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PubMed1997

A second generation of terminological systems is coming.

Diverse achievements by recent computer-based terminological systems are outlining a new generation of systems (i.e. a "second generation"). We collected the relevant features of various advanced terminological systems and we systematized these features into four components of a unique framework. We review a set of systems according to our framework, and we discuss how standardization activities can support the evolution of computer-based terminological systems towards a complete set of new performances.

Humans↗
PubMed1987

Computers in the cognitive rehabilitation of brain-injured persons.

Currently there is a rapid expansion of work among rehabilitation professionals in applying computer-assisted instructional technology to remediate cognitive deficits resulting from brain injury. The present article presents a framework for relating the various theoretical, empirical, and clinical challenges raised by the coalescence of two such recently emerging disciplines as computer-assisted instruction and cognitive rehabilitation. These challenges are presented from the perspectives of diverse disciplines, including cognitive science, rehabilitation professions, and computer science. A set of guiding principles are derived for evaluating the potential efficacy of currently existing programs and for directing future developmental work in software design, evaluation research, and service delivery.

Animals↗
PubMed2003

Wavelet-like receptive fields emerges by non-linear minimization of neuron error.

Redundancy reduction as a form of neural coding has been since the early sixties a topic of large research interest. A number of strategies has been proposed, but the one which is attracting most attention recently assumes that this coding is carried out so that the output signals are mutually independent. In this work we go one step further and suggest an strategy to deal also with non-orthogonal signals (i.e., "dependent" signals). Moreover, instead of working with the usual squared error, we design a neuron where the non-linearity is operating on the error. It is computationally more economic and, importantly, the permutation/scaling problem is avoided. The framework is given with a biological background, as we avocate throughout the manuscript that the algorithm fits well the single neuron and redundancy reduction doctrine. Moreover, we show that wavelet-like receptive fields emerges from natural images processed by this algorithm.

Algorithms↗
PubMed2003

Ultrastructure of pigment-dispersing hormone-immunoreactive neurons in a three-dimensional model of the accessory medulla of the cockroach Leucophaea maderae.

Locomotor activity rhythms of the cockroach Leucophaea maderae are orchestrated by two bilaterally symmetric, mutually coupled, circadian pacemakers. They lie in the optic lobes of the brain and are confined to the accessory medulla (AMe), ventro-medially to the medulla. The AMe is innervated by approximately 12 pigment-dispersing hormone (PDH)-immunoreactive anterior medulla neurons (PDHMe), which are circadian pacemaker candidates in the fruitfly and the cockroach. We have developed a three-dimensional computer model of the AMe and associated structures as a framework for neuroanatomical studies. Our greatly improved understanding of this structure in space has allowed us further to subdivide the anterior PDHMe into three subgroups, i.e., large, medium-sized, and small anterior PDHMe. The synaptic connections of two of these subgroups have been examined within subcompartments of the AMe by light and electron microscopy. The large, intensely staining, anterior PDHMe contain medium-sized dense-core vesicles and form input and output synapses with profiles densely filled with clear vesicles primarily in the anterior and shell neuropil of the AMe. The medium-sized anterior PDHMe contain large dense-core vesicles and constitute input and output synapses either with profiles being densely filled with clear vesicles, or with profiles containing granular dense-core vesicles. The small, weakly staining anterior PDHMe belong to a morphological group different from the large and medium-sized PDHMe and cannot be further identified at the electron-microscopic level because of their weak PDH immunoreactivity.

Animals↗
PubMed2006

Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling.

The complexity of the acute inflammatory response (AIR) is, by now, generally recognized. The primary manifestation of this property has been the difficulty in translating the information derived from reductionist, basic science research into effective clinical treatment regimens for sepsis. However, the recognition of the "complexity" of the AIR is not without its pitfalls. Despite its limitations, reductionism remains the primary means of obtaining scientific information. Furthermore, a functional shortcoming of use of the term complex has been to make it equivalent to "essentially unsolvable." Therefore, a mechanism is needed to integrate the apparatus of reductionist analysis into a complex synthetic methodology that overcomes the current limitations of both. Toward this end, I propose a structure for a class of collaborative, community-wide in silico models that use the framework of agent-based modeling. Agent-based modeling is a type of mathematical modeling that focuses on the behaviors of the components of complex systems and is well suited for translating the results of basic science experiments. I will also introduce a preliminary version of a syntactical "grammar" that can potentially be used to facilitate the transfer of basic science data into computer code. It is hoped that when a mature version of this framework is implemented, the resulting models will provide a functional, synthetic data base on the AIR that could be used for directing research, testing hypotheses, teaching and training, and drug discovery/testing.

Acute Disease↗
PubMed1983

A computer-compatible method for observing falling asleep behavior of hospitalized children.

A family-organizational linkage framework was used to conceptualize the nighttime separation behaviors of 18 hospitalized children, ages 3 to 8, whose parents did not room-in. All children were observed for three consecutive nights during the falling asleep period. A bedtime story, tape recorded by the parent, was played on the second and third nights for one group. Frequency and duration of falling asleep behaviors were recorded and analyzed with the Senders Signals and Receivers System, a computer-compatible method of recording behavioral data. Eight conceptual behavioral categories emerged from the data: sleepy, contact, active, inactive, neutral, communication, distress, and pleasure. The story-children fell asleep sooner (23 minutes vs. 28 minutes), exhibited more sleepy behaviors, and displayed fewer active behaviors. Duration of contact behaviors also was greater in this group (22 minutes vs. 14 minutes). Hospitalized children who hear a bedtime story recorded by a parent appear to use self-soothing behaviors to cope with the separation experience.

Child↗
PubMedDate not supplied

A self-learning segmentation framework--the Taguchi approach.

The detection of object boundary is an interesting and challenging task in computer vision and medical image processing. The active contour model (snake model) has attracted much attention for object boundary detection in the past decade. However, due to the lack of understanding on the effect of different energy terms to the behavior of related objective functions for an image, the assignment of weights for different energy terms in this model is usually fulfilled empirically. Few discussions have been brought out specifically for assigning these weights automatically. In this paper, a novel self-learning segmentation framework, based on the snake model is proposed and applied to the detection of cardiac boundaries from ultrasonic images. The framework consists of a learning section and a detection section, and provides a training mechanism to obtain the weights from a desired object contour given manually. This mechanism first employs Taguchi's method to determine the weight ratios among distinct energy terms, followed by a weight refinement step with a genetic algorithm. The refined weights can be treated as the a priori knowledge embedded in the manually defined contour and be used for subsequent contour detection. Experiments with both synthetic and real echocardiac images were conducted with satisfactory outcomes. Results also show that the present method can be used to analyze successive images of the same object with only one training contour. Finally, the validity of the weight determining process was verified by the analysis of variance method (ANOVA).

Algorithms↗
PubMed2006

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment.

Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Differences in conformational sampling of DNA with two sets of atomic radii that are used to define the dielectric interface between the solute and the continuum dielectric model of the solvent are investigated. Results suggest that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations. Furthermore, partial conformational transitions toward A-DNA conformations when salt is added within the implicit solvent framework are observed.

Computer Simulation↗
PubMedDate not supplied

Impact of manual and computer-assisted PACS for automated PACS.

Considerations of totally electronic picture archiving system (PACS) often neglect the fact that every radiology practice currently has some system for storing and retrieving images and related alphanumeric data. Although these systems are usually manual, many departments now use on-line computers to help manage film flow. In either event, the creation of electronic PACS can be viewed as a classic data processing problem of automating an existing system, and the conversion should proceed through the usual steps of documenting the existing system in detail, and conducting feasibility studies and cost-benefit analyses. Documenting current systems should be facilitated by computer-assisted PACS--particularly documenting transaction volumes which can be provided as a by-product of radiology information management systems. Similarly cost-benefit analysis should be facilitated, although the cost/benefit ratio may be less favorable when comparing automated to computer-assisted PACS. Finally, information management features such as those provided by current on-line radiology systems provide a framework necessary to realize the full benefits of automated PACS.

Computers↗
PubMed1999

A CORBA-based object framework with patient identification translation and dynamic linking. Methods for exchanging patient data.

Exchanging and integration of patient data across heterogeneous databases and institutional boundaries offers many problems. We focused on two issues: (1) how to identify identical patients between different systems and institutions while lacking universal patient identifiers; and (2) how to link patient data across heterogeneous databases and institutional boundaries. To solve these problems, we created a patient identification (ID) translation model and a dynamic linking method in the Common Object Request Broker Architecture (CORBA) environment. The algorithm for the patient ID translation is based on patient attribute matching plus computer-based human checking; the method for dynamic linking is temporal mapping. By implementing these methods into computer systems with help of the distributed object computing technology, we built a prototype of a CORBA-based object framework in which the patient ID translation and dynamic linking methods were embedded. Our experiments with a Web-based user interface using the object framework and dynamic linking-through the object framework were successful. These methods are important for exchanging and integrating patient data across heterogeneous databases and institutional boundaries.

Database Management Systems↗
PubMed2006

Using a white matter reference to remove the dependency of global signal on experimental conditions in SPECT analyses.

Proportional scaling models are often used in functional imaging studies to remove confounding of local signals by global effects. It is generally assumed that global effects are uncorrelated with experimental conditions. However, when the global effect is estimated by the global signal, defined as the intracerebral average, incorrect inference may result from the dependency of the global signal on preexisting conditions or experimental manipulations. In this paper, we propose a simple alternative method of estimating the global effect to be used in a proportional scaling model. Specifically, by defining the global signal with reference strictly to a white matter region within the centrum semiovale, the dependency is removed in experiments where white matter is unaffected by the disease effect or experimental treatments. The increase in the ability to detect changes in regional blood flow is demonstrated in a SPECT study of healthy and ill Gulf War veterans in whom it is suspected that brain abnormalities influence the traditional calculation of the global signal. Controlling for the global effect, ill veterans have significantly lower intracerebral averages than healthy controls (P = 0.0038), evidence that choice of global signal has an impact on inference. Scaling by the modified global signal proposed here results in an increase in sensitivity leading to the identification of several regions in the insula and frontal cortex where ill veterans have significantly lower SPECT emissions. Scaling by the traditional global signal results in the loss of sensitivity to detect these regional differences. Advantages of this alternative method are its computational simplicity and its ability to be easily integrated into existing analysis frameworks such as SPM.

Brain↗
PubMed2006

Lossless watermarking for image authentication: a new framework and an implementation.

We present a novel framework for lossless (invertible) authentication watermarking, which enables zero-distortion reconstruction of the un-watermarked images upon verification. As opposed to earlier lossless authentication methods that required reconstruction of the original image prior to validation, the new framework allows validation of the watermarked images before recovery of the original image. This reduces computational requirements in situations when either the verification step fails or the zero-distortion reconstruction is not needed. For verified images, integrity of the reconstructed image is ensured by the uniqueness of the reconstruction procedure. The framework also enables public(-key) authentication without granting access to the perfect original and allows for efficient tamper localization. Effectiveness of the framework is demonstrated by implementing the framework using hierarchical image authentication along with lossless generalized-least significant bit data embedding.

Algorithms↗
PubMed2005

Hypothetical binodal zeolitic frameworks.

Hypothetical binodal zeolitic structures (structures containing two kinds of tetrahedral sites) were systematically enumerated using tiling theory and characterized by computational chemistry methods. Each of the 109 refineable topologies based on "simple tilings" was converted into a silica polymorph and its energy minimized using the GULP program with the Sanders-Catlow silica potential. Optimized structural parameters, framework energies relative to alpha-quartz and volumes accessible to sorption have been calculated. Eleven of the 30 known binodal topologies listed in the Atlas of Zeolite Framework Types were found, leaving 98 topologies that were unknown previously. The chemical feasibility of each structure as a zeolite was evaluated by means of a feasibility factor derived from the correlation between lattice energy and framework density. Structures are divided into 15 families, based on common structural features. Many "feasible" structures contain only small pores. Several very open structures were also enumerated, although they contain three-membered rings which are thermodynamically disfavoured and not found in conventional zeolites. We believe that such topologies may be realizable as framework materials, but with different elemental compositions to those normally associated with zeolites.

Computing Methodologies↗
PubMed2003

EXCAVATOR: a computer program for efficiently mining gene expression data.

Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.

Algorithms↗
PubMed2026

Advancing proteomic discovery through optimized multi-stage scoring and deep learning-enhanced open search.

MOTIVATION: Protein search engines are essential for interpreting mass spectrometry data into biological insight. Current tools often face limitations in sensitivity when analyzing complex modern datasets, and lack a unified framework that effectively integrates deep learning features for both restricted and open searches, especially for scenarios aimed at discovering unknown modifications. RESULTS: We present pFind+, a high-performance search engine for data-dependent acquisition (DDA) proteomics, extending pFind. It introduces an enhanced raw scoring that delivers substantially improved pre-filtering ability, while recovering most of the computational overhead through a tailored acceleration strategy. Coupled with an enhanced rescoring framework that effectively integrates deep learning features, pFind+ uniquely supports high-sensitivity, DL-enhanced open search, enabling comprehensive PTM discovery while incorporating hardware-aware inference optimizations for practical deployment. Evaluations across diverse datasets demonstrate its superior sensitivity, with gains of 12.7%-29.3% (average 17.9%) in restricted search and 8.0%-38.4% (average 25.8%) in open search over the best existing tools.

Deep Learning↗
PubMed1993

To test or not to test, that is the question.

This paper describes a system that is used in Maastricht, the Netherlands, to provide general practitioners with feedback about the adequateness of their test requesting behaviour. The system has proven to be effective. Since the screening of test requests and additional patient data is work-intensive a project was started in the framework of the AIM programme OPENLABS to design a computer-based feedback system. In this system the general practitioner sends test requests to the laboratory decision support system by means of electronic data interchange (EDI). The authors were involved in the development of the EDI messages, which are now accepted standards in the Netherlands. The requests are stored in a database that is part of the laboratory decision support system. The other part of the decision support system, an expert system, obtains the request data (including patient data) from the database, screens the requests for adequateness and provides feedback when necessary.

Clinical Laboratory Information Systems↗
PubMed2002

Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q.

The electronic structures of key species involved in methane hydroxylation performed by the hydroxylase component of soluble methane monooxygenase (sMMO), as proposed previously on the basis of high-level density functional theory, were investigated. The reaction starts with initial approach of methane at one of the bridging oxo atoms in intermediate Q, a di(mu-oxo)diiron(IV) unit. This step is accompanied by a proton-coupled outer-sphere transfer of the first electron from a C-H sigma-bond in methane to one of the metal centers. The second electron transfer, also an outer-sphere electron transfer process, occurs along a two-component reaction pathway. Both redox reactions are strongly coupled to structural distortions of the diiron core. The electronic consequence and driving force of these distortions are intuitively explained by using the computed Kohn-Sham orbitals in the broken-symmetry framework to incorporate the experimentally observed antiferromagnetic coupling of the unpaired electrons at the metal centers. The broken-symmetry orbital scheme is essential for describing the C-H bond activation process in a consistent and complete manner, enabling derivation of both an intuitive and quantitative understanding of the most salient electronic features that govern the details of the hydroxylation.

Electrons↗