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At least 703 records · Page 39Linked to original sources
PubMed1999

An intelligent framework for the classification of the 12-lead ECG.

An intelligent framework has been proposed to classify an unknown 12-Lead electrocardiogram into one of a possible number of mutually exclusive and combined diagnostic classes. The framework segregates the classification problem into a number of bi-dimensional classification problems, requiring individual bi-group classifiers for each individual diagnostic class. The bi-group classifiers were generated employing Neural Networks (NN), combined with a combination framework containing an Evidential Reasoning framework to accommodate for any conflicting situations between the bi-group classifiers. A number of different feature selection techniques were investigated with the aim of generating the most appropriate input vector for the bi-group classifiers. It was found that by reducing the original input feature vector, the generalisation ability of the classifiers, when exposed to unseen data, was enhanced and subsequently this reduced the computational requirements of the network itself. The entire framework was compared with a conventional approach to NN classification and a rule based classification approach. The framework attained a significantly higher level of classification in comparison with the other methods; 80.0% compared with 66.7% for the rule based technique and 68.00% for the conventional neural approach.

Computer Simulation↗
PubMed2003

Non-equilibrium gating in cardiac Na+ channels: an original mechanism of arrhythmia.

BACKGROUND: Many long-QT syndrome (LQTS) mutations in the cardiac Na+ channel result in a gain of function due to a fraction of channels that fail to inactivate (burst), leading to sustained current (Isus) during depolarization. However, some Na+ channel mutations that are causally linked to cardiac arrhythmia do not result in an obvious gain of function as measured using standard patch-clamp techniques. An example presented here, the SCN5A LQTS mutant I1768V, does not act to increase Isus (<0.1% of peak) compared with wild-type (WT) channels. In fact, it is difficult to reconcile the seemingly innocuous kinetic alterations in I1768V as measured during standard protocols under steady-state conditions with the disease phenotype. METHODS AND RESULTS: We developed new experimental approaches based on theoretical analyses to investigate Na+ channel gating under non-equilibrium conditions, which more closely approximate physiological changes in membrane potential that occur during the course of a cardiac action potential. We used this new approach to investigate channel-gating transitions that occur subsequent to channel activation. CONCLUSIONS: Our data suggest an original mechanism for development of LQT-3 arrhythmias. This work demonstrates that a combination of computational and experimental analysis of mutations provides a framework to understand complex mechanisms underlying a range of disorders, from molecular defect to cellular and systems function.

Action Potentials↗
PubMed2002

Simulating the formation of cosmic structure.

A timely combination of new theoretical ideas and observational discoveries has brought about significant advances in our understanding of cosmic evolution. Computer simulations have played a key role in these developments by providing the means to interpret astronomical data in the context of physical and cosmological theory. In the current paradigm, our Universe has a flat geometry, is undergoing accelerated expansion and is gravitationally dominated by elementary particles that make up cold dark matter. Within this framework, it is possible to simulate in a computer the emergence of galaxies and other structures from small quantum fluctuations imprinted during an epoch of inflationary expansion shortly after the Big Bang. The simulations must take into account the evolution of the dark matter as well as the gaseous processes involved in the formation of stars and other visible components. Although many unresolved questions remain, a coherent picture for the formation of cosmic structure is now beginning to emerge.

Astronomy↗
PubMed2025

CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of CaXML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

Machine Learning↗
PubMed2002

The IUPS human Physiome Project.

The Physiome Project of the International Union of Physiological Sciences (IUPS) is attempting to provide a comprehensive framework for modelling the human body using computational methods which can incorporate the biochemistry, biophysics and anatomy of cells, tissues and organs. A major goal of the project is to use computational modelling to analyse integrative biological function in terms of underlying structure and molecular mechanisms. To support that goal the project is establishing web-accessible physiological databases dealing with model-related data, including bibliographic information, at the cell, tissue, organ and organ system levels. Here we discuss the background and goals of the project, the problems of modelling across multiple spatial and temporal scales, and the development of model ontologies and markup languages at all levels of biological function.

Anatomy↗
PubMed1993

Simulation of stochastic micropopulation models--III. COGNET: an artificial neural network for visual recognition.

COGNET, based on a neural network first described by Fukushima, demonstrates the relationship between connectionist and other micropopulation models. Its success and physiological orientation led to an implementation using the SUMMERS simulation shell. After self-supervised learning, COGNET uses forward and backward propagation of signals to recognize partial and noisy patterns, and to reconstruct the originals. Stochastic features include variable thresholds for neuronal firing and occasional cell death. The successful implementation of COGNET demonstrates the generality of the concepts embodied in SUMMERS, which in turn promotes the reusability of software and facilitates the extension of computational models in biomedical research. COGNET itself forms a framework for building other physiologically oriented neural network models.

Computer Simulation↗
PubMed1990

An algorithm for approximating conditional probabilities.

When diagnostic programs are constructed within a probabilistic framework, it is often the case that computation of joint probabilities of exhaustive combinations of events is easy, but computation of the kind of conditional probabilities the user wishes to know, is hard. This paper describes a simple algorithm for computing the required values, and then suggests several heuristic optimizations that may enable suitable approximations to be obtained in a feasible time when the task is otherwise intractable. An account is given of a specific application of the method in the construction of a medical diagnostic program, which is described in more detail elsewhere.

Algorithms↗
PubMed1995

Bone strain gage data and theoretical models of functional adaptation.

The in vivo implantation of strain gages on the surface of bones has proven to be a very useful technique for studying the relationship between in vivo loading and bone growth and adaptation. However, data from such experiments have yet to be well incorporated within the context of theoretical models of bone adaptation. Methods for analyzing bone rosette strain gage recordings within the framework of strain energy density-based computational modeling/remodeling theories are presented. A new strain energy density based parameter, energy equivalent strain, is proposed as a single scalar measure of cyclic strain magnitudes and the concept of a daily strain stimulus is also introduced. As an illustrative example, the approach is applied to analyze previously reported in vivo data from the anteromedial human tibia (Lanyon et al., 1975, Acta orthop. Scand. 46, 256-268).

Adaptation, Physiological↗
PubMed2026

Leveraging Interradiomic Feature Relationships for Enhanced Prediction of Distant Metastasis and Characterization of Heterogeneity in Head and Neck Cancer.

PURPOSE: Distant metastasis remains a major cause of treatment failure in head and neck (HN) cancer, highlighting the need for more accurate early risk stratification. This study developed and validated a deep radiomics framework to characterize tumor heterogeneity from pretreatment computed tomography (CT) images and improve prediction of distant metastasis-free survival (DMFS). METHODS AND MATERIALS: This multicenter study included 3421 patients with HN cancer from 4 cohorts across 12 institutions. Radiomics features were extracted from primary tumors and transformed into OmicsMaps, a structured representation that spatially organizes interfeature relationships to facilitate learning of complex prognostic patterns. A convolutional neural network was trained to derive prognostic signatures, which were integrated with key clinical variables to construct an OmicsMap-clinical fusion model for patient risk stratification. Model performance was assessed using the concordance index (C-index) and time-dependent area under the receiver operating characteristic curve (AUC) in the CT Images from Large Head and Neck Cohort (RADCURE), HEAD-NECK-RADIOMICS-HN1 (HN1), and Head-Neck-Positron Emission Tomography-Computed Tomography (HN-PET-CT) cohorts. Radiogenomic analyses using RNA-seq data were conducted in the Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) cohort to investigate biological characteristics associated with the imaging-defined risk groups. RESULTS: The OmicsMap achieved C-index values of 0.742, 0.768, and 0.671 in the RADCURE, HN1, and HN-PET-CT cohorts, outperforming the conventional radiomics approach by 5.40%-6.37%. Incorporating clinical variables further improved generalizability, yielding a C-index of 0.864 (HN1) and 0.730 (HN-PET-CT), with time-dependent AUC of 0.727-0.895. The fusion model consistently stratified patients into distinct high- and low-risk groups for both DMFS and overall survival across cohorts (P <.01). Radiogenomic analyses revealed enrichment of immune-related pathways in the low-risk group, whereas the high-risk group exhibited a more aggressive phenotype enriched for proliferation, hypoxia, and epithelial-mesenchymal transition pathways, along with a fibrosis-prone tumor microenvironment characterized by extracellular matrix remodeling. CONCLUSIONS: Modeling interradiomic feature relationships using the OmicsMap representation substantially improves CT-based prediction of DMFS and characterization of tumor heterogeneity in HN cancer, supporting precision risk stratification in clinical oncology.

Journal Article↗
PubMed2005

Estimation of diagnostic-test sensitivity and specificity through Bayesian modeling.

We review recent Bayesian approaches to estimation (based on cross-sectional sampling designs) of the sensitivity and specificity of one or more diagnostic tests. Our primary goal is to provide veterinary researchers with a concise presentation of the computational aspects involved in using the Bayesian framework for test evaluation. We consider estimation of diagnostic-test sensitivity and specificity in the following settings: (i) one test in one population, (ii) two conditionally independent tests in two or more populations, (iii) two correlated tests in two or more populations, and (iv) three tests in two or more populations, where two tests are correlated but jointly independent of the third test. For each scenario, we describe a Bayesian model that incorporates parameters of interest. The WinBUGS code used to fit each model, which is available at http://www.epi.ucdavis.edu/diagnos-tictests/, can be altered readily to conform to different data.

Animals↗
PubMed1996

Subject-verb agreement in Spanish and English: differences in the role of conceptual constraints.

This paper reports studies of subject-verb agreement errors with speakers of Spanish and English; we used a sentence completion task, first introduced by Bock and Miller (1991). In a series of four experiments, we assessed the role of semantic information carried by the sentential subject in the induction of subject-verb agreement errors. For Spanish speakers, a sentence preamble such as la etiqueta score las botellas (the label on the bottles), which is usually interpreted to denote several labels, induced more agreement errors than preambles that normally denote a single entity. This finding replicates previous research with Italian (Vigliocco et al., 1995). English speakers, on the other hand, were not sensitive to this semantic dimension, as was found earlier by Bock and Miller (1991). This cross-linguistic difference is discussed in the framework of a modified version of the computational model of grammatical encoding proposed by Kempen and Hoenkamp (1987). In this version of the model agreement is computed through a unification operation instead of feature-copying, allowing for an independent retrieval of agreement features from the conceptual representation for the subject and the verb. We propose that languages differ in the extent to which the selection of the verb is controlled by features on the subject and features from the conceptual representation.

Adult↗
PubMed2001

Electron-rich bonding and the importance of s,p mixing as one moves across a period: a lesson from the LiSn system.

The electronic structure of an unusual LiSn phase (computed using band structure calculations in the framework of the extended Hückel tight binding theory) is the starting point for a general analysis of the variation of electron-rich multicenter bonding across a period. The LiSn crystal structure of Müller and Schäfer in question contains 2D slabs of Sn atoms arranged as microscopic stairs and intercalated by Li atoms. Discrepancies between an electron count derived from a recent extension of the Zintl-Klemm rules to electron-rich systems (5(2/3) electrons) and the experimental one (5 electrons for the Sn sublattice) and other failures of chemical "common sense" emerge in the analysis. The key for interpretation of a series of puzzling results was found in the comparative analysis of the Sn net with other main group element hypervalent slabs. Increasing s,p-mixing as one moves from the right to the left side of the same row of the periodic table is responsible for these effects. The result is that a lower electron count is found in the Sn slabs relative to the one expected from the extended Zintl-Klemm theory. The effect should also occur in discrete molecules. We also showed that the Li atoms have a role in the determination of the final structure, not only because of their small size but also through the degree of the electron transfer to the Sn sublattice.

Journal Article↗
PubMed2005

A mechanism for error detection in speeded response time tasks.

The concept of error detection plays a central role in theories of executive control. In this article, the authors present a mechanism that can rapidly detect errors in speeded response time tasks. This error monitor assigns values to the output of cognitive processes involved in stimulus categorization and response generation and detects errors by identifying states of the system associated with negative value. The mechanism is formalized in a computational model based on a recent theoretical framework for understanding error processing in humans (C. B. Holroyd & M. G. H. Coles, 2002). The model is used to simulate behavioral and event-related brain potential data in a speeded response time task, and the results of the simulation are compared with empirical data.

Attention↗
PubMed2003

Integration from proteins to organs: the Physiome Project.

The Physiome Project will provide a framework for modelling the human body, using computational methods that incorporate biochemical, biophysical and anatomical information on cells, tissues and organs. The main project goals are to use computational modelling to analyse integrative biological function and to provide a system for hypothesis testing.

Computer Simulation↗
PubMedDate not supplied

The ICNP's relevance in the US.

Efforts to develop an International Classification for Nursing Practice (ICNP) were initiated nearly a decade ago. To update nurses on progress, below is a critical review of the ICNP using the Computer-based Patient Record Institute (CPRI) Features Framework and a discussion of its relevance to current US efforts: 1) the activities of the American Nurses' Association (ANA) Steering Committee on Databases To Support Clinical Nursing Practice; 2) implementation of formal approaches for representing nursing concepts and 3) Health Level 7 standards.

American Nurses' Association↗
PubMed2004

Calculation of the fourth-rank molecular hypermagnetizability of some small molecules.

A computational scheme has been developed within the framework of Rayleigh-Schrödinger perturbation theory to evaluate nonlinear interaction energy contributions for a molecule in the presence of an external spatially uniform, time-independent magnetic field. Terms connected with the fourth power of the perturbing field, representing the fourth-rank hypermagnetizabilities of five small molecules, have been evaluated at the coupled Hartree-Fock level of accuracy within the conventional common-origin approach. Gaugeless basis sets of increasing size and flexibility have been employed in a numerical test, adopting two different coordinate systems to estimate the degree of convergence of theoretical tensor components.

Journal Article↗
PubMed2003

Evaluating a spoken dialogue system for recording clinical observations during an endoscopic examination.

Paper, keyboard or mouse-driven systems may not be suitable for data capture because of the hands-busy constraint imposed by an endoscopic examination. A Spoken Dialogue System (SDS) has a number of advantages when compared to keyboard and mouse-driven input modalities, particularly with respect to hands free and eyes-free control of a system. However, any emerging technology will never deliver improved organizational effectiveness if it is not accepted and used. The Technology Acceptance Model (TAM) provides a framework that helps explain the determinants of computer acceptance. This study, through the application of TAM, demonstrates a high level of user acceptance with clinicians wanting to use spoken dialogue technology for recording clinical observations during an endoscopic examination. Clinicians would also prefer to use a SDS for recording endoscopy rather than use a paper-based or keyboard and mouse-driven system. Using a clinical narrative during an endoscopic examination was also perceived to be a natural way to record findings. Relationships between basic TAM variables were confirmed and relationships between quality of dialogue measures and TAM variables were established.

Adult↗
PubMed1998

Quantitative cardiac SPECT in three dimensions: validation by experimental phantom studies.

A mathematical framework for quantitative SPECT (single photon emission computed tomography) reconstruction of the heart is presented. An efficient simultaneous compensation approach to the reconstruction task is described. The implementation of the approach on a digital computer is delineated. The approach was validated by experimental data acquired from chest phantoms. The phantoms consisted of a cylindrical elliptical tank of Plexiglass, a cardiac insert made of Plexiglass, a spine insert of packed bone meal and lung inserts made of styrofoam beads alone. Water bags were added to simulate different body characteristics. Comparison between the quantitative reconstruction and the conventional FBP (filtered backprojection) method was performed. The FBP reconstruction had a poor quantitative accuracy and varied for different body configurations. Significant improvement in reconstruction accuracy by the quantitative approach was demonstrated with a moderate computing time on a currently available desktop computer. Furthermore, the quantitative reconstruction was robust for different body characteristics. Therefore, the quantitative approach has the potential for clinical use.

Body Composition↗