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Incremental communication for adaptive resonance theory networks.

We have proposed earlier the incremental internode communication method to reduce the communication cost as well as the time of the learning process in artificial neural networks (ANNs). In this paper, the limited precision incremental communication method is applied to a class of recurrent neural networks, the adaptive resonance theory 2 (ART2) networks. Simulation studies are carried out to examine the effects of the incremental communication method on the convergence behavior of ART2 networks. We have found that, 7-13-b precision is sufficient to obtain almost the same results as those with full (32-b) precision conventional communication. A theoretical error analysis is also carried out to analyze the effects of the limited precision incremental communication. The simulation and analytical results show that the limited precision errors are bounded and do not seriously degrade the convergence of ART2 networks. Therefore, the incremental communication can be incorporated in parallel and special-purpose very large scale integration (VLSI) implementations of the ART2 networks.

Algorithms↗

[Goals of medical monitoring].

The paper deals with the problems of medical monitoring, namely how to solve those in the detection and classification of human abnormalities. The medical monitor is a complex hierarchic system and the authors state problems and tasks for each level of hierarchy and the objectives of studies in medical diagnosis and prediction while designing the hierarchic network structure of a medical computer monitor. A parallel is drawn between the image recognition theory and medical diagnosis.

Algorithms↗

Fast Algorithm for X-ray Cone-beam Microtomography.

Cone-beam X-ray microtomography attracts increasing attention due to its applications in biomedical sciences, material engineering, and industrial nondestructive evaluation. Rapid volumetric image reconstruction is highly desirable in all these areas for prompt visualization and analysis of complex structures of interest. In this article, we reformulate a generalized Feldkamp cone-beam image reconstruction algorithm, utilize curved voxels and mapping tables, improve the reconstruction efficiency by an order of magnitude relative to a direct implementation of the standard algorithm, and demonstrate the feasibility with numerical simulation and experiments using a prototype cone-beam X-ray microtomographic system. Our fast algorithm reconstructs a 256-voxel cube from 100 projections within 2 min on an Intel Pentium II(R) 233 MHz personal computer, produces satisfactory image quality, and can be further accelerated using special hardware and/or parallel processing techniques.

Journal Article↗

A new method for the characterization of chemical libraries--solely by HPLC retention times.

A method has been developed for the assignment of HPLC peaks to their corresponding compounds in libraries of single compounds (parallel syntheses). The basis of the new method is the correlation of the product retention times with the different substituents in the variable positions of the molecule. The correlation is performed automatically by a new algorithm which is part of the computer program LIBFINDER. This practical, easy-to-use tool accelerates the analysis, characterization and purification of chemical libraries, without the need for expensive HPLC-MS equipment.

Chromatography, High Pressure Liquid↗

Strategy execution in cognitive skill learning: an item-level test of candidate models.

This article investigates the transition to memory-based performance that commonly occurs with practice on tasks that initially require use of a multistep algorithm. In an alphabet arithmetic task, item response times exhibited pronounced step-function decreases after moderate practice that were uniquely predicted by T. C. Rickard's (1997) component power laws model. The results challenge parallel strategy execution models as developed to date and they demonstrate that the shift to retrieval is an item-specific, as opposed to task-general, learning phenomenon. The results also call into question the entire class of smooth speed-up functions as global empirical learning laws. It is shown that overlaying of averaged item fits on averaged data can provide a sensitive test for model sufficiency. Strategy probes agreed with strategy inferences that were based on step-function speed-up patterns, supporting the validity of the probing technique.

Cognition↗

The benefit of multislice CT in the emergency room management of polytraumatized patients.

The early treatment of polytraumatized patients needs an effective and standardized approach. Reducing time requirements for the primary diagnostic evaluation is a major concern in the early phase of polytrauma management. Multislice-CT (MSCT) is a quick and reliable method for the initial diagnostic evaluation. Computed tomography provides more detailed and more consistent information than conventional radiography. It has the great advantage of allowing rapid examination of the head, vertebral column, chest, abdomen and pelvis during one single examination. The CT-suite needs to be adequately equipped for resuscitation and reanimation, which is done parallel to the radiological investigations. Since polytrauma management is based on a multidisciplinary approach characterized by a coordinated interaction between trauma surgeons, anaesthesiologists and radiologists, members of all involved disciplines need adequate teaching. Guidelines and algorithms contribute to optimize the early management.

Humans↗

Pre-clinical evaluation of a two-channel microwave hyperthermia system with adaptive phase control in a large animal.

A pre-clinical assessment of the heating capabilities of a two-channel 915 MHz Microfocus-1000 hyperthermia system, with adaptive phase control, was carried out in a series of experiments using a large animal model. The results of the experimental measurements of specific absorption rate (SAR) and tissue temperature show that when muscle tissue of the hind legs of pigs was compressed to 6.5-7 cm, then a pair of parallel opposed, coherently driven, transverse electromagnetic wave applicators could elevate the temperature in deep tissue to therapeutic levels without overheating superficial tissues when the phase difference between applicators was determined by the adaptive phase control algorithm.

Animals↗

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix workstations to massively parallel systems, and is available from the Ribosomal Database Project (RDP) by anonymous FTP. Our program uses a maximum likelihood approach and is based on version 3.3 of Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance and reduce memory usage, making it feasible to construct even very large trees. Trees containing 40-100 taxa have been easily generated, and phylogenetic estimates are possible even when hundreds of sequences exist. We are currently using the tool to construct a phylogenetic tree based on 473 small subunit rRNA sequences from prokaryotes.

Algorithms↗

[Use of voxel-oriented femur models for stress analysis. Generation, calculation and validation of CT-based FEM models].

A means of interfacing computed tomography with the finite element method for the analysis of stress distribution in human femurs is described. With the aid of data transfer and image processing programs, three-dimensional voxel models of four macerated and a fresh-frozen cadaveric femur were generated from CT data sets. The underlying basic principle is direct generation of model elements from one or more adjacent CT-voxels, which are characterised by their coordinates and local absorption coefficients. A new algorithm was used for smoothing the edges of the model. All the models were analysed with respect to their stress distribution under different load situations, and the results were compared with the data of a parallel study utilizing the strain-gauge technique. Using the method of linear regression, a high correlation (coefficient of determination r2: 0.80-0.91) was found between the calculated and experimentally measured principal stresses at the surface of the bones.

Biomechanical Phenomena↗

Application of spatial modulation of magnetization (SPAMM) to children: the effect of image resolution on tagging pattern.

BACKGROUND AND OBJECTIVE: Spatial modulation of magnetization (SPAMM) is a valuable magnetic resonance imaging technique for studying ventricular biomechanics. In order to track the intersection points of the stripes to calculate regional wall motion and strain, the stripe spacing should be at most half the wall thickness, yet sufficiently larger than the image pixel size in order that the stripes be well resolved. These conflicting requirements, that the grid spacing be much smaller than the wall thickness yet much larger than the pixel size, are relatively easy to meet in adult subjects but are difficult in children because of their small size. The purpose of this study was to delineate the effect of pixel size relative to SPAMM grid spacing on the stripe pattern produced by SPAMM with application towards its use in children and to present a new approach to the analysis of these images. METHODS: We performed SPAMM imaging on a 1.5 Telsa Siemen's Vision MR system on a phantom, using an artificial ECG (R-R interval = 450 ms for triggering), holding the pixel size constant and varying the degree of stripe spacing. We used both square (1 mm) and rectangular (1 mm by 2 mm) pixels. We express the ratio of grid to pixel size as the ratio of the center-center spacing of the grid lines to the horizontal pixel size. We retrospectively reviewed the SPAMM images on 10 patients with a ratio of grid to pixel size approximately 4:1 and 10 with a ratio of grid to pixel size approximately 8:1. We further performed SPAMM imaging in four patients with different grid to pixel size ratios in the same patient. Finally, we tested a new algorithm to track the signal intense regions rather than the signal poor intersection points of the grid lines, which were compared on three ventricles with SPAMM tagging. RESULTS: In a phantom, the effect of decreasing the separation between stripes while keeping the resolution of the image constant changed the stripe pattern from a series of two parallel lines perpendicular to each other to a "checkerboard" pattern. With a relative grid:pixel ratio of 8:1 as used with adult studies, the dark bands and the crossing points are well defined. As the ratio decreases from 8:1 to 6:1, the black band is less well resolved. When the resolution is reduced further to a grid:pixel ratio of 4:1, the image appears to be a checkerboard of white and dark squares. This occurred with both square and rectangular pixels. The effect in vivo is similar. When the ratio is approximately 8:1, all patients demonstrated a stripe pattern as a set of parallel lines perpendicular to each other. When the ratio was approximately 4:1, all patients demonstrated the stripe pattern as checkerboard. This was found to be the case in the same patient, whether varying the pixel size by changing the field of view or matrix or by changing the grid spacing. We also found that tracking the signal intense regions was equivalent to tracking the signal poor intersection points of the grid, and this approach was much easier to implement. CONCLUSION: With decreasing ratio of grid spacing to pixel size, SPAMM stripe patterns change from a set of parallel lines perpendicular to each other to a "checkerboard" pattern. This effect has implications for tracking techniques to determine strain and wall motion. At smaller ratios, as is needed sometimes in children, it is easier to track the signal intense regions rather than the "intersection" points of the stripes. Both these approaches to tracking are equivalent.

Adolescent↗

Cone beam tomography of the heart using single-photon emission-computed tomography.

The authors evaluated cone beam single-photon emission-computed tomography (SPECT) of the heart. A new cone beam reconstruction algorithm was used to reconstruct data collected from "short scan" acquisitions (of slightly more than 180 degrees) of a detector anteriorally traversing a noncircular orbit. The less than 360 degrees acquisition was used to minimize the attenuation artifacts that result from reconstructing posterior projections of 201T1 emissions from the heart. The algorithm includes a new method for reconstructing truncated projections of background tissue activity that eliminates reconstruction ring artifacts. Phantom and patient results are presented which compare a high-resolution cone beam collimator (50-cm focal length; 6.0-mm full width at half maximum [FWHM] at 10 cm) to a low-energy general purpose (LEGP) parallel hole collimator (8.2-mm FWHM at 10 cm) which is 1.33 times more sensitive. The cone beam tomographic results are free of reconstruction artifacts and show improved spatial and contrast resolution over that obtained with the LEGP parallel hole collimator. The limited angular sampling restrictions and truncation problems associated with cone beam tomography do not deter from obtaining diagnostic information. However, even though these preliminary results are encouraging, a thorough clinical study is still needed to investigate the specificity and sensitivity of cone beam tomography.

Algorithms↗

Distributed data mining on grids: services, tools, and applications.

Data mining algorithms are widely used today for the analysis of large corporate and scientific datasets stored in databases and data archives. Industry, science, and commerce fields often need to analyze very large datasets maintained over geographically distributed sites by using the computational power of distributed and parallel systems. The grid can play a significant role in providing an effective computational support for distributed knowledge discovery applications. For the development of data mining applications on grids we designed a system called Knowledge Grid. This paper describes the Knowledge Grid framework and presents the toolset provided by the Knowledge Grid for implementing distributed knowledge discovery. The paper discusses how to design and implement data mining applications by using the Knowledge Grid tools starting from searching grid resources, composing software and data components, and executing the resulting data mining process on a grid. Some performance results are also discussed.

Algorithms↗

Value of a screening algorithm for celiac disease using tissue transglutaminase antibodies as first level in a population-based study.

OBJECTIVE: Serological screening for celiac disease (CD) can detect a large number of otherwise undiagnosed patients based on the sequential evaluation of serological tests and intestinal biopsy. The aim of this study was to compare the screening value for CD of two different protocols for the same community-based population. METHODS: We screened 1,000 consecutive subjects (497 women, age range 16-71 yr) attending a centralized laboratory for obligatory prenuptial blood tests. Serum samples obtained from all subjects were processed using two different protocols: I) a three-level classic screening consisting of the parallel use of IgG and IgA antigliadin antibodies as first level, followed by endomysial antibodies and total serum IgA for positive patients, and finally, intestinal biopsy of positive patients; and 2) a study screening protocol consisting of the parallel use of a commercial guinea pig antitissue transglutaminase antibody and total serum IgA as first line, endomysial antibodies (type IgA and/or IgG) for positive patients, and finally, intestinal biopsy. RESULTS: The classic screening protocol identified five subjects who were eligible for intestinal biopsy, which confirmed the presence of CD in all (prevalence 5.0 x 1,000, 95% CI = 1.6-11.6). Using the study algorithm, we detected seven new patients including the five patients detected by the first protocol (prevalence 7.0 x 1,000, 95% CI = 2.8-14.4). The two additional patients diagnosed using the proposed algorithm had positive IgG antigliadin antibodies and normal total serum IgA and were not detected by the classic protocol. Both patients were endomysial antibodies positive. The comparative analysis showed that the classic approach was more expensive (U.S. $4,687 per new patient detected) compared with the proposed study algorithm (U.S. $3,006). CONCLUSIONS: Our data showed that a new screening protocol using antitissue transglutaminase as first line followed by endomysial antibodies is a cost-effective screening and yielded more realistic figures of prevalence for CD in a community setting than the classic three-level sequential evaluation using antigliadin antibodies.

Adolescent↗

Automated feature extraction and identification of colon carcinoma.

OBJECTIVE: To assess an automated algorithm, developed for the classification of normal and cancerous colonic mucosa, using geometric analysis of features and texture analysis. STUDY DESIGN: Twenty-one images were analyzed, 10 from normal and 11 from cancerous mucosa. The classification was based on a regularity index dependent on shape, object orientation for establishing parallelism and five texture features derived using the co-occurrence image analysis method. RESULTS: Geometric analysis yielded an overall classification accuracy of 80%. The corresponding sensitivity and specificity were 94% and 64%, respectively. Using texture analysis, the overall classification accuracy was 90%, with a sensitivity and specificity of 82% and 100%, respectively. CONCLUSION: This initial study demonstrated that geometric and texture analysis techniques show promise for automated analysis of colon cancer.

Algorithms↗

Particle filters, a quasi-Monte-Carlo-solution for segmentation of coronaries.

In this paper we propose a Particle Filter-based approach for the segmentation of coronary arteries. To this end, successive planes of the vessel are modeled as unknown states of a sequential process. Such states consist of the orientation, position, shape model and appearance (in statistical terms) of the vessel that are recovered in an incremental fashion, using a sequential Bayesian filter (Particle Filter). In order to account for bifurcations and branchings, we consider a Monte Carlo sampling rule that propagates in parallel multiple hypotheses. Promising results on the segmentation of coronary arteries demonstrate the potential of the proposed approach.

Algorithms↗

Cardiac material markers from tagged MR images.

Tagged magnetic resonance imaging (MRI) has shown great promise in non-invasive analysis of heart motion. To replace implanted markers as a gold standard, however, tagged MRI must be able to track a sparse set of material points, so-called material markers, with high accuracy. This paper presents a new method for generating accurate motion estimates over a sparse set of material points using standard, parallel-tagged MR images. Each tracked point is located at the intersection of three tag surfaces, each of which is estimated using a thin-plate spline. The intersections are determined by an iterative alternating projections algorithm for which a proof of convergence is provided. The resulting data sets are compatible with applications developed to exploit implanted marker data. One set of these material markers from a normal human volunteer is examined in detail using several methods to visualize the markers. Numerical results that include additional studies are also discussed. Finally, an error analysis is presented using a computer-simulated left ventricle for which material markers are tracked with an RMS error of approximately 0.2 mm for typical imaging parameters and noise levels.

Algorithms↗

Prosit, an online service to calculate pseudorotational parameters of nucleosides and nucleotides.

The online service PROSIT (Pseudo-Rotational Online Service and Interactive Tool) is a free service available at http://cactus.nci.nci.gov/prosit/ that performs pseudorotational analysis of nucleosides(tides). PROSIT reads the 3D coordinates of nucleosides and returns the pseudorotational phase angle P, puckering amplitude vmax and other related information. As examples, the sugar conformations in a parallel-stranded guanine tetraplex and a four-way Holliday junction are presented here.

Algorithms↗

A sticker-based model for DNA computation.

We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is represented and of separation by hybridization as a central mechanism. However, unlike previous models, the stickers model has a random access memory that requires no strand extension and uses no enzymes; also (at least in theory), its materials are reusable. The paper describes computation under the stickers model and discusses possible means for physically implementing each operation. Finally, we go on to propose a specific machine architecture for implementing the stickers model as a microprocessor-controlled parallel robotic workstation. In the course of this development a number of previous general concerns about molecular computation (Smith, 1996; Hartmanis, 1995; Linial et al., 1995) are addressed. First, it is clear that general-purpose algorithms can be implemented by DNA-based computers, potentially solving a wide class of search problems. Second, we find that there are challenging problems, for which only modest volumes of DNA should suffice. Third, we demonstrate that the formation and breaking of covalent bonds is not intrinsic to DNA-based computation. Fourth, we show that a single essential biotechnology, sequence-specific separation, suffices for constructing a general-purpose molecular computer. Concerns about errors in this separation operation and means to reduce them are addressed elsewhere (Karp et al., 1995; Roweis and Winfree, 1999). Despite these encouraging theoretical advances, we emphasize that substantial engineering challenges remain at almost all stages and that the ultimate success or failure of DNA computing will certainly depend on whether these challenges can be met in laboratory investigations.

Computer Simulation↗