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PubMedDate not supplied

Whole word morphologizer: expanding the word-based lexicon: a nonstochastic computational approach.

Whole Word Morphologizer is a small computer implementation of word-based morphology. The program automatically identifies morphological relations in a small word-based lexicon, literally learning its morphology, and uses the knowledge it acquires to generate new words. It is based on a model of the mental lexicon in which all entries are whole, entire, fully fledged words and relies solely on basic cognitive principles (differentiation and generalization) for the automatic acquisition of morphological relations and the population of the lexicon.

Humans↗
PubMed2001

Computational approaches to motor control.

New concepts and computational models that integrate behavioral and neurophysiological observations have addressed several of the most fundamental long-standing problems in motor control. These problems include the selection of particular trajectories among the large number of possibilities, the solution of inverse kinematics and dynamics problems, motor adaptation and the learning of sequential behaviors.

Adaptation, Physiological↗
PubMed1998

Computational approach to the physical chemistry of fullerenes and their derivatives.

A critical review is presented of results obtained with different computational methods (mainly ab initio) on C60, C70, and specific fullerene derivatives, also in comparison with experimental data. From the discussion of diverse systems, the (often underestimated) complexity of their physical and chemical behavior emerges, and hence the importance of an accurate description and the need for a careful inspection of the experimental data, with which comparison is often intrinsically difficult. The ambition of this review is to help establish a basis not only for a nonsuperficial reading of the existing literature, but also for a constructive approach with computations to the challenge posed by recent promising applications of fullerenes in nanotechnology, optoelectronics, and biology.

Journal Article↗
PubMed2004

A computational approach to characterization of bovine sperm chromatin alterations.

We describe here a computational morphology-based approach to the investigation of possible causes of chromatin alterations in sperm. A comprehensive set of state-of-the-art and geometric measures are computationally extracted from toluidine blue stained images and analyzed to infer the possible processes leading to normal and abnormal chromatin formation while seeking a possible taxonomy of chromatin alterations and their influence on sperm head morphology. Using this methodology, we have identified higher chromatin fragility at some specific points of the sperm head. Despite the lack of correlation between morphologies of sperm head and chromatin structure, four main morphological types of chromatin alterations in bull spermatozoa have been identified and their possible causes discussed.

Animals↗
PubMed1993

Glucagon adsorption on polymer surfaces with alpha-helical and extended beta-strand conformations: a computational approach.

The adsorption of glucagon with alpha-helical and extended beta-strand conformations on polymer surfaces was investigated using a computer simulation approach. An X-ray crystallographic structure of glucagon was employed in the study of the alpha-helical glucagon adsorption. The X-ray structure was then modified to simulate an extended beta-strand structure in the study of the beta-strand glucagon adsorption. Totally, 1632 different adsorption orientations of glucagon with each conformation were examined on polystyrene, polypropylene, polyethylene, poly(hydroxyethyl methacrylate) and poly(vinyl alcohol) surfaces. The calculation of the average adsorption energies among different orientations did not reveal any marked difference between the two conformations. However, when the lowest-energy orientations were compared, the adsorption energy of the extended beta-strand glucagon was always much lower than that of the alpha-helical glucagon, indicating that the adsorption of extended beta-strand glucagon was more energy favorable. The lower adsorption energy for the extended beta-strand glucagon than for the alpha-helical glucagon appeared to be contributed by the lower interaction potential energy of the former conformation. A greater number of the surface atoms in the extended beta-strand glucagon than in the alpha-helical glucagon was also observed. Fourier transform infrared spectroscopic (FTIR) studies in the literature showed conformational changes in adsorption of various larger proteins. Our study appears to provide a theoretical insight for the results from the FTIR studies.

Adsorption↗
PubMed2006

A guide through present computational approaches for the identification of mammalian microRNA targets.

Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.

3' Untranslated Regions↗
PubMed1997

Computational approaches to molecular recognition.

Recent advances in the computation of free energies have facilitated the understanding of host-guest and protein-ligand recognition. Rigorous perturbation methods have been assessed and expanded, and more approximate techniques have been developed that allow faster treatment of diverse systems.

Binding Sites↗
PubMed2002

Modeling civil violence: an agent-based computational approach.

This article presents an agent-based computational model of civil violence. Two variants of the civil violence model are presented. In the first a central authority seeks to suppress decentralized rebellion. In the second a central authority seeks to suppress communal violence between two warring ethnic groups.

Civil Disorders↗
PubMed2005

Rearrangement of the endoplasmic reticulum and calcium transient formation: the computational approach.

Experiments affecting calcium signaling often lead to changes in the calcium transient height. The present work is designed to approach this effect theoretically. Use of computational model let us to follow results of precisely designed changes in the endoplasmic reticulum distribution as a possible cause of cytoplasmic free calcium ion level. Obtained results suggest that indeed, rearrangement of the endoplasmic reticulum elements may be responsible for modulation of calcium signal's strength. We have also noticed that even if the endoplasmic reticulum concentration levels are local, the resulting changes in free calcium concentration are global and evenly distributed throughout the cell. The used mathematical method proved to be a powerful tool which made us understand the chemical dynamics of nonequilibrium processes of calcium transient formation. Presented data show how Ca2+ signal resulting from IP3 provoked release of calcium from the endoplasmic reticulum may depend on the cytoskeleton structure.

Calcium Signaling↗
PubMed1991

On the computational approach to immobilized pH gradients.

The unified treatment for computing the pH of complex mixtures of mono- and polyprotic buffers, including ampholytes, as utilized in the gradient simulation program PGS, is presented. Its ability to compute pH, buffering power and ionic strength is shown by discussing a few simulations. The problems arising in the automatic formulation of optimal mixtures are presented, as well as the merits and limits of several target functions utilized in such optimizations. It is shown that no universal target function exists and that a proper optimization method should account for the fact that more than one formulation is possible for a given pH range.

Buffers↗
PubMed1999

Computational approaches to structure-based ligand design.

The first computational structure-based drug design methods came into existence in the early 1980s and are, to an extent, still in their infancy. There have been a few successes to date. With dramatic increases in computer speed, improved accuracy in ligand scoring functions, and the advent of combinatorial chemistry, there promises to be many more. In addition, the virtual explosion in the amount of available sequence and structural information has increased the need to develop these computational techniques to exploit this vast body of information. In this review, recent advances in computational methods for database searching and docking, de novo drug design, and estimation of ligand binding affinities are discussed.

Combinatorial Chemistry Techniques↗
PubMed2025

Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.

Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell receptor-engineered T (TCR-T), chimeric antigen receptor T (CAR-T), and therapeutic cancer vaccines (TCVs). After recognizing presented neoantigens, the immune system becomes activated and triggers the death of tumor cells. Neoantigens may be derived from multiple origins, including somatic mutations (single nucleotide variants, insertions/deletions, and gene fusions), circular RNAs, alternative splicing, RNA editing, and polymorphic microbiomes. An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources, which may require inputs from different multi-omics data. In addition, calculating the peptide-major histocompatibility complex (MHC) affinity can aid in selecting putative neoantigens, as high binding affinities facilitate antigen presentation. Based on these approaches and previous experiments, many resources have been developed to reveal the landscape of tumor neoantigens across multiple cancer types. Herein, we summarize these tools, algorithms, and resources to provide an overview of computational analysis for neoantigen discovery and prioritization, as well as the future development of potential clinical utilities in this field.

Humans↗
PubMed1996

Recognition-by-parts: a computational approach to human learning and generalization of shapes.

In this paper human pattern recognition is modeled in terms of how human observers learn to describe patterns in terms of their perceived parts, their unary (part) and binary (relational) attributes and the way in which such attribute states "evidence' different classes of shapes. This approach, originally developed in the area of computer vision, is concerned with algorithms which enable the learning of shape descriptions from examples and the classification of new data (generalization) efficiently and accurately. An object in such an "evidence-based' system is represented by a set of rules, where each rule provides a certain amount of evidence for each object class in the database. The accumulated class evidence over all activated rules can then be used to determine the classification probability. We have examined how well this model reflects human perception by training observers to classify compound Gabor patterns and then testing them with versions of such patterns which were segmented (gray-level transformed) versions of the original training set. If the observers were to construct rules to define each pattern class in terms of perceived parts and their relations, then it should be expected that classification performance would generalize to these new patterns from the original set. Results confirm this hypothesis and the specific feature extraction, learning and rule generation model used to predict performance.

Attention↗
PubMed2000

Predicting human safety: screening and computational approaches.

Current preclinical safety evaluation programs use a combination of computational methods, mechanistic in vitro screening and - primarily - in vivo experimentation to predict human toxicity. The rapid transition of pharmaceutical R&D into electronic R&D (e-R&D) makes it imperative that predictive safety testing also develops into an information-rich, knowledge-based process in the near future. Accordingly, enhanced databases and computational tools are expected to change the way the pharmaceutical industry assesses drug toxicity during discovery and early development. Expert use of prediction tools should lead to lower failure rates in drug development and decrease the cost and time involved in successful drug approval.

Journal Article↗
PubMed1980

Perception of surface slant and edge labels from optical flow: a computational approach.

I present here two results from investigations of a computational theory of how the human visual system may obtain information about the physical environment directly from optically sensed velocity fields (optical flow). Previous work has shown how optical flow arises when an observer moves through the static environment. The inverse problem is investigated here: how to recover intrinsic characteristics of the environment from optical flow patterns. The first result is a method for computing the local slant of surfaces relative to the moving observer. The second result is a method for detecting and discriminating among the five types of edges that form the boundaries of surfaces. The results have been formalised as mathematical equations, a physiological model, and a computer program. Properties and predictions resulting from these formal models are discussed with regard to experimental findings in psychophysics.

Computers↗
PubMed2003

Computational approach to quantifying hemodynamic forces in giant cerebral aneurysms.

BACKGROUND AND PURPOSE: The options for treating giant fusiform basilar aneurysms are limited, and the potential impact of planned interventions is difficult to assess. We developed a computational framework to evaluate the impact that interventions might have on hemodynamic conditions. METHODS: A computational fluid dynamics approach was used to determine the velocity field, wall shear stress, and pressure distribution within a model of a basilar artery before and after a simulated occlusion of one vertebral artery. The vascular geometry in a patient with a giant fusiform basilar artery aneurysm was determined by using contrast-enhanced MR angiography, and the numerical simulation approach was used to calculate the flow fields in the presenting geometry and to predict the flow field that would occur if a vertebral artery were occluded. RESULTS: In the model geometry, computational fluid dynamics indicated that there would be a symmetric flow pattern with a strong central stream and large recirculation zones at the walls. After simulated occlusion of one vertebral artery, the primary stream was diverted to one side, resulting in high pressure and increased wall shear stress. For the patient-specific geometry, flow patterns were shown to depend strongly on how much flow there was in each vertebral artery. CONCLUSION: Contrast-enhanced MR angiography is an effective tool for demonstrating the luminal boundaries of large intracranial aneurysms. Computational fluid dynamics is a powerful tool for determining the prevailing flow conditions in vascular territories and for modeling the possible alterations of the flow field that would result from interventional treatments.

Basilar Artery↗
PubMed1991

Isoelectric membrane simulator: a computational approach for isoelectric immobiline membranes.

Isoelectric membrane simulator (IMS) is a computer program meant for computation of pH, buffering power (beta), ionic strength (I) and dissociation degree (a) of a mixture of up to 3 buffering and 1 titrant Immobilines, for generating in a reproducible manner isoelectric membranes. Such membranes, of precise isoelectric point, are then used for large-scale protein purification by isoelectric focusing in multicompartment electrolyzers. IMS can be used, in a more general application, for titrating mixtures of buffers to a desired pH value. This versatile program is written in M.Q.BASIC rel. 2.5 and it runs on any IBM hardware or compatible machine supported by MS-DOS. An example of purification of superoxide dismutase in a multicompartment electrolyzer with a set of fixed pI membranes of widely differing composition is shown.

Acrylamides↗