Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational methods”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54Linked to original sources
PubMed2002

A comparative genomic method for computational identification of prokaryotic translation initiation sites.

The ever growing number of completely sequenced prokaryotic genomes facilitates cross-species comparisons by genomic annotation algorithms. This paper introduces a new probabilistic framework for comparative genomic analysis and demonstrates its utility in the context of improving the accuracy of prokaryotic gene start site detection. Our frame work employs a product hidden Markov model (PROD-HMM) with state architecture to model the species-specific trinucleotide frequency patterns in sequences immediately upstream and downstream of a translation start site and to detect the contrasting non-synonymous (amino acid changing) and synonymous (silent) substitution rates that differentiate prokaryotic coding from intergenic regions. Depending on the intricacy of the features modeled by the hidden state architecture, intergenic, regulatory, promoter and coding regions can be delimited by this method. The new system is evaluated using a preliminary set of orthologous Pyrococcus gene pairs, for which it demonstrates an improved accuracy of detection. Its robustness is confirmed by analysis with cross-validation of an experimentally verified set of Escherichia coli K-12 and Salmonella thyphimurium LT2 orthologs. The novel architecture has a number of attractive features that distinguish it from previous comparative models such as pair-HMMs.

Algorithms↗
PubMed1999

Automated registration of multimodal brain image sets using computer vision methods.

We present a new method of registering three dimensional image volumes of the brain of a given patient acquired at different times or with different imaging modalities, or both. Registration is an essential requirement for fusing the data from the two image sets so as to either increase the available information by exploiting complementary imaging modalities, or to measure small changes over time for prognostication, disease assessment, etc. The new technique exploits an external, removable, remountable reference frame which is attached to the head. Computer vision techniques are used to determine the positions of fiducial marks in every image. The transformation required to map each image of one image volume onto the other image volume is developed using the theory of quaternions. The results indicate that the new technique is robust and practical in a clinical setting.

Algorithms↗
PubMed1988

Evaluation of a computer-assisted method of analysing SDS-PAGE protein profiles in tracing a hospital outbreak of Serratia marcescens.

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles of bacterial proteins have been successfully used for taxonomical purposes. More recently this technique has been applied to epidemiological investigations in respect of various micro-organisms including Neisseria meningitidis, Staphylococcus aureus and Clostridium difficile. The main limitations of the methods so far described are lack of standardisation in extraction and separation as well as in the analysis of results. Although reproducibility in the same laboratory has been shown to be satisfactory, comparison of results among laboratories is still difficult. Moreover, assessment of differences and/or similarities among chromatograms or autoradiographs showing many bands depends upon qualitative descriptions. Interpretation of densitometric scannings is laborious and time-consuming. In this paper we present our experience of a completely standardised, fully computer-controlled procedure for SDS-PAGE (AMBIS System) in analysing 35S-methionine-labelled total proteins. The methodology proved very useful in monitoring a hospital outbreak of Serratia marcescens. It allowed us to make quantitative comparison in a shorter time as well as to handle easily a great amount of data and usefully integrate it with those obtained with other systems such as serotyping. Furthermore, when the two systems are used together, more precise information can be gained. In this epidemic, serotyping indicated the presence of two groups which would have been missed by PAGE analysis alone. Electrophoretotyping, however, focused on similarities of cellular proteins among the epidemic strains. This allowed us to distinguish them from epidemiologically unrelated strains of the same serogroup.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Infections↗
PubMed2003

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Manual curation has long been held to be the "gold standard" for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an "uninformative filter" that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Animals↗
PubMed2003

FRAME and the Royal Commission on Environmental Pollution: common recommendations for assessing risks posed by chemicals under the EU REACH system.

This document discusses recommendations made by FRAME and the Royal Commission on Environmental Pollution (RCEP) with regard to the current European Commission proposals on the Registration, Evaluation and Authorisation of Chemicals (REACH) system for assessing the risks of chemicals to humans, wildlife and the environment. Of several common aims and recommendations, the two most important are: a) the greater use of non-animal testing methods, especially computational prediction methods (for example, [quantitative] structure-activity relationships, expert systems and biokinetic modelling) for prioritising chemicals for hazard assessment; and b) the greater use of intelligent exposure-based targeted risk assessment, with less emphasis being placed on tonnage-triggers. FRAME has produced a decision-tree testing scheme to illustrate the way in which these approaches could be used, together with in vitro test methods. This scheme has been slightly modified to take account of proposals subsequently made by the RCEP. In addition, FRAME points out that new and improved computational methods are needed through more coordinated research, and that these and existing methods need to be validated. The similarities between the independent publications of FRAME and the RCEP add weight to the recommendations that each have made concerning the implementation of the REACH system.

Animal Testing Alternatives↗
PubMed2003

Data mining and computationally intensive methods: summary of Group 7 contributions to Genetic Analysis Workshop 13.

The Framingham Heart Study data, as well as a related simulated data set, were generously provided to the participants of the Genetic Analysis Workshop 13 in order that newly developed and emerging statistical methodologies could be tested on that well-characterized data set. The impetus driving the development of novel methods is to elucidate the contributions of genes, environment, and interactions between and among them, as well as to allow comparison between and validation of methods. The seven papers that comprise this group used data-mining methodologies (tree-based methods, neural networks, discriminant analysis, and Bayesian variable selection) in an attempt to identify the underlying genetics of cardiovascular disease and related traits in the presence of environmental and genetic covariates. Data-mining strategies are gaining popularity because they are extremely flexible and may have greater efficiency and potential in identifying the factors involved in complex disorders. While the methods grouped together here constitute a diverse collection, some papers asked similar questions with very different methods, while others used the same underlying methodology to ask very different questions. This paper briefly describes the data-mining methodologies applied to the Genetic Analysis Workshop 13 data sets and the results of those investigations.

Bayes Theorem↗
PubMed1986

A computer assisted method to obtain the prothrombin activation velocity in whole plasma independent of thrombin decay processes.

A method is described that, on the basis of the time course of amidolytic activity after the triggering of thrombin generation in normal plasma, allows the calculation of the velocity of prothrombin conversion independent of thrombin inactivating processes. It is shown how the reaction constants for the alpha 2M-dependent and the alpha 2M-independent thrombin inactivation processes can be obtained in a sample of whole plasma. The method is verified by demonstrating that the experimentally observed time courses of residual prothrombin and of alpha 2M-thrombin complex coincide with those calculated from the time course of amidolytic activity, and by showing that the course of prothrombin conversion in plasma without alpha 2-macroglobulin or AT III is adequately described if the alpha 2M or AT III-dependent breakdown constants are taken zero in the calculations. It appears that the inactivation of thrombin, endogenously generated in whole plasma, is about half as fast as that of exogenous thrombin added to the plasma. A computer program is presented that carries out the relevant calculations.

Brain↗
PubMed1992

Retinal vessel measurement: comparison between observer and computer driven methods.

A method of semi-automated image analysis for the measurement of retinal vessel diameters is described. This was compared with an observer-driven method for reproducibility and accuracy. The coefficient of variation for the data from the semi-automated method was 1.5-7.5% (depending on the vessel diameter) compared to 6-34% with the observer-driven method. The mean vessel diameters using the observer-driven method tended to be higher; however, this did not reach significance. The speed and low inter- and intra-observer variability for the semi-automated method make it a useful technique for measuring retinal blood vessel diameters. A larger variability was found between photographs taken at different times. This may be due to changes in retinal vessel diameter with changes in retinal perfusion pressure during the cardiac cycle.

Diabetic Retinopathy↗
PubMed1987

A method for computing spectral reflectance.

Psychophysical experiments show that the perceived colour of an object is relatively independent of the spectrum of the incident illumination and mainly depends on the surface spectral reflectance. We first demonstrate a possible solution to this undetermined problem for a Mondrian world of flat rectangular patches. We expand the illumination and surface reflectances in terms of a finite number of basis functions. We assume that the number of colour receptors is greater than the number of basis functions. This yields a set of nonlinear equations for each colour patch. Number counting arguments show that, given a sufficient number of surface patches with the same illumination, there are enough equations to determine the surface reflectances up to an overall scaling factor. This theory is similar to previous and independent work by Maloney and Wandell (Maloney 1985). We demonstrate a simple method of solving these non-linear equations. We generalize to situations where the illumination varies in space and the objects are three dimensional shapes. To do this we define a method for detecting material changes, a colour edge detector, and illustrate a way of detecting the colour of a material at its boundaries and propagating it inwards.

Color Perception↗
PubMed2004

A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptor-regulated genes.

A novel computational method based on a genetic algorithm was developed to study composite structure of promoters of coexpressed genes. Our method enabled an identification of combinations of multiple transcription factor binding sites regulating the concerted expression of genes. In this article, we study genes whose expression is regulated by a ligand-activated transcription factor, aryl hydrocarbon receptor (AhR), that mediates responses to a variety of toxins. AhR-mediated change in expression of AhR target genes was measured by oligonucleotide microarrays and by reverse transcription-polymerase chain reaction in human and rat hepatocytes. Promoters and long-distance regulatory regions (>10 kb) of AhR-responsive genes were analyzed by the genetic algorithm and a variety of other computational methods. Rules were established on the local oligonucleotide context in the flanks of the AhR binding sites, on the occurrence of clusters of AhR recognition elements, and on the presence in the promoters of specific combinations of multiple binding sites for the transcription factors cooperating in the AhR regulatory network. Our rules were applied to search for yet unknown Ah-receptor target genes. Experimental evidence is presented to demonstrate high fidelity of this novel in silico approach.

Algorithms↗
PubMed1984

FFT method to compute solution X-ray scattering curves.

We present an efficient algorithm to compute X-ray intensities scattered by macromolecules in solution, from atomic positions found in crystal structures. The algorithm applies the Fast Fourier Transform to an electron density map created from the atomic coordinates and corrected for solvent density. We compute scattering curves for both allosteric forms of E. coli aspartate carbamoyltransferase. Calculated intensities are in agreement with the ones measured by Moody et al. which shows that the structures observed in solution in the presence or in the absence of a substrate analogue do correspond to those of two crystal forms analyzed by Lipscomb and collaborators .

Aspartate Carbamoyltransferase↗
PubMed1985

Solubility of inorganic kidney stone components in the presence of acid-base sensitive complexing agents.

Computation methods used to calculate the solubilities of the main inorganic kidney stone components in the absence or presence of acid-base-sensitive complexants as a function of pH are described. The solubilities of whewellite, brushite, whitlockite, octocalcium phosphate, hydroxyapatite and struvite were calculated in the presence of ethylenediaminetetraacetate (EDTA), trans-cyclohexane-1,2-diaminetetraacetate (CDTA), citrate, tripolyphosphate and alpha-hydroxyisobutyrate. The results explain why kidney irrigations with citrate give extremely variable results. The calculated solubility curves show that only EDTA and CDTA solutions with a pH of 8 or higher will have good litholytic properties for all compounds concerned. The computation methods presented in this paper can be used to calculate the solubility of a large number of salts. These salts may contain non-acid-base-sensitive cations capable of forming complexes, acid-base-sensitive anions, hydroxyl ions, hydrogen ions or other acid-base-sensitive cations (e.g. NH4+), and the solubilities can be calculated in the presence or absence of acid-base-sensitive complexing agents.

Calcium Oxalate↗
PubMed2006

FRAME and the Royal Commission on Environmental Pollution: common recommendations for assessing risks posed by chemicals under the EU REACH system.

This document discusses recommendations made by FRAME and the Royal Commission on Environmental Pollution (RCEP) with regard to the current European Commission proposals on the Registration, Evaluation and Authorisation of Chemicals (REACH) system for assessing the risks of chemicals to humans, wildlife and the environment. Of several common aims and recommendations, the two most important are: a) the greater use of non-animal testing methods, especially computational prediction methods (for example, [quantitative] structure-activity relationships, expert systems and biokinetic modelling) for prioritising chemicals for hazard assessment; and b) the greater use of intelligent exposure-based targeted risk assessment, with less emphasis being placed on tonnage-triggers. FRAME has produced a decision-tree testing scheme to illustrate the way in which these approaches could be used, together with in vitro test methods. This scheme has been slightly modified to take account of proposals subsequently made by the RCEP. In addition, FRAME points out that new and improved computational methods are needed through more coordinated research, and that these and existing methods need to be validated. The similarities between the independent publications of FRAME and the RCEP add weight to the recommendations that each have made concerning the implementation of the REACH system.

Journal Article↗
PubMed1990

[A computer-supported method for the direct production of shielding blocks and compensators for radiotherapy].

The homogeneous irradiation of irregularly shaped targets with high doses and the simultaneous protection of the equally irregular surrounding high risk regions can be carried out with the help of shielding blocks and compensation filters specially cut for individual use. The machines offered on the market that help in their production have serious drawbacks in spite of the advanced technology used. These machines with limited usage are not only expensive but also require personnel to control the several steps the production of the blocks and filters involves. Safer radiotherapy however demands a more intensive use of these protective measures. However, it is now possible to overcome the drawbacks we have mentioned. The projection of the contours of the block marked on the X-ray on the shielding blocks can be carried out directly with the help of the computer that directs the radiotherapy. This computer could be connected to a multipurpose CNC milling machine. Similarly, one could, in the near future, use the data from computed tomograms in the computer used to plan the radiotherapy to mould three dimensional compensation filters. The cutting out of the negative moulds from Styrodur, the casting with fluid metal alloys, the imprecision that follows, as well as the health hazards and environmental pollution attached to his process could then be avoided, not to speak of the possibility of total reutilization of the rests. The positioning of the block ensemble can follow effortlessly and with precision on the lucite plates which have been drilled to accommodate the blocks.

Equipment Design↗
PubMed2004

Contracted basis Lanczos methods for computing numerically exact rovibrational levels of methane.

We present a numerically exact calculation of rovibrational levels of a five-atom molecule. Two contracted basis Lanczos strategies are proposed. The first and preferred strategy is a two-stage contraction. Products of eigenfunctions of a four-dimensional (4D) stretch problem and eigenfunctions of 5D bend-rotation problems, one for each K, are used as basis functions for computing eigenfunctions and eigenvalues (for each K) of the Hamiltonian without the Coriolis coupling term, denoted H0. Finally, energy levels of the full Hamiltonian are calculated in a basis of the eigenfunctions of H0. The second strategy is a one-stage contraction in which energy levels of the full Hamiltonian are computed in the product contracted basis (without first computing eigenfunctions of H0). The two-stage contraction strategy, albeit more complicated, has the crucial advantage that it is trivial to parallelize the calculation so that the CPU and memory costs are independent of J. For the one-stage contraction strategy the CPU and memory costs of the difficult part of the calculation scale linearly with J. We use the polar coordinates associated with orthogonal Radau vectors and spherical harmonic type rovibrational basis functions. A parity-adapted rovibrational basis suitable for a five-atom molecule is proposed and employed to obtain bend-rotation eigenfunctions in the first step of both contraction methods. The effectiveness of the two methods is demonstrated by calculating a large number of converged J = 1 rovibrational levels of methane using a global potential energy surface.

Journal Article↗
PubMed2001

Computing the optimally fitted spike train for a synapse.

Experimental data have shown that synapses are heterogeneous: different synapses respond with different sequences of amplitudes of postsynaptic responses to the same spike train. Neither the role of synaptic dynamics itself nor the role of the heterogeneity of synaptic dynamics for computations in neural circuits is well understood. We present in this article two computational methods that make it feasible to compute for a given synapse with known synaptic parameters the spike train that is optimally fitted to the synapse in a certain sense. With the help of these methods, one can compute, for example, the temporal pattern of a spike train (with a given number of spikes) that produces the largest sum of postsynaptic responses for a specific synapse. Several other applications are also discussed. To our surprise, we find that most of these optimally fitted spike trains match common firing patterns of specific types of neurons that are discussed in the literature. Hence, our analysis provides a possible functional explanation for the experimentally observed regularity in the combination of specific types of synapses with specific types of neurons in neural circuits.

Action Potentials↗
PubMed1982

Computer-assisted method for performing impedance cardiography calculations.

Impedance cardiography provides a noninvasive technique to monitor stroke volume on a beat-by-beat basis. It correlates well with other techniques at rest, with both cycle and arm-ergometer exercise, and during head-up tilt. It has the advantage that it does not require active subject participation, as does the CO2-rebreathing technique; yet it is still noninvasive. The method described herein facilitates the measurement and calculation of stroke volume, cardiac output, and indices of ventricular function when this technique is used - whether a few or many beats are recorded. This method utilizes a recording of the impedance cardiogram, which may include a simultaneously recorded electrocardiogram and phonocardiogram; a digitizer for reading the coordinates from the recording; a CRT terminal with keyboard for additional data input and for monitoring output; a printer; and a minicomputer for calculation of variables and data analysis. Data related to approximately 100 cardiac beats can be read, calculated, printed, and statistically analyzed in about an hour.

Cardiography, Impedance↗
PubMedDate not supplied

[A new approach to assessment of the impairment of higher cortical function in psychoneurological diseases in children and adolescents by instrumental computer-assisted methods].

The authors discuss the possibility and efficacy of instrumental methods of psychophysiological examinations: automated devices Ritmotest, Mnemotest, and Binatest for assessing the disorders of the higher cortical functions in children with psychoneurological diseases. The main protocols and parameters for examination of children aged 7 to 15 years with various diseases are offered, test performance by children of different age shown, and score values fit for practical use of the above devices obtained.

Adolescent↗