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PubMed1989

A set of Macintosh computer programs for the design and analysis of synthetic genes.

Computer programs that can be used for the design of synthetic genes and that are run on an Apple Macintosh computer are described. These programs determine nucleic acid sequences encoding amino acid sequences. They select DNA sequences based on codon usage as specified by the user, and determine the placement of base changes that can be used to create restriction enzyme sites without altering the amino acid sequence. A new algorithm for finding restriction sites by translating the restriction endonuclease target sequence in all three reading frames and then searching the given peptide or protein amino acid sequence with these short restriction enzyme peptide sequences is described. Examples are given for the creation of synthetic DNA sequences for the bovine prethrombin-2 and ribonuclease A genes.

Algorithms↗
PubMed2001

Computer program supporting the diagnostic accuracy of cellular BALF analysis: a new release.

Recently we developed a validated computer program based on polychotomous logistic regression analysis using bronchoalveolar avage fluid (BALF) results to distinguish between the three most common interstitial lung diseases (ILD): sarcoidosis, idiopathic pulmonary fibrosis (IPF) and extrinsic allergic alveolitis (EAA) or drug-induced pneumonitis. One of the limitations of this program was that it was not useful in discriminating between infectious disorders and non-infectious disorders. Therefore, we added BALF samples obtained from patients with a confirmed bacterial pulmonary infection based on culture results > or = 10(4) cfum l(-1) (group I: n=31) to the study population mentioned above (group II: n=272). Notably, just one variable, i.e. the percentage of polymorphonuclear neutrophils, allowed us to distinguish between infectious and non-infectious disorders. The agreement of predicted with the actual diagnostic group membership was 99.67% (groups I and II). Additionally, 91.2% of the cases with ILD were correctly classified. In conclusion, this updated Windows version 2000 of the validated computer program provides a very reliable prediction of the correct diagnosis for an arbitrary patient with suspected pneumonia or with ILD given information obtained from BALF analysis results, and is thought to improve the diagnostic power of BALF analysis.

Alveolitis, Extrinsic Allergic↗
PubMed1980

[An ALGOL computer program for extensive automatic data processing and evaluation of karyometric studies].

A short survey is given upon ALGOL-computer programs which are ready for use also for a biomathematical treatment of morphometrical findings. Thereafter, the numerical and the nonnumerical steps are described following the caryometrical measurements. These steps are formulated algorithmically, constituting the main parts of a computer program for data transforming and evaluation of caryometrical studies by a data processing system.

Cell Nucleus↗
PubMed2001

Computer program to assist in making decisions about adjuvant therapy for women with early breast cancer.

PURPOSE: The goal of the computer program Adjuvant! is to allow health professionals and their patients with early breast cancer to make more informed decisions about adjuvant therapy. METHODS: Actuarial analysis was used to project outcomes of patients with and without adjuvant therapy based on estimates of prognosis largely derived from Surveillance, Epidemiology, and End-Results data and estimates of the efficacy of adjuvant therapy based on the 1998 overviews of randomized trials of adjuvant therapy. These estimates can be refined using the Prognostic Factor Impact Calculator, which uses a Bayesian method to make adjustments based on relative risks conferred and prevalence of positive test results. RESULTS: From the entries of patient information (age, menopausal status, comorbidity estimate) and tumor staging and characteristics (tumor size, number of positive axillary nodes, estrogen receptor status), baseline prognostic estimates are made. Estimates for the efficacy of endocrine therapy (5 years of tamoxifen) and of polychemotherapy (cyclophosphamide/methotrexate/fluorouracil-like regimens, or anthracycline-based therapy, or therapy based on both an anthracycline and a taxane) can then be used to project outcomes presented in both numerical and graphical formats. Outcomes for overall survival and disease-free survival and the improvement seen in clinical trials, are reasonably modeled by Adjuvant!, although an ideal validation for all patient subsets with all treatment options is not possible. Additional speculative estimates of years of remaining life expectancy and long-term survival curves can also be produced. Help files supply general information about breast cancer. The program's Internet links supply national treatment guidelines, cooperative group trial options, and other related information. CONCLUSION: The computer program Adjuvant! can play practical and educational roles in clinical settings.

Actuarial Analysis↗
PubMed1999

An assessment of the Nam Pehchan computer program for the identification of names of south Asian ethnic origin.

BACKGROUND: An assessment was made of the usefulness and accuracy of a computer program for the identification of the south Asian population through the classification of names on a disease register. METHODS: The computer program, Nam Pehchan, was used to classify names as either south Asian or non south Asian. The results were compared with a reference standard, which combined use of the program with visual inspection. The latter was facilitated by a computer-generated dictionary of common non south Asian names. The data set consisted of 356,555 cases of incident cancer (ICD9: 140-208) registered between 1990 and 1992 by Thames, Trent, West Midlands and Yorkshire cancer registries. RESULTS: Nam Pehchan classified 5506 cases as south Asian. Visual inspection identified 2024 false positives (36.8 per cent of all cases identified as south Asian by Nam Pehchan) and 363 false negatives (9.5 per cent of those identified by the reference standard). Compared with the reference standard, Nam Pehchan had a sensitivity of 90.5 per cent and a positive predictive value of 63.2 per cent. CONCLUSION: The Nam Pehchan program quickly identified a high proportion of the names classified as south Asian by the reference standard, but the high false positive rate means that the program alone is not an adequate single strategy. The time-consuming process of inspection of program negatives for large data sets can be substantially reduced by comparison with dictionaries of common non south Asian names.

Asia↗
PubMed1984

Simplified computer programs for search of homology within nucleotide sequences.

Four new computer programs for search of homology within nucleotide sequences are presented. The main scope of the program design is flexibility, independence of sequence length and the capability to be used by any molecular biologist without any prior computer experience. The programs offer a linear search, a search for maximal identity, an alignment along a given sequence and a search based on homology within the amino acid coding capacity of nucleotide sequences. The language is Fortran V. Copies are available on request.

Amino Acid Sequence↗
PubMed2006

Partitioning reference values of several Gaussian subpopulations with unequal prevalence--a procedure with computer program support.

BACKGROUND: To be able to interpret laboratory values, it is essential to develop population-based reference intervals. A crucial consideration is whether a reference interval should be divided into subpopulations or not, so-called partitioning. There are established methods for deciding whether partitioning should be done or not. However, these methods are only applicable when partitioning into two subpopulations is considered. The primary aim of this study was to suggest a procedure that was also valid for several subpopulations. The method assumes that these subpopulations are Gaussian. Furthermore, a secondary aim was to provide a tailor-made computer program to support calculations. METHODS: The fundamental idea is to partition reference intervals if the proportions of the distributions of the subpopulations outside the combined reference limit deviate from the nominal value of 0.025. This is made possible by finding the combined reference interval using an equation solver algorithm. RESULTS: It was found that an equation solver algorithm could easily identify the combined reference interval when combining two or more subpopulations, even if these subpopulations had unequal prevalences. It was also found that this could be done even if the ratio between samples does not reflect the ratio between prevalences. Using this algorithm, it was possible to study whether the proportion outside the combined reference limits in any of several subpopulations deviated from the nominal 0.025 by such a magnitude that partitioning was recommended. When similar figures to those found in earlier studies with other methods were tested, the procedure showed consistent results with these methods. The procedure was also found to be applicable when several subpopulations were considered. As a practical result of the study, a tailor-made computer program was developed and is now provided over the Internet. CONCLUSIONS: The suggested procedure could serve as an alternative or complement to existing methods. The procedure provides calculations of the combined reference interval, even if sample fractions do not reflect prevalence fractions. The important advantage with the suggested procedure is the generalisation to the situation when several Gaussian subpopulations, possibly with unequal prevalences, are considered. Finally, since a tailor-made computer program is provided, the procedure is simple to use.

Algorithms↗
PubMed1974

Computer program designed to follow fluctuations in microbial populations and its application in a study of Chesapeake Bay microflora.

A computer program has been developed which performs cluster analysis of microorganisms using methods of numerical taxonomy. The program is designed to group related strains, identify the groups by reference to known strains, and calculate a hypothetical median organism (HMO) for each group. The HMO serves to condense taxonomic information and provides a tag for each strain cluster. Every strain in a group is compared with the HMO established for that group. A representative strain for the group is obtained by selection of the strain showing highest similarity to the HMO. New data sets can be compared with data sets of previous analyses. Hence, the occurrence of the same taxonomic groups within separate data sets can be determined. Quantitative or qualitative differences in distribution of taxonomic groups within or between data sets can be measured. The output from the computer is a graphical display, using an on-line plotter; thus, the investigator is provided with visual comparison of data sets. Results obtained from a study applying the computer program in an analysis of taxonomic data obtained for 43 bacterial strains isolated from Chesapeake Bay indicate the usefulness of this method of taxonomic analysis in microbial ecology.

Bacteria↗
PubMed1984

Analys. DNA: a computer program for nucleic acid sequence data processing.

A computer program written in BASIC language is described. The program allows processing and analysis of DNA data and has been designed to be used by persons with little or no computer experience. The operator using different options can search for direct homologies with varying degrees of matching, generate complementary strands, find restriction sites, invert the polarity of the sequence and edit a print-out.

Animals↗
PubMed1996

A computer program for sample size and power calculations in the design of multi-arm and factorial clinical trials with survival time endpoints.

This paper presents a computer program for use in the design of long-term clinical trials with multiple treatment arms in which the primary outcome variables are censored survival times. The treatment arms may be structured as a one-way or multi-way factorial design. It is assumed that patients are entered and randomized to a treatment arm during an accrual period. The patients are then followed for a fixed period during which there may be dropouts. Various distributional assumptions can be used to model the survival times. These include an option in which there is an effect of treatment duly after a lag or delay time. The program then computes the power of various statistical tests of hypotheses concerning treatment differences, interactions and trends. The power computations are "exact" in that they use the Monte Carlo method to obtain Type I and II error probabilities. However the program also outputs the normal approximations for comparison, although they are typically not accurate in these situations. Fisher's LSD method is used to adjust for the multiple comparisons. By comparing the power for various sets of design parameters, such as sample size, numbers of factor levels, patient accrual rate, and length of follow-up, an appropriate design can be constructed. Two examples are provided. The first is a simple one-way layout with multiple treatment arms; the second a two-way factorial design for a proposed large scale cancer chemoprevention trial.

Clinical Trials as Topic↗
PubMed1998

BrainView: a computer program for reconstruction and interactive visualization of 3D data sets.

A computer program, BrainView, is presented which has been developed to reconstruct, visualize, and evaluate three dimensional (3D) biological and medical imaging data, such as images from histological sections, confocal microscopy, or magnetic resonance tomography. The program allows the simultaneous display of three orthogonal sectional planes, i.e. the horizontal, frontal, and sagittal planes, of reconstructed data and to move interactively through the brain to optimally assess the 3D data set. Furthermore, any arbitrary sectioning plane through a data set can be visualized. Implemented warping algorithms allow the geometric normalization of data sets of different animals, modalities or developmental stages as a preprocessing for the comparative evaluation of the data. For a quantitative analysis, data sets can be segmented based on equal grey levels and the corresponding equidensities were calculated. The program works on Apple-Macintosh computers and has a user-friendly graphical interface. The BrainView program is discussed in comparison to related programs.

Animals↗
PubMed1985

SIMP: a computer program in BASIC for nonlinear curve fitting.

A computer program for nonlinear regression analysis is described. The program, SIMP, is written in BASIC for use with a wide range of microcomputers. The simplex algorithm is used to minimize the sum of the squared residuals around the fitted line, and the data can be weighted if required. The program is applicable to a wide range of pharmacological procedures requiring curve fitting, and the analysis of protein-binding data is given as an example.

Animals↗
PubMed2002

A comparison of a lecture and computer program to teach fundamentals of the Draw-a-Person test.

BACKGROUND: Although computer-assisted education has been used to augment education in many areas, there are few studies of programs designed to replace lectures in a medical curriculum. OBJECTIVE: To test whether a thoughtfully designed computer program can replace a standard lecture in a pediatrics curriculum while teaching the subject matter equally well. METHODS: A computer program was developed to teach the Draw-a-Person developmental test using the multimedia-authoring tool Director. One of us (A.E.C.) tested and modified the program several times during its creation after submitting it to several objective evaluators. Thirty-nine students taking the clinical pediatrics rotation were chosen by month to interact with the program or attend the lecture. All students then scored 3 drawings and assigned them a developmental age according to the Draw-a-Person test rules. Students assigned to the computer program also completed a questionnaire evaluating the program in several subjective areas. A t test for 2 samples assuming equal variance was used to analyze the test results. RESULTS: Students receiving the lecture (control group) scored the 3 drawings as 5.43 years (age range, 4.5-8 years), 9.08 years (age range, 7-12 years), and 3.5 years (age range, 2-5 years), respectively. Those using the computer program (study group) scored the 3 drawings as 5.91 years (age range, 5-7 years), 7.68 years (age range, 7-8 years), and 4.34 years (age range, 3-5 years), respectively. The correct answers for the ages were 6, 7.75, and 4.25 years, respectively. A t test for 2 samples assuming equal variance showed that students using the computer program performed better on all 3 drawings (P<.05, P<.02, and P<.002, respectively). CONCLUSIONS: Students using the computer program were more accurate than students attending the lecture when scoring drawings and estimating a developmental age from them. These results support the conclusion that a thoughtfully designed computer program can replace a standard lecture in a pediatrics curriculum.

Attitude to Computers↗
PubMed1985

A BASIC computer program for analysis of the Farnsworth 100-hue test.

A computer program in BASIC has been written which will compute all scores for the Farnsworth 100-hue test, and plot them in the appropriate colour on a polar co-ordinate graph. Hard copy can be obtained on a dot-matrix printer. The program is simple to use, and considerably curtails the analysis time for this test, as well as eliminating possible computational errors.

Color Perception Tests↗
PubMed1986

AUC-RPP: BASIC computer program for compartment model independent pharmacokinetic analysis.

A computer program in BASIC for compartment model independent analysis (AUC-RPP) is presented. The program is based on regression analysis of the terminal phase, the area under the curve and the area under the first moment curve. It is designed for i.v. constant rate infusion, i.v. push and extravascular administration. For the latter route a simple estimate on the absorption rate constant is performed.

Computer Simulation↗
PubMed1986

PROLIF: a computer program for calculation and comparison of cultured lymphocyte proliferation.

A computer program which expedites the quantitation and comparison of cultured lymphocyte proliferative responses is described. The program, entitled PROLIF, is written in VAX BASIC and computes this in vitro activity by collating and reducing radioactive count data obtained from tritiated-thymidine incorporation studies. The report generated by this program includes descriptive statistics such as the mean, percentage change from control and t-test probability. Special program features allow for flexibility in experimental protocol design, user-defined default program options, and automatic result storage on disk for subsequent archiving purposes.

Computers↗