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At least 1,765 records · Page 98Linked to original sources
PubMed2001

Mixed echo train acquisition displacement encoding with stimulated echoes: an optimized DENSE method for in vivo functional imaging of the human heart.

Mixed echo train acquisition displacement encoding with stimulated echoes (meta-DENSE) is a phase-based displacement mapping technique suitable for imaging myocardial function. This method has been optimized for use with patients who have a history of myocardial infarction. The total scan time is 12-14 heartbeats for an in-plane resolution of 2.8 x 2.8 mm2. Myocardial strain is mapped at this resolution with an accuracy of 2% strain in vivo. Compared to standard stimulated echo (STE) methods, both data acquisition speed and resolution are improved with inversion-recovery FID suppression and the meta-DENSE readout scheme. Data processing requires minimal user intervention and provides a rapid quantitative feedback on the MRI scanner for evaluating cardiac function. Published 2001 Wiley-Liss, Inc.

Artifacts↗
PubMed1999

Dynamic three-dimensional freehand echocardiography using raw digital ultrasound data.

In this paper, we present a new method for simple acquisition of dynamic three-dimensional (3-D) ultrasound data. We used a magnetic position sensor device attached to the ultrasound probe for spatial location of the probe, which was slowly tilted in the transthoracic scanning position. The 3-D data were recorded in 10-20 s, and the analysis was performed on an external PC within 2 min after transferring the raw digital ultrasound data directly from the scanner. The spatial and temporal resolutions of the reconstruction were evaluated, and were superior to video-based 3-D systems. Examples of volume reconstructions with better than 7 ms temporal resolution are given. The raw data with Doppler measurements were used to reconstruct both blood and tissue velocity volumes. The velocity estimates were available for optimal visualization and for quantitative analysis. The freehand data reconstruction accuracy was tested by volume estimation of balloon phantoms, giving high correlation with true volumes. Results show in vivo 3-D reconstruction and visualization of mitral and aortic valve morphology and blood flow, and myocardial tissue velocity. We conclude that it was possible to construct multimodality 3-D data in a limited region of the human heart within one respiration cycle, with reconstruction errors smaller than the resolution of the original ultrasound beam, and with a temporal resolution of up to 150 frames per second.

Adult↗
PubMed2003

New three-dimensional echocardiographic system using digital radiofrequency data--visualization and quantitative analysis of aortic valve dynamics with high resolution: methods, feasibility, and initial clinical experience.

BACKGROUND: Common 3D systems have only limited spatial and temporal resolution (frame rate of 25 Hz). Thin structures such as cardiac valves are not imaged exactly; rapid movement patterns cannot be precisely recorded. The objective of the present project was to achieve radiofrequency (RF) data transmission to the 3D workstation to improve image resolution. METHODS AND RESULTS: A commercially available echocardiographic system (5-MHz transesophageal echocardiography probe) with an integrated raw data interface enables transmission of RF data (up to 40 megabytes per second). A 3D data set may contain up to 3 gigabytes, so that all of the high-resolution ultrasound information of the 2D image is available. Frame rates of up to 168 Hz result in temporal resolution 6 times that of standard 3D systems. The applicability of the system and the image quality were tested in 10 patients. The structure of the aortic valve and the dynamic changes were depicted by volume rendering. The changes in the orifice areas were measured in frame-by-frame planimetry. The mean number of frames recorded per cardiac cycle was 122+/-16. The improved structural resolution enabled a detailed imaging of the morphology of the aortic cusps. The rapid systolic movement patterns were recorded with up to 51 frames. The high number of frames enabled creation of precise area-time diagrams. Thus, the individual phases of aortic valve movement (rapid opening, slow valve closing, and rapid valve closing) could be analyzed quantitatively. CONCLUSIONS: A 3D system based on RF data enables high-resolution imaging of cardiac movement patterns. This offers new perspectives for qualitative and quantitative analyses, especially of cardiac valves.

Aortic Valve↗
PubMed2003

Simultaneous variation of multipole parameters and Gram-Charlier coefficients in a charge-density study of tetrafluoroterephthalonitrile based on X-ray and neutron data.

Difficulties encountered in modelling the scattering of fluorine in organic compounds have been investigated through refinements of accurate X-ray and neutron diffraction data measured on tetrafluoroterephthalonitrile, TFT, at 122.4 K. Multipole refinements led to a highly contracted octopole on fluorine. The subsequent analysis revealed that fluorine does not possess a valence octopole but exhibits anharmonic thermal motion that can be modelled by the octopole multipole parameters. The scattering contribution from the octopole shows the same cubic dependence in the scattering vector as the Gram-Charlier expansion of the nuclear displacements to third order. The analysis also showed that refinement of third-order Gram-Charlier coefficients on fluorine requires data to at least 0.93 A(-1) resolution in sinthetas/lambda. The X-ray data extending to 1.27 A(-1) were of sufficient resolution to include third-order Gram-Charlier coefficients for N, F and the cyano C atoms in the refinement, whereas the neutron data only enabled refinement of the third-order Gram-Charlier coefficients for nitrogen. The refinements of the neutron and X-ray diffraction data yielded identical atomic displacement parameters for all the atoms. Though inclusion of anharmonic motion for N and F atoms provides the best model, it does not affect the crystal electron density, and all intramolecular bond critical points have identical features. Application of the anharmonic model, however, leads to small differences in the intermolecular interactions, which is illustrated by the electrostatic potential adjacent to the N atom. The characteristics of the C-F bond were elucidated by the topological analysis of the crystal electron density, which also supported the proposed quinonoid structure of the benzene ring.

Journal Article↗
PubMed1997

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.

Algorithms↗
PubMed1993

Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution.

The crystal structure of a complex of ribonuclease from Streptomyces aureofaciens (RNase Sa) with guanosine-2'-monophosphate (2'-GMP) has been refined against synchrotron data recorded from a single crystal using radiation from beamline X31 at EMBL, Hamburg, and an imaging plate scanner. The crystals are in space group P2(1)2(1)2(1) with cell dimensions a = 64.7, b = 78.8 and c = 39.1 A. The structure has two enzyme molecules in the asymmetric unit, complexed with 2'-GMP inhibitor with occupancies of 1 and 2/3 (different to the 3'-GMP complex crystal structure where only one of the two independent RNase Sa molecules binds nucleotide), 492 associated water molecules and one sulfate ion, and was refined using all data between 10.0 and 1.7 A to a final crystallographic R factor of 13.25%. Binding of the base to the enzyme confirms the basis for the guanine specificity but the structural results still do not provide direct evidence of the identity and role of the particular residues involved in the catalytic process. New native RNase Sa data to 1.8 A were recorded to provide a reference set measured under comparable experimental conditions. The crystals are in the same space group and have the same lattice as those of the 2'-GMP complex. The native structure with 423 water molecules was refined in a similar manner to the complex to a final R factor of 13.87%. 1.77 A resolution data were independently measured on a 2'-GMP complex crystal at UCLA using an R-AXIS II image plate scanner mounted on a conventional source. The cell dimensions were essentially the same as above. 2'-GMP was bound more fully to molecule A than to molecule B of the RNase Sa. The structure was refined to an R factor of 14.64% with 388 water molecules. This work follows on from the structure determination of native RNase Sa and its complex with 3'-GMP [Sevcik, Dodson & Dodson (1991). Acta Cryst. B47, 240-253].

Journal Article↗
PubMed2000

P1 Shake-and-Bake: can success be guaranteed?

The multi-trial direct-methods procedure known as Shake-and-Bake has been applied to three small proteins (alpha-1 peptide, vancomycin and lysozyme) that crystallize in space group P1. Phase refinement was accomplished through parameter-shift optimization using both the cosine and exponential forms of the minimal function. By extending error-free data to sufficiently high resolution, 100% convergence of trial structures to solution could be achieved in all three cases by using the exponential minimal function and a shift angle in the range 130-150 degrees. These results suggest optimum parameters for other P1 structures and emphasize the importance of collecting data to the highest possible resolution.

Algorithms↗
PubMed1992

The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution.

The crystal and molecular structure of a triacylglyceride lipase (EC 3.1.1.3) from the fungus Rhizomucor miehei was analyzed using X-ray single crystal diffraction data to 1.9 A resolution. The structure was refined to an R-factor of 0.169 for all available data. The details of the molecular architecture and the crystal structure of the enzyme are described. A single polypeptide chain of 269 residues is folded into a rather unusual singly wound beta-sheet domain with predominantly parallel strands, connected by a variety of hairpins, loops and helical segments. All the loops are right-handed, creating an uncommon situation in which the central sheet is asymmetric in that all the connecting fragments are located on one side of the sheet. A single N-terminal alpha-helix provides the support for the other, distal, side of the sheet. Three disulfide bonds (residues 29-268, 40-43, 235-244) stabilize the molecule. There are four cis peptide bonds, all of which precede proline residues. In all, 230 ordered water molecules have been identified; 12 of them have a distinct internal character. The catalytic center of the enzyme is made up of a constellation of three residues (His257, Asp203 and Ser144) similar in structure and function to the analogous (but not homologous) triad found in both of the known families of serine proteinases. The fourth residue in this system equivalent to Thr/Ser in proteinases), hydrogen bonded to Asp, is Tyr260. The catalytic site is concealed under a short amphipatic helix (residues 85 to 91), which acts as "lid", opening the active site when the enzyme is adsorbed at the oil-water interface. In the native enzyme the "lid" is held in place by hydrophobic interactions.

Amino Acid Sequence↗
PubMed1998

Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Eight protein crystal structures, which have been refined against X-ray diffraction data extending to atomic resolution, 1.2 A or better, were inspected using four different validation tools, PROCHECK, PROVE, SQUID and WHATCHECK. Two general questions were addressed. (1) Do the structures imply changes in "expected" stereochemical properties and are the target values used for restraints in the validation programs and the refinement protocol appropriate? (2) Can errors in models be detected and how reliable are the coordinates after refinement? Preliminary analysis by members of the network led to modifications both to the validation programs and to the refinement protocols. The results of the final analyses are reported here. Apparent discrepancies in cell dimensions were identified. Most stereochemical properties are shown to be more tightly clustered than for lower resolution analyses. In contrast the omega angle has a wider distribution. The validation software is generally available and can be accessed at servers listed at the end of the paper.

Bacterial Proteins↗
PubMed2004

Does the location of a vascular loop in the cerebellopontine angle explain pulsatile and non-pulsatile tinnitus?

The purpose was to investigate patients with unexplained pulsatile and non-pulsatile tinnitus by means of MR imaging of the cerebellopontine angle (CPA) and to correlate the clinical subtype of tinnitus with the location of a blood vessel (in the internal auditory canal or at the cisternal part of the VIIIth cranial nerve). Clinical presentation of tinnitus and perceptive hearing loss were correlated. In 47 patients with unexplained tinnitus, an MR examination of the CPA was performed. Virtual endoscopy reconstructions were obtained using a 3D axial thin-section high-resolution heavily T2-weighted gradient echo constructive interference in steady state (CISS) data-set. High-resolution T2-weighted CISS images showed a significantly higher number of vascular loops in the internal auditory canal in patients with arterial pulsatile tinnitus compared to patients with non-pulsatile tinnitus (P<0.00001). Virtual endoscopy images were used to investigate vascular contacts at the cisternal part of the VIIIth cranial nerve in patients with low pitch and high pitch non-pulsatile tinnitus. A significantly different distribution of the vascular contacts (P=0.0320) was found. Furthermore, a correlation between the clinical presentation of non-pulsatile tinnitus (high pitch and low pitch) and the perceptive hearing loss was found (P=0.0235). High-resolution heavily T2-weighted CISS images and virtual endoscopy of the CPA can be used to evaluate whether a vascular contact is present in the internal auditory canal or at the cisternal part of the VIIIth cranial nerve and whether the location of the vascular contact correlates with the clinical subtype of tinnitus. Our findings suggest that there is a tonotopical structure of the cisternal part of the VIIIth cranial nerve. A correlation between the clinical presentation of tinnitus and hearing loss was found.

Adolescent↗
PubMed2001

A refined structure of human aquaporin-1.

A refined structure of the human water channel aquaporin-1 is presented. The model rests on the high resolution X-ray structure of the homologous bacterial glycerol transporter GlpF, electron crystallographic data at 3.8 A resolution and a multiple sequence alignment of the aquaporin superfamily. The crystallographic R and free R values (36.7% and 37.8%) for the refined structure are significantly lower than for previous models. Improved geometry and enhanced stability in molecular dynamics simulations demonstrate a significant improvement of the aquaporin-1 structure. Comparison with previous aquaporin-1 models shows significant differences, not only in the loop regions, but also in the core of the water channel.

Aquaporin 1↗
PubMed2002

Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution.

The crystal structure of the 19-mer RNA, 5'-GAAUGCCUGCGAGCAUCCC-3' has been determined from X-ray diffraction data to 1.6 A resolution by the multiwavelength anomalous diffraction method from crystals containing a brominated uridine. In the crystal, this RNA forms an 18-mer self-complementary double helix with the 19th nucleotide flipped out of the helix. This helix contains most of the target stem recognized by the bacteriophage Mu Com protein (control of mom), which activates translation of an unusual DNA modification enzyme, Mom. The 19-mer duplex, which contains one A.C mismatch and one A.C/G.U tandem wobble pair, was shown to bind to the Com protein by native gel electrophoresis shift assay. Comparison of the geometries and base stacking properties between Watson-Crick base pairs and the mismatches in the crystal structure suggest that both hydrogen bonding and base stacking are important for stabilizing these mismatched base pairs, and that the unusual geometry adopted by the A.C mismatch may reveal a unique structural motif required for the function of Com.

Bacteriophage mu↗
PubMed1987

Tracer-kinetic models for measuring cerebral blood flow using externally detected radiotracers.

All tracer-kinetic models currently employed with positron-emission tomography (PET) are based on compartmental assumptions. Our first indication that a compartmental model might suffer from severe limitations in certain circumstances when used with PET occurred when we implemented the Kety tissue-autoradiography technique for measuring CBF and observed that the resulting CBF estimates, rather than remaining constant (to within predictable statistical uncertainty) as expected, fell with increasing scan duration T when T greater than 1 min. After ruling out other explanations, we concluded that a one-compartment model does not possess sufficient realism for adequately describing the movement of labeled water in brain. This article recounts our search for more realistic substitute models. We give our derivations and results for the residue-detection impulse responses for unit capillary-tissue systems of our two candidate distributed-parameter models. In a sequence of trials beginning with the simplest, we tested four progressively more detailed candidate models against data from appropriate residue-detection experiments. In these, we generated high-temporal-resolution counting-rate data reflecting the history of radiolabeled-water uptake and washout in the brains of rhesus monkeys. We describe our treatment of the data to yield model-independent empirical values of CBF and of other parameters. By substituting these into our trial-model functions, we were able to make direct comparisons of the model predictions with the experimental dynamic counting-rate histories, confirming that our reservations concerning the one-compartment model were well founded and obliging us to reject two others. We conclude that a two-barrier distributed-parameter model has the potential of serving as a substitute for the Kety model in PET measurements of CBF in patients, especially when scan durations for T greater than 1 min are desired.

Animals↗
PubMed2003

Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase.

Cytosine deaminase is an attractive candidate for anticancer gene therapy through its catalysis of the deamination of the prodrug 5-fluorocytosine to 5-fluorouracil. Recombinant yeast cytosine deaminase has been crystallized with the inhibitor 2-hydroxypyrimidine in 10% 2-propanol, 20% polyethylene glycol 4000, 0.1 M HEPES pH 7.5. The crystals belong to space group P2(1), with unit-cell parameters a = 45.31, b = 53.33, c = 64.29 A, beta = 99.98 degrees and one dimer per asymmetric unit. The crystals diffract X-rays beyond 1.5 A resolution and an initial atomic model has been built based on selenomethionyl multiwavelength anomalous data at 2 A resolution.

Crystallization↗
PubMed2004

Crystallization and preliminary crystallographic analysis of Bacillus subtilis guanine deaminase.

Guanine deaminase, a key enzyme in nucleotide metabolism, catalyzes the hydrolytic deamination of guanine to xanthine. The first guanine deaminase crystal from Bacillus subtilis was grown in the absence or presence of the inhibitor hypoxanthine in 30% polyethylene glycol 4000, 0.2 M ammonium acetate and 0.1 M sodium citrate pH 6.5. The crystals belong to space group C222(1), with unit-cell parameters a = 84.91, b = 90.90, c = 80.19 angstroms, with one dimer per asymmetric unit. The crystals diffract X-rays to beyond 1.2 angstroms resolution and an initial atomic model has been built based on selenomethionyl multiwavelength anomalous data at 2 angstroms resolution. Unexpectedly, this is the first domain-swapped structure in the cytidine deaminase superfamily.

Acetates↗
PubMed2004

Crystallization and preliminary X-ray analysis of the outer membrane pyoverdine receptor FpvA from Pseudomonas aeruginosa.

FpvA, the pyoverdine outer-membrane receptor from Pseudomonas aeruginosa, is involved in iron uptake when bacteria grow under iron limitation. Crystals of the in vivo pyoverdine-loaded FpvA were obtained under several crystallization conditions using different detergents. A native data set was collected at 3.6 A resolution and a three-wavelength MAD data set was collected at 3.6 A resolution using crystals of selenomethionine-substituted protein. The crystals grew under similar conditions and both belong to space group C2, but have different unit-cell parameters.

Bacterial Outer Membrane Proteins↗
PubMed2006

The size of the cochlea and predictions of insertion depth angles for cochlear implant electrodes.

AIMS: To establish normative data on the size of the basal turn of the cochlea using high-resolution computed tomography of the temporal bone in adults and children. To determine whether final insertion depth angle for a perimodiolar cochlear implant electrode varies according to cochlear size. METHODS: Forty-two patients screened for cochlear anomaly using computed tomography were randomly selected from patients with otologic disease. Reconstruction of the full basal turn was performed for both ears using a 1.0-mm layer, minimum intensity projection. The largest distance from the round window to the lateral wall (distance A) and the perpendicular distance (B) were measured. Distances were averaged between ears for each individual. In addition, 15 patients were implanted with the Nucleus 24 Contour Advance electrode array using a linear insertion depth of either 17 mm (n = 9) or 19 mm (n = 6). Postoperative X-rays were analyzed using the method of Xu et al. [Am J Otol 2000;21:49-56] to obtain the insertion depth angles for individual electrodes. RESULTS: Mean distance A was 9.23 mm (SD = 0.53, range 7.9-10.8 mm). Perpendicular distance B was significantly correlated with distance A (r2 = 0.57, p < 0.001). The mean difference in insertion depth angle between the 17 and 19 mm groups was 80 degrees . A statistically significant correlation (r2 = 0.51) was found between distance A and the insertion depth angle for the 17 mm group. CONCLUSIONS: The cochlear size measure distance A was repeatable to within the resolution of the high-resolution computed tomography image data. The basal turn of the normally formed cochlea is variable in size. These variations in size would produce >5.0 mm variation in the length of the lateral wall to the point consistent with an insertion depth angle of 360 degrees . Cochlear size influenced final insertion depth angles obtained for the perimodiolar Nucleus 24 Contour Advance electrode.

Adolescent↗
PubMed1999

Estimation of epicardial activation maps from intravascular recordings.

Multielectrode catheters provide a percutaneous means of recording activation near the epicardium but only for a relatively small number of sites that are restricted to the major coronary vessels. We have applied a statistical signal processing technique to estimate the value of activation time over the entire epicardium (490 sites) from leadsets consisting of 4 to 40 sites aligned with major branches of the coronary veins. We tested this method using data from high-resolution epicardial mapping from six dog hearts and 153 activation sequences. A study including data from both normal and infarcted dog hearts yielded estimates of activation time, with mean correlation coefficients ranging from 0.97 to 0.84 and achieved localization of earliest site of activation to within 3 to 15 mm, depending on training parameters and leadset. These results suggest that with 10 to 15 catheter-mounted electrodes, it may be possible to reconstruct epicardial activation maps from percutaneous recordings.

Algorithms↗