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PubMed1993

X-ray scattering using synchrotron radiation shows nitrite reductase from Achromobacter xylosoxidans to be a trimer in solution.

We demonstrate here the applicability of X-ray scattering for studying molecular conformation of multimeric proteins in solution by using synchrotron radiation to extend the range of data collection to include medium angles (ca. 3-4 degrees). We have been able to define the solution structure of the dissimilatory nitrite reductase of Achromobacter xylosoxidans (AxNiR), an enzyme for which there are conflicting reports as to the nature of its multimeric structure. Quantitative interpretation of the X-ray scattering profile, based on a modeling study using the high-resolution crystal structure data for the nitrite reductase from the related organism Achromobacter cycloclastes (AcNiR), provides a detailed model for the trimeric structure of AxNiR in solution. Sedimentation equilibrium centrifugation gave an M(r) of 103,000, consistent with such a trimeric structure.

Alcaligenes↗
PubMed1997

Optimizing the malaria data recording system through a study of case detection and treatment in Sri Lanka.

The potential of using malaria incidence data routinely collected from endemic regions for disease control and research has increased with the availability of advanced computer-based technologies, but will depend on the quality of the data itself. We report here an investigation into the relevance of malaria statistics provided by the routine data collection system in Moneragala, a rural malaria-endemic region in Sri Lanka. All patients (n = 321) treated for malaria in 2 clusters of health care centres (HCCs) of both the private and the public sector in the administrative regions of Moneragala and Buttala Divisional Secretariat (D.S.). Divisions were studied in December 1995/ January 1996. The catchment area of these HCCs included a population resident in 53 Grama Niladhari (GN) areas, the smallest administrative units of the country. Almost equal numbers of malaria patients were detected and treated at Government and private health care institutions, and in 70% of them treatment was based on a diagnosis confirmed by microscopy. The routine data recording system, however, included only statistics from the Government sector, and only of patients whose diagnosis was microscopically confirmed. In compiling data, the origin of a case of malaria is attributed to the D.S. Division in which the institution (at which the patient was treated) was located, rather than the area in which the patient was resident, which was inaccurate because 90% of malaria patients sought health care at institutions located closest to their residence, thus crossing administrative boundaries. It also led to a loss of resolution of spatial data because patients' addresses recorded at the Government HCCs to the village-level are replaced in the statistics by the D.S. Division, which is a coarse spatial unit. Modifications to the system for malaria case recording needed to correct these anomalies are defined here. If implemented, these could result in major improvements to the quality of data, a valuable resource for the future of malaria control. The paper reiterates the call for the use of a standard spatial unit within a country to facilitate exchange of data among health and other sectors for the control of tropical diseases.

Data Collection↗
PubMed2004

Digital video for the documentation of colonoscopy.

BACKGROUND: The aim of this study was to determine whether digital video is suitable for the documentation of colonoscopy. Standards are required for the visual documentation of endoscopic findings and to optimize image quality while limiting file size and bandwidth requirements. METHODS: Video recordings of colonoscopy procedures were encoded using a common video compression method at selected data rates and resolutions. Twelve reviewers were selected, each of whom was assigned 8 video review sessions, each consisting of 5 colonoscopy procedures. The reviewers rated the following: level of confidence that the cecum was demonstrated, subjective quality of the video compared with actual videocolonoscopy, and whether the video was of "diagnostic quality." RESULTS: Reviewers were confident that the cecum was demonstrated in all cases except at the lowest data rate. The 1.0 Mbps standard interchange format video provided an optimal balance between quality and file size. CONCLUSIONS: For the documentation of colonoscopy, 1.0 Mbps is acceptable and results in a file size of 7.5 Mbytes/min, which is manageable for most modern hospital and telehealth networks.

Colonoscopy↗
PubMed1990

A ray tracing approach to restoration and resolution enhancement in experimental ultrasound tomography.

Recursive ray tracing is applied for experimental time-of-flight projection data to achieve a resolution enhancement over the initial straight-ray reconstructed velocity image. Curved-ray reconstruction is performed using the dedicated simultaneous algebraic reconstruction technique (SART). Tomographic reconstructions from experimental data are compared to images obtained from simulated projection data for a refractive field mimicking the actual tissue-equivalent phantom. The simulation study adequately explains the macrostructural geometric distortion and loss of resolution in the straight-ray image due to refraction effects that are unaccounted for.

Computer Simulation↗
PubMed1997

Crystals of cytochrome c-553 from Bacillus pasteurii show diffraction to 0.97 A resolution.

We report here the purification and characterization of a c-type cytochrome present in the soluble fraction of the gram-positive, alkaliphilic, and highly ureolytic soil bacterium Bacillus pasteurii. The cytochrome is acidic (pI = 3.3), has a molecular mass of 9.5 kDa, and appears to dimerize in 150 mM ionic strength solution. The electronic spectrum is typical of a low-spin hexa-coordinated heme iron. Crystals of the protein in the oxidized state were grown by vapor diffusion at pH 5, by using 3.2 M ammonium sulfate as precipitant. Diffraction data at ultrahigh resolution (0.97 A) and completeness (99.9%) have been collected under cryogenic conditions, by using synchrotron radiation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with cell constants a = 37.14, b = 39.42, c = 44.02 A, and one protein monomer per asymmetric unit. Attempts to solve the crystal structure by ab initio methods are in progress.

Bacillus↗
PubMed1993

[Clinical evaluation of two- and three-dimensional imaging of helical scanning CT in the upper abdomen].

To evaluate the usefulness of helical scanning CT of the upper abdomen, 30 patients with hepatic, adrenal, pancreatic and renal disease were examined using a Toshiba CT system, the Xforce. Helical scanning CT data were acquired using up to 20 continuous 1.5-second rotations, with a 1.5-3 ml bolus injection of contrast medium, and during a single breath-hold. Helical scanning provided both better data continuity and resolution than conventional scanning. The axial images with a slice thickness of 5 mm were not inferior in quality to equivalent images acquired by conventional CT, and multiplanar reconstruction images were superior. Targeted structures could be easily obtained because helical scanning CT permits image reconstruction in any direction. Using a CEMAX-VIPstation, we generated three-dimensional display images of high-density structures from the postcontrast data acquired with helical scanning. On these images, it was easy to observe the high-density tumors three-dimensionally and to determine the position of the tumors relative to the high-density surrounding organs. In conclusion, helical scanning CT was considered to be useful in clinical diagnosis involving the upper abdomen.

Adult↗
PubMed2005

Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution.

This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A(2) (PLA(2)) and also to a PLA(2) with Asp 49. The fatty acid identified as n-tridecanoic acid is observed at the substrate recognition site of PLA(2) hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA(2) was determined using the cDNA method. Three-dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 A. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n-tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium-binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n-tridecanoic acid was clearly fitted. The MALDI-TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA(2) by 212 Da over the native PLA(2). A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA(2) in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium-binding loop.

Alkanes↗
PubMed2006

The use of soil survey data to determine the magnitude and extent of historic metal deposition related to atmospheric smelter emissions across Humberside, UK.

When a smelter has ceased operation, and in the absence of historical emission data, high-resolution geochemical surveys of the soil can reveal historical loads to the surrounding land. We use measurements of lead and tin in the soil at two depths to estimate the total quantities of these metals deposited on 286 km(2) of land around the former Capper Pass smelter (north-east England). We subtracted median background concentrations for three parent material types outside the region of deposition from the data within it. We then constructed a statistical model of metal deposition based on the adjusted data. The data were from irregularly spaced sites and were strongly skewed with a spatial trend. We mapped the concentrations of the metals by lognormal universal kriging with the parameters for the trend and residuals modelled simultaneously by residual maximum likelihood (REML). The maps suggest that metal was deposited up to 24 km to the north-east of the smelter by the prevailing wind. We estimated total excess metal in the soil over the area of deposition to be 2500 t of lead and 830 t of tin.

Air Pollutants↗
PubMed2003

Comparison of functional activation foci in children and adults using a common stereotactic space.

The development of methods allowing direct comparisons between child and adult neuroimaging data is an important prerequisite for studying the neural bases of cognitive development. Several issues arise when attempting to make such direct comparisons, including the comparability of anatomical localization of functional responses and the magnitude and time course of the hemodynamic responses themselves. Previous results suggest that, after transformation into a common stereotactic space, anatomical differences between children (ages 7 and 8) and adults are small relative to the resolution of fMRI data. Here, we investigate whether time courses (BOLD responses) and locations of functional activation foci show similarities as well. Event-related fMRI was performed on 16 children (ages 7 and 8) and 16 adults, who pressed buttons in response to a visual stimulus. After transforming images into Talairach space, the coordinates of four consistent activations in each hemisphere were determined for each subject: two foci in the sensorimotor cortex, one focus in the visual cortex, and one focus in the supplementary motor area (eight activations in total). In seven foci, time courses were similar between children and adults, and peak amplitudes of time courses were comparable in all eight foci. There were negligible between-group differences in location of all foci. Variability of activation location was statistically similar in the two groups. In voxelwise group comparison images, minimal differences were found between children and adults in visual and motor cortex regions. The small differences in time courses and locations of activation foci between child and adult brains validate the feasibility of direct statistical comparison of these groups within a common space.

Adult↗
PubMed1991

Beta-lactamase of Bacillus licheniformis 749/C. Refinement at 2 A resolution and analysis of hydration.

The crystallographic and molecular structure of the class A beta-lactamase (penicillinase) of Bacillus licheniformis 749/C has been refined with X-ray diffraction data to 2 A resolution. For the 27,330 data with F greater than or equal to 3 sigma(F), the R factor is 0.15; for all 30,090 data, R is 0.16. The estimated co-ordinate error is 0.15 A. In the final model, the deviation of covalent bonds and angles from ideality is 0.012 A and 2.2 degrees, respectively. The model includes two molecules of 29,500 daltons each in the asymmetric unit of space group P2(1), 484 water molecules and two tetrahedral buffer anions. Overlay of the two protein molecules results in a root-mean-square difference of 0.17 A and 0.41 A for alpha-carbon atoms and for all atoms, respectively. Twenty-six water molecules fall within 0.25 A of matching water molecules associated with the second protein molecule. The reactive Ser70 is on a turn of 3(10) helix at the N terminus of a longer alpha-helix (72-83). The penicillin-binding site near this helix contains at least seven water molecules. Upon penicillin entry, a water molecule in the oxyanion hole, hydrogen-bonded between the N terminus of helix (80-83) and beta-strand (230-238), would be displaced by the oxygen atom of the beta-lactam carbonyl group. An unexpelled molecule of water is proposed to be the catalytic water required for penicillin hydrolysis. The water is hydrogen-bonded to Glu166, a conserved residue in all beta-lactamases, and it lies 3 A from the alpha-face of a previously modeled penicillin. The position of the water-Glu166 pair is stabilized in the active site by a cis peptide bond at Pro167.

Amino Acid Sequence↗
PubMed1990

Towards the understanding of the function of Rb sphaeroides Y wild type reaction center: gene cloning, protein and detergent structures in the three-dimensional crystals.

We report various experiments aimed at the resolution of the 3-dimensional structure of the photosynthetic reaction center from wild type Y Rhodobacter sphaeroides. The genes encoding the L and M polypeptides have been cloned and sequenced. They bear 2 mutations each when compared to those already sequenced in another Rb sphaeroides strain (2.4.1). In the L gene, these codon changes are silent. In the M gene, one is silent and the other one leads to a Leu-Met substitution at position 140. At the present stage of the refinement of the X-ray data (0.3 nm resolution) the structure of the Y reaction center is shown to be highly similar to that of the Rhodopseudomonas viridis reaction center. The binding of spheroidene on the M side of the Y reaction center is shown to be determined by hydrophobic interactions with neighboring amino acids and by steric factors. Preliminary results concerning the localization of the detergent (beta-octylglucoside) in the unit cell are presented. This method combines low angle neutron scattering at different contrasts in H2O/D2O with X-ray crystallographic data.

Carotenoids↗
PubMed2003

A fractal analysis of human cranial sutures.

OBJECTIVES: Many biological structures are products of repeated iteration functions. As such, they demonstrate characteristic, scale-invariant features. Fractal analysis of these features elucidates the mechanism of their formation. The objectives of this project were to determine whether human cranial sutures demonstrate self-similarity and measure their exponents of similarity (fractal dimensions). DESIGN: One hundred three documented human skulls from the Terry Collection of the Smithsonian Institution were used. Their sagittal sutures were digitized and the data converted to bitmap images for analysis using box-counting method of fractal software. RESULTS: The log-log plots of the number of boxes containing the sutural pattern, N(r), and the size of the boxes, r, were all linear, indicating that human sagittal sutures possess scale-invariant features and thus are fractals. The linear portion of these log-log plots has limits because of the finite resolution used for data acquisition. The mean box dimension, D(b), was 1.29289 +/- 0.078457 with a 95% confidence interval of 1.27634 to 1.30944. CONCLUSIONS: Human sagittal sutures are self-similar and have a fractal dimension of 1.29 by the box-counting method. The significance of these findings includes: sutural morphogenesis can be described as a repeated iteration function, and mathematical models can be constructed to produce self-similar curves with such D(b). This elucidates the mechanism of actual pattern formation. Whatever the mechanisms at the cellular and molecular levels, human sagittal suture follows the equation log N(r) = 1.29 log 1/r, where N(r) is the number of square boxes with sides r that are needed to contain the sutural pattern and r equals the length of the sides of the boxes.

Adolescent↗
PubMed1992

The electrocardiographic inverse problem.

Using the boundary element method in conjunction with Tikhonov zero-order regularization, we have computed epicardial potentials from body surface potential data in a realistic geometry heart-torso system. The inverse-reconstructed epicardial potentials were compared to the actual measured potentials throughout a normal cardiac cycle. Potential features (maxima, minima) were recovered with an accuracy better than 1 cm in their location. In this chapter, we use these data to illustrate and discuss computational issues related to the inverse-reconstruction procedure. These include the boundary element method, the choice of a regularization scheme to stabilize the inversion, and the effects of incorporating a priori information on the accuracy of the solution. In particular, emphasis is on the use of temporal information in the regularization procedure. The sensitivity of the solution to geometrical errors and to the spatial and temporal resolution of the data is discussed.

Animals↗
PubMed2001

Determination of volatile components in peptic powder by gas chromatography-mass spectrometry and chemometric resolution.

Gas chromatography-mass spectrometry (GC-MS) coupled with chemometric resolution upon two-dimensional data was proposed as a method for the analysis of volatile components in a traditional Chinese medicinal preparation peptic powder which contains Rhizoma Atractylodis, Pericarpium Citri Reticulatae, Cortex Magnoliae Officinalis and Radix Glycyrrhizae. Ninety-three components were separated and 65 of them were qualitatively and quantitatively analyzed which represented about 90.28% of the total content. With the help of chemometric resolution, the data were resolved into a pure chromatogram and a mass spectrum of each chemical component. The accuracy of qualitative and quantitative results was greatly improved by using the two-dimensional comprehensive information of chromatograms and mass spectra. The example showed that chemometric resolution could greatly enhance separation ability. This makes it possible to analyze complicated practical systems like traditional Chinese medicinal preparations with the help of coupled instruments and chemometric resolution methods.

Drugs, Chinese Herbal↗
PubMed1994

Refined structure of trichosanthin at 1.73 A resolution.

An X-ray reflection data set of the orthorhombic crystal of Trichosanthin (TCS) at 1.73 A resolution had been collected using the area detector. We determined TCS crystal structure by the molecular replacement method using the data of the known alpha-momocharin model and TCS intensities, and then TCS structure refinement at 1.73 A resolution was performed with the restrained least-squares refinement. A final R-factor of 0.186 was obtained with a model obeying standard geometry within 0.013 A in bond lengths and 2.48 degrees in bond angles. The final model contains 133 solvent molecules in the asymmetric unit. This paper gives a detailed description of TCS molecule structure, temperature factors, hydrogen bonds, bound water, the distribution of conserved residues and the interactions between the TCS molecules. The hydrogen bond between the hydroxyl group of conserved residue 14Tyr and O157 plays an important role in maintaining the active site conformation. Conserved residue 160Glu and its conformation at the active site play a key role in the catalytic activity.

Crystallography, X-Ray↗
PubMed2000

Are changes in myocardial integrated backscatter restricted to the ischemic zone in acute induced ischemia? An in vivo animal study.

Integrated backscatter (IB) from a myocardial region, calculated from radiofrequency echocardiographic data, has been proposed as a useful parameter for investigating changes in myocardial tissue induced by ischemia. In 10 closed-chest dogs, 5 minutes of myocardial ischemia was induced by either a proximal occlusion of the circumflex coronary artery (CX) (5 dogs), resulting in extensive ischemia in the posterior wall, or by occluding the distal CX vessel (5 dogs) to produce a small localized ischemic zone in the posterior wall. High-resolution digital radiofrequency data from the whole left ventricular myocardium, in the imaging plane during one complete heart cycle, were acquired with a whole-image real-time acquisition approach. Regions in the septum and posterior wall (both ischemic tissue and, in the case of distal occlusions, tissue surrounding the ischemic zone) were chosen for analysis, and IB and cyclic variation (CV) of IB were calculated. Post occlusion, an increase in mean IB values was found in the ischemic segment. However, an increase in CV was also observed in the peri-ischemic zone for the distal CX occlusion and in the septum after proximal CX occlusion. These findings show that changes in CV are not restricted to the ischemic zone but may also occur in distal myocardium. This may be explained by changes in the regional contractile state and loading conditions of the "normal" myocardium, which are altered in response to the distal ischemia.

Animals↗
PubMed2001

Whiplash syndrome: kinematic factors influencing pain patterns.

STUDY DESIGN: The overall, local, and segmental kinematic responses of intact human cadaver head-neck complexes undergoing an inertia-type rear-end impact were quantified. High-speed, high-resolution digital video data of individual facet joint motions during the event were statistically evaluated. OBJECTIVES: To deduce the potential for various vertebral column components to be exposed to adverse strains that could result in their participation as pain generators, and to evaluate the abnormal motions that occur during this traumatic event. SUMMARY OF BACKGROUND DATA: The vertebral column is known to incur a nonphysiologic curvature during the application of an inertial-type rear-end impact. No previous studies, however, have quantified the local component motions (facet joint compression and sliding) that occur as a result of rear-impact loading. METHODS: Intact human cadaver head-neck complexes underwent inertia-type rear-end impact with predominant moments in the sagittal plane. High-resolution digital video was used to track the motions of individual facet joints during the event. Localized angular motion changes at each vertebral segment were analyzed to quantify the abnormal curvature changes. Facet joint motions were analyzed statistically to obtain differences between anterior and posterior strains. RESULTS: The spine initially assumed an S-curve, with the upper spinal levels in flexion and the lower spinal levels in extension. The upper C-spine flexion occurred early in the event (approximately 60 ms) during the time the head maintained its static inertia. The lower cervical spine facet joints demonstrated statistically greater compressive motions in the dorsal aspect than in the ventral aspect, whereas the sliding anteroposterior motions were the same. CONCLUSIONS: The nonphysiologic kinematic responses during a whiplash impact may induce stresses in certain upper cervical neural structures or lower facet joints, resulting in possible compromise sufficient to elicit either neuropathic or nociceptive pain. These dynamic alterations of the upper level (occiput to C2) could impart potentially adverse forces to related neural structures, with subsequent development of a neuropathic pain process. The pinching of the lower facet joints may lead to potential for local tissue injury and nociceptive pain.

Aged↗
PubMed1999

Pneumonia in febrile neutropenic patients and in bone marrow and blood stem-cell transplant recipients: use of high-resolution computed tomography.

PURPOSE: To obtain statistical data on the use of high-resolution computed tomography (HRCT) for early detection of pneumonia in febrile neutropenic patients with unknown focus of infection. MATERIALS AND METHODS: One hundred eighty-eight HRCT studies were performed prospectively in 112 neutropenic patients with fever of unknown origin persisting for more than 48 hours despite empiric antibiotic treatment. Fifty-four of these studies were performed in transplant recipients. All patients had normal chest roentgenograms. If pneumonia was detected by HRCT, guided bronchoalveolar lavage was recommended. Evidence of pneumonia on chest roentgenograms during follow-up and micro-organisms detected during follow-up were regarded as documentation of pneumonia. RESULTS: Of the 188 HRCT studies, 112 (60%) showed pneumonia and 76 were normal. Documentation of pneumonia was possible in 61 cases by chest roentgenography or micro-organism detection (54%) (P < 10(-6)). Sensitivity of HRCT was 87% (88% in transplant recipients), specificity was 57% (67%), and the negative predictive value was 88% (97%). A time gain of 5 days was achieved by the additional use of HRCT compared to an exclusive use of chest roentgenography. CONCLUSION: The high frequency of inflammatory pulmonary disease after a suspicious HRCT scan (> 50%) proves that pneumonia is not excluded by a normal chest roentgenogram. Given the significantly longer duration of febrile episodes in transplant recipients, HRCT findings are particularly relevant in this subgroup. Patients with normal HRCT scans, particularly transplant recipients, have a low risk of pneumonia during follow-up. All neutropenic patients with fever of unknown origin and normal chest roentgenograms should undergo HRCT.

Adult↗