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PubMed2000

Computer-based methods for measuring joint space and estimating erosion volume in the finger and wrist joints of patients with rheumatoid arthritis.

OBJECTIVE: This study was conducted 1) to determine the feasibility of using computer programs to measure radiographic joint space width and estimate erosion volume in the hands of patients with rheumatoid arthritis (RA), and 2) to compare the new computer-based methods with established scoring methods. METHODS: To measure the joint space width in the finger and wrist joints of RA patients, hand and wrist radiographic films were scanned using a tabletop scanner and analyzed with programs written using the "macro" capabilities of NIH Image software. Estimation of erosion volume was determined by utilizing gray-scale intensity to calibrate bone density units per mm3, which made possible comparisons between the erosions and noneroded, anatomically similar sites. RESULTS: In 3 sets of duplicate measurements of joint space width on 79, 48, and 48 finger and wrist joints, the mean absolute deviation from the mean of the 2 measurements was 0.036 mm (SD 0.034), 0.032 mm (SD 0.049), and 0.021 mm (SD 0.016), respectively. Joint space measurements and scoring of joint space narrowing both demonstrated a difference between active treatment and placebo in an old trial set on gold therapy (P = 0.03 and P = 0.01, respectively). Two repeated measurements of bone density units in the bones of 3 different hands differed from the mean of the measurement by 2.29-4.04%. In 2 experiments, estimates of erosion volume showed a greater difference between gold therapy and placebo than did erosion scores in the trial set (P = 0.049 and P = 0.016 versus P = 0.27). CONCLUSION: Computer-based methods for measuring finger and wrist joint spaces and estimating erosion volume in patients with RA agree with the results of radiographic scoring of erosions and joint space narrowing.

Arthritis, Rheumatoid↗
PubMed2004

A simple method for computing exact probabilities of mutation numbers.

We describe a method for the recursive computation of exact probability distributions for the number of neutral mutations segregating in samples of arbitrary size and configuration. Construction of the recursions requires only characterization of evolutionary changes as a Markov process and determination of one-step transition matrices. We address the pattern of nucleotide diversity at a neutral marker locus linked to a determinant of mating type. Under a reformulation of parameters, the method also applies directly to metapopulation models with island migration among demes. Characterization of complete probability distributions facilitates parameter estimation and hypothesis testing by likelihood- as well as moment-based approaches.

Algorithms↗
PubMed1997

Using automated analysis of the resting twelve-lead ECG to identify patients at risk of developing transient myocardial ischaemia--an application of an adaptive logic network.

The aim of this study was to introduce an adaptive logic network computing method for detecting patients who were likely to show transient ischaemic episodes during ambulatory Holter monitoring, using parameters from a previously recorded standard twelve-lead resting electrocardiogram (ECG). In the present study, the adaptive logic network computing method is compared with other commonly used classification methods, such as backpropagation network and discriminant analysis techniques. Of 1367 study subjects aged 65 and above, 733 were women and 634 were men. Ambulatory Holter recordings were made to detect episodic ischaemia in study patients. Those subjects showing ischaemic episodes were classified as 'ischaemic' patients, and the remaining subjects were 'non-ischaemic'. Accuracy was 67% using the adaptive logic network computing method, 56% using the backpropagation network computing method, and 65% using statistical discriminant analysis. We concluded that the adaptive logic network technique offers a slightly higher accuracy and shows several potential advantages for automated detection of ischaemia in resting electrocardiograms.

Adult↗
PubMed2006

Cement mantle fatigue failure in total hip replacement: experimental and computational testing.

One possible loosening mechanism of the femoral component in total hip replacement is fatigue cracking of the cement mantle. A computational method capable of simulating this process may therefore be a useful tool in the preclinical evaluation of prospective implants. In this study, we investigated the ability of a computational method to predict fatigue cracking in experimental models of the implanted femur construct. Experimental specimens were fabricated such that cement mantle visualisation was possible throughout the test. Two different implant surface finishes were considered: grit blasted and polished. Loading was applied to represent level gait for two million cycles. Computational (finite element) models were generated to the same geometry as the experimental specimens, with residual stress and porosity simulated in the cement mantle. Cement fatigue and creep were modelled over a simulated two million cycles. For the polished stem surface finish, the predicted fracture locations in the finite element models closely matched those on the experimental specimens, and the recorded stem displacements were also comparable. For the grit blasted stem surface finish, no cement mantle fractures were predicted by the computational method, which was again in agreement with the experimental results. It was concluded that the computational method was capable of predicting cement mantle fracture and subsequent stem displacement for the structure considered.

Arthroplasty, Replacement, Hip↗
PubMed2005

From structure to function: methods and applications.

The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming universally accepted that the scale of the accumulated data for analysis and for prediction necessitate highly efficient computational tools with appropriate application capabilities. The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations. We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments. We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending movements). We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment.

Algorithms↗
PubMed2005

[Computer assisted methods in reconstructive and function-preserving orbital surgery. New capabilities of computer assisted preoperative surgical planning (CAPP) and computer assisted surgery (CAS)].

BACKGROUND: Orbital reconstruction after tumor or trauma makes high demands on the surgeon when restoring the optic axis and cosmetic features. Computer-assisted preoperative planning surgery (CAPP) and computer-assisted surgery (CAS) allow calculation of the form of the orbital cavity to be reconstructed preoperatively as well as the process of its realization intraoperatively. METHODS: We developed new planning software methods for this surgical procedure. For validation the deviation of accuracy was assessed between the virtual and the real model in eight patients with surgical reconstruction of the orbit. RESULTS: The check of accuracy of the reconstructions compared to the planning of the surgery by fusion of preoperative and postoperative data resulted in a mean deviation of 1.74 mm. The volumetric measurements presented a mean deviation of 0.2 cm(3) with an accuracy of >99%. The accuracy of linear measurements with the techniques of image fusion of the "feature-based" method was 0.38 mm and thus close to the technical threshold of effective data accuracy of 0.35 mm. The enophthalmus could be assessed more objectively with this method compared to using the Hertel index. CONCLUSIONS: CAPP and CAS are helpful in reconstructive orbital surgery to verify the position of the optic axis and the cosmetic result intraoperatively.

Adult↗
PubMed2004

Assessment of medical communication skills by computer: assessment method and student experiences.

BACKGROUND: A computer-assisted assessment (CAA) program for communication skills designated ACT was developed using the objective structured video examination (OSVE) format. This method features assessment of cognitive scripts underlying communication behaviour, a broad range of communication problems covered in 1 assessment, highly standardised assessment and rating procedures, and large group assessments without complex organisation. SETTING: The Academic Medical Centre (AMC) at the University of Amsterdam, the Netherlands. Aims To describe the development of the AMC Communication Test (ACT); to describe our experiences with the examination and rating procedures; to present test score descriptives, and to present the students' opinions of ACT. DESIGN: The ACT presents films on history taking, breaking bad news and shared decision making. Each film is accompanied by 3 types of short essay questions derived from our assessment model: "knows", "knows why/when" and "knows how". Evaluation questions about ACT were integrated into the assessment. Participants A total of 210 third year medical undergraduates were assessed. This study reports on the 110 (53%) students who completed all evaluation questions. RESULTS: Marking 210 examinations took about 17 days. The test score matched a normal distribution and showed a good level of discrimination of the students. About 75% passed the examination. Some support for the validity of our assessment model was found in the students' differential performance on the 3 types of questions. The ACT was well received. Student evaluations confirmed our efforts to develop realistic films that related well to the communication training programme. CONCLUSIONS: The ACT is a useful assessment method which complements interpersonal assessment methods for the evaluation of the medical communication skills of undergraduates.

Attitude of Health Personnel↗
PubMed2001

A computer-based method for the assessment of body-image distortions in anorexia-nervosa patients.

A computer-based method for the assessment of body-image distortions in anorexia nervosa and other eating-disorder patients is presented in this paper. At the core of the method is a realistic pictorial simulation of lifelike weight changes, applied to a real source image of the patient. The patients, using a graphical user interface, adjust their body shapes until they meet their self-perceived appearance. Measuring the extent of virtual fattening or slimming of a body with respect to its real shape and size allows direct quantitative evaluation of the cognitive distortion in body image. In a preliminary experiment involving 33 anorexia-nervosa patients, 70% of the subjects chose an image with simulated visual weight gain between 8%-16% as their "real" body image, while only one of them recognized the original body image. In a second experiment involving 30 healthy participants, the quality of the weight modified images was evaluated by pairwise selection trials. Over a weight change range from -16% to +28%, in about 30% of the trials, artificially modified images were mistakenly taken as "original" images, thus demonstrating the quality of the artificial images. The method presented is currently in a clinical validation phase, toward application in the research, diagnosis, evaluation, and treatment of eating disorders.

Agnosia↗
PubMed1981

[Serial computed tomography -- methods and early experience (author's transl)].

Serial computed tomography following intravenous bolus injection of contrast agent is an important development in computed tomographic diagnosis. The technical necessities and methods of examination are discussed. Our experience with 108 examinations is evaluated. The additional information in terms of morphology and function is described.

Arterial Occlusive Diseases↗
PubMedDate not supplied

[Quantification of pulmonary emphysema with computerized tomography. Comparison with various methods].

Computed Tomography (CT) has been proved to be the most accurate imaging modality to diagnose emphysema in vivo. Our study was aimed at comparing different CT methods for pulmonary emphysema quantification in patients with severe chronic obstructive pulmonary disease (COPD). Forty-six consecutive inpatients affected with COPD underwent high resolution CT (HRCT). Three scans were acquired at 3 preselected anatomic levels at both full inspiration and expiration. Three different observers were asked to subjectively evaluate, under blind conditions, the extent alone and both the severity and the extent of emphysema on the 6 scans. HRCT findings were also analyzed quantitatively by measuring the mean CT number in Hounsfield Units (HU) and the % of lung area with CT numbers < -900 HU (pixel index). Quantitative CT data were compared with reference values obtained in 7 normal nonsmokers. The CT visual score of emphysema exhibited medium-high interobserver reproducibility with correlation coefficients ranging from 0.80 to 0.96 and a good correlation with pulmonary function tests, particularly relative to the assessment of the extent of emphysema alone as expressed by one observer. CT quantification demonstrated an excellent correlation with functional indices of expiratory airflow, lung volumes and diffusion coefficients (p < 0.001). The expiratory measurements were better than the inspiratory ones while the analysis of both CT number and pixel index gave comparable results. Only the CT expiratory quantitative data allowed to differentiate the patients affected with COPD from the controls. In conclusion, the severity of emphysema as expressed by CT correctly reflects the functional impairment of patients with severe COPD.(ABSTRACT TRUNCATED AT 250 WORDS)

Aged↗
PubMed1999

A computationally efficient method for tracking reference position displacements for motion compensation in magnetic resonance imaging.

A fast and computationally efficient method for detecting and tracking the displacement of a reference structure within the body using MR imaging is described. This method is used to determine the position of the diaphragm in order to synchronize the data acquisition to the same relative position of the abdominal and thoracic organs, thereby minimizing or eliminating respiratory motion artifacts. The method described uses the time domain linear phase shift of a reference structure to determine its spatial positional displacement as a function of the respiratory cycle. The signal from a two-dimensional rectangular excitation column is first Fourier-transformed to the image domain, apodized, and then transformed back to the time domain. The relative displacement of a target edge in the image domain is determined from an autocorrelation of the resulting time domain information. This technique was found to require between three and eight times less computation than either cross-correlation or least-squares analysis, depending on the navigator parameters. Magn Reson Med 42:548-553, 1999.

Algorithms↗
PubMedDate not supplied

Differences between manual and computer-based methods for clinical learning assignments.

Two methods of assigning nursing students to clinical learning settings were compared for accuracy and speed. The first, a manually prepared method, was based on student preferences and experiential knowledge of nursing faculty. The second, a computer program designed for the project, used decision rules derived from ratings of student learning capabilities and ratings of the perceived demand for such capabilities by clinical settings. Ratings were assigned numerical values and were processed by the computer to obtain the best matches between students and settings. The same ratings were applied to the hand-prepared method after this assignment was completed. Comparison of the results showed that the best fit (least total numerical differences) between students and settings for the whole class was found by the computer, indicating that the computer method was superior. A completely randomized computer assignment that was run as an added source for comparison was much less effective than the assignment completed by hand, suggesting that human decision-making is an important factor in making clinical assignments. In terms of speed, 5.5 hours were used to prepare an assignment by hand and to make an adjustment; the computer completed the assigning task in less than 3 minutes. An alternate computing algorithm, used subsequently, completed the task in 3 seconds. The authors concluded that human judgment is necessary in making clinical assignments, but use of a tailored computer matching program can improve the quality of the decision making and can reduce the time and energy spent on this task.

Computer Systems↗
PubMed2006

Prediction of the variance of stereological volume estimates from systematic sections using computer-intensive methods.

The Cavalieri method is an unbiased estimator of the total volume of a body from its transectional areas on systematic sections. The coefficient of error (CE) of the Cavalieri estimator was predicted by a computer-intensive method. The method is based on polynomial regression of area values on section number and simulation of systematic sectioning. The measurement function is modelled as a quadratic polynomial, with an error term superimposed. The relative influence of the trend and the error component is estimated by techniques of analysis of variance. This predictor was compared with two established short-cut estimators of the CE based on transitive theory. First, all predictors were applied to data sets from six deterministic models with analytically known CE. For these models, the CE was best predicted by the older short-cut estimator and by the computer-intensive approach, if the measurement function had finite jumps. The best prediction was provided by the newer short-cut estimator when the measurement function was continuous. The predictors were also applied to published empirical datasets. The first data set consisted of 10 series of areas of systematically sectioned rat hearts with 10-13 items, the second data set consisted of 13 series of systematically sampled transectional areas of various biological structures with 38-90 items. On the whole, similar mean values for the predicted CE were obtained with the older short-cut estimator and the computer-intensive method. These ranged in the same order of magnitude as resampling estimates of the CE from the empirical data sets, which were used as a cross-check. The mean values according to the newer short-cut CE estimator ranged distinctly lower than the resampling estimates. However, for individual data sets, it happened that the closest prediction as compared to the cross-check value could be provided by any of the three methods. This finding is discussed in terms of the statistical variability of the resampling estimate itself.

Analysis of Variance↗
PubMed2006

A computer-aided method to expedite the evaluation of prognosis for childhood acute lymphoblastic leukemia.

This study presented a fully-automated computer-aided method (scheme) to detect metaphase chromosomes depicted on microscopic digital images, count the total number of chromosomes in each metaphase cell, compute the DNA index, and correlate the results to the prognosis of childhood acute lymphoblastic leukemia (ALL). The computer scheme first uses image filtering, threshold, and labeling algorithms to segment and count the number of the suspicious "chromosome," and then computes a feature vector for each "detected chromosome." Based on these features, a knowledge-based classifier is used to eliminate those "non-chromosome" objects (i.e., inter-phase cells, stain debris, and other kinds of background noises). Due to the possible overlap of the chromosomes, a classification criterion was used to identify the overlapped chromosomes and adjust the initially counted number of the total chromosomes in each image. In this preliminary study with 60 testing images (depicting metaphase chromosome cells) acquired from three pediatric patients, the computer scheme generated results matched with the diagnostic results provided by the clinical cytogeneticists. The results demonstrated the feasibility or potential of using a computerized method to replace the tedious and the reader-dependent diagnostic methods commonly used in genetic laboratories to date.

Algorithms↗
PubMed2004

An efficient method for computing leave-one-out error in support vector machines with Gaussian kernels.

In this paper, we give an efficient method for computing the leave-one-out (LOO) error for support vector machines (SVMs) with Gaussian kernels quite accurately. It is particularly suitable for iterative decomposition methods of solving SVMs. The importance of various steps of the method is illustrated in detail by showing the performance on six benchmark datasets. The new method often leads to speedups of 10-50 times compared to standard LOO error computation. It has good promise for use in hyperparameter tuning and model comparison

Computing Methodologies↗
PubMed1982

A simplified method for computer analysis of autoradiograms from two-dimensional gels.

A simple method is described for computer analysis of a discrete number of spots on autoradiograms from two-dimensional gels. The method involves digitizing the density data on an autoradiograph with a rotating drum densitometer and displaying the data on a graphics computer terminal. The software allows the operator to select the boundaries of the spots to be analyzed from the terminal, then integrates the the density of the spots and tabulates the data. Graphics options allow the operator to display a computer-generated image of the area of the film being analyzed. Accurate integration of weak or overlapping spots is accomplished by a nonlinear least squares fit of the density data to normal Gaussian curves in the x and y dimensions followed by analytical integration of the equations. Since the software is written in Fortran IV and the equipment required to run the programs is available in most computing centers, this technique should allow laboratories of modest resources to quantitate information from two-dimensional gels.

Animals↗
PubMed2006

Computationally efficient method for retrieving aerosol optical depth from ATSR-2 and AATSR data.

We present a robust and computationally efficient method for retrieving aerosol optical depth (AOD) from top-of-atmosphere ATSR-2 (Along-Track Scanning Radiometer) and AATSR (Advanced ATSR) reflectance data that is formulated to allow retrieval of the AOD from the 11 year archive of (A)ATSR data on the global scale. The approach uses a physical model of light scattering that requires no a priori information on the land surface. Computational efficiency is achieved by using precalculated lookup tables (LUTs) for the numerical inversion of a radiative-transfer model of the atmosphere. Estimates of AOD retrieved by the LUT approach are tested on AATSR data for a range of global land surfaces and are shown to be highly correlated with sunphotometer measurements of the AOD at 550 nm. (Pearson's correlation coefficient r(2) is 0.71.).

Journal Article↗