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PubMed1986

MINMOD: a computer program to calculate insulin sensitivity and pancreatic responsivity from the frequently sampled intravenous glucose tolerance test.

Insulin sensitivity and pancreatic responsivity are the two main factors controlling glucose tolerance. We have proposed a method for measuring these two factors, using computer analysis of a frequently-sampled intravenous glucose tolerance test (FSIGT). This 'minimal modelling approach' fits two mathematical models with FSIGT glucose and insulin data: one of glucose disappearance and one of insulin kinetics. MINMOD is the computer program which identifies the model parameters for each individual. A nonlinear least squares estimation technique is used, employing a gradient-type of estimation algorithm, and the first derivatives (not known analytically) are computed according to the 'sensitivity approach'. The program yields the parameter estimates and the precision of their estimation. From the model parameters, it is possible to extract four indices: SG, the ability of glucose per se to enhance its own disappearance at basal insulin, SI, the tissue insulin sensitivity index, phi 1, first phase pancreatic responsivity, and phi 2, second phase pancreatic responsivity. These four characteristic parameters have been shown to represent an integrated metabolic portrait of a single individual.

Computer Simulation↗

PubMed1992

SILMUT: a computer program for the identification of regions suitable for silent mutagenesis to introduce restriction enzyme recognition sequences.

We describe a set of IBM-compatible computer programs designed to selectively identify the potential sites for silent mutagenesis within a target DNA sequence. This program is based on a novel strategy of identifying amino acid motifs compatible with each restriction site (BioTechniques 12:382-384, 1991). The programs can be used to identify the suitability for the introduction of any 6-base nucleic acid sequences, such as restriction enzyme sites in cassette mutagenesis strategies. The Table program generates a table of multiple amino acid motifs for each restriction enzyme, obtained by translating each unique recognition sequence in all three reading frames. The Silmut program, which utilizes the features of Table, will further identify the presence of a match between any amino acid motif of each restriction enzyme and the input target sequence. Minor manipulations of the data base files will enable the individual researcher to identify the potential for introduction of any 6-base sequences by silent mutagenesis.

Base Sequence↗

PubMed1992

[Prognostication of chronic Ph+ myeloid leukemia using the PHCML.EXE computer program].

In 193 patients with Ph-positive chronic myeloid leukaemia (CML) Sokal's calculation formulae prognosticating initial risk status were applied, using the computer program PHCML. The aim of this study was to the prognostic reproducibility of these prognostic staging systems in our patient population. Our results confirm the previous conclusions that prognostic discrimination is possible at the time of diagnosis of CML but in our patients with poorer prognosis the stratification seems to be more accurate. No significant advantage was achieved when we prognosticated our patients younger than 46 years using the formula recommended by Sokal et al. specifically for younger patients. We analyzed different criteria when segregating patients in groups with better or poorer prognosis. We found that the coefficient of the patient's relative risk as the boundary, was 1.9 our patient's group contrary to 1.2 in Sokal's studies.

Adolescent↗

PubMed1999

Assessment of quality of life in the younger child: the use of an animated computer program.

BACKGROUND: In the past, quality of life was primarily assessed using objective measurements of the condition of the patient. Today, most quality-of-life measurements include several aspects regarding the patient's opinions and feelings. There has been an extensive development of quality-of-life instruments particularly in adults, including those for people with inflammatory bowel disease (IBD). However, only a few instruments, mostly questionnaires, have been developed for the pediatric population. It has been noted, even in young patients with IBD, that there is reduced self-esteem and more anxiety and depression. Altogether, these are important aspects for early measurement of psychosocial functioning and possibly intervention during the treatment of children with IBD. METHODS: For the current study, an instrument was developed for young children aged 5 years or more in which a computer-based animated program was used to measure quality of life in children with inflammatory bowel disease. The instrument was designed to be similar for boys and girls with no reference to racial identity. In addition, it was culturally acceptable for all Dutch children. The program was in the form of a story of a bear and a clown playing in an attic of an old house where they come across many objects with which they play and where many adventures occur. All 35 questions were interwoven in this story. RESULTS: The animated computer program was well accepted and easily used by 16 children between the ages of 5 and 12 in a small pilot study. In those older than 11 years, another approach is probably necessary, using an age-appropriate animated program. CONCLUSIONS: The computer program can easily be used in an outpatient setting and thus ensures that quality-of-life measurement will become a routine part of a medical visit.

Child↗

PubMed1983

A computer program using a nested analysis of variance in morphometric sampling.

The quality of the sample set is absolutely essential in a morphometric analysis. In this paper a computer program is described which uses a nested analysis of variance in defining the sample. The program denotes those levels of the sampling protocol at which additional sampling should be performed to reduce the variance within the sample set. Furthermore, the program is written for use on a microcomputer which allows it to be used routinely in monitoring a sample set.

Analysis of Variance↗

PubMed1984

A computer program for quality control in the blood gas laboratory.

In blood gas laboratory quality-assurance programs, which are routinely included with materials sold for quality control, raw data are sent to a data processing center for reduction to statistics meaningful to the laboratory's quality-control effort. This data reduction service usually requires a turn-around time of 2 weeks or more. I describe a computer program for the more timely, in-house computation of a laboratory's mean, standard deviation, and coefficient of variation. We have also found this program useful in calculating values for a new lot number of controls during the period between receipt of the controls and receipt of the first set of statistics from the data processing center. Comparing these values to the assayed values in the manufacturer's insert provides timely feedback and augments the manufacturer's professional data reduction service.

Blood Gas Analysis↗

PubMed1999

Z-curve: a computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature.

In order to predict curvature of DNA fragments, we previously developed a computer program for simply calculating a vectorial sum of all individual roll, tilt and twist wedge angles between the nearest base pairs for a given DNA fragment [Lee et al., (1991)]. Now, a new program, called Z-curve, was developed to calculate three-dimensional coordinates of the helical center of each base pair along the DNA, using helical axis deviations from B-form DNA by wedge angles. The output file of the new program was designed to become an input file for a graphics program, Insight II. Thus, we were able to obtain three-dimensional graphic presentations of DNA helical axis curvatures of any length. It visualized spatial details of the DNA curvature, where and how much it curves, and to which direction. It also allowed calculation of the three-dimensional distance between two ends of a DNA fragment, which could provide a measure of its curvature. Here, three DNA fragments, both curved and straight, were subjected to the Z-curve and Insight II programs. The results showed that their curvature details could be visualized to the level of the base pair, whether the DNA fragments contained an oligo(A) track or not. Their estimated curvatures were consistent with the experimental results of permutation gel mobility assay.

Algorithms↗

PubMed1997

Theory and computer programs for calculating solution pH, buffer formula, and buffer capacity for multiple component system at a given ionic strength and temperature.

PURPOSE: A theory and computer programs running on Microsoft Excel for Windows for calculation of solution pH, buffer formula, and buffer capacity at a given ionic strength and temperature were developed. The theory does not limit the category of buffer components, the number of buffer components, or the number of ionizations for each buffer component. The usefulness of the programs was examined. METHODS: The formulas for 7 single component buffer solutions and 2 multiple component buffer solutions composed of citrate, phosphate, Tris, borate, and glycine were calculated. The solution pH values were measured at 25, 40, 55 and 70 degrees C for comparison with the calculated pH values. RESULTS: Of the 108 predictions made, 96 were of pH values with +/- 0.1 pH unit of the measured values, at temperatures ranging from 25 degrees C to 70 degrees C and at ionic strengths ranging from 0.1 M to 0.5 M. CONCLUSIONS: These programs will be useful for identifying appropriate buffer solutions at various temperatures and/or ionic strengths.

Buffers↗

PubMed1989

A computer program to determine diagnostic decision thresholds and likelihood ratios illustrated with aspartate aminotransferase activities after a myocardial infarction.

We describe an enhancement of our earlier computer program which allows calculation of decision thresholds, sensitivity and specificity, and likelihood ratios of negative and positive test results for any chosen value of sensitivity or specificity. The program will also plot continuous receiver operating characteristic and decision level curves which permit examination of the contours created by using all the available data. We illustrate the value of these routines by showing that the sensitivity and specificity of serum aspartate aminotransferase changes during the course of a myocardial infarction.

Aspartate Aminotransferases↗

PubMedDate not supplied

[Description of the computer program used at the Hospital de Bellvitge for monitoring and control in the Parenteral Nutrition Unit].

The purpose of this paper is to introduce a computer program to control the Pharmacy Service Parenteral Nutrition Unit. The program's main feature is a broad menu of possibilities for the clinical monitoring of patients receiving PN. We explain its operation, potential and applications and give some practical examples of some of those applications.

Clinical Pharmacy Information Systems↗

PubMed1996

A computer program for quantification of SH groups generated after reduction of monoclonal antibodies.

Reduction of disulfide bonds to sulfhydryl (SH) groups for direct radiolabeling of antibodies for immunoscintigraphic studies of colorectal and other cancers continues to be of considerable research interest. We have developed a general strategy and a versatile computer program for the quantification of the number of SH per molecule of antibody (Ab) generated after the treatment of monoclonal antibodies (MAbs) with reducing agents such as 2-mercaptoethanol (2-ME), stannous chloride (SnCl2), dithiothreitol (DTT), dithioerythritol (DTE), ascorbic acid (AA), and the like. The program we describe here performs an unweighted least-squares regression analysis of the cysteine standard curve and interpolates the cysteine concentration of the samples. The number of SH groups per molecule of antibody in the 2-mercaptoethanol and in the other reducing agents was calculated from the cysteine standard curve using Ellman's reagent to develop the yellow color. The linear least-squares method fit the standard data with a high degree of accuracy and with the correlation coefficient r of 0.999. A program has been written for the IBM PC compatible computer utilizing a friendly menu to interact with the users. The package allows the user to change parameters of the assay, to calculate regression coefficients slope, intercept and its standard errors, to perform statistical analysis, together with detailed analysis of variance, and to produce an output of the results in a printed format.

Animals↗

PubMed2005

A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program.

Post-translational modification by small ubiquitin-like modifier 1 (SUMO-1) is a highly conserved process from yeast to humans and plays important regulatory roles in many cellular processes. Sumoylation occurs at certain internal lysine residues of target proteins via an isopeptide bond linkage. Unlike ubiquitin whose carboxyl-terminal sequence is RGG, the tripeptide at the carboxyl terminus of SUMO is TGG. The presence of the arginine residue at the carboxyl terminus of ubiquitin allows tryptic digestion of ubiquitin conjugates to yield a signature peptide containing a diglycine remnant attached to the target lysine residue and rapid identification of the ubiquitination site by mass spectrometry. The absence of lysine or arginine residues in the carboxyl terminus of mammalian SUMO makes it difficult to apply this approach to mapping sumoylation sites. We performed Arg scanning mutagenesis by systematically substituting amino acid residues surrounding the diglycine motif and found that a SUMO variant terminated with RGG can be conjugated efficiently to its target protein under normal sumoylation conditions. We developed a Programmed Data Acquisition (PDA) mass spectrometric approach to map target sumoylation sites using this SUMO variant. A web-based computational program designed for efficient identification of the modified peptides is described.

Amino Acid Sequence↗

PubMed2000

Description of a computer program to assess cancer antigen 15.3, carcinoembryonic antigen, and tissue polypeptide antigen information during monitoring of metastatic breast cancer.

It is time-consuming to process and compare the clinical and marker information registered during monitoring of breast cancer patients. To facilitate the assessment, we developed a computer program for interpreting consecutive measurements. The intraindividual biological variation, the analytical precision profile, the cutoff limit, and the detection limit for each marker are entered and stored in the program. The assessment procedure for marker signals considers the analytical and biological variation of the applied markers. The software package contains a database that can store the interpretation of the measurements as evaluation codes together with patient demographics, information about treatment type, dates for treatment periods, control periods, and evaluation codes for clinical activity of disease. The consecutive concentrations for a patient are imported temporarily into the program from outside sources and presented graphically. Marker concentrations to be compared are selected with the computer mouse and the significance of the difference is calculated by the program. The program has an option for calculating the lead time of marker signals vs clinical information. The program facilitates the monitoring of individual breast cancer patients with tumor marker measurements. It may also be implemented in trials investigating the utility of potential new markers in breast cancer as well as in other malignancies.

Antibiotics, Antineoplastic↗

PubMed1989

Incidence density matching with a simple SAS computer program.

Incidence density matching is the method of choice for selecting controls in nested case-control studies, but its use has been limited by its computational complexity. We describe incidence density matching in nested case-control studies with a simple and flexible SAS computer program. The program contains no restrictions on the number of matching factors, although it is usually only necessary to match on age (in incidence density fashion) and on gender. The program is illustrated with data from an historical cohort study of the mortality experience of workers at an asbestos textile manufacturing plant.

Case-Control Studies↗

PubMed1989

AAQUANT: a computer program for quantitative amino acid analysis of proteins and peptides.

Quantitative amino acid analysis is an important tool used in the characterization and structural determination of peptides and proteins. A new computer program, AAQUANT, has been developed specifically to aid researchers in analyzing amino acid composition data. AAQUANT calculates amino acid recoveries, including 95% confidence intervals, following acid hydrolysis of peptides and proteins, and also includes useful routines to locate regions of a specified amino acid composition in known protein sequences, compute amino acid composition reports of known protein sequences, generate proteolytic digestion maps of proteins, and create and edit protein sequence data files. This report describes the AAQUANT routines, and demonstrates the use of the program.

Amino Acid Sequence↗

PubMed1984

Design and analysis of accelerated degradation tests for the stability of biological standards II. A flexible computer program for data analysis.

The accelerated degradation test is commonly used to predict the stability of a biological standard during long-term storage at low temperature. A flexible computer program is described which has been written to analyse degradation test results by the method of maximum likelihood. In addition to predicting the degradation rate at low temperature, the program furnishes estimates of statistical precision and it carried out a test of goodness of fit of the data to the assumed Arrhenius equation model.

Biological Products↗

PubMed1995

Quantitative forensic evaluation of bite marks with the aid of a shape analysis computer program: Part 2; "SCIP" and bite marks in skin and foodstuffs.

In a previous paper 1, we have shown that the use of an interactive shape analysis computer program ("SCIP") and the derivation of a quantitative Similarity Index 1 greatly facilitated the comparison of experimental flat wax bite marks with the dentition of various 'suspects' and the identification of the agent producing the bite. In this study, "SCIP" was employed in an attempt to quantify the comparison, in the form of the Similarity Index (S.I.), between the "offender's" teeth and the bite marks produced on foodstuffs and on human skin, under experimental conditions. The use of "SCIP" and the S.I. is recommended as a routine means of eliminating suspects in bite mark cases. If a reasonable number of reference points have been registered in the bitten material and particularly if the perpetrator has any unusual features in the anterior dentition, the matching of the bite mark with the actual offender is a possibility with this method.

Bites, Human↗

PubMed1977

Computer program for evaluation, physicochemical characterization and optimization of competitive protein binding assays: comparison of four curve-fitting models in peptide and steroid radioimmunoassays.

A modular construced computer program for evaluation, physicochemical characterization and optimization of compititive protein binding assays is put forward. The program allows standard curve fitting by the following models: spline approximation, semi-logarithmic interpolation, logit-log regression and logit-log interpolation. The suitability of these models was studied in a series of routine steroid radioimmunoassays (deoxycorticosterone, deoxycortisol, cortisol and aldosterone) and peptide radioimmunoassays (angiotensin I and angiotensin II). The spline approximation model was used as an approximate reference model. In all assays the logit-log interpolation model exhibited the best correlation with the spline approximation model. In the steroid assays the logit-log regression model was found to be inferior to the other models; in the peptide assays it was equal to or superior to the semi-logarithmic interpolation model. The study on the physicochemical parameters of the antigen-antibody reactions demonstrated that affinity of steroid antibodies was much lower than that of the peptide antibodies. Consequently the degree of antibody saturation at zero dose in the routine peptide assays was greater than 50% and in the routine steroid assays was less than 50%. The relationship of assay characteristics to the applicability of particular curve-fitting models is discussed.

Adrenal Cortex Hormones↗