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At least 523 records · Page 29Linked to original sources
PubMed2003

Visualization of ischaemic penumbra using a computed tomography perfusion method.

A computed tomography (CT) perfusion imaging and a diffusion/perfusion magnetic resonance imaging (MRI) were performed in a 51-year-old man at 15 and 15.5 h of onset of left middle cerebral artery infarction, respectively. The established infarct, as revealed by the diffusion-weighted MRI, had low values of cerebral blood flow (CBF) and cerebral blood volume (CBV) on the CT perfusion study. The ischaemic penumbra, as reflected by the perfusion-diffusion mismatch on MRI, had reduced CBF, prolonged mean transit time (MTT) and compensated CBV. Spontaneous bleeding occurred in the medial part of the left lentiform nucleus, immediately following decompressive craniectomy. CT measurements of CBF, CBV and MTT may visualize the ischaemic penumbra and explain the site of bleeding after surgical decompression.

Brain Ischemia↗
PubMed1995

A computerized method for determination of microvascular density.

Currently accepted stereological methods for vascular density measurements involve manual counting of labeled vessels with a grid image overlay and determination of vessel-grid intersections. This method both is tedious and may be prone to error; therefore, our laboratory has developed a method for computer-automated determination of microvascular density using digital image processing techniques. An image of the microvasculature is acquired using computer videomicroscopy. The image is processed in three general steps, involving (1) background correction, (2) thresholding of the gray level image to create a binary image, and (3) processing of the binary image using erosion, dilation, and skeletonization algorithms. Testing of this procedure was performed on 328 typical images of skeletal muscle tissue sections taken from the hindlimb of Sprague-Dawley rats and quantitated by both traditional measures and our new computer method. Results from this comparison reveal that the automated vessel counting is highly correlated (r2 = 0.71) and decreased analysis time from 15 min/image to 30 sec/image when compared with manual counting methods. Our computer-based method also appears to be superior to the traditional method due to the unbiased and nonsubjective nature of determining vessel-grid intersections.

Animals↗
PubMed2001

A quick method for computing approximate thresholds for quantitative trait loci detection.

This article proposes a quick method for computing approximate threshold levels that control the genome-wise type I error rate of tests for quantitative trait locus (QTL) detection in interval mapping (IM) and composite interval mapping (CIM). The procedure is completely general, allowing any population structure to be handled, e.g., BC(1), advanced backcross, F(2), and advanced intercross lines. Its main advantage is applicability in complex situations where no closed form approximate thresholds are available. Extensive simulations demonstrate that the method works well over a range of situations. Moreover, the method is computationally inexpensive and may thus be used as an alternative to permutation procedures. For given values of the likelihood-ratio (LR)-profile, computations involve just a few seconds on a Pentium PC. Computations are simple to perform, requiring only the values of the LR statistics (or LOD scores) of a QTL scan across the genome as input. For CIM, the window size and the position of cofactors are also needed. For the approximation to work well, it is suggested that scans be performed with a relatively small step size between 1 and 2 cM.

Biometry↗
PubMed2005

Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria.

BACKGROUND: Identification of a bacterial protein's subcellular localization (SCL) is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation. RESULTS: In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods. CONCLUSION: We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high-throughput laboratory approaches. We note that analysis of all cellular fractions collectively is required to effectively provide localization information from laboratory studies, and we propose an overall approach to genome-wide subcellular localization characterization that capitalizes on the complementary nature of current laboratory and computational methods.

Bacterial Proteins↗
PubMed1985

[A new 3-dimensional imaging method in computed tomography].

A new imaging method for computerized tomography is presented and some examples are demonstrated. The method is based on the collection of all image data of a chosen block of tissue and enables the examiner to perform multiplanar reconstructions of high quality in any direction, even in oblique planes. In order to achieve a better orientation, the block of tissue can also be visualized at the same time on the reconstruction.

Aged↗
PubMed1989

Reliability of the Cobb angle index derived by traditional and computer assisted methods.

The reliability of the traditional Cobb angle index, which at present exhibits a wide range of reported values, was determined in this study and amounted to a within subject error of +/-4.3 degrees and a between subject error of +/-4.9 degrees. An attempt to pinpoint the source of this variability by investigating the influence of choice of end vertebrae proved inconclusive. The reliability of a computer assisted Cobb angle index, developed to improve measurement accuracy, was also examined and an estimated within subject error of +/-1.5 degrees and a between subject error of +/-1.6 degrees obtained. A comparison of the traditional and computer assisted methods indicates a high correlation between the Cobb angle derived using the two methods when measuring like curves and an improved reliability obtained by the computer method. Such an improvement is worth implementing clinically but of course the availability of a computer and digitizer and a little extra time for an operator to input the X-ray coordinates may be a barrier to its general use.

Diagnostic Errors↗
PubMed1979

"Circumferential profiles:" a new method for computer analysis of thallium-201 myocardial perfusion images.

A method for computer analysis of thallium-201 scintigrams is described, in which the left-ventricular activity is measured along radii constructed from the center of the left ventricle (LV) to each point on the LV circumference. Data are then displayed graphically as a "circumferential profile" of normalized activity against radial location. Thallium defects are identified and scored by comparison of the profile curve with empirically determined normal limits. In patients with coronary artery disease, defect scores were found to be quantitative and reproducible, and to agree generally with subjective visual analysis.

Adult↗
PubMed1994

Correlates of reactivity: problems with regression based methods.

Computer simulations were used to compare change score and regression methods for identifying relationships between a third variable and reactivity. When the third variable was not correlated with baseline, the two methods were equally effective for detecting relationships between the third variable and change. However when there was a correlation between the third variable and baseline, regression measures of change yielded a high rate of Type one errors. Regression methods also had less power for detecting a relationship between the third variable and change when the relationship was in the direction opposite to the sign of the correlation with baseline. The implication of these findings for two areas of research are discussed: the relationship of fitness to heart rate reactivity and the relationship of hypertension to blood pressure reactivity.

Computer Simulation↗
PubMed2001

Volumetric quantification of the gastric emptying: computer-based method for generation of volumetric index from fluoroscopic images.

We developed an automated software-based procedure for estimation of the volume variation of the stomach using videofluoroscopic analysis of the gastric emptying. We used radiological images with postero-anterior incidence of eight healthy volunteers and in vitro experimental tests, with different volumes and concentrations of the contrast medium. This computational method generates an index that measures, in the three dimensions, the dynamic behaviour of gastric emptying. Using adequate contrast concentration (barium sulphate solution), it is possible to determine volume behaviour from density variations. This software can automate this computation, facilitating the amount of work, avoiding mistakes and improving reproducibility.

Adult↗
PubMed2001

Myocardial fibrosis assessment by semiquantitative, point-counting and computer-based methods in patients with heart muscle disease: a comparative study.

AIMS: No study has directly compared different histomorphometric methods of quantification of myocardial fibrosis. Therefore we compared the results of semiquantitative, point-counting and computer-based methods in the assessement of myocardial fibrosis in a consecutive series of endomyocardial biopsy samples from patients with heart muscle disease. METHODS AND RESULTS: Histological samples (at least three per patient) were obtained by endomyocardial biopsy from 11 patients with focal myocarditis and from 24 ambulatory patients with idiopathic dilated cardiomyopathy, or during surgery in 10 patients who underwent partial left ventriculectomy. Samples were cut and stained with Masson-trichrome for better contrast. From each sample, a representative field was digitized, and the amount of fibrosis was assessed by semiquantitative scoring, by point-counting, and by computer-based software. Semiquantitative scoring correlated with both point-counting (Spearman's r = 0.69, P < 0.0001) and computer-based (Spearman's r = 0.83, P < 0.0001) methods. There was also a good correlation between point-counting and computer-based methods (r = 0.71, P < 0.0001). However, when compared with the point-counting method, the computer-based method overestimated percent fibrosis by 3.0 +/- 6.7% (P = 0.004). This overestimation correlated with the mean percent fibrosis (r = 0.38, P = 0.014). CONCLUSIONS: Our data show good correlations between the three methods of myocardial fibrosis assessment. However, systematic differences between them emphasize that this should be taken into consideration when comparing results of the studies using different methods of fibrosis assessment.

Biopsy↗
PubMed2003

A hybrid numerical method to compute erythrocyte TMP in low-frequency electric fields.

This paper presents a coupling method of the finite element method and the boundary element method to compute the transmembrane potential (TMP) of an erythrocyte in a low-frequency electric field. We compute an in vitro erythrocyte's TMP induced by external electric fields by this hybrid method. It takes advantage of the homogeneous characteristics from both intracellular region and extracellular region. Moreover, we may use a fine three-dimensional (3-D) mesh around the thin membrane and avoid 3-D meshes in other regions. Numerical results of a spherical cell show that the hybrid method is accurate. The computed threshold of the applied electric field for membrane electric breakdown agrees well with those experimental results. Numerical results can also guide us to locate the maximum induced TMP on the erythrocyte membrane in various electric fields. Some further applications of the hybrid method are also discussed.

Algorithms↗
PubMed2003

New method for computing finite-time Lyapunov exponents.

We present a novel method for computing finite-time Lyapunov exponents and vectors, via generalizing a correction given by Goldhirsch, Sulem, and Orszag [Physica (Amsterdam) 27D, 311 (1987)]] into higher-order corrections. This method is a generalized LR method, which is, in contrast to the existing methods, applicable to multidimensional systems with degenerate spectra. The efficiency and accuracy is demonstrated by applying it to multidimensional dynamical systems. Without these corrections, we could not accurately detect, as an example, the coexistence of qualitatively different Lyapunov instabilities along a trajectory for a multidimensional oscillator system.

Journal Article↗
PubMed2005

Advanced soft computing diagnosis method for tumour grading.

OBJECTIVE: To develop an advanced diagnostic method for urinary bladder tumour grading. A novel soft computing modelling methodology based on the augmentation of fuzzy cognitive maps (FCMs) with the unsupervised active Hebbian learning (AHL) algorithm is applied. MATERIAL AND METHODS: One hundred and twenty-eight cases of urinary bladder cancer were retrieved from the archives of the Department of Histopathology, University Hospital of Patras, Greece. All tumours had been characterized according to the classical World Health Organization (WHO) grading system. To design the FCM model for tumour grading, three experts histopathologists defined the main histopathological features (concepts) and their impact on grade characterization. The resulted FCM model consisted of nine concepts. Eight concepts represented the main histopathological features for tumour grading. The ninth concept represented the tumour grade. To increase the classification ability of the FCM model, the AHL algorithm was applied to adjust the weights of the FCM. RESULTS: The proposed FCM grading model achieved a classification accuracy of 72.5%, 74.42% and 95.55% for tumours of grades I, II and III, respectively. CONCLUSIONS: An advanced computerized method to support tumour grade diagnosis decision was proposed and developed. The novelty of the method is based on employing the soft computing method of FCMs to represent specialized knowledge on histopathology and on augmenting FCMs ability using an unsupervised learning algorithm, the AHL. The proposed method performs with reasonably high accuracy compared to other existing methods and at the same time meets the physicians' requirements for transparency and explicability.

Algorithms↗
PubMed1975

[Plea for the application of statistical methods by computer to stomatological research].

In face of the double reflex of fascination and defiance which is right away created by statistical methods by computers, the authors have attempted by means of precise examples to demystify these methods by recalling: 1) That computer statistics can be defined as the association of a service and a machine, the combination should be considered as an instrument and only an instrument. 2) That the application of computer statistics to odonto-stomatological research of course evidently enables the resolution of problems which would be otherwise insoluble, but above all considerably enlarges the field of research by rendering visible phenomena which would otherwise remain hidden. In this way, statistical methods by computer can be compared with the microscope; a low magnification with the optical microscope justifies only an overall view of the section while changing to higher magnifications permits the demonstration of details which would remain unsuspected. Use of the electromicroscope opens up another world for research. 3) In the same way as the biologist who uses the microscope, if he knows the principle of it is not in so far a specialist in optics, neither does the research woker who uses statistics necessarily have to be a trained statistician, on the one condition that evidently he disposes of professional computer logistics. This is the case of the ACB (Nantes) rush technical units, who cosigned this work, where the engineers who pose the problems to be resolved and emit the working hypotheses from the results supplied by the statistical studies are not the same people who carry out these very studies. 4) An essential fact, the research worker's independance is complete, only he can pose the problems and emit the hypothesis from the correlation, i. e. point of fact concomitance between the various isolated parameters. It therefore does not seem that weighty statistical techniques presently occupy the place of choice which should be theirs in stomatological research and more particularly in research concerning growth and development of the face where their use seems to be electively implied in face of the number and complexity of the parameters looked at.

Computers↗
PubMed1991

Efficient methods for computing linkage likelihoods of recessive diseases in inbred pedigrees.

Traditional methods for computing linkage likelihoods can be infeasible for data that involve considerable inbreeding and missing information, characteristics of large pedigrees affected by rare recessive diseases. For this type of data, we propose alternative procedures that can efficiently provide good approximates of linkage likelihoods. These approximation procedures are constructed based on a new mathematical representation of the multiloci inheritance model. Instead of representing each person by a single variable, the genotype, the disease gene alleles, and the marker alleles are taken as separate variables. This allows us to break down the computations into manageable pieces. This new representation is also potentially useful for multipoint mapping.

Algorithms↗
PubMed1984

Method of computed tomography-based stereotactic biopsy with arteriographic control.

A method for computed tomography (CT)-based stereotactic biopsy of intracranial neoplasms with arteriographic control is described. Stereotactic CT and digitized stereotactic arteriographic data are input to a three-dimensional computer matrix that corresponds to the coordinate system of a stereotactic frame located in the operating room. A site for biopsy is selected by cursor from the CT display screen. The computer calculates and outputs the mechanical adjustments of the stereotactic frame necessary to place the target point into the focal point of the frame. Horizontal and vertical approach angles are determined from the digitized arteriogram and are displayed as settings on the stereotactic frame that represent an avascular trajectory along which the lesion may be biopsied safely. This procedure has been used successfully in 86 patients, with no morbidity or mortality.

Biopsy↗