The World Health Organization oral rehydration solution in pediatric practice: a comment on the methodology.
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Bicarbonates↗
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Results for “Computing Methodologies”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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On Bayesian calculations for mixture likelihoods and priors.
We present methodology for calculating Bayes factors between models as well as posterior probabilities of the models when the indicator variables of the models are integrated out of the posterior before Markov chain Monte Carlo (MCMC) computations. Standard methodology would include the indicator functions as part of the MCMC computations. We demonstrate that our methodology can give substantially greater accuracy than the traditional approach. We illustrate the methodology using the model selection prior of George and McCulloch applied to logistic regression and to a mixture model for observations in a hierarchical random effects model.
Bayes Theorem↗
Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins.
The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso-1-cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed.
Algorithms↗
Identifying revolutionary computing technologies.
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Brain Mapping↗
A novel method for tracking pedestrians from real-time video.
This novel method of Pedestrian Tracking using Support Vector (PTSV) proposed for a video surveillance instrument combines the Support Vector Machine (SVM) classifier into an optic-flow based tracker. The traditional method using optical flow tracks objects by minimizing an intensity difference function between successive frames, while PTSV tracks objects by maximizing the SVM classification score. As the SVM classifier for object and non-object is pre-trained, there is need only to classify an image block as object or non-object without having to compare the pixel region of the tracked object in the previous frame. To account for large motions between successive frames we build pyramids from the support vectors and use a coarse-to-fine scan in the classification stage. To accelerate the training of SVM, a Sequential Minimal Optimization Method (SMO) is adopted. The results of using a kernel-PTSV for pedestrian tracking from real time video are shown at the end. Comparative experimental results showed that PTSV improves the reliability of tracking compared to that of traditional tracking method using optical flow.
Algorithms↗
Automatic motion correction in dynamic radionuclide renography using image registration.
Time-activity curves from dynamic renograms can be analysed to yield important quantitative parameters. However, accurate results are dependent on curves being free from artefacts caused by patient movement. We describe a method to correct for both translational and rotational motion during renography. The method is image-based and does not require markers. Sequential dynamic frames are registered using an affine transform from which rotational and translational components are extracted by singular-value decomposition. Computer simulations demonstrate correction to < 1 pixel and < 1 degree. The method is also fast, with renograms comprising 75 frames of 64 x 64 pixels taking under 1 min for correction on a Sun SPARC 5.
Automation↗
Support vector machine-based expert system for reliable heartbeat recognition.
This paper presents a new solution to the expert system for reliable heartbeat recognition. The recognition system uses the support vector machine (SVM) working in the classification mode. Two different preprocessing methods for generation of features are applied. One method involves the higher order statistics (HOS) while the second the Hermite characterization of QRS complex of the registered electrocardiogram (ECG) waveform. Combining the SVM network with these preprocessing methods yields two neural classifiers, which have been combined into one final expert system. The combination of classifiers utilizes the least mean square method to optimize the weights of the weighted voting integrating scheme. The results of the performed numerical experiments for the recognition of 13 heart rhythm types on the basis of ECG waveforms confirmed the reliability and advantage of the proposed approach.
Algorithms↗
Medical image informatics infrastructure design and applications.
Picture archiving and communication systems (PACS) is a system integration of multimodality images and health information systems designed for improving the operation of a radiology department. As it evolves, PACS becomes a hospital image document management system with a voluminous image and related data file repository. A medical image informatics infrastructure can be designed to take advantage of existing data, providing PACS with add-on value for health care service, research, and education. A medical image informatics infrastructure (MIII) consists of the following components: medical images and associated data (including PACS database), image processing, data/knowledge base management, visualization, graphic user interface, communication networking, and application oriented software. This paper describes these components and their logical connection, and illustrates some applications based on the concept of the MIII.
Age Determination by Skeleton↗
[Concept of multi-functional LEONARDO workstation].
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Computer Graphics↗
A data mining approach for analyzing density maps representing macromolecular structures.
Results of electron microscopy-based three-dimensional reconstructions of macromolecules or their complexes are usually stored as density maps. Each point ("voxel") in the map represents a density value and one approach for studying details of the map is to display an isosurface enclosing areas of interest. We have taken a data mining approach not only focusing on the areas of immediate interest but determining all possible separate entities ("blobs") from a density map. After the entire density map is analyzed with our mining program BLOBBER, properties of all detected blobs can be browsed and sets of blobs can be visualized using our VIZBLOB program. Since BLOBBER analyzes density maps using only density information and relates it to spatial relationships, BLOBBER can be used to analyze symmetrical or asymmetrical density maps from any source. To test our program we have analyzed published bacteriophage PRD1 reconstructions. We identified various structural details ranging from individual proteins to major complexes such as the whole capsid shell and more elaborate details of possible connections between membrane interfaces. This approach can also be a useful preprocessing tool for visualizing reconstructions.
Bacteriophages↗
High-performance computing and networking as tools for accurate emission computed tomography reconstruction.
It is well known that the quantitative potential of emission computed tomography (ECT) relies on the ability to compensate for resolution, attenuation and scatter effects. Reconstruction algorithms which are able to take these effects into account are highly demanding in terms of computing resources. The reported work aimed to investigate the use of a parallel high-performance computing platform for ECT reconstruction taking into account an accurate model of the acquisition of single-photon emission tomographic (SPET) data. An iterative algorithm with an accurate model of the variable system response was ported on the MIMD (Multiple Instruction Multiple Data) parallel architecture of a 64-node Cray T3D massively parallel computer. The system was organized to make it easily accessible even from low-cost PC-based workstations through standard TCP/IP networking. A complete brain study of 30 (64x64) slices could be reconstructed from a set of 90 (64x64) projections with ten iterations of the conjugate gradients algorithm in 9 s, corresponding to an actual speed-up factor of 135. This work demonstrated the possibility of exploiting remote high-performance computing and networking resources from hospital sites by means of low-cost workstations using standard communication protocols without particular problems for routine use. The achievable speed-up factors allow the assessment of the clinical benefit of advanced reconstruction techniques which require a heavy computational burden for the compensation effects such as variable spatial resolution, scatter and attenuation. The possibility of using the same software on the same hardware platform with data acquired in different laboratories with various kinds of SPET instrumentation is appealing for software quality control and for the evaluation of the clinical impact of the reconstruction methods.
Algorithms↗
Quantization errors of the echoes in ultrasonic pulsed flowmeter employing time domain correlation.
The implementation of Time Domain Correlation Method for blood flow velocity estimation requires the conversion of the reflected ultrasonic signals into digital format in order that the computer can be utilized to investigate the technique. A number of quanitization errors, namely, that the A/D has a finite bit resolution, only a limited number of samples of the waveform may be taken per wavelength and correlation function only exits at discrete points, have an effect on the velocity estimate. This paper discusses the effect of errors associated with A/D conversion process on the accuracy of the velocity estimate. A computer simulation was performed to achieve this goal. A band passed white Gaussian noise segment was used to simulate the reflected ultrasonic signal. The jitters of the velocity estimates corresponding various A/D resolutions were calculated and plotted. Effects of interpolating the correlation function rather than determining the complete function were presented.
Algorithms↗
Inferring qualitative relations in genetic networks and metabolic pathways.
MOTIVATION: Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics. Although inference algorithms based on the Boolean network were proposed, the Boolean network was not sufficient as a model of a genetic network. RESULTS: First, a Boolean network model with noise is proposed, together with an inference algorithm for it. Next, a qualitative network model is proposed, in which regulation rules are represented as qualitative rules and embedded in the network structure. Algorithms are also presented for inferring qualitative relations from time series data. Then, an algorithm for inferring S-systems (synergistic and saturable systems) from time series data is presented, where S-systems are based on a particular kind of nonlinear differential equation and have been applied to the analysis of various biological systems. Theoretical results are shown for Boolean networks with noises and simple qualitative networks. Computational results are shown for Boolean networks with noises and S-systems, where real data are not used because the proposed models are still conceptual and the quantity and quality of currently available data are not enough for the application of the proposed methods.
Algorithms↗
Cellular neural networks for real-time DNA microarray analysis.
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Algorithms↗
Introduction to the special issue on virtual reality environments in behavioral sciences.
Virtual reality (VR) is usually described in biology and in medicine as a collection of technologies that allow people to interact efficiently with three-dimensional (3-D) computerized databases in real time using their natural senses. This definition lacks any reference to head-mounted displays (HMDs) and instrumented clothing such as gloves or suits. In fact, less than 10% of VR healthcare applications in medicine are actually using any immersive equipment. However, if we focus our attention on behavioral sciences, where immersion is used by more than 50% of the applications, VR is described as an advanced form of human- computer interface that allows the user to interact with and become immersed in a computer-generated environment. This difference outlines a different vision of VR shared by psychologists, psychotherapists, and neuropsychologists: VR provides a new human-computer interaction paradigm in which users are no longer simply external observers of images on a computer screen but are active participants within a computer-generated 3-D virtual world. This special issue investigates this vision, presenting some of the most interesting applications actually developed in the area. Moreover, it discusses the clinical principles, human factors, and technological issues associated with the use of VR in the behavioral sciences.
Behavioral Sciences↗
Analyzing holistic parsers: implications for robust parsing and systematicity.
Holistic parsers offer a viable alternative to traditional algorithmic parsers. They have good generalization performance and are robust inherently. In a holistic parser, parsing is achieved by mapping the connectionist representation of the input sentence to the connectionist representation of the target parse tree directly. Little prior knowledge of the underlying parsing mechanism thus needs to be assumed. However, it also makes holistic parsing difficult to understand. In this article, an analysis is presented for studying the operations of the confluent preorder parser (CPP). In the analysis, the CPP is viewed as a dynamical system, and holistic parsing is perceived as a sequence of state transitions through its state-space. The seemingly one-shot parsing mechanism can thus be elucidated as a step-by-step inference process, with the intermediate parsing decisions being reflected by the states visited during parsing. The study serves two purposes. First, it improves our understanding of how grammatical errors are corrected by the CPP. The occurrence of an error in a sentence will cause the CPP to deviate from the normal track that is followed when the original sentence is parsed. But as the remaining terminals are read, the two trajectories will gradually converge until finally the correct parse tree is produced. Second, it reveals that having systematic parse tree representations alone cannot guarantee good generalization performance in holistic parsing. More important, they need to be distributed in certain useful locations of the representational space. Sentences with similar trailing terminals should have their corresponding parse tree representations mapped to nearby locations in the representational space. The study provides concrete evidence that encoding the linearized parse trees as obtained via preorder traversal can satisfy such a requirement.
Algorithms↗
SignStream: a tool for linguistic and computer vision research on visual-gestural language data.
Research on recognition and generation of signed languages and the gestural component of spoken languages has been held back by the unavailability of large-scale linguistically annotated corpora of the kind that led to significant advances in the area of spoken language. A major obstacle has been the lack of computational tools to assist in efficient analysis and transcription of visual language data. Here we describe SignStream, a computer program that we have designed to facilitate transcription and linguistic analysis of visual language. Machine vision methods to assist linguists in detailed annotation of gestures of the head, face, hands, and body are being developed. We have been using SignStream to analyze data from native signers of American Sign Language (ASL) collected in our new video collection facility, equipped with multiple synchronized digital video cameras. The video data and associated linguistic annotations are being made publicly available in multiple formats.
Computer Simulation↗
The impact of a computer generated patient held health record.
OBJECTIVE: To examine the use and impact of a computer generated, patient held health record (PHR) on information sharing, responsibility sharing and preventive health care. SETTING: An academic group, private solo and private group general practice in Adelaide, South Australia. METHODS: Patients with chronic health problem(s) were randomly assigned to an experimental control or post test only group. Pre and post intervention data were collected using a standardised audit and abstraction of the patient records into a computer based record system. In addition, patient and doctor questionnaires, telephone follow ups and face to face interviews were conducted. OUTCOME MEASURES: Patient and GP use of, and satisfaction with the PHR; effectiveness of information and responsibility sharing; and uptake and performance of selected preventive health care by patient and GP. RESULTS: Seventy-two patients were recruited (29 received the PHR, and 22 each were in the control and post test only groups). The PHR was well received and used in both primary and secondary care settings. No statistically significant differences in the outcome measures were found between the groups as well as before and after the intervention (Kruskal-Wallis, p > 0.05). Data trends suggested that the PHR may increase information and responsibility sharing as well as improve patient awareness of the issues involved, with patient participation in information sharing, preventive health care and clinical decision making. Provided training and resources were made available, participating GPs believed that the computer based methodology developed was a practical option for use in practice. CONCLUSION: The computer generated PHR is an important determinant of patient participation in information and responsibility sharing, health promotion, and disease management. Implementation and evaluation studies are recommended.
Adolescent↗