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At least 163 records · Page 9Linked to original sources
PubMedDate not supplied

[A compressed form for presenting data to banks on the primary and spatial structure of biopolymers. Means for accessing compressed data banks].

Description of open CAN format (Compressed Amino acids and Nucleotides) is presented for storing genetic information in compressed form in data banks (DB). Data compression principles are demonstrated in detail on examples of EMBL DB (sequences of nucleotides), SWISSPROT DB (sequences of amino acids) and PDB DB (3D structures). A unified compressed data format provides a possibility to integrate EMBL, SWISSPROT, and PDB DB in one data bank. We are going to use this approach for integration of GENBANK and other similar DBs. One of the outcomes of the research is a library of data retrieval procedures for access to DB, providing developers of the application software packages with a uniform interface to DBs with biologically related data. The proposed scheme for data representation was recommended by the Expert Commission of the Informatics Section of the RSSIP "Human Genome" as a standard for distribution of data banks in Russia.

Amino Acid Sequence↗
PubMed2006

The Gurnham equation in characterizing the compressibility of pharmaceutical materials.

Limitations of the Heckel equation in characterizing material compression behavior have been well reported. In this work, the Gurnham equation, which was first introduced in chemical engineering, is proposed as an alternate method of evaluating the compressibility of pharmaceutical powders. The Gurnham equation was adapted for tablet compression and the estimated slope parameter c was proposed to represent material compressibility. Data from the compression of four commonly used excipients (microcrystalline cellulose, corn starch, lactose monohydrate, and dibasic calcium phosphate dihydrate) and one drug (acetaminophen) were evaluated using the Gurnham equation. Using compression data at different peak pressures, linear relationships between porosity and lnPressure of the five materials were obtained. The determined parameter c expresses the compressibility of materials. The analysis of previous experimental data, including granulations, mixtures and co-processed materials also indicates that c might be a representative parameter for material compressibility.

Acetaminophen↗
PubMedDate not supplied

Fast and efficient compression of floating-point data.

Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.

Journal Article↗
PubMed2000

Compression of real time volumetric echocardiographic data using modified SPIHT based on the three-dimensional wavelet packet transform.

Real-time three-dimensional echocardiography has been introduced to provide improved quantification and description of cardiac function. Data compression is desired to allow efficient storage and improve data transmission. Previous work has suggested improved results utilizing wavelet transforms in the compression of medical data including 2D echocardiogram. Set partitioning in hierarchical trees (SPIHT) was extended to compress volumetric echocardiographic data by modifying the algorithm based on the three-dimensional wavelet packet transform. A compression ratio of at least 40:1 resulted in preserved image quality.

Aerospace Medicine↗
PubMed1996

The dependence of shear failure properties of trabecular bone on apparent density and trabecular orientation.

The shear properties of trabecular bone, in particular the shear failure strains, are not well understood despite their potential importance in age-related fractures and prosthesis loosening. We hypothesized that shear failure strains (yield and ultimate) are independent of apparent density and trabecular orientation, i.e. are homogeneous and isotropic. We measured the shear failure properties of bovine tibial trabecular bone, where specimens were loaded to failure in torsion longitudinally (n = 25) or transversely (n = 23) relative to the primary trabecular orientation. We found that although failure stresses depended strongly on apparent density (r2 = 0.61 - 0.80), failure strains were independent of apparent density for both trabecular orientations. Although the mean (+/-S.D.) yield strain in the longitudinal group (1.46 +/- 0.19%) was 10% higher (p = 0.01) than in the transverse group (1.33 +/- 0.15%), indicating a slight anisotropy of shear yield strains, the mean ultimate strains did not depend on trabecular orientation (longitudinal group 4.60 +/- 0.77% vs transverse group 4.24 +/- 1.25%, p = 0.20). These findings indicate that shear failure strains are homogeneous and largely isotropic. By combining our shear data with compressive data from a previous experiment, we also predicted that trabecular bone can fail in shear when subjected to compressive loads that are not aligned with the principal trabecular orientation. If this prediction holds for human bone, shear may be a dominant failure mode during off-axis loading of trabecular bone in vivo, such as during falls on the hip.

Animals↗
PubMed2000

Power laws, highly optimized tolerance, and generalized source coding

We introduce a family of robust design problems for complex systems in uncertain environments which are based on tradeoffs between resource allocations and losses. Optimized solutions yield the "robust, yet fragile" features of highly optimized tolerance and exhibit power law tails in the distributions of events for all but the special case of Shannon coding for data compression. In addition to data compression, we construct specific solutions for world wide web traffic and forest fires, and obtain excellent agreement with measured data.

Journal Article↗
PubMedDate not supplied

Ground and on-orbit command and data handling architectures for the Active Rack Isolation System microgravity flight experiment.

The Active Rack Isolation System [ARIS] International Space Station [ISS] Characterization Experiment, or ARIS-ICE for short, is a long duration microgravity characterization experiment aboard the ISS. The objective of the experiment is to fully characterize active microgravity performance of the first ARIS rack deployed on the ISS. Efficient ground and on-orbit command and data handling [C&DH] segments are the crux in achieving the challenging objectives of the mission. The objective of the paper is to provide an overview of the C&DH architectures developed for ARIS-ICE, with the view that these architectures may serve as a model for future ISS microgravity payloads. Both ground and on-orbit segments, and their interaction with corresponding ISS C&DH systems are presented. The heart of the on-orbit segment is the ARIS-ICE Payload On-orbit Processor, ARIS-ICE POP for short. The POP manages communication with the ISS C&DH system and other ISS subsystems and payloads, enables automation of test/data collection sequences, and provides a wide range of utilities such as efficient file downlinks/uplinks, data post-processing, data compression and data storage. The hardware and software architecture of the POP is presented and it is shown that the built-in functionality helps to dramatically streamline the efficiency of on-orbit operations. The ground segment has at its heart special ARIS-ICE Ground Support Equipment [GSE] software developed for the experiment. The software enables efficient command and file uplinks, and reconstruction and display of science telemetry packets. The GSE software architecture is discussed along with its interactions with ISS ground C&DH elements. A test sequence example is used to demonstrate the interplay between the ground and on-orbit segments.

Acceleration↗
PubMed2006

Optimization of requantization codebook for vector quantization.

Requantization is a key technology for reducing the bit rate of a previously compressed data. When recompression ratio is high, the requantizer may cause unacceptable quality degradation. To improve the quality of the requantized image, an optimization scheme for the requantization codebook has been proposed. The proposed scheme constructs an optimal requantization codebook in an iterative manner for a given original quantization codebook of transmitter. The construction of codebook is iteratively repeated until they reach a local optimum solution. Our approach can be applied not only to the scalar quantization, but to any method which employs vector quantization-based system. Simulation results show that the optimized system based on the proposed algorithm outperforms the conventional system which is made without consideration of requantization. The proposed algorithm enables a reliable image communication over heterogeneous networks.

Algorithms↗
PubMed1998

The Austrian Academic Computer Network and its usefulness for teleradiology.

To study the value of the Austrian Academic Computer Network (ACOnet) for teleradiology, 1740 test image data-sets and 620 image data-sets were exchanged between the departments of diagnostic radiology of the Universities of Innsbruck and Graz using the ACOnet service. Data transmission was reliable and fast with an average transfer capacity of 170 kByte/s (range 94-341). During the test phase, no major problems with image transfer occurred. Assuming that problems like security of patient data-sets, data compression and data verification can be solved, the ACOnet service would be a useful additional tool for telemedicine applications throughout Austria and eastern Europe.

Austria↗
PubMed2001

TeleMedMail: free software to facilitate telemedicine in developing countries.

Telemedicine offers the potential to alleviate the severe shortage of medical specialists in developing countries. However lack of equipment and poor network connections usually rule out video-conferencing systems. This paper describes a software application to facilitate store-and-forward telemedicine by email of images from digital cameras. TeleMedMail is written in Java and allows structured text entry, image processing, image and data compression, and data encryption. The design, implementation, and initial evaluation are described.

Computer Communication Networks↗
PubMed2003

Optimizing spectral power compression with respect to inference performance for recognition of tumor patterns in ultrasound images.

Imaging modalities are widely used to explore and diagnose diseases. Feature extraction methods are used to quantitatively describe and identify objects of interest in acquired images, typically involving data compression. The extracted features are subject to clinical inference, whereby the compression ratio used for feature extraction can affect the inference performance. In this paper, a new method is introduced which allows for optimal data compression with respect to performance maximization of uncertain inference. The model introduced herein identifies objects of interest using selective data compression in the frequency domain. It quantifies the amount of information provided by the inference involving these objects, calculates the inference efficiency, and estimates its cost. By analyzing the effect of data compression on inference efficiency and cost, the method allows for the optimal selection of the compression ratio. The method is applied to prostate cancer diagnosis in ultrasound images.

Data Compression↗
PubMed1990

High compression of nuclear medicine dynamic studies.

As data compression plays now an important role in the development of medical PACS, a technique has been developed for medical image sequences storage and transmission in order to obtain very high compression ratio: in dynamic nuclear medicine studies it can achieve a compression ratio as high as 100:1 without significant degradation. The implemented technique combines two methods which multiply their effects. In a first step, a principal component analysis (PCA) of the image series is performed. It extracts a limited number of principal components and their associated images. For data compression it is not necessary to perform an oblique factor analysis to estimate the so-called 'physiological functions' and their spatial distributions as in factor analysis of dynamic structures (FADS). In a second step, the principal images are compressed by means of a transform coding procedure: an adaptive block-quantization technique using the 2D discrete cosine transform (DCT) is implemented, followed by a statistical quantization method to encode the DCT coefficients. To reconstruct the principal images, an inverse DCT is applied. Then the original series is computed from the reconstructed images combined with the principal components which have been stored without any modification. The reconstructed series is compared to the original series, as well as the time activity curves generated on different regions of interest (ROI) and the factor estimates obtained using FADS performed on the two series. Method and evaluation are illustrated on an example of first pass radionuclide angiocardiography.

Humans↗
PubMed2006

Rate distortion optimal bit allocation methods for volumetric data using JPEG 2000.

Computer modeling programs that generate three-dimensional (3-D) data on fine grids are capable of generating very large amounts of information. These data sets, as well as 3-D sensor/measured data sets, are prime candidates for the application of data compression algorithms. A very flexible and powerful compression algorithm for imagery data is the newly released JPEG 2000 standard. JPEG 2000 also has the capability to compress volumetric data, as described in Part 2 of the standard, by treating the 3-D data as separate slices. As a decoder standard, JPEG 2000 does not describe any specific method to allocate bits among the separate slices. This paper proposes two new bit allocation algorithms for accomplishing this task. The first procedure is rate distortion optimal (for mean squared error), and is conceptually similar to postcompression rate distortion optimization used for coding codeblocks within JPEG 2000. The disadvantage of this approach is its high computational complexity. The second bit allocation algorithm, here called the mixed model (MM) approach, mathematically models each slice's rate distortion curve using two distinct regions to get more accurate modeling at low bit rates. These two bit allocation algorithms are applied to a 3-D Meteorological data set. Test results show that the MM approach gives distortion results that are nearly identical to the optimal approach, while significantly reducing computational complexity.

Algorithms↗
PubMed2001

Generation, description and storage of dendritic morphology data.

It is generally assumed that the variability of neuronal morphology has an important effect on both the connectivity and the activity of the nervous system, but this effect has not been thoroughly investigated. Neuroanatomical archives represent a crucial tool to explore structure-function relationships in the brain. We are developing computational tools to describe, generate, store and render large sets of three-dimensional neuronal structures in a format that is compact, quantitative, accurate and readily accessible to the neuroscientist. Single-cell neuroanatomy can be characterized quantitatively at several levels. In computer-aided neuronal tracing files, a dendritic tree is described as a series of cylinders, each represented by diameter, spatial coordinates and the connectivity to other cylinders in the tree. This 'Cartesian' description constitutes a completely accurate mapping of dendritic morphology but it bears little intuitive information for the neuroscientist. In contrast, a classical neuroanatomical analysis characterizes neuronal dendrites on the basis of the statistical distributions of morphological parameters, e.g. maximum branching order or bifurcation asymmetry. This description is intuitively more accessible, but it only yields information on the collective anatomy of a group of dendrites, i.e. it is not complete enough to provide a precise 'blueprint' of the original data. We are adopting a third, intermediate level of description, which consists of the algorithmic generation of neuronal structures within a certain morphological class based on a set of 'fundamental', measured parameters. This description is as intuitive as a classical neuroanatomical analysis (parameters have an intuitive interpretation), and as complete as a Cartesian file (the algorithms generate and display complete neurons). The advantages of the algorithmic description of neuronal structure are immense. If an algorithm can measure the values of a handful of parameters from an experimental database and generate virtual neurons whose anatomy is statistically indistinguishable from that of their real counterparts, a great deal of data compression and amplification can be achieved. Data compression results from the quantitative and complete description of thousands of neurons with a handful of statistical distributions of parameters. Data amplification is possible because, from a set of experimental neurons, many more virtual analogues can be generated. This approach could allow one, in principle, to create and store a neuroanatomical database containing data for an entire human brain in a personal computer. We are using two programs, L-NEURON and ARBORVITAE, to investigate systematically the potential of several different algorithms for the generation of virtual neurons. Using these programs, we have generated anatomically plausible virtual neurons for several morphological classes, including guinea pig cerebellar Purkinje cells and cat spinal cord motor neurons. These virtual neurons are stored in an online electronic archive of dendritic morphology. This process highlights the potential and the limitations of the 'computational neuroanatomy' strategy for neuroscience databases.

Algorithms↗
PubMed1994

A comparison of methods used to calculate ultrasonic myocardial backscatter in the time domain.

The cyclic variation of ultrasonic integrated backscatter from the left ventricular posterior wall and interventricular septum of the heart is now well documented in the literature, with minimal values occurring at end-systole and maximal at end-diastole. However, little work has been performed to date to determine whether cyclic cardiac variation of other, more easily derived, backscatter parameters exists. In this study, 20 baseline, epicardial, long-axis cardiac-cycle sequences were obtained from eight open-chest pigs, yielding a total of 285 ultrasonic frames of RF data, which were analysed off-line on a Sun workstation. In addition, the video data from these studies was digitised and collected from each scan. Five backscatter parameters, calculated in the time-domain, including (1) the average integrated backscatter; (2) the average of the backscatter power from the log-compressed data; (3) the square of the average of the uncompressed radio frequency (RF) amplitude; (4) the square of the average of the RF amplitude from the log-compressed data; and (5) the square of the average grey-scale video data, were analysed and their variation throughout the cardiac cycle correlated against that obtained from integrated backscatter measurements. The backscatter values obtained were referenced to a gel calibration phantom widely used for 2-D calibration studies. Significant (p < 0.001), good correlation existed between the four backscatter parameters derived from the RF data. Reduced correlation was obtained between the video backscatter parameter and those derived from the RF data. Maximum cyclic variation between systole and diastole was measured from the integrated backscatter parameter and minimum from the three log-compressed data sets.

Analog-Digital Conversion↗
PubMed1996

Adaptive estimation of QRS complex wave features of ECG signal by the Hermite model.

The most characteristic wave set in ECG signals is the QRS complex. Automatic procedures to classify the QRS are very useful in the diagnosis of cardiac dysfunctions. Early detection and classification of QRS changes are important in real-time monitoring. ECG data compression is also important for storage and data transmission. An Adaptive Hermite Model Estimation System (AHMES) is presented for on-line beat-to-beat estimation of the features that describe the QRS complex with the Hermite model. The AHMES is based on the multiple-input adaptive linear combiner, using as inputs the succession of the QRS complexes and the Hermite functions, where a procedure has been incorporated to adaptively estimate a width related parameter b. The system allows an efficient real-time parameter extraction for classification and data compression. The performance of the AHMES is compared with that of direct feature estimation, studying the improvement in signal-to-noise ratio. In addition, the effect of misalignment at the QRS mark is shown to become a neglecting low-pass effect. The results allow the conditions in which the AHMES improves the direct estimate to be established. The application is shown, for subsequent classification, of the AHMES in extracting the QRS features of an ECG signal with the bigeminy phenomena. Another application is highlighted that helps wide ectopic beats detection using the width parameter b.

Electrocardiography↗