Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “computational frameworks”

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 847 records · Page 47Linked to original sources
PubMed2005

Physical exposure of sign language interpreters: baseline measures and reliability analysis.

Measurement of physical exposure to musculoskeletal disorder risk factors must generally be performed directly in the field to assess the effectiveness of ergonomic interventions. To perform such an evaluation, the reliability of physical exposure measures under similar field conditions must be known. The objectives of this study were to estimate the reliability of physical exposure measures performed in the field and to establish the baseline values of physical exposure in sign language interpreters (SLI) before the implementation of an intervention. The electromyography (EMG) of the trapezius muscles as well as the wrist motions of the dominant arm were measured using goniometry on nine SLI on four different days. Several exposure parameters, proposed in the literature, were computed and the generalizability theory was used as a framework to assess reliability. Overall, SLI showed a relatively low level of trapezius muscle activity, but with little time at rest, and highly dynamic wrist motions. Electromyography exposure parameters showed poor to moderate reliability, while goniometry parameter reliability was moderate to excellent. For EMG parameters, performing repeated measurements on different days was more effective in increasing reliability than extending the duration of the measurement over one day. For goniometry, repeating measurements on different days was also effective in improving reliability, although good reliability could be obtained with a single sufficiently long measurement period.

Adult↗
PubMed1989

Testing between the TRACE model and the fuzzy logical model of speech perception.

The TRACE model of speech perception (McClelland & Elman, 1986) is contrasted with a fuzzy logical model of perception (FLMP) (Oden & Massaro, 1978). The central question is how the models account for the influence of multiple sources of information on perceptual judgment. Although the two models can make somewhat similar predictions, the assumptions underlying the models are fundamentally different. The TRACE model is built around the concept of interactive activation, whereas the FLMP is structured in terms of the integration of independent sources of information. The models are tested against test results of an experiment involving the independent manipulation of bottom-up and top-down sources of information. Using a signal detection framework, sensitivity and bias measures of performance can be computed. The TRACE model predicts that top-down influences from the word level influence sensitivity at the phoneme level, whereas the FLMP does not. The empirical results of a study involving the influence of phonological context and segmental information on the perceptual recognition of a speech segment are best described without any assumed changes in sensitivity. To date, not only is a mechanism of interactive activation not necessary to describe speech perception, it is shown to be wrong when instantiated in the TRACE model.

Adult↗
PubMed1996

Metaphors, models and bioinformation.

The notion of bioinformation is central to the biosciences. This short paper examines a number of metaphors which are intimately related to this idea. These include metaphors about 'system' as well as metaphors associated with biosystem as 'text'. A framework its presented which allows ideas about biosystems and computer systems to be displaced and a number of specific topics are then discussed. Firstly, information processing in non-neural tissues is given as an example of parallel distributed processing. This is followed with a number of metaphors associated with 'text', including 'glue', 'verbs' and 'interpretation'. The paper concludes with a proposal on how to integrate general ideas of bioinformation using the idea of the 'ecology of domains'.

Information Theory↗
PubMed2004

The association of parity with mortality outcomes among triplets.

OBJECTIVE: The purpose of this study was to evaluate the association of parity with stillbirth and neonatal and infant death among triplets. STUDY DESIGN: This was a retrospective cohort study of 15,930 triplets who were delivered in the United States between 1995 and 1997. Infants of nulliparous mothers were compared with infants of multiparous mothers. Adjusted relative risks for death by parity were computed with the use of the generalized estimating equations framework. RESULTS: The likelihood for stillbirth (odds ratio, 3.40; 95% CI, 2.20-5.26) was significantly greater among nulliparous mothers. Neonatal (odds ratio, 1.17; 95% CI, 0.95-1.43) and infant mortality rates (odds ratio, 1.10; 95% CI, 0.92-1.32) were comparable, however. With an increase in parity, there was a consistent declining trend in the risk for stillbirth (P<.0001). CONCLUSION: Nulliparity more than triples the risk for intrauterine fetal death among triplets. This parity-related disparity underscores the need for care providers to be particularly concerned about triplet gestations among nulliparous mothers.

Adult↗
PubMed2005

An object-oriented designed finite-difference time-domain simulator for electromagnetic analysis and design in MRI--applications to high field analyses.

This paper presents a finite-difference time-domain (FDTD) simulator for electromagnetic analysis and design applications in MRI. It is intended to be a complete FDTD model of an MRI system including all RF and low-frequency field generating units and electrical models of the patient. The program has been constructed in an object-oriented framework. The design procedure is detailed and the numerical solver has been verified against analytical solutions for simple cases and also applied to various field calculation problems. In particular, the simulator is demonstrated for inverse RF coil design, optimized source profile generation, and parallel imaging in high-frequency situations. The examples show new developments enabled by the simulator and demonstrate that the proposed FDTD framework can be used to analyze large-scale computational electromagnetic problems in modern MRI engineering.

Algorithms↗
PubMed2002

Calculation of forces at focal adhesions from elastic substrate data: the effect of localized force and the need for regularization.

Forces exerted by stationary cells have been investigated on the level of single focal adhesions by combining elastic substrates, fluorescence labeling of focal adhesions, and the assumption of localized force when solving the inverse problem of linear elasticity theory. Data simulation confirms that the inverse problem is ill-posed in the presence of noise and shows that in general a regularization scheme is needed to arrive at a reliable force estimate. Spatial and force resolution are restricted by the smoothing action of the elastic kernel, depend on the details of the force and displacement patterns, and are estimated by data simulation. Corrections arising from the spatial distribution of force and from finite substrate size are treated in the framework of a force multipolar expansion. Our method is computationally cheap and could be used to study mechanical activity of cells in real time.

Algorithms↗
PubMed2003

Stochastic model of autocrine and paracrine signals in cell culture assays.

Autocrine signaling systems are commonly studied under cell culture conditions. In a typical cell culture assay, a layer of liquid medium covers a random two-dimensional dispersion of cells, which secrete ligands. In a growing number of experiments, it is important to characterize the spatial range of autocrine and paracrine cell communication. Currently, the spatial distribution of diffusing signals can be analyzed only indirectly, from their effects on the intracellular signaling or physiological responses of autocrine cells. To directly characterize the spatial range of secreted ligands, we propose a stochastic model for autocrine cell cultures and analyze it using a combination of analytical and computational tools. The two main results derived within the framework of this model are 1), an expression for the fraction of autocrine trajectories, i.e., the probability for a ligand to be trapped by the same cell from which it has been secreted; and 2), an expression for the spatial distribution of trapping points of paracrine trajectories. We test these analytical results by stochastic simulations with efficient Brownian dynamics code and apply our model to analyze the spatial operation of autocrine epidermal growth factor receptor systems.

Algorithms↗
PubMed1999

A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

We describe application of the implicit solvation model (see the first paper of this series), to Monte Carlo simulations of several peptides in bilayer- and water-mimetic environments, and in vacuum. The membrane-bound peptides chosen were transmembrane segments A and B of bacteriorhodopsin, the hydrophobic segment of surfactant lipoprotein, and magainin2. Their conformations in membrane-like media are known from the experiments. Also, molecular dynamics study of surfactant lipoprotein with different explicit solvents has been reported (Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. J. Mol. Biol. 247:808-822). The principal goal of this work is to compare the results obtained in the framework of our solvation model with available experimental and computational data. The findings could be summarized as follows: 1) structural and energetic properties of studied molecules strongly depend on the solvent; membrane-mimetic media significantly promote formation of alpha-helices capable of traversing the bilayer, whereas a polar environment destabilizes alpha-helical conformation via reduction of solvent-exposed surface area and packing; 2) the structures calculated in a membrane-like environment agree with the experimental ones; 3) noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carlo simulation with implicit solvent (this work) and molecular dynamics in explicit solvent were observed; 4) in vacuo simulations do not correctly reproduce protein-membrane interactions, and hence should be avoided in modeling membrane proteins.

Amino Acid Sequence↗
PubMedDate not supplied

Advances in the computational study of language acquisition.

This paper provides a tutorial introduction to computational studies of how children learn their native languages. Its aim is to make recent advances accessible to the broader research community, and to place them in the context of current theoretical issues. The first section locates computational studies and behavioral studies within a common theoretical framework. The next two sections review two papers that appear in this volume: one on learning the meanings of words and one or learning the sounds of words. The following section highlights an idea which emerges independently in these two papers and which I have dubbed autonomous bootstrapping. Classical bootstrapping hypotheses propose that children begin to get a toc-hold in a particular linguistic domain, such as syntax, by exploiting information from another domain, such as semantics. Autonomous bootstrapping complements the cross-domain acquisition strategies of classical bootstrapping with strategies that apply within a single domain. Autonomous bootstrapping strategies work by representing partial and/or uncertain linguistic knowledge and using it to analyze the input. The next two sections review two more more contributions to this special issue: one on learning word meanings via selectional preferences and one on algorithms for setting grammatical parameters. The final section suggests directions for future research.

Algorithms↗
PubMed2002

The TEAM methodology for the evaluation of information systems in biomedicine.

The TEAM evaluation methodology for information systems in biomedicine (Total Evaluation and Acceptance Methodology) is a unifying methodology for any computer-based information system based on a three dimensional framework; these dimensions being Role, Time and Structure. The theory is derived from how the information system relates to the general system where it should operate, the properties of information flow within a general system and the relation between a system and its models. As a system can in theory be modelled from many perspectives, a perspective to be modelled is built up by formulating criteria relevant to that perspective which can be evaluated by quantitative and qualitative assessment methods. Key characteristics of the methodology include the insistence on a global rather than partial approach to the evaluation of information systems, also the dynamic nature of an information system which is continually in modification as it more successfully deals with the inherent complexity of the environment in which it is operating. The role dimension identifies four main categories, designer, specialist user, end user and stakeholder from which several sub-categories may be identified. The time dimension has four main phases towards relative stability of the information system. The structural dimension distinguishes strategic, tactical or organisational and operational levels that often are confused together with risk of dilution in current approaches. It is believed that this framework and methodology can provide a basis for future standardisation of evaluation methodologies.

Evaluation Studies as Topic↗
PubMed2001

Modeling a medical environment: an ontology for integrated medical informatics design.

Modern medical environments have seen an increase in technological complexity and pressures of handling more patients with fewer resources, resulting in higher demands on medical practitioners. Medical informatics designers will have to focus on the problem of organizing medical information more effectively to enable practitioners to cope with these challenges. This article addresses this research problem for the particular area of medical problem solving in patient care. First, we describe a traditional modeling approach for medical reasoning used as a basis for developing some decision support systems. We argue these models may be faithful to what is known about biomedical knowledge, but they have limitations for human problem solving, especially in unanticipated situations. Second, we present an ontological framework, known as the abstraction hierarchy (Rasmussen, IEEE Trans. Man. Cybernetics 15 (1985) 234-243), for integrating patient representations that are faithful to existing biomedical knowledge and that are consistent with what is known about human problem solving. Through an example of a critical event in the operating room, we reveal how this framework can support medical problem solving in unanticipated situations. Third, we show how to use these representations as a frame of reference for mapping medical roles, responsibilities, sensors, and controls in an operating room context. Finally, we provide some insight for medical informatics designers in using this framework to design novel training programs and human-computer displays.

Decision Support Techniques↗
PubMed2003

Interaction design theory.

OBJECTIVE: This paper presents a framework for the design of interactions between human and computational agents working in organisations, mediation by technological systems. DESIGN: The design of interactions within an organisation is viewed from the point of view, not of the technology mediating the new interaction, but of the human and computational agents who interact with each other. RESULTS: Understanding the limits to individual agent resources permits an analysis of the impact that a new interaction will have in a given setting. When we look beyond simple interaction settings, we can use the notion of interaction equilibria to predict the impact of new information and communication technologies within an organisation. Economic supply and demand curves, for example, may allow us to make both qualitative and quantitative predictions about technological adoption of communication systems. CONCLUSION: Rather than focusing solely on characteristics of individual technologies, or psychological and social issues, these can be combined to explain the overall decisions that individuals make when using technologies. Without necessarily understanding all the local decision criteria used by any individual, we can make robust predictions about how a group as a whole will interact.

Humans↗
PubMed1999

Tyrosine, phenylalanine, and disulfide contributions to the circular dichroism of proteins: circular dichroism spectra of wild-type and mutant bovine pancreatic trypsin inhibitor.

Improved descriptions of the lowest energy excited states of tyrosine and phenylalanine side chains have been developed in order to extend the capabilities of calculating the circular dichroism (CD) spectra of proteins. Four transitions (Lb, La, Bb, and Ba) for each of the side-chain chromophores were considered, and the transition monopole charges were obtained from a CNDO/S calculation on models representing the individual groups. Monopole charges at midpoints of the bonds, corresponding to the maximum transition charge densities in the Lb band, and monopole charges representing the vibronic coupling with the B transitions for the La transition were also included. The aromatic transitions were combined with the peptide transitions (npi, pi0pi n'pi, and pi+pi) and disulfide transitions (n1sigma and n4sigma) in the framework of the origin-independent matrix method to compute the CD spectra of different crystal forms and Y --> L and F --> L mutants of bovine pancreatic trypsin inhibitor (BPTI). The structures of the mutants were obtained by replacing the appropriate tyrosine or phenylalanine residue by leucine in the wild-type crystal structure. The CD calculations were performed on the energy-minimized structures. The CD spectrum calculated for the form II crystal structure of BPTI showed the best agreement with experiment. In the far UV, the calculated and experimental CD spectra agree to various extents for the wild-type and mutant BPTI. Among the mutants, the calculated CD spectra of Y4L, Y10L, Y23L, and F45L showed reasonable agreement with experiment, while those of Y21L and F22L, the two residues interacting with most aromatic groups, showed poor agreement. In the near UV, the negative bands predicted for the wild-type and mutant BPTI have much less intensity than observed experimentally.

Animals↗
PubMed2006

Molecular dynamics simulation of liquid water: hybrid density functionals.

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.

Algorithms↗
PubMed2000

Standardization of the 24-hour diet recall calibration method used in the european prospective investigation into cancer and nutrition (EPIC): general concepts and preliminary results.

OBJECTIVES: Despite increasing interest in the concept of calibration in dietary surveys, there is still little experience in the use and standardization of a common reference dietary method, especially in international studies. In this paper, we present the general theoretical framework and the approaches developed to standardize the computer-assisted 24 h diet recall method (EPIC-SOFT) used to collect about 37 000 24-h dietary recall measurements (24-HDR) from the 10 countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC). In addition, an analysis of variance was performed to examine the level of standardization of EPIC-SOFT across the 90 interviewers involved in the study. METHODS: The analysis of variance used a random effects model in which mean energy intake per interviewer was used as the dependent variable, while age, body mass index (BMI), energy requirement, week day, season, special diet, special day, physical activity and the EPIC-SOFT version were used as independent variables. The analysis was performed separately for men and women. RESULTS: The results show no statistical difference between interviewers in all countries for men and five out of eight countries for women, after adjustment for physical activity and the EPIC-SOFT program version used, and the exclusion of one interviewer in Germany (for men), and one in Denmark (for women). These results showed an interviewer effect in certain countries and a significant difference between gender, suggesting an underlying respondent's effect due to the higher under-reporting among women that was consistently observed in EPIC. However, the actual difference between interviewer and country mean energy intakes is about 10%. Furthermore, no statistical differences in mean energy intakes were observed across centres from the same country, except in Italy and Germany for men, and France and Spain for women, where the populations were recruited from areas scattered throughout the countries. CONCLUSION: Despite these encouraging results and the efforts to standardize the 24-HDR interview method, conscious or unconscious behaviour of respondents and/or interviewer bias cannot be prevented entirely. Further evaluation of the reliability of EPIC-SOFT measurements will be conducted through validation against independent biological markers (nitrogen, potassium).

Analysis of Variance↗
PubMed2002

Nuclear masses: evidence of order-chaos coexistence.

Shell corrections are important in the determination of nuclear ground-state masses and shapes. Although general arguments favor a regular single-particle dynamics, symmetry breaking and the presence of chaotic layers cannot be excluded. The latter provide a natural framework that explains the observed differences between experimental and computed masses.

Journal Article↗
PubMed2005

Myocardial motion analysis from B-mode echocardiograms.

The quantitative assessment of cardiac motion is a fundamental concept to evaluate ventricular malfunction. We present a new optical-flow-based method for estimating heart motion from two-dimensional echocardiographic sequences. To account for typical heart motions, such as contraction/expansion and shear, we analyze the images locally by using a local-affine model for the velocity in space and a linear model in time. The regional motion parameters are estimated in the least-squares sense inside a sliding spatiotemporal B-spline window. Robustness and spatial adaptability is achieved by estimating the model parameters at multiple scales within a coarse-to-fine multiresoluion framework. We use a wavelet-like algorithm for computing B-spline-weighted inner products and moments at dyadic scales to increase computational efficiency. In order to characterize myocardial contractility and to simplify the detection of myocardial dysfunction, the radial component of the velocity with respect to a reference point is color coded and visualized inside a time-varying region of interest. The algorithm was first validated on synthetic data sets that simulate a beating heart with a speckle-like appearance of echocardiograms. The ability to estimate motion from real ultrasound sequences was demonstrated by a rotating phantom experiment. The method was also applied to a set of in vivo echocardiograms from an animal study. Motion estimation results were in good agreement with the expert echocardiographic reading.

Algorithms↗
PubMed2000

Staged growth of optimized arterial model trees.

There is a marked difference in the structure of the arterial tree between epi- and endocardial layers of the human heart. To model these structural variations, we developed an extension to the computational method of constrained constructive optimization (CCO). Within the framework of CCO, a model tree is represented as a dichotomously branching network of straight cylindrical tubes, with flow conditions governed by Poiseuille's law. The tree is grown by successively adding new terminal segments from randomly selected points within the perfusion volume while optimizing the geometric location and topological site of each new connection with respect to minimum intravascular volume. The proposed method of "staged growth" guides the generation of new terminal sites by means of an additional time-dependent boundary condition, thereby inducing a sequence of domains of vascular growth within the given perfusion volume. Model trees generated in this way are very similar to reality in their visual appearance and predict diameter ratios of parent and daughter segments, the distribution of symmetry, the transmural distribution of flow, the volume of large arteries, as well as the ratio of small arterial volume in subendocardial and subepicardial layers in good agreement with experimental data. From this study we conclude that the method of CCO combined with staged growth reproduces many characteristics of the different arterial branching patterns in the subendocardium and the subepicardium, which could not be obtained by applying the principle of minimum volume alone.

Algorithms↗