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At least 667 records · Page 37Linked to original sources
PubMed1999

What object attributes determine canonical views?

We investigated preferred or canonical views for familiar and three-dimensional nonsense objects using computer-graphics psychophysics. We assessed the canonical views for objects by allowing participants to actively rotate realistically shaded three-dimensional models in real-time. Objects were viewed on a Silicon Graphics workstation and manipulated in virtual space with a three-degree-of-freedom input device. In the first experiment, participants adjusted each object to the viewpoint from which they would take a photograph if they planned to use the object to illustrate a brochure. In the second experiment, participants mentally imaged each object on the basis of the name and then adjusted the object to the viewpoint from which they imagined it. In both experiments, there was a large degree of consistency across participants in terms of the preferred view for a given object. Our results provide new insights on the geometrical, experiential, and functional attributes that determine canonical views under ecological conditions.

Adolescent↗
PubMed1995

A mathematically based classification of root canal curvatures on natural human teeth.

Testing of root canal-shaping instruments on natural human teeth has many difficulties, because of the different anatomical forms of root canals. There is a lack of an internationally accepted and mathematically based classification of root canal morphology. The aim of this study was to give a mathematical description of root canal forms with the help of differentiated geometrical pattern analysis and computer graphics. The measurements of 433 roots were conducted on isometric radiographs taken from the clinical view. Measured points of the same radiographs were approximated using fourth degree polynomial functions describing the imaginary axis of canals. The classification of root canal morphology on the basis of Schneider's angle differs from the classification of geometrical pattern analysis. Fourth-degree function approximation as a new method for the description of the shape of root canal curvatures seems to be exact and reliably repeatable. This type of classification of root canals is suitable for standardizing test specimens, including natural human teeth used for testing root forms: I (straight), J (apical curve), C (entirely curved), or S (multicurved).

Chi-Square Distribution↗
PubMed1996

The three-dimensional bone interface of an osseointegrated implant. I: A morphometric evaluation in initial healing.

Direct bone-implant interface as an indicator of endosseous implant success appears to have been overinterpreted because 100% bone apposition is not necessarily obtained at the surface of the endosseous dental implant. The purpose of this study was to obtain quantitative information about the three-dimensional bone structure around three hydroxyapatite-coated titanium alloy dental implants. Implants were placed in the mandible in three monkeys, and the surface bone contact ratio in the buccal, lingual, mesial, and distal directions was computed. Computer graphics were generated by the integration of data for serial ground surfaces obtained at 75 microm intervals of the tissue block involved with the implant. The bone contact ratio of the whole surface of each of the three implants was 80.8%, 68.1%, and 68.8%, and the bone contact ratio for each direction and portion varied with the conditions of implant placement. The bone volume ratios around the implant at the 0 to 300 microm zone were also calculated, and total ratios ranged from 58% to 81%. These results may provide useful quantitative information about the bone structure around the hydroxyapatite-coated implants and contribute to the development of realistic finite element analysis models based on the biologic bone structure around the implants.

Animals↗
PubMed1990

Comparative study on specificities of rat cathepsin L and papain: amino acid differences at substrate-binding sites are involved in their specificities.

Sixty-nine rat cathepsin L-susceptible peptide bonds were analyzed employing various peptide substrates. The proteolytic specificities of rat cathepsin L and papain were compared and the results are discussed in relation to differences in amino acid residues around their binding sites. The specificity of cathepsin L, which is characterized by a remarkable preference for hydrophobic amino acids at the P2 site of the scissile peptide bonds, was analogous to that of papain as a whole. This analogous specificity suggests that the binding sites of the two proteases are analogous, as expected from their homologous amino acid sequences. However, there is a slight difference in the preference for S3 site between them. That is, cathepsin L showed a greater preference for bulky and hydrophobic amino acids at the S3 site than did papain. Based on the computer-graphically deduced structure of the binding sites of cathepsin L, the preferences for hydrophobic amino acids at the S2 site and for bulky and hydrophobic amino acids at the S3 site of the protease are supposed to be related to the compensating amino acid substitutions at the S2 site (V133A and V157L) and the reduction in size at the S3 site (Y61Q and Y67L), respectively. The discussion of the effect of the amino acid substitutions on the proteolytic activities of cathepsin L and papain in this paper provides a basis for more advanced studies of the relationship between structure and function of proteases belonging to the papain superfamily by means of protein engineering.

Amino Acid Sequence↗
PubMed2002

Partnership status and the temporal context of relationships influence human female preferences for sexual dimorphism in male face shape.

Secondary sexual characteristics may indicate quality of the immune system and therefore a preference for masculinity may confer genetic benefits to offspring; however, high masculinity may be associated with costs of decreased paternal investment. The current study examined women's preferences for masculinity in male faces by using computer graphics to allow transformation between feminine and masculine versions of individual male faces. We found that preferences for masculinity are increased when women either have a partner or are considering a short-term relationship. Such preferences are potentially adaptive, serving to: (i) maximize parental investment and cooperation in long-term relationships by biasing choices towards feminine faced males, and (ii) maximize possible good-gene benefits of short-term or extra-pair partners by biasing choices towards masculine faced males. We also found that individuals using oral contraception do not show the above effects, indicating that such hormonal intervention potentially disrupts women's choices for evolutionarily relevant benefits from males.

Adolescent↗
PubMed1999

Structure based development of novel specific inhibitors for cathepsin L and cathepsin S in vitro and in vivo.

Specific inhibitors for cathepsin L and cathepsin S have been developed with the help of computer-graphic modeling based on the stereo-structure. The common fragment, N-(L-trans-carbamoyloxyrane-2-carbonyl)-phenylalanine-dimethyla mide, is required for specific inhibition of cathepsin L. Seven novel inhibitors of the cathepsin L inhibitor Katunuma (CLIK) specifically inhibited cathepsin L at a concentration of 10(-7) M in vitro, while almost no inhibition of cathepsins B, C, S and K was observed. Four of the CLIKs are stable, and showed highly selective inhibition for hepatic cathepsin L in vivo. One of the CLIK inhibitors contains an aldehyde group, and specifically inhibits cathepsin S at 10(-7) M in vitro.

Animals↗
PubMed2000

[Effects of different types of disparity cues on the response of axis-orientation selective cells in the monkey parietal cortex].

PURPOSE: To specify the cues for the discrimination of orientation in depth in axis orientation selective (AOS) neurons. METHODS: We analyzed the responses of AOS neurons in the monkey caudal intraparietal sulcus (cIPS) region using binocular disparity stimuli generated by stereoscopic 3 D computer graphics. RESULTS: Most AOS neurons (20/27) were sensitive to binocular disparity and showed tuning to the orientation of a slit in the sagittal plane with orientation disparity cues. For 12 neurons we also used an array of discs or dots instead of slits to eliminate orientation disparity. Half of the neurons (6/12) responded better to the slits than to the discs or dots, suggesting that they were sensitive to orientation disparity. Five neurons (5/12) responded equally well to the discs or dots suggesting that they were more sensitive to the gradient of horizontal disparity than to the orientation disparity. CONCLUSION: Both orientation disparity and disparity gradient were likely to be integrated in the cIPS area to represent axis orientation of an object in space.

Animals↗
PubMed2000

A tactile display for international space station (ISS) extravehicular activity (EVA).

BACKGROUND: A tactile display to increase an astronaut's situational awareness during an extravehicular activity (EVA) has been developed and ground tested. The Tactor Locator System (TLS) is a non-intrusive, intuitive display capable of conveying position and velocity information via a vibrotactile stimulus applied to the subject's neck and torso. In the Earth's 1 G environment, perception of position and velocity is determined by the body's individual sensory systems. Under normal sensory conditions, redundant information from these sensory systems provides humans with an accurate sense of their position and motion. However, altered environments, including exposure to weightlessness, can lead to conflicting visual and vestibular cues, resulting in decreased situational awareness. The TLS was designed to provide somatosensory cues to complement the visual system during EVA operations. METHODS: An EVA task was simulated on a computer graphics workstation with a display of the International Space Station (ISS) and a target astronaut at an unknown location. Subjects were required to move about the ISS and acquire the target astronaut using either an auditory cue at the outset, or the TLS. Subjects used a 6 degree of freedom input device to command translational and rotational motion. The TLS was configured to act as a position aid, providing target direction information to the subject through a localized stimulus. RESULTS: Results show that the TLS decreases reaction time (p = 0.001) and movement time (p = 0.001) for simulated subject (astronaut) motion around the ISS. CONCLUSION: The TLS is a useful aid in increasing an astronaut's situational awareness, and warrants further testing to explore other uses, tasks and configurations.

Aerospace Medicine↗
PubMed2006

LAFIRE: software for automating the refinement process of protein-structure analysis.

Manual intervention is usually required in the multiple rounds of refinement of protein crystal structures, including linking and/or extending the fragments of the initial model and rebuilding (fitting) ill-matched residues using computer-graphics software. Such manual modification is both time-consuming and requires a great deal of expertise in crystallography. Consequently, the refinement process becomes the bottleneck for high-throughput structure analysis. A program, Local correlation coefficient-based Automatic FItting for REfinement (LAFIRE), has been developed to achieve manual intervention-free refinement. This program was designed to perform the entire process of protein structural refinement automatically using the refinement programs CNS1.1 (CNS v.1.1) or REFMAC5. The automatic process begins from an initial model, which can be approximate, fragmentary or even only main-chain, and refines it to the final model including water molecules, controlled by monitoring the R(free) factor. More than 30 structures have now been refined successfully in a fully or semi-automatic manner within a few hours or days using LAFIRE.

Animals↗
PubMedDate not supplied

3-D mapping of body surface potentials.

A new system has been developed in which the human body surface potentials are displayed in a 3-dimensional format using computer graphics. A wire-frame model of the human torso is constructed using geometrical data from several cross-sectional slices. The body surface potentials are measured and the isopotential lines drawn. By mapping the co-ordinates obtained with the isopotential line subroutine to the X, Y and Z torso arrays, a 3-dimensional representation of the depolarization wave travelling across the body surface can be displayed. The deviations from its normal path are clearly seen in the 2 clinical cardiac conditions presented (right bundle branch block and left ventricular premature beat). The increased realism and spatial resolution, as compared to ECG and the 2-dimensional contour map, lead to a clear understanding and interpretation of the underlying electrical phenomena of the heart while making a diagnosis or presenting experimental results.

Bundle-Branch Block↗
PubMed1990

L-alpha-glycerophosphate binding to bovine gamma-crystallin: a potential link between metabolism and supramolecular order.

The highly selective nature of protein-ligand interactions provides a sensitive mechanism for the modulation of cellular activity by proteins. In the eye lens the supramolecular order of the lens crystallins, which is expected to be susceptible to protein electrostatic charge, in part defines transparency. The binding of charged ligands to proteins is one way of achieving an alteration in protein electrostatic charge. Evidence is presented that L-alpha-glycerophosphate, a major phosphorus metabolite of eye lens metabolism, binds to the globular protein, gamma-crystallin with moderately high affinity and in a positive cooperative manner. The following binding parameters were obtained from equilibrium measurements: minimum number of binding sites, n = 2; Kassoc = 6.2 +/- 0.5 x 10(3) M-1; cooperativity parameter, alpha H = 1.9 +/- 0.1. Interactive computer graphics display techniques were used to locate putative ligand binding sites, and in turn, to identify the possible molecular interactions responsible for the binding of ligand to protein at one of the sites. One putative binding site was located in the cleft between the two domains of gamma II-crystallin. Arginyl residues 79 and 147 are involved in ligand binding as are the peptide carbonyl oxygens of residues Tyrosyl-50 and Aspartyl-156. Five hydrogen bonds between the ligand and the protein structure are predicted for the binding of L-alpha-glycerophosphate, whereas only 3 occur for the binding of the "unnatural" D-enantiomorph. Modulation of both lens protein supramolecular organization and lens metabolism is predicted to be a consequence of L-alpha-glycerophosphate binding to gamma-crystallin in the lens.

Animals↗
PubMed1996

Sub-pixel accuracy: psychophysical validation of an algorithm for fine positioning and movement of dots on visual displays.

Many visual experiments call for visual displays in which dots are plotted with very fine positional accuracy. Spatial hyperacuities and motion displacement thresholds can be as low as 5 sec arc. On computer graphics displays small angular displacements of a pixel can be obtained only with long viewing distances which impose a small field of view. To overcome this problem, we describe a method for positioning the centroid of a quadrel (a 2 x 2 block of pixels) with very high accuracy, equivalent to 0.4% of a pixel width. This enables dot displays to be plotted with high positional accuracy at short viewing distances with larger fields of view. We show psychophysically that hyperacuities can be measured with sub-pixel accuracy in quadrel displays. Motion displacement thresholds of 16 sec arc were measured in multiple-dot and single-dot displays even though the pixel spacing was 1.2 min arc. Quadrel displays may be especially useful in studies of optic flow and structure-from-motion which demand a fairly large field of view along with fine positional accuracy.

Algorithms↗
PubMed1988

A model for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome.

A three-dimensional model for the arrangement of 29 of the 33 proteins from the Escherichia coli large ribosomal subunit has been generated by interactive computer graphics. The topographical information that served as input in the model building process was obtained by combining the immunoelectron microscopically determined network of epitope-epitope distances on the surface of the large ribosomal subunit with in situ protein-protein cross-linking data. These two independent sets of data were shown to be compatible by geometric analysis, thus allowing the construction of an inherently consistent model. The model shows (i) that the lower third of the large subunit is protein-poor, (ii) that proteins known to be functionally involved in peptide bond formation and translocation are clustered in two separate regions, (iii) that proteins functionally interdependent during the self-assembly of the large subunit are close neighbours in the mature subunit and (iv) that proteins forming the early assembly nucleus are grouped together in a distinct region at the 'back' of the subunit.

Bacterial Proteins↗
PubMed1991

Three-dimensional structure and molecular dynamics of cis(Z)- and trans(E)-chlorprothixene.

cis(Z)-Chlorprothixene has antidopaminergic potency, while trans(E)-chlorprothixene is virtually inactive. In order to reveal the structural features causing the difference in activity, the three-dimensional molecular and electronic structures of cis(Z)- and trans(E)-chlorprothixene were examined by computer graphics and molecular mechanical and quantum mechanical calculations. The internal molecular motions of the isomers were studied by molecular dynamics simulations in vacuo and in aqueous solution. The cis(Z)-isomer had lower potential molecular energy than the trans(E)-isomer, mainly due to electrostatic interactions within the side-chain and between the dimethylamino group and the chlorine atom. During molecular dynamics simulations in aqueous solution, the side-chain of the trans(E)-isomer stayed closer to the central S-C axis of the ring system than did the side-chain of the cis(Z)-isomer. The molecular electrostatic potentials were significantly lower in the vicinity of the chlorine atom in the trans(E)- than in the cis(Z)-isomer. Differences in molecular electrostatic potentials and in three-dimensional structure are suggested to be the main reasons for the difference in pharmacological activities of cis(Z)- and trans(E)-chlorprothixene.

Chlorprothixene↗
PubMed1997

Development of the computerized dental cast form analyzing system--three dimensional diagnosis of dental arch form and the investigation of measuring condition.

To analyze the functional and morphological harmonies of the tooth and dental arch, a computerized system to measure a dental cast and to detect the apex of dental cusps and angle points of incisors was developed. Detailed morphology in the measured dental cast could be displayed distinctively by computer graphics (CG) with a surface model. Accuracy in determining the position of the apex of the dental cusp was examined by increasing the measuring pitch from 50 microns to 400 microns, the error increased gradually with increased measuring pitch. Taking the measuring error, the time for measurement and the memory size for analysis into account, a measuring pitch of 200 microns was determined to be reasonable. Three-dimensional data measurements from the apex of the dental cusp in molar, and the mesial and distal angles in canine and incisor were fitted to a polynomial formula. In the present measured model, the 4th order polynomial formula was used for the dental arch, and the 2nd order polynomial formula was used for the anteroposterior and lateral occlusal curves. These formulae could be simultaneously superimposed on the surface model of the dental cast, and displayed using CG.

Computer Graphics↗
PubMed1988

Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.

Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has provided useful structural information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinases to provide a structurally based sequence alignment: alpha-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat mast cell protease 2 (RMCP2). The root mean square differences in alpha-carbon atom positions among these four structures when compared in a pairwise fashion range from 0.79 to 0.97 A for structurally equivalent residues. The sequences of the two lymphocyte enzymes were then aligned to these proteinases using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. With RMCP2 as a template for CCP1 and the two enzymes RMCP2 and BT as templates for HF, the molecular models were constructed. Intramolecular steric clashes that resulted from the replacement of amino acid side chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angles in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginine residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 position of the substrate. Both CCP1 and HF have a free cysteine in the segment of polypeptide 88 to 93.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1988

Color vision defects in ocular hypertension and glaucoma. Quantification with a computer-driven color television system.

In order to detect early defects of color vision caused by increased intraocular pressure, a computer graphics device and color monitor system were used to measure color contrast sensitivity. The system determines the threshold chrominance of a colored grating in which there is no change in luminance. The study included 13 control subjects aged 10 to 57 years and 19 patients with ocular hypertension or glaucoma aged 20 to 58 years. In the 13 eyes with visual field loss, color contrast sensitivity was profoundly reduced when the grating colors fell on a tritan color confusion line. In the eyes without visual field loss, tritan color contrast sensitivity was reduced to an average level considerably below the extreme limits of the control group. These results were compared with those of other color vision tests and diagnostic criteria for glaucoma. The findings suggest that among the tests used, color contrast sensitivity testing was able to discriminate most effectively between patients who had retinal damage and the normal population.

Color Perception Tests↗
PubMed1991

A model of the lac repressor-operator complex based on physical and genetic data.

Computer graphics were used to build a molecular model of the complex of Lac repressor and lac operator. The model is based (a) on the NMR data of the Kaptein group [Boelens, R., Lamerichs, R. M. J. N., Rullmann, J. A. C., van Boom, J. H. & Kaptein, R. (1988) Protein Sequence Data Anal. 1, 487-498] and (b) on our genetic and biochemical data including specificity changes [Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1990) EMBO J. 9, 615-621]. Effects of amino acid exchanges in the recognition helix could be predicted by the model and were subsequently tested and confirmed by genetic experiments. Comparison of the modelled lac complex with the known crystallographic structures of several helix-turn-helix DNA complexes reveals striking similarities and suggests rules which govern the recognition between particular amino acid side chains and particular base pairs in these systems.

Amino Acid Sequence↗