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This paper describes a comprehensive program for translating one or two DNA sequences into amino acid sequences. Written in FORTRAN, it was designed for maximum flexibility of use and easy maintenance, modification and portability. It has full comments throughout.
The algorithm of this program for estimating rate constants of drug absorption is mainly based on the Loo-Riegelman method. In order to improve the flexibility of the program, several options for the users were included: one-, two- as well as three-compartment open models with first-order elimination; two optional methods to calculate the area under the curve, i.e. the simple trapezoidal method and the Lagrange method combined with log-trapezoidal approximation and others. In addition to the estimation of the rate constant of drug absorption, this program can be applied for the design of optimal sampling schemes. For this purpose an extra subroutine for simulating plasma drug concentration-time courses is also included.
Modern information technology offers new opportunities for the storage and manipulation of clinical data within hospital departments. We have designed and put into use a microcomputer system for urology. Its basic structure and main functions are described.
A program is described, which performs automatic uptake, plotting and processing of radio-hippuran renograms obtained from a gamma camera, using an on-line minicomputer system. The program is written in machine language for a ND 50/50 system equipped with a PDP8-L processor, but translation for other nuclear medicine EDP system is easy. Minimum configuration requirements are: (i) 4K processor with TTY; (ii) external clock; (iii) magnetic tape transport; and (iv) 4K + 4K buffered camera interface or additional 8K of storage plus camera interface. Camera interface is computer-controlled and includes two AD-converters, a display unit for buffer storage and interest-areas selection facility. Operation starts recording 40 scintiphotographs of 30 sec each. Then, kidney uptake curves are obtained by subtraction of blood and tissue background, and diagnostic parameters, such as the initial slope, the maximum uptake point and 50% activity time, are computed. The only manual intervention required is the computer-assisted selection of interest-areas of kidneys, and blood and tissue background. Time required is 20 min for uptake of renograms and 5 min for processing and output, thus allowing routine execution of good quality renography, including hardcopy printout of both kidney uptake curves and diagnostic paramerers.
The effect of some steroid hormones and their synthetic analogs--dexamethasone, estradiol, progesterone, testosterone, and cytostatics--on the fibroblast nuclei in a monolayer culture was studied. Their proliferation was studied at the same time by the radioindicator method. The method of computerized morphodensitometry with the use of the apparatus-programmer complex DiaMorf (Russia) showed that the compounds under study induce reorganization of interphase chromatin of fibroblast nuclei over the molecules, the amount of which may be recorded by means of the computer system of analysis of cell and tissue images.
The exponential model for a regulatory enzyme with two ligands (either two substrates or one substrate and an effector) provides an expression for the initial velocity of the catalysed reaction in terms of the fractional saturation of the enzyme by each ligand. This paper describes a program which determines the constants of the model from velocity data, measured with respect to the concentrations of the two ligands, when the corresponding fractional saturations are unknown. Listings of the essential routines, written in BASIC, are provided.
A method has been developed to locate biological complexes in a digitized electron micrograph by matching small windows to a set of reference images using a series of simple criteria. From the reference images, the program calculates parameters such as the radius of gyration, the density sum and variance. It compares them with corresponding values from a moving square window of densities extracted from the micrograph and records the coordinates of successfully matched candidate squares. Since the same particle is detected in a series of overlapping windows, candidates found to be within close proximity are grouped and the best-fitting one is selected from each cluster. The user is required only to select a small stack of boxed reference images and provide a few parameters, such as the particle radius and the minimum acceptable distance between particle centres. Micrograph labels and other areas that do not contain appropriate specimens are automatically ignored in order to minimize false positives. The program has been tested successfully on a variety of different biological structures, from both negatively stained and ice-embedded specimens.
Oligonucleotide microarrays have demonstrated potential for the analysis of gene expression, genotyping, and mutational analysis. Our work focuses primarily on the detection and identification of bacteria based on known short sequences of DNA. Oligo Design, the software described here, automates several design aspects that enable the improved selection of oligonucleotides for use with microarrays for these applications. Two major features of the program are: (i) a tiling algorithm for the design of short overlapping temperature-matched oligonucleotides of variable length, which are useful for the analysis of single nucleotide polymorphisms and (ii) a set of tools for the analysis of multiple alignments of gene families and related short DNA sequences, which allow for the identification of conserved DNA sequences for PCR primer selection and variable DNA sequences for the selection of unique probes for identification. Note that the program does not address the full genome perspective but, instead, is focused on the genetic analysis of short segments of DNA. The program is Internet-enabled and includes a built-in browser and the automated ability to download sequences from GenBank by specifying the GI number. The program also includes several utilities, including audio recital of a DNA sequence (useful for verifying sequences against a written document), a random sequence generator that provides insight into the relationship between melting temperature and GC content, and a PCR calculator.
A method of model discrimination and parameter estimation in enzyme kinetics is proposed. The experimental design and analysis of the model are carried out simultaneously and the stopping rule for experimentation is deduced by the experimenter when the probabilities a posteriori indicate that one model is clearly superior to the rest. A FORTRAN77 program specifically developed for joint designs is given. The method is very powerful, as indicated by its usefulness in the discrimination between models. For example, it has been successfully applied to three cases of enzyme kinetics (a single-substrate Michaelian reaction with product inhibition, a single-substrate complex reaction and a two-substrate reaction). By using this method the most probable model and the estimates of the parameters can be obtained in one experimental session. The FORTRAN77 program is deposited as Supplementary Publication SUP 50134 (19 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1986) 233, 5.
An algorithm is given in order to quantify the similarity of a couple's test profile in the Giessen-Test as concerns that 16 typical test profiles discovered by Brähler and Brähler (1993). The German Giessen-Test is a personality-inventory based on psychoanalysis. The Euklidian distance was chosen as a measuring unit. The identification of that typical test profile to which any couple belongs succeeds very easily, a task which is otherwise only possible with difficulty. However, any allocation is merely for reasons of description, not based on statistical decisions. As a special service, the respective computer programme is placed at everyone's disposal.
We are attempting to adapt the two-dimensional polyacrylamide gel technology to the search for mutations that after the electrophoretic mobility of proteins. These events are expected to have a frequency on the order of 10(-6). To this end, programs that run on the CytocomputerTM are being developed for comparing the pattern of the gel derived from a child's blood sample with those of the gels of corresponding samples from its parents. We anticipate examining thousands of such trios. Programs are described that perform background normalization, noise filtering, spot detection, gel registration, and, finally, compare the father/mother/child gel trios for the presence of unique protein moieties in the child that are consistent with a mutational event.
BACKGROUND: Ruptured abdominal aortic aneurysms (AAAs) are the 13th leading cause of death in the United States. While AAA rupture may occur without significant warning, its risk assessment is generally based on critical values of the maximum AAA diameter (> 5 cm) and AAA-growth rate (> 0.5 cm/year). These criteria may be insufficient for reliable AAA-rupture risk assessment especially when predicting possible rupture of smaller AAAs. METHODS: Based on clinical evidence, eight biomechanical factors with associated weighting coefficients were determined and summed up in terms of a dimensionless, time-dependent severity parameter, SP(t). The most important factor is the maximum wall stress for which a semi-empirical correlation has been developed. RESULTS: The patient-specific SP(t) indicates the risk level of AAA rupture and provides a threshold value when surgical intervention becomes necessary. The severity parameter was validated with four clinical cases and its application is demonstrated for two AAA cases. CONCLUSION: As part of computational AAA-risk assessment and medical management, a patient-specific severity parameter 0 < SP(t) < 1.0 has been developed. The time-dependent, normalized SP(t) depends on eight biomechanical factors, to be obtained via a patient's pressure and AAA-geometry measurements. The resulting program is an easy-to-use tool which allows medical practitioners to make scientific diagnoses, which may save lives and should lead to an improved quality of life.
Educating individuals who seek information about genetic testing for cancer susceptibility is a complex task. Because of the psychological and social risks to patients of being identified as susceptible to a genetic disorder, it is important that education take place before a patient undergoes gene testing. However, it is not known who will provide such education. Since primary care physicians have limited knowledge, time, and confidence with genetic counseling, they are not ideal educators. Genetic counselors are well trained to provide the service, but many patients lack access to them. Other specialists are scare. Interactive computers hold much promise as a supplemental or alternative modality for education. The authors describe their experience with developing an interactive CD-ROM on gene testing and breast cancer, and respond to anticipated criticisms of this technology.
Over-dispersed binary and count data occur frequently in many fields of application. Examples include occurrence of cavities in one or more teeth, and development of tumors in one or more animals of a litter. Methods of statistical analyses that ignore correlation between observations underestimate the standard errors. Consequently, coverage proportions of confidence intervals and significance levels of tests are distorted. To implement methods for the analysis of correlated binary or count data requires a level of sophistication for data analysis such that one can specify a model for over-dispersion and the correlation between observations. To analyze the over-dispersed binary or count data, one could postulate a specific statistical model and use maximum likelihood methods for the estimation of parameters. However, it may be preferable to employ an approach that does not rely on modeling because the true model is hard to know with confidence. Rao and Scott (J.N.K. Rao and A.J. Scott, Biometrics 48 (1992) 577-585)y and Scott and Rao (A.J. Scott and J.N.K. Rao, submitted for publication, 1995) proposed simple methods for analyzing correlated binary and count data exhibiting over-dispersion relative to a binomial and homogeneous Poisson model. This paper presents the SAS program to implement their methods to analyze over-dispersed binary and count data. To demonstrate the implementation and the usefulness of their methods, we present an application involving sensitivity of a monoclonal antibody and the number of mammary tumors developing in rats.
In this paper, we describe our design for advanced drug dosing programs that "reason" using a combination of Bayesian pharmacokinetic modeling and symbolic modeling of patient status and drug response. Our design is similar to the design of the Digitalis Therapy Advisor program, but extends this previous work by incorporating a Bayesian pharmacokinetic model, performing a "meta-level" analysis of drug concentrations to identify sampling errors and changes in pharmacokinetics, and including the results of this analysis in reasoning for dosing and therapeutic monitoring recommendations. The design has been implemented in a program for aminoglycoside antibiotics called Aminoglycoside Therapy Manager. The program is user-friendly and runs on low-cost general-purpose hardware. The initial validation study showed that the program was as accurate in predicting future drug concentrations as an expert using commercial Bayesian forecasting software and that its dosing recommendations were similar to those of an expert.
The paper describes a non-linear multiple regression program to analyse the kinetic parameters Vm and Km as functions of pH, assuming that the activity of particular enzyme forms is determined by the ionisation of two groups, the active form of the enzyme being the half-ionised species.
Contrast medium administration with the contrast medium injector system XD 5500 has proved to be an ideal supplement to the Somatom Plus. The specially developed programs for specific organ regions and differential diagnosis allow an optimization of the diagnosis. The contrast medium administration is thereby standardized and reproducible at any time. Contrast medium enhancement is constant and homogenous with density values of the aorta definitely over 60 Hounsfield units and in most cases over 100 HU. Operation is simple for the proficient investigator and is performed from outside the examination room. The function of a particle filter and an air bubble detector were convincing and certainly ensure the safety of the patient. As a disadvantage, it must be mentioned that the injector carries out program selected even in the event of a perivascular injection. This only occurred three times during our examinations on a total of approximately 5600 patients, without any lasting harm to the patient.
Listings of BASIC and TI-59 programs are included to obtain the HPLC retention factors for beta-lactam antibiotics at given antibiotic pK's, pH, and capacity factor values, which are useful in considering the different chromatographic behaviour of antibiotics as the pH varies.