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PubMed1991

Accurate control of contrast on microcomputer displays.

Off-the-shelf microcomputers can now display arbitrary 8-bit images, but accurate control of these images requires dealing with several undesirable properties of real digital to analog converters (DACs) and analog video monitors. The limitations of DACs and video monitors are presented in the form of a model for their calibration and use in vision experiments. Low contrasts can be accurately rendered by summing a small accurate a.c. signal and a large less-accurate d.c. signal (Watson et al., 1986; Behavior Research, Method, Instrument and Computers, 18, 587-594). Exploiting that idea, this note presents an easy-to-build passive resistor network, a video attenuator, that combines the outputs of three 8-bit DACs to render low contrasts with 12-bit accuracy at the display. Measurements confirm the 12-bit accuracy.

Analog-Digital Conversion↗
PubMed1991

A programmable digital video pattern generator controlled by microprocessor for basic research and clinical applications.

A programmable digital video pattern generator controlled by a microprocessor is described as a part of any commercial or specific visual evoked potential analysis system. The generator handles all kinds of patterns (uniform, orthogonal and radial) with all known presentation modes (onset, offset and reversal) and resolution 640 x 200 square pixels. The frame rate of the generator is adjusted to be compatible to either low cost 50 Hz video monitor or expensive ones of higher frame rate. The operation parameters defined by software are: pattern selection, trigger mode, field selection and stimulation rate. The development of software applications for special research demands is desirable because of the control of the generator by a microprocessor.

Computer Graphics↗
PubMed1992

Contrast sensitivity as a function of spatial frequency, viewing distance and eccentricity with and without spatial noise.

Using computer graphics and a two-alternative forced-choice method we measured threshold contrast as a function of viewing distance, spatial frequency, and eccentricity for gratings with and without added, white two-dimensional spatial noise. Our experiments showed that in spatial noise contrast sensitivity was independent of viewing distance as long as contrast sensitivity was lower with noise than without. With increasing spatial frequency (f) the grating area (A) was reduced in order to keep the relative grating size (Af2) constant. At all spatial frequencies the test gratings thus had the same amount of detail and contour. Noise spectral density was reduced in direct proportion to grating area in order to keep the physical signal-to-noise ratio constant. An increase in spatial frequency was thus accompanied with reductions in grating area and noise spectral density similar to those produced by a corresponding increase in viewing distance. In agreement, contrast detection in spatial noise was found to be independent of spatial frequency as long as contrast sensitivity was lower with noise than without. The effect of increasing eccentricity on visual performance can be compensated for by reducing the viewing distance (M-scaling). Hence, without M-scaling the effect of increasing eccentricity is similar to that of increasing viewing distance. In agreement, we found that contrast sensitivity in spatial noise was independent of eccentricity as long as contrast sensitivity was lower with noise than without.

Adult↗
PubMed1996

Does the human visual system implement an ideal observer theory of slant from texture?

Texture information about surface shape can be decomposed into three constituents: compression, density and scaling. Blake, Bülthoff and Sheinberg's (1993, Vision Research, 33, 1723-1737) Ideal Observer theory of slant from texture predicts that the relative contribution of compression and density to the percept of planar surface slant should vary with field of view (FOV). The contribution of compression and density should both increase as FOV increases but statistical analysis shows that the reliability, and hence the expected contribution, of density increases at a greater rate than compression with increasing FOV. Specific predictions are that at FOV < 20 deg compression should be more effective than density, at FOV approximately 20 deg, compression and density should be equally effective, and at FOV > 20 deg, compression should be less effective than density. These predictions were tested by pitting these components of texture against one another. The method used was similar to that described in Frisby and Buckley [1992 In Orban, G. & Nagel H.-H. (Eds) Artificial and biological visual systems. Berlin: Springer]: observers judged binocularly the slant of a large table on to which was projected a texture created using computer graphics to contain various texture component cues to slant. The size of the projected texture patch determined the FOV which was by this means set to either 10, 20 or 30 deg. It was found that compression was the dominant cue irrespective of FOV, even if it was perturbed by noise. Possible reasons for this divergence of human observers from predictions of the Ideal Observer theory of slant from texture are discussed.

Adolescent↗
PubMed1988

Evidence that multiple residues on both the alpha-helices of the class I MHC molecule are simultaneously recognized by the T cell receptor.

Single amino acid substitutions at nine different positions on the H-2Kb molecules from in vitro-mutagenized, immunologically altered, somatic cell variants were correlated with their patterns of recognition by monoclonal antibodies (MAbs) and allogeneic cytotoxic T lymphocyte (CTL) clones. While MAbs were found to detect spatially discrete, domain-specific sites, CTLs interacted simultaneously with multiple residues on the alpha 1 and alpha 2 domains of the Kb molecule. The computer graphic three-dimensional Kb model structure showed that, of the seven CTL-specific residues analyzed, six residues were located on the alpha-helical regions of the two domains. Every CTL clone was found to interact with a distinct pattern of residues composed of a specific subset of the CTL-specific residues.

Amino Acid Sequence↗
PubMedDate not supplied

Telescience at the University of California, Berkeley.

The University of California at Berkeley (UCB) is a member of a university consortium involved in telescience testbed activities under the sponsorship of NASA. Our Telescience Testbed Project consists of three experiments using flight hardware being developed for the Extreme Ultraviolet Explorer project at UCB's Space Sciences Laboratory. The first one is a teleoperation experiment investigating remote instrument control using a computer network such as the Internet. The second experiment is an effort to develop a system for operation of a network of remote workstations allowing coordinated software development, evaluation, and use by widely dispersed groups. The final experiment concerns simulation as a method to facilitate the concurrent development of instrument hardware and support software. We describe our progress in these areas.

Astronomy↗
PubMed1991

A proposed molecular model for the carboxy terminus of HIV-1 gp120 showing structural features consistent with the presence of a T-cell alloepitope.

A computer graphics molecular model of the C terminus of gp120 of HIV has been constructed using predicted secondary structure based on homologies with proteins for which X-ray crystallographic data have been published. The model shows sequences known to be important in CD4 binding in close proximity to regions with a high probability of forming alpha helical and beta strand motifs. The orientation adopted by these domains approximates to the known 3D structure of HLA-A2 alpha 2 chain without constraints based on HLA-A2 as a template being introduced. The model may therefore represent an energetically favourable conformation for a part of gp120 which mimics the binding domain for the T-cell receptor on MHC molecules. Recognition of gp120 as an alloepitope in high affinity association with CD4 would explain many of the sequelae of acquired immune deficiency on HIV infection.

Amino Acid Sequence↗
PubMed1988

Issues and themes in computer aided design for external prosthetics and orthotics.

Computer aided design systems are finding use in prosthetics and orthotics in the production of customized components to match to and support body segments. Such systems consist essentially at present of shape measurement, computer manipulation of shape, and manufacture of the support surface or its mould. General themes of design philosophy, relationship of shape and pressure for body segments, representation and presentation of shape information by computer, surface adjustments, measurements and manufacturing geometry are considered. Aspects of existing systems are presented to highlight issues which may be the subject of future developments.

Computer Graphics↗
PubMed1990

Computer model of an inhomogeneous human torso.

Based on the atlas of sectional human anatomy, a three dimensional computer model of a human torso, including four cavities of the heart (LV, RV, LA, RA), two lobes of the lung and the body surface, and a three dimensional model of the myocardium is introduced. The torso model, with more than 10,000 surface triangles, depicts the structures and appropriate proportions of the internal organs, especially of the heart. Algorithms for the model construction are given in detail and the validity of the models for the purpose of simulation research into the electrocardiogram is discussed.

Algorithms↗
PubMed1990

Three-dimensional structure of a hybrid light chain dimer: protein engineering of a binding cavity.

An attempt was made to engineer a binding site and check its structure by X-ray analysis. Two human light chains (Mcg and Weir), with "variable" domain sequences differing in 36 positions, were hybridized into a heterologous dimer and crystallized in ammonium sulfate by the same procedure used for the trigonal form of the Mcg dimer. The three-dimensional structure of the hybrid was determined at 3.5-A resolution by difference Fourier analysis, interactive model building with computer graphics and crystallographic refinement. In the heterologous dimer, the Weir protein behaved as the structural analog of the heavy chain in an antigen binding fragment, while the Mcg protein assumed the role of the light chain component. The hybrid and the Mcg dimer were closely similar in overall structure, an observation probably correlated with the deliberate cleavage of the intrachain disulfide bond in the variable domain of the Weir protein during the hybridization procedure. Examination of the crystal structure of the hybrid suggested that the cleavage resulted in the relaxation of restraints which might otherwise have interfered with the formation of an Mcg-like dimer. There were six substitutions among the residues lining the binding cavities of the hybrid and Mcg dimer. These substitutions significantly affected the sizes, shapes and binding properties of the two cavities.

Amino Acid Sequence↗
PubMed1981

A lucite plate method for 3-dimensional reconstruction of neuronal populations.

A Lucite plate reconstruction method is described which, when combined with HRP histochemistry, provides an excellent means of visualizing, in 3-dimensional fashion, the functional organization of neuronal populations. Color photomicrographs of representative serial sections were made through the baboon oculomotor nucleus. Each color slide was then projected onto a 9 X 12 in. Lucite plate and the configuration of the nucleus at each representative level drawn to scale on the plates. These plates were then stacked one in front of the other yielding a see-through, 3-dimensional reconstruction of the entire nucleus. Color transparencies of every sixth HRP-processed section were made and the image of each section projected onto the Lucite plates on which the configuration of the oculomotor nucleus was previously outline. Using different colored stars to represent the neurons which supply different oculomotor muscles, the number and location of HRP-positive neurons was then plotted. The end result was an anatomically accurate 3-dimensional reconstruction of the entire labeled population of the oculomotor nucleus including the location of subnuclei that can be viewed from any side or at any angle. With adequate reference points these data can be entered into a computer graphics device, then viewed and manipulated in 3-dimensional fashion.

Animals↗
PubMed1987

Montage: a system for three-dimensional reconstruction by personal computer.

This paper describes a simplified system for serial section three-dimensional (3-D) reconstruction. A set of 9 software programs runs on a standard personal computer and produces camera-ready illustrations suitable for publication. The user enters trace points on a digitizing tablet from sections that have been already aligned. A 3-D view of the reconstructed object is generated which can be displayed with hidden lines removed. Analysis of volume, surface area and autoradiographic grain density are performed automatically. A relational database query language allows display and analysis of a selected subset of the data. The system runs under the UNIX operating system which allows the programs to be easily transported to new hardware or modified for other purposes.

Animals↗
PubMed1995

Object-oriented approach to fast display of electrophysiological data under MS-windows.

Microcomputers provide neuroscientists an alternative to a host of laboratory equipment to record and analyze electrophysiological data. Object-oriented programming tools bring an essential link between custom needs for data acquisition and analysis with general software packages. In this paper, we outline the layout of basic objects that display and manipulate electrophysiological data files. Visual inspection of the recordings is a basic requirement of any data analysis software. We present an approach that allows flexible and fast display of large data sets. This approach involves constructing an intermediate representation of the data in order to lower the number of actual points displayed while preserving the aspect of the data. The second group of objects is related to the management of lists of data files. Typical experiments designed to test the biological activity of pharmacological products include scores of files. Data manipulation and analysis are facilitated by creating multi-document objects that include the names of all experiment files. Implementation steps of both objects are described for an MS-Windows hosted application.

Animals↗
PubMed1989

Structural characterization of kappa II Inc, a new amyloid immunoglobulin.

Light chain Inc, obtained from a patient with amyloid arthropathy, has an Mr of 23,550 and consists of 219 amino acid residues. The complete primary structure of its variable domain has been determined by sequence analysis of the corresponding tryptic peptides, aligned by fragments derived from cyanogen bromide digestion, and by partially sequencing the intact protein. Although closely related to protein of the V kappa II subgroup, light chain Inc differs from its counterpart by the replacement of some invariant residues in its variable domain. By comparing its sequence with that of the nonamyloid kappa II Nim, a different distribution of some polar and apolar amino acid residues through the molecule is evidenced. A computer graphic analysis shows that some of the replaced amino acid residues cannot be readily accommodated in the known three-dimensional structure of the immunoglobulin light chains.

Amino Acid Sequence↗
PubMedDate not supplied

Electrocardiomultigraphimeter using a home computer.

The drop in hardware costs has fostered the widespread use of home-computer systems. Because of this situation, the home computer can be profitably employed in some highly specialized fields. We believe electrocardiographic instrumentation to be one such field. We have built an electrocardiomultigraphimeter (ECXGM), which can be considered as a development of the traditional electrocardiograph that performs some additional functions. Our prototype features vectorcardiography, polar coordinate tracing, automatic measurements between fiducial points selected by the user with a joystick and screen cursor and trace filing by patient on labelled floppy disks. The standard hardware consists of a Commodore 64 console, a monitor, two floppy disk drives and an Epson HI-80 plotter, all of which are readily available. The special hardware consists of an A/D converter, which receives the electrocardiographic signal downstream of the amplifying stage, which is a standard feature of any electrocardiograph. Prototype development mostly involved the software. Difficulties were posed by the limited resources available on home computers, an important point in view of the problem to be tackled. The solutions adopted are based on the use of assembler language and overloading techniques and minimizing the interconnections among the software modules defined in a compactly built program. The result is an instrument with significantly advanced clinico-scientific capabilities as compared to current electrocardiographic instruments. This fact, and the class of the hardware used and special software built, confer originality to this work. The new instrument ought to be especially suitable for the offices of cardiologists who have an interest in such capabilities, and for schools of electrocardiography.

Computer Graphics↗
PubMed1989

The automation of routine calculations and graphing for alkaline filter elution analysis on a computer-controlled liquid scintillation analyzer.

The data calculations and graphing functions for the widely used alkaline filter elution technique have been completely automated. This saves considerable time and increases both efficiency and accuracy by eliminating human error. The automation was accomplished utilizing Lotus 1-2-3 and Lotus Graphwriter II on a Packard Tri-Carb 1900CA liquid scintillation analyzer containing a built-in pico-XTE computer. A batch file is used to control the overall execution of the process. It copies the data stored by the 1900CA into the Lotus subdirectory and invokes Lotus 1-2-3. A Lotus macro automatically imports the data file, performs the calculations, and prints the results. Graphwriter II is then invoked by the batch file and the charts are composed and graphed. Finally, the instrument operating software for the 1900CA is reentered and sample analysis can be resumed for any unanalyzed samples.

Alkalies↗
PubMed1991

A system for compartmental modelling and simulation.

The paper describes a software package for modelling and simulating compartmental systems based upon a generalisation of the equations of compartmental systems. The aim is a versatile package which can be used for rapid model development. Its use is first illustrated in a number of simple classical examples. The power of the software--and more generally the methodology--is demonstrated by showing its application in developing a model-based system for insulin planning for diabetic patients. The software has been written in Pascal and runs on IBM PC and compatible computers.

Algorithms↗