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PubMed1999

Time-resolved analysis and visualization of dynamic processes in living cells.

Recent development of in vivo microscopy techniques, including green fluorescent proteins, has allowed the visualization of a wide range of dynamic processes in living cells. For quantitative and visual interpretation of such processes, new concepts for time-resolved image analysis and continuous time-space visualization are required. Here, we describe a versatile and fully automated approach consisting of four techniques, namely highly sensitive object detection, fuzzy logic-based dynamic object tracking, computer graphical visualization, and measurement in time-space. Systematic model simulations were performed to evaluate the reliability of the automated object detection and tracking method. To demonstrate potential applications, the method was applied to the analysis of secretory membrane traffic and the functional dynamics of nuclear compartments enriched in pre-mRNA splicing factors.

Animals↗

PubMed1985

Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins.

A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge. The location of the guanine ring is unusual; the purine ring is located on the outer edge of the domain, not deep within a hydrophobic pocket. The amino acids from Pro10 to Arg44 and from Gly59 to Glu190 have been assigned to the electron density with computer graphic techniques, and the resulting model is consistent with all known biochemical data. An analysis of the structure reveals that four regions of the amino acid sequence that are homologous with the family of ras oncogene proteins, termed p21, are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the proteins interact directly with the GDP ligand.

Amino Acid Sequence↗

PubMed1983

Computer-assisted facility planning: a formidable weapon in project cost management.

What are the goals of space planning? They are to predict the probable future of various alternative combinations of space, their layouts, the operating movement, the economic effect and the visual effect of these solutions. Computer graphics, a simple and reliable communication tool in the hands of experienced space planners, can help planners and clients to make real contributions to the design process. This technology will allow them to become, for the first time, not a client and designer, but rather a true partnership, contributing from a broader base of knowledge in an accountable way to the solution of complex problems. This can make a real difference in the future of healthcare facilities.

Computers↗

PubMed2004

Anatomy- and physics-based facial animation for craniofacial surgery simulations.

A modelling approach for the realistic simulation of facial expressions of emotion in craniofacial surgery planning is presented. The method is different from conventional, non-physical techniques for character animation in computer graphics. A consistent physiological mechanism for facial expressions was assumed, which was the effect of contracting muscles on soft tissues. For the numerical solution of the linear elastic boundary values, the finite element method on tetrahedral grids was used. The approach was validated on a geometrical model of a human head derived from tomographic data. Using this model, individual facial expressions of emotion were estimated by the superpositioning of precomputed single muscle actions.

Computer Simulation↗

PubMed2004

Preoperative evaluation of submucosal myoma by virtual hysteroscopy.

STUDY OBJECTIVE: To assess the utility of a new technique called virtual hysteroscopy in the evaluation of the size and location of submucosal myomas before hysteroscopic myomectomy. DESIGN: Retrospective analysis (Canadian Task Force classification II-1). SETTING: Department of gynecology at a general hospital. PATIENTS: Thirteen consecutive women. INTERVENTION: Sixteen-slice computed tomography (CT) scanner. MEASUREMENTS AND MAIN RESULTS: Thirteen women with submucosal myomas were examined by virtual hysteroscopy. The lesions were filmed by multislice CT scanner, immediately after CO2 injection into the uterine cavity with an intravenous dosage of iodide contrast media. The filmed image was subsequently reconstituted and analyzed by endoscopy mode and volume mode using three-dimensional computer graphics software. The size and depth of invasion of the submucosal myoma were clearly identified by the procedure. CONCLUSION: Accurate preoperative evaluation of the size and location of submucosal myomas before hysteroscopic myomectomy is important for a safe surgical procedure. Virtual hysteroscopy can provide such information with good reproducibility and is superior to previously described diagnostic procedures.

Adult↗

PubMed1995

Characterization of the spatial-frequency spectrum in the perception of shape from texture.

The major cue to shape from texture is the compression of texture as a function of surface curvature [J. Exp. Psychol. 13, 242 (1987); Vision Res. 33, 827 (1993)]. A number of computational models have been proposed in which compression is measured by detection of changes in the spatial-frequency spectrum [Comput. Graphics Image Process. 5, (1976)]. We propose that the visual system uses a strategy of characterizing the frequency spectrum by a simple set of measures and of tracking the changes in this characterization rather than determining changes in the shape of the actual spectra. Our evidence is based on a number of psychophysical demonstrations that use stimuli with specifically tailored frequency spectra, constructed from white noise filtered in the frequency domain. Our evidence suggests that the visual system determines the average peak frequency of the spectrum and uses this measure as its characterization. Changes in fp are strongly correlated with the degree of surface curvature, and, over a range of stimuli, fp takes account of the variance in local estimates of the frequency spectrum. One computes fp by determining the peak frequency at each spatial location and then averaging these frequency values over a local spatial region. We show that fp is related to the second-order moment but is more biologically plausible and shows superior ability to function in the presence of noise. As a test of this model, we have constructed a neural network architecture for computing shape from texture. Our model is limited to orthographically projected, homogeneous textures without in-surface rotation. The early stages of the model consist of multiple simple-cell units tuned to different orientations and spatial frequencies. We show that these simple cells are inadequate for the determination of compression but that the outputs of complex-cell-like units after normalization generate estimates of surface slant and tilt. The network shows qualitative agreement with human perception of shape from texture over a wide range of real and artificial stimuli.

Form Perception↗

PubMed1988

Bile acids with a cyclopropyl-containing side chain. 3. Separation, identification, and properties of all four stereoisomers of 3 alpha,7 beta-dihydroxy-22,23-methylene-5 beta-cholan-24-oic acid.

3 alpha,7 beta-Dihydroxy-22,23-methylene-5 beta-cholan-24-oic acid (CUDCA) (2a), a side-chain cyclopropylog of ursodeoxycholic acid (UDCA) was shown to be a mixture of four stereoisomers (CUDCA A-D). The 22S,23R, and 22R,23S diastereoisomers have been separated, their respective configurations assigned by 13C NMR spectroscopy, and original synthetic schemes for their preparation elaborated. Moreover, theoretical models of the structure of UDCA and CUDCA A-D were built by using molecular computer graphic techniques. It was shown that the four diastereoisomers greatly differ in hydrophilicity, in critical micellar concentration (CMC) in water, and exhibit a different interaction with intestinal bacterial enzymes. It was also shown that CUDCA A-C are not conjugated with glycine or taurine in the liver, while CUDCA D is secreted into bile predominantly as taurine and glycine conjugate.

Animals↗

PubMed1990

Testing of insulin hexamer-stabilizing ligands using theoretical binding, microcalorimetry, and nuclear magnetic resonance (NMR) line broadening techniques.

In a study aimed at the development of a long-acting insulin preparation, Manallack and co-workers (5) reported on the design of small organic molecules which have the potential to bind to insulin and stabilize its hexameric aggregate. Two of the molecules that were designed with their computer graphics program were thought to be particularly promising as ligands: benzene-p-disulfonate and benzene-p-diphosphonate. In the present work, the insulin binding abilities of these molecules have been thoroughly tested. A theoretical binding program, GRID, was used to calculate the binding energetics of the molecules and to predict the most probable site of their binding. Microcalorimetry and NMR line broadening techniques were used to measure the actual binding reactions of the ligands. For both compounds, no evidence of binding to insulin was ever observed in either the microcalorimetry or the NMR studies. In contrast, a series of phenolic ligands commonly used as preservatives for insulin showed evidence of substantial binding using either method. An explanation has been proposed for this apparent discrepancy between computer predictions and actual experimental data: The theoretical programs do not take solvation effects of the aqueous medium into account. Solvation effects would tend to inhibit binding of the ionized ligand molecules due to charge delocalization and steric crowding.

Benzenesulfonates↗

PubMed1987

Mean geometry of the thiopeptide unit and conformational features of dithiopeptides and polythiopeptides.

The mean geometry of the thiopeptide [Ca-N-C(=S)-Ca] unit has been derived from an analysis of X-ray crystal structure data, as well as MM2 and Gaussian 80/82 calculations. The conformational flexibilities of dithiopeptides with glycl- and alanyl-side chains have been investigated by molecular mechanics. Minimum energy conformations were examined using interactive computer graphics molecular modeling techniques. Alanyl-dithiopeptide substitution within an oligopeptide results in considerable restriction of conformational freedom whereas the effect is minimal for glycyl-dithiopeptide substitution. Polyglycyl-thiopeptide adopts a left-handed three or fourfold or right-handed threefold helical structure with favorable interchain C = S...H-N hydrogen bond interactions. A poly-L-alanyl-thiopeptide prefers a left-handed threefold poly-L-proline-like helical structure.

Amides↗

PubMed1989

Corneal topographic changes after radial keratotomy.

A high resolution photokeratoscope using digital video image acquisition and computer graphics was used to describe anterior corneal topography before and after radial keratotomy. After radial keratotomy, the entire cornea is flattened, but this effect is more pronounced centrally. The flat central "optical zone" varies in size, shape, and location. Regional variations in corneal power may explain phenomena observed after radial keratotomy, such as visual acuity that is better than would be expected on the basis of refractive error, and the occurrence of ghost images.

Adult↗

PubMed1996

Three-dimensional reconstruction of the rat triceps surae muscle and finite element mesh generation of the gastrocnemius medialis muscle.

In order to simulate blood flow in skeletal muscle, our group has developed a finite element description of perfused skeletal muscle. This model requires input parameters concerning the vascular system, muscle contraction and the geometry of a muscle, including its aponeuroses. The objective of the present paper is to create a geometrical reconstruction of the rat gastrocnemius medialis muscle that can be incorporated in the finite element model. Since this muscle is connected to the plantaris and the gastrocnemius lateralis muscle, a detailed computer graphical reconstruction of the triceps surae muscle, based on histological cross-sections, has been accomplished first. Using this reconstruction, relevant sections were selected to create the finite element mesh of the gastrocnemius medialis muscle. Special attention was payed to the location of the aponeuroses. The mesh can be used in finite element simulations of perfused skeletal muscle.

Animals↗

PubMed1991

Recent advances in radiotherapy treatment planning.

Radiation treatment planning is currently in a state of rapid change. Dissatisfaction with past planning technology stems from the growing realization that: (1) Increases in the local regional tumor control rate will increase the cure rate in many malignancies. (2) Even at the best treatment centers geometric tumor misses are commonplace. (3) Traditional constraints on treatment techniques, originally imposed for simplicity and reproducibility, are no longer necessary, and can result in suboptimal treatment. (4) Treatment plans judged "optimal" in two dimensions may be far from optimal when viewed over the entire treatment volume. (5) Lack of treatment reproducibility is also commonplace, and can be demonstrated to adversely affect treatment outcome. On the positive side, recent developments in computer graphics, image processing, radiation physics, and radiation biology are now making it possible to define, design, and deliver sophisticated 3D radiation treatments. However, because many of these technologies are being developed for other disciplines, their applicability to radiation therapy treatment planning is not widely appreciated. We outline the current status and new developments in radiation therapy treatment planning.

Artificial Intelligence↗

PubMed1991

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗

PubMed1993

Craniofacial morphometry by photographic evaluations.

Frontal and lateral oriented profile photographs of 108 healthy young adults (57 men and 51 women) were taken, and a standardized protocol was used to quantitatively describe the depicted craniofacial soft tissue structure, the relationships among facial structures, and head posture relative to the ground. Pictures were taken in two body positions, standing and sitting. The male faces were, on average, wider and longer than the female faces, in both frontal and lateral views, with greater differences in the mouth and chin regions. Both sexes were generally symmetrical. Persons who were asymmetric compensated for their appearance by changing head posture relative to the ground, so that in the frontal plane, the interpupillary axis and the occlusal plane were parallel to the ground. Measurements can be employed in computer graphic reconstructions used in orthognathic, maxillofacial, and plastic surgery. In the standing position, the Frankfurt plane was directed upward and forward, with a mean angle of 13 degrees relative to the ground. In seated subjects, it was more nearly horizontal (5 degrees in the men, 8 degrees in the women). This result confirms the need for a careful reevaluation of standard cephalometric and photographic protocols.

Adult↗

PubMed2004

High-resolution 3-D shape integration of dentition and face measured by new laser scanner.

Face and dentition were measured using a high-resolution three-dimensional laser scanner to circumvent problems of radiation exposure and metal-streak artifacts associated with X-ray computed tomography. The resulting range data were integrated in order to visualize the dentition relative to the face. The acquisition interval for dentition by laser scanner was 0.18 mm, and complicated morphologies of the occlusal surface could be sufficiently reproduced. Reproduction of occlusal condition of upper and lower dentitions was conducted by matching the surface of the occlusal impression record with upper dentition data. To integrate dentition and face, a marker plate interface was devised and adopted on the lower dental cast or by the subject directly. Integration was performed by matching both sets of interface data. Reproduction of the occlusal condition and integration of the dentition and face were accomplished and visualized satisfactorily by computer graphics. The integration accuracy was examined by changing the attachment angle of the marker plate, and the marker plate attached at 45 degrees showed the smallest error of 0.2 mm. The current noninvasive method is applicable to clinical examination, diagnosis and explanation to the patient when dealing with the physical relationship between face and dentition.

Adult↗

PubMed2005

Software system for three-dimensional volumetric reconstruction of histological sections: a case study for the snake chondrocranium.

Volumetric digital computer-assisted reconstruction of histological sections is an attractive possibility for developmental studies. Commercial solutions are very expensive for many educational institutions. Therefore, we developed a software system for three-dimensional reconstruction of anatomical virtual models. The input data for the system are the digitized images from the histological samples of the chondrocranium of two crotalines, Bothrops jararaca and Crotalus durissus terrificus, and one colubrid, Philodryas olfersii, using a stereomicroscope connected to a digital camera. These images are then manually registered and segmented. We use computer graphics visualization algorithms such as marching cubes and ray casting to generate three-dimensional visualizations of the volumes. The results show that the digital reconstruction is as good as the manual reconstruction with the advantages of speed of reconstruction, accuracy, and flexibility to handle and study the volume. Compared with commercial options, our system has approximately the same features, and it is available free for the scientific community.

Animals↗

PubMed1984

Macro-structural organization of phosphoglycerate mutase.

The three-dimensional structure of phosphoglycerate mutase has been analyzed using a contoured distance matrix and by visual inspection using three-dimensional computer graphics. Three folding lobes have been identified and their internal structure tentatively characterized. The active site is located at a lobe interface with a channel providing possible access from above and below. The arrangement of active site residues on two lobes suggests that the active site might be conformationally flexible. The remaining interface not associated with the active site channel appears to be predominately hydrophobic and thus may contribute to inter-lobe stability.

Binding Sites↗

PubMed1981

Tonotopic organization of the anteroventral cochlear nucleus of the cat.

A quantitatively accurate map of the tonotopic organization of the anteroventral cochlear nucleus (AVCN) was derived from single unit recordings. Histologically localized single unit recordings from many animals were mapped onto a computerized atlas of the cochlear nucleus, and surfaces of constant characteristic frequency (CF) estimated with the aid of computer graphics. In anterior AVCN the surfaces of constant CF were found to be parallel planes, whereas in posterior AVCN they progressively deviated from this simple description. A further complication was noted in the most posterior portion of the AVCN where units with very different CF was found in close proximity. Comparison of the tonotopic map with descriptions of cellular organization shows conclusively that different CF ranges are dominant in the various cytoarchitectonic regions of the AVCN.

Animals↗