Theory and method of a priori computation of catalytic acts of aspartic and serine proteinases.
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Aspartic Acid Endopeptidases↗
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ART: mathematics and applications. A report on the mathematical foundations and on the applicability to real data of the algebraic reconstruction techniques.
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Computers↗
A multivariate logistic model (MLM) for analyzing binary family data.
We consider modeling the familial correlation between 2 related individuals using a multiple logistic regressive model. It is shown that there is a discrepancy in the marginal probability of the second individual. We investigate the conditions under which this discrepancy can be minimized and show how it can have a direct effect on handling missing values and ascertainment. We derive a functional relationship between the parameters in the model that eliminates this discrepancy, hence solving the problems that can arise in the handling of missing values and ascertainment. Because this methodology fails when there are more than 2 related individuals, we present a new model based on a multivariate logistic distribution. Residual familial correlations can be directly related to the parameters of this model. The likelihood for family data under this model is independent of the order in which the family members enter the calculation. The marginal probabilities can be easily computed.
Data Interpretation, Statistical↗
MathNMR: spin and spatial tensor manipulations in Mathematica.
Spin and spatial tensor manipulations are frequently required to describe the theory of NMR experiments. A Mathematica package is presented here, which provides some of the most common functions for these calculations. Examples are the calculation of matrix representations of operators, commutators, projections, rotations, Redfield matrix elements, matrix decomposition into basis operators, change of basis, coherence filtering, and the manipulation of Hamiltonians. The calculations can be performed for any spin system, containing spins 1/2 and quadrupolar spins alike, subject to computational limitations. The package will be available from upon acceptance of the article.
Magnetic Resonance Spectroscopy↗
Calculations of proton-binding thermodynamics in proteins.
Computational models of proton binding can range from the chemically complex and statistically simple (as in the quantum calculations) to the chemically simple and statistically complex. Much progress has been made in the multiple-site titration problem. Calculations have improved with the inclusion of more flexibility in regard to both the geometry of the proton binding and the larger scale protein motions associated with titration. This article concentrated on the principles of current calculations, but did not attempt to survey their quantitative performance. This is (1) because such comparisons are given in the cited papers and (2) because continued developments in understanding conformational flexibility and interaction energies will be needed to develop robust methods with strong predictive power. Nevertheless, the advances achieved over the past few years should not be underestimated: serious calculations of protonation behavior and its coupling to conformational change can now be confidently pursued against a backdrop of increasing understanding of the strengths and limitations of such models. It is hoped that such theoretical advances will also spur renewed experimental interest in measuring both overall titration curves and individual pKa values or pKa shifts. Exploration of the shapes of individual titration curves (as measured by Hill coefficients and other parameters) would also be useful in assessing the accuracy of computations and in drawing connections to functional behavior.
Hemoglobins↗
Comparison of a new method for computer analysis with standard techniques for measuring survival rates in the rat transverse rectus abdominis musculocutaneous flap.
Many methods have been used to measure experimental flap survival in animal models. These have previously included planimetry, computer programs, and (routinely by the authors) the simple measurement of the weight of a template traced according to the dimensions of a given flap. To test the validity of their method, an alternative technique was developed by the authors' biostatiticians. Initially, in a study of rat transverse rectus abdominis musculocutaneous (TRAM) flaps, all templates were also scanned electronically to form bitmaps. Using commonly available software programs, each bitmap was colorized corresponding to viable and nonviable areas of the flaps. A summation of individual pixels by color could then be used to calculate the percentage of flap survival. A comparison of both methodologies in 64 rat TRAM flaps found that the survival rate was slightly greater overall when a computer analysis had been performed (3.1 +/- 1.7%), but this was not a significant difference (p = 0.479). Thus, the previous standard method was proven reliable, but just as precise calculations are now possible using the convenience of any personal computer.
Animals↗
TETCORR: a computer program to compute smoothed tetrachoric correlation matrices.
Although many programs exist for computing tetrachoric correlations, these programs typically lack one or more of the following features: (1) efficient processing of a large number of variables and computing of a matrix of coefficients; (2) a matrix-smoothing capability; (3) an accurate, reliable computing algorithm; (4) the ability to handle missing data; and (5) nominal cost. TETCORR, which combines an algorithm developed by Brown (1977) with starting values obtained from Divgi (1979a) for more efficient computation, was created to address these and other user concerns.
Algorithms↗
[Choice of the optimal method of numerical analysis in taxonometric study of mollicutes based on electrophoresis of their proteins].
Different procedures of numerical analysis are evaluated to select the most convenient of them for processing the results of mycoplasm protein electrophoresis in polyacrylamide gel (EPAAG) when solving problems of their taxonomy and systematics. This aim is satisfied most of all by the method of Sokal which permits revealing relations at the rank of species, genus and higher taxons. This method as well as the approaches developed by the authors for transforming results of EPAAG of proteins into the numerical form are recommended to improve the systematics of mollicutes with application of computers.
Bacterial Proteins↗
Biostatistical science as a discipline: a look into the future.
The field of biostatistics is enjoying unparalleled developments. Never before have members of our profession been in such demand. Current applications are significantly influencing the direction of research in statistical methodology. It is not clear whether there is a discipline which can be termed 'biostatistics', but we are part of the emergence of a discipline which is termed 'biostatistical science'. It refers to the applications of statistics, probability, computing and mathematics to the life sciences, with the goal of advancing our knowledge of a subject-matter field in this area. This paper discusses the role of computing, some aspects of training, and future directions of biostatistical science. A special role is envisioned for the Biometric Society to be more active in problems associated with developing countries.
Animals↗
The dynamics of HIV spread: a computer simulation model.
Mathematical modeling of the AIDS pandemic has been limited by the difficulty of satisfactorily representing the marked behavioral heterogeneity that characterizes the various populations at risk. We propose an approach which models the spread of infection as a discrete-event simulation using SIMSCRIPT, a powerful simulation language. The program developed provides sufficient flexibility to adequately represent and study a wide range of risk-group dynamics. Using this tool we have verified the May-Anderson prediction relating contact rate heterogeneity to the rate of HIV spread. We have also been able to assess the sensitivity of the model to the particular choice of distribution for contact rates, disease stage durations, and intercontact intervals. It is thought that this approach will permit the empirical testing of hypotheses which do not lend themselves to a purely mathematical treatment.
Acquired Immunodeficiency Syndrome↗
Improved designs for dose escalation studies using pharmacokinetic measurements.
We describe a method for incorporating pharmacokinetic (PK) data into dose escalation clinical trial designs. Doing so can improve the efficiency and accuracy of these studies. The method proposed uses a parametric dose response function that models the probability of response in each person with two effects: the dose of drug administered and an ancillary pharmacokinetic measurements. After treatment and observation of each subject (or group of subjects) for response, one calculates the dose to be administered to the next individual (or group) to yield the target probability of response from the current best estimate of the dose-response curve. This procedure is a variant of the continual reassessment method (CRM). Statistical simulations employing a logistic dose-response model (that is, we model the logit of the response probability as a linear combination of predictors), dose of drug, and the area under the time-concentration curve (AUC) demonstrate that the addition of pharmacokinetic information to the CRM is a practical and useful way to improve both dose-response modelling and the design of dose escalation studies.
Area Under Curve↗
Fractal system--a time domain approach.
A method to analyze the fractal system in the time domain is presented so that the dynamic behavior of the system can be studied. The fractal system is represented by a set of linear time-varying differential equations whose order depends on the order of the system under non-fractal condition. Four different types of fractal system are considered and their solutions in the time domain are presented. These analyses show that the fractal system is dynamically more stable with smooth changes of magnitude and less oscillatory than the non-fractal system. Examples of the physiological system of the conduction pathways in the heart and also the polarization phenomena of noble metal are presented to illustrate the phenomena.
Bundle of His↗
[German Database of Gene Transfer Clinical Trials. Implementation of a central registry of gene transfer clinical trials in Germany].
Continuous biotechnical development and rapid increase in knowledge in the field of research on human gene transfer raise scientific, medical, and ethical considerations in the scientific community and general public. Dissemination of new scientific findings is needed. Gene transfer studies today not only focus on monogenic diseases or life-threatening conditions such as cancer, but also comprise trials for diagnosis and prophylaxis and common medical conditions such as cardiovascular disease. This raises special attention and public discussion and requires even more the systematic monitoring and assessment of clinical trails being conducted. Whereas the number of gene transfer trials in the USA can be clearly specified, this had not been possible in Germany prior to the establishment of the DeReG database. The aim is implementation of a permanent registry comprehending all clinical gene transfer trials being conducted in Germany. Only a complete and updated database serves as a common foundation of knowledge for various groups and facilitates addressing scientific projects.
Clinical Trials as Topic↗
Evaluation of a computer program for teaching laboratory diagnosis of acid-base disorders.
A computer program was evaluated as a tool for increasing the diagnostic acumen of medical housestaff and students in identifying acid-base disorders. The participants were randomized into two groups; group A (N = 20) was encouraged to use the software, and group B (N = 19) was denied access. Pre- and post-tests were administered to delineate the groups' ability to identify correctly an acid-base disorder from laboratory data (electrolytes and arterial blood gas). During 6 weeks, group A used the computer for a mean of 2.83 h (range 1 to 6). The mean +/- SE number of correct answers out of 20 questions, prior to use of the computer program, were 5.7 +/- 0.8 (95% confidence interval 3.9 to 7.5) for group A and 5.2 +/- 0.6 (95% confidence interval 3.9 to 6.5) for group B. These results were not statistically different. Correct responses increased significantly in group A to 10.3 +/- 0.9 (P < 0.0001, 95% confidence interval 8.4 to 12.2) but did not increase significantly in group B. The data suggest that this software program was effective in increasing the diagnostic capabilities of medical housestaff and students for identifying acid-base disorders.
Acid-Base Imbalance↗
Compound action potential and single acoustic nerve fibres activity generation: an equivalent neuron approach.
The peripheral acoustic system can be easily subdivided into three distinct subsystems: a mechanical one (middle ear and basilar membrane), the set of mechanical-to-neural transducers (the inner and outer hair cells) and the neural part. The functional behaviour of the external and middle ear is well known, but the processes concerned with the transduction of mechanical motion into neural activity are still under investigation. Actually the mechanism of transmission of information concerning acoustic stimuli to the central nervous pathways is not clearly known. On the basis of physiological knowledge, a mathematical model reproducing the pattern of activity of the acoustic nerve, in response to the most typical acoustic stimuli, is proposed. This has been simulated on a digital computer.
Action Potentials↗
Use of resampling techniques to estimate the variance of parameters in pharmacological assays when experimental protocols preclude independent replication: an example using Schild regressions.
Estimates of variance in pharmacological assays are usually made by repeating the experiment with different tissues. Biological factors, such as the inability to wash a drug from tissue, may preclude the type of replication that is appropriate for the statistics of interest. For example, in Schild regressions, replication is usually done at each concentration of antagonist. In some test systems, replication of dose-response curves is not possible. For example, some persistent agonists cannot be removed from tissues after exposure, while in other systems, rapid desensitization severely alters tissue sensitivity to repeated challenge with agonist. In this paper, we demonstrate how a statistical resampling method, bootstrapping, can be used to derive estimates of the confidence intervals for pA2, pKB, and slope from Schild plots. This method utilizes the speed of the computer to estimate variance by repeatedly resampling the data. The advantage to this method is that it can be used for many different experimental designs. For a data set obtained from a Schild regression of atenolol antagonism of isoproterenol in the guinea pig left atrium, bootstrap estimates of confidence limits were calculated for cases where dose ratios were derived from the same tissue and randomly paired tissues. These estimates showed good agreement with estimates obtained using conventional analytical methods, thus suggesting that this method may be useful in practice.
Adrenergic beta-Agonists↗
Unveiling synaptic plasticity: a new graphical and analytical approach.
Short-term synaptic plasticity has a key role in information processing in the CNS, whereas memories can be formed through long-lasting changes in synaptic strength. Despite the importance of these phenomena, it remains difficult to determine whether a synaptic modulation is expressed at a presynaptic or postsynaptic site. This article describes a new approach that, in its simplest form, can identify the site of expression by direct graphical means. A more-sophisticated form of the technique can quantify functional synaptic properties and determine which of these properties is altered following a modulation of synaptic strength.
6-Cyano-7-nitroquinoxaline-2,3-dione↗
Diminished recall and the cohort effect of major depression: a simulation study.
Several large-scale epidemiological surveys have reported increasing lifetime rates of psychopathology among recently born cohorts. In the case of Major Depressive Disorder (MDD) younger cohorts tend to manifest higher lifetime prevalences of the condition than older cohorts, at any given age. In some studies, cohort differences are so large that the youngest cohort exceeds the lifetime prevalence of the oldest cohort well before passing through their total period of risk. The data on lifetime prevalences that support the existence of secular differences, however, has typically been collected in cross-sectional studies. Thus, individuals are interviewed at a single point in time and asked to recall all prior psychopathology. Due to poor recall, this design may greatly underestimate earlier experiences. In fact, cohort differences are not limited to MDD; similar results have been reported for a wide range of psychopathology, suggesting methodological problems at data collection. We have conducted a simulation study to examine the magnitude of annual rates of forgetting that could produce the secular trends reported for MDD. Small, but constant annual rates produce striking, 'cohort effect-like' curves. The rates needed to reconstruct the reported effect are compatible with published values for test-retest studies of lifetime recall of MDD. This simulation study does not rule out the existence of a cohort effect in some psychiatric disorders, but stresses the possible limitations of using cross-sectional studies to investigate secular trends.
Adolescent↗