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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↗

PubMed2006

Statistical, computational and visualization methodologies to unveil gene primary structure features.

OBJECTIVES: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. trinucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis. METHODS: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods--contingency table analysis, residual analysis, multivariate analysis (cluster analysis)--to analyze the codon bias under various aspects (degree of association, contexts and clustering). RESULTS: The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicans and Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples. CONCLUSIONS: The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

Algorithms↗

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↗

PubMedDate not supplied

Evaluation of CT during arterial portography for preoperative diagnosis of intrahepatic cholangiocarcinoma.

BACKGROUND/AIMS: To evaluate computed tomography during arterial portography for preoperative evaluation in patients with intrahepatic cholangiocarcinoma. METHODOLOGY: Computed tomography during arterial portography was performed in 11 intrahepatic cholangiocarcinoma patients undergoing hepatectomy. Segmental perfusion defect, sensitivity of the main tumor, and sensitivity of intrahepatic metastasis on computed tomography during arterial portography were retrospectively evaluated. RESULTS: In 9 of 11 patients (81.8%), a segmental perfusion defect was seen. The sensitivities for detecting the main tumor and intrahepatic metastasis were 81.8% and 20%, respectively. In 2 patients, the main tumors existed in segmental perfusion defects and thus were not depicted. In 4 false-negative cases, intrahepatic metastatic lesions existed in the segments that were the counterparts of segmental perfusion defects on computed tomography during arterial portography. CONCLUSIONS: The sensitivity of computed tomography during arterial portography for diagnosing intrahepatic cholangiocarcinoma and its intrahepatic metastasis was low due to segmental perfusion defect. It is necessary for intrahepatic cholangiocarcinoma to be subjected to systematic segmentectomy including all areas corresponding to the segmental perfusion defect.

Adult↗

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↗

PubMed2005

Y-aromaticity: why is the trimethylenemethane dication more stable than the butadienyl dication?

[reactions: see text] Resonance energies of the trimethylenemethane dication (1) and the butadienyl dication (4) were evaluated using two independent computational methodologies to provide insight into the validity of Y-aromaticity. One methodology employed density functional theory calculations and examined the resonance contribution of the C=C double bond toward the double hydride abstraction enthalpies of methylpropene (6) and 2-butene (8), yielding 1 and 4, respectively. These resonance contributions by the double bond were determined by calculating the double hydride abstraction enthalpies of both the parallel and perpendicular conformations of vinylogues of 6 and 8, in which n = 1-4 vinyl units were inserted between the central carbon-carbon double bond and each of the reaction centers. Extrapolation of the resonance contribution in each vinylogue to n = 0 yielded the resonance contribution in the respective parent molecules. The second methodology employed an orbital deletion procedure (ODP), which effectively allowed us to examine the energies of individual resonance structures. The resonance energy of each dication is computed as the difference between the most stable resonance structure and that of the delocalized species. The two methodologies are in agreement, suggesting that the resonance energy of the trimethylenemethane dication is substantially greater than that of the butadienyl dication. The origin of this difference in resonance stabilization is discussed.

Journal Article↗

PubMed2005

Hydrodynamic models and computational methods for NMR relaxation.

Interpretation of NMR relaxation data of macromolecules is based on the analysis of their dynamic behavior in solution. For quasirigid molecules, in addition to a minor, separable contribution from local mobility, the main contribution corresponds to the overall rotational diffusion of the complete molecule. Therefore, theoretical descriptions and computational methodologies for hydrodynamic calculations, which yield the full, anisotropic rotational diffusion tensor of rigid molecules, are extremely helpful in the analysis of NMR relaxation. Recent approaches allow realistic predictions of the rotational diffusion tensor from structures at atomic detail. This enables measured relaxation rates and structural models to be compared. Such a comparison (1) provides an independent test of the structural model, (2) provides a framework for the interpretation of local motion, even for highly anisotropic systems, (3) provides a simple method for the detection of additional sources of relaxation, such as chemical exchange, and (4) provides a sensitive method for the detection of nonspecific aggregation or oligomer formation. Although hydrodynamic calculations usually assume a rigid structure, Brownian dynamics simulations extend their range of applications to flexible multidomain structures. Hydrodynamic applications are not restricted to globular proteins. Small DNA fragments, which could be otherwise considered cylindrical objects, can also be treated with atomic detail using the same methodology used for proteins.

Computational Biology↗

PubMedDate not supplied

Daily duration of vitamin D synthesis in human skin with relation to latitude, total ozone, altitude, ground cover, aerosols and cloud thickness.

Vitamin D production in human skin occurs only when incident UV radiation exceeds a certain threshold. From simulations of UV irradiances worldwide and throughout the year, we have studied the dependency of the extent and duration of cutaneous vitamin D production in terms of latitude, time, total ozone, clouds, aerosols, surface reflectivity and altitude. For clear atmospheric conditions, no cutaneous vitamin D production occurs at 51 degrees latitude and higher during some periods of the year. At 70 degrees latitude, vitamin D synthesis can be absent for 5 months. Clouds, aerosols and thick ozone events reduce the duration of vitamin D synthesis considerably, and can suppress vitamin D synthesis completely even at the equator. A web page allowing the computation of the duration of cutaneous vitamin D production worldwide throughout the year, for various atmospheric and surface conditions, is available on the Internet at http://zardoz.nilu.no/~olaeng/fastrt/VitD.html and http://zardoz.nilu.no/~olaeng/fastrt/VitD-ez.html. The computational methodology is outlined here.

Aerosols↗

PubMed2005

Computational study of turbulent laminar patterns in couette flow.

Turbulent-laminar patterns near transition are simulated in plane Couette flow using an extension of the minimal-flow-unit methodology. Computational domains are of minimal size in two directions but large in the third. The long direction can be tilted at any prescribed angle to the streamwise direction. Three types of patterned states are found and studied: periodic, localized, and intermittent. These correspond closely to observations in large-aspect-ratio experiments.

Journal Article↗

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↗

PubMed2006

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

The computation of ionic solvation free energies from atomistic simulations is a surprisingly difficult problem that has found no satisfactory solution for more than 15 years. The reason is that the charging free energies evaluated from such simulations are affected by very large errors. One of these is related to the choice of a specific convention for summing up the contributions of solvent charges to the electrostatic potential in the ionic cavity, namely, on the basis of point charges within entire solvent molecules (M scheme) or on the basis of individual point charges (P scheme). The use of an inappropriate convention may lead to a charge-independent offset in the calculated potential, which depends on the details of the summation scheme, on the quadrupole-moment trace of the solvent molecule, and on the approximate form used to represent electrostatic interactions in the system. However, whether the M or P scheme (if any) represents the appropriate convention is still a matter of on-going debate. The goal of the present article is to settle this long-standing controversy by carefully analyzing (both analytically and numerically) the properties of the electrostatic potential in molecular liquids (and inside cavities within them). Restricting the discussion to real liquids of "spherical" solvent molecules (represented by a classical solvent model with a single van der Waals interaction site), it is concluded that (i) for Coulombic (or straight-cutoff truncated) electrostatic interactions, the M scheme is the appropriate way of calculating the electrostatic potential; (ii) for non-Coulombic interactions deriving from a continuously differentiable function, both M and P schemes generally deliver an incorrect result (for which an analytical correction must be applied); and (iii) finite-temperature effects, including intermolecular orientation correlations and a preferential orientational structure in the neighborhood of a liquid-vacuum interface, must be taken into account. Applications of these results to the computation methodology-independent ionic solvation free energies from molecular simulations will be the scope of a forthcoming article.

Journal Article↗

PubMed2002

Mining genome databases to identify and understand new gene regulatory systems.

The availability of a large number of sequenced microbial genomes allows us to conduct systematic studies on microbial gene regulatory systems. Computational methods, using comparative genomics approaches, are powerful tools to understand their mechanisms and evolutionary history. Recent advances in computational methodology for uncovering transcriptional regulatory components and their interactions are discussed.

Computational Biology↗