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At least 1,261 records · Page 70Linked to original sources
PubMed2001

[Rapid interactive 3-D imaging of the temporal bone with "direct volume rendering"].

INTRODUCTION: For the first time, the relatively new method of interactive direct volume rendering (dVR) allows for a fast and direct three-dimensional visualization of spiral CT data without any manual, explicit segmentation. This study was performed to prove whether dVR is capable of providing a meaningful three-dimensional visualization of the structures within the temporal bone. PATIENTS AND METHODS: In ten patients a three-dimensional visualization of the structures of the inner and middle ear was performed from spiral CT data on a commercially available graphics workstation. RESULTS: The cochlea and semicircular canals were visualized in good quality in all patients. The ossicles and bony facial canal were visualized in good or fair quality in most cases. The time needed for the visualization of the data and all target structures was less than 15 min in all cases. CONCLUSIONS: Three-dimensional visualization of the structures within the temporal bone from high-resolution spiral CT data using dVR is easily performed in a very short time on standard graphics workstations. This allows integrating three-dimensional visualizations into routine clinical work.

Computer Graphics↗
PubMed1982

Polyoma virus capsid structure at 22.5 A resolution.

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.

Capsid↗
PubMed1992

Quality assurance and reproducibility of high-resolution two-dimensional electrophoresis and silver staining in polyacrylamide gels.

Qualitative data from high-resolution two-dimensional electrophoresis (2DE) have become clinically useful in immunoglobulin clonality analysis, in resolution of ambiguities in immunofixation typing of paraproteins, and in genetic typing of serum proteins. Since 1986, the authors have been evaluating the College of American Pathologists Reference Preparation for Serum Proteins (RPSP) as a quality control material for 2DE because (1) it is prepared exclusively from pooled human sera, (2) the pool yields a reference pattern of mixed heterozygosity for genetic markers, and (3) RPSP is widely available as a lyophilized preparation that currently serves in the authors' laboratory as a qualitative quality control preparation and that may become a quantitative quality control material or external quality assessment material for 2DE. Using the ISO-DALT 2DE system and silver-staining, the peptide patterns were examined in 11 lots of RPSP and compared with fresh serum and with each other. Consistent differences in the 2DE pattern between RPSP and fresh serum included the presence of freeze-thaw peptides, the presence of degradation spots of apolipoprotein A-I, and the diminution of apolipoprotein spot intensities in RPSP. All lots of RPSP yielded clear identification of the eight serum proteins used for quality control calculations. Run-to-run coefficients of variation for a single lot of RPSP for four parameters of 2DE spot location and gradient reproducibility were comparable with band location reproducibility for the one-dimensional procedures of serum protein electrophoresis and lactate dehydrogenase isoenzyme electrophoresis. It is concluded that the reproducibility, that is, imprecision, of 2DE is the same as one-dimensional clinical electrophoresis techniques and that either RPSP or pooled fresh serum can serve as a satisfactory internal quality control material.

Blood Protein Electrophoresis↗
PubMedDate not supplied

Teleradiology at Gunma University Hospital.

Using NEC MediFile 1000 and the public telephone system, the Department of Radiology of Gunma University Hospital and Saitama Medical School deliver image diagnosis to fellow clinicians and affiliated hospitals. The system consists of digitizing, filing, processing, retrieving and archiving units for radiographs and documents. Images were digitized by CCD and filed in 2 Gbyte double sided optical disk, which can accommodate 500 sheets of 14 x 17 films on 1500 of the smallest size slats without data compression. Image resolution was evaluated by ROC curve using multiple pulmonary nodules. The time taken for image transfer over 24 km was tested with various film sizes, image varieties and data compression rates.

Computer Communication Networks↗
PubMed2002

Crystallization and preliminary X-ray diffraction studies of Escherichia coli branching enzyme.

Branching enzyme catalyzes the formation of the branch points in glycogen and starch by cleavage of the alpha-1,4 link and its subsequent transfer to the alpha-1,6 position. This paper reports the crystallization and preliminary structural studies of an amino-terminally truncated branching enzyme from Escherichia coli. High-resolution diffracting crystals were obtained and a complete native data set to a resolution of 2.3 A was collected. These crystals belong to the P2(1) space group, with unit-cell parameters a = 91.44, b = 102.58, c = 185.41 A, beta = 91.38 degrees. A native data set with 99.6% completeness, an overall R(merge) of 0.086 and I/sigma(I) of 10.43 was obtained.

1,4-alpha-Glucan Branching Enzyme↗
PubMed2004

Ultra-high resolution 3D NMR spectra from limited-size data sets.

The advantage of the filter diagonalization method (FDM) for analysis of triple-resonance NMR experiments is demonstrated by application to a 3D constant time (CT) HNCO experiment. With a 15N-,13C-labeled human ubiquitin sample (1.0 mM), high spectral resolution was obtained at 500 MHz in 25 min with only 6-8 increments in each of the CT dimensions. This data set size is about a factor of 50-100 smaller than typically required, yet FDM analysis results in a fully resolved spectrum with a sharp peak for each HNCO resonance. Unlike Fourier transform (FT) processing, in which spectral resolution in each dimension is inversely proportional to the acquisition time in this dimension, FDM is a true multi-dimensional method; the resolution in all dimensions is determined by the total information content of the entire signal. As the CT dimensions of the 3D HNCO signal have approximate time-reversal symmetry, they can each be doubled by combining the usual four hyper-complex data sets. This apparent quadrupling of the data is important to the success of the method. Thus, whenever raw sensitivity is not limiting, well-resolved n-dimensional spectra can now be obtained in a small fraction of the usual time. Alternatively, to maximize sensitivity, evolution periods of faster relaxing nuclei may be radically shortened, the total required resolution being obtained through chemical shift encoding of other, more slowly relaxing, spins. Improvements similar to those illustrated with a 3D HNCO spectrum are expected for other triple-resonance spectra, where CT evolution in the indirect dimensions is implemented.

Algorithms↗
PubMed2006

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.

Algorithms↗
PubMed1989

Quantitative comparison of cerebral glucose metabolic rates from two positron emission tomographs.

The rapid progress in positron emission tomography technology has created the dilemma of how to compare data from old and new tomographs. We examined cerebral metabolic data from two scanners, with different spatial resolutions and methods of attenuation correction, to see if data from the lower resolution tomograph (ECAT II) could be "corrected" and then compared to data from the higher resolution scanner (Scanditronix PC1024-7B). Nine subjects were scanned on both tomographs after a single injection of [18F]2-fluoro-2-deoxy-D-glucose. Regional and lobar gray matter metabolic rates for glucose were obtained from comparable images from each scanner. Ratios of lobar to global gray matter metabolism also were calculated. Regression coefficients and percent differences were computed to compare ECAT II and PC1024 data. Twenty-four of the 36 regions showed significant regression slopes, and PC1024 measures of glucose utilization ranged from 30% to 120% higher than those from the ECAT II. Lobar differences between the two machines were less variable (50% to 80%), and ratios generally differed by only +/- 5%. Since there was no simple and consistent relation between regional metabolic rates on the two tomographs, an overall adjustment of regional ECAT values for comparison to PC1024 values would be impossible. A region-by-region adjustment would be necessary. On the other hand, ratios are sufficiently similar that direct comparisons could be made.

Aged↗
PubMed1990

Analysis of side-chain conformational distributions in neutrophil peptide-5 NMR structures.

The side-chain conformations have been analyzed in the antimicrobial peptide, Neutrophil Peptide-5 (NP-5), whose structure was independently generated from nmr-derived distance constraints using a distance geometry algorithm. The side-chain and peptide dihedral angle distributions in the nmr structures were compared with those constructed from a data base of high-resolution protein crystal structures. The side-chain conformational preferences for NP-5 in solution are significantly different from those observed in the crystal structure data base. These results indicate that the side-chain conformations are quite disordered for many of the residues of NP-5. The absence of a correlation between the width of the conformational distribution and surface accessibility suggests that the disorder may be due to limitations in the structural information extracted from the nmr data rather than to molecular motion. However, it is also observed that the degree of conformational disorder is only weakly correlated with the number of nuclear Overhauser enhancements to a given side chain. Possible reasons for this are discussed. Molecular mechanics refinement of these structures did not significantly change the side-chain populations. Anomolously wide distributions are observed for rotations about the peptide bonds and the disulfide bonds in the NP-5 distance geometry structures, which are improved by the refinement. The very high degree of order observed for the central dihedral angle of the disulfide bond in the high-resolution crystal data base suggests that the rotation about this bond in proteins is determined by the local potential.

Algorithms↗
PubMed2004

Optimization of technetium-99m Sestamibi single-photon emission tomography to define multidrug resistance with confidence.

BACKGROUND: The efflux rate of technetium-99m Sestamibi (99mTc-Sestamibi) is a kinetic phenomenon related to the response of cancer cells to chemotherapy, and may be used to determine drug resistance. Measurement of the efflux rate requires accurate quantitative single-photon emission tomography (SPET) imaging within the time constraints imposed by the kinetics of the process. METHODS: A phantom study, at activity concentrations typically found with 99mTc-Sestamibi in vivo, was undertaken to optimize the SPET parameters and, in particular, to determine whether 180 degrees acquisition arcs with heads in 'L' configuration could be used for accurate quantification. Following the development of the most appropriate SPET protocol, a small patient pilot study was undertaken. RESULTS: Studies designed to evaluate statistical uncertainty (noise), contrast restitution and spatial resolution of the data sets, using different acquisition and reconstruction parameters, showed that 180 degrees SPET using a 64 x 64 matrix, 6 degrees angular sampling and iterative reconstruction was optimal. Finer linear and/or angular sampling afforded negligible improvement in resolution, but markedly increased the statistical uncertainty. Comparison of 360 degrees and 180 degrees acquisitions, utilizing conventional filtered backprojection and iterative reconstruction algorithms, demonstrated that the statistical uncertainty was reduced to a greater extent for 180 degrees data collection. For 360 degrees (64 x 64) data acquisition, statistical uncertainty decreased from 15% to 11% using the iterative algorithm, whilst the 180 degrees (64 x 64) data showed a reduction from 20% to 7%, and approached values obtained by planar imaging. The efflux measurements obtained in the patient pilot study were consistent with the observed chemotherapy response. CONCLUSION: Our study shows that 180 degrees acquisition arcs are a practical option for accurate quantitative SPET kinetic imaging for potential studies of chemotherapy response in patients with lung cancer.

Algorithms↗
PubMed1993

Crystallization and preliminary crystallographic analysis of Streptomyces griseus aminopeptidase.

Streptomyces griseus excretes a small molecular mass (30 kDa) aminopeptidase that could be used for various biotechnological applications. This enzyme was isolated from an extracellular protease mixture of Streptomyces griseus (Pronase E. Sigma) and single crystals were obtained by the vapor diffusion method using polyethylene glycol 4000 as the precipitant. The crystals belong to the tetragonal space group P4(1)2(1)2 (P4(3)2(1)2), with cell dimensions of a = b = 61.82(3) A and c = 145.88(4) A. These crystals are mechanically strong, they are stable in the X-ray beam and they diffract to better than 1.8 A resolution. The cell dimensions and the cell symmetry are consistent with one molecule in the asymmetric unit and the crystals are suitable for a detailed high-resolution crystallographic analysis. A complete native data set to 1.9 A resolution has been collected on a Rigaku R-AXIS-IIC Imaging Plate Detector system and a heavy-atom derivative search is in progress.

Aminopeptidases↗
PubMed2006

Performance of list mode data acquisition with ECAT EXACT HR and ECAT EXACT HR+ positron emission scanners.

Recently, list mode (event-by-event) data acquisition with positron emission tomography (PET) has been widely noticed because list mode acquisition is superior to conventional frame mode data acquisition in terms of (1) higher efficiency of data storage, (2) higher temporal resolution, and (3) higher flexibility of data manipulation. The aim of this study is to investigate the performance of list mode data acquisition with ECAT EXACT HR and HR+ PET scanners (CTI PET Systems) and its feasibility in clinical applications. A cylindrical phantom (16 cm in diameter and length) filled with a 11C solution for the HR and a 15O solution for the HR+ was scanned several times by varying the radioactivity concentration with the list mode and frame mode acquisitions. The scans were also carried out with a septa (2D mode) and without a septa (3D mode) in order to evaluate the effect of the interplane septa on the quality of the list mode data. The acquired list mode data were sorted into a sinogram and reconstructed using a filtered back-projection algorithm. The count rate performance of the list mode data was comparable to that of the frame mode data. However, the list mode acquisition could not be performed when the radioactivity concentration in the field-of-view was high (exceeding 24 kBq/ml for the 3D mode) due to a lack of sufficient transfer speed for sending data from the memory to hard disk. In order to estimate the pixel noise in a reconstructed image, ten replicated data sets were generated from one list mode data. The reconstructed images with the 3D mode had a signal-to-noise ratio that was more than 60% better than that of the image with the 2D mode. The file size of the generated list mode data was also evaluated. In the case of ECAT EXACT HR+ with the 3D list mode, the list mode data with a generated file size of 2.31 Mbytes/ s were generated for 37 MBq injections. Our results suggest that careful attention must be paid to the protocol of the list mode data acquisition in order to obtain the highest performance of the PET scanner.

Algorithms↗
PubMed1996

RNA hydration: a detailed look.

The crystal structure of the RNA duplex [r(CCCCGGGG)]2 has been refined to 1.46 A resolution with room temperature synchrotron diffraction data. This represents the highest resolution reported to date for an all-RNA oligonucleotide and is well beyond the best resolution ever achieved with an A-form DNA duplex. The analysis of the ordered hydration around the octamer duplex reveals conserved regular arrangements of water molecules in both grooves. In the major groove, all located first shell water molecules can be fitted into a pattern that is repeated through all eight base pairs, involves half the phosphate oxygens, and joins the two strands. In the minor groove, roughly across its narrowest dimension, tandem water molecules link the 2'-hydroxyl groups of adjacent nucleotides in base-pair steps in a similarly regular fashion. The structure provides evidence for an important role of the 2'-hydroxyl groups in the thermodynamic stabilization of RNA, beyond their known functions of locking the sugar pucker and mediating 3' --> 5' intrastrand O2'...O4' hydrogen bonds. The ribose 2'-hydroxyls lay the foundation for the enthalpic stability of the RNA relative to the DNA duplex, both as a scaffold for the water network in the minor groove and through their extensive individual hydration.

Crystallography, X-Ray↗
PubMed1995

Refined 3.2 A structure of glycosomal holo glyceraldehyde phosphate dehydrogenase from Trypanosoma brucei brucei.

The three-dimensional crystal structure of the enzyme glyceraldehyde phosphate dehydrogenase from the kinetoplastid Trypanosoma brucei brucei has been determined at 3.2 A resolution from a 37% complete data set collected using the Laue method. The crystals used in the structure determination contain one and a half tetrameric enzyme molecules in the asymmetric unit, i.e. six identical subunits. Initial phasing was carried out by the method of molecular replacement using the refined coordinates of holo glyceraldehyde phosphate dehydrogenase from Bacillus stearothermophilus as a search model. The initial electron-density distribution, obtained from the molecular-replacement solution, was greatly improved by a procedure consisting of 36 cycles of iterative non-crystallographic density averaging. During the averaging procedure, the missing reflections (63% of the data) were gradually introduced as map-inversion structure factors. At completion of the procedure, the R-factor between averaged map-inversion amplitudes and observed structure-factor amplitudes was 19.0% for all data between 7.0 and 3.2 A resolution, and that between the map-inversion amplitudes and later recorded structure-factor amplitudes was 41.9%. After model building into the resulting averaged electron-density map, refinement by molecular-dynamics procedures with X-PLOR provided the current model, which has an R-factor of 17.6% for 34 835 reflections between 7.0 and 3.2 A resolution. The refined model, comprising 2735 protein atoms plus one NAD(+) molecule and two sulfate ions per subunit, has r.m.s. deviations from ideality of 0.02 A for bond lengths and 3.6 degrees for bond angles. All subunits, located either within the tetrameric molecule or within the half tetramer present in the asymmetric unit, are related to each other by almost exact twofold symmetry. The overall structure of the glycosomal glyceraldehyde phosphate dehydrogenase subunit and its quaternary arrangement in the tetrameric molecule are similar to that of the enzyme of lobster and Bacillus stearothermophilus (with r.m.s. differences between equivalent Calpha positions of 0.71 and 0.64 A, respectively). The main differences between the structures is the presence of three insertions, plus the substitution of a beta-strand by a short alpha-helix, both occurring at the surface of the glycosomal enzyme subunit.

Journal Article↗
PubMed2001

From data to knowledge--the Visible Human Project continues.

The U. S. National Library of Medicine (NLM) has long been a world leader in the archiving and distribution of the print-based images of biology and medicine. NLM has also been a pioneer in the use of computer systems to encode and distribute textual knowledge of the life sciences. NLM's Long Range Planning effort of 1985-86 foresaw a coming era where NLM's Bibliographic and factual database services would be complemented by libraries of digital images, distributed over high speed computer networks. The NLM Planning Panel on Electronic Imaging recommended that NLM should undertake the building a digital image library consisting of computerized tomography (CT) and magnetic resonance (MR) images, and cryosection images of a representative, carefully selected and prepared male and female cadaver--the "Visible Human Project ." The male and female Visible Human data sets are now being made available through a license agreement with the NLM. The data sets are supporting a wide range of educational, diagnostic, treatment planning, and commercial uses. The NLM, in partnership with other U.S. government research agencies has begun a three prong effort within the Visible Human Project to address: the creation of a new online, interactive, digital head-and-neck atlas; the development of a tool kit of computational programs capable of automatically performing many of the basic data handling functions required for using Visible Human data in applications; and the improved resolution of future Visible Human data sets through the reduction of the anatomical artifacts introduced by the methods used to stabilize and section the anatomical materials and the development of staining and wide-spectrum methods for increasing tissue contrast.

Anatomy, Artistic↗
PubMed2000

Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 A resolution.

The phospholipase A(2 )from Daboia russelli pulchella (DPLA(2)) is the only known member of subclass II of group IIA. The three-dimensional structure of this presynaptic neurotoxic DPLA(2) enzyme has been determined at 2.4 A resolution. The structure was determined by the molecular replacement method using the model Crotalus atrox, and refined using X-PLOR to a final R-factor of 18.8 % for all data in the resolution range 20.0 A-2.4 A. The final refined model comprises 1888 atoms from two crystallographically independent protein molecules and 160 water oxygen atoms. The overall folding of DPLA(2), with three long helices and two short antiparallel beta-strands is grossly similar to those observed for other PLA(2)s. In the present structure, the calcium binding site is empty but the conformation of the calcium binding loop is similar to those observed in the calcium bound states. Two spatially adjacent regions of residues 55-61 (a typical beta-turn I) and 83-94 (a well defined loop) are remarkably different in conformation, electrostatic characteristics and inter-segmental interactions from those found in non-neurotoxic PLA(2)s. Yet another striking structural feature in DPLA(2 )pertains to the stretch of residues 53-77, which has a series of positively charged residues protruding outwardly. The above segment is presumed to be involved in the anticoagulant activity. A unique hydrophobic patch including residues Leu17, Ala18, Ile19, Pro20, Phe106 and Leu110 is found on the surface together with an equally emphatic region of -OH groups containing residues such as Ser21, Tyr22, Ser23, Ser24, Tyr25 and Tyr28. The interactions between two molecules of DPLA(2) in the asymmetric unit are remarkably different from those observed in the standard dimers and trimers of PLA(2)s, leaving the enzyme's active site fully exposed for enzyme-substrate reactions, it makes this structure one of the most favourable examples for structure-based drug design through soaking experiments.

Amino Acid Sequence↗
PubMed1991

Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3'-guanylic acid at 1.8 A resolution.

The crystal structures of ribonuclease from Streptomyces aureofaciens (RNase Sa) and its complex with 3'-guanylic acid (guanosine 3'-monophosphate, 3'-GMP) have been determined by the method of isomorphous replacement. The atomic parameters have been refined by restrained least-squares minimization using data in the resolution range 10.0-1.8 A. All protein atoms and more than 230 water atoms in the two crystal structures have been refined to crystallographic R factors of 0.172 and 0.175 respectively. The estimated r.m.s. error in the atomic positions ranges from 0.2 A for well-defined atoms to about 0.5 A for more poorly defined atoms. There are two enzyme molecules in the asymmetric unit, built independently, and referred to as molecules A and B. The value of the average B factor for protein atoms in both structures is about 19 A2 and for water molecules about 35 A2. Electron density for the substrate analogue 3'-GMP was found only at the active site of molecule A. The density was very clear and the positions of all 3'-GMP atoms were refined with precision comparable to that of the protein.

Amino Acid Sequence↗