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At least 163 records · Page 9Linked to original sources
PubMed1992

Computer methods in child language research: four principles for the use of archived data.

With the increasing use of computers in language research, there is a need for caution concerning several new issues of data accountability. This paper presents four principles for archive-based language research: Maximum Readability and Minimum Bias; Consistent Encoding for exhaustive computer search; Systematic Contrastiveness; and Data Comparability in elicitation, transcription and coding. These and related principles are illustrated by examples from existing computer archives, and strategies are suggested for minimizing detrimental effects of violations. Finally, the paper describes some implications of the principles for properties of a field-wide and international standard of transcription of language data.

Archives↗
PubMed2002

Progress in computational methods for the prediction of ADMET properties.

This review surveys recent progress in the development and application of computational techniques for the prediction of absorption, distribution, metabolism, elimination and toxicity (ADMET) properties, including intestinal permeability, blood-brain barrier penetration, active transport/efflux, aqueous solubility, metabolism and toxicity. While much effort continues to be expended in this field with some success on existing datasets, perhaps the most pressing need at this time is for larger, high-quality sets of experimental data to provide a sound basis for model building.

Absorption↗
PubMed2000

Fluctuations of spherical waves in a turbulent atmosphere: effect of the axisymmetric approximation in computational methods.

The validity of the axisymmetric parabolic-equation (PE) method for line-of-sight sound propagation in a turbulent atmosphere is investigated. The axisymmetric PE method is a finite-difference method for solving a 2D parabolic wave equation, which follows from the 3D wave equation by the assumption of axial symmetry around the vertical axis through the source. It is found that this axisymmetric approximation has a considerable spurious effect on the fluctuations of the sound field. This is concluded from analytical expressions for the log-amplitude and phase variances, derived both for isotropic turbulence and for axisymmetric turbulence. The expressions for axisymmetric turbulence are compared with the results of numerical computations with the PE method.

Acoustics↗
PubMed1991

Computational method for the design of enzymes with altered substrate specificity.

A combination of enzyme kinetics and X-ray crystallographic analysis of site-specific mutants has been used to probe the determinants of substrate specificity for the enzyme alpha-lytic protease. We now present a generalized model for understanding the effects of mutagenesis on enzyme substrate specificity. This algorithm uses a library of side-chain rotamers to sample conformation space within the binding site for the enzyme-substrate complex. The free energy of each conformation is evaluated with a standard molecular mechanics force field, modified to include a solvation energy term. This rapid energy calculation based on coarse conformation sampling quite accurately predicts the relative catalytic efficiency of over 40 different alpha-lytic protease-substrate combinations. Unlike other computational approaches, with this method it is feasible to evaluate all possible mutations within the binding site. Using this algorithm, we have successfully designed a protease that is both highly active and selective for a non-natural substrate. These encouraging results indicate that it is possible to design altered enzymes solely on the basis of empirical energy calculations.

Algorithms↗
PubMed2000

Structural analysis of transition metal beta-X substituent interactions. Toward the use of soft computing methods for catalyst modeling

Fuzzy logic and neural network techniques are used to classify intramolecular interactions between transition metals (M) and beta-X substituents in the following structural motif (LnMC(alpha)(A1)(A2)-C(beta)(B1)(B2)X). These interactions are relevant to the direct polymerization of functionalized olefins by Ziegler-Natta (ZN) catalysis. The efficiency and effectiveness of different soft computing techniques are compared. These methods give not only encouraging results with respect to general data mining issues but also insight into the factors that effect interactions between transition metals and beta-X substituents.

Journal Article↗
PubMed1989

A least-squares computer method for the determination of the molecular ratio of conjugates between two different proteins from the results of the amino acid analysis.

A method for the determination of the composition of a conjugate between two different proteins by amino acid analysis followed by least-squares evaluation of the concentration ratio of the two components is presented. The method is based solely on calculations and avoids the use of labeled residues. A computer program, written in BASIC, is also presented to perform the calculations.

Amino Acids↗
PubMed2002

The computational challenges of applying comparative-based computational methods to whole genomes.

The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tools will play a fundamental role in analysing the enormous amount of new data that is currently being generated. The synthesis of computationally intensive comparative computational approaches with the requirement for whole genome analysis represents both an unprecedented challenge and opportunity for computational scientists. We focus on a few of these challenges, using by way of example the problems of alignment, gene finding and regulatory element discovery, and discuss the issues that have arisen in attempts to solve these problems in the context of whole genome analysis pipelines.

Computational Biology↗
PubMed1991

A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences.

We describe a new computer program that identifies conserved secondary structures in aligned nucleotide sequences of related single-stranded RNAs. The program employs a series of hash tables to identify and sort common base paired helices that are located in identical positions in more than one sequence. The program gives information on the total number of base paired helices that are conserved between related sequences and provides detailed information about common helices that have a minimum of one or more compensating base changes. The program is useful in the analysis of large biological sequences. We have used it to examine the number and type of complementary segments (potential base paired helices) that can be found in common among related random sequences similar in base composition to 16S rRNA from Escherichia coli. Two types of random sequences were analyzed. One set consisted of sequences that were independent but they had the same mononucleotide composition as the 16S rRNA. The second set contained sequences that were 80% similar to one another. Different results were obtained in the analysis of these two types of random sequences. When 5 sequences that were 80% similar to one another were analyzed, significant numbers of potential helices with two or more independent base changes were observed. When 5 independent sequences were analyzed, no potential helices were found in common. The results of the analyses with random sequences were compared with the number and type of helices found in the phylogenetic model of the secondary structure of 16S ribosomal RNA. Many more helices are conserved among the ribosomal sequences than are found in common among similar random sequences. In addition, conserved helices in the 16S rRNAs are, on the average, longer than the complementary segments that are found in comparable random sequences. The significance of these results and their application in the analysis of long non-ribosomal nucleotide sequences is discussed.

Base Composition↗
PubMed2002

Quantitative fluorescence lifetime spectroscopy in turbid media: comparison of theoretical, experimental and computational methods.

A Monte Carlo model developed to simulate time-resolved fluorescence propagation in a semi-infinite turbid medium was validated against previously reported theoretical and computational results. Model simulations were compared to experimental measurements of fluorescence spectra and lifetimes on tissue-simulating phantoms for single and dual fibre-optic probe geometries. Experiments and simulations using a single probe revealed that scattering-induced artefacts appeared in fluorescence emission spectra, while fluorescence lifetimes were unchanged. Although fluorescence lifetime measurements are generally more robust to scattering artefacts than are measurements of fluorescence spectra, in the dual-probe geometry scattering-induced changes in apparent lifetime were predicted both from diffusion theory and via Monte Carlo simulation, as well as measured experimentally. In all cases, the recovered apparent lifetime increased with increasing scattering and increasing source-detector separation. Diffusion theory consistently underestimated the magnitude of these increases in apparent lifetime (predicting a maximum increase of approximately 15%), while Monte Carlo simulations and experiment were closely matched (showing increases as large as 30%). These results indicate that quantitative simulations of time-resolved fluorescence propagation in turbid media will be important for accurate recovery of fluorophore lifetimes in biological spectroscopy and imaging applications.

Computer Simulation↗
PubMed1982

Comparison of computer methods for taxonomy of some streptococci using gas chromatographic chemotaxonomic data.

Gas chromatographic fingerprints of eighty-three strains of Streptococcus were analysed by computer. Seven measures of association were compared for their ability to identify strains. The most effective measure was the Stack coefficient which correctly identified 68% of strains, mostly of oral origin. Clustering of strains was carried out by median, average, single-linkage, furthest neighbour, and centroid linkage, Andrew's plots, and Minimum Spanning Trees. Of the clustering methods, centroid linkage produced the most inclusive and compact clusters. Clusters of strains of S. mitis, S. mutans, S. salivarius and S. sanguis showed varying degrees of heterogeneity; while, S. milleri was comprised of three chemotypes corresponding to oral isolates, biochemically atypical vaginal isolates, and biochemically typical strains from other sources.

Chromatography, Gas↗