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PubMedDate not supplied

A data mining approach for analyzing density maps representing macromolecular structures.

Results of electron microscopy-based three-dimensional reconstructions of macromolecules or their complexes are usually stored as density maps. Each point ("voxel") in the map represents a density value and one approach for studying details of the map is to display an isosurface enclosing areas of interest. We have taken a data mining approach not only focusing on the areas of immediate interest but determining all possible separate entities ("blobs") from a density map. After the entire density map is analyzed with our mining program BLOBBER, properties of all detected blobs can be browsed and sets of blobs can be visualized using our VIZBLOB program. Since BLOBBER analyzes density maps using only density information and relates it to spatial relationships, BLOBBER can be used to analyze symmetrical or asymmetrical density maps from any source. To test our program we have analyzed published bacteriophage PRD1 reconstructions. We identified various structural details ranging from individual proteins to major complexes such as the whole capsid shell and more elaborate details of possible connections between membrane interfaces. This approach can also be a useful preprocessing tool for visualizing reconstructions.

Bacteriophages↗
PubMed1997

High-performance computing and networking as tools for accurate emission computed tomography reconstruction.

It is well known that the quantitative potential of emission computed tomography (ECT) relies on the ability to compensate for resolution, attenuation and scatter effects. Reconstruction algorithms which are able to take these effects into account are highly demanding in terms of computing resources. The reported work aimed to investigate the use of a parallel high-performance computing platform for ECT reconstruction taking into account an accurate model of the acquisition of single-photon emission tomographic (SPET) data. An iterative algorithm with an accurate model of the variable system response was ported on the MIMD (Multiple Instruction Multiple Data) parallel architecture of a 64-node Cray T3D massively parallel computer. The system was organized to make it easily accessible even from low-cost PC-based workstations through standard TCP/IP networking. A complete brain study of 30 (64x64) slices could be reconstructed from a set of 90 (64x64) projections with ten iterations of the conjugate gradients algorithm in 9 s, corresponding to an actual speed-up factor of 135. This work demonstrated the possibility of exploiting remote high-performance computing and networking resources from hospital sites by means of low-cost workstations using standard communication protocols without particular problems for routine use. The achievable speed-up factors allow the assessment of the clinical benefit of advanced reconstruction techniques which require a heavy computational burden for the compensation effects such as variable spatial resolution, scatter and attenuation. The possibility of using the same software on the same hardware platform with data acquired in different laboratories with various kinds of SPET instrumentation is appealing for software quality control and for the evaluation of the clinical impact of the reconstruction methods.

Algorithms↗
PubMed1997

Quantization errors of the echoes in ultrasonic pulsed flowmeter employing time domain correlation.

The implementation of Time Domain Correlation Method for blood flow velocity estimation requires the conversion of the reflected ultrasonic signals into digital format in order that the computer can be utilized to investigate the technique. A number of quanitization errors, namely, that the A/D has a finite bit resolution, only a limited number of samples of the waveform may be taken per wavelength and correlation function only exits at discrete points, have an effect on the velocity estimate. This paper discusses the effect of errors associated with A/D conversion process on the accuracy of the velocity estimate. A computer simulation was performed to achieve this goal. A band passed white Gaussian noise segment was used to simulate the reflected ultrasonic signal. The jitters of the velocity estimates corresponding various A/D resolutions were calculated and plotted. Effects of interpolating the correlation function rather than determining the complete function were presented.

Algorithms↗
PubMed2000

Inferring qualitative relations in genetic networks and metabolic pathways.

MOTIVATION: Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics. Although inference algorithms based on the Boolean network were proposed, the Boolean network was not sufficient as a model of a genetic network. RESULTS: First, a Boolean network model with noise is proposed, together with an inference algorithm for it. Next, a qualitative network model is proposed, in which regulation rules are represented as qualitative rules and embedded in the network structure. Algorithms are also presented for inferring qualitative relations from time series data. Then, an algorithm for inferring S-systems (synergistic and saturable systems) from time series data is presented, where S-systems are based on a particular kind of nonlinear differential equation and have been applied to the analysis of various biological systems. Theoretical results are shown for Boolean networks with noises and simple qualitative networks. Computational results are shown for Boolean networks with noises and S-systems, where real data are not used because the proposed models are still conceptual and the quantity and quality of currently available data are not enough for the application of the proposed methods.

Algorithms↗
PubMed2002

Introduction to the special issue on virtual reality environments in behavioral sciences.

Virtual reality (VR) is usually described in biology and in medicine as a collection of technologies that allow people to interact efficiently with three-dimensional (3-D) computerized databases in real time using their natural senses. This definition lacks any reference to head-mounted displays (HMDs) and instrumented clothing such as gloves or suits. In fact, less than 10% of VR healthcare applications in medicine are actually using any immersive equipment. However, if we focus our attention on behavioral sciences, where immersion is used by more than 50% of the applications, VR is described as an advanced form of human- computer interface that allows the user to interact with and become immersed in a computer-generated environment. This difference outlines a different vision of VR shared by psychologists, psychotherapists, and neuropsychologists: VR provides a new human-computer interaction paradigm in which users are no longer simply external observers of images on a computer screen but are active participants within a computer-generated 3-D virtual world. This special issue investigates this vision, presenting some of the most interesting applications actually developed in the area. Moreover, it discusses the clinical principles, human factors, and technological issues associated with the use of VR in the behavioral sciences.

Behavioral Sciences↗
PubMed2001

Analyzing holistic parsers: implications for robust parsing and systematicity.

Holistic parsers offer a viable alternative to traditional algorithmic parsers. They have good generalization performance and are robust inherently. In a holistic parser, parsing is achieved by mapping the connectionist representation of the input sentence to the connectionist representation of the target parse tree directly. Little prior knowledge of the underlying parsing mechanism thus needs to be assumed. However, it also makes holistic parsing difficult to understand. In this article, an analysis is presented for studying the operations of the confluent preorder parser (CPP). In the analysis, the CPP is viewed as a dynamical system, and holistic parsing is perceived as a sequence of state transitions through its state-space. The seemingly one-shot parsing mechanism can thus be elucidated as a step-by-step inference process, with the intermediate parsing decisions being reflected by the states visited during parsing. The study serves two purposes. First, it improves our understanding of how grammatical errors are corrected by the CPP. The occurrence of an error in a sentence will cause the CPP to deviate from the normal track that is followed when the original sentence is parsed. But as the remaining terminals are read, the two trajectories will gradually converge until finally the correct parse tree is produced. Second, it reveals that having systematic parse tree representations alone cannot guarantee good generalization performance in holistic parsing. More important, they need to be distributed in certain useful locations of the representational space. Sentences with similar trailing terminals should have their corresponding parse tree representations mapped to nearby locations in the representational space. The study provides concrete evidence that encoding the linearized parse trees as obtained via preorder traversal can satisfy such a requirement.

Algorithms↗
PubMed2001

SignStream: a tool for linguistic and computer vision research on visual-gestural language data.

Research on recognition and generation of signed languages and the gestural component of spoken languages has been held back by the unavailability of large-scale linguistically annotated corpora of the kind that led to significant advances in the area of spoken language. A major obstacle has been the lack of computational tools to assist in efficient analysis and transcription of visual language data. Here we describe SignStream, a computer program that we have designed to facilitate transcription and linguistic analysis of visual language. Machine vision methods to assist linguists in detailed annotation of gestures of the head, face, hands, and body are being developed. We have been using SignStream to analyze data from native signers of American Sign Language (ASL) collected in our new video collection facility, equipped with multiple synchronized digital video cameras. The video data and associated linguistic annotations are being made publicly available in multiple formats.

Computer Simulation↗
PubMed2003

Support vector machine applications in bioinformatics.

The support vector machine (SVM) approach represents a data-driven method for solving classification tasks. It has been shown to produce lower prediction error compared to classifiers based on other methods like artificial neural networks, especially when large numbers of features are considered for sample description. In this review, the theory and main principles of the SVM approach are outlined, and successful applications in traditional areas of bioinformatics research are described. Current developments in techniques related to the SVM approach are reviewed which might become relevant for future functional genomics and chemogenomics projects. In a comparative study, we developed neural network and SVM models to identify small organic molecules that potentially modulate the function of G-protein coupled receptors. The SVM system was able to correctly classify approximately 90% of the compounds in a cross-validation study yielding a Matthews correlation coefficient of 0.78. This classifier can be used for fast filtering of compound libraries in virtual screening applications.

Algorithms↗
PubMed1998

The impact of a computer generated patient held health record.

OBJECTIVE: To examine the use and impact of a computer generated, patient held health record (PHR) on information sharing, responsibility sharing and preventive health care. SETTING: An academic group, private solo and private group general practice in Adelaide, South Australia. METHODS: Patients with chronic health problem(s) were randomly assigned to an experimental control or post test only group. Pre and post intervention data were collected using a standardised audit and abstraction of the patient records into a computer based record system. In addition, patient and doctor questionnaires, telephone follow ups and face to face interviews were conducted. OUTCOME MEASURES: Patient and GP use of, and satisfaction with the PHR; effectiveness of information and responsibility sharing; and uptake and performance of selected preventive health care by patient and GP. RESULTS: Seventy-two patients were recruited (29 received the PHR, and 22 each were in the control and post test only groups). The PHR was well received and used in both primary and secondary care settings. No statistically significant differences in the outcome measures were found between the groups as well as before and after the intervention (Kruskal-Wallis, p > 0.05). Data trends suggested that the PHR may increase information and responsibility sharing as well as improve patient awareness of the issues involved, with patient participation in information sharing, preventive health care and clinical decision making. Provided training and resources were made available, participating GPs believed that the computer based methodology developed was a practical option for use in practice. CONCLUSION: The computer generated PHR is an important determinant of patient participation in information and responsibility sharing, health promotion, and disease management. Implementation and evaluation studies are recommended.

Adolescent↗
PubMed1998

Concepts, knowledge and language in healthcare information systems: follow-up 30 months later.

The paper reviews the last IMIA-WG6 recommendations, issued along two themes: (1) how to better share common results and (2) how to conduct new research and development efforts. Some of the major discrepancies in the field are reviewed. The paper intends to offer insight into two areas, first, in the issue of knowledge representation and, second, in the science of meaning, incorporating the broad intersection of computational linguistics, semantics, conceptual approach, and denotation. The Ogden-Richards meaning triangle is used as a convenient organizing principle to maximize the scope of understanding among the different schools, particularly in areas of linguistics and semantics on the one side and denotation and conceptual approach on the other. In conclusion, there is a need for clarification and for more scientific pragmatism.

Artificial Intelligence↗
PubMedDate not supplied

[Method of computing the geometrical parameters of contact lenses].

Contact lenses of home-made production are classified, and the methodology of computing their structural elements for several types of lenses is presented. Some design features of the parameters are considered with regard to the properties of the water-receptive material used for soft lenses.

Contact Lenses↗
PubMedDate not supplied

An integrated methodological approach to the computer-assisted gas chromatographic screening of basic drugs in biological fluids using nitrogen selective detection.

This paper presents the methodological aspects of a computerized system for the gas-chromatographic screening and primary identification of central nervous system stimulants and narcotic analgesics (including some of their respective metabolites) extracted from urine. The operating conditions of a selective nitrogen detector for optimized analytical functions are discussed, particularly the effect of carrier and fuel gas on the detector's sensitivity to nitrogen-containing molecules and discriminating performance toward biological matrix interferences. Application of simple extraction techniques, combined with rapid derivatization procedures, computer data acquisition, and reduction of chromatographic data are presented. Results show that this system approach allows for the screening of several drugs and their metabolites in a short amount of time. The reliability and stability of the system have been tested by analyzing several thousand samples for doping control at major international sporting events and for monitoring drug intake in addicts participating in a rehabilitation program. Results indicate that these techniques can be used and adapted to many different analytical toxicology situations.

Body Fluids↗
PubMedDate not supplied

[Structural principles in the creation of training in medical information retrieval systems].

The systems approach has been used to consider the principles in the creation of the popular medical information retrieval systems (IRSs) BodyWorks, 3DBody, MAYO Clinic on IBM personal computers. The methodological problems in the use of IRSs in a training process, requirements for computer resources, strategy for development of such systems under the Russian conditions are discussed in the paper. Guidelines for further developments are also forwarded.

Information Systems↗
PubMed1997

Two complementary methods for predicting peptides binding major histocompatibility complex molecules.

Peptides that bind to major histocompatibility complex products (MHC) are known to exhibit certain sequence motifs which, though common, are neither necessary nor sufficient for binding: MHCs bind certain peptides that do not have the characteristic motifs and only about 30% of the peptides having the required motif, bind. In order to develop and test more accurate methods we measured the binding affinity of 463 nonamer peptides to HLA-A2.1. We describe two methods for predicting whether a given peptide will bind to an MHC and apply them to these peptides. One method is based on simulating a neural network and another, called the polynomial method, is based on statistical parameter estimation assuming independent binding of the side-chains of residues. We compare these methods with each other and with standard motif-based methods. The two methods are complementary, and both are superior to sequence motifs. The neural net is superior to simple motif searches in eliminating false positives. Its behavior can be coarsely tuned to the strength of binding desired and it is extendable in a straightforward fashion to other alleles. The polynomial method, on the other hand, has high sensitivity and is a superior method for eliminating false negatives. We discuss the validity of the independent binding assumption in such predictions.

Artificial Intelligence↗
PubMed1984

Analyzing and comparing the performance of two real-time playback systems.

A technique used in animated computer graphics involves the use of real-time playback. This method is used when it is not possible to display frames of display code in real-time. Instead, frames are compiled in advance at non realtime rates, saved in secondary storage, and played back at desired realtime speeds. The basic design and operation of two such systems will be considered. The more powerful of the two is built upon an Evans and Sutherland picture System I and utilizes animated vector graphics. The other playback system is built upon a Terak micro computer display and represents an example of rudimentary raster graphics animation. The synchronization, buffering, blocking and man-machine interfaces of both systems are detailed thus spotlighting their operational behavior. A comparison of the two systems show: that similarities in the logical organization of each system exist; that both systems are input bound; and both require their image files to be built on other computer systems. The differences in the performance of the two systems can be attributed to technological differences between the two systems; the retrieval rates of their respective disk subsystems; and differences in the intent and purpose behind the design of each machine. The systems are demonstrated by applying them to chemical modeling. It is determined that playback is a useful technique for examining complicated sequential situations or for providing the concise and convenient representation of large amounts of data.

Computer Graphics↗
PubMedDate not supplied

Parallel computation of simple arithmetic using peptide-antibody interactions.

We propose a theoretical model for representing and manipulating binary numbers using peptide-antibody interactions. In particular, we present models to solve simple binary arithmetical problems like addition and subtraction. As the interactions can take place in parallel we show that the number of steps is independent of the size (bits) of the numbers.

Algorithms↗
PubMed1997

World Wide Web interface for advanced SPECT reconstruction algorithms implemented on a remote massively parallel computer.

Data from Single Photon Emission Computed Tomography (SPECT) studies are blurred by inevitable physical phenomena occurring during data acquisition. These errors may be compensated by means of reconstruction algorithms which take into account accurate physical models of the data acquisition procedure. Unfortunately, this approach involves high memory requirements as well as a high computational burden which cannot be afforded by the computer systems of SPECT acquisition devices. In this work the possibility of accessing High Performance Computing and Networking (HPCN) resources through a World Wide Web interface for the advanced reconstruction of SPECT data in a clinical environment was investigated. An iterative algorithm with an accurate model of the variable system response was ported on the Multiple Instruction Multiple Data (MIMD) parallel architecture of a Cray T3D massively parallel computer. The system was accessible even from low cost PC-based workstations through standard TCP/IP networking. A speedup factor of 148 was predicted by the benchmarks run on the Cray T3D. A complete brain study of 30 (64 x 64) slices was reconstructed from a set of 90 (64 x 64) projections with ten iterations of the conjugate gradients algorithm in 9 s which corresponds to an actual speed-up factor of 135. The technique was extended to a more accurate 3D modeling of the system response for a true 3D reconstruction of SPECT data; the reconstruction time of the same data set with this more accurate model was 5 min. This work demonstrates the possibility of exploiting remote HPCN resources from hospital sites by means of low cost workstations using standard communication protocols and an user-friendly WWW interface without particular problems for routine use.

Algorithms↗