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At least 289 records · Page 16Linked to original sources

PubMed1997

A computer program based on parallel line assay for analysis of skin tests.

A computer program for the analysis of differences or changes in skin sensitivity has been developed. It is based on parallel line assay, and its main features are its ability to conduct a validation process which ensures that the data from skin tests conform to the conditions imposed by the analysis which is carried out (regression, parallelism, etc.), the estimation of the difference or change in skin sensitivity, and the determination of the 95% and 99% confidence intervals of this estimation. This program is capable of managing data from independent groups, as well as paired data, and it may be applied to the comparison of allergen extracts, with the aim of determining their biologic activity, as well as to the analysis of changes in skin sensitivity appearing as a consequence of treatment such as immunotherapy.

Analysis of Variance↗

PubMed1980

'Recipe', a computer program for calculating the nutrient contents of foods.

The paper describes a computer program which calculates the amounts of each of 39 nutrients in a food, presented to it as a list of ingredients. Allowances can be made for losses of water and vitamins on cooking. The recipe can be compared with other foods already listed in the food tables. Other comparisons can also be made in terms of percent recommended daily intake. The new food may be retained as an addition to the food tables.

Adolescent↗

PubMed1979

Computer programs for the assembly of DNA sequences.

A collection of user-interactive computer programs is described which aid in the assembly of DNA sequences. This is achieved by searching for the positions of overlapping common nucleotide sequences within the blocks of sequence obtained as primary data. Such overlapping segments are then melded into one continuous string of nucleotides. Strategies for determining the accuracy of the sequence being analyzed and reducing the error rate resulting from the manual manipulation of sequence data are discussed. Sequences mapping from 97.3 to 100% of the Ad2 virus genome were used to demonstrate the performance of these programs.

Adenoviridae↗

PubMed1976

A computer program for an open two compartment system distinguishing three models.

A digital computer program is described for the estimation of parameters in an open two compartment system distinguishing 3 models. The mathematical function to be fitted to a given set of experimental data is given initial estimates for the parameters of the function. The program uses an iterative procedure to adjust the parameters until the sum of squares of residuals has converged to a minimum. Assuming that a given substance is introduced into compartment 1, the function can be fitted to the set of experiment data of that compartment. A set of experimental data from compartment 2 can also be included in the minimizing function. Two optional weighting functions are presented. From the constants of the two-exponential functions the physiological parameters of the three models are determined. Experimental observations of compartment 1 only allow for calculation of physiological parameters of two of the models.

Computers↗

PubMed1999

Clinical experience with a decision support computer program using Bayes' theorem to diagnose chest pain patients.

A decision support computer program (DSP) was used by the emergency room physician as a diagnostic tool on patients admitted with acute chest pain to guide the referral of these patients either to the Coronary Care Unit (CCU) or general ward. The DSP used Bayes' theorem on 38 anamnestic and clinical variables to classify patients into one of nine diagnoses. During a six months trial period 32 physicians used the DSP to diagnose 493 patients admitted with acute chest pain. The physicians referred the patients to CCU or general ward based on their clinical judgements, the ECG findings and the diagnostic estimates given by the DSP. The program correctly diagnosed 150 (84%) of 178 patients with acute myocardial infarction and 63 of 112 patients with unstable angina. However, acute ischemic heart disease (acute myocardial infarction or unstable angina) was correctly classified by the DSP for 259 (89%) of 290 patients. By using the DSP, the number of patients unnecessarily referred to CCU was reduced from 35% to 19% and the number of patients in need of CCU observation misallocated to general ward was reduced from 13% to 10%. Thus, use of the DSP in the emergency room on easily available anamnestic and clinical variables may improve referrals to the CCU, optimize therapy and resource use.

Adult↗

PubMed1995

Metal search: a computer program that helps design tetrahedral metal-binding sites.

We describe a computer program (Metal Search) that helps design tetrahedrally coordinated metal binding sites in proteins of known structure. The program takes as input the backbone coordinates of a protein and outputs lists of four residues that might form tetrahedral sites if wild-type amino acids were replaced by cysteine or histidine. The program also outputs the side chain dihedral angles of the amino acids and the coordinates of the predicted metal ion. The only function evaluated by Metal Search is the ability of side chains to meet simple geometric criteria for formation of a tetrahedral site, but these criteria are sufficient to produce a manageably small list that can then be evaluated by other means. The program has been used in the introduction of zinc binding sites in the designed four-helix bundle protein alpha 4 and in the B1 domain of streptococcal protein G, and in both cases the tetrahedral coordination of a bound metal ion has been confirmed (Klemba, M., Gardner, K. H., Marino, S., Clarke, N.D., and Regan, L., Nature: Structural Biology 2:368-373, 1995).

Amino Acids↗

PubMed1991

The use of a personal computer program for monitoring wound infections and other complications in orthopedics.

A personal computer program to monitor wound infections and other complications after orthopedic operations was developed, adopting international criteria and definitions. The program offers fixed data entry screens, and a free text editor, and produces user-specified variations of seven screen pages comprising most of the epidemiological data needed for surveillance and complication control. Furthermore a number of special lists can be generated for use in the daily work. For all reports and lists it is possible to generate subpopulations with up to twelve criteria. The program was tested in four danish orthopedic departments and serves well as a simple local tool for the operating staff, offering fast information on complication rates. Results consisting 2,583 operations are presented. The overall rates of complications were 1.8% superficial wound infections, 0.6% deep wound infections, 2.6% other infections and 3.8 other complications. The system is lowcost and an effective method of providing a widespread uniform surveillance of surgical wound infections and other complications in the orthopedic wards.

Adolescent↗

PubMed2004

JECP/PCED--a computer program for simulation of polycrystalline electron diffraction pattern and phase identification.

A computer program for simulation of polycrystalline electron diffraction pattern and phase identification is described. In addition to simulating electron diffraction pattern for a single phase, the program has the ability to model two phases with selected mass ratio. Experimental polycrystalline electron diffraction patterns can be directly compared to simulated patterns for phase identification. Examples of how to use the program are also given.

Journal Article↗

PubMed1997

BBReader: a computer program for the combined use of the BioMagResBank and PDB databases.

A computer program ('BBReader') was developed which performs an inverse search in the BioMagResBank database. Given (cross) peak positions of a protein, the program searches for atoms with matching chemical shifts and suggests possible assignments for user-specified homo- and heteronuclear one- to three-dimensional COSY- and NOESY-type experiments. It can handle 1H, 13C and 15N spectra. Distance information from PDB files can be utilized for filtering possible NOESY cross peak assignments.

Databases, Factual↗

PubMed1992

A personal computer program for large-scale comparisons of related nucleotide sequences.

A personal computer program (COMPSEQ) has been developed which can present an informative listing of pre-aligned exonic nucleotide sequences and of their translations to amino acid sequences as well run triplet-oriented analyses on these sequences in a given reading frame. The sequence listing focuses on the differences between related sequences by suppressing the concordances between them.

Algorithms↗

PubMed1984

A computer program package for storing and retrieving DNA/RNA and protein sequence data.

A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and protein sequence data, respectively. They contain various options to help users in analyzing DNA/RNA and protein sequence data. With program NUCDAT, it is also possible to get access to the EMBO Nucleotide Data Library. This can be achieved by running program COPY to create two data files from the library. Program LITRAT enables users to prepare a scientific literature file convenient for writing scientific articles, and program STRAIN for storing information concerning bacterial and/or plasmid strains.

Amino Acid Sequence↗

PubMed1988

[Determination of antibiotype by a computer program. Epidemiological significance and antibiogram-identification correlates].

By means of a computer program disk diffusion diameter were analysed and an antibiotic susceptibility code (antibiotype) was determined for enterobacteriaceae. This code was a 6 figure-number. Each figure summarised susceptibility (susceptible or resistant) to 3 antibiotics. Thus a 18 serial antibiotics was necessary to calculate the 6 figure-code. At least following antibiotics were chosen for their characteristic behavior: amoxycillin, ticarcillin, amoxycillin + clavulanic acid, cephalothin, ticarcillin + clavulanic acid, cefotaxime, gentamycin, tobramycin, amikacin, nalidixic acid, pefloxacin, ciprofloxacin, fosfomycin and colistin. This code allowed three kind of utilisation: epidemiology by comparing biochemical and susceptibility patterns of same isolated species; laboratory control: a data base with main antibiotic susceptibility patterns for each species allowed a rapid compatibility control of biochemical identification with antibiogram. An inconsistent result lead to a checking of biochemical and susceptibility tests or to record a new code in a file to a further enrichment of the data base. Impression of a message depending of the code for a therapeutic purpose.

Drug Resistance, Microbial↗

PubMed1984

Interactive computer programs for the graphic analysis of nucleotide sequence data.

A group of interactive computer programs have been developed which aid in the collection and graphical analysis of nucleotide and protein sequence data. The programs perform the following basic functions: a) enter, edit, list, and rearrange sequence data; b) permit automatic entry of nucleotide sequence data directly from an autoradiograph into the computer; c) search for restriction sites or other specified patterns and plot a linear or circular restriction map, or print their locations; d) plot base composition; e) analyze homology between sequences by plotting a two-dimensional graphic matrix; and f) aid in plotting predicted secondary structures of RNA molecules.

Amino Acid Sequence↗

PubMed1992

OLIGSCAN: a computer program to assist in the design of PCR primers homologous to multiple DNA sequences.

OLIGSCAN (oligonucleotide scanner) is a computer program for IBM-PC-compatible computers that allows the user to scan up to 200 DNA sequences for homology to oligonucleotide sequences of interest. Once a core sequence of longer than the user-defined minimum length is found, the remainder of the oligonucleotide is compared to the corresponding positions of the larger sequence to identify matches or mismatches flanking the core region. This algorithm results in identification of the longest possible homologous regions first. The program was originally designed to assist in the identification of potential annealing sites for polymerase chain reaction (PCR) primers in the genomic DNA of related strains of viruses. However, it may also be used for more general pattern-identification purposes, including scanning for various sequence motifs of functional importance. We present the analysis of homology to an oligonucleotide primer in 16 complete genomic sequences of the human and simian immunodeficiency viruses.

Algorithms↗

PubMed1991

A compiled computer program for assisting the diagnosis of gastrointestinal helminths of humans and animals.

A compiled computer program for assisting the diagnosis of gastrointestinal helminths in fecal examinations of humans and animals is described. The characteristics of this program which distinguish it from previous similar programs are that it does not require specific software, it does not need a lot of computer memory, and it covers both humans and animals, making it easier to use.

Animals↗

PubMed1979

A computer program for analysis of clotting factor assays and other parallel-line bioassays.

A computer program for the analysis of coagulation factor assays is presented. It can be run on small computers utilizing FORTRAN. It allows considerable flexibility in assay design, accommodates any sample dilution scheme, different numbers of standard and test doses, and missing data points. The report lists the input data for each assay, the analysis of variance for the regression lines, and the potency ratio, as well as statistics that allow estimates of the precision of the potency ratio. It is suggested that interpretation of clotting factor assay results would be facilitated if reports regularly included such information about the reliability of the potency ratio measurements.

Analysis of Variance↗

PubMed1977

A computer program for the analysis of controllability, observability and structural identifiability of biological compartmental systems.

A computer program to check structural identifiability of biological compartmental systems, that is the priori possibility of estamating all unknown system parameters through a multi input-multi output tracer experiment is presented. The procedure, as based only on the adopted compartmental structure and the chosen input-output experiment, is independent of the numerical values of the parameters: therefore the program can be usefully employed before parameter estimation algorithms, to assure that all the unknown parameters evidenced in the model can be estimated from the experimental data. After a short review on compartmental models, controllability observability and structural identifiability are defined and techniques to check them are provided. The digital computer implementation of the whole procedure is discussed in detail. Some typical program runs regarding the application to biological systems are given.

Computers↗

PubMed1995

ORDMKV: a computer program fitting proportional odds model for multi-state Markov process.

ORDMKV is a computer program designed to fit a multi-state discrete-time Markov model for k-stages disease processes having an ordinal structure. The model consists of k transient states representing the increasing severity of the disease process, and the final state can be optionally chosen to be an absorbing state in cases such as death. The ordinal structure of the stages of the disease is modelled by using ordinal response models. Each row of the one-step transition probability matrix is modelled using a proportional odds model based on the cumulative transition probabilities. By using these ordinal response models, the number of parameters used to model the disease process can be reduced significantly not only with respect to a general discrete-time model, but also compared with a parsimonuos continuous-time model. A restricted model can be fitted by assuming that the effect of the covariables in the cumulative probability has common regression coefficients in all stages of the disease process. This assumption, if it holds, reduces the number of regression coefficients associated with each covariate to only one. The regression coefficients of this model are estimated via the method of maximum likelihood, using a quasi-Newton optimization algorithm. When the last state is considered as an absorbing state, it is possible to compute survival curves from the transient states of the process. The program was written in standard FORTRAN 77 and is illustrated using a four-state model to determine factors influencing diabetic retinopathy in young subjects with insulin-dependent diabetes mellitus.

Diabetes Mellitus, Type 1↗