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PubMed1980

A method for the evaluation of dose-effect data utilizing a programmable calculator.

A program for the calculation of the median effective dose (ED50) and the slope of the dose-effect line was developed for a programmable calculator. The method employed approximated the solution described by Bliss. Experimental data were evaluated and compared to both hand calculated results and results of other computer methods. This method produced results which differed from other computer methods by less than 1 percent. This program provided information necessary for the test for parallelism and estimate of relative potency of two dose-effect lines.

Computers↗
PubMedDate not supplied

A computer-based method for determination of the cell-free layer width in microcirculation.

OBJECTIVES: The cell-free layer between the erythrocyte column and the vessel wall is an important determinant of hydrodynamic resistance in microcirculatory vessels. The authors report a method for continuous measurement of the width of this layer. METHODS: The light intensity of a linear array of pixels perpendicular to the vessel axis is continuously determined from a video image of a microcirculatory vessel. A threshold level based on Otsu's method is used to establish the interface between the cell-free layer and the erythrocyte column. To test the method, video images at 750-4500 frames/s were obtained from venules and arterioles in rat spinotrapezius muscle at normal and reduced arterial pressures before and after induction of erythrocyte aggregation with Dextran 500. The current measurements were compared to manual measurements of the same images. RESULTS: Values obtained by the manual and the new methods were in agreement within the 95% confidence limit by the Bland-Altman analysis and within 90-95% range by the correlation coefficient (R2). The more frequent measurements reveal substantial, rapid variations in cell-free layer width and changes in mean values with alteration of arterial pressure and red cell aggregability. CONCLUSIONS: A new, computer-based technique has been developed that provides measurements of rapid, time-dependent variations in the width of the cell-free layer in the microcirculation.

Animals↗
PubMed1982

Evaluation of a computer-assisted method for individualized anticoagulation: retrospective and prospective studies with a pharmacodynamic model.

We studied the effectiveness of a computer program based on a mathematic model of warfarin dynamics in assisting with the initial phases of anticoagulation. In retrospective evaluations the program was successful in predicting prothrombin complex activity (PCA) responses for three different groups of subjects, indicating that the model is a good representation of the physiologic system. In a prospective evaluation of the program a computer-assisted group of 10 patients was compared with a control of 10 patients who did not receive computer assistance. Because of the program's very conservative upper limits for warfarin dosage in the first few days of therapy, the computer-assisted patient require slightly more time (6 days), on the average, to first reach PCA values in the 20% to 30% therapeutic range than did the control patients (4.8 days). After the desired PCA had been achieved, however, the computer-assisted group remained within the therapeutic range for 83% of the time compared to only 60% for the control group. This difference was due primarily to much less overanticoagulation of the computer-assisted patients than of the controls.

Blood Coagulation↗
PubMedDate not supplied

[Computer-assisted method of representation of sperm movement in the evaluation of the quality of ejaculate].

The paper describes computer-aided processing of video images of mobile biological objects in view of forming tracks and of evaluating their individual kinetic characteristics. The proposed processing procedure allows one avoid lower information quality associated with resultant image contract reduction when combining video frames are summarized and the signal/ratio decreases.

Ejaculation↗
PubMed2002

A method for computing identity by descent probabilities and quantitative trait loci mapping with dominant (AFLP) markers.

Amplified fragment length polymorphisms (AFLPs) are a widely used marker system: the technique is very cost-effective, easy and rapid, and reproducibly generates hundreds of markers. Unfortunately, AFLP alleles are typically scored as the presence or absence of a band and, thus, heterozygous and dominant homozygous genotypes cannot be distinguished. This results in a significant loss of information, especially as regards mapping of quantitative trait loci (QTLs). We present a Monte Carlo Markov Chain method that allows us to compute the identity by descent probabilities (IBD) in a general pedigree whose individuals have been typed for dominant markers. The method allows us to include the information provided by the fluorescent band intensities of the markers, the rationale being that homozygous individuals have on average higher band intensities than heterozygous individuals, as well as information from linked markers in each individual and its relatives. Once IBD probabilities are obtained, they can be combined into the QTL mapping strategy of choice. We illustrate the method with two simulated populations: an outbred population consisting of full sib families, and an F2 cross between inbred lines. Two marker spacings were considered, 5 or 20 cM, in the outbred population. There was almost no difference, for the practical purpose of QTL estimation, between AFLPs and biallelic codominant markers when the band density is taken into account, especially at the 5 cM spacing. The performance of AFLPs every 5 cM was also comparable to that of highly polymorphic markers (microsatellites) spaced every 20 cM. In economic terms, QTL mapping with a dense map of AFLPs is clearly better than microsatellite QTL mapping and little is lost in terms of accuracy of position. Nevertheless, at low marker densities, AFLPs or other biallelic markers result in very inaccurate estimates of QTL position.

Algorithms↗
PubMed1976

Comparison of graphical and computerized methods for calculating binding parameters for two strongly bound drugs to human serum albumin.

The determination of drug-protein binding parameters (n's and K's) can lead to important information on the required therapeutic dosage regimen and possible clinical complications associated with competitive displacement of one drug by a concurrently administered agent. Graphical and computer estimates of the data are often incorrectly formulated, and and seldom are adequate data obtained at low binding ratios. Commonly used graphical procedures, inadequately formulated computer methods, and a statistically correct computer method were used to compare results obtained from a circular dichroic examination of dicumarol-human serum albumin and fenoprofen-human serum albumin interactions. Literature binding constants for dicumarol-albumin range from 1 X 10(5) to 30 times that figure, and it is shown here that a wide range in parameter estimates may be obtained depending on the method of data analysis. The parameter estimates in the case of fenoprofen-albumin are even more variable.

Binding Sites↗
PubMed2006

A comparison of an interactive computer-based method with a conventional reading approach for learning pelvic anatomy.

OBJECTIVE: This study was undertaken to assess the impact of interactive, computer-based versus conventional, paper-based format in student, resident, and fellow learning and retention of anatomy knowledge. STUDY DESIGN: Randomized longitudinal cohort design with scores repeated as pre-, post-, and follow-up tests. Subjects were randomly assigned to an anatomy module in computer-based (CD-ROM) format and 1 in paper-based format. A follow-up examination was administered 3 weeks after the posttest to evaluate retention of knowledge. Tests results were analyzed by using Student t tests and analysis of variance. RESULTS: Thirty-nine subjects completed all testing. Regardless of instructional method, pretest to posttest scores improved (P < .01), and posttest to follow-up test scores decreased among all levels of training (P < .01). Student satisfaction was highest with CD-ROM format. CONCLUSION: Improvement and retention of anatomy knowledge was not significantly different when comparing a new CD-ROM interactive approach with a traditional paper-based method.

Anatomy↗
PubMed2001

Resolvent method for computations of localized defect modes of H-polarization in two-dimensional photonic crystals.

We have developed and tested a version of the resolvent (or Green's function) method, based on the shift-inverse of the Maxwellian operator, that ensures stable convergence of iterative computations of localized defect modes of H-polarization in two-dimensional (2D) photonic crystals. The defect states are obtained by solving the eigenvalue problem for an associated compact operator with the expansion in Bloch eigenfunctions of the unperturbed Maxwellian operator. This method can be extended to 3D photonic crystals. We apply the method to a 2D square lattice of square dielectric rods in a dielectric background and compute (with controlled precision of approximately 1%) the defect modes induced by the replacement of one rod (the defect). We investigate the rise and variation of the defect frequencies in a photonic band gap, caused by the increase of the dielectric strength of the defect, for four branches of localized modes of various symmetries.

Journal Article↗
PubMed1995

A new computer-assisted method for fabrication of crowns and fixed partial dentures.

The availability of high-technology systems that use computer-aided design and computer-aided machining is on the increase. One such system is the Procera system, which is currently providing cost-effective, high-quality dental restorative services to dental laboratories and to dentists. A reduction in cost to the dentist, and ultimately to the patient, is a major advantage of the Procera system. Cost benefits combined with its continued success in producing crowns and fixed partial dentures that meet professional standards of care should enhance the acceptance of this new technology.

Computer-Aided Design↗
PubMed2025

Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework.

MOTIVATION: Therapeutic peptide is an important ingredient in the treatment of various diseases and drug discovery. The toxicity of peptides is one of the major challenges in peptide drug therapy. With the abundance of therapeutic peptides generated in the post-genomics era, it is a challenge to promptly identify toxicity peptides using computational methods. Although several efforts have been made, few algorithms are designed to identify whether a query peptide exhibits toxicity. Considering the varied levels of biological activities, the toxicity peptides should be further classified into multi-functional peptides. RESULTS: This study introduces a two-level predictor, ToxPre-2L, developed using the multi-view tensor learning and latent semantic learning framework. The proposed method utilized multi-label learning with feature induced labels to avoid the redundancy of information from each view. Then the multi-view tensor learning was employed to establish the latent semantic information among different views, while low-rank constraint learning was leveraged to exploit the correlation information among multi-labels. Finally, we constructed an updated toxicity peptide benchmark dataset to assess the effectiveness of the proposed method. Experimental results demonstrated that ToxPre-2L achieves a better performance than alternative computational methods in the prediction of toxicity peptides and their multi-functional types. AVAILABILITY AND IMPLEMENTATION: The source code and data of ToxPre-2L can be accessed at http://bliulab.net/ToxPre-2L.

Peptides↗
PubMed2004

The effects of different mesh generation methods on computational fluid dynamic analysis and power loss assessment in total cavopulmonary connection.

The flow field and energetic efficiency of total cavopulmonary connection (TCPC) models have been studied by both in vitro experiment and computational fluid dynamics (CFD). All the previous CFD studies have employed the structured mesh generation method to create the TCPC simulation model. In this study, a realistic TCPC model with complete anatomical features was numerically simulated using both structured and unstructured mesh generation methods. The flow fields and energy losses were compared in these two meshes. Two different energy loss calculation methods, the control volume and viscous dissipation methods, were investigated. The energy losses were also compared to the in vitro experimental results. The results demonstrated that: (1) the flow fields in the structured model were qualitatively similar to the unstructured model; (2) more vortices were present in the structured model than in the unstructured model; (3) both models had the least energy loss when flow was equally distributed to the left and right pulmonary arteries, while high losses occurred for extreme pulmonary arterial flow splits; (4) the energy loss results calculated using the same method were significantly different for different meshes; and (5) the energy loss results calculated using different methods were significantly different for the same mesh.

Animals↗
PubMed2004

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

G-protein-coupled receptors (GPCRs) are involved in cell communication processes and with mediating such senses as vision, smell, taste, and pain. They constitute a prominent superfamily of drug targets, but an atomic-level structure is available for only one GPCR, bovine rhodopsin, making it difficult to use structure-based methods to design receptor-specific drugs. We have developed the MembStruk first principles computational method for predicting the three-dimensional structure of GPCRs. In this article we validate the MembStruk procedure by comparing its predictions with the high-resolution crystal structure of bovine rhodopsin. The crystal structure of bovine rhodopsin has the second extracellular (EC-II) loop closed over the transmembrane regions by making a disulfide linkage between Cys-110 and Cys-187, but we speculate that opening this loop may play a role in the activation process of the receptor through the cysteine linkage with helix 3. Consequently we predicted two structures for bovine rhodopsin from the primary sequence (with no input from the crystal structure)-one with the EC-II loop closed as in the crystal structure, and the other with the EC-II loop open. The MembStruk-predicted structure of bovine rhodopsin with the closed EC-II loop deviates from the crystal by 2.84 A coordinate root mean-square (CRMS) in the transmembrane region main-chain atoms. The predicted three-dimensional structures for other GPCRs can be validated only by predicting binding sites and energies for various ligands. For such predictions we developed the HierDock first principles computational method. We validate HierDock by predicting the binding site of 11-cis-retinal in the crystal structure of bovine rhodopsin. Scanning the whole protein without using any prior knowledge of the binding site, we find that the best scoring conformation in rhodopsin is 1.1 A CRMS from the crystal structure for the ligand atoms. This predicted conformation has the carbonyl O only 2.82 A from the N of Lys-296. Making this Schiff base bond and minimizing leads to a final conformation only 0.62 A CRMS from the crystal structure. We also used HierDock to predict the binding site of 11-cis-retinal in the MembStruk-predicted structure of bovine rhodopsin (closed loop). Scanning the whole protein structure leads to a structure in which the carbonyl O is only 2.85 A from the N of Lys-296. Making this Schiff base bond and minimizing leads to a final conformation only 2.92 A CRMS from the crystal structure. The good agreement of the ab initio-predicted protein structures and ligand binding site with experiment validates the use of the MembStruk and HierDock first principles' methods. Since these methods are generic and applicable to any GPCR, they should be useful in predicting the structures of other GPCRs and the binding site of ligands to these proteins.

Algorithms↗
PubMed1985

A computer-based method of filing photographs and procedures.

Careful preoperative and postoperative photographs are an essential part of facial plastic surgery for medical and legal documentation, publication, patient education, and lectures. Computers play an increasing role in many aspects of the medical practice. A method of filing photographs and procedures and a related data base system allows rapid access by multiple factors, including name, procedure, age, surgeon, assistants, anesthetic, complications, dates of all photographs, multiple procedure subheadings, and so on. Additional variables can be added as a date base for analysis of operation results and postoperative recall of patients. This system is based on a personal computer (IBM-PC Computer) and readily available software. The system allow simple entry and retrieval of photographs on any of the multiple variables. We found it to be a superb adjunct to photography in facial plastic and reconstructive surgery.

Computers↗
PubMed2004

New nomogram for foetal weight estimation based on Hadlock's two-parameter formula.

AIM: To develop and validate a graphical method for ultrasonic foetal weight estimation with predictive qualities comparable to state-of-the-art computational methods. METHOD: Study data were obtained from 3839 consecutive singleton pregnancies with ultrasound examination within 7 days of delivery. We translated the well established Hadlock 2-parameter formula based on abdomen circumference and femur length into a nomogram [corrected]. We compared the measured foetal weight with estimations obtained from this new nomogram and three other methods. RESULTS: Measured by the foetal weight percentage error the new nomogram underestimates the foetal weight on average by 2.5 % (9.86) (mean [SD]) with uniform results over the complete birth weight spectrum. By the same measurement the Hadlock 4-parameter formula underestimates the foetal weight by 1.2 % (9.3) whereas the Hansmann nomogram overestimates the foetal weight by 14.5 % (16.1) The difference between the estimated foetal weight percentage error obtained from the new nomogram and from the Hadlock 2-parameter formula is 0.06 % (0.27) and hence clinically irrelevant. CONCLUSION: The new nomogram has predictive qualities comparable to state-of-the-art computational methods and is thus not only as reliable but also easy to use in situations when computers are not available. It can be recommended for foetal weight estimation over the whole spectrum of birth weight.

Embryonic and Fetal Development↗
PubMed1998

A personal computer-based method of stereo chronometry for measuring neuroretinal rim width: a pilot study.

PURPOSE: Quantifying neuroretinal rim width from optic disc photographs to study glaucomatous progression requires precise, reproducible measurements. We explored the use of a personal computer with three-dimensional capabilities to enhance measurement accuracy and repeatability. METHODS: A simultaneous stereo retinal camera was used to serially photograph the optic discs often glaucomatous eyes with a mean interval of 18 months. The neuroretinal rims were qualitatively assessed as either stable (five) or narrowing (five). The images were measured using software written for an IBM compatible personal computer The measurements were compared from the earliest to the most recent image and the five narrowed rims were correctly identified. RESULTS: This simple, low-cost method allowed both three-dimensional viewing and measurement of the optic disc rim from simultaneous stereo images. CONCLUSIONS: This method is, potentially, more sensitive in identifying glaucomatous rim changes than conventional, subjective image comparison techniques.

Glaucoma↗
PubMed1995

Five methods for computing significant individual client change and improvement rates: support for an individual growth curve approach.

Interest has been renewed in methods for determining individual client change. Currently, there are at least 4 pretreatment-posttreatment (pre-post) difference score methods. A 5th method, based on a random effects model and multiwave data, represents a growth curve approach and was hypothesized to be more sensitive to detecting significant (p < .05) change than the pre-post methods. The change rates produced by the 5 methods were compared in a sample of 73 older outpatients with 3 to 5 assessments per client on a measure of well-being (H. J. Dupuy, 1977). Results indicated that the growth curve approach improvement rate was the highest (68.5%). The growth curve and the Edwards-Nunnally (63.0%) methods produced significantly (p < .05) higher improvement rates than the other 3 methods, with 1 exception.

Adaptation, Psychological↗