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At least 1,693 records · Page 94Linked to original sources
PubMed2000

Darwin v. 2.0: an interpreted computer language for the biosciences.

MOTIVATION: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. RESULTS: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs. AVAILABILITY: Darwin is made available for most operating systems free of char ge from the Computational Biochemistry Research Group (CBRG), reachable at http://chrg.inf.ethz.ch. CONTACT: darwin@inf.ethz.ch

Algorithms↗
PubMed1990

Restriction site mapping for three or more enzymes.

Restriction site mapping requires a generator to put forward possible maps and a constraint checker to reject false maps. Ideally these combine to give an algorithm which calculates a sound and complete solution set. Three algorithms for generation are presented and compared. Two decompose a multi-enzyme problem (greater than or equal to 3) into subproblems. The constraint checker is based on separation theory. Some insights into the extent of constraint checking involved in and feasibility of more checking for three or more enzymes are discussed. The trade-off between computation time and the soundness of the solution set is examined.

Algorithms↗
PubMed2005

Applying the stochastic difference equation to DNA conformational transitions: a study of B-Z and B-A DNA transitions.

Despite the existence of numerous models to account for the B-Z DNA transition, experimenters have not yet arrived at a conclusive answer to the structural and dynamical features of the B-Z transition. By applying the stochastic difference equation to simulate the B-Z DNA transition, we have shown that the stretched intermediate model of the B-Z transition is more probable than other B-Z transition models such as the Harvey model. This is accomplished by comparing potential energy profiles of various B-Z DNA transition models and calculating relative probabilities based on the stochastic difference equation with respect to length (SDEL) formalism. The results garnered in this article allow for new approaches in determining the structural transition of B-DNA to Z-DNA experimentally. We have also simulated the B-A DNA transition using the stochastic difference equation. Unlike the B-Z DNA transition, the mechanism for the B-A DNA transition is well established. The variation in the pseudorotation angle during the transition is in good agreement with experimental results. Qualitative features of the simulated B-A transition also agree well with experimental data. The SDEL approach is thus a suitable numerical technique to compute long-time molecular dynamics trajectory for DNA molecules.

DNA↗
PubMed2005

Recalibration methods to enhance information on prevalence rates from large mental health surveys.

Comparisons between self-report and clinical psychiatric measures have revealed considerable disagreement. It is unsafe to consider these measures as directly equivalent, so it would be valuable to have a reliable recalibration of one measure in terms of the other. We evaluated multiple imputation incorporating a Bayesian approach, and a fully Bayesian method, to recalibrate diagnoses from a self-report survey interview in terms of those from a clinical interview with data from a two-phase national household survey for a practical application, and artificial data for simulation studies. The most important factors in obtaining a precise and accurate 'clinical' prevalence estimate from self-report data were (a) good agreement between the two diagnostic measures and (b) a sufficiently large set of calibration data with diagnoses based on both kinds of interview from the same group of subjects. From the case study, calibration data on 612 subjects were sufficient to yield estimates of the total prevalence of anxiety, depression or neurosis with a precision in the region of +/-2%. The limitations of the calibration method demonstrate the need to increase agreement between survey and reference measures by improving lay interviews and their diagnostic algorithms.

Adult↗
PubMed1994

Computation of multifactorial receiver operator and predictive accuracy characteristics.

The computation of the so-called receiver operator characteristics (i.e. functions that assign the maximum specificity to each value of sensitivity) is simple when the characteristics are based on univariate data. On the contrary, multivariate characteristics are difficult to compute, as the complexity of their calculation increases exponentially with the dimension of the data. This paper describes an algorithm for computation of multivariate receiver operator characteristics and derived functions (namely positive and negative predictive characteristics). The algorithm is based on several concepts that increase its computational efficiency. The most important of them is a pre-sorting of the data in each dimension and the division of each dimension into groups in which the positive and negative cases are 100% stratified. The paper also presents a risk stratification study that utilised this algorithm. The study was aimed at identifying those survivors of acute myocardial infarction who are at risk of early death. A cohort of 539 patients was stratified based on time-domain (three variables) and spectral turbulence (six variables) indices of signal-averaged electrocardiogram. The computing times of the algorithm in this study are presented in the text, and the efficiency of the computation is discussed in detail.

Algorithms↗
PubMed1997

A least squares algorithm for estimating epidemiological indices in case-control studies with non-differential misclassification.

A least squares method for determining two integer 4-tuples representing, in a non-differentially misclassified case-control study with exposure factor E and confounder C, the 'true' case and control frequencies respectively, is presented. Each of the four integer frequencies in the 4-tuple related to cases represents the number of patients whose exposure status to the factors E and C is characterized by one of the four possible combinations of occurrence or non-occurrence of E and C, while quite analog remarks hold for the meaning of the elements of the 4-tuple which is related to controls. As an additional product of the relevant algorithm the two groups (alpha, beta) and (gamma, delta) of the 'true' misclassification probabilities referring to exposure E and confounder C respectively, are calculated. The parameters alpha and beta denote the probability that subjects exposed to E are classified as non-exposed and the probability that non-exposed ones will be classified as exposed, respectively. Similarly, delta and gamma stand for the probability that those who have been exposed to C will be classified as non-exposed and the probability that non-exposed subjects are classified as exposed, respectively. The final objective of the method is to use the above determined least squares substitutes of the true case and/or control frequencies in the formulas giving the epidemiological indices, in the hope to compute values for these parameters conforming as far as possible with the real ones. A numerical experiment illustrates such a use of the method and indicates the deviations which may be observed between epidemiological indices when no correction for misclassification is taken into account and those computed by means of the method outlined in this paper.

Algorithms↗
PubMed1999

Dynamics of palmitic acid complexed with rat intestinal fatty acid binding protein.

Dynamics of palmitic acid (PA), isotopically enriched with 13C at the second, seventh, or terminal methyl position, were investigated by 13C NMR. Relaxation measurements were made on PA bound to recombinant rat intestinal fatty acid binding protein (I-FABP) at pH 5.5 and 23 degreesC, and, for comparison, on PA incorporated into 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (MPPC) micelles, and dissolved in methanol. The 13C relaxation data, T1, and steady-state nuclear Overhauser effect (NOE) obtained at two different magnetic fields were interpreted using the model-free approach [Lipari, G., and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559]. The overall rotational correlation time of the fatty acid.protein complex was 2.5 +/- 0.4 ns, which is substantially less than the value expected for the protein itself (>6 ns). Order parameters (S2), which are a measure of the amplitude of the internal motion of individual C-H vectors with respect to the PA molecule, while largest for C-2 and smallest for the methyl carbon, were relatively small (<0.4) in the protein complex. S2 values for given C-H vectors also were smaller for PA in the MPPC micelles and in methanol than in the protein complex. Correlation times reflective of the time scale of the internal motion of the C-H vectors were in all cases <60 ps. These results support the view that the fatty acid is not rigidly anchored within the I-FABP binding pocket, but rather has considerable freedom to move within the pocket.

Animals↗
PubMed2003

[Detection of liver lesions with gadolinium-enhanced VIBE sequence in comparison with SPIO-enhanced MRI].

PURPOSE: Detection of malignant liver lesions with gadolinium-enhanced volumetric interpolated breath-hold examination (VIBE) in comparison with SPIO-enhanced MRT (four different SPIO-enhanced T2w sequences) and histological and imaging follow-up in non-cirrhotic livers at 1.5 T. PATIENTS AND METHODS: Twenty-two patients with suspected focal liver lesions prospectively underwent a gadolinium-enhanced 3D VIBE. Four T2w sequences (HASTE sequence, fast spin-echo-sequence with and without fat-saturation, FLASH 2D gradient echo-sequence) after administration of superparamagnetic iron oxide (SPIO) served as gold standard combined with histological work-up in 17 patients and histological and imaging follow-up in five patients. The image quality was evaluated and the detectability of intrahepatic lesions was rated by the alternative free-response receiver operating characteristic (AFROC) analysis. In addition, the contrast-to-noise ratio was compared. RESULTS: Altogether 49 malignant and 35 benign liver lesions were found. Concerning the image quality, VIBE turned out to be of slightly poorer image quality than the SPIO-enhanced examination with HASTE sequence (4.95 vs. 5.0). The fast spin-echo-sequence without fat-saturation demonstrated the highest contrast-to-noise ratio. All sequences showed a comparable certainty in detecting lesion (area under the curve 0.68-0.73) and identifying malignant liver lesions. CONCLUSION: Despite the small number of patients, VIBE seems to be a comparable, inexpensive and fast method in diagnosing malignant liver lesions.

Adult↗
PubMed2001

A model and application for estimating completeness of registration.

Completeness of population-based registration systems is recognized to be an important aspect of the quality of information in registries which has to be examined. In this paper a model is presented which was used to estimate completeness of reporting of Down syndrome data notified to the Styrian Malformation registry between 1985-92. The model introduced is based on the two-source capture-recapture method allowing for time-varying parameters. For estimation of the parameters a discrete-time filtering algorithm was developed. For the used data set, an estimate of completeness derived from this model was in good agreement with an independent estimator based on demographic data and maternal age-specific Down syndrome risks whereas the usual two-source capture-recapture method gave a higher estimate.

Algorithms↗
PubMed2005

Empirical Eigenfunctions and medial surface dynamics of a human vocal fold.

OBJECTIVES: The purpose of this investigation was to use an excised human larynx to substantiate physical mechanisms of sustained vocal fold oscillation over a variety of phonatory conditions. During sustained, flow-induced oscillation, dynamical data was collected from the medial surface of the vocal fold. The method of Empirical Eigenfunctions was used to analyze the data and to probe physical mechanisms of sustained oscillation. METHODS: Thirty microsutures were mounted on the medial margin of a human vocal fold. Across five distinct phonatory conditions, the vocal fold was set into oscillation and imaged with a high-speed digital imaging system. The position coordinates of the sutures were extracted from the images and converted into physical coordinates. Empirical Eigenfunctions were computed from the time-varying physical coordinates, and mechanisms of sustained oscillation were explored. RESULTS: Using the method of Empirical Eigenfunctions, physical mechanisms of sustained vocal fold oscillation were substantiated. In particular, the essential dynamics of vocal fold vibration were captured by two dominant Empirical Eigenfunctions. The largest Eigenfunction primarily captured the alternating convergent/divergent shape of the medial surface of the vocal fold, while the second largest Eigenfunction primarily captured the lateral vibrations of the vocal fold. CONCLUSIONS: The hemi-larynx setup yielded a view of the medial surface of the vocal folds, revealing the tissue vibrations which produced sound. Through the use of Empirical Eigenfunctions, the underlying modes of vibration were computed, disclosing physical mechanisms of sustained vocal fold oscillation. The investigation substantiated previous theoretical analyses and yielded significant data to help evaluate and refine computational models of vocal fold vibration.

Aged, 80 and over↗
PubMed1988

The Gemini conundrum--a problem of unpairable data: statistical comparison of ratios each derived from two separately estimated parameters.

In biological studies it may be necessary to compare ratios of two separately estimated parameters under test and control conditions. Since it is not always possible technically to obtain paired data for the two parameters, how does one take account of their variances? By extending previously described approximations in a modified t-test we present a BASIC computer program which may be used to solve this problem.

Algorithms↗
PubMed1994

A computer program for non-parametric analysis of incomplete repeated measures from two samples.

RMNP2 is an easy-to-use FORTRAN program for the analysis of repeated measures using the non-parametric two-sample tests of Wei and Lachin (J. Am. Stat. Assoc. 79 (1984) 653-661) and Wei and Johnson (Biometrika 72 (1985) 359-364). The program compares two groups of subjects or experimental units when measurements are obtained at multiple time points, or under multiple conditions, from each subject. A strength of the methodology is that subjects with missing responses at one or more time points can be included in the analysis, under the assumption that the missing value mechanism is independent of the response. In contrast to other methods that require parametric assumptions concerning the distribution of the outcome variable, RMNP2 is applicable when the response variable is continuous but not normally distributed. The program is also useful in the analysis of ordered categorical outcomes when the number of possible responses is too large to permit application of general categorical data methodology. The program can be run on microcomputers, workstations and mainframe computers. Two examples illustrating the use and features of RMNP2 are provided.

Analgesia, Obstetrical↗
PubMed1993

Supplementing tests of statistical significance: variation accounted for. Tutorial.

This tutorial summarizes some of the widely known limitations of tests of statistical significance and then focuses on extracting measures of variation accounted for as a supplement to significance testing. Computation details are presented for research consumers. Some cautions in interpreting these measures are also reviewed.

Data Interpretation, Statistical↗
PubMed2001

Challenges and benefits of assessment, diagnosis, and taxonomy for clinical practice and research.

OBJECTIVE: To outline nosological (top-down) and empirically based (bottom-up) approaches to assessment and taxonomy of psychopathology. METHOD: The two approaches were compared and contrasted to highlight similarities and differences between them. RESULTS AND CONCLUSIONS: To advance services and research, we need to make optimal use of assessment data (i) to identify the distinguishing features of each case, and (ii) to link individual patterns of functioning with taxonomic constructs that can help us apply previously accumulated knowledge to new cases. The time may be ripe for integrating nosological and empirically based approaches. One way to integrate these approaches is to construct empirically based and DSM-oriented scales from the same item pools and to generate age- and gender-specific standard scores and cut-off points from the same normative samples. Integration of the approaches was illustrated with profiles of empirically based and DSM-oriented scales scored from the same item pools and quantified in relation to the same normative samples. To facilitate use by clinicians and researchers under diverse conditions, data are readily obtained on forms completed independently by parents, teachers and others. The data can be quickly scored by hand or computer. To take account of situational and informant variations, the computer software systematically compares data from multiple informants on empirically based and DSM-oriented scales.

Adolescent↗
PubMed2004

Evolutionary dynamics of biological games.

Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

Adaptation, Biological↗
PubMed2006

Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions.

BACKGROUND: Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. RESULTS: The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were determined using several different chip evaluation methods, among which the MAS 5.0 signal algorithm appeared to be most robust. The computed mRNA proportions agreed well with the cell proportions determined by immunohistochemistry except for a minor number of outliers. Genes that were either regulated (i.e. differentially-expressed in tissue and isolated cell fractions) or robustly-expressed in all patients were identified using different test statistics. CONCLUSION: Robust Computational Reconstitution uses an intermediate number of robustly-expressed genes to estimate the relative mRNA proportions. This avoids both the exclusive dependence on the robust expression of individual, highly cell type-specific marker genes and the bias towards an equal distribution upon inclusion of all genes for computation.

Arthritis, Rheumatoid↗