Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data.
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Algorithms↗
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Results for “Mathematical Computing”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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BACTID: a microcomputer implementation of a PASCAL program for bacterial identification based on Bayesean probability.
A computer program (BACTID) is described which enables the identification of bacteria based on a priori data and Bayesean probability testing. The program is not limited to a specific format, has a short execution time, can be easily applied to a variety of situations, and can be run on almost any microcomputer system operating under either 8-bit CP/M or 16-bit MS-DOS or PC-DOS. Additionally, BACTID is not limited to one type of computer (hardware independent); is not limited by size of the computer's random access memory (RAM independent); can recognize various database matrices (format independent); is able to compensate for missing data; and allows for various methods of data entry. The efficacy of the program was checked against a commercially available test system and a 99.34% agreement was obtained. Also, the execution time for a 46 x 21 data matrix was as little as 3.5 seconds. These results show that microcomputer identification programs not only are viable alternatives to code-book registers, but also offer flexibility which is not found in commercial systems.
Bacteria↗
From simple to complex oscillatory behaviour: analysis of bursting in a multiply regulated biochemical system.
We analyze the transition from simple to complex oscillatory behaviour in a three-variable biochemical system that consists of the coupling in series of two autocatalytic enzyme reactions. Complex periodic behaviour occurs in the form of bursting in which clusters of spikes are separated by phases of relative quiescence. The generation of such temporal patterns is investigated by a series of complementary approaches. The dynamics of the system is first cast into two different time-scales, and one of the variables is taken as a slowly-varying parameter influencing the behaviour of the two remaining variables. This analysis shows how complex oscillations develop from simple periodic behaviour and accounts for the existence of various modes of bursting as well as for the dependence of the number of spikes per period on key parameters of the model. We further reduce the number of variables by analyzing bursting by means of one-dimensional return maps obtained from the time evolution of the three-dimensional system. The analysis of a related piecewise linear map allows for a detailed understanding of the complex sequence leading from a bursting pattern with p spikes to a pattern with p + 1 spikes per period. We show that this transition possesses properties of self-similarity associated with the occurrence of more and more complex patterns of bursting. In addition to bursting, period-doubling bifurcations leading to chaos are observed, as in the differential system, when the piecewise-linear map becomes nonlinear.
Catalysis↗
Hands-on to handle-turning man.
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Humans↗
METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.
METAMOD, a BBC microcomputer-based software package for steady-state modelling and control analysis of model metabolic pathways, is described, The package consists of two programs. METADEF allows the user to define the pathway in terms of reactions, rate equations and initial concentrations of metabolites. METACAL uses one of two algorithms to calculate the steady-state concentrations and fluxes. One algorithm uses the current ratio of production and consumption rates of variable metabolites to adjust iteratively their concentrations in such a way that they converge towards the steady state. The other algorithm solves the roots of the system equations by means of a quasi-Newtonian procedure. Control analysis allows the calculation of elasticity, control and response coefficients, by means of finite difference approximation. METAMOD is interactive and easy to use, and suitable for teaching and research purposes.
Algorithms↗
A demonstration of pharmacokinetics and physiological modelling using a microcomputer for data capture and analysis.
We describe a simple and inexpensive demonstration of mass transport and exchange using dye clearance from a hydrodynamic model. A microcomputer was used for data acquisition and storage, non-linear least squares curve fitting, compartmental analysis and parameter estimation. The system is useful for demonstrating the indicator-dilution technique for fluid volume measurement and compartmental analysis in pharmacokinetics.
Algorithms↗
An evaluation of some statistics packages for the BBC microcomputer.
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Computers↗
Microcomputer package for statistical analysis of microbial populations.
We have developed a Pascal system to compare microbial populations from different ecological sites using microcomputers. The values calculated are: the coverage value and its standard error, the minimum similarity and the geometric similarity between two biological samples, and the Lambda test consisting of calculating the ratio of the mean similarity between two subsets by the mean similarity within subsets. This system is written for Apple II, IBM or compatible computers, but it can work for any computer which can use CP/M, if the programs are recompiled for such a system.
Algorithms↗
Matrix algebra routines for the Acorn Archimedes microcomputer: example applications.
A set of matrix algebra routines have been written, as BASICV procedures, for the Acorn Archimedes microcomputer. It is shown that these procedures are executed so quickly that programs, which require matrix algebra computations, can be written in interpreted BASIC. Two example applications, reciprocal averaging and principal components analysis, are demonstrated.
Computers↗
Use of simultaneous curve fitting and a four-parameter logistic model to evaluate the nutritional quality of protein sources at growth rates of rats from maintenance to maximum gain.
A four-parameter logistic model was used to describe the dose-response relationship of rats fed diets containing 12 levels of casein, peanut meal or wheat gluten. The model was capable of accurately describing the entire response curve of rats fed diets containing each of the three protein sources. Incorporation of a technique known as parameter sharing into the curve-fitting process facilitated convergence of the parameter estimates for b (the response of rats fed a protein-free diet) and Rmax (maximum response) for all curves when compared with the values observed experimentally. Parameter sharing also provided a method by which the curves could be differentiated on a statistical basis. These data indicate that the relative value of a protein source is dependent on the concentration of the protein in the diet. The application of nonlinear models combined with parameter sharing provides a technique by which protein values can be evaluated at levels of animal response from maintenance to maximum growth.
Animals↗
Cognitive remediation in pediatric head injury: a case study.
Little work has been done in delineating cognitive remediation approaches for pediatric survivors of head injury. The use of a cognitive remediation approach is described in a case study of a 16-year-old male, who was 1 1/2 years post severe traumatic brain injury. Specific techniques and treatment course are outlined to demonstrate the model offered as one meeting the unique needs of the pediatric survivor. This model emphasizes a behavioral, individually tailored approach with clear delineation of a functional academic skill goal of competence in mathematical computation. Results indicate accomplishment of goals and some generalization of skills obtained to a math domain that was not the major focus of the remediation attempts.
Achievement↗
Electron dose-rate conversion factors for external exposure of the skin from uniformly deposited activity on the body surface.
Dose-rate conversion factors have been calculated for external exposure of the skin from electrons emitted by sources that are deposited uniformly on the body surface. The dose-rate factors are obtained from electron scaled point kernels developed by Berger (Be71; Be73; Be74). The dose-rate factors are calculated at depths of 4, 8, and 40 mg cm-2 below the body surface as recommended by Whitton (Wh73), and at a depth of 7 mg cm-2 as recommended in ICRP Publication 26 (ICRP77). The dependence of the dose-rate factors at selected depths on the energy of the emitted electrons is displayed. The dose-rate factors for selected radionuclides of potential importance in radiological assessments are tabulated.
Beta Particles↗
The realization of a pulsatile implantable impeller pump with low hemolysis.
A pulsatile implantable impeller pump with low hemolysis was developed without markedly increasing the complexity of the system compared with the nonpulsatile pump. The key to the question is to design a three-dimensional impeller with twisted vanes, compacted by an axial helical spiral and a radial logarithmic spiral so as to reduce the turbulent shear in the pump as the impeller changes its rotations per minute periodically to generate a physiologic pulsatile flow. Both mathematic computation of velocity distribution in the impeller and geometric illustration of the velocity triangle at the top of the vane have demonstrated that the peripheral velocity variation of blood cells in a twisted impeller will be less than that in an untwisted impeller. Thus, the main mechanical factor of hemolysis in the impeller pump, namely, the turbulent shear, should be reduced because it is proportional to the product of velocity variations measured in two perpendicular directions. In the in vitro experiments, the pump delivered 4 L/min mean flow at 100 mm Hg mean pressure (pulsed between 80-120 mm Hg) for more than 3 h in a circulatory model containing 700 ml of fresh citrated porcine blood. Every half hour, the free hemoglobin level in the plasma was tested, and the resulting index of hemolysis was about 0.020, slightly more than that of a nonpulsatile impeller pump developed in Shanghai. To compare hemolysis, the index of hemolysis of this pump is about 1/6 of that of the self-made diaphragm pump and 1/13 of that of the Polystan Pulsatile Pump.(ABSTRACT TRUNCATED AT 250 WORDS)
Animals↗
Dynamic oscillations in the membrane potential of pancreatic islet cells.
Glucose and other metabolizable sugars which elicit insulin release from the beta-cell of the pancreatic islet induce repetitive oscillations in the beta-cell transmembrane potential. Upon each phasic depolarization are superimposed rapid fluctuations in potentials, i.e. 'action potentials' or 'spikes' which occur as bursts of electrical activity; the duration and frequency of each burst is a function of glucose concentration. These established electrophysiological features of glucose-islet cell interaction are described in detail together with a consideration of their possible molecular and ionic basis. Based on these observations, a dynamic mathematical computer model of the beta-cell membrane electrical behaviour is presented which utilizes the Goldman equation extended to include divalent ions. The model illustrates how the ionic mechanisms deduced from experimental observations can account for the electrical patterns produced by the beta-cells in the presence of D-glucose; it also allows systematic changes to be made in a number of state variables in order to assess their relative importance and possible contribution to the integrated processes actually observed. Finally, distinction is made between aspects of the model which are well supported by experimental results and those areas which require further analysis.
Animals↗
Large language models in bioinformatics: a comprehensive survey.
The emergence of foundation models with trillion-level parameters has redefined the landscape of artificial intelligence. Various fields are developing their own large-scale models, which can solve many problems within the field and improve work efficiency. Biological large-scale models are a cross-disciplinary research field that combines mathematics, computer science, and biology, aiming to simulate and understand the structure, function, and dynamic changes of biological systems through the establishment of complex computational models. This field covers multiple levels such as biological pathways, population dynamics, protein folding, etc., providing us with tools for deep exploration of the mysteries of life and applications in medicine, ecology, and other fields. This article reviews the background and research status of biological large-scale models, and discusses future directions. Large language models (LLMs) and other large-scale foundation models have rapidly advanced in recent years, enabling powerful representation learning and generation across text, sequences, and multimodal data. In bioinformatics and biomedicine, these models are increasingly used to analyze genomic sequences, infer protein properties and structures, support drug discovery, and integrate heterogeneous biomedical evidence. This survey reviews the basic principles of LLMs and summarizes representative applications in (i) gene and genome sequence analysis, (ii) protein structure and function prediction, and (iii) drug design, including virtual screening and personalized medicine. We also discuss emerging multi-model modeling approaches, as well as key challenges such as data quality and privacy, interpretability, generalization to new organisms and tasks, and responsible deployment in health-related settings. Finally, we outline future directions for developing reliable, scalable, and explainable bioinformatics foundation models.
bioinformatics↗
On some two-way barriers between models and mechanisms.
A number of recent as well as classic ideas suggest that there are constraints and limits on the explanatory role that computational, mathematical, and neural net models of visual and other cognitive processes can play that have not been generally appreciated. These ideas come from mathematics, automata theory, chaos theory, thermodynamics, neurophysiology, and psychology. Collectively, these ideas suggest that the neural or cognitive mechanisms underlying many kinds of formal models are untestable and unverifiable. Models may be good descriptions of perceptual and other cognitive processes, but they cannot in principle be reductive explanations nor can we use them to predict behavior at the molar level from what we know of the neural primitives. This discussion is an effort to clarify the appropriate meanings of these models, not to dissuade workers from forging ahead in the modeling endeavor, which I acknowledge is progressing and is making possible our increasingly deep appreciation of plausible and interesting cognitive processes.
Brain↗
[HLA immunogenetic markers in predicting therapeutic resistance in paranoid schizophrenia].
A study was made of the incidence of HLA histocompatibility antigens of A, B and C loci in 100 male patients suffering from paranoid continuous schizophrenia associated with hallucinatory paranoid symptomatology during the formation in them of therapeutic resistance. In accordance with the clinico-pathogenetic philosophy, 2 groups of resistant patients were formed: an "endogenous" one (because of rapid progression) and a "pharmacogenous" one (secondary, formed by the mechanisms of "adaptation" to neuroleptics). In addition, a group of "nonresistant" patients (a reference one) was also distinguished. The data were compared to those obtained in normal subjects (50 men) and to those derived within the distinguished groups, employing mathematic computation of the risk coefficient. It has been shown that in contrast to the group of normal subjects, the general group of patients suffering from paranoid schizophrenia manifested the accumulation of the HLA antigens A2, A9, W7 and B15. The accumulation of the HLA antigens A2 and A11 was characteristic of the patients suffering from "endogenous" resistance, which distinguished those patients from normal subjects, from "nonresistant" patients and those with "pharmacogenous" resistance. The HLA phenotype A2,11 can be regarded as a potential marker of progression (risk grades 9.8). Besides, it has been demonstrated that the HLA antigens B7 may attest to risk of tolerance to psychopharmacotherapy and formation of "pharmacogenous" resistance (risk grades 4.3).
Adult↗
An instrument to monitor physiological and environmental parameters associated with heat stress on an ambulatory subject.
This paper outlines the development and construction of an instrument for use on an ambulatory subject which monitors selected physiological and environmental parameters that are a reflection of the degree of physiological strain associated with heat stress. The resulting instrument is rugged, reliable, and uses existing practical technology for in-the-field ambulatory monitoring, and provides minimal restriction to subject movement. The physiological parameters monitored (heart rate and skin temperature) were selected following examination of systemic, skin, and psychoneurotic heat disorders, with the environmental parameters (wind velocity, ambient temperature and relative humidity) based on existing heat stress indices' correlation with physiological parameters. A microprocessor is utilized for data acquisition, mathematical computation and long term storage, and software for downloading the data to a large mainframe computer is provided. Following calibration of the transduction circuits, the instrument was assembled and tested. Improvements are required to obtain the reliability originally envisaged. Additional field trials would see the collection of data to establish criteria to determine the values of the parameters monitored enabling prediction of the onset of heat stress in hot, humid environments.
Ambulatory Care↗