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PubMed1977

[Method of computer processing of genealogic material].

The essential moments of the computer algorithms - a construction of pedigree patterns and determination of inbreeding coefficients - are described. The main attention is given to the field material prossesing for the computer system. The common program is composed to three subprograms: pedigree construction, F estimation and evaluation of information quantity concerning the ancestors. The principal algorithms of the pedigree subprogram is based on computations of a parents computer adress from the proband's code. Such a run is repeated from generation to generation, until the information of ancestors comees to zero. Common ancestors for Wright's inbreeding estimation have been found by sorting out and comparison of husband's and wife's ancestors. The inbreeding coefficient has been formed as the kinship coefficient of parents.

Computers↗
PubMedDate not supplied

Comparison of manual microscopic and computer-assisted methods for analysis of sperm count and motility.

This investigation was conducted to determine which of three methods, manual analysis, and two different commercially available computer-assisted semen analyzers (CASA), was the most reproducible. Semen samples from donors participating in an artificial insemination program (n = 1) and from patients being seen for andrology procedures (n = 12) were acquired at 0.5 h after ejaculation. Each specimen was loaded into one chamber of a 20-microns microcell slide (Conception Technologies, San Diego, CA, USA) and the port was sealed with petroleum jelly to prevent drying of the specimen. The specimens were assessed for sperm count (SC) and motility (MOT) first by manual analysis using an eyepiece reticle and brightfield light microscopy at 400 x total magnification, second using the Hamilton-Thorn 2030 analyzer (Hamilton-Thorn Research, Danvers, MA, USA), and third, using the Cell Trak/S system (CTS; Motion Analysis Corporation, Santa Rosa, CA, USA). Each analysis was repeated five times for each specimen on the same microcell by the same technician. The three methods were compared in terms of means and standard deviations of the SC and MOT over repeated measures-of a specimen using sign tests. The CTS system measured significantly lower sperm counts than the HTM system. MAN was intermediate and not significantly different from either. For MOT, there were no significant differences. Comparison of the standard deviations demonstrated that the three methods were not equally reproducible. For SC, the manual method was significantly less reproducible than the HTM system; the CTS system was intermediate. For MOT, the manual method was less reproducible than either CASA system, both of which were not significantly different from each other. CASA methodology in general provides a more reproducible (less variable) analysis than the manual microscopic method for assessing sperm count and motility.

Humans↗
PubMed2004

Computation of conversion coefficients relating air Kerma to Hp(0.07,alpha), Hp(10,alpha), and H*(10) for x-ray narrow spectrum from 40 to 140 kV.

A computation method was implemented to predict the conversion coefficients and the angular dependence factors relating air Kerma to Hp(0.07,alpha), Hp(10,alpha), and H*(10) in an ICRU slab phantom for tungsten anode x-ray spectra for tube potentials from 40 to 140 kV. The simulation of the unfiltered x-ray spectra is based on the Boone and Seibert model. The calculation of conversion coefficients were performed for an x-ray narrow spectrum at any filtration material and tube potentials in the diagnostic radiology range. This computation method has been checked for five narrow x-ray spectra using a comparison of the results with published data given by the International Organization for Standardization (ISO), and American National Standards Institute (ANSI). In all cases, the mean deviation of the calculated mean conversion coefficients values do not exceed 1% for Hp (0.07,alpha) and 1.5% for Hp (10,alpha), except at 60 degrees where a mean deviation from the ISO values of 1.72% and of 2.27% was, respectively, found. But it is still lower than the mean deviation of 2.31% for Hp(0.07,alpha), and of 3.08% for Hp(10,alpha) observed at this angle between ISO and ANSI values. Otherwise, the computed values of conversion coefficients of H*(10) differ by only 0.41% from the ISO values. The results of this computation method can be considered satisfactory considering the accuracy required in radioprotection fields, and can allow an appreciable estimation of conversion coefficients for the narrow x-ray spectra indispensable to calibrate the personnel dosimeters in terms of the personal dose equivalent.

Air↗
PubMed1984

Stewart-Hamilton and gamma variate methods in computer analysis of dye curves.

The conventional Stewart-Hamilton (SH) principle was compared to the gamma variate function fitting (G) method in on-line computer determination of cardiac output from dye dilution curves on anaesthetized animals (dogs, cats and reindeer), and on an artificial circulation model with known flows. In animal experiments, indicator was injected into the pulmonary artery (n = 674), the coefficient of linear correlation (Rlin) between G and SH was 0.982, and the regression line of G was 1.101 x SH-0.072 l/min. When the right atrium was the site of indicator injection (n = 88), Rlin was 0.982, and the regression line nearly agreed with the line of unity. In the artificial circulation model with the single circulation arrangement (n = 81), Rlin between SH and known flow (Q) was 0.959, and between G and Q it was 0.951; both methods over-estimated the flows, with the over-estimation being greater in the case of G. In the artificial model with recirculation effect (n = 31), Rlin between SH and Q was 0.953, and between G and Q 0.942, G again over-estimating the real flow essentially more than SH. Thus, in most cases the Stewart-Hamilton principle seems to be the more reliable way of analysis of dye dilution curves also in modern computer practice.

Anesthetics↗
PubMed2006

Ram sperm motility after intermittent scrotal insulation evaluated by manual and computer-assisted methods.

AIM: To study whether additional measurements of motility characteristics of spermatozoa by computer assisted semen analysis (CASA) were more sensitive indicators of reduced semen quality than estimates of percentages of motile, rapid or progressive cells. METHODS: Intermittent scrotal insulation was applied to 6 rams for 16 h per day for 21 days or to 2 of these for 12 h per day for 28 days in the following year. Semen was collected and evaluated by CASA immediately and either frozen or stored at 30 degrees Celsius or 5 degrees Celsius before re-evaluation. RESULTS: Intermittent scrotal insulation caused falls in the percentage of motile, progressive and rapid sperm, as did freezing-thawing and storage at 30 degrees Celsius or 5 degrees Celsius. Motility characteristics (amplitude of lateral head displacement, mean path velocity, mean progressive velocity and curvilinear velocity), as determined by CASA fell only when the percentage of motile sperm was already reduced. Freezing and thawing or liquid storage of the semen from insulated rams caused a greater fall in the percentage of motile and rapid sperm than control semen, but only affected the motility characteristics when the percentage of motile sperm was already reduced. CONCLUSION: Intermittent scrotal insulation affected not only the motility of the freshly collected sperm, but also their ability to withstand the additional stress of storage. The additional data on motility characteristics obtained by CASA appeared to be no more a sensitive indicator than the percentage of motile cells of reductions in semen quality.

Animals↗
PubMed1986

Videodensitometric quantitation of aortic regurgitation by digital subtraction aortography using a computer-based method analyzing time-density curves.

To assess the clinical role of computer analysis of time-density curves in the evaluation of aortic regurgitation (AR), digital subtraction aortography (DSA) and cineaortography were performed sequentially in 17 patients with varying degrees of AR (1+ to 4+) and in 4 control patients. DSA was performed at a rate of 30 frames/s on a 512 X 512 X 8 bit pixel matrix using the same total volume and injection rate, but with half the amount of contrast agent as standard cineaortography. A 30 X 30 pixel area of interest was identified in the aorta above the valve plane and in the left ventricle where the AR stream was seen. The density of both areas of interest and the ratio of left ventricular/aortic area of interest density was calculated in each frame and then plotted vs time. The ratio at the end of injection (LVd/Aod) had an excellent correlation with cineaortography (chi 2 = 19, p less than 0.001), ranging from 0 to 0.2 in patients with no AR, 0.2 to 0.5 in those with 1+ AR, 0.5 to 0.7 in those with 2+ AR, 0.7 to 0.9 in those with 3+ AR and more than 0.9 in those with 4+ AR. Thus, quantitative assessment of AR by computer analysis of time-density curves derived from DSA is a new and objective technique with significant clinical potential.

Aortic Valve Insufficiency↗
PubMedDate not supplied

A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models.

An increased availability of genotypes at marker loci has prompted the development of models that include the effect of individual genes. Selection based on these models is known as marker-assisted selection (MAS). MAS is known to be efficient especially for traits that have low heritability and non-additive gene action. BLUP methodology under non-additive gene action is not feasible for large inbred or crossbred pedigrees. It is easy to incorporate non-additive gene action in a finite locus model. Under such a model, the unobservable genotypic values can be predicted using the conditional mean of the genotypic values given the data. To compute this conditional mean, conditional genotype probabilities must be computed. In this study these probabilities were computed using iterative peeling, and three Markov chain Monte Carlo (MCMC) methods--scalar Gibbs, blocking Gibbs, and a sampler that combines the Elston Stewart algorithm with iterative peeling (ESIP). The performance of these four methods was assessed using simulated data. For pedigrees with loops, iterative peeling fails to provide accurate genotype probability estimates for some pedigree members. Also, computing time is exponentially related to the number of loci in the model. For MCMC methods, a linear relationship can be maintained by sampling genotypes one locus at a time. Out of the three MCMC methods considered, ESIP, performed the best while scalar Gibbs performed the worst.

Genotype↗
PubMed2006

Mammographic density measured with quantitative computer-aided method: comparison with radiologists' estimates and BI-RADS categories.

PURPOSE: To retrospectively compare computer-aided mammographic density estimation (MDEST) with radiologist estimates of percentage density and Breast Imaging Reporting and Data System (BI-RADS) density classification. MATERIALS AND METHODS: Institutional Review Board approval was obtained for this HIPAA-compliant study; patient informed consent requirements were waived. A fully automated MDEST computer program was used to measure breast density on digitized mammograms in 65 women (mean age, 53 years; range, 24-89 years). Pixel gray levels in detected breast borders were analyzed, and dense areas were segmented. Percentage density was calculated by dividing the number of dense pixels by the total number of pixels within the borders. Seven breast radiologists (five trained with MDEST, two not trained) prospectively assigned qualitative BI-RADS density categories and visually estimated percentage density on 260 mammograms. Qualitative BI-RADS assessments were compared with new quantitative BI-RADS standards. The reference standard density for this study was established by allowing the five trained radiologists to manipulate the MDEST gray-level thresholds, which segmented mammograms into dense and nondense areas. Statistical tests performed include Pearson correlation coefficients, Bland-Altman agreement method, kappa statistics, and unpaired t tests. RESULTS: There was a close correlation between the reference standard and radiologist-estimated density (R = 0.90-0.95) and MDEST density (R = 0.89). Untrained radiologists overestimated percentage density by an average of 37%, versus 6% for trained radiologists (P < .001). MDEST showed better agreement with the reference standard (average overestimate, 1%; range, -15% to +18%). MDEST correlated better with percentage density than with qualitative BI-RADS categories. There were large overlaps and ranges of percentage density in qualitative BI-RADS categories 2-4. Qualitative BI-RADS categories correlated poorly with new quantitative BI-RADS categories, and 16 (6%) of 260 views were erroneously classified by MDEST. CONCLUSION: MDEST compared favorably with radiologist estimates of percentage density and is more reproducible than radiologist estimates when qualitative BI-RADS density categories are used. Qualitative and quantitative BI-RADS density assessments differed markedly.

Adult↗
PubMedDate not supplied

A hybrid method to compute accurate efficiencies for volume samples in gamma-ray spectrometry.

In recent years, Monte Carlo (MC) methods have been increasingly applied to cope with variability in photopeak efficiencies due to matrix effects. But to obtain proper results only by numerical simulation, especially at low energies, sample bulk density and chemical composition must be well characterized. In this paper, we propose a method that combines both experimental measurements and MC simulations, being applicable to matrices of unknown composition. A transmission measurement of a 210Pb point source through the sample allows one to compute accurately its photopeak efficiencies at energies above 46.5 keV. The method is validated for several inorganic and organic matrices measured in Petri dishes geometry.

Algorithms↗
PubMed2005

A digital image-based method for computational tissue fate mapping during early avian morphogenesis.

The early stages of vertebrate development, encompassing gastrulation, segmentation, and caudal axis formation, presumably involve large (finite) morphogenetic deformations; however, there are few quantitative biomechanical data available for describing such large-scale or tissue-level deformations in the embryo. In this study, we present a new method for automated computational "tissue fate mapping," by combining a recently developed high-resolution time-lapse digital microscopy system for whole-avian embryo imaging with particle image velocimetry (PIV), a well-established digital image correlation technique for measuring continuum deformations. Tissue fate mapping, as opposed to classical cell fate mapping or other cell tracking methods, is used to track the spatiotemporal trajectories of arbitrary (virtual) tissue material points in various layers of the embryo, which can then be used to calculate finite morphogenetic deformation or strain maps. To illustrate the method, we present representative tissue fate and strain mapping data for normal early-stage quail embryos. These data demonstrate, to our knowledge, for the first time, large tissue-level deformations that are shared between different germ layers in the embryo, suggesting a more global morphogenetic patterning mechanism than had been previously appreciated.

Animals↗
PubMed1983

Method for computation of cardiac output in mitral stenosis independent of left ventricular dimensions and kinetic state: correlation with cardiac catheterization via the Fick method.

An hydraulic orifice formula offering the possibility of quantifying cardiac output in conditions of mitral stenosis is tested using potentially noninvasive portions of catheterization data from patients evaluated for obstructive mitral valve disease. The equation studied is V = (1/21) R A T2, where V is the cardiac output (ml/min), R is the heart frequency, A is the mitral valve area (cm2), and T is the diastolic filling interval (sec/min). The mitral valve area was determined by the Gorlin formula, and R and T were measured from the pressure tracings recorded at cardiac catheterization. The degree of correspondence between the equation tested and the measured cardiac output as determined by the Fick principle technique is characterized by r = 0.87, SE = 450 ml/min, N = 10. The results suggest that the new formulation may offer a noninvasive method for estimating the cardiac output status of patients with mitral valve disease once mitral valve area is measured either at catheterization or by two-dimensional echocardiography.

Cardiac Catheterization↗
PubMed2006

Enhanced visualization methods for computed radiography images.

This paper focuses on the application of two image enhancement techniques for the picture archiving and communications systems imaging diagnostic workstation applied to computed radiography (CR) and digital radiography images. The first method is a contrast enhancement technique based on a class of nonlinear intensity transformations described by analytic transfer functions derived from Hurter and Driffield characteristic curves. The second method employs antialiasing techniques preventing the formation of Moiré patterns on subsampled CR images containing antiscatter grid lines, designed to achieve a good balance between artifact suppression and resolution degradation. These techniques are likely to become standard features for all high-end medical imaging workstations in the near future, and thus, we are suggesting that more powerful descriptions of these types of processing should be included in the Digital Imaging and Communications in Medicine standard.

Humans↗
PubMed2001

Comparison of a new method for computer analysis with standard techniques for measuring survival rates in the rat transverse rectus abdominis musculocutaneous flap.

Many methods have been used to measure experimental flap survival in animal models. These have previously included planimetry, computer programs, and (routinely by the authors) the simple measurement of the weight of a template traced according to the dimensions of a given flap. To test the validity of their method, an alternative technique was developed by the authors' biostatiticians. Initially, in a study of rat transverse rectus abdominis musculocutaneous (TRAM) flaps, all templates were also scanned electronically to form bitmaps. Using commonly available software programs, each bitmap was colorized corresponding to viable and nonviable areas of the flaps. A summation of individual pixels by color could then be used to calculate the percentage of flap survival. A comparison of both methodologies in 64 rat TRAM flaps found that the survival rate was slightly greater overall when a computer analysis had been performed (3.1 +/- 1.7%), but this was not a significant difference (p = 0.479). Thus, the previous standard method was proven reliable, but just as precise calculations are now possible using the convenience of any personal computer.

Animals↗
PubMed1996

Computational screening of combinatorial libraries.

We first review existing computational methods with an intrinsic combinatorial feature, then describe a new computational method for screening combinatorial libraries using a recently developed multicopy sampling technique. The new method differs from the existing ones in that it can be used to screen simultaneously an entire library of molecules, instead of the individual molecules in a library. As an example, we have applied the method to study site-directed amino acid substitutions in a protein. After two rounds of library screening, we identified the energetically most stable substitutions along with their optimal conformations from all natural amino acids. In principle, the method is generally applicable to study ligand-host systems.

Amino Acids↗
PubMed2006

Finding function: evaluation methods for functional genomic data.

BACKGROUND: Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. There is currently no standard approach to evaluation in functional genomics. Our analysis of existing approaches shows that they are inconsistent and contain substantial functional biases that render the resulting evaluations misleading both quantitatively and qualitatively. These problems make it essentially impossible to compare computational methods or large-scale experimental datasets and also result in conclusions that generalize poorly in most biological applications. RESULTS: We reveal issues with current evaluation methods here and suggest new approaches to evaluation that facilitate accurate and representative characterization of genomic methods and data. Specifically, we describe a functional genomics gold standard based on curation by expert biologists and demonstrate its use as an effective means of evaluation of genomic approaches. Our evaluation framework and gold standard are freely available to the community through our website. CONCLUSION: Proper methods for evaluating genomic data and computational approaches will determine how much we, as a community, are able to learn from the wealth of available data. We propose one possible solution to this problem here but emphasize that this topic warrants broader community discussion.

Algorithms↗
PubMed1978

Computer-assisted method for intracavitary radiotherapy of cancer of the uterine cervix.

This paper describes a simple computer system for calculating the radiation dose rate to selected points in the pelvis of a patient treated by gynaecological insertion of applicators loaded with radioactive sources. The calculations are performed on the basis of radiographs made before the sources are placed in the applicators. The system consists of a minicomputer, a teletype and a digitizer. The method allows an optimum loading distribution to be determined within a few minutes once the radiographic images are available.

Computers↗
PubMed1986

A simple coding method for computer storage and handling of drug information.

An ever-growing body of knowledge in pharmacology has created a need for devising improved methods for handling drug information. We have developed an eleven digit comprehensive cardiovascular number to represent vital information on the effects of a drug on the cardiovascular system. Each digit of the number signifies an important cardiovascular phenomenon, and can vary from 0 to 9. This coding method provides a simple technique for computer handling of vital information on the effects of pharmacoactive agents in a semi-quantitative manner. Using this procedure, similar numbers for neuromuscular and immune systems can be easily developed.

Cardiovascular Physiological Phenomena↗