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At least 145 records · Page 8Linked to original sources
PubMed1979

Computing in the bio-sciences with hypernumbers: a survey.

A survey of higher types of number, with more sophisticated arithmetics than square root -1, is presented. Such powerful embodiments of the number concept are capable of representing entities and operations in the bio-sciences, where phenomena are characteristically more recondite than in naively reductionist, mechanistic physics or chemistry, which today even quantum theory (which itself deploys two kinds of hypernumber) has shown to be inadequate to explain observed phenomena. When the bio-sciences enter the picture, four other kinds of hypernumber are needed, one of them (w) relating also to the frontiers of quantum theory, in terms of the resolution of problems such as the breakdown of parity conservation and of time reversal, and the concomitant elimination of unwanted divergences (infinities). A brief statement of the relevance of each of the additional kinds of hypernumbers in bio-scientific computing is furnished, as an introduction to an approach that is not only viable in terms of digital computing, but is fraught with new implications for bio-scientific research.

Computers↗
PubMed1985

Computer-assisted studies of molecular structure-biological activity relationships.

Computer-assisted methods can be used to investigate the relationships between the molecular structures of compounds and their biological activity. A number of approaches have been reported in the literature, including correlations of activity with substituent constants, conformational analysis and display, quantum mechanical methods, and methods relying on discriminant development and pattern-recognition techniques. Application areas for this technology include drug design, agricultural chemical design, and studies of chemical toxicity and genetic toxicity (mutagenic or carcinogenic potential). These structure-activity methods are introduced, and citations are given. Several current structure-activity relationship (SAR) studies using pattern recognition are presented as examples of typical projects that are feasible with this approach. These include the investigation of a set of 122 antiinflammatory steroids, a study of 153 retinoids for cancer prevention, and a study of chemicals that have been tested in a sister chromatid exchange mutagen screen.

Animals↗
PubMedDate not supplied

Fluorescence photograph of stomach cancer tumors in Wistar rats: computerized analysis.

Detection of cancer in early stages with hematoporphyrin derivatives (HpD) is highly limited by the low fluorescence quantum yield, the strong autofluorescent components of the tissue, and the low contrast between normal and tumoral tissue when fluorescent photographs are taken. A new computer analysis based on digital subtraction of photographs before and after the administration of HpD, allows a total autofluorescence extraction, resulting in a remarkable increase of contrast between tumors and normal tissue. Experiments, with this computerized imaging system in adenocarcinoma of the stomach in Wistar rats, confirms the reliability of this method.

Animals↗
PubMed1983

Quantitative structure-activity relationships employing independent quantum chemical indices.

Derivation of quantitative structure-activity relationships between pharmacological potencies and the electronic structure of molecules may often result in chance correlations, because of the large number of quantum chemical indices. Interrelationships between the parameters complicate the interpretation of the results. Quantum chemical indices of benzylamines, tetracyclines, and 1,4-benzodiazepines were transformed into mutually independent components using principal component analysis. The number of essential components was 3, 4, and 3, respectively. The computational efforts needed to develop multivariate linear regression equations between these components and the pharmacological activities were reduced, since the regression coefficients were not affected by the inclusion of new parameters. In each example, the first component, which accounted for the highest part of the total sample variance in the electronic structure, was the most important one in determining pharmacological activity. It seems that besides the electrostatic forces, charge transfer also affected the inhibitory potencies of benzylamines.

Amines↗
PubMed1989

Molecular determinants of benzodiazepine receptor affinities and anticonvulsant activities.

In vivo convulsant activities profiles and receptor binding studies together with the techniques of theoretical chemistry were used to characterize 15 compounds, from five different chemical families, known to bind to the BDZ receptor. The experimental goals of this study were to determine the affinity of these analogs for this receptor, the effect of gamma-aminobutyric acid on the affinity, and, in a self-consistent manner, the nature of the activity, agonist (anticonvulsant), antagonist, or inverse agonist (proconvulsant, convulsant), elicited by binding to this receptor. To these ends, in vivo studies were made to determine the proconvulsant, convulsant, and anticonvulsant activities and antagonism to anticonvulsant activities of the 15 analogs. Their receptor affinities at 25 degrees were also determined by competitive inhibition of [3H] flunitrazepam and [3H]Ro 15-1788 in the absence and presence of gamma-aminobutyric acid. The goal of the theoretical studies was to identify and calculate molecular properties that modulate these affinities and types of activities and from them to develop a model of receptor recognition and activation that could consistently explain observed behavior and predict new results. Thus, molecular orbital calculations were carried out for all analogs, using semiempirical quantum mechanical methods. In addition to the optimization of structures, a number of electronic properties, such as polarizations, partition coefficients, and proton and electron affinities were computed and examined for their ability to modulate relative affinities and modes of activation of the receptor. From these studies, a model for receptor recognition involving two anchoring hydrogen bond-acceptor sites and for activation involving interaction of the most lipophilic aromatic region of each compound with the receptor was developed, which could systematically account for the three different types of behavior, agonist, antagonist, and inverse agonist, observed for these analogs. Electronic rather than structural properties were found to be the principal modulator of both recognition and activation. A possible mechanism of agonist activation of the receptor involving electron transfer to the agonist, as well as a possible induced conformational change in the receptor, is also suggested by these results. Finally, by complementarity, some steric and electronic characteristics of the receptor binding site could be deduced.

Animals↗
PubMed1990

Stacking interactions between demethylated ellipticines and DNA base pairs--a quantum mechanical study.

A study of the binding behaviour of ellipticine compounds, derivatives of pyrido (4-3b) carbazole, has been carried out to elucidate the relationship between the drug-activity and demethylation of ellipticine. An all valence electron method (CNDO/2) has been employed to compute molecular charge distribution corresponding to various atomic centres of ellipticines and DNA base pairs. Using these atomic charges and dipoles, intermolecular interaction energy has been calculated with the help of second order perturbation theory and multicentered-multipole expansion technique. A comparative analysis of the binding patterns for nor-5,11-dimethyl-ellipticine and nor-11-methyl-ellipticine has been presented vis-a-vis ellipticine. Attempt has been made to correlate interaction energy studies with demethylation of ellipticine and the possible binding patterns.

Base Composition↗
PubMed1984

[Observation of magnetic fields from three directions, and the moving image of the heart in a normal subject].

Three components of the magnetic field generated by the heart over the anterior aspect of the chest in a normal subject were detected using a Superconducting Quantum Interference Device (SQUID) magnetometer with a single detecting coil in a magnetically shielded room. Contour maps and color density maps of the field were prepared by computer. Movies of sequential magnetic fields of the vertical component on the anterior aspect of the chest were made from these maps. In the movies, the maximum moved from the upper central portion to right lower portion in the early stage of ventricular excitation. It moved to the central portion in the middle stage, then returned to the upper central portion in the late stage. Three-dimensional maps of instantaneous magnetic fields over the anterior portion of the chest were derived from maps of three components of the field, and from presumed heart vectors and were drawn as arrows, based on the Viot-Savart theorem. Heart vectors from these field maps corresponded well with septal forces in the early stage, left ventricular free wall force in the middle stage and the basal force in the late stage, respectively. However, large circulating vectors in the form of clockwise rotation in the central portion were also presumed. These circulating heart vectors did not correspond with the sequence of cardiac excitation as reported by Durrer et al. This discrepancy may have been caused by the fact that the vertical electric current could not be expressed from our display for presuming an electric force. Therefore, new displays and interpretations may be required for the expression of heart vectors.

Heart↗
PubMed1990

Solution structure studies of d(AC)4.d(GT)4 via restrained molecular dynamics simulations with NMR constraints derived from two-dimensional NOE and double-quantum-filtered COSY experiments.

The structure of d(AC)4.d(GT)4 is investigated by constrained molecular dynamics simulations. The constraints include proton pair distances derived from 2D NOE intensities by using the iterative relaxation matrix analysis algorithm MARDIGRAS and sugar pucker phases and amplitudes derived from double-quantum-filtered COSY spectra. Molecular dynamics runs on simulated intensity and distance sets as well as the experimental data were carried out to determine the effects of starting structure, distance constraint derivation, energy functions, and experimental errors on the end result. It was found that structural details could not be elucidated within about 1.5-A overall atomic deviation. This limitation is due in part to the accuracy of the experimental data but, more importantly, is attributable to the quantity of experimental constraints available and to imperfections in the force field utilized in the molecular dynamics calculations. Within the limits of the method, some structural characteristics of d(AC)4.d(GT)4 could be elucidated.

Computer Simulation↗
PubMed1982

Cooperative effects in water-biomolecule crystal systems.

Monte Carlo computer simulation techniques have been used to model non-pair-additive (cooperative) effects in the water organization around several biomolecules. Although most models for water assume pair-additive potentials, both quantum mechanical calculations and experimental data indicate that cooperative effects are not negligible in hydrogen-bounded systems such as water. The many-body polarizable electropole (PE) model for water is used to examine the extent and the consequences of this cooperative behavior in several biomolecule hydrate crystals. Increases in the dipole moments of water molecules are predicted in all systems studied so far and can be as much as 50% more than the monomer value of 1.855 debyes. The average value of the individual dipole moments for any one system differs from that of another system and, therefore, should be considered a property of the system and not of the water molecule itself. When this previously calculated average value of the dipole moment for water molecules in a given system is used as a fixed parameter in the simulation, we find differences between this fixed calculation and the original unfixed simulation. An alternative procedure, which allows for a spread in dipole moments and is not dependent on a predetermined average value, has been developed to make simulations of large water-protein systems, including cooperative effects, computationally feasible.

Arginine↗
PubMed1986

Refined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions compatible with more efficient calculations.

A reappraisal has been made of interatomic potential functions for protein structure calculations using the all-atom approximation (except CH, CH2 and CH3, which are treated as "united atoms"). Some key problems are identified and treated. The potential functions are somewhat novel in form and consistent with more efficient and robust folding algorithms. In addition, the potentials are calibrated for for the rigid geometry approximation, since use of fixed standard bond lengths and valence angles (and fixed trans planar peptide groups) reduces the number of conformational variables and saves a great deal of computer time. Though these algorithms demand the use of potential functions of this special type, these functions can be readily implemented in more classical programs for the conformational analysis of proteins. They are calibrated or tested against a large body of experimental data, including extended basis set ab initio, quantum mechanical calculations, nuclear magnetic resonance spectroscopic data and dipole moment data for di- and oligopeptides, characteristic ratio data for random coil homopolypeptides, extensive data from peptide solubility studies, and experimental structures of polyalanine fibres and globular proteins. This paper will form the basis of a further report, which will include investigations of how water might be more realistically represented subject to the computing power available.

Amino Acid Sequence↗
PubMed1987

A simple quantitative analysis system for coronary cineangiograms using a personal computer.

We have developed a simple quantitative analysis system for coronary cineangiograms using a personal computer and a standard projector-video camera system. The selected frame of cinefilm was projected onto the target area of a CCD video camera. To decrease spatial fluctuations due to quantum noise, the digital data were smoothed spatially by applying a moving averaged filter and a median filter. Following the smoothing process, the digital data with gray level were transformed to binary data by quantifying the threshold property of their gray level. To minimize the geometric influence, mainly pincushion effect, a cinefilm of a 1 cm grid was placed against the input screen of the image intensifier to correct the distortion by using 3rd degree polynomials. The accuracy of the contour detection procedure was validated on the basis of phantom models filled with a contrast medium. Despite the potential influence of many radiographic variables on computerized diameter measurements, the overall accuracy was found to be 0.26-0.33 mm over a wide range of clinically relevant artery diameters and radiographic conditions. Using this system we demonstrated one method of examining the effects of acetylcholine and nitroglycerin on coronary artery diameter in adult humans.

Acetylcholine↗
PubMed1973

Spontaneous quantal transmitter release: a statistical analysis and some implications.

1. Miniature end-plate potentials (m.e.p.p.s) were intra- and extracellularly recorded from neuromuscular junctions in rat phrenic nerve-diaphragm preparations in vitro.2. Statistical analysis of the intervals between m.e.p.p.s showed that when the mean number of events in time t was plotted as a function of the variance of the events in time t there was a significant deviation from the straight line relationship expected for a Poisson process. Computer simulation showed that this deviation is explicable if release was generated by the random phasing of the activity of a number of releasing sites.3. There was no indication that release of one quantum influences the probability of release of remaining quanta (drag, clustering). It is suggested that m.e.p.p.s whose amplitude is larger than the mode result from the release of the contents of vesicles whose volume is also supramodal.4. The effects of depolarization of nerve terminals upon the variance-mean curve suggest an increase in the activity of sites rather than an increase in their number.5. Statistical analysis indicated at least 200 +/- 100 (mean +/- 1 S.E.) releasing sites. This number is of the same order as the number of sites of vesicle aggregation and presynaptic membrane density seen in electron micrographs of nerve terminals of this preparation.

Animals↗
PubMed1984

[Digital radiography using a computed tomography instrument in comparison with conventional film-screen images].

Parameters of image quality, comprising spatial resolution and contrast, have been determined in the form of a contrast/detail diagram for a digital system (Topogram) and a film-screen system. The digital system was particularly examined concerning its contrast sensitivity in relation to quantum noise. The clinical implications of the comparison of the systems, where evaluated on chest x-rays of 250 patients. Despite lower image sharpness, the digital method is already able to produce equivalent or better diagnostic results in certain circumstances. The advantages and disadvantages of both systems are discussed in detail.

Breast Neoplasms↗
PubMed1992

Superresolved tomography by convex projections and detector motion.

If the spatial resolution of an image-acquisition system is limited by the size of its component detector elements, then scanning may be required for the signal to be fully sampled. In such cases interpolation methods are normally applied to reproduce a uniformly sampled signal from the set of observations. Alternatively, however, this step can be treated as a restoration problem, in which case the extra measurements made accessible by detector motion may contain sufficient information to superresolve the signal, i.e., to recover information beyond the limit normally associated with finite detector size. We describe the application of this concept to the problem of constructing the projection matrix from a set of noise-corrupted tomographic measurements made by a moving detector array. In particular we focus on the case encountered in many tomographic applications in which the spatial response functions are approximately stationary with object depth. The method of projections onto convex sets is used in conjunction with an underrelaxation scheme to recover the projection matrix, from which the image is reconstructed by the standard filtered backprojection algorithm. Simulation results demonstrate that this approach applied to data acquired by a wobbling positron emission tomography system can substantially enhance the quality of the reconstructed image, even in the presence of high levels of quantum noise. The projection-matrix recovery step can be performed in a matter of seconds; thus the benefits of signal recovery are gained without a significant sacrifice in computation time.

Image Processing, Computer-Assisted↗
PubMed1978

Proem to a quantum leap in audiometric data collection and management.

A revolution began in 1961 when Weiss first mated a minicomputer to an audiometer. Today's technology offers a number of aids to the audiometrist in standardizing stimulus presentation patterns, objectifying and validating responses, computing HTL from a response pattern, computing significant threshold shifts from baseline audiograms, computing percentage binaural hearing impairment for a person, etc. Audiometers can be made which self-calibrate and are fail-safe. Furthermore, a revolution has occurred in replacing an audiogram written record, for example a card, with a system in which the audiometer transfers HTL data directly into computer storage without the possibility of transcription error. A group of turnkey and interlocking terminals allows the audiometric data of any individual serviced to be retrieved and/or updated from any terminal in the system. This paper lists commercial models simulating standard manual audiometry, models computerizing Bekesy audiometry, and some experimental models on yet other principles. Psychometric methods and methods for response validation suitable for audiometry are discussed, and out of many possible suggestions a few are offered for audiometric paradigms which may go beyond simulation of ASHA guidelines and ANSI specifications for manual threshold audiometry in order to take advantage of the power available from the computer as a tool in audiometry. For example, a computer can scan the responses of as many as 32 subjects simultaneously, offer each an adaptive program based on his response, and printout HTL's in conventional audiometric format.

Adolescent↗