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PubMed1989

Novel computer optimization methodology for pharmaceutical formulations investigated by using sustained-release granules of indomethacin.

A modified optimization technique, based on the response surface methodology, was developed for selecting pharmaceutical formulations. In general optimization methods, it is difficult to insure that the optimum formulation is strictly obtainable. Thus, the combined use of random number techniques and Andrews' plots with general optimization methods was investigated for seeking the optimum formulation. The method developed in this study was applied to the optimization of a sustained-release formulation based on the interpolymer complex of polyvinylpyrrolidone with carboxyvinyl polymer. Indomethacin was selected as a model drug for which sustained-release formulations are desirable. Experimental results obtained for the optimum formulation agreed well with the predictions, indicating the usefulness of this approach.

Chemistry, Pharmaceutical↗
PubMed1993

Determining heart-rate variability: comparing methodologies using computer simulations.

Heart rate variation due to respiration is a window onto autonomic nervous system function and many measures exist that quantify this variability. Computer-based simulations of 1-minute deep-breathing tests, along with common artifacts, were used to compare the most frequently used measures. We found distinct differences in the performance of the measures. Some measures (e.g., SDRR and MSSD) are strongly influenced by the underlying mean heart rate while others (e.g., Max-Min and SDHR) are not. All of the measures tested, except R, were influenced by both shifting mean heart rate and single-beat anomalies. R, on the other hand, is strongly influenced by test duration and breathing asynchronies. Sensitivity to phenomena unrelated to ANS function can reduce the diagnostic discrimination of these measures. We suggest simple improvements to the measures and discuss how some measures may be theoretically superior to others.

Computer Simulation↗
PubMedDate not supplied

Profiling of endogenous brain peptides and small proteins: methodology, computer-assisted analysis, and application to aging and lesion models.

Significant advances in the technology for the isolation of peptides and small proteins have permitted their identification as biologic markers and enhanced the study of the posttranslational life of proteins. The protocol described here examined large numbers of tissue-derived peptides and small proteins, extracted in low pH and boiled so that proteolysis was interrupted. These were then fractionated batchwise using size exclusion and ion-exchange chromatography. Profiles of species in the peptide pools were then generated on reverse-phase high-performance liquid chromatography (HPLC). The HPLC profiles were evaluated with chromatographic analysis software to identify and quantify peptide peaks and with data compilation programs to sort this information into spreadsheets for comparison of profiles among groups. Using rodent brain, the effects of postmortem delay or age were examined. Postmortem delay produced limited alterations to the profiles, but the effect of age was more pronounced. Many changes were apparent until 12 months, after which the profiles became more constant. Additional peptide profiling of the hippocampus demonstrated changes in peptide content as a function of perforant pathway ablation. The major strengths of HPLC-mediated peptide profiling are that it lends itself to automation and can be used to detect changes in peptides and small proteins among experimental groups or subjects without any prior assumptions concerning which ones might be altered.

Aged↗
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↗
PubMed2002

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.

By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue alpha-helical protein from the villin headpiece. The total simulated time exceeds 300 micros, orders of magnitude more than previous simulations of a molecule of this size. Starting from an extended state, we obtained an ensemble of folded structures, which is on average 1.7A and 1.9A away from the native state in C(alpha) distance-based root-mean-square deviation (dRMS) and C(beta) dRMS sense, respectively. The folding mechanism of villin is most consistent with the hydrophobic collapse view of folding: the molecule collapses non-specifically very quickly ( approximately 20ns), which greatly reduces the size of the conformational space that needs to be explored in search of the native state. The conformational search in the collapsed state appears to be rate-limited by the formation of the aromatic core: in a significant fraction of our simulations, the C-terminal phenylalanine residue packs improperly with the rest of the hydrophobic core. We suggest that the breaking of this interaction may be the rate-determining step in the course of folding. On the basis of our simulations we estimate the folding rate of villin to be approximately 5micros. By analyzing the average features of the folded ensemble obtained by simulation, we see that the mean folded structure is more similar to the native fold than any individual folded structure. This finding highlights the need for simulating ensembles of molecules and averaging the results in an experiment-like fashion if meaningful comparison between simulation and experiment is to be attempted. Moreover, our results demonstrate that (1) the computational methodology exists to simulate the multi-microsecond regime using distributed computing and (2) that potential sets used to describe interatomic interactions may be sufficiently accurate to reach the folded state, at least for small proteins. We conclude with a comparison between our results and current protein-folding theory.

Amino Acid Sequence↗
PubMed1999

Evaluating the performance of detection algorithms in digital mammography.

The initial and relative evaluation of computer methodologies developed for assisting diagnosis in mammography is usually done by comparing the computer output to ground truth data provided by experts and/or biopsy. Reported studies, however, give little information on how the performance indices of computer assisted diagnosis (CAD) algorithms are determined in this initial stage of evaluation. Several strategies exist in the estimation of the true positive (TP) and false positive (FP) rates with respect to ground truth. Adopting one strategy over another yields different performance rates that can be over- or underestimates of the true performance. Furthermore, the estimation of pairs of TP and FP rates gives a partial picture of the performance of an algorithm. It is shown in this work that new performance indices are needed to fully describe the degree of detection (part or whole) and the type of detection (single calcification, cluster of calcifications, mass, or artifact). Several evaluation strategies were tested. The one that yielded the most realistic performances included the following criteria: The detected area should be at least 50% of the true area and no more than four times the true area in order to be considered TP. At least three true calcifications should be detected to within 1 cm2 with nearest neighbor distances of less than square root(2) cm for a cluster to be considered TP. Separate detection measures should be established and used for artifacts and naturally occurring structures to maximize the benefits of the evaluation. Finally, it is critical that CAD investigators provide information on the tested image set as well as the criteria used for the evaluation of the algorithms to allow comparisons and better understanding of their methodologies.

Algorithms↗
PubMed1999

Using a hand-held computer to collect data in an orthopedic outpatient clinic: a randomized trial of two survey methods.

OBJECTIVES: In a randomized study, the authors examine how data can be collected at the point of care. Specifically, examining to what extent handheld computer data collection systems introduce bias or increase respondent difficulty. METHODS: Volunteers were randomized to 1 of 2 survey methods: the hand-held computer or a paper and pencil form of similar content. Differences between group scale scores were compared using the Wilcoxon (rank sum) test. RESULTS: The hand-held computer system produced comparable scores to paper and pencil surveys. However, there was evidence of lower internal consistency reliability with the handheld computer. CONCLUSIONS: This study demonstrated the comparability of the hand-held computer methodology to the paper and pencil methodology in obtaining survey information in an ambulatory clinic. The hand-held computer method of survey data collection offers an alternative to paper methods when point-of-care administration is acceptable. Preliminary evidence shows that this method produces comparable results to paper forms.

Adolescent↗
PubMed2001

Advances in sequence analysis.

In its early days, the entire field of computational biology revolved almost entirely around biological sequence analysis. Over the past few years, however, a number of new non-sequence-based areas of investigation have become mainstream, from the analysis of gene expression data from microarrays, to whole-genome association discovery, and to the reverse engineering of gene regulatory pathways. Nonetheless, with the completion of private and public efforts to map the human genome, as well as those of other organisms, sequence data continue to be a veritable mother lode of valuable biological information that can be mined in a variety of contexts. Furthermore, the integration of sequence data with a variety of alternative information is providing valuable and fundamentally new insight into biological processes, as well as an array of new computational methodologies for the analysis of biological data.

Computational Biology↗
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↗
PubMed2000

Analyzing human random time generation behavior: a methodology and a computer program.

In the present article, it is argued that in addition to the traditional random generation tasks discussed by Towse and Neil (1998), random time interval generation tasks should be considered as useful alternatives, because they allow a better empirical control of the executive task component in dual-task situations. First, a framework for discussing randomness over time is presented. Then, the article goes on to present three methods for the analysis of such tasks. A first method is based on the correlation between the intervals produced. The second method calculates the approximate entropy, and the third method converts the time sequences into binary sequences and estimates the statistical properties of the sequence on the basis of these binary data. A principal components analysis on 19 different measures based on 1,381 sequences produced in a number of single-task and dual-task experiments shows that the proposed measures form two general clusters, one related to output probability, perseveration, and alternation, and one related to sequential commonalities. The article also briefly describes a computer program that implements these methodologies.

Humans↗