Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational methods”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources
PubMed1996

[Computer graphics methods for 3-dimensional imaging of intrapulmonary space-occupying lesions of CT and MRI images].

AIM: To improve the pre-operative planning of interventional procedures in thorax surgery different methods of computer-graphical visualization of intrapulmonary lesions and adjacent anatomical structures based on CT and MR data were realized and compared to each other. DESIGN: In 21 patients with intrapulmonary lesions the image data was segmented by interactive and automatic algorithms and different reconstruction techniques were applied (maximum intensity projection; color-encoded and transparent surfaces; volume rendering). Based on these three-dimensional reconstructions, different views from arbitrary perspectives (including simulated endoscopic images) were generated and animated film sequences of the 3D scene were displayed with 30 frames/second. RESULTS: For all patients under review, a high-quality presentation of the relevant structures was obtained by use of the applied computer-graphical techniques. Even combinations of different visualization methods in one image can be generated with the software we developed. CONCLUSIONS: The various methods for image segmentation allow a fast and comfortable processing even of large data sets. The calculated values of tumor surface and volume can be used for quantitative studies and therapy control. The planning of surgical and interventional procedures can be supported by the simultaneous visualization of the intrathoracic lesion and the surrounding structures.

Aged↗
PubMed2006

[Computer simulation methods of cardiac electrophysiology].

Computer simulation is one of the powerful protocols to study electrophysiology theoretically. In this paper,the algorithm of Rush and Larsen was used to solve the ordinary differential equations (ODE's) in the Luo-Rudy models of mammalian ventricular cell. The operator splitting and adaptive time step methods were used to solve the partial differential equations (PDE's) in cardiac tissue conduction models. Using these methods we accomplished the simulation programs of single ventricular cell model and two-dimensional (2-D) tissue model. The methods of initiating spiral waves were studied with this software. The data obtained from 2-D simulation can be used for further study on isopotential contour lines, spiral wave tip trajectories, and pseudo-ECG.

Algorithms↗
PubMedDate not supplied

An evaluation method of computer usability based on human-to-computer information transmission model.

This paper proposes a new evaluation and prediction method for computer usability. This method is based on our two previously proposed information transmission measures created from a human-to-computer information transmission model. The model has three information transmission levels: the device, software, and task content levels. Two measures, called the device independent information measure (DI) and the computer independent information measure (CI), defined on the software and task content levels respectively, are given as the amount of information transmitted. Two information transmission rates are defined as DI/T and CI/T, where T is the task completion time: the device independent information transmission rate (RDI), and the computer independent information transmission rate (RCI). The method utilizes the RDI and RCI rates to evaluate relatively the usability of software and device operations on different computer systems. Experiments using three different systems, in this case a graphical information input task, confirm that the method offers an efficient way of determining computer usability.

Computer Literacy↗
PubMedDate not supplied

Comparison of convolution and ray-tracing methods for computing small blood vessel images in angiography.

Two methods for computing x-ray images of small blood vessels in angiography are presently available, namely, convolution and ray tracing. The convolution method, which is simpler and more powerful than the ray-tracing method, is based on the assumption that blood vessel imaging is isoplantic, whereas ray tracing is considered to provide correct images. In this study, the approximation error (difference between two images, normalized by the maximum value) due to nonisoplanatic imaging was determined by computation of blood vessel images according to both methods. The approximation error for geometric conditions normally encountered in angiography was less than 0.01. It is concluded that an approximation error of this magnitude is negligible and that the convolution method can be applied instead of the ray-tracing method for the computation of images of small blood vessels.

Angiography↗
PubMed2001

A computer-based method for calculation of orbital floor fractures from coronal computed tomography scans.

PURPOSE: A computer program recently developed for the calculation of the orbital floor and fracture areas from coronal computed tomography (CT) scans was used in a study to evaluate the accuracy and ability of this new method. MATERIAL AND METHODS: The size of orbital floors and fabricated fractures in 14 dried, anatomic specimens were measured in coronal CT scans by 3 independent observers. Based on this data set, the orbital floor and fracture regions were calculated with the newly developed computer program. These calculated regions were then compared with a direct measurement of the specimens that had been obtained by digital photography. The accuracy of the computer-based calculations was assessed using Lin's concordance correlation coefficient. RESULTS: The size of the orbital floor (mean +/- SD) was found to be 5.21 +/- 0.39 cm(2) by direct measurement of the specimens and 5.30 +/- 0.52 cm(2) by calculation with the computer program. The region of the fracture (mean +/- SD) was 1.05 +/- 0.64 cm(2) by direct measurement and 1.01 +/- 0.62 cm(2) by computer calculation. The between-method mean difference (direct measurement minus computer based calculation) was -0.09 cm(2) (or 1.7% of mean orbital floor region) for orbital floor region and 0.04 cm(2) (or 3.8% of mean fracture region) for fracture region. CONCLUSIONS: This accurate and time-saving method is practicable for determining the size and location of orbital floor fractures. This calculation program can be advantageously applied in the clinical management of blowout fractures of the orbit.

Algorithms↗
PubMed2005

Computational calibration method for optical tomography.

We propose a computational calibration method for optical tomography. The model of the calibration scheme is based on the rotation symmetry of source and detector positions in the measurement setup. The relative amplitude losses and phase shifts at the optic fibers are modeled by complex-valued coupling coefficients. The coupling coefficients can be estimated when optical tomography data from a homogeneous and isotropic object are given. Once these coupling coefficients have been estimated, any data measured with the same measurement setup can be corrected for the relative variation in the data due to source and detector losses. The final calibration of the data for the source and detector losses and the source calibration between the data and the forward model are obtained as part of the initial estimation for reconstruction. The calibration method was tested with simulations and measurements. The results show that the coupling coefficients of the sources and detectors can be estimated with good accuracy. Furthermore, the results show that the method can significantly improve the quality of reconstructed images.

Algorithms↗
PubMed2006

Immunohistochemistry quantification by a digital computer-assisted method compared to semiquantitative analysis.

PURPOSE: To compare immunostaining quantification obtained by a digital computer-assisted method with the well-established semiquantitative analysis. METHODS: Cytoplasmic staining of galectin-3 was obtained by standard immunohistochemical reactions in 25 cases of well-differentiated thyroid carcinoma. The expression index that associates the conventional area fraction of labeled cells with the immunostaining intensity score based on visual qualitative observation was used as the semiquantitative analysis. A digital computer-assisted method is described based on the use of an image processing program (ImageLab). Three parameters were obtained: (1) percentage of labeled cells; (2) digital immunostaining intensity, and (3) digital expression index. The proposed method allows numerical analysis of the immunostaining intensity. RESULTS: There was a strong correlation between the immunostaining intensity obtained by the two methods (Pearson correlation coefficient, r = 0.71, P = 0.0001). The same was observed between expression indexes (Pearson correlation coefficient, r = 0.66, P = 0.0001). CONCLUSION: Results obtained with our proposed digital computer-assisted method for immunoexpression analysis were concordant with the semiquantitative analysis. In addition, digital values can also resolve disagreement among different observers about the quality of staining intensity because the digital method does not classify the results into groups, but rather provides a numerical value for each individual case; thus, it increases the diagnostic and, more importantly, the prognostic sensitivity of the immunohistochemical analysis.

Analysis of Variance↗
PubMed1993

Computer-assisted functional assessment and documentation.

Occupational therapy personnel spend considerable time on functional assessment and documentation. The rapid and error-free information processing ability of computers offers methods for data collection, clinical decision making, and reporting of functional assessment results, which may be more effective and efficient than the current paper-and-pencil methods. Computers can provide assistance throughout the many steps of the functional assessment and reporting process. Software is available to assist in direct data collection, data reduction, and analysis, or to assess complex data systems and databases. Additionally, computers can use assessment techniques, such as dynamic question sets and expert systems, which have not been possible with paper-and-pencil methods. Furthermore, data collected on computers are readily available to be integrated in computer-assisted report writing and can be compiled into large databases for analysis. These databases can be used for program evaluation, continuous quality improvement exercises, and other research objectives. This paper provides a snapshot of these computer uses in the assessment process.

Computers↗
PubMed2001

Computationally accessible method for estimating free energy changes resulting from site-specific mutations of biomolecules: systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins.

A practical computational method for the molecular modeling of free-energy changes associated with protein mutations is reported. The de novo generation, optimization, and thermodynamic analysis of a wide variety of deoxy and oxy hemoglobin mutants are described in detail. Hemoglobin is shown to be an ideal candidate protein for study because both the native deoxy and oxy states have been crystallographically determined, and a large and diverse population of its mutants has been thermodynamically characterized. Noncovalent interactions for all computationally generated hemoglobin mutants are quantitatively examined with the molecular modeling program HINT (Hydropathic INTeractions). HINT scores all biomolecular noncovalent interactions, including hydrogen bonding, acid-base, hydrophobic-hydrophobic, acid-acid, base-base, and hydrophobic-polar, to generate dimer-dimer interface "scores" that are translated into free-energy estimates. Analysis of 23 hemoglobin mutants, in both deoxy and oxy states, indicates that the effects of mutant residues on structurally bound waters (and visa versa) are important for generating accurate free-energy estimates. For several mutants, the addition/elimination of structural waters is key to understanding the thermodynamic consequences of residue mutation. Good agreement is found between calculated and experimental data for deoxy hemoglobin mutants (r = 0.79, slope = 0.78, standard error = 1.4 kcal mol(-1), n = 23). Less accurate estimates were initially obtained for oxy hemoglobin mutants (r = 0.48, slope = 0.47, standard error = 1.4 kcal mol(-1), n = 23). However, the elimination of three outliers from this data set results in a better correlation of r = 0.87 (slope = 0.72, standard error = 0.75, n = 20). These three mutations may significantly perturb the hemoglobin quaternary structure beyond the scope of our structural optimization procedure. The method described is also useful in the examination of residue ionization states in protein structures. Specifically, we find an acidic residue within the native deoxy hemoglobin dimer-dimer interface that may be protonated at physiological pH. The final analysis is a model design of novel hemoglobin mutants that modify cooperative free energy (deltaGc)--the energy barrier between the allosteric transition from deoxy to oxy hemoglobin.

Computational Biology↗
PubMed2004

[Evaluation of tibial torsion--comparison of clinical methods and computed tomography].

PURPOSE: To determine variability between clinical goniometric methods and computed tomography (CT) in measuring posttraumatic malrotation of the tibia. MATERIALS AND METHODS: In a prospective study, absolute tibial torsion of both legs after unilateral fracture of the tibia as well as the difference between both legs (intra-individual torsional difference) was postoperatively determined with two goniometric and two CT methods in 40 patients (female : male = 16 : 24, mean age = 46 +/- 34 years). RESULTS: The mean difference between goniometric and CT methods in determining intra-individual torsional difference was not significant. Nevertheless, variance of values was higher in goniometric measurement (up to +/- 11 degree), with the measurements of torsional difference showing two times greater standard deviation in interobserver variability of goniometric methods as compared to CT. CONCLUSION: Goniometric methods do not significantly differ from the CT methods for determination of intraindividual torsional difference. The higher variance of interobserver values limits accuracy of goniometric methods. Therefore, goniometric determination of tibial torsion can only be considered an estimate but not a precise measurement.

Adolescent↗
PubMed2004

A new computer-assisted method for measuring the tibio-femoral angle in patients with osteoarthritis of the knee.

OBJECTIVE: The purpose of this study was to evaluate the inter- and intraobserver variability in measuring the tibio-femoral angle using our new computer-assisted method, and to compare it with a conventional manual method. METHODS: Radiography of all patients of osteoarthritis of the knee in outpatient were performed with standing on both legs, and with conventional antero-posterior weight bearing view of the knee fully extended. Three examiners measured the tibio-femoral angle with the computerized method in 52 subjects with osteoarthritis (73 knees). The tibio-femoral angle was measured using a computer-assisted method in which the observer must visually determine and select eight points on the margins of the femur and tibia on a radiographic image displayed on a computer monitor. The inter- and intraobserver Intra-class correlation (ICC) was analyzed. RESULTS: The interobserver mean correlation of computer-assisted method was 0.970 with a mean difference of 0.38 degrees (S.D. 1.125 degrees). The intraobserver mean ICC of computer-assisted method was 0.973, with a mean difference of 0.16 degrees (S.D. 1.12 degrees). An analysis of the difference between conventional methods and our new system showed a mean ICC of 0.922, with an intersystem mean difference of 0.295 degrees (S.D. 1.82 degrees). CONCLUSION: Our computer-assisted method of measuring the tibio-femoral angle was simple, easy, and quick, and should be considered as an alternate method for measurement.

Adult↗
PubMed1998

Comparison of reliability of manual and computer-intensive methods for radiodensity measures of alveolar bone loss.

OBJECTIVE: To compare the reliability of radiodensity measurements made from dental radiographs with manual and a novel computer-intensive methods. METHODS: As part of a prospective study of postmenopausal women, a series of seven vertical bitewing radiographs were taken of 36 patients. One of each set of radiographs was repeated. The original and the corresponding duplicate radiographs were used in this study. Radiographs were digitized at 50 microns spatial resolution and 12-bit gray-scale resolution. For the Manual Method, original and duplicate radiographs were manually cropped to improve image homology, histogram matched and mean pixel gray-scale values determined for an alveolar bone ROI within each image. For the computer-intensive method, images were put into registration with ANALYZE software (Mayo Foundation, Rochester, MINN, USA), cropped automatically, histogram matched and color-coded on the basis of the per cent difference. Alveolar bone ROIs adjacent to clinical crowns and root surfaces whose color code indicated less than a 5% change were sampled. Method error (ME) and the coefficient of variation of method error (CVME) were calculated. RESULTS: With the Manual Method the SD between original and duplicate measures was 95.21 out of 4096 gray scale values; ME = 67.32; CVME = 3.78%. For the computer-intensive method, the corresponding values were 54.74, 38.71, and 2.29%. CONCLUSIONS: The new computer-intensive method resulted in a 40% improvement over the Manual Method in the precision of radiodensity measurements.

Absorptiometry, Photon↗
PubMed1994

A method for computing random chord length distributions in geometrical objects.

A method is described that uses a Monte Carlo approach for computing the distribution of random chord lengths in objects traversed by rays originating uniformly in space (mu-randomness). The resulting distributions converge identically to the analytical solutions for a sphere and satisfy the Cauchy relationship for mean chord lengths in circular cylinders. The method can easily be applied to geometrical shapes that are not convex such as the region between nested cylinders to simulate the sensitive volume of a detector. Comparisons with other computational methods are presented.

Monte Carlo Method↗
PubMed2005

Toward a robust and general molecular simulation method for computing solid-liquid coexistence.

A rigorous and generally applicable method for computing solid-liquid coexistence is presented. The method overcomes some of the technical difficulties associated with other solid-liquid simulation procedures and can be implemented within either a molecular dynamics or Monte Carlo framework. The method consists of three steps: First, relative Gibbs free energy curves are created for the solid and liquid phases using histogram reweighting. Next, the free energy difference between the solid and liquid phases is evaluated at a single state point by integrating along a pseudosupercritical transformation path that connects the two phases. Using this result, the solid and liquid free energy curves are referenced to a common point, allowing a single coexistence point to be determined. Finally, Gibbs-Duhem integration is used to determine the full coexistence curve. To evaluate its utility, this method is applied to the Lennard-Jones and NaCl systems. Results for solid-liquid coexistence agree with previous calculations for these systems. In addition, it is shown that the NaCl model does not correctly describe solid-liquid coexistence at high pressures. An analysis of the accuracy of the method indicates that the results are most sensitive to the transformation free energy calculation.

Computer Simulation↗
PubMed2005

Method for computing protein binding affinity.

A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.

Binding Sites↗
PubMed1975

A simple method for computing acid-base state.

Simple methods are described for computing the variables derived from the Siggaard-Andersen nomogram, where the in vitro buffer line is either established by direct measurement or calculated from measurements of pH, Pco2 and haemoglobin. Calculations are performed using the equation of the pH-log Pco2 buffer line, the Henderson-Hasselbalch equation, and the polynomials: BE=-38.402+1.8970 (SB)-0.013342 (SB)-2 m-equiv/litre; SL=-69.046+17.377 (pH40)-1.1121 (pH40)-2; SH=-123.30+31.357 (pH40)-2.0143 (pH40)-2. Then haemoglobin=7.5 (1+(S-SL)/(SH-SL)) G/100 ml, where S is the slope of the buffer line. Results are sufficiently accurate for clinical purposes.

Acid-Base Equilibrium↗