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At least 1,441 records · Page 80Linked to original sources
PubMed2005

A hybrid approach for efficient and robust parameter estimation in biochemical pathways.

Developing suitable dynamic models of biochemical pathways is a key issue in Systems Biology. Predictive models for cells or whole organisms could ultimately lead to model-based predictive and/or preventive medicine. Parameter estimation (i.e. model calibration) in these dynamic models is therefore a critical problem. In a recent contribution [Moles, C.G., Mendes, P., Banga, J.R., 2003b. Parameter estimation in biochemical pathways: a comparison of global optimisation methods. Genome Res. 13, 2467-2474], the challenging nature of such inverse problems was highlighted considering a benchmark problem, and concluding that only a certain type of stochastic global optimisation method, Evolution Strategies (ES), was able to solve it successfully, although at a rather large computational cost. In this new contribution, we present a new integrated optimisation methodology with a number of very significant improvements: (i) computation time is reduced by one order of magnitude by means of a hybrid method which increases efficiency while guaranteeing robustness, (ii) measurement noise (errors) and partial observations are handled adequately, (iii) automatic testing of identifiability of the model (both local and practical) is included and (iv) the information content of the experiments is evaluated via the Fisher information matrix, with subsequent application to design of new optimal experiments through dynamic optimisation.

Algorithms↗
PubMedDate not supplied

Computer support for continuous quality improvement.

Continuous quality improvement (CQI) methodology is predicated on data-based decision making, using both statistical and nonstatistical data tools. The current generation of commercially available quality management computer software does not integrate the basic CQI tools. A variety of off-the-shelf programs can be used to supplement the resource needs of CQI methodology.

Database Management Systems↗
PubMed2006

From systems biology to dynamical neuropharmacology: proposal for a new methodology.

The concepts and methods of systems biology are extended to neuropharmacology in order to test and design drugs for the treatment of neurological and psychiatric disorders. Computational modelling by integrating compartmental neural modelling techniques and detailed kinetic descriptions of pharmacological modulation of transmitter-receptor interaction is offered as a method to test the electrophysiological and behavioural effects of putative drugs. Even more, an inverse method is suggested as a method for controlling a neural system to realise a prescribed temporal pattern. In particular, as an application of the proposed new methodology, a computational platform is offered to analyse the generation and pharmacological modulation of theta rhythm related to anxiety.

Action Potentials↗
PubMed1997

Visualization-based analysis of multiparameter models using environment for N-dimensional model analysis.

We present a methodology, based on N-dimensional computer visualization, for analyzing multiparameter models. This approach originally consisted of three steps: behavior analysis, sensitivity analysis, identifiability analysis. We have now developed a new way of calculating sensitivity based on the statistical measure of the coefficient of variation. Furthermore, we extended the methodology through the addition of an extra step, visual regression. Visual regression allows the user to visualize the process of actual parameter identification and presents a combined, empirical view of the first three steps in a single image. Next we applied this methodology to pulmonary capillary-transport models. Finally, we implemented the model analysis process as a stand-alone program. EN-DIMAN, the resulting software, allows researchers to carry out model analysis in a graphical user interface (GUI)-based environment.

Algorithms↗
PubMed1978

Effective atomic number and electron density as measured with a computed tomography scanner: computation and correlation with brain tumor histology.

The mathematical basis and methodology for determining the effective atomic number and electron density of a tissue are presented. Cranial computed tomography (CT) scanning is performed at two different energy levels, both with and without contrast enhancement. The histology of 15 brain tumors has been correlated with the effective atomic number and electron density of the tumor, with parameters of the linear attenuation coefficient, and with statistical values of the CT numbers. The most useful value in separating gliomas from meningiomas from metastases appears to be the percentage change of effective atomic number following contrast enhancement.

Absorptiometry, Photon↗
PubMed2005

Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2.

The accurate description of solvation effects is highly desirable in numerous computational chemistry applications. One widely used methodology treats the solvent as a uniform continuum ("implicit solvation"), and describes its net interaction with the solute by solving the Poisson-Boltzmann (PB) equation using the Boundary Element Method (BEM). These calculations are very time consuming using conventional computers. A new, efficient way of solving the PB equation on the special-purpose hardware chip MDGRAPE-2 is presented. The MDGRAPE-2 chip was originally developed to speed up the calculation of pairwise van der Waals and electrostatic interactions. By recasting the BEM equations and applying an iterative solution procedure, a hardware-accelerated PB solver on MDGRAPE-2 could be implemented. The performance and reliability of the method is demonstrated on three examples ranging from small peptides to large proteins, whereby the obtained acceleration factors range from 15-fold to up to 40-fold with no loss of accuracy compared to the conventional approach.

Algorithms↗
PubMed1990

Covariances among sire by breed group of dam interaction effects in multibreed sire evaluation procedures.

In multibreed populations, bulls need to be evaluated for additive and nonadditive genetic effects. When the nonadditive genetic effects associated with a bull are defined as sire x breed-group-of-dam interactions, they can be expressed as linear combinations of interactions between alleles of one or more breeds at one or more loci. If these specific allelic interactions are assumed to be independent, then variances and covariances between sire x breed-group-of-dam interaction subclasses can be shown to be linear combinations of variances and covariances of specific intra- and interlocus intra- and interbreed allelic interactions. Furthermore, covariances between sire x breed-group-of-dam interactions due to specific interactions at one, two, or more loci are zero. If dams are assumed to be unrelated to bulls and among themselves, except through their sires and maternal grandsires, efficient procedures to compute the inverse of the covariance matrices of nonadditive genetic effects can be devised, both in subclass and in regression models. Recursive procedures developed make possible the evaluation of large numbers of bulls for nonadditive genetic effects using mixed-model methodology. For completeness, recursive procedures to compute nonadditive covariance matrices in subclass and in regression models also were developed. The prediction of nonadditive genetic values for bulls, in addition to their additive genetic values, will help plan matings, make selection decisions more accurate and, possibly, make economic projections better.

Alleles↗
PubMed2002

Estimating the elastographic signal-to-noise ratio using correlation coefficients.

In conventional elastography, strain is estimated from the gradient of the displacement (time-delay) estimates. The displacement estimates involve estimating the peak location of the cross-correlation function between matching pre- and post-compression A-lines. Bias errors in estimating the peak location of the cross-correlation function, amplified by the gradient operation on the displacement estimates (needed for the computation of the strain), could result in values of elastographic signal-to-noise ratio (SNR(e)) that exceed the theoretical upper bounds, thereby hindering a consistent interpretation of this parameter. These algorithmic errors have not been accounted for by the theory. We propose the use of the measured correlation coefficients in the theoretical SNR(e) expressions to estimate the SNR(e), rather than computing them directly from the elastograms. This methodology results in values of SNR(e) that are lower than the theoretical upper bounds, thereby avoiding the problems associated with computing SNR(e) directly from the elastograms. Using simulated models of uniformly elastic phantoms, a proof of principle of such an SNR(e) measure is shown.

Algorithms↗
PubMed2002

Computed tomography diagnosis utilizing compressed image data: an ROC analysis using acute appendicitis as a model.

Using receiver-operating characteristic (ROC) methodology, the ability to diagnose acute appendicitis with computed tomography (CT) images displayed at varying levels of lossy compression was evaluated. Nine sequential images over the ileocecal region were obtained from 53 consecutive patients with right lower quadrant pain who were clinically suspected to have acute appendicitis. Thirty were proven surgically to have acute appendicitis, alternative diagnoses confirmed in 23. The image sets were subjected to a lossy wavelet-based compression algorithm "Embedded Predictive Wavelet Image Coder" (EPWIC). Compression levels were: none, 8:1, 16:1, and 24:1, resulting in 4 sets of images per patient. Image sets were randomized and evaluated separately by 4 body radiologists on a 1,024 x 768-pixel SVGA color PC monitor in 512 x 512 format. The readers were aware of the clinical suspicion of appendicitis but were unaware of the positive fraction of cases. Individual and combined reader ROC and c2 analyses of sensitivity, specificity, and accuracy were determined. For all readers, sensitivity decreases at 16:1 and 24:1 levels (P <0.01, P <0.001, respectively). Accuracy decreased at 24:1 levels (P <0.01). Specificity was unaffected. By ROC analysis there was statistically significantly decreased area under the curve at 24:1 levels (P <0.02) as compared with uncompressed images. Finite levels of lossy wavelet compression may be applied to CT images without compromising diagnostic performance.

Acute Disease↗
PubMed1994

Screening for cognitive impairment in older individuals. Validation study of a computer-based test.

OBJECTIVE: This study examined the validity of a computer-based cognitive test that was recently designed to screen the elderly for cognitive impairment. DESIGN: Criterion-related validity was examined by comparing test scores of impaired patients and normal control subjects. Construct-related validity was computed through correlations between computer-based subtests and related conventional neuropsychological subtests. SETTING: University center for memory disorders. PARTICIPANTS: Fifty-two patients with mild cognitive impairment by strict clinical criteria and 50 unimpaired, age- and education-matched control subjects. Control subjects were rigorously screened by neurological, neuropsychological, imaging, and electrophysiological criteria to identify and exclude individuals with occult abnormalities. RESULTS: Using a cut-off total score of 126, this computer-based instrument had a sensitivity of 0.83 and a specificity of 0.96. Using a prevalence estimate of 10%, predictive values, positive and negative, were 0.70 and 0.96, respectively. Computer-based subtests correlated significantly with conventional neuropsychological tests measuring similar cognitive domains. Thirteen (17.8%) of 73 volunteers with normal medical histories were excluded from the control group, with unsuspected abnormalities on standard neuropsychological tests, electroencephalograms, or magnetic resonance imaging scans. CONCLUSIONS: Computer-based testing is a valid screening methodology for the detection of mild cognitive impairment in the elderly, although this particular test has important limitations. Broader applications of computer-based testing will require extensive population-based validation. Future studies should recognize that normal control subjects without a history of disease who are typically used in validation studies may have a high incidence of unsuspected abnormalities on neurodiagnostic studies.

Aged↗
PubMed1995

Interfacing electrochromic spectacles to computer IO ports.

Many important properties of molecules depend on their precise three-dimensional (3D) structure. It is therefore useful to be able to view a molecule in 3D on a 2D computer screen when manipulating it. An inexpensive method for viewing in 3D using liquid crystal glasses and a PC is presented. The methodology used is easily extended to other computers and workstations.

Computer Graphics↗
PubMed2005

Comparative evaluation of strain-based and model-based modulus elastography.

Elastography based on strain imaging currently endures mechanical artefacts and limited contrast transfer efficiency. Solving the inverse elasticity problem (IEP) should obviate these difficulties; however, this approach to elastography is often fraught with problems because of the ill-posed nature of the IEP. The aim of the present study was to determine how the quality of modulus elastograms computed by solving the IEP compared with those produced using standard strain imaging methodology. Strain-based modulus elastograms (i.e., modulus elastograms computed by simply inverting strain elastograms based on the assumption of stress uniformity) and model-based modulus elastograms (i.e., modulus elastograms computed by solving the IEP) were computed from a common cohort of simulated and gelatin-based phantoms that contained inclusions of varying size and modulus contrast. The ensuing elastograms were evaluated by employing the contrast-to-noise ratio (CNR(e)) and the contrast transfer efficiency (CTE(e)) performance metrics. The results demonstrated that, at a fixed spatial resolution, the CNR(e) of strain-based modulus elastograms was statistically equivalent to those computed by solving the IEP. At low modulus contrast, the CTE(e) of both elastographic imaging approaches was comparable; however, at high modulus, the CTE(e) of model-based modulus elastograms was superior.

Algorithms↗
PubMed1984

A physicomathematical approach to the structure of the mandible.

Classical methods of anatomical study and experimentation have reached an endpoint with respect to the advancement of our knowledge of certain aspects of bone, i.e. its mechanical properties, investigation of the constraints acting on bone and the organization of bone allowing resistance to such mechanical stress. Indeed, current knowledge is rather limited regarding bone as a material. Furthermore, bone from the cadaver cannot be considered a reliable source of study material since its physicochemical composition and mechanical properties are highly different from those of living bone. The types of experimentation used to date, although allowing to study the phenomena occurring on the surface of the bone, do not allow to evaluate those that occur within the bone without modification of its mechanical features. Finally, the number and complexity of the parameters to be taken into account in this respect largely supersede the possibilities of classical study techniques. Accordingly, new types of methodology are required to evaluate the many parameters involved, to perform the corresponding computations and resolve the great number of unknown variables. Such methodology must allow experimentation to be performed without modifying the object of study and to determine the phenomena occurring within the bone itself, i.e. the mandible. A method of computer assisted simulation of a physicomathematical model was used to analyse the structural properties of the mandible.(ABSTRACT TRUNCATED AT 250 WORDS)

Biomechanical Phenomena↗
PubMed2002

Motor recovery after stroke: a systematic review of the literature.

OBJECTIVE: To collect and integrate existing data concerning the occurrence, extent, time course, and prognostic determinants of motor recovery after stroke using a systematic methodologic approach. DATA SOURCES: A computer-aided search in bibliographic databases was done of longitudinal cohort studies, original prognostic studies, and randomized controlled trials published in the period 1966 to November 2001, which was expanded by references from retrieved articles and narrative reviews. STUDY SELECTION: After a preliminary screening, internal, external, and statistical validity was assessed by a priori methodologic criteria, with special emphasis on the internal validity. DATA EXTRACTION: The studies finally selected were discussed, based on the quantitative analysis of the outcome measures and prognostic determinants. Meta-analysis was pursued, but was not possible because of substantial heterogeneity. DATA SYNTHESIS: The search resulted in 174 potentially relevant studies, of which 80 passed the preliminary screening and were subjected to further methodologic assessment; 14 studies were finally selected. Approximately 65% of the hospitalized stroke survivors with initial motor deficits of the lower extremity showed some degree of motor recovery. In the case of paralysis, complete motor recovery occurred in less than 15% of the patients, both for the upper and lower extremities. Hospitalized patients with small lacunar strokes showed relatively good motor recovery. The recovery period in patients with severe stroke was twice as long as in patients with mild stroke. The initial grade of paresis was the most important predictor for motor recovery (odds ratios [OR], >4). Objective analysis of the motor pathways by motor-evoked potentials (MEPs) showed even higher ORs (ORs, >20). CONCLUSIONS: Our knowledge of motor recovery after stroke in more accurate, quantitative, and qualitive terms is still limited. Nevertheless, our data synthesis and quantitative analysis comprises data from many methodologically robust studies, which may support the clinician in the management of stroke patients. With respect to early prognosis of motor recovery, our review confirms clinical experience that the initial grade of paresis (as measured on admission in the hospital) is the most important predictor, although the accuracy of prediction rapidly improves during the first few days after stroke. Initial paralysis implies the worst prognosis for subsequent motor recovery. Remarkably, the prognostic accuracy of MEPs appears much higher than that of clinical examination for different subgroups of patients.

Activities of Daily Living↗
PubMed2001

Methodology of the 1997 New Zealand National Nutrition Survey.

AIMS: To describe the development and use of the methodologies in the 1997 New Zealand National Nutrition Survey (NNS97). METHODS: NNS97 was a voluntary cross-sectional population survey conducted over a twelve month period on 4,636 non-institutionalized urban and rural New Zealand residents aged fifteen years and older. Survey data were collected in the participants' home and included: a self-administered qualitative food frequency questionnaire, including questions on food preparation habits; a three-pass 24-hour diet recall; interviewer-administered questions on diet supplement use, barriers to dietary change and participant perception of household food security; physical measurements including weight, height, three circumferences, two skinfolds and elbow breadth; blood pressure; and a blood sample to determine cholesterol and iron status. RESULTS: New methodologies developed for NNS97 included a computer based interview system, probability analyses for estimating prevalence of inadequate intake of selected nutrients, determination of iron status by both dietary and biochemical assessment, assessments of dietary supplement use and food security. A full range of quality control procedures at each stage of the data collection were also initiated. CONCLUSION: NNS97 has improved on previous New Zealand national nutrition survey methodologies, particularly with direct data capture and rigorous quality control procedures used in the collection of survey data.

Adolescent↗
PubMed2025

Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data.

Recent advances in ultra-low coverage whole-genome sequencing (WGS) of single cells have enabled detailed analysis of copy number variation at a throughput approaching that of single-cell RNA sequencing. However, downstream computational methods have not seen comparable advances and are largely adaptations of deep sequencing methodology with reduced precision. Here, we present ASCENT, a computational method built to take full advantage of modern direct tagmentation-based WGS at ultra-low depth. Using joint segmentation with high-resolution bins, we accurately detect small segments, achieving accurate copy number profiles even at 100 000 reads per cell. ASCENT implements true absolute copy state inference for single cells, based on statistical modeling of coverage rather than comparison to a reference, while taking variable segment copy state into account. Further, ASCENT implements per-segment copy-neutral loss of heterozygosity (LOH) calling without the need for non-tumor or bulk WGS reference. When applied to a pediatric B-ALL sample, ASCENT finds copy-neutral LOH in a small segment and a minor subclone defined by breakpoints missed in bulk WGS. Thus, by applying appropriate computational methods, single-cell WGS provides clear advantages over bulk, even at a relatively low cell number and sequencing depth.

DNA Copy Number Variations↗
PubMed2006

Towards systemic theories in biological psychiatry.

Although still rather controversial, empirical data on the neurobiology of schizophrenia have reached a degree of complexity that makes it hard to obtain a coherent picture of the malfunctions of the brain in schizophrenia. Theoretical neuropsychiatry should therefore use the tools of theoretical sciences like cybernetics, informatics, computational neuroscience or systems science. The methodology of systems science permits the modeling of complex dynamic nonlinear systems. Such procedures might help us to understand brain functions and the disorders and actions of psychiatric drugs better.

Antipsychotic Agents↗
PubMedDate not supplied

Meeting the computer technology needs of community faculty: building new models for faculty development.

OBJECTIVE: We aimed to identify the evolving computer technology needs and interests of community faculty in order to design an effective faculty development program focused on computer skills: the Teaching and Learning Through Educational Technology (TeLeTET) program. METHODOLOGY: Repeated surveys were conducted between 1994 and 2002 to assess computer resources and needs in a pool of over 800 primary care physician-educators in community practice in East Texas. Based on the results, we developed and evaluated several models to teach community preceptors about computer technologies that are useful for education. RESULTS: Before 1998, only half of our community faculty identified a strong interest in developing their technology skills. As the revolution in telecommunications advanced, however, preceptors' needs and interests changed, and the use of this technology to support community-based teaching became feasible. In 1998 and 1999, resource surveys showed that many of our community teaching sites had computers and Internet access. By 2001, the desire for teletechnology skills development was strong in a nucleus of community faculty, although lack of infrastructure, time, and skills were identified barriers. The TeLeTET project developed several innovative models for technology workshops and conferences, supplemented by online resources, that were well attended and positively evaluated by 181 community faculty over a 3-year period. CONCLUSIONS: We have identified the evolving needs of community faculty through iterative needs assessments, developed a flexible faculty development curriculum, and used open-ended, formative evaluation techniques to keep the TeLeTET program responsive to a rapidly changing environment for community-based education in computer technology.

Community Health Services↗