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At least 217 records · Page 12Linked to original sources
PubMed2006

An experimental metagenome data management and analysis system.

The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi.doe.gov/m.

Bacterial Physiological Phenomena↗
PubMed1999

A practical gait analysis system using gyroscopes.

This study investigated the possibility of using uni-axial gyroscopes to develop a simple portable gait analysis system. Gyroscopes were attached on the skin surface of the shank and thigh segments and the angular velocity for each segment was recorded in each segment. Segment inclinations and knee angle were derived from segment angular velocities. The angular signals from a motion analysis system were used to evaluate the angular velocities and the derived signals from the gyroscopes. There was a good correlation between these signals. When performing a turn the signals of segment inclination and knee angle drifted. Two methods were used to solve this: automatically resetting the system to re-initialise the angle in each gait cycle, and high-pass filtering. They both successfully corrected this drift. A single gyroscope on the shank segment could provide information on segment inclination range, cadence, number of steps, and an estimation of stride length and walking speed.

Algorithms↗
PubMed2000

Intraoperative PAR corneal topography system (CTS): comparison of its keratometric readings to manual keratometer, auto-keratometer, EyeSys Corneal Analysis system, and slit lamp PAR CTS in healthy eyes.

PURPOSE: To compare the keratometric readings obtained from Intraoperative PAR Corneal Topography System (IOPAR) to those produced by manual keratometer (Mnl-Km), autokeratometer (Auto-Km), EyeSys CAS (EyeSys Corneal Analysis System) and slit lamp PAR CTS in healthy eyes. METHODS: All instruments were calibrated prior to use and only data from the best image obtained was used for statistical analysis. Simulated keratometry readings obtained from the central 3-mm zone of the corneas by IOPAR, including flat (K1) and steep (K2) keratometry readings, average keratometric power (AK), astigmatism (As) (difference between steep and flat keratometry readings) and the axis of the steep meridian (Ax) were compared to those from four other units. The latter units were also compared among themselves. Statistical analysis was done for right and left eyes separately. For each variable, average differences between the measurements taken from pairs of instruments were estimated, with corresponding 95% confidence intervals. The degree of agreement between pairs of instruments on individual measurements was additionally assessed, via the use of "Bland-Altman"-type plots, and estimates of the proportion of cases achieving satisfactory agreement. Additionally, for every variable, the average of the measurements taken from the different instruments were compared. RESULTS: Forty-five (22 right and 23 left) normal corneas of 26 volunteers were examined. On the average, IOPAR tended to measure K1 higher than slit lamp PAR CTS system. Because K2 measurements taken by the IOPAR were higher than that of all other instruments, the As measurements, on the average, were also higher than that of others, with the exception of the PAR CTS. For the same reasons, the IOPAR produced average AK readings that were higher than those taken by EyeSys CAS and PAR CTS. When the individual measurements taken by the IOPAR were compared with each of the other units, according to the arbitrary designation of satisfactory agreement within +/-0.5 D (for K1, K2, AK, and As) and +/-20 degrees (for Ax), for almost all parameters, proportion of differences that were within the agreement range varied from 0.33 to 0.82, with wide confidence intervals (confidence interval lower limits ranging from 0.20 to 0.61 and upper limits ranging from 0.62 to 0.94). CONCLUSIONS: IOPAR is a clinically useful topographic system, producing qualitative and quantitative data in the operating environment that, in normal corneas, on the average, matches those produced by the other units in the clinic. When individually analyzed, its keratometric measurements may show greater variations with respect to other units. Further studies with multiple examiners, in corneas with high or irregular astigmatism are required to establish its reproducibility and efficacy.

Adult↗
PubMed2005

Gait analysis system for assessment of dynamic loading axis of the knee.

The purpose of this study was (1) to demonstrate a computer-assisted gait analysis system that can visualize the locus of the dynamic loading axis on the proximal tibia joint surface, and (2) to assess the accuracy of this system in a patient with bilateral knee osteoarthritis (OA). This system uses force plate data, CT skeletal structure data and motion capture data obtained from an infrared position sensor. The relative positions between bones and markers were used to calculate skeletal model movement based on movement of the markers. The locus of the dynamic loading axis on the knee joint was defined as the point on the proximal tibia joint surface that intersected with the loading axis of the lower limb, which passed through the centre of the femoral head and the centroid of multiple points surrounded by the distal tibia joint surface contour. To assess the accuracy of this system, open MRI was used to evaluate positions of skin markers against bones in six healthy volunteers. The locus in a patient was affected by differences between the varus knee with medial compartment OA on the non-operative side and the knee treated with high tibial osteotomy (HTO) on the opposite side. At knee flexion angles of 0 degrees, 15 degrees and 30 degrees, the mean value of measurement error for point locations on the locus was within 5.6% of joint width in the lateral direction (JWLD) on the proximal tibia joint. This system can provide clinically useful information for evaluation of the dynamic loading axis on the knee joint surface.

Aged↗
PubMed1991

Stochastic interpretation of linear pharmacokinetics: a linear system analysis approach.

Linear drug disposition is most generally defined in terms of the superposition principle. This principle is explained on the molecular level by probability principles involving stochastic, independent kinetic behavior of drug molecules. A stochastic modeling approach is presented that is more general than pharmacokinetic models typically employed in stochastic approaches. First-order microscopic transfer rate constants (Kij) are not employed or assumed in the analysis. The approach is a linear system analysis approach that makes use of the simplest possible kinetic structure that enables a differentiation of the drug disposition into elimination and distribution components. This is done by applying stochastic principles in the context of the disposition decomposition analysis (DDA). The DDA approach in its linear form is a generalization of linear pharmacokinetic systems that assume a homogeneous sampling space. Disposition kinetics is partitioned into two kinetic spaces, a homogeneous sampling space, and a heterogeneous peripheral kinetic space. A structure differentiation beyond this is difficult to justify in common situations when only the parent drug is determined from a single iv sampling site. A stochastic independent molecule (SIM) model is formulated in the structure context of DDA. The model is employed to identify core relationships by isolating elementary stochastic building blocks of the disposition kinetics and absorption kinetics. It is shown how the stochastic building blocks of the SIM-DDA model are related to various mean time parameters. Residence probability functions and drug delivery probability functions provided by the approach appear useful for extending kinetic bioavailability concepts into a purely stochastic realm. The emphasis on transit time concepts enables a kinetic differentiation and a more intrinsic characterization than possible by the use of common residence time principles. Relationships are presented that link stochastic and kinetic elements. Formulas are presented for the practical calculations of the mean time parameters and stochastic functions presented. Practical examples are given of the concepts presented using data from several drugs.

Biological Availability↗
PubMed2005

Multicolour digital image analysis system for identification of bacteria and concurrent assessment of their respiratory activity.

AIMS: To develop a rapid and simple multicolour digital image analysis system for simultaneous identification of bacteria and assessment of their metabolic activity. METHODS AND RESULTS: We developed an image analyser capable of distinguishing triple-stained bacterial cells. Bacteria were stained with a nucleic acid stain, a fluorescent antibody and a fluorescent metabolic indicator for enumeration, species identification and assessment of metabolic activity. This multicolour image analyser was used to simultaneously identify Escherichia coli O157:H7 in milk samples and assess their respiratory activity. The images of the triple-stained bacteria were captured using a combination of blue light and u.v. excitation and an epifluorescence microscope and were processed by our image analyser. We found a good correlation between the counts of actively respiring (r = 0.93) and total (r = 0.94) E. coli O157:H7 measured by digital image analysis and visual observation. CONCLUSION: The multicolour digital image analysis system described here was able to quantify active pathogenic micro-organisms within 2 h. SIGNIFICANCE AND IMPACT OF THE STUDY: This multicolour image analysis allows the rapid and simultaneous quantification of bacteria, identification of species and assessment of metabolic activity.

Animals↗
PubMed1988

Computer video acquisition and analysis system for biological data.

The BIAS (Biological Image Analysis System) was developed to: (i) permit accurate entry and image processing of biological data; (ii) minimize the need for specialized hardware; and (iii) aid in the human genome mapping and other projects. The first mouse/cursor key-driven module was designed to be user interactive and readily accessible to many laboratories. It contains the DRSNDS programs which automate the entering of data in a systematic format. The types of data that can be entered utilizing this module are DNA-RNA gels from either a positive or negative Polaroid image, autoradiograms or biotinylated images from Southern, Northern and dot or slot blot hybridization analyses. The image is acquired using a video camera and then digitized for subsequent analysis. During the analysis graphical representations of the intermediate results are provided to assure user confidence. At any point within the program the user may obtain on-line help with the current task. The output displays the mol. wt of each individual component in the appropriate context. The present version of the program produces results comparable with a human interpreter for some data. Band shifting and optical density calculations are in a prototype form to permit evaluation of various techniques. Future work is directed at expanding the system's capabilities to interpret data from other biological analyses including DNA sequencing gels.

Algorithms↗
PubMed1988

Automated measurement of the concentration and 13C enrichment of carbon dioxide in breath and blood samples using the Finnigan MAT Breath Gas Analysis System.

The operation and performance of the Finnigan MAT automated Breath Gas Analysis System for the routine analysis of 13C breath tests taken in 20-ml Vacutainers is described. Up to four samples per hour can be analysed with a standard deviation of delta 13C of less than 0.05% being achieved over the range 10-50 mumol CO2. The equipment can also be used for the automatic measurement of the concentration and 13C enrichment of CO2 derived from carbonate or bicarbonate solutions, including blood and other physiological fluids.

Autoanalysis↗
PubMed2001

Adaptive frequency decomposition of EEG with subsequent expert system analysis.

We present a hybrid system for automatic analysis of clinical routine EEG, comprising a spectral analysis and an expert system. EEG raw data are transformed into the time-frequency domain by the so-called adaptive frequency decomposition. The resulting frequency components are converted into pseudo-linguistic facts via fuzzification. Finally, an expert system applies symbolic rules formulated by the neurologist to evaluate the extracted EEG features. The system detects artefacts, describes alpha rhythm by frequency, amplitude, and stability and after artefact rejection detects pathologic slow activity. All results are displayed as linguistic terms, numerical values and maps of temporal extent, giving an overview about the clinical routine EEG.

Adolescent↗
PubMed1992

One year's experience with two different image analysis systems for automated reading of the contrast fluorescence test.

We have tested two different personal-computer-based color image analysis systems for automated reading of the microlymphocytotoxicity test (LCT) for HLA-A,B,C typing and screening. Over 17,000 single LCT reactions were prepared using the simultaneous double fluorescent variant of the LCT (contrast fluorescence test, CFT). All tests were read visually by experienced laboratory staff members. For digital image analysis, an automated scanning system was used. The reactions were first recorded on a videotape recorder using a color (CCD) videocamera und subsequently analyzed with the two different image analysis systems by specifically developed programs. Good correlation (r = 0.89) of the score values assigned by digital image analysis with the visual tray reading was obtained. Since also the other main performance characteristics of the prototype system were acceptable for routine application, we may conclude that digital image analysis is a feasible and very interesting new technique for automated evaluation of the LCT.

Algorithms↗
PubMedDate not supplied

Interactive statistical analysis system for clinical investigators.

We have developed an interactive statistical analysis system (ISAS-Q) with which clinical investigators with little experience in computers and programming can easily perform statistical analyses. ISAS-Q can perform most of the frequently used statistical methods, including multivariate analysis, in an interactive mode. Furthermore, ISAS-Q has self-consistent and extensive help functions.

Data Interpretation, Statistical↗
PubMed1992

[An image analysis system for optic disc in glaucoma].

An image analysis system for glaucomatous optic disc was developed. The key for optic disc measurement was to trace accurately the boundaries of the optic cup and disc. The 2-dimension measurement modality adopted was the heuristic boundary tracing method, and the 3-dimension measurement was performed by observation of the photographs, arbitrary selection of points, and automatic plotting and calculation. In order to measure accurately the optic disc in glaucoma follow-up, the authors made use of the cross correlation line by line scanning method, after proper correction of the photographs, to detect any positional shift in two photographs. By clinical verification, the 95% confidence criterion of normal optic cup boundary shifting was 1.7 pixels. The optic disc diameter of the disc images was over 200 pixels, and any shift over 2 pixels (1%) would have clinical significance, which was a high degree of precision.

Glaucoma↗
PubMed1992

One year's experiences with two different image analysis systems for automated reading of the contrast fluorescence test.

We have tested two different personal-computer based color image analysis systems for automated reading of the microlymphocytotoxicity test (LCT) for HLA-A,B,C-typing and screening. Over 17,000 single LCT-reactions were prepared using the simultaneous double fluorescent variant of the LCT (contrast fluorescence test, CFT). All tests were read visually by experienced laboratory staff members. For image analysis, an automated scanning system was used. In a first step, reactions were recorded on a videotape recorder using a color(CCD)-video camera. In a second step, the recorded reactions were analyzed with the two different image analysis systems by specifically developed programs. Good correlation (r = 0.89) of the score values assigned by digital image analysis with the visual tray reading was obtained. Since also the other main performance characteristics of the prototype system (throughput, reliability, compatibility) were acceptable for routine application, we may conclude that digital image analysis is a feasible and very interesting new technique for automated evaluation of the LCT.

Algorithms↗
PubMedDate not supplied

Using computer based data acquisition and analysis system for nasal potential difference measurement in cystic fibrosis.

Nasal potential difference (PD) measurement has been used as a diagnostic test for cystic fibrosis (CF). It has been shown that large differences in reproducibility of nasal PD measurement can exist between different study sites. These differences reduce the validity of studies. In our study we tried to measure nasal PD values for a group of Turkish CF patients by using a computer based data acquisition system, which could eliminate the bias due to using different voltmeters. The CF group (n=40, mean age 9.3 years) value was -39.21+/-1.74 mV, and the control group (n=36, mean age 17.08 years) value was -18.24+/-1.48 mV (mean+/-SEM). Using the electronic data acquisition and analysis systems gave reliable results with high specificity (92%), sensitivity (79%), positive predictive value (95%) and negative predictive value (72%). Computer based data acquisition and analysis system provides suitable monitoring and continuous recording during measurements and facilitates repeat readings at the same distances along the nasal floor. Using electronic data acquisition may help to minimize the subjectivity in voltmeter measurements and hand analysis.

Adolescent↗
PubMed2002

The validity of using a video-based motion analysis system for measuring maximal area of fingertip motion and angular variation.

The aim of the study was to verify the application of a three-dimensional video motion analysis system to evaluate maximal fingertip motion area and angular variation of the hand by comparison and correlation with videofluoroscopic analysis. Eight normal subjects were recruited in this study. The maximal motion area of the fingertip and the angles of the metacarpal phalangeal (MP), proximal interphalangeal (PIP) and distal interphalangeal (DIP) joints in performing five sequential postures for functional evaluation of the hand were measured using a video motion analysis system and a fluoroscopy system respectively. The results indicated that the intraclass correlation coefficient (ICC) of the calculated maximal fingertip motion area between the two methods was 0.9597. The ICC for total active motion (TAM) measurements of three finger joints was 0.940 between the surface and bony landmarks by fluoroscopy, 0.952 between the surface landmarks from fluoroscopy and motion analysis, and 0.927 between the bony landmark from fluoroscopy and surface markers from motion analysis. The ICC for angular measurements between three different paired assessments was 0.9650, 0.8896 and 0.8799 for the MP, PIP and DIP joints respectively. The results indicate that motion analysis is a practical method for assessing impairment of the hand.

Adult↗
PubMed1992

Proficiency of the Tradescantia-micronucleus image analysis system for scoring micronucleus frequencies and data analysis.

The Tradescantia-micronucleus (Trad-MCN) bioassay is an efficient short-term test for genotoxicity of pollutants. In order to increase the efficiency and to standardize the micronucleus (MCN) scoring process, an automated scoring system was developed using the principle of image analysis in computer science. This assemblage is called the Tradescantia-micronucleus image analysis (Trad-MCNIA) system. The MCN frequencies scored by this system were compared with those scored by human observation for its proficiency. A set of low MCN frequency (around 5 MCN/100 tetrads) slides prepared from a control group, a set of medium MCN frequency (around 20 MCN/100 tetrads) slides prepared from sodium azide treated plant cuttings and a set of high MCN frequency (around 50 MCN/100 tetrads) slides prepared from X-ray treated materials were used for this study. In the low MCN frequency slides, the Trad-MCNIA system scored about the same value as human observation. In the medium and high frequency slides, MCN frequencies scored by the system were lower than those scored by human observers. This discrepancy was corrected by increasing the power of the objective of the microscope in the system. The MCN frequencies scored by the system attained 90% congruity with those scored by human observers after the correction. The scoring speed of the system was about 3.5 times as fast as that by human observers, and the data could be statistically analyzed immediately after the data scores were recorded. Further improvements can be made by upgrading the video camera and the computer speed.

Azides↗
PubMed1997

A rule-based expert system for the automatic classification of DNA "ploidy" histograms measured by the CAS 200 image analysis system.

DNA "ploidy" histogram interpretation is one of the most important sources of variation in DNA image cytometry and is influenced by multiple technical factors such as scaling, selection of peaks, and variable classification criteria. A rule-based expert system was developed to automate and eliminate subjectivity from this interpretative process. Ninety-eight Feulgen stained histologic sections from patients with breast, colon, and lung cancer were measured with the CAS 200 image analysis system (Becton Dickinson, Santa Clara, CA); they included diploid (n = 42), aneuploid (n = 46), tetraploid (n = 7), and multiploid (n = 3) examples. The data was converted from listmode format into ASCII with the aid of CELLSHEET software (JVC Imaging, Elmhurst, IL). Individual microphotometric nuclear measurements were sorted to one of 64 bins based on DNA index. The 64 bins were then divided into 5 semi-arbitrarily defined ranges: hypodiploid, diploid, aneuploid, tetraploid, and hypertetraploid. The nuclear percentages in each range were calculated with EXCEL 4.0 (Microsoft, Redmond, WA). The histograms were divided into 2 equal sets: training and testing. The data from the training set were used to develop 16 IF-THEN rules to classify the histograms into diploid, aneuploid, or tetraploid. A macro was programmed in EXCEL to automate all these operations. The rule-based expert system classified correctly 45/50 histograms of the training set. Two tetraploid histograms were classified as aneuploid. Three multiploid histograms were classified as tetraploid. All histograms in the testing set were correctly classified by the expert system. The potential role of rule-based expert system technology for the objective classification of DNA "ploidy" histograms measured by image cytometry is discussed.

Automation↗