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At least 883 records · Page 49Linked to original sources
PubMed2004

Time-oriented hierarchical method for computation of principal components using subspace learning algorithm.

Principal Component Analysis (PCA) and Principal Subspace Analysis (PSA) are classic techniques in statistical data analysis, feature extraction and data compression. Given a set of multivariate measurements, PCA and PSA provide a smaller set of "basis vectors" with less redundancy, and a subspace spanned by them, respectively. Artificial neurons and neural networks have been shown to perform PSA and PCA when gradient ascent (descent) learning rules are used, which is related to the constrained maximization (minimization) of statistical objective functions. Due to their low complexity, such algorithms and their implementation in neural networks are potentially useful in cases of tracking slow changes of correlations in the input data or in updating eigenvectors with new samples. In this paper we propose PCA learning algorithm that is fully homogeneous with respect to neurons. The algorithm is obtained by modification of one of the most famous PSA learning algorithms--Subspace Learning Algorithm (SLA). Modification of the algorithm is based on Time-Oriented Hierarchical Method (TOHM). The method uses two distinct time scales. On a faster time scale PSA algorithm is responsible for the "behavior" of all output neurons. On a slower scale, output neurons will compete for fulfillment of their "own interests". On this scale, basis vectors in the principal subspace are rotated toward the principal eigenvectors. At the end of the paper it will be briefly analyzed how (or why) time-oriented hierarchical method can be used for transformation of any of the existing neural network PSA method, into PCA method.

Algorithms↗
PubMed1998

Mechanical properties of human trabecular bone lamellae quantified by nanoindentation.

Improved preventive and therapeutic strategies for skeletal diseases such as osteoporosis rely on a better understanding of the mechanical properties of trabecular bone and their influence on cell mediated adaptation processes. The mechanical properties of trabecular bone are determined by composition as well as structural (trabecular architecture), microstructural (trabecular packets) and nanostructural (lamellae) organization. Density is the major predictor of the mechanical properties of trabecular structures and has been extended to the concept of fabric to include architectural anisotropy and improve even further the power of prediction. Recent advances in QCT and MRI technologies allow for precise assessment of 3D trabecular architecture and the mechanical consequences of structural changes can be increasingly well quantified by the means of computational methods. While single trabeculae have been tested using various techniques with contrasting results, little is known about the intrinsic mechanical properties of trabecular bone lamellae on which these computational methods rely. For instance, water and mineral content have a significant effect on the elastic, viscous, yield and postyield properties of bone tissue. In addition, collagen fiber orientation affects the mechanics of single remodeling units. Variations in composition and organization determined by age, accumulated damage or disease may therefore reduce the mechanical integrity of trabecular bone and deserve more attention. The aim of this work was to utilize a nanoindentation technique to quantify elastic modulus and hardness of human trabecular bone lamellae.

Aged↗
PubMed1997

[Trial of analysis of esophageal wall motion using optical flow method on esophagogram].

Several studies have indicated that the analysis of esophageal motion provides a valid means of identifying esophageal diseases. Although this motion can be seen on esophagogram, its quantification leaves much room for improvement. This study presents a computer method to quantify the apparent motion (optical flow) observed on sequences of esophagogram. This method computes at every point of a sequence of digitized images the two-dimensional velocity vector which characterized its motion from one image to the next image. The information on motion of the esophagus can be displayed by superimposing the local velocity vector on the original image.

Algorithms↗
PubMed1999

Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations.

We have ranked 13 different TIBO derivatives with respect to their relative free energies of binding using two approximate computational methods: adaptive chemical Monte Carlo/molecular dynamics (CMC/MD) and Poisson-Boltzmann/solvent accessibility (PB/SA) calculations. Eight of these derivatives have experimentally determined binding affinities. The remaining new derivatives were constructed based on contour maps around R86183 (8Cl-TIBO), generated with the program PROFEC (pictorial representation of free energy changes). The rank order among the derivatives with known binding affinity was in good agreement with experimental results for both methods, with average errors in the binding free energies of 1. 0 kcal/mol for CMC/MD and 1.3 kcal/mol for the PB/SA method. With both methods, we found that one of the new derivatives was predicted to bind 1-2 kcal/mol better than R86183, which is the hitherto most tightly binding derivative. This result was subsequently supported by the most rigorous free energy computational methods: free energy perturbation (FEP) and thermodynamic integration (TI). The strategy we have used here should be generally useful in structure-based drug optimization. An initial ligand is derivatized based on PROFEC suggestions, and the derivatives are ranked with CMC/MD and PB/SA to identify promising compounds. Since these two methods rely on different sets of approximations, they serve as a good complement to each other. Predictions of the improved affinity can be reinforced with FEP or TI and the best compounds synthesized and tested. Such a computational strategy would allow many different derivatives to be tested in a reasonable time, focusing synthetic efforts on the most promising modifications.

Algorithms↗
PubMed1985

Practical use of computer-assisted EEG interpretation in epilepsy.

Computer methods can automatically recognize interictal spikes and seizures quite reliably, but they still make a large number of false detections because of physiological or artifactual nonepileptiform transients. In the context of long-term monitoring, these methods can be used efficiently and safely despite their imperfection. They allow considerable data reduction, by selecting epileptiform activity and discarding the largest part of the recording. In addition to data reduction, computer methods can be useful in refining the analysis of epileptic seizures, revealing information not available from visual inspection of the paper tracing. Recent technological advances make these applications affordable in a clinical EEG laboratory.

Cerebral Cortex↗
PubMed2005

Computer based safety training: an investigation of methods.

BACKGROUND: Computer based methods are increasingly being used for training workers, although our understanding of how to structure this training has not kept pace with the changing abilities of computers. Information on a computer can be presented in many different ways and the style of presentation can greatly affect learning outcomes and the effectiveness of the learning intervention. Many questions about how adults learn from different types of presentations and which methods best support learning remain unanswered. AIMS: To determine if computer based methods, which have been shown to be effective on younger students, can also be an effective method for older workers in occupational health and safety training. METHODS: Three versions of a computer based respirator training module were developed and presented to manufacturing workers: one consisting of text only; one with text, pictures, and animation; and one with narration, pictures, and animation. After instruction, participants were given two tests: a multiple choice test measuring low level, rote learning; and a transfer test measuring higher level learning. RESULTS: Participants receiving the concurrent narration with pictures and animation scored significantly higher on the transfer test than did workers receiving the other two types of instruction. There were no significant differences between groups on the multiple choice test. CONCLUSIONS: Narration with pictures and text may be a more effective method for training workers about respirator safety than other popular methods of computer based training. Further study is needed to determine the conditions for the effective use of this technology.

Adult↗
PubMed1998

A multi-media, computer-based method for stroboscopy rating training.

Methods of training individuals to rate stroboscopic examinations vary widely in rating criteria, viewing times, samples, and length of training. Consequently, problems occur in both inter- and intrajudge agreement. Computer-aided instruction (CAI) provides a means to integrate and control key learning factors that facilitate learning. This study attempted to determine if CAI could train individuals to make accurate and reliable visuo-perceptual judgments of stroboscopy. Experienced and inexperienced subjects rated 45 samples before and after training. Following 4 to 5 hours of CAI training, the subjects with no previous experience demonstrated improved interjudge agreement with a panel of expert raters. The training was not effective for the experienced group. Regardless of the rater's experience, the parameters that required evaluation of movement were more difficult to rate than those requiring only an assessment of structure.

Computer-Assisted Instruction↗
PubMed2003

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

BACKGROUND: Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. RESULTS: This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. CONCLUSION: As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Alternative Splicing↗
PubMed1981

Computer-assisted method for identification of Bacillus species isolated from liquid antacids.

One hundred nineteen species of Bacillus were isolated from five heavily contaminated liquid antacids and their constituent chemicals. The 66 different reaction profiles obtained were expressed in probability figures and stored in a computer. A total of 13 Bacillus species were identified, with B. coagulans, B. licheniformis, B. subtilis, and B. polymyxa present at particularly high frequencies. The potential advantage of using a computer in the identification of aerobic sporeformers is demonstrated.

Antacids↗
PubMed2006

Analytic IMRT dose calculations utilizing Monte Carlo to predict MLC fluence modulation.

A hybrid dose-computation method is designed which accurately accounts for multileaf collimator (MLC)-induced intensity modulation in intensity modulated radiation therapy (IMRT) dose calculations. The method employs Monte Carlo (MC) modeling to determine the fluence modulation caused by the delivery of dynamic or multisegmental (step-and-shoot) MLC fields, and a conventional dose-computation algorithm to estimate the delivered dose to a phantom or a patient. Thus, it determines the IMRT fluence prediction accuracy achievable by analytic methods in the limit that the analytic method includes all details of the MLC leaf transport and scatter. The hybrid method is validated and benchmarked by comparison with in-phantom film dose measurements, as well as dose calculations from two in-house, and two commercial treatment planning system analytic fluence estimation methods. All computation methods utilize the same dose algorithm to calculate dose to a phantom, varying only in the estimation of the MLC modulation of the incident photon energy fluence. Gamma analysis, with respect to measured two-dimensional (2D) dose planes, is used to benchmark each algorithm's performance. The analyzed fields include static and dynamic test patterns, as well as fields from ten DMLC IMRT treatment plans (79 fields) and five SMLC treatment plans (29 fields). The test fields (fully closed MLC, picket fence, sliding windows of different size, and leaf-tip profiles) cover the extremes of MLC usage during IMRT, while the patient fields represent realistic clinical conditions. Of the methods tested, the hybrid method most accurately reproduces measurements. For the hybrid method, 79 of 79 DMLC field calculations have gamma < 1 (3%/3 mm) for more than 95% of the points (per field) while for SMLC fields, 27 of 29 pass the same criteria. The analytic energy fluence estimation methods show inferior pass rates, with 76 of 79 DMLC and 24 of 29 SMLC fields having more than 95% of the test points with gamma < or = 1 (3%/3 mm). Paired one-way ANOVA tests of the gamma analysis results found that the hybrid method better predicts measurements in terms of both the fraction of points with gamma < or = 1 and the average gamma for both 2%/2 mm and 3%/3 mm criteria. These results quantify the enhancement in accuracy in IMRT dose calculations when MC is used to model the MLC field modulation.

Body Burden↗
PubMed2007

Fully automated segmentation and morphometrical analysis of muscle fiber images.

BACKGROUND: Measurement of muscle fiber size and determination of size distribution is important in the assessment of neuromuscular disease. Fiber size estimation by simple inspection is inaccurate and subjective. Manual segmentation and measurement are time-consuming and tedious. We therefore propose an automated image analysis method for objective, reproducible, and time-saving measurement of muscle fibers in routinely hematoxylin-eosin stained cryostat sections. METHODS: The proposed segmentation technique makes use of recent advances in level set based segmentation, where classical edge based active contours are extended by region based cues, such as color and texture. Segmentation and measurement are performed fully automatically. Multiple morphometric parameters, i.e., cross sectional area, lesser diameter, and perimeter are assessed in a single pass. The performance of the computed method was compared to results obtained by manual measurement by experts. RESULTS: The correct classification rate of the computed method was high (98%). Segmentation and measurement results obtained manually or automatically did not reveal any significant differences. CONCLUSIONS: The presented region based active contour approach has been proven to accurately segment and measure muscle fibers. Complete automation minimizes user interaction, thus, batch processing, as well as objective and reproducible muscle fiber morphometry are provided.

Algorithms↗
PubMed2004

Receptor flexibility in the in silico screening of reagents in the S1' pocket of human collagenase.

A major difficulty in structure-based molecular design is the prediction of the structure of the protein-ligand complex because of the enormous number of degrees of freedom. Commonly, the target protein is kept rigid in a single low-energy conformation. However, this does not reflect the dynamic nature of protein structures. In this work, we investigate the influence of receptor flexibility in virtual screening of reagents on a common scaffold in the S1' pocket of human collagenase (matrix metalloproteinase-1). We compare screening using a single-crystal structure and multiple NMR structures, both apo and holo forms. We also investigate two computational methods of addressing receptor flexibility that can be used when NMR data are not available. The results from virtual screening using the experimental structures are compared to those obtained using the two computational methods. From the results, we draw conclusions about the impact of target flexibility on the identification of active and diverse reagents in a virtual screening protocol.

Apoenzymes↗