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PubMed1995

Developing interactive computer-based simulations: an object-oriented development methodology enhances computer-assisted instruction.

The purpose of this research was to investigate the application of object-oriented technology and AI techniques to enhance development of computer-based training simulations. Towards that end, a comprehensive computer-assisted instructional unit was developed to teach the skills and concepts of window-based applications, the OS/2 desktop, and the use of a patient care information system. By taking advantage of sophisticated computer graphics for the visual representation of objects and the behavioral modeling capabilities of the object-oriented language, domain knowledge modeling and human-computer interactions were implemented without complex natural language processing techniques. The results of this research indicate that nurses and physicians are able to learn the basic skills and concepts of computer systems and how to query for patient information. The new methodology described for building these computer-assisted instructional simulations significantly eased the training and teaching of large numbers of nurses and physicians and simplified their transition to a complex, computer-based hospital information system environment.

Computer Graphics↗

PubMed1992

[Computers in urology].

The present state of computer utilization in urology has been described. Nowadays, use of computer is becoming essential in the urological diagnosis and treatment. Recently computers have been so rapidly developed so that it became much smaller and yet offers higher performance. The methods and problems of utilizing computers have been explained by presenting actual examples. An important point that must be recognized in utilizing computers is that the computer is meant to be a part of method in resolving problems and its use itself is not conclusion. In other words, computers are a means of methodology. Computers have been used for frequency analysis in urophonograms, diagnosis in a simultaneous pressure-flow study in lower urinary tract, and for supporting the data entry by photoscanner. Moreover, computers have been used for digital differentiation to materialize higher performance uroflowmeter. Computers have also been applied to litholytic fluid pressure-flow control system for renal stones, and played important role in long hours's intra pelvic pressure monitoring system in support of the large amount of data accumulation and noise reduction. Recently, in the expert system in the pressure-flow study etc., computer plays an essential role which covers most territory of the system. Finally, its future applications have also been speculated.

Computers↗

PubMed1981

Teaching vowel articulation with the computer vowel trainer. Methodology and results.

The Computer Vowel Trainer (CVT) uses linear prediction to estimate and display the shape of the speaker's vocal tract during an utterance. The assessment of the CVT was carried out over a period of three years with 14 profoundly deaf children divided into an experimental and a matched control group. Two main results were obtained: (a) children learning to articulate with the CVT achieve consistently higher articulation scores than those trained with conventional methods; (b) the younger the children, the greater their progress in vowel learning, retention and generalization.

Age Factors↗

PubMed1991

Parallel distributed processing and neural networks: origins, methodology and cognitive functions.

Parallel Distributed Processing (PDP), a computational methodology with origins in Associationism, is used to provide empirical information regarding neurobiological systems. Recently, supercomputers have enabled neuroscientists to model brain behavior-relationships. An overview of supercomputer architecture demonstrates the advantages of parallel over serial processing. Histological data provide physical evidence of the parallel distributed nature of certain aspects of the human brain, as do corresponding computer simulations. Whereas sensory networks follow more sequential neural network pathways, in vivo brain imaging studies of attention and rudimentary language tasks appear to involve multiple cortical and subcortical areas. Controversy remains as to whether associative models or Artificial Intelligence symbolic models better reflect neural networks of cognitive functions; however, considerable interest has shifted towards associative models.

Artificial Intelligence↗

PubMed2025

OmnibusX: A unified platform for accessible multi-omics analysis.

OmnibusX is an integrated, privacy-centric platform that enables code-free multi-omics data analysis by bridging computational methodologies with user-friendly interfaces. Designed to overcome challenges posed by fragmented analytical tools and high computational barriers, OmnibusX consolidates workflows for diverse technologies - including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics - into a single, cohesive application. The application integrates established open-source tools such as Scanpy, DESeq2, SciPy, and scikit-learn into transparent, reproducible pipelines, offering users control over analytical parameters. Additionally, OmnibusX features proprietary modules, including a highly accurate cell-type prediction engine and an interactive plotting editor for generating publication-quality visualizations. Available as a standalone desktop application and an enterprise edition for centralized server deployment, OmnibusX ensures all data processing is conducted locally, eliminating external data transfer and usage tracking. By lowering technical barriers and enhancing reproducibility, OmnibusX aims to accelerate biological discovery and foster robust, data-driven collaborations. A fully documented trial version is accessible at: https://omnibusx.com/apps.

Computational Biology↗

PubMed1987

Computer instruction as part of a course on analytic medicine for first-year students.

The Medical University of South Carolina integrated instruction in information science and computer technology into a required freshman-level course. Analytic and Community Medicine. The advantages of this placement in the curriculum are two-fold. First, the course provides an opportunity to integrate computer methodology with clinically relevant topics such as medical decision-making. This integration enhances the students' view of the computer as a useful tool that can aid the physician in the practice of medicine. Course organizers are convinced that the success of the first offering is attributable to this integration. Second, the instruction comes early in the medical education process and allows the concepts learned to be utilized throughout the students' medical school careers. The degree to which these concepts and methods are actually utilized by students will depend upon the degree of reinforcement of these ideas in the clinical years and residency. Thus, faculty members must act as role models who not only acknowledge the importance of mastering the use of computers in medicine but also manifest those skills.

Community Medicine↗

PubMed1995

Computational methods for Markov series with large state spaces, with application to AIDS modeling.

AIDS models, and epidemiological models generally, are almost exclusively either differential equations or Markov processes. Of course, the phenomena are fundamentally random, so at best differential equations track the expectation of the process and variability is masked. There are few techniques in the literature for numerical analysis of Markov chains of any size, and so those wishing to analyze stochastic epidemics presently have little alternative to simulation. The contribution of the present paper is to propose numerical techniques capable of finding marginal probabilities of Markov chains having thousands and even millions of states. The ideas are illustrated by application to AIDS models in the literature which formerly had been investigated only through Monte Carlo. This introductory foray has not plumbed the depths of the computational methodology, which yet needs refinement and streamlining that comes through experience. Yet in its primitive form, it is shown herein to be adequate for a computation on the scale of a two-population partition of the San Francisco homosexual epidemic. The closing discussion compares the strengths and weaknesses of the present numerical techniques with the simulation approach to investigation of Markov epidemics.

Acquired Immunodeficiency Syndrome↗

PubMed2027

Inferring Gene Regulatory Networks in Stem Cells: Methods and Applications.

Gene regulatory networks (GRNs) represent the complex interplay of transcription factors, regulatory elements, and target genes that orchestrate cellular identity and function, playing a crucial role in the differentiation and maintenance of stem cells. This chapter provides an overview of experimental and computational methodologies for inferring GRNs, with particular emphasis on single-cell approaches. We first review key experimental techniques for detecting transcription factor binding sites, chromatin accessibility, and DNA motifs, alongside essential databases that support GRN reconstruction. We then introduce computational inference methods that can be categorized into four principal frameworks: correlation-based approaches, regression and machine learning models, probabilistic and deep learning methods, and integrative or message-passing frameworks. To illustrate practical application, we present a case study applying the pySCENIC workflow to a peripheral blood mononuclear cell single-cell RNA sequencing dataset from mouse, demonstrating how regulon-based analysis can reveal cell-type-specific regulatory programs. This chapter aims to serve as a practical guide for researchers seeking to understand and implement GRN inference methodologies in stem cell biology and related fields.

Gene Regulatory Networks↗

PubMed1992

AIDA: an automated insulin dosage advisor.

A prototype computer system utilising a model of carbohydrate metabolism linked to an expert system is described. The prototype which integrates quantitative and qualitative computational methodologies can be used to predict blood glucose profiles and adjust insulin doses in type I diabetic subjects.

Blood Glucose↗

PubMed1987

The role of computerized ECG interpretation in clinical trials.

The Lipid Research Clinics project consisted of the Prevalence Study and the Coronary Primary Prevention Study. The first study characterized the levels of blood lipids in the population studied, and related these to the presence of coronary artery disease as detected by medical history, symptom analysis, resting ECG and treadmill exercise ECG tests. The prevention trial tested whether a reduction of elevated serum cholesterol would reduce the incidence of coronary events (Table I). Both projects collected resting 12-lead ECGs and treadmill exercise test data on the participants. Instrumentation and methodology were standardized. Rest and exercise electrocardiographic data were recorded on analog magnetic tape. Tapes were sent to the ECG Center where they were digitized, analyzed and also reproduced for visual analysis according to the Minnesota Code of Blackburn. There were two reasons for using both visual coding and computer analyses in these projects. It was thought that computer methodology would enhance the accuracy of the electrocardiographic data, but on the other hand its accuracy had not been adequately documented and its output statements were not in the language of the Minnesota Code, which is traditionally accepted by epidemiologists. The other and more pressing reason for using the Minnesota Code is that the computer programming had not been completed at the start of the project, and visual coding was required in order to provide the ECG data necessary for the randomization of the Prevention Trial participants.

Clinical Trials as Topic↗

PubMed1979

Multiexponential and multicompartmental approaches for analysis of tracer washout data from animal.

A comparison is made between multiexponential and multicompartmental analyses of tracer washout data from biological tissues. Various analytical and computer methods are used to explore the relations between kinetic parameters of three-compartment models and parameters of three-exponential functions fitted to typical observed tracer washout records and also to examine relations between kinetic parameters of the same three-compartment models determined analytically and numerically. It is concluded that exponential factors and coefficients cannot always be equated respectively with conpartmental transport rate constants or compartment sizes. Sufficient analytical and computer methodologies exist so that selection of meaningful biological models should not be hampered by a lack of appropriate solution procedures.

Animals↗

PubMed1983

Evolving methodologies in computerized European Registries.

The histories and present roles of four European Registries are described. Three are transplant sharing organizations, Eurotransplant (ET), Scandiatransplant (ST), and the United Kingdom Transplant Service (UKTS). The Registry of the European Dialysis and Transplant Association is a patient Registry that tracks patients on dialysis as well as after transplantation and follows them from center to center. The transplant organizations collaborate by linking patient records on the EDTA Register. These large central Registries have evolved specialized computer methodologies for recording the follow-up of patients, researching the patient file, and improving the service to centers. The log-rank test is useful for the evaluation of pooled results. Reliability of donor typings can be verified by testing results for the Hardy-Weinberg equilibrium. A method for the prediction of pool size required to find matched recipients is described. Collaborative studies have been carried out in an attempt to discover the factor(s) responsible for the "center effect." New trends in analysis of transplant results will include detailed documentation of rejection episodes. Compliance by centers contributing to the transplant organizations is ensured by the need for organ interchange, whereas the EDTA Registry depends on the directors of centers being motivated by the publication of pooled statistics and results and by the provision of feedback information to the individual units.

Computers↗

PubMed1979

Characterization of normal human cells by pyrolysis gas chromatography mass spectrometry.

Differentiation of normal human cells has been accomplished by pyrolysis gas chromatography mass spectrometry. Normal cells from human kidney, spleen, liver and brain tissues have been pyrolyzed and the products chromatographically separated and characterized by mass spectrometry. Molecular pyrolysis products giving rise to the characteristic pyro-mass chromatograms include, but are not limited to, alkenes, alkanes, nitriles and various ring compounds. Single ion mass chromatograms as well as multiple ion mass chromatograms have been used to explore the characteristic differences between various tissue materials. A dynamic computer methodology for comparing pyro-mass chromatograms has been developed for use in automatic identification and classification of the human cellular material.

Brain↗

PubMed2024

Sparse spectral graph analysis and its application to gastric cancer drug resistance-specific molecular interplays identification.

Uncovering acquired drug resistance mechanisms has garnered considerable attention as drug resistance leads to treatment failure and death in patients with cancer. Although several bioinformatics studies developed various computational methodologies to uncover the drug resistance mechanisms in cancer chemotherapy, most studies were based on individual or differential gene expression analysis. However the single gene-based analysis is not enough, because perturbations in complex molecular networks are involved in anti-cancer drug resistance mechanisms. The main goal of this study is to reveal crucial molecular interplay that plays key roles in mechanism underlying acquired gastric cancer drug resistance. To uncover the mechanism and molecular characteristics of drug resistance, we propose a novel computational strategy that identified the differentially regulated gene networks. Our method measures dissimilarity of networks based on the eigenvalues of the Laplacian matrix. Especially, our strategy determined the networks' eigenstructure based on sparse eigen loadings, thus, the only crucial features to describe the graph structure are involved in the eigenanalysis without noise disturbance. We incorporated the network biology knowledge into eigenanalysis based on the network-constrained regularization. Therefore, we can achieve a biologically reliable interpretation of the differentially regulated gene network identification. Monte Carlo simulations show the outstanding performances of the proposed methodology for differentially regulated gene network identification. We applied our strategy to gastric cancer drug-resistant-specific molecular interplays and related markers. The identified drug resistance markers are verified through the literature. Our results suggest that the suppression and/or induction of COL4A1, PXDN and TGFBI and their molecular interplays enriched in the Extracellular-related pathways may provide crucial clues to enhance the chemosensitivity of gastric cancer. The developed strategy will be a useful tool to identify phenotype-specific molecular characteristics that can provide essential clues to uncover the complex cancer mechanism.

Stomach Neoplasms↗

PubMed1997

Different dietary calcium intake and relative supersaturation of calcium oxalate in the urine of patients forming renal stones.

1. Dietary calcium restriction, an efficient practice in reducing urinary calcium excretion, has been reported to induce either an increase or no change in oxalate excretion, questioning its use in hypercalciuric stone-forming patients. In addition, calcium restriction has been previously demonstrated to induce other urinary changes which might influence the relative supersaturation of calcium oxalate. So the overall effect of calcium deprivation on the relative supersaturation of calcium oxalate is unpredictable. 2. The aim of the study was to evaluate the effect of dietary calcium restriction on the relative supersaturation of calcium oxalate in the urine of stone-forming patients utilizing a computer methodology which takes into account the main soluble complex species of oxalate. 3. We studied 34 stone-forming patients on both a free-choice diet, whose Ca and oxalate content (24 and 1.2 mmol respectively) was assessed by dietary inquiry, and after 30 days on a prescribed low-calcium and normal oxalate diet (11 and 1.1 mmol respectively). Under both conditions, the excretion of the main urinary parameters related to dietary composition, electrolytes, oxalate and daily citrate urinary excretion, were measured. The relative supersaturation of calcium oxalate was calculated by means of an iterative computer method which takes into account the main soluble complex species on which the solubility of calcium oxalate is dependent. In addition, intact parathyroid hormone and 1,25-dihydroxyvitamin D blood levels were also evaluated. In 13 of the patients intestinal calcium absorption was evaluated during both a free- and a low-calcium diet, utilizing kinetics methodology. 4. The low-calcium diet induced, together with an expected reduction of calcium excretion, a marked increase in oxalate urinary output. This finding was independent of the presence or otherwise of hypercalciuria and of the serum levels of parathyroid hormone and vitamin D. Intestinal calcium absorption was also stimulated by calcium deprivation and its levels were well correlated with oxalate excretion. Minor changes in magnesium and citrate excretion were also observed. The overall effect on the relative supersaturation of calcium oxalate consisted in a substantial increase in this parameter during the low-calcium diet. 5. In conclusion, our data reinforce the concept that dietary calcium restriction has potentially deleterious effects on lithogenesis, by increasing the relative supersaturation of calcium oxalate.

Adult↗

PubMed1996

Impact of the mass media on calls to the CDC National AIDS Hotline.

This paper considers new computer methodologies for assessing the impact of different types of public health information. The example used public service announcements (PSAs) and mass media news to predict the volume of attempts to call the CDC National AIDS Hotline from December 1992 through to the end of 1993. The analysis relied solely on data from electronic databases. Newspaper stories and television news transcripts were obtained from the NEXIS electronic database and were scored by machine for AIDS coverage. The PSA database was generated by computer monitoring of advertising distributed by the Centers for Disease Control and Prevention (CDC) and by others. The volume of call attempts was collected automatically by the public branch exchange (PBX) of the Hotline telephone system. The call attempts, the PSAs and the news story data were related to each other using both a standard time series method and the statistical model of ideodynamics. The analysis indicated that the only significant explanatory variable for the call attempts was PSAs produced by the CDC. One possible explanation was that these commercials all included the Hotline telephone number while the other information sources did not.

Acquired Immunodeficiency Syndrome↗

PubMed1996

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly].

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L- and D-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Adrenocorticotropic Hormone↗

PubMed1996

Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design.

One relatively new computational approach to the drug discovery process involves calculating functional group maps of a target structure. Experimental functional group mapping techniques have also recently emerged. In this paper, the structure of RNase A with two bound formates (i.e. carboxylate functionalities) is used as a model system to test the computational methodology. Functional group maps of the RNase A structure were calculated using the Multiple Copy Simultaneous Search (MCSS) method and compared with experimentally determined formate and water positions. The calculations indicate that the protonation state of active-site histidines determines the ability of the enzyme to bind formate. The results also suggest an ordered binding mechanism for the two formates. An improved strategy for using the MCSS method to design new candidate ligands is discussed.

Animals↗