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At least 973 records · Page 54Linked to original sources

PubMed1985

A predicted structure of calmodulin suggests an electrostatic basis for its function.

By using interactive computer graphics, two models for calmodulin have been constructed based on the structures of two functionally and structurally related proteins, intestinal calcium-binding protein and carp parvalbumin. The two models have been compared and contrasted to the parent proteins with respect to proportion of solvent-exposed hydrophobic residues, solvent-accessible surface area, and side-chain packing. Electrostatic potential surfaces generated for the models suggest a probable binding site for basic amphiphilic alpha-helical peptides located between the last E and F helices in the second domain of calmodulin. Both electrostatic and hydrophobic complementarity can contribute to stabilization of a peptide-protein complex in this region.

Animals↗

PubMed1994

Analysis and modelling of the structures of beta-cyclodextrin complexes.

A systematic computer graphics study of all available beta-cyclodextrin crystal structures has been carried out specifically to aid in the modelling and design of beta-cyclodextrin-drug complexes. The analyses show that the basic conformation of the molecule remains constant among natural, mono-substituted and partially permethylated beta-cyclodextrins, with major changes observed only in the case of full permethylation. In all the structures, however, there are no significant perturbations caused by guest molecule inclusion. On the basis of these observations models are proposed for the structures of beta-cyclodextrin-indomethacin complexes, the principal features of which are shown to be consistent with the data obtained in 1H-NMR studies.

Carbohydrate Sequence↗

PubMed1992

6R instrumented spatial linkages for anatomical joint motion measurement--Part 1: Design.

Six-revolute-joint instrumented spatial linkages (6R ISLs) have become often-used devices to measure the complete six-degree-of-freedom motion of anatomical joints. Accuracy of motion measurement depends on ISL design and calibration technique. In this paper, a design process is outlined that uses computer graphics and numerical methods as aids in developing 6R ISLs that (i) physically assemble within the desired range of motion of the joint; (ii) do not collide with either the experimental apparatus or the subject joint; (iii) avoid singular linkage configurations that can cause forces to be applied to the joint; and (iv) measure selected anatomical motions most accurately. It is found that a certain subgroup of 6R linkages are suitable for accurate measurement of specific motions, and can be the basis for new ISL designs. General guidelines are developed that can assist in the generation of unique linkage designs for different anatomical joints. The design process is demonstrated in the creation of an ISL to measure knee motion.

Computer Simulation↗

PubMed2006

Computer assisted image analyses of corpora lutea in relation to peripheral concentrations of progesterone: a comparison between breeds of sheep with different ovulation rates.

Transrectal ovarian ultrasonography is a non-invasive technique that permits the real-time serial visualization of ovarian structures. Previous studies have reported correlations between serum progesterone concentrations and physical characteristics of the corpus luteum (CL) in different species. The aim of the present study was to investigate whether or not there were correlations between ultrasound image attributes of the CL and changing progesterone concentrations over time, in prolific and non-prolific ewes. Ultrasonographic images of CL were taken, once daily, from 12 Western White Face ewes and 7 Finn ewes for the duration of one luteal phase. Blood samples were collected daily prior to each scanning session and assayed to determine mean serum concentrations of progesterone. Analysis of ultrasound images was performed using a series of custom-developed computer algorithms optimized for ultrasonography on a computer graphics workstation. Both total luteal area and mean pixel values were correlated with the pattern of serum concentrations of progesterone from days 3 to 15 after ovulation in Western White Face ewes and from days 3 to 14 in Finn ewes. There was no significant correlation between progesterone concentrations and spot pixel heterogeneity for either Western White Face ewes or Finn ewes. We concluded that pixel heterogeneity is a poor indicator of progesterone secretory ability of the CL when compared to mean pixel values. However, luteal area and mean spot pixel values are better but not strong indicators of the functional status of the CL in cyclic ewes.

Algorithms↗

PubMed1993

Computer modelling in predicting carcinogenicity.

The cytochrome P450-dependent mixed-function oxidases are the most important enzyme system in the oxidation of chemicals to their reactive intermediates which then interact with cellular components to provoke toxicity and carcinogenicity. These enzymes comprise a multifamily of proteins, two families of which, namely CYP1A and CYP2E, activate planar and small molecular weight compounds, respectively. A computer graphic procedure (COMPACT) has been developed which, based on the molecular shape and electronic structure of the chemical, determines whether the chemical will interact with these two particular cytochrome P450 families and thus be metabolized to toxic and carcinogenic intermediates. As the basal levels of these enzyme families are low, the ability of the chemical to induce them selectively, on repeated administration, is an important determinant of its carcinogenic potential. Inductive capability may be determined in short-term experiments (ENACT) utilizing a small number of animals. Thus the combination of COMPACT and ENACT provides a rapid and inexpensive means for the preliminary screening of chemicals, before the long term and expensive rodent lifetime bioassays are undertaken.

Animals↗

PubMed1994

Preexisting nuclear architecture defines the intranuclear location of herpesvirus DNA replication structures.

Herpes simplex virus DNA replication proteins localize in characteristic patterns corresponding to viral DNA replication structures in the infected cell nucleus. The intranuclear spatial organization of the HSV DNA replication structures and the factors regulating their nuclear location remain to be defined. We have used the HSV ICP8 DNA-binding protein and bromodeoxyuridine labeling as markers for sites of herpesviral DNA synthesis to examine the spatial organization of these structures within the cell nucleus. Confocal microscopy and three-dimensional computer graphics reconstruction of optical series through infected cells indicated that viral DNA replication structures extend through the interior of the cell nucleus and appear to be spatially separate from the nuclear lamina. Examination of viral DNA replication structures in infected, binucleate cells showed similar or virtually identical patterns of DNA replication structures oriented along a twofold axis of symmetry between many of the sister nuclei. These results demonstrate that HSV DNA replication structures are organized in the interior of the nucleus and that their location is defined by preexisting host cell nuclear architecture, probably the internal nuclear matrix.

Animals↗

PubMed1998

Volumetric object modeling for surgical simulation.

Surgical simulation has many applications in medical education, surgical training, surgical planning and intra-operative assistance. However, extending current surface-based computer graphics methods to model phenomena such as the deformation, cutting, tearing or repairing of soft tissues poses significant challenges for real-time interactions. This paper discusses the use of volumetric methods for modeling complex anatomy and tissue interactions. New techniques are introduced that use volumetric methods for modeling soft-tissue deformation and tissue cutting at interactive rates. An initial prototype for simulating arthroscopic knee surgery is described which uses volumetric models of the knee derived from 3-D magnetic resonance imaging, visual feedback via real-time volume and polygon rendering, and haptic feedback provided by a force-feedback device.

Arthroscopy↗

PubMed1984

Computed spatial homology between the L12 protein of chloroplast ribosome and 1.7 A structure of Escherichia coli L12 domain.

A computer-graphic model of the tertiary structure of a functional domain in an organelle ribosomal protein was generated using the amino acid sequence of chloroplast ribosomal protein L12 from spinach (Bartsch, Kimura and Subramanian, Proc. Natl. Acad. Sci. USA 79, 6871-6875, 1982) and 1.7 A resolution coordinates of the E. coli L12 C-terminal fragment crystal (Leijonmarck, Eriksson and Liljas, Nature 286, 824-826, 1980). A comparison between the model and the experimentally derived structure shows that although 40% of the primary structure of this part of the two proteins has undergone amino acid replacements, the gross spatial structure of the domain is maintained and the character of the surfaces of possible functional importance are not significantly altered.

Amino Acid Sequence↗

PubMed1985

New technique for showing the relation of tomographic myocardial perfusion images obtained with thallium-201 to the coronary arteries.

A new technique has been developed for presenting myocardial tomograms that allows the observer to perceive the shape of the thallium-201 distribution directly. The surface of the myocardium was found by applying an interactive thresholding technique to a set of conventional transverse slices. Computer graphics techniques were used to display a shaded image of that surface on a television screen, showing the three dimensional shape of the myocardial surface from any chosen aspect. A set of normal preserved coronary arteries was digitised, and using scaling and transformation techniques these arteries were mapped on to the myocardial tomograms and a shaded surface image produced with superimposed coronary arteries. This provided a familiar anatomical framework for locating perfusion defects. Its value in identifying various diseased vessels was confirmed by a comparison of the tomographic findings with the angiographic findings in five individual cases.

Adult↗

PubMed1997

Three-dimensional image reconstruction of large nuclear RNP (lnRNP) particles by automated electron tomography.

Nuclear RNA transcripts of split genes and their splicing products, as well as the general population of nuclear polyadenylated RNA are packaged in multi-component large nuclear ribonucleoprotein (lnRNP) particles. These lnRNP particles, which sediment at the 200 S region in sucrose gradients, contain all U small nuclear RNPs required for precursor messenger RNA (pre-mRNA) splicing and several protein splicing factors, including U2AF and the SR proteins. Electron microscopy of lnRNP particles revealed a large compact structure of 50 nm in diameter. In this study we employed automated computed tomography from electron micrographs for the three-dimensional (3D) image reconstruction of individual lnRNP particles isolated from mammalian cells nuclei and negatively stained. For each particle, a tilt series of 71 images was collected by direct digital recording of the images on a CCD camera attached to a computer controlled TEM facility. The 3D image was reconstructed according to the back projection principle. For rendering, real time display and comparison of the reconstructed particles, interactive computer graphics was employed. The reconstructed 3D images show a compact structure composed of four major subunits connected to each other. Comparison of the reconstructed lnRNP particles revealed morphological similarity of the individual particles, as well as similarity among the sub-structures. Based on these observations we propose a model for the packaging of nuclear pre-mRNAs in lnRNP particles where each substructure represents a functional unit. This model is compatible with the requirements for alternative splicing in multi-intronic pre-mRNAs, and with the fact that the splicing of multi-intronic pre-mRNAs does not occur in a sequential manner.

Animals↗

PubMedDate not supplied

Methods for evaluating cardiac wall motion in three dimensions using bifurcation points of the coronary arterial tree.

An accurate three-dimensional (3D) representation of heart wall motion would be an important means of evaluating cardiac function. To accomplish this, we have developed an interactive computer graphics system designed to enter the time-dependent 3D positions of bifurcations of the coronary arterial tree. These bifurcations are precise markers of the epicardial surface, and their motions accurately represent the motion of the underlying heart wall. We demonstrate techniques for calculating local wall motion, including displacement and velocity, for determining a time-dependent center-of-contraction point towards which the epicardium tends to move and for tracking the mechanical contraction wave using cross-correlation methods. We have applied these techniques to study seven patients with normal left ventriculograms and coronary arteriograms. We have found these methods to be generally applicable and to provide information not obtainable without 3D analysis.

Cineangiography↗

PubMedDate not supplied

An in vivo experiment to test composite resin wear using the Latin-Square analysis.

The Michigan Computer Graphics Coordinate Measurement System was used to measure the wear of three composite resins and an amalgam alloy control. The validity of the Latin Square experimental design for analysis in a clinical study was demonstrated, and statistically significant differences in wear were established for main effect for the materials under investigation. None of the composite resins examined approximated the amalgam alloy control in wear properties. Rank ordering of the materials with respect to wear was possible using this experimental design. Ranking of the materials for wear resistance using this research approach opens up other future research opportunities to correlate such properties as filler particle size, composition, and distribution with the data derived.

Analysis of Variance↗

PubMed1996

Cellular differentiation and development of pyloric mucosal metaplasia in the human gall-bladder.

The development of pyloric mucosal metaplasia (PMM) with regard to cellular differentiation in the human gallbladder was studied by mucin staining (paradoxical concanavalin A (Con A), galactose oxidase-Schiff (GOS) and alcian blue (pH 2.5) PAS (AB-PAS) and immunohistochemistry (pepsinogen II (PgII) and SH-9, and proliferating cell nuclear antigen (PCNA). PMM was divided into three stages of development by three-dimensional (3D) computer graphic reconstruction analysis. In the early stage, a transitional zone of PCNA positive cells was observed between areas of SH-9 and/or GOS reactive cells and class III and/or Pg II positive cells in flat monolayered epithelium. In the middle stage, shallow pits became apparent as areas enlarged, with these becoming deeper in the advanced stage, whereby SH-9 and/or GOS reactive cells and class III and/or Pg II positive cells were observed at the upper and lower portion of the pits, respectively, with PCNA-positive cells forming a narrow zone between the two cell populations. Consequently, the structure of PMM gradually resembles that of the normal gastric pyloric mucosa.

Cell Differentiation↗

PubMed1991

Molecular structure and dynamics of cis(Z)-and trans(E)-flupenthixol and clopenthixol.

The three-dimensional structures and molecular electrostatic potentials of the cis(Z) and trans(E)-isomers of flupenthixol and clopenthixol were examined by computer graphics and molecular mechanical and quantum mechanical calculations, and their internal molecular motions were studied by molecular dynamics simulations in vacuo and in aqueous solution. The simulations demonstrated that both the side chains and the tricyclic ring systems of clopenthixol and flupenthixol are highly flexible. The angle between the two phenyl ring planes varied between 105 and 171 degrees during the simulations in solution. The electrostatic potentials around the 2-substituent were significantly more negative in the trans(E)-isomers than in the cis(Z)-isomers. The stronger negative potentials may weaken electrostatic receptor interactions and, thereby, cause the trans(E)-isomers to be less active than cis(Z)-isomers. Differences both in three-dimensional structure and in electronic structure may cause the difference in pharmacological activity between cis(Z)- and trans(E)-thioxanthenes.

Clopenthixol↗

PubMed1993

Molecular dynamics of the 5-HT1a receptor and ligands.

A 3-D model of the human 5-HT1a receptor was constructed from its amino acid sequence by computer graphics techniques, molecular mechanics calculations and molecular dynamics simulations. The model has seven alpha-helical membrane spanning segments, which form a central core containing a putative ligand binding site. Electrostatic potentials 1.4 A outside the water accessible surface were mainly negative on the synaptic side of the receptor model and at the postulated ligand binding site, and positive in the cytoplasmic domains. The negative electrostatic potentials around the synaptic domains indicate that positively charged ligands are attracted to the receptor by electrostatic forces. Molecular dynamics simulations of the receptor model with serotonin, ipsapirone, R(-)-methiothepin or S(+)-methiothepin in the central core suggested that up to 22 different amino acid residues may form a ligand binding pocket, and contribute to the specificity of ligand recognition and binding.

Binding Sites↗

PubMed1992

Initial results for automated computational modeling of patient-specific electromagnetic hyperthermia.

Developments in finite-difference time-domain (FD-TD) computational modeling of Maxwell's equations, super-computer technology, and computed tomography (CT) imagery open the possibility of accurate numerical simulation of electromagnetic (EM) wave interactions with specific, complex, biological tissue structures. One application of this technology is in the area of treatment planning for EM hyperthermia. In this paper, we report the first highly automated CT image segmentation and interpolation scheme applied to model patient-specific EM hyperthermia. This novel system is based on sophisticated tools from the artificial intelligence, computer vision, and computer graphics disciplines. It permits CT-based patient-specific hyperthermia models to be constructed without tedious manual contouring on digitizing pads or CRT screens. The system permits in principle near real-time assistance in hyperthermia treatment planning. We apply this system to interpret actual patient CT data, reconstructing a 3-D model of the human thigh from a collection of 29 serial CT images at 10 mm intervals. Then, using FD-TD, we obtain 2-D and 3-D models of EM hyperthermia of this thigh due to a waveguide applicator. We find that different results are obtained from the 2-D and 3-D models, and conclude that full 3-D tissue models are required for future clinical usage.

Computer Simulation↗

PubMed1994

Computer-stimulated test fitting of an implantable hearing aid using implantable hearing aid using three-dimensional CT scans of the temporal bone: preliminary study.

In preparation for future implantation of the implantable middle ear transducer in patients, a method was sought for preoperatively test fitting a model of the device, using computer generated three-dimensional (3-D) temporal bone images derived from spiral computed tomography (CT) data. A 3-D model of the implantable middle ear transducer was designed using NIH Image software on a Macintosh computer. High resolution human temporal bone CT scans were obtained using a spiral CT scanner (Siemens Somatom Plus S). The 3-D transducer model was superimposed onto 3-D reconstructions of the temporal bone using ANALYZE software on a computer graphics workstation (Sun SPARCstation 10), showing the transducer "implanted" in the temporal bone. Measurements were validated using a cadaver temporal bone. This process produced images demonstrating the "fit" of the current transducer design in the mastoid region of the adult temporal bone. It permitted assessment of the proximity of surrounding structures such as the external auditory meatus, dura, or sigmoid sinus. Preliminary cadaver validation measurements confirmed the accuracy of this method. Three-dimensional CT is a feasible method for preoperative planning of the surgical implantation of devices in the temporal bone. This method of 3-D test fitting will be used in the future to determine optimum orientation and size limitations for human implantable devices.

Cochlear Implants↗

PubMed1984

Mechanisms of phase 1a and 1b early ventricular arrhythmias during acute myocardial ischemia in the dog.

Two phases of ventricular arrhythmia occur within the first 30 minutes of experimental myocardial ischemia. Possible differences in their mechanisms of pathogenesis were investigated in anesthetized dogs by detailed mapping of patterns of epicardial activation and regional myocardial blood flow during phase 1a and phase 1b early ventricular arrhythmias induced by high ligation of the left anterior descending coronary artery. Data were derived from 80 sites in a 4 by 5 cm area of left ventricular anterior free wall and displayed using computer graphics. Regional myocardial blood flow and the relation of regional flow to epicardial delay did not differ significantly during the 2 phases of arrhythmia in central ischemic or nonischemic areas, although epicardial flow in border region segments was increased during phase 1b. Significantly greater mean epicardial delays and spatial heterogeneity of epicardial delay (assessed by intersite variance within the ischemic area) occurred during phase 1a arrhythmias. Serial studies show striking increases in spatial heterogeneity of delays during phase 1a, but not during phase 1b, relating to temporal dispersion of a phenomenon of transient prolongation of activation delay at individual electrode sites. These data are consistent with the concept that phase 1a and 1b arrhythmias arise through different electrophysiologic mechanisms independent of flow-dependent effects.

Acute Disease↗