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At least 595 records · Page 33Linked to original sources
PubMed2003

GGUMLINK: a computer program to link parameter estimates of the generalized graded unfolding model from item response theory.

The generalized graded unfolding model (GGUM) is an item response theory (IRT) model that implements symmetric, nonmonotonic, single-peaked item characteristic curves. The GGUM is appropriate for measuring individual differences for a variety of psychological constructs, especially attitudes. Like other IRT models, the location and scale (i.e., the metric) of parameter estimates from the GGUM are data dependent. Therefore, parameter estimates from alternative calibrations will generally not be comparable, even when responses to the same items are analyzed. GGUMLINK is a computer program developed to reexpress parameter estimates from two separate GGUM calibrations in a common metric. In this way, the results from separate calibrations of model parameters can be compared. GGUMLINK can secure a common metric by using one of five methods that have recently been generalized to the GGUM. The GGUMLINK executable program is available free and may be downloaded from http://www.education.umd.edu/EDMS.

Calibration↗
PubMed1988

A computer program allows the separation of a wide range of chromosome sizes by pulsed field gel electrophoresis.

The introduction of Pulsed Field Gel Electrophoresis techniques, which allow the separation of DNA molecules of molecular weights as high as chromosomes of lower eukaryotes, has given a powerful tool to geneticists. The resolution expected from these techniques is dependent on numerous parameters, among them pulse time and field strength. A given set of these parameters allows only a limited range of molecular weights to be resolved. To allow the separation of a broader molecular weight range on a single gel, we designed a computer program, driving a simple switching device, to take care of switching electrodes and power supplies in OFAGE migrations. This program has been designed to be used with any technique calling for periodic switching or inversion of the electric field, and/or variation of the electric field applied during electrophoresis. As an example, we show the results obtained with yeast genera in which chromosome sizes range from 260 to 9,000 kilobase pairs.

Chromosomes↗
PubMed1988

An interactive computer program for the analysis of HLA class II restriction fragment patterns.

There is considerable current interest in the application of Southern blotting and hybridization, with locus-specific HLA class II probes, to HLA typing. The work of several laboratories has shown that, under suitable conditions, restriction fragment patterns that correlate with DR and DQ serology and with DP cellular reactivities can be obtained from homozygous cell lines. Although the identification of class II specificities from restriction fragment patterns is relatively straightforward in homozygotes, the increased complexity of the patterns obtained from heterozygotes makes the interpretation considerably more difficult; this difficulty is compounded by even slight variation between and within gels. We have developed an interactive computer program that allows HLA-DR and DQ typing by the visual matching of restriction fragment pattern data with standard data derived from a panel of well-characterized homozygous cell lines. The program also uses a simple algorithm (after Southern) to estimate the fragment sizes in the unknown track. The screen display can be printed out to give a convenient record of the match; a numerical measure is also given of the goodness of fit of the new data.

Algorithms↗
PubMedDate not supplied

Macroevolution simulated with autonomously replicating computer programs.

The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. The evolutionary outcome of selection acting on novel variation arising over long periods is therefore difficult to predict. The classical problem of this kind is whether 'replaying the tape of life' would invariably lead to the familiar organisms of the modern biota. Here we study the long-term behaviour of populations of autonomously replicating computer programs and find that the same type, introduced into the same simple environment, evolves on any given occasion along a unique trajectory towards one of many well-adapted end points.

Adaptation, Biological↗
PubMed1993

A computer program for non-parametric receiver operating characteristic analysis.

Sensitivity and specificity are key measures of the performance of a given test in detecting a given disorder. For tests yielding numerical scores, sensitivity and specificity usually vary inversely over the range of theoretically possible cutoff scores, complicating the task of quantifying and comparing the diagnostic accuracy of tests. Receiver Operating Characteristic analysis (ROC) approaches this problem by plotting the curve of sensitivity versus 1-specificity for all possible cutoff scores of the test. The area under the ROC curve (AUC) can be used to describe the diagnostic accuracy of the test. Parametric and non-parametric methods exist that allow the calculation of the AUC and the comparison of tests. A disadvantage of parametric formulations is the assumption of a normal or Gaussian distribution of test scores. The present article presents a computer program that utilizes non-parametric formulations that do not require the normal distribution of test scores. The program calculates the sensitivity and specificity of a test at all possible cutoff scores, plots the ROC curve, calculates the AUC, its standard error and 95% confidence limits, and allows the comparison of tests on independent and correlated samples.

Confidence Intervals↗
PubMedDate not supplied

PARSAFE: computer program for safety assessment and optimization of parenteral nutrition formulations based on chemical speciation analysis.

Instability arising from the formation of precipitates and lipid emulsion aggregates is common in parenteral nutrition formulations due to the concentration- and pH-dependent incompatibility of some of the vital ingredients. Previously, the boundaries between stability and instability could only be established through the use of laborious and expensive empirical methods. The predictive technique with the concept of chemical speciation (based on the analysis of many competitive thermodynamic equilibriums) has been adapted for use with parenteral fluids so that these detrimental events may now be avoided. A comprehensive computer program, PARSAFE ((C) 1991. Sponsors interested in this program should contact D.R.W.) has been developed for this purpose. PARSAFE encompasses chemical-speciation techniques and contains a large data base of commonly used intravenous fluid constituents together with the appropriate thermodynamic equilibrium constants describing their interactions so that stability prediction may be readily achieved in hospital pharmacy laboratories. We review the relevant physical chemistry required for the successful implementation of PARSAFE and outline the audit trails involved in the development of the predictive model.

Algorithms↗
PubMed1992

Computer programs to identify and classify amphipathic alpha helical domains.

The amphipathic alpha helix is an often-encountered secondary structural motif in biologically active peptides and proteins. An amphipathic helix is defined as an alpha helix with opposing polar and nonpolar faces oriented along the long axis of the helix. In a recent review article we grouped amphipathic helixes into seven distinct classes (A, H, L, G, K, C, and M) based upon a detailed analysis of their physical-chemical and structural properties (Segrest, J. P., et al. Amphipathic helix motif: classes and properties. Proteins. 1990. 8: 103-117). We have developed five computer programs that automate analysis and classification of potential amphipathic helical domains from primary amino acid sequence data. Here we describe these five programs and illustrate their usefulness by comparing two data sets of sequences representing different amphipathic alpha helical motifs from the exchangeable apolipoproteins. In a companion review article (Segrest, J. P., et al. The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function. J. Lipid Res. 1992. 33: 000-000) these five programs are used to localize and characterize the putative amphipathic helixes in the exchangeable apolipoproteins.

Amino Acid Sequence↗
PubMedDate not supplied

Mini-computer programs for bioequivalence testing of pharmaceutical drug formulations in two-way cross-over studies. Including a survey of current parametric evaluation techniques.

For bioequivalence testing of pharmaceutical formulations of the same drug entity, it is not sufficient to carry out an analysis of variance on the characteristic to be evaluated (e.g., area under the plasma level vs time curve, half-life of elimination, time to plasma-peak level, plasma peak level) and to establish 'classical' 95% confidence intervals for the difference or the ratio of the characteristic concerned. In the past 10 years, several approaches have been proposed as an aid in decision-making: Westlake's 95% intervals, Rodda and Davis' probabilities, Fluehler's posterior probability histograms and the evaluation of the residual variation coefficient. A survey of these approaches is given, together with a discussion of their merits, their differences and their similarities. It is recommended that the final evaluation should be supported by probability density plots, which facilitate easy understanding of the differences and similarities between the various approaches. A bioequivalence study with two types of oral tablets containing bepridil, a new anti-anginal drug, is used as an example. Computer programs are presented, which enable the user to easily apply the various approaches in order to meet requirements of regulatory agencies.

Analysis of Variance↗
PubMed1998

Method and computer program for controlling the family-wise alpha rate in gene association studies involving multiple phenotypes.

Multiple significance testing involving multiple phenotypes is not uncommon in the context of gene association studies but has remained largely unaddressed. If no adjustment is made for the multiple tests conducted, the type I error probability will exceed the nominal (per test) alpha level. Nevertheless, many investigators do not implement such adjustments. This may, in part, be because most available methods for adjusting the alpha rate either: 1) do not take the correlation structure among the variables into account and, therefore, tend to be overly stringent; or 2) do not allow statements to be made about specific variables but only about multivariate composites of variables. In this paper we develop a simulation-based method and computer program that holds the actual alpha rate to the nominal alpha rate but takes the correlation structure into account. We show that this method is more powerful than several common alternative approaches and that this power advantage increases as the number of variables and their intercorrelations increase. The method appears robust to marked non-normality and variance heterogeneity even with unequal numbers of subjects in each group. The fact that gene association studies with biallelic loci will have (at most) three groups (i.e., AA, Aa, aa) implies by the closure principle that, after detection of a significant result for a specific variable, pairwise comparisons for that variable can be conducted without further adjustment of the alpha level.

Analysis of Variance↗
PubMed1995

A computer program for predicting recovery of SDS-protein in the automated HPGE-1000 apparatus.

The commercial automated gel electrophoresis apparatus (HPGE-1000 of LabIntelligence, Menlo Park, CA) allows one to recover the material migrating and visualized as a fluorescent-labeled band by electrophoresis into a collection cup located above the band at a right angle to the orientation of the separation path. The degree of recovery is a function of sample load (peak area), electrophoresis time at constant field strength, the mobility of the material and band width. Neglecting the latter, recovery of several SDS-proteins was measured as a function of the first three parameters. These measurements were used as a data base for a computer program capable of predicting, by interpolation of the experimental values, the time of electrophoresis needed to obtain a specified degree of recovery, or the degree of recovery obtained after a desired time of electrophoresis into the collection cup.

Autoanalysis↗
PubMed1998

Computer programs and datasheets. Initiative on quality control of the German Working-Group on Pediatric Diabetology.

Despite modern treatment regimens, late complications in IDDM patients are still prevalent. Even in developed countries, a significant number of patients do not get the treatment which would be considered optimal based on the present state of medical knowledge. Quality documentation provides a successful approach to unmask deficits and to improve the outcome of care. Structural aspects as well as process and outcome indicators are different in pediatric diabetology compared to the care of adult patients. The German Working Group on Pediatric Diabetology has discussed and finalized a Statement on Quality Control, including specific parameters to be recorded prospectively in all patients. Under the auspices of the German Ministry of Health, a Computer Program designed for inpatient and outpatient care in pediatric diabetology was developed. Among many other features, internal and external quality control according to the guidelines of the German Working Group are facilitated by this approach, as no separate data entry is required. This program is now widely used among pediatric--as well as some adult--diabetes centers in Germany. Regular external comparisons of quality indicators are organized by the Working Group.

Adolescent↗
PubMed1977

HIDACSYS: computer programs for interactive scanning cytophotometry.

A description is given of a combination of three programs developed for computer-assisted stage scanning cytophotometry and cytofluorometry of isolated, close-lying, or touching objects in different types of microscopical preparations. The advantages and limitations of the individual programs are discussed, as well as the local specimen conditions determining the optimal application range of each of the programs. The applicability of these programs was investigated by determination of the integrated absorbance values of Feulgen or gallocyanin-chrome alum stained chicken erythrocytes, human leucocytes, and skin biopsy cells in imprint preparations, as well as of guinea pig peritoneal granulocytes which had been submitted to a simultaneous coupling azo dye incubation for alkaline phosphatase activity.

Alkaline Phosphatase↗
PubMed1993

An expanded nomenclature scheme for labeling peptide fragmentations and its use with 'AMASS', a computer program for generating all possible fragment ion structures from known precursors.

A nomenclature scheme for exhaustively labeling peptide fragment ions is proposed. The scheme is based on IUPAC nomenclature and the previously proposed Roepstorff nomenclature scheme used to label fragment ions in linear peptides. The descriptor used is specifically defined in order to increase the number of peptide and side chain linkages to which the nomenclature scheme can be applied compared with the Roepstorff scheme. The proposed descriptor can be used unambiguously to assign all possible fragments from linear, cyclized, branched, extended (i.e. beta-amino acids) and retro inverso peptides. A significant advantage of the proposed scheme is its simple interface with the currently accepted Roepstorff scheme. This nomenclature scheme is able to label all theoretical fragments generated by the computer program 'AMASS'. AMASS is proposed as a means of systematically calculating the mass of all possible fragment ions from known precursor structures. The program can help determine whether a peptide fragment was derived from an internal sequence fragment or a combination of side chain and backbone cleavages. The program AMASS and the proposed nomenclature scheme are used to illustrate a procedure for identifying fragment ions in the metastable product ion spectrum of somatostatin-14. We envisage that this procedure will be useful for identifying fragment ions which are characteristic of particular structural arrangements in dicyclic and polycyclic peptides.

Amino Acid Sequence↗
PubMed1983

The influence of editing on the performance of a computer program for serial comparison of electrocardiograms.

In this study, three tests of computer ECG analysis function were conducted: 1) interpretation of serial tracings using the single record analysis program, i.e. without serial comparisons; 2) interpretation of the same tracings using a computer-comparison program; and 3) interpretation of these tracings using not only a computer-comparison program but also an editing program which allows amending of each serial record and insertion of any corrections into the computer data base before the next comparison. There was an over-all reduction of 84% in the number of statement changes needed to produce a correct final report by using the combined comparison and editing program. When this combined program was used, 81% of all computer interpretations required no alteration, --a considerable saving of time in analyzing serial electrocardiographic tracings. Serial comparison was required in in 27--45% of all ECG's taken in four medical centers.

Arrhythmias, Cardiac↗
PubMed1998

The PCR-SSP Manager computer program: a tool for maintaining sequence alignments and automatically updating the specificities of PCR-SSP primers and primer mixes.

An emerging problem of molecular typing methods such as PCR amplification using sequence-specific primers (PCR-SSP) is that they frequently require updating as new alleles are constantly being described which potentially affect the specificity of every PCR-SSP reaction. PCR-SSP uses pairs of primers to detect cis-linked polymorphisms and thus each new allele described must be compared to each individual primer pair. Furthermore, sequence homology between the various loci for class I and class II means that, for example, new HLA-A sequences have to be compared with HLA-B and HLA-C primer mixes to rule out cross-locus amplification. We have developed a computer program known as SSP Manager which is capable of aligning HLA class I and class II sequences obtained from Internet-accessible databases such as GenBank. The program then updates all individual primer specificities held in its database before updating the specificities of all primer mixes. Sets of primer mixes can then be combined from the primer mix directory to create PCR-SSP typing trays which are subsequently analysed by the program. A report is generated which stipulates whether all known sequences are amplified and the reason for apparent failure to test for individual alleles, e.g. a lack of relevant sequence information. SSP Manager has the flexibility to cope with unusual sequences (deletions and insertions), primers with internal mismatches and primers with a deliberate mismatch. The program also has many tools for developing new primer mixes, such as the facility to search for novel reactions using Boolean operators. The organisation and operational use of the SSP Manager program is described and its uses are illustrated with an updated allele list for our previously described Phototyping PCR-SSP class I and class II typing set. The SSP Manager is available on request from the authors.

Antisense Elements (Genetics)↗
PubMed1996

Structural analysis and identification of gel-purified proteins, available in the femtomole range, using a novel computer program for peptide sequence assignment, by matrix-assisted laser desorption ionization-reflectron time-of-flight-mass spectrometry.

A procedure is described for structural characterization and identification of proteins, purified by either one- or two-dimensional gel electrophoresis in the low picomole to femtomole range. The purified proteins are first detected in the primary gels by the sensitive reverse staining procedure described by Fernandez-Patron et al. (Anal. Biochem. 1995, 224, 203-211) and consecutively reeluted from combined get pieces and concentrated in the tip of a Pasteur pipette in a secondary gel matrix consisting of either sodium dodecyl sulfate-polyacrylamide or agarose. The concentrated proteins are in-matrix-digested and the resulting peptides are separated by reverse-phase high performance liquid chromatography (HPLC) combined with microsequencing or analyzed by matrix-assisted laser desorption ionization--time of flight--mass spectrometry. Protein identification is based on sequence homology or on the peptide mass pattern. The matching peptide sequences can additionally be verified by matching their measured post-source decay spectra with the calculated fragmentation patterns of the isobaric candidate peptides appearing on the search list. This is done by a computer program referred to as MassFrag, described in this paper. We demonstrate that it is possible to identify protein that are only available in the femtomole range and whose sequences are stored in nonredundant protein databases or nucleotide and expressed sequence tag databases.

Amino Acid Sequence↗
PubMed2006

Benefits and risks of fish consumption Part II. RIBEPEIX, a computer program to optimize the balance between the intake of omega-3 fatty acids and chemical contaminants.

In recent years, and based on the importance of fish as a part of a healthy diet, there has been a notable promotion of fish and seafood consumption. However, a number of recent studies have shown that fish may be a potential source of exposure to chemical pollutants, some of them with well known adverse effects on human health. Recently, we determined in 14 edible marine species the concentrations of eicosapentaenoic acid (EPA) and docosohexaenoic acid (DHA), as well as those of a number of chemical contaminants: Cd, Hg, Pb, polychlorinated dibenzo-p-dioxins and furans, polychlorinated biphenyls, hexachlorobenzene, polycyclic aromatic hydrocarbons, polychlorinated naphthalenes, polybrominated diphenylethers and polychlorinated diphenylethers. To quantitative establish the intake of these pollutants (risks) versus that of EPA+DHA (benefits), we designed a simple computer program, RIBEPEIX. The concentrations of EPA, DHA, and the chemical pollutants were introduced into the program. We here present how RIBEPEIX may be used as an easy tool to optimize fish consumption: most suitable species, frequency of consumption, and size of meals. RIBEPEIX can be useful not only for professionals (cardiologists, general physicians, nutritionists, toxicologists, etc.), but also for the general population. It is available at: .

Animals↗
PubMed1996

A computer program using BALF-analysis results as a diagnostic tool in interstitial lung diseases.

Recently, we showed that it is possible to distinguish between three common interstitial lung diseases (ILD) with similarities in clinical presentation by using a number of selected variables derived from bronchoalveolar lavage fluid (BALF) analysis. The aim of this study was to develop a more general discriminant model, based on polychotomous logistic regression analysis. The 277 patients involved in the study belonged to diagnostic groups with sarcoidosis (n = 193), extrinsic allergic alveolitis (EAA; n = 39), and idiopathic pulmonary fibrosis (IPF; n = 45). The diagnosis had been established independently of the BALF-analysis results. The variables used to discriminate among these patient groups were the yield of recovered BALF, total cell count, and percentages of alveolar macrophages, lymphocytes, neutrophils, and eosinophils. In order to test the predictive power of the logistic model, we used 128 patients having sarcoidosis (n = 91), EAA (n = 5), or IPF (n = 32) from another hospital. In this test set the agreement of predicted with actual diagnostic-group membership was the same as in the learning set in which the logistic model was fitted: 94.5% of the cases were correctly classified. A validated computer program based on the polychotomous logistic regression model can be used to predict the diagnosis for an arbitrary patient with information provided by BALF analysis, and is thought to be of diagnostic value in patients suspected of having ILD.

Adolescent↗