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At least 1,207 records · Page 67Linked to original sources
PubMed1998

Automated spectral analysis III: application to in vivo proton MR spectroscopy and spectroscopic imaging.

An automated method for analysis of in vivo proton magnetic resonance (MR) spectra and reconstruction of metabolite distributions from MR spectroscopic imaging (MRSI) data is described. A parametric spectral model using acquisition specific, a priori information is combined with a wavelet-based, nonparametric characterization of baseline signals. For image reconstruction, the initial fit estimates were additionally modified according to a priori spatial constraints. The automated fitting procedure was applied to four different examples of MRS data obtained at 1.5 T and 4.1 T. For analysis of major metabolites at medium TE values, the method was shown to perform reliably even in the presence of large baseline signals and relatively poor signal-to-noise ratios typical of in vivo proton MRSI. Identification of additional metabolites was also demonstrated for short TE data. Automated formation of metabolite images will greatly facilitate and expand the clinical applications of MR spectroscopic imaging.

Aspartic Acid↗
PubMed2004

Identification of patients with Churg-Strauss syndrome (CSS) using automated data.

PURPOSE: Our aim was to identify individuals with Churg-Strauss syndrome (CSS) among asthma drug users, based on patterns of diagnostic and procedural codes (termed 'algorithms') contained in automated claims data. METHODS: A retrospective study was conducted among patients who had been dispensed asthma drugs at three HMOs. Individuals who received > or =3 dispensings of an asthma drug during any consecutive 12-month period beginning 1 January 1994 through 20 June 2000 were identified. Information on patient age, gender, enrollment status, asthma drugs dispensed, inpatient and outpatient diagnoses and procedures were obtained from the HMO automated databases. Twelve combinations of diagnostic and billing codes ('algorithms') were developed using the claims data to identify potential cases of CSS. Chart reviews blinded to drug exposure were performed using a standardized abstraction form. A rheumatologist reviewed abstracted information on all subjects, and those who met two or more American College of Rheumatology (ACR) criteria for CSS were further reviewed by two clinical experts. Cases were classified as unlikely, possible, or probable/definite CSS. Each clinical expert independently rated the cases; disagreements were resolved by consensus. RESULTS: A total of 185 604 patients who had been dispensed asthma drugs were identified. Three hundred fifty subjects were selected for chart review, and 15 were classified as having 'probable/definite' CSS. The algorithms that were most successful in identifying patients with CSS were as follows: (1) two or more codes for vasculitis (13 confirmed cases from 129 reviewed; positive predictive value 10%); (2) codes for both vasculitis and neurologic symptoms (6 confirmed cases from 15 reviewed; positive predictive value 40%) and (3) codes for both eosinophilia and vasculitis (4 confirmed cases from 5 reviewed; positive predictive value 80%). CONCLUSION: Automated claims data can be used to identify patients with CSS. This approach can facilitate better epidemiologic study of the risk factors for the condition.

Algorithms↗
PubMed2005

Liquid ultraviolet matrix-assisted laser desorption/ionization -- mass spectrometry for automated proteomic analysis.

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet -- matrix-assisted laser desorption/ionisation -- mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. The low-femtomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydroxybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and low-mass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2003

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known structure and to build long loop insertions (and N-and C-terminal extensions) in cases where a structural template was available. Encouraging results were obtained both for the de novo predictions and for the long loop insertions; we describe here the successes as well as the failures in the context of current efforts to improve the Rosetta method. In particular, de novo predictions failed for large proteins that were incorrectly parsed into domains and for topologically complex (high contact order) proteins with swapping of segments between domains. However, for the remaining targets, at least one of the five submitted models had a long fragment with significant similarity to the native structure. A fully automated version of the CASP5 protocol produced results that were comparable to the human-assisted predictions for most of the targets, suggesting that automated genomic-scale, de novo protein structure prediction may soon be worthwhile. For the three targets where the human-assisted predictions were significantly closer to the native structure, we identify the steps that remain to be automated.

Algorithms↗
PubMed2006

Critical assessment of the automated AutoDock as a new docking tool for virtual screening.

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure-based virtual screening.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2006

Feasibility of different mass spectrometric techniques and programs for automated metabolite profiling of tramadol in human urine.

The purpose of the study was to determine the advantages of different mass spectrometric instruments and commercially available metabolite identification programs for metabolite profiling. Metabolism of tramadol hydrochloride and the excretion of it and its metabolites into human urine were used as a test case because the metabolism of tramadol is extensive and well known. Accurate mass measurements were carried out with a quadrupole time-of-flight mass spectrometer (Q-TOF) equipped with a LockSpray dual-electrospray ionization source. A triple quadrupole mass spectrometer (QqQ) was applied for full scan, product ion scan, precursor ion scan and neutral loss scan measurements and an ion trap instrument for full scan and product ion measurements. The performance of two metabolite identification programs was tested. The results showed that metabolite programs are time-saving tools but not yet capable of fully automated metabolite profiling. Detection of non-expected metabolites, especially at low concentrations in a complex matrix, is still almost impossible. With low-resolution instruments urine samples proved to be challenging even in a search for expected metabolites. Many false-positive hits were obtained with the automated searching and manual evaluation of the resulting data was required. False positives were avoided by using the higher mass accuracy Q-TOF. Automated programs were useful for constructing product ion methods, but the time-consuming interpretation of mass spectra was done manually. High-quality MS/MS spectra acquired on the QqQ instrument were used for confirmation of the tramadol metabolites. Although the ion trap instrument is of undisputable benefit in MS(n), the low mass cutoff of the ion trap made the identification of tramadol metabolites difficult. Some previously unreported metabolites of tramadol were found in the tramadol urine sample, and their identification was based solely on LC/MS and LC/MS/MS measurements.

Adult↗
PubMed2002

Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra.

Glycoprotein function is controlled by several biological factors, one of them being the structure of carbohydrate chains (glycans) attached to specific amino acids of the protein backbone. Changes in glycan structures have been shown to modify the secondary and tertiary conformation of glycoproteins, thus their function. Powerful analytical tools are available for the characterization of sugar structures, and recently mass spectrometry (MS) has been increasingly useful for this purpose. Manual interpretation of tandem mass spectrum is possible but tedious. Automated interpretation should speed the analysis and enhance the results obtained. A new computer program for automated interpretation of tandem MS spectra of complex N-linked glycans oligosaccharides from mammals will be described. N-Linked oligosaccharides standards were derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP) and analyzed by matrix-assisted laser desorption/ionization (MALDI)-tandem MS. Simulated tandem mass spectra of other common glycans were also generated to test the algorithm. The MALDI-MS/MS spectra featured resolved isotopic distributions for the [M + H](+) and fragment ions of oligosaccharides. These isotopic distributions complicated the automated analysis of the spectra and were removed to leave only monoisotopic peaks. An algorithm was written for this purpose, yielding simplified tandem mass spectra. Another algorithm is then used to determine the structure of the oligosaccharide. A score is then given to each structure, depending on agreement with experimental results. The program successfully assigned the true structure in 24 out of the 28 cases (86%) and the true structure was among the three top scoring structures in all cases.

Algorithms↗
PubMed2006

Automated detection of infectious disease outbreaks: hierarchical time series models.

The purpose of infectious disease surveillance is to inform the public health policy makers on the incidence and trends of infectious diseases and to trigger appropriate actions to control infectious disease outbreaks. The enormous amount of data collected with automated laboratory-based surveillance systems require automated algorithms for detecting unexpected aberrations that may signal infectious disease outbreaks. In this paper, we explore the potential of hierarchical time series models to detect deviations from expected incidence. As these count data are extremely noisy it can be expected that these models are suitable to detect signal from noise and accommodate for possible autocorrelation. The proposed procedure consists of three steps; (1) the model parameters are estimated by empirical Bayes on a training period of, e.g. a year; (2) the expected values are updated for small time steps (e.g. daily) as new data arrive; (3) threshold levels are updated conditionally on the past expected values and an alarm is triggered when the threshold level is exceeded. To test the potential of the models we estimated sensitivity, specificity and timeliness on simulated time series and compared the results with an alternative approach of a linear regression model adjusted for trends and season. We also used two observed series for Rubella notifications and Salmonella infections and compared our findings with the expert opinions on these series. The hierarchical time series models approach shows high sensitivity and specificity and correctly identifies outbreaks at an early stage. This, in our opinion, makes the proposed model a reliable tool for adequate automated detection of infectious disease outbreaks.

Algorithms↗
PubMed1997

Preparative electrophoresis in a concentrated polymer solution: automated procedure for microsome isolation.

A recently introduced automated gel electrophoresis apparatus with an intermittent scanning of the migration path, the HPGE 1000 apparatus (LabIntelligence, Belmont, CA) has a unique preparative feature: A recovery cup can be automatically positioned on the band of interest, which is then electroeluted with fluorescence monitoring of recovery. Electroelution time is extended stepwise until quantitative recovery is attained. This preparative procedure has been extended from electrophoresis in gels to that of subcellularsized particles in concentrated polymer solutions Chang et al., Electrophoresis 17, 776-780, 1996). However, that application required manual rather than computer-directed positioning of the recovery chamber over the band. The present report details a modification of instrumentation and procedure by which automated operation was restored. The modified procedure extends the benefits of automation and known quantitative recovery to isolation of particles too large to enter into gels.

Animals↗
PubMed1994

An automated technique for identification and analysis of activation fronts in a two-dimensional electrogram array.

Cardiac activation sequences are normally determined by (i) the detection and timing of local activations in cardiac electrograms, (ii) the grouping together of activations in different electrodes that are generated by the same activation fronts, and (iii) the construction by interpolation of isochronal maps showing the pathways of the activation fronts. This process is typically carried out by manual or semiautomated methods. These methods are usually adequate for stable, repeatable rhythms in normal hearts. However, in situations in which the electrograms are distorted, as in those recorded from abnormal myocardium, or the mapped rhythms are rapidly changing, as in ventricular fibrillation, they are tedious and time-consuming and yield results that are subjective and not repeatable from one investigator to another. Therefore, we developed a computer-based method for automating the identification and analysis of activation fronts recorded from a large array of electrodes. The electrodes are closely spaced (1 mm) so that interpolation is not required. Electrodes are identified as recording an activation when the temporal derivative of the potential is more negative than a user-specified value. Activations occurring less than a user-specified distance apart in time and space are identified as part of the same activation front. Characteristics of the activation fronts, such as their number, size, and the presence of reentry or collision, are then quantified. The differences between the results obtained by this automated method and those obtained by four human investigators was no greater than the differences in results among the four investigators themselves. Because the method is automated and algorithmic, it is both rapid and repeatable.

Algorithms↗
PubMed1993

Orphan peak analysis: a novel method for detection of point mutations using an automated fluorescence DNA sequencer.

Automated DNA sequencers draw the four-base profiles of a sample with four different colors, but it is also possible to draw the profiles of a base-specific reaction of four different samples with four colors. PCR-amplified DNAs from four individuals were subjected to a single base-specific sequencing reaction and the products were applied to a set of four lanes of an automated DNA sequencer. A base substitution in an individual was clearly identified as an individual-specific peak with a color specific for the individual. In this way, we analyzed more than 50 individuals and identified several polymorphic base substitutions. The sensitivity of this method was high enough to allow detection of the mutation/polymorphism even if samples from several individuals were applied to one lane. Thus, our method is applicable to screening of a large number of samples in an automated manner.

Amyloid beta-Protein Precursor↗
PubMed2001

Selective automated indexing of findings and diagnoses in radiology reports.

The recent improvements in capabilities of desktop computers and communications networks give impetus for the development of clinical image repositories that can be used for patient care and medical education. A challenge in the use of these systems is the accurate indexing of images for retrieval performance acceptable to users. This paper describes a series of experiments aiming to adapt the SAPHIRE system, which matches text to concepts in the UMLS Metathesaurus, for the automated indexing of image reports. A series of enhancements to the baseline system resulted in a recall of 63% but a precision of only 30% in detecting concepts. At this level of performance, such a system might be problematic for users in a purely automated indexing environment. However, if the ability to retrieve images in repositories based on content in their reports is desired by clinical users, and no other current systems offer this functionality, then follow-up research questions include whether these imperfect results would be useful in a completely or partially automated indexing environment and/or whether other approaches can improve upon them.

Abstracting and Indexing↗
PubMed2002

Urinary glycosaminoglycan excretion quantified by an automated semimicro method in specimens conveniently transported from around the globe.

Current and future treatments for children with mucopolysaccharidosis (MPS) diseases require early, presymptomatic diagnosis, yet existing diagnostic methods to quantitate urinary glycosaminoglycan (GAG) are labor-intensive, and thus not applicable for newborn screening. Direct and rapid quantification of GAG excretion with 1,9-dimethylmethylene blue (DMB) is applicable to small volumes of urine collected, dried, and mailed on a paper matrix (MPS Test). To determine if this assay could be automated, a robotic instrument was programmed to accomplish the procedure; the pilot method simultaneously determined GAG and creatinine concentrations in 10 patient specimens/run. Each analyte is measured in 4 dilutions, thus increasing the operating range to cover a broad spectrum of normal and pathologic levels. Samples and reagents are mixed in a 96-well tray format in approximately 20 min, and densitometric measurements are recorded in less than 60 s. Optical density measurements are electronically transmitted to a desktop computer to select optimal dilutions, identify values above or below the level of reliability, make calculations, and print reports. This automated method was applied to 255 specimens from 101 subjects representing each of the MPS diseases--specifically, types I (n = 126), II (n = 47), III (n = 48), IV (n = 17), VI (n = 14) and VII (n = 3). This method discriminated pathologic elevations of GAG excretion of MPS patients particularly when multiple specimens were available. Patients with non-MPS lysosomal diseases had normal GAG excretion, except for a patient with fucosidosis who had markedly elevated levels. Automation of the direct DMB method provides the key technology necessary for newborn screening for MPS diseases.

Adolescent↗
PubMed1997

Mutual information for automated unwarping of rat brain autoradiographs.

An automated multimodal warping based on mutual information metric (MI) as a mapping cost function is demonstrated. Mutual information (I) is calculated from a two-dimensional (2D) gray scale histogram of an image pair, and MI (= -I) provides a matching cost function which can be effective in registration of two- or three-dimensional data sets independent of modality. Most histological image data, though information rich and high resolution, present nonlinear deformations due to the specimen sectioning and need reconstitution into deformation-corrected volumes prior to geometric mapping to an anatomical volume for spatial analyses. Section alignment via automatic 2D registrations employing MI as a global cost function and thin-plate-spline (TPS) warping is applied to deoxy-D-[14C]glucose autoradiographic image slices of a rat brain with video reference images of the uncut block face to reconstitute a cerebral glucose metabolic volume data. Unlike the traditional feature-based TPS warping algorithms, initial control points are defined independently from feature landmarks. Registration quality using automated multimodal image warping is validated by comparing MIs of the image pair registered by automated affine registration and manual warping method. The MI proves to be a robust objective matching cost function effective for automatic multimodality warping for 2D data sets and can be readily applied to volume registrations.

Algorithms↗
PubMed2002

Accurate, robust, and automated longitudinal and cross-sectional brain change analysis.

Quantitative measurement of brain size, shape, and temporal change (for example, in order to estimate atrophy) is increasingly important in biomedical image analysis applications. New methods of structural analysis attempt to improve robustness, accuracy, and extent of automation. A fully automated method of longitudinal (temporal change) analysis, SIENA, was presented previously. In this paper, improvements to this method are described, and also an extension of SIENA to a new method for cross-sectional (single time point) analysis. The methods are fully automated, robust, and accurate: 0.15% brain volume change error (longitudinal): 0.5-1% brain volume accuracy for single-time point (cross-sectional). A particular advantage is the relative insensitivity to differences in scanning parameters. The methods provide easy manual review of their output by the automatic production of summary images which show the results of the brain extraction, registration, tissue segmentation, and final atrophy estimation.

Algorithms↗
PubMed1983

A comparison of automated data collection and manual data collection for toxicology studies.

Automated data collection was compared with manual data collection in terms of accuracy and man-hours devoted to data manipulation and checking. The comparison was based on experience with an automated data collection system (DOLPHIN)TM1 developed at Toxigenics for use in conducting toxicological studies. It was found that on-line data collection increases the quality of the data gathered because: 1) it facilitates scientific observation by displaying historical data and statistics on changes since the last observation period; 2) it virtually eliminates errors due to oversight and transcription; 3) it allows more careful monitoring of the course of the study by providing immediate access to interim summary statistics; 4) it provides complete documentation of all changes made to the data after initial collection. In addition, automated data collection enables more rapid completion of the final report of results because: 1) fewer departmental transfers are required; 2) auditing by Quality Assurance (Q.A.) personnel is facilitated.

Data Collection↗
PubMed1992

Discrepancies between single stimulus and multiple stimulus visual field examinations with the Peritest semi-automated perimeter in glaucoma patients.

In a total of 24 randomly selected eyes of glaucoma patients, tested with the automated (single stimulus) and the manual (multiple stimulus) modes of the semi-automated Peritest perimeter, the numbers and depths of defects were compared as estimated with these two different measurement strategies. It was found that with the manual technique considerably less defects were detected than with the automated strategy.

Glaucoma↗
PubMed1982

Use of Fieldmaster automated perimeter for the detection of early visual field changes in glaucoma.

The efficacy of automated suprathreshold perimetry with Fieldmaster automated perimeter (model 101 PR and 200) was evaluated in the screening for very early glaucomatous visual field defects which failed to be detected with kinetic perimetry using a Goldman perimeter. Evaluation of 117 eyes with elevated intraocular pressure revealed a small, relative defect in the central field in 14 eyes which was confirmed by static perimetry with a Tübinger perimeter. Although Fieldmaster model 200 is equipped with more target positions than model 101 PR, detectability of early defects was almost identical between two models. Automated suprathreshold perimetry with either model of Fieldmaster perimeter is useful in detecting the early changes which may be missed by kinetic perimetry with a Goldman perimeter. Based on the difference in the false positive rate (45.6% with model 200 vs 26.7% with model 101 PR) the screening with 101 PR seems to be more rewarding.

Adult↗