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PubMed1997

A computational theory of executive cognitive processes and multiple-task performance: Part 1. Basic mechanisms.

A new theoretical framework, executive-process interactive control (EPIC), is introduced for characterizing human performance of concurrent perceptual-motor and cognitive tasks. On the basis of EPIC, computational models may be formulated to simulate multiple-task performance under a variety of circumstances. These models account well for reaction-time data from representative situations such as the psychological refractory-period procedure. EPIC's goodness of fit supports several key conclusions: (a) At a cognitive level, people can apply distinct sets of production rules simultaneously for executing the procedures of multiple tasks; (b) people's capacity to process information at "peripheral" perceptual-motor levels is limited; (c) to cope with such limits and to satisfy task priorities, flexible scheduling strategies are used; and (d) these strategies are mediated by executive cognitive processes that coordinate concurrent tasks adaptively.

Attention↗

PubMed1986

Dynamics of rural-urban migration in India: 1960-1981.

"This paper analyzes a multi-sectoral simulation model of the Indian economy designed to isolate the sources of Indian economic growth and urbanization since 1960. The model shares many common traits with other computable general equilibrium (CGE) simulation models, and its underlying framework is neoclassical. The model stresses spatial issues so that it can provide predictions on rural/urban labor demands, and hence on migration flows. The central issue we seek to evaluate is whether a neoclassical development paradigm can explain adequately the somewhat paradoxical patterns of urbanization and economic growth observed in India since 1960. Our conclusion is a qualified, affirmative response, based on the model's ability to replicate key macroeconomic variables."

Asia↗

PubMed2004

Vibrationally inelastic collisions in H+ +CO system: comparing quantum calculations with experiments.

State-resolved cross beam experiments [H. Udseth et al., J. Chem. Phys. 60, 3051 (1974); J. Krutein and F. Linder, J. Chem. Phys. 71, 599 (1979); G. Niedner-Schatteburg and J. P. Toennies, Adv. Chem. Phys. LXXXII, 553 (1992)], coupled with proton energy loss spectroscopy for the inelastic scattering of H(+) from CO in the collision range of 10-30 eV show very low vibrational excitation of the target molecule. Stimulated by the experimentally observed low vibrational inelasticity in the system the ground and the first two low-lying excited electronic potential-energy surfaces have been computed using the ab initio multireference configuration interaction method. Quantum dynamics has been performed on the ground potential energy surface in the framework of vibrational close-coupling rotational infinite-order sudden approximation. The various computed dynamical attributes such as differential and integral cross sections, and average vibrational energy transfer are analyzed in detail, and compared successfully with the available experimental results.

Journal Article↗

PubMed2003

An examination of the process of relapse prevention therapy designed to aid smoking cessation.

The process of relapse prevention (RP) therapy is examined. Patients' responses were recorded primarily during telephonic, RP counseling designed to facilitate smoking cessation. A computer program that prompted counselor initiatives and provided a framework for the recording of patient responses guided counselor interaction with patients. A total of 437 patients took part in 1650 counseling sessions and reported 2882 urge/lapse situations. The 2531 situations, for which complete data were available, and 4879 coping responses were analyzed. The main findings are (1) the descriptions of urge/lapse situations provided by patients in treatment are similar to those derived by research that aimed to discover the determinants of relapse without specific treatment, (2) number of coping responses rather than number of situations is related to treatment outcome, and (3) the more coping responses discussed during treatment, the better the treatment outcome.

Adaptation, Psychological↗

PubMed2006

Computational modeling of arterial wall growth. Attempts towards patient-specific simulations based on computer tomography.

The present manuscript documents our first experiences with a computational model for stress-induced arterial wall growth and in-stent restenosis related to atherosclerosis. The underlying theoretical framework is provided by the kinematics of finite growth combined with open system thermodynamics. The computational simulation is embedded in a finite element approach in which growth is essentially captured by a single scalar-valued growth factor introduced as internal variable on the integration point level. The conceptual simplicity of the model enables its straightforward implementation into standard commercial finite element codes. Qualitative studies of stress-induced changes of the arterial wall thickness in response to balloon angioplasty or stenting are presented to illustrate the features of the suggested growth model. First attempts towards a patient-specific simulation based on realistic artery morphologies generated from computer tomography data are discussed.

Aorta↗

PubMed2005

Evidence and diagnostic reporting in the IHE context.

Capturing clinical observations and findings during the diagnostic imaging process is increasingly becoming a critical step in diagnostic reporting. Standards developers-notably HL7 and DICOM-are making significant progress toward standards that enable exchanging clinical observations and findings among the various information systems of the healthcare enterprise. DICOM-like the HL7 Clinical Document Architecture (CDA) -uses templates and constrained, coded vocabulary (SNOMED, LOINC, etc.). Such a representation facilitates automated software recognition of findings and observations, intrapatient comparison, correlation to norms, and outcomes research. The scope of DICOM Structured Reporting (SR) includes many findings that products routinely create in digital form (measurements, computed estimates, etc.). In the Integrating the Healthcare Enterprise (IHE) framework, two Integration Profiles are defined for clinical data capture and diagnostic reporting: Evidence Document, and Simple Image and Numeric Report. This report describes these two DICOM SR-based integration profiles in the diagnostic reporting process.

Computer Systems↗

PubMed2005

Three-dimensional representation of complex muscle architectures and geometries.

Almost all computer models of the musculoskeletal system represent muscle geometry using a series of line segments. This simplification (i) limits the ability of models to accurately represent the paths of muscles with complex geometry and (ii) assumes that moment arms are equivalent for all fibers within a muscle (or muscle compartment). The goal of this work was to develop and evaluate a new method for creating three-dimensional (3D) finite-element models that represent complex muscle geometry and the variation in moment arms across fibers within a muscle. We created 3D models of the psoas, iliacus, gluteus maximus, and gluteus medius muscles from magnetic resonance (MR) images. Peak fiber moment arms varied substantially among fibers within each muscle (e.g., for the psoas the peak fiber hip flexion moment arms varied from 2 to 3 cm, and for the gluteus maximus the peak fiber hip extension moment arms varied from 1 to 7 cm). Moment arms from the literature were generally within the range of fiber moment arms predicted by the 3D models. The models accurately predicted changes in muscle surface geometry over a 55 degrees range of hip flexion, as compared to changes in shape predicted from MR images (average errors between the model and measured surfaces were between 1.7 and 5.2 mm). This new framework for representing muscle will enhance the accuracy of computer models of the musculoskeletal system.

Adult↗

PubMed2004

Suppression of intensity transition artifacts in statistical x-ray computer tomography reconstruction through radon inversion initialization.

Statistical reconstruction (SR) methods provide a general and flexible framework for obtaining tomographic images from projections. For several applications SR has been shown to outperform analytical algorithms in terms of resolution-noise trade-off achieved in the reconstructions. A disadvantage of SR is the long computational time required to obtain the reconstructions, in particular when large data sets characteristic for x-ray computer tomography (CT) are involved. As was shown recently, by combining statistical methods with block iterative acceleration schemes [e.g., like in the ordered subsets convex (OSC) algorithm], the reconstruction time for x-ray CT applications can be reduced by about two orders of magnitude. There are, however, some factors lengthening the reconstruction process that hamper both accelerated and standard statistical algorithms to similar degree. In this simulation study based on monoenergetic and scatter-free projection data, we demonstrate that one of these factors is the extremely high number of iterations needed to remove artifacts that can appear around high-contrast structures. We also show (using the OSC method) that these artifacts can be adequately suppressed if statistical reconstruction is initialized with images generated by means of Radon inversion algorithms like filtered back projection (FBP). This allows the reconstruction time to be shortened by even as much as one order of magnitude. Although the initialization of the statistical algorithm with FBP image introduces some additional noise into the first iteration of OSC reconstruction, the resolution-noise trade-off and the contrast-to-noise ratio of final images are not markedly compromised.

Algorithms↗

PubMed2004

Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations.

Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion. The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1.

Anisotropy↗

PubMed2005

QCD and a holographic model of hadrons.

We propose a five-dimensional framework for modeling low-energy properties of QCD. In the simplest three parameter model we compute masses, decay rates and couplings of the lightest mesons. The model fits experimental data to within 10%. The framework is a holographic version of the QCD sum rules, motivated by the anti-de Sitter/conformal field theory correspondence. The model naturally incorporates properties of QCD dictated by chiral symmetry, which we demonstrate by deriving the Gell-Mann-Oakes-Renner relationship for the pion mass.

Journal Article↗

PubMed2000

The reliability issue of computer-aided breast cancer diagnosis.

This paper introduces a number of reliability criteria for computer-aided diagnostic systems for breast cancer. These criteria are then used to analyze some published neural network systems. It is also shown that the property of monotonicity for the data is rather natural in this medical domain, and it has the potential to significantly improve the reliability of breast cancer diagnosis while maintaining a general representation power. A central part of this paper is devoted to the representation/narrow vicinity hypothesis, upon which existing computer-aided diagnostic methods heavily rely. The paper also develops a framework for determining the validity of this hypothesis. The same framework can be used to construct a diagnostic procedure with improved reliability.

Breast Neoplasms↗

PubMed2001

Recognition of imagined hand movements with low resolution surface Laplacian and linear classifiers.

EEG-based Brain Computer Interfaces (BCIs) require on-line detection of mental states from spontaneous EEG signals. In this framework, it was suggested that EEG patterns can be better detected with EEG data transformed with Surface Laplacian computation (SL) than with the unprocessed raw potentials. However, accurate SL estimates require the use of many EEG electrodes, when local estimation methods are used. Since BCI devices have to use a limited number of electrodes for practical reasons, we investigated the performances of spline methods for SL estimates using a limited number of electrodes (low resolution SL). Recognition of mental activity was attempted on both raw and SL-transformed EEG data from five healthy people performing two mental tasks, namely imagined right and left hand movements. Linear classifiers were used including Signal Space Projection (SSP) and Fisher's linear discriminant. Results showed an acceptable average correlation between the waveforms obtained with the low resolution SL and these obtained with the SL computed from 26 electrodes (full resolution SL). More importantly, satisfactorily recognition scores for mental EEG-patterns were obtained with the low-resolution surface Laplacian transformation of the recorded potentials when compared with those obtained by using full resolution SL (82%). These results demonstrated also the utility of linear classifiers for the detection of mental patterns in the BCI field.

Biomedical Engineering↗

PubMed2026

FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.

MOTIVATION: Since the introduction of single-cell RNA sequencing (scRNA-seq), numerous computational approaches have been developed to reconstruct dynamic cellular processes from static transcriptional profiles. These methods order cells along continuous trajectories by assessing their similarity in the gene-expression space. However, they rely on several assumptions, such as prior knowledge of the structure and directionality of the expected genealogy. These assumptions can limit their application to complex cellular systems with poorly understood developmental paths. RESULTS: To address this challenge, we introduce FIERCE (Framework for InfERence of the veloCity of Entropy), a novel computational pipeline designed to predict the changes in the differentiation potency of single cells during dynamic processes. Through a fully unsupervised approach, FIERCE enables the inference of cell lineages directly on the differentiation landscape of the biological system, thus eliminating the need for prior specification of developmental parameters. We demonstrate the efficacy of FIERCE by reconstructing three well-known mouse differentiation systems and by quantifying its accuracy on simulated data. AVAILABILITY AND IMPLEMENTATION: The FIERCE R package is available on GitHub at https://github.com/bicciatolab/FIERCE.

Cell Differentiation↗

PubMed2006

Computational studies of enzyme mechanism: linking theory with experiment in the analysis of enzymic H-tunnelling.

Hydrogen transfer--an essential component of most biological reactions--is a quantum problem. A crucial question of great current interest is how enzymes modulate the quantum dynamics of hydrogen transfer to achieve their outstanding catalytic properties. That tunnelling occurs is now widely accepted, with the conceptual frameworks incorporating protein motion into the enzymic H-tunnelling process. Computational simulation can be used to help elucidate how enzymes work and facilitate H-tunnelling at the atomic level. We review the strength of a multidisciplinary approach--combining computational simulations with enzyme kinetics and structural biology--in revealing tunnelling mechanisms in enzymes. We focus on two paradigm systems--aromatic amine dehydrogenase, in which H-tunnelling is facilitated by fast (sub-picosecond) short range motions, and dihydrofolate reductase, in which a network of long-range coupled motions drives the tunnelling event.

Biophysics↗

PubMed1989

Evaluation of a generalized model of human postural dynamics and control in the sagittal plane.

A two-step identification method is used to evaluate a generalized model of human postural control in the sagittal plane. Postural dynamics are represented as a planar open-chain linkage system supported by a triangular foot. The control mechanism is modeled as a state feedback element in which the torque acting at a given link is an arbitrary function of the state variables--angles and angular velocities. To validate the approach, six normal subjects underwent two series of experiments. The first series were used to determine an appropriate model of the system dynamics. The second series were used to estimate the parameters of the feedback model. A computer simulation of the complete system shows that the model predictions closely match the observed responses. These results suggest that the proposed model provides a useful framework for analysis of postural control mechanisms.

Computer Simulation↗

PubMed2000

Architecture for an artificial immune system.

An artificial immune system (ARTIS) is described which incorporates many properties of natural immune systems, including diversity, distributed computation, error tolerance, dynamic learning and adaptation, and self-monitoring. ARTIS is a general framework for a distributed adaptive system and could, in principle, be applied to many domains. In this paper, ARTIS is applied to computer security in the form of a network intrusion detection system called LISYS. LISYS is described and shown to be effective at detecting intrusions, while maintaining low false positive rates. Finally, similarities and differences between ARTIS and Holland's classifier systems are discussed.

Animals↗

PubMed1997

A physiological model for motion-stereo integration and a unified explanation of Pulfrich-like phenomena.

Many psychophysical and physiological experiments indicate that visual motion analysis and stereoscopic depth perception are processed together in the brain. However, little computational effort has been devoted to combining these two visual modalities into a common framework based on physiological mechanisms. We present such an integrated model in this paper. We have previously developed a physiologically realistic model for binocular disparity computation (Qian, 1994). Here we demonstrate that under some general and physiological assumptions, our stereo vision model can be combined naturally with motion energy models to achieve motion-stereo integration. The integrated model may be used to explain a wide range of experimental observations regarding motion-stereo interaction. As an example, we show that the model can provide a unified account of the classical Pulfrich effect (Morgan & Thompson, 1975) and the generalized Pulfrich phenomena to dynamic noise patterns (Tyler, 1974; Falk, 1980) and stroboscopic stimuli (Burr & Ross, 1979).

Depth Perception↗

PubMed2026

CancerOmicsStudio (CoS): a web server for integrative and interpretable analysis of multi-omics cancer data.

MOTIVATION: Large-scale omics resources, including The Cancer Genome Atlas, Genomics of Drug Sensitivity in Cancer, and the Cancer Dependency Map, have become essential for cancer research. However, these datasets are distributed across different platforms, formats and analysis frameworks, which limits their practical use by researchers without extensive computational expertise. RESULTS: We developed CancerOmicsStudio (CoS), a web server for integrative and interpretable analysis of multi-omics cancer data across 33 cancer types. CoS provides five major modules: CosAI, Traditional Analysis, Drug Sensitivity, CRISPR Dependency and Single-Cell Tumor Microenvironment. The Traditional Analysis module supports expression comparison, diagnostic evaluation, survival analysis, enrichment analysis and gene correlation. The Drug Sensitivity and CRISPR Dependency modules enable systematic evaluation of gene-drug response associations and gene essentiality in cancer cell lines. The Single-Cell Tumor Microenvironment module supports tumor microenvironment analysis at single-cell resolution. In total, approximately 1.23 million results have been precomputed to enable rapid retrieval. CosAI further allows users to submit natural-language queries and obtain results through a Real-time Analysis as Retrieval framework, with responses summarized by a lightweight language model. AVAILABILITY AND IMPLEMENTATION: CancerOmicsStudio is freely available at Zenodo (doi: 10.5281/zenodo.18744990) and https://cos.wanglab.bio.

Humans↗