSION: This small series suggests that aortic intimal injuries smaller than 20 mm in hemodynamically stable patients treated with beta-blockade resolve within several days. This approach appears safe when monitored by serial TEE studies performed by experienced experts, and continuous invasive hemodynamic monitoring.

Adrenergic beta-Antagonists↗
PubMed2001

Structure of beta-trimyristin and beta-tristearin from high-resolution X-ray powder diffraction data.

The crystal structures of beta-1,2,3-tritetradecanoylglycerol (beta-trimyristin or beta-MMM) and beta-1,2,3-trioctadecanoylglycerol (beta-tristearin or beta-SSS) have been determined from high-resolution synchrotron X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine and refine the structure, respectively. Both substances crystallize in space group P1; with Z = 2. The unit-cell parameters for beta-MMM are a = 12.0626 (6), b = 41.714 (1), c = 5.4588 (3) A, alpha = 73.388 (4), beta = 100.408 (5) and gamma = 118.274 (4) degrees. For beta-SSS the unit-cell parameters are a = 12.0053 (7), b = 51.902 (2), c = 5.4450 (3) A, alpha = 73.752 (5), beta = 100.256 (6) and gamma = 117.691 (5) degrees. Soft-distance restraints have been applied to the molecules during refinement. For beta-MMM the final R(p) value obtained is 0.053 and for beta-SSS the final R(p) value is 0.041.

Journal Article↗
PubMed1998

[High-resolution virtual laryngoscopy based on spiral CT data].

This pilot study investigated the feasibility and clinical value of high-resolution virtual real-time laryngoscopy based on helical CT data sets. Nine patients with laryngeal pathology (three with tumors of the vocal cords, two laryngeal carcinomas, one with invasion of the larynx by thyroid carcinoma and six subglottic stenoses) underwent examination by helical CT at a collimation of 1 mm. Following acquisition, the images were processed at a workstation with standard visualization software, such that virtual endoscopy (VE) in real time was possible. The images were then compared with the findings of conventional endoscopy. Because of swallowing artifacts, reconstruction failed in 2 of 12 patients. None of the carcinomas of the vocal cords was recognized at VE or in the cross-sectional CT images. VE provided the correct diagnosis in 8 of 12 cases (laryngeal tumors, subglottic stenoses). Virtual laryngoscopy is capable of simulating the visual findings of endoscopy in cases of laryngeal tumors and subglottic stenoses. Small tumors of the vocal cords are not adequately visualized. The major problem affecting results is motion artifacts resulting from involuntary swallowing.

Aged↗
PubMed1999

On the application of phase relationships to complex structures. XXXVI: some experiments with a small protein without heavy atoms.

The direct-methods program MULTAN88 has been applied to a known protein, ribonuclease (RNAP1), containing 808 non-H atoms, including five S atoms, plus 83 ordered solvent water molecules. Phase sets with mean phase errors between 69 and 75 degrees were selected by modified figures of merit for trials with the full data at 1.17 A resolution and also with restricted data at 1.25 and 1.5 A resolution. These figures of merit had previously only been applied to protein structures containing heavy atoms, and this is the first demonstration of their usefulness with no heavy atom present. An initial set of 1091 phases from a 1.17 A trial was developed by an objective procedure to give the full structure with a residual of 0. 21, which agrees well with the published structure.

Crystallography, X-Ray↗
PubMed2005

Estimation of biogenic emissions with satellite-derived land use and land cover data for air quality modeling of Houston-Galveston ozone nonattainment area.

The Houston-Galveston Area (HGA) is one of the most severe ozone non-attainment regions in the US. To study the effectiveness of controlling anthropogenic emissions to mitigate regional ozone nonattainment problems, it is necessary to utilize adequate datasets describing the environmental conditions that influence the photochemical reactivity of the ambient atmosphere. Compared to the anthropogenic emissions from point and mobile sources, there are large uncertainties in the locations and amounts of biogenic emissions. For regional air quality modeling applications, biogenic emissions are not directly measured but are usually estimated with meteorological data such as photo-synthetically active solar radiation, surface temperature, land type, and vegetation database. In this paper, we characterize these meteorological input parameters and two different land use land cover datasets available for HGA: the conventional biogenic vegetation/land use data and satellite-derived high-resolution land cover data. We describe the procedures used for the estimation of biogenic emissions with the satellite derived land cover data and leaf mass density information. Air quality model simulations were performed using both the original and the new biogenic emissions estimates. The results showed that there were considerable uncertainties in biogenic emissions inputs. Subsequently, ozone predictions were affected up to 10 ppb, but the magnitudes and locations of peak ozone varied each day depending on the upwind or downwind positions of the biogenic emission sources relative to the anthropogenic NOx and VOC sources. Although the assessment had limitations such as heterogeneity in the spatial resolutions, the study highlighted the significance of biogenic emissions uncertainty on air quality predictions. However, the study did not allow extrapolation of the directional changes in air quality corresponding to the changes in LULC because the two datasets were based on vastly different LULC category definitions and uncertainties in the vegetation distributions.

Air Pollution↗
PubMed2006

Adsorption and in situ scanning tunneling microscopy of cysteine on Au(111): Structure, energy, and tunneling contrasts.

The amino acid L-cysteine (Cys) adsorbs in highly ordered (3 square root of 3 x 6) R30 degrees lattices on Au(111) electrodes from 50 mM ammonium acetate, pH 4.6. We provide new high-resolution in situ scanning tunneling microscopy (STM) data for the L-Cys adlayer. The data substantiate previous data with higher resolution, now at the submolecular level, where each L-Cys molecule shows a bilobed feature. The high image resolution has warranted a quantum chemical computational effort. The present work offers a density functional study of the geometry optimized adsorption of four L-Cys forms-the molecule, the anion, the neutral radical, and its zwitterion adsorbed a-top-at the bridge and at the threefold hollow site of a planar Au(111) Au12 cluster. This model is crude but enables the inclusion of other effects, particularly the tungsten tip represented as a single or small cluster of W-atoms, and the solvation of the L-Cys surface cluster. The computational data are recast as constant current-height profiles as the most common in situ STM mode. The computations show that the approximately neutral radical, with the carboxyl group pointing toward and the amino group pointing away from the surface, gives the most stable adsorption, with little difference between the a-top and threefold sites. Attractive dipolar interactions screened by a dielectric medium stabilize around a cluster size of six L-Cys entities, as observed experimentally. The computed STM images are different for the different L-Cys forms. Both lateral and vertical dimensions of the radical accord with the observed dimensions, while those of the molecule and anion are significantly more extended. A-top L-Cys radical adsorption further gives a bilobed height profile resembling the observed images, with comparable contributions from sulfur and the amino group. L-Cys radical a-top adsorption therefore emerges as the best representation of L-Cys adsorption on Au(111).

Adsorption↗
PubMed2000

The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.

X-ray diffraction analysis of protein structure is often limited by the availability of suitable crystals. However, the absence of single crystals need not present an insurmountable obstacle in protein crystallography any more than it does in materials science, where powder diffraction techniques have developed to the point where complex oxide, zeolite and small organic molecular structures can often be solved from powder data alone. Here, that fact is demonstrated with the structure solution and refinement of a new variant of the T(3)R(3) Zn-human insulin complex produced by mechanical grinding of a polycrystalline sample. High-resolution synchrotron X-ray powder diffraction data were used to solve this crystal structure by molecular replacement adapted for Rietveld refinement. A complete Rietveld refinement of the 1630-atom protein was achieved by combining 7981 stereochemical restraints with a 4800-step (d(min) = 3.24 A) powder diffraction pattern and yielded the residuals R(wp) = 3.73%, R(p) = 2.84%, R(F)(2) = 8.25%. It was determined that the grinding-induced phase change is accompanied by 9.5 and 17.2 degrees rotations of the two T(3)R(3) complexes that comprise the crystal structure. The material reverts over 2-3 d to recover the original T(3)R(3) crystal structure. A Rietveld refinement of this 815-atom protein by combining 3886 stereochemical restraints with a 6000-step (d(min) = 3.06 A) powder diffraction pattern yielded the residuals R(wp) = 3.46%, R(p) = 2.64%, R(F)(2) = 7.10%. The demonstrated ability to solve and refine a protein crystal structure from powder diffraction data suggests that this approach can be employed, for example, to examine structural changes in a series of protein derivatives in which the structure of one member is known from a single-crystal study.

Humans↗
PubMed1995

Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data.

The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.

Journal Article↗
PubMed2002

Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein.

Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 A and 1.00 A resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8 % for 7.0-0.92 A resolution data of the form I and 11.2 % for the 13.3-1.0 A resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 A resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C(alpha)-C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D(2d) symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.

Bacillus↗
PubMed2006

Natural linewidth chemical shift imaging (NL-CSI).

The discrete Fourier transform (FT) is a conventional method for spatial reconstruction of chemical shifting imaging (CSI) data. Due to point spread function (PSF) effects, FT reconstruction leads to intervoxel signal leakage (Gibbs ringing). Spectral localization by imaging (SLIM) reconstruction was previously proposed to overcome this intervoxel signal contamination. However, the existence of magnetic field inhomogeneities creates an additional source of intervoxel signal leakage. It is demonstrated herein that even small field inhomogeneities substantially amplify intervoxel signal leakage in both FT and SLIM reconstruction approaches. A new CSI data acquisition strategy and reconstruction algorithm (natural linewidth (NL) CSI) is presented that eliminates effects of magnetic field inhomogeneity-induced intervoxel signal leakage and intravoxel phase dispersion on acquired data. The approach is based on acquired CSI data, high-resolution images, and magnetic field maps. The data are reconstructed based on the imaged object structure (as in the SLIM approach) and a reconstruction matrix that takes into account the inhomogeneous field distribution inside anatomically homogeneous compartments. Phantom and in vivo results show that the new method allows field inhomogeneity effects from the acquired MR signal to be removed so that the signal decay is determined only by the "natural" R2 relaxation rate constant (hence the term "natural linewidth" CSI).

Algorithms↗
PubMed2001

[Multislice CT of the lung. Technique and clinical applications].

With the advent of multislice technology computed tomography experienced a boost in image quality, comparable to the introduction of spiral CT one decade ago. In the chest, the improved performance may be utilised to scan faster or to obtain an almost isotropic spatial resolution. For examinations of the lungs multislice CT offers considerable advantages over single slice spiral CT: reduced breathing and pulsation artefacts, the ability to cover large volumes with thin slices, the simultaneous evaluation of high resolution and standard imaging protocols from one data acquisition, high resolution multiplanar sections through the lung parenchyma, and 3D techniques like volume rendering and virtual bronchoscopy. In this review the technical principles of multislice CT of the lungs are discussed. Major clinical applications such as evaluation of focal and diffuse lung disease are reviewed.

Artifacts↗
PubMed2001

Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism.

The structure of Bacillus pasteurii urease (BPU) inhibited with phosphate was solved and refined using synchrotron X-ray diffraction data from a vitrified crystal (1.85 A resolution, 99.3% completeness, data redundancy 4.6, R-factor 17.3%, PDB code 6UBP). A distance of 3.5 A separates the two Ni ions in the active site. The binding mode of the inhibitor involves the formation of four coordination bonds with the two Ni ions: one phosphate oxygen atom symmetrically bridges the two metal ions (1.9-2.0 A), while two of the remaining phosphate oxygen atoms bind to the Ni atoms at 2.4 A. The fourth phosphate oxygen is directed into the active site channel. Analysis of the H-bonding network around the bound inhibitor indicates that phosphate is bound as the H2PO4- anion, and that an additional proton is present on the Odelta2 atom of Asp(alpha363), an active site residue involved in Ni coordination through Odelta1. The flexible flap flanking the active site cavity is in the open conformation. Analysis of the complex reveals why phosphate is a relatively weak inhibitor and why sulfate does not bind to the nickels in the active site. The implications of the results for the understanding of the urease catalytic mechanism are reviewed. A novel alternative for the proton donor is presented.

Bacillus↗
PubMed1989

Correlation between occupancy and temperature factors of solvent molecules in crystal structures of proteins.

Correlation between occupancy and temperature factors during the refinement of a disordered molecule is discussed on the basis of their effects on an atomic scattering factor curve. When the resolution of the data is limited, occupancy and temperature factors affect scattering-factor curves in a similar fashion, and therefore they are correlated. An examination of this correlation suggests that small deviations (0.1) of occupancy factors from their tentative values may be compensated by suitable changes in temperature factors when the data are limited to medium (2.5 A) resolution.

Chemical Phenomena↗
PubMed2004

Crystallization of GcnA, an N-acetyl-beta-D-glucosaminidase, from Streptococcus gordonii.

Streptococcus gordonii is a primary colonizer of the surface of human teeth. The gcnA gene is one of a number of genes involved in glycoside metabolism. GcnA has N-acetyl-beta-D-glucosaminidase (EC 3.2.1.52) activity; it has been overexpressed, purified and crystallized. Diffraction has been observed to beyond 1.5 A resolution and synchrotron data have been recorded to 1.55 A resolution. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 112.5, b = 104.0, c = 110.0 A. The crystals contain either a monomer or a dimer in the asymmetric unit.

Acetylglucosaminidase↗
PubMed1986

Replication and resolution of cloned poxvirus telomeres in vivo generates linear minichromosomes with intact viral hairpin termini.

The covalently closed terminal hairpins of the linear duplex-DNA genomes of the orthopoxvirus vaccinia and the leporipoxvirus Shope fibroma virus (SFV) have been cloned as imperfect palindromes within circular plasmids in yeast cells and recombination-deficient Escherichia coli. The viral telomeres inserted within these recombinant plasmids are equivalent to the inverted-repeat structures detected as telomeric replicative intermediates during poxvirus replication in vivo. Although the telomeres of vaccinia and SFV show little sequence homology, the termini from both viral genomes exist as AT-rich terminal hairpins with extrahelical bases and alternate "flip-flop" configurations. Using an in vivo replication assay in which circular plasmid DNA was transfected into poxvirus-infected cells, we demonstrated the efficient replication and resolution of the cloned imperfect palindromes to bona fide hairpin termini. The resulting linear minichromosomes, which were readily purified from transfected cells, were shown by restriction enzyme mapping and by electron microscopy to have intact covalently closed hairpin termini at both ends. In addition, staggered unidirectional deletion derivatives of both the cloned vaccinia and SFV telomeric palindromes localized an approximately 200-base-pair DNA region in which the sequence organization was highly conserved and which was necessary for the resolution event. These data suggest a conserved mechanism of the resolution of poxvirus telomeres.

Base Sequence↗