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At least 685 records · Page 38Linked to original sources
PubMed1999

Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.

Automation↗
PubMed2001

Determination of nonsteroidal anti-inflammatory drugs in biological fluids by automatic on-line integration of solid-phase extraction and capillary electrophoresis.

A new, automatic method for the clean-up, preconcentration, separation, and quantitation of nonsteroidal anti-inflammatory drugs (NSAIDs) in biological samples (human urine and serum) using solid-phase extraction coupled on-line to capillary electrophoresis is proposed. Automatic pretreatment is carried out by using a continuous flow system operating simultaneously with the capillary electrophoresis equipment, to which it is linked via a laboratory-made mechanical arm. This integrated system is controlled by an electronic interface governed via a program developed in GWBasic. Capillary electrophoresis is conducted by using a separation buffer consisting of 20 mM NaHPO4, 20 mM beta-cyclodextrin and 50 mM SDS at pH 9.0, an applied potential of 20 kV and a temperature of 20 degrees C. The analysis time is 10 min and the detection limits were between 0.88 and 1.71 microg mL(-1). Automatic clean-up and preconcentration is accomplished by using a C-18 minicolumn and 75% methanol as eluent. The limit of detection of NSAIDs can be up to 400-fold improved when using sample clean-up. The extraction efficiency for these compounds is between 71.1 and 109.7 microg mL(-1) (RSD 2.0-7.7%) for urine samples and from 77.2 to 107.1 microg mL(-1) (RSD 3.5-7.1%) for serum samples.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2001

Automatic inducer addition and harvesting of recombinant Escherichia coli cultures based on indirect on-line estimation of biomass concentration and specific growth rate.

This article describes a novel bioreactor configuration for production optimization of recombinant proteins in Escherichia coli. Inducer addition and harvesting are controlled on-line based on indirect estimation of biomass concentration and specific growth rate from addition of NaOH to maintain constant pH. When either a predetermined biomass concentration is reached or the cultures have obtained, a constant specific growth rate inducer is introduced automatically. The induction period is ended by automatic harvesting of the cultures either at a predetermined biomass concentration or when substrate (in this study glucose) is depleted, detected as an increase of pH, or dissolved oxygen tension. During harvesting, metabolic activities are quenched within 3 min by cooling of the cell suspension. The system has been used to optimize expression of glutathione S-transferase (GST) fusion protein of the ligand binding domain of mouse peroxisome proliferator-activated receptor, GST-PPARalpha LBD. Total yield of GST-PPARalpha LBD was independent of the time of inducer addition as long as the length of induction period corresponded to at least 0.25 cell divisions while the yield of soluble GST-PPARalpha LBD, the only active form, increased with the length of induction period. Highest yields were obtained when the inducer was added at low cell concentration as soon as constant specific growth rate was detected, resulting in induction periods corresponding to 3.4 +/- 0.4 cell divisions. The specific growth rate remained almost constant for one cell division after inducer addition, whereafter it decreased. No decrease of specific growth rate was observed when inducer was added in the lag-phase, and no soluble protein was produced. These results suggest that solely soluble GST-PPARalpha LBD acts as a growth inhibitor and that GST-PPARalpha LBD is expressed predominantly as inclusion bodies immediately after inducer addition whereas the proportion expressed as soluble protein is increased after 1 h of induction. Compared to the procedures, which are generally used for protein expression in the laboratory, this system is less labor intensive, it automatically provides recording of biomass concentration and specific growth rate, and it allows direct comparisons between expression of different proteins and performance of different constructs since the induction period is linked to growth.

Animals↗
PubMed1983

Safety and effectiveness of a portable external automatic defibrillator-pacemaker.

Sudden cardiac death in the community can be reduced by early resuscitation. The commonest arrhythmia encountered in this setting is ventricular fibrillation. A portable external automatic defibrillator-pacing machine for use by emergency services and laymen after basic training, has recently been introduced. This device has a tongue-abdominal pathway for sensing the electrocardiogram and respiration, as well as delivery of current. In its automatic mode, the machine cannot defibrillate unless the patient's breathing and gag reflex are virtually absent. The decision-making characteristics of the machine were defined in isolation from the patient using simulated ECG signals and recordings of arrhythmias obtained during cardiac surgery and during electrophysiological studies. The pathway was evaluated separately by attaching it to a conventional defibrillator and using it in the elective cardioversion of 15 patients. Electrode sites were examined and creatine phosphokinase (CPK) and creatinine phosphokinase isoenzyme (CPKMB) release determined following conversion. Repeated playback of the same 34 minutes of selected recordings showed that decisions were consistent 95% of the time. Automatic pacing always occurred with asystole. ECG signals less than 0.35 mV in amplitude were not recognized, but a manual override switch could be operated in those circumstances where there was failure to act upon fine ventricular fibrillation. Defibrillation of 50% of the recordings of supraventricular and ventricular tachycardia did occur, but this could not have happened in practice unless the patient was unconscious, and in addition, the operator failed to countermand this decision. The tongue-abdominal pathway yielded good recordings of the ECG.(ABSTRACT TRUNCATED AT 250 WORDS)

Creatine Kinase↗
PubMed2005

Automatic telomere length measurements in interphase nuclei by IQ-FISH.

To benefit from the fluorescence-based automatic microscope (FLAME), we have adapted a PNA FISH technique to automatically determine telomere length in interphase nuclei. The method relies on the simultaneous acquisition of pan-telomeric signals and reference probe signals. We compared the quantitative figures to those for existing methods, i.e. Southern blot analysis and quantitative FISH (Q-FISH). Quantitative-FISH on interphase nuclei (IQ-FISH) allows the exact quantification of telomere length in interphase nuclei. Thus, this enables us to obtain not only exact information on the telomere length, but also morphological and topological details. The automatic measurement of large cell numbers allows the measurement of statistically relevant cell populations.

Adult↗
PubMed1988

Wheat cultivar identification by a totally automatic soft-laser scanning densitometry and computer-aided analysis of protein electropherograms.

A computer-aided analysis based on soft-laser densitometry of electrophoretic patterns is described. The system has the potential to automatically identify wheat cultivars from normalized sodium dodecyl sulfate-polyacrylamide gel electropherograms. The principle encompasses autocalibration of the relative mobilities of components of the unknown pattern using standards of Mr that bracket each pattern on the pictures, automatic identification of peaks and baseline correction, and simplified estimation of the peak intensities. The algorithm provides a normalized array that can be automatically compared with a library of standard cultivar patterns in order to determine those having the highest similarity percentage. The outputs of the program are 1) relative similarity plots which show the percentage of similarity between the unknown cultivar to that of each of the common standard cultivars put in a pattern library, 2) the names of cultivars in the library having the most similar patterns and 3) computer-generated electrophoretic graphics of these cultivars. This system is not intended to identify closely related cultivars but it is particularly recommended for cultivar identification without well-trained personnel, familiar with band location and nomenclature.

Densitometry↗
PubMed2005

Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection).

For use in routine prenatal diagnostics, we developed software and methods for automatic aneuploidy detection based on a commercial multiplex ligation-dependent probe amplification (MLPA) kit. Software and methods ensure a reliable, objective, and fast workflow, and may be applied to other types of MLPA kits. Following CE of MLPA amplification products, the software automatically identified the peak area for each probe, normalized it in relation to the neighboring peak areas of the test sample, computed the ratio relative to a reference created from normal samples, and compensated the ratio for a side effect of the normalization procedure that scaled all chromosomally normal DNA peak areas slightly up or down depending on the kind of aneuploidy present. For the chromosomes 13, 18, 21, X, and Y, probe reliability weighted mean ratio values and corresponding SDs were calculated, and the significance for being outside a reference interval around ratio 1.0 was tested. p < or = 1% suggested aneuploidy and 1 < p < or = 5% suggested potential aneuploidy. Individual peaks, where the normalized area was situated more than 4 SD from the corresponding reference, suggested possible partial deletion or gain. Sample quality was automatically assessed. Control probes were not required. Having used the software and methods for two years, we conclude that a reliable, objective, and fast workflow is obtained.

Aneuploidy↗
PubMed1994

Automatic scoring of sister chromatid exchanges by image analysis in a dose response experiment.

A system which automatically selects second division metaphases and then, automatically scores the number of SCEs of each cell is described. In an initial set of experiments, the performance of the components of the system was measured using a data set in which metaphases had been visually classified as either 2nd division or other; and in 2nd division metaphases, every SCE had been marked on a hard copy. SCE scoring had a true positive rate of about 75% and a false positive rate of about 1.5 false SCEs per metaphase analyzed. Second division detection had a true positive rate of 80% and a false positive rate of about 10% of the non-2nd division cells. Next, the overall system was compared to human visual scoring in a dose-response experiment by analyzing the effect of mitomycin C on human chromosomes scored visually by two observers and by the fully automatic scoring. Human visual scoring and machine analysis showed similar dose responses, but the variability between them was considerable.

Cell Division↗
PubMed1996

The role of ultrasonography and automatic-needle biopsy in outpatient percutaneous liver biopsy.

The risk of complications from percutaneous liver biopsy is low, but discomfort is common and complications require hospitalization in approximately 4% of patients. The optimal method of performing these biopsies is unknown. The goal of our study was to determine whether the use of ultrasonography in the biopsy room immediately prior to or during the procedure would lessen the risk of complications and to compare the safety and efficacy in obtaining tissue by use of a Trucut needle versus an automatic biopsy needle. Between 1992 and 1994, 836 patients were entered into a randomized study (489 in Rochester, MN; 347 in Barcelona, Spain). Patients were randomized immediately prior to liver biopsy into four groups: Trucut needle, or automatic biopsy needle, and with or without ultrasonography. Fisher's Exact Test and a logistic regression model were also used to assess the effect of needle and ultrasonography on the odds for complications. The four biopsy groups were well-matched at entry with respect to age, sex, underlying liver disease, hemoglobin, prothrombin time, and platelet count. The use of ultrasound was associated with a decreased rate of hospitalization for pain, hypotension, or bleeding (2 vs. 9, P < .05). No difference in safety was found between the two types of needles. The number of passes needed to obtain specimens was similar for all four groups. The average length of the specimen was slightly greater with ultrasonographic-guided biopsies (1.7 mm vs. 1.6 mm, P < .05) and with biopsies obtained using the automatic biopsy needle when compared with the Trucut needle (1.7 mm vs. 1.5 mm, P < .05), but this did not seem to be clinically important. The addition of ultrasonography reduces complications in patients undergoing percutaneous liver biopsy. The type of needle appears to offer little difference in safety or yield of diagnostic tissue. The use of ultrasonography for guidance of percutaneous liver biopsy will lead to a lower rate of complications. The value of this benefit must be weighed against the added cost of ultrasonographic guidance.

Adolescent↗
PubMed1992

Application of automatic image analysis for quantitative morphological studies of peroxisomes in rat liver in conjunction with cytochemical staining with 3-3'-diaminobenzidine and immunocytochemistry.

We describe the application of automatic image analysis for quantitative morphological studies of peroxisomes in rat liver. For automatic detection by light and electron microscopy peroxisomes must be stained with the alkaline DAB procedure for catalase. There is a good agreement between the results obtained by conventional morphometric techniques and by automatic image analysis of DAB-stained electron microscopic preparations. Moreover, the image analyzer may be used in conjunction with a light microscope for evaluation of semithin sections (1-0.25 microns), provided the section thickness factor is taken into consideration. This latter approach has proven highly efficient in estimation of peroxisome proliferation. The limitations of this method and the relevance of volume density as a reliable morphometric parameter for evaluation of peroxisome proliferation are discussed. In the second part of this study we present the application of image analysis for quantitation of alterations of individual peroxisomal enzyme proteins after treatment with bezafibrate in immunogold stained ultrathin sections. There is good agreement between the results of quantitative immunocytochemistry and Western (immuno) blot analysis of highly purified peroxisomal fractions. In our experience quantitative immunoelectron microscopy provides a versatile, highly sensitive, and efficient method for detection of modulations of various proteins in peroxisomes. Finally the limitations and prospects of quantitative immunocytochemistry for investigation of peroxisomal proteins are discussed.

3,3'-Diaminobenzidine↗
PubMed2005

Automatic tuning of flexible interventional RF receiver coils.

Microcontroller-based circuitry was built and tested for automatically tuning flexible RF receiver coils at the touch of a button. This circuitry is robust to 10% changes in probe center frequency, is in line with the scanner, and requires less than 1 s to tune a simple probe. Images were acquired using this circuitry with a varactor-tunable 1-inch flexible probe in a phantom and in an in vitro porcine knee model. The phantom experiments support the use of automatic tuning by demonstrating 30% signal-to-noise ratio (SNR) losses for 5% changes in coil center frequency, in agreement with theoretical calculations. Comparisons between patellofemoral cartilage images obtained using a 3-inch surface coil and the surgically-implanted 1-inch flexible coil reveal a worst-case local SNR advantage of a factor of 4 for the smaller coil. This work confirms that surgically implanted coils can greatly improve resolution in small-field-of-view (FOV) applications, and demonstrates the importance and feasibility of automatically tuning such probes.

Animals↗
PubMed2006

Fast automatic linear off-resonance correction method for spiral imaging.

Field inhomogeneity and susceptibility variations, coupled with a long readout, can result in image blurring in spiral imaging. Many correction methods based on a priori off-resonance information, such as an acquired field map, have been proposed in the literature. Automatic off-resonance correction methods are alternative approaches that estimate a field map from the image data themselves. In this paper we propose a fast automatic off-resonance correction method that performs linear correction without acquiring a field map. The method requires only about two times the total computation time compared to image reconstruction by gridding. It can also be used in combination with a full field map automatic off-resonance correction method to increase the extent of correction. The method is demonstrated by in vivo coronary artery imaging.

Algorithms↗
PubMed1989

Evaluation of an automatic method of measuring features of motor unit action potentials.

This study was performed to evaluate an automatic method of motor unit action potential (MUAP) analysis developed in our laboratory. MUAPs were recorded from the biceps brachii muscle of 68 normal subjects and 122 patients with nerve or muscle disease. The values of mean MUAP durations from normal subjects obtained by automatic analysis were similar to those reported in the literature. However, the normal range of MUAP amplitude and the incidence of polyphasic MUAPs were much higher. Normal ranges of mean MUAP area, area/amplitude ratio, and the number of turns were also defined. Automatic analysis demonstrated an abnormality of at least one MUAP feature in 70% of patients. There was concordance between automated analysis and visual assessment of MUAPs in 76% of patients with neuropathy but in only 50% of patients with myopathy. The relationships between different MUAP features seen in neuropathy and myopathy are explained in physiologic terms.

Action Potentials↗
PubMed2005

Automatic repositioning of single voxels in longitudinal 1H MRS studies.

An automatic procedure, allowing the prospective registration of brain MRI images and the acquisition of nearly identical brain volumes (coverage and orientation) in longitudinal exams, is presented. This procedure, based on a fast registration algorithm and a tailored pulse sequence, is used to reposition single voxels for 1H MRS data acquired in vivo. The impact of the repositioning method on the extent of voxel overlap and on the reproducibility of metabolite concentration measurements is studied. A statistically significant increase in voxel overlap and generally decreased short-term measurement variability (decreased coefficients of variation and increased reproducibility coefficients) are observed. Differences in the long-term variances of metabolite concentrations and concentration ratios measured using the eye and automatic repositioning scheme, however, do not reach statistical significance. The improved workflow associated with the use of the automatic repositioning process, which obviates the need for skilled operator intervention for voxel repositioning, suggests that approaches similar to the one presented here may be a standard element in tomorrow's longitudinal MRI and MRS exams.

Algorithms↗
PubMed2003

Preprocessing of tandem mass spectrometric data to support automatic protein identification.

Liquid chromatography tandem mass spectrometry is a major tool for identifying proteins. The fragment spectra of peptides can be interpreted automatically in conjunction with a sequence database search. With the development of powerful automatic search engines, research now focuses on optimizing the result returned from database searches. We present a series of preprocessing steps for fragment spectra to increase the accuracy and specificity of automatic database searches. After processing, the correct amino acid sequences from the database can be related better to the fragment spectra. This increases the sensitivity and reliability of protein identifications, especially with very large genomic databanks, and can be important for the systematic characterization of post-translational modifications.

Algorithms↗
PubMed2003

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller.

CASP provides a unique opportunity to compare the performance of automatic fold recognition methods with the performance of manual experts who might use these methods. Here, we show that a novel automatic fold recognition server, Pmodeller, is getting close to the performance of manual experts. Although a small group of experts still perform better, most of the experts participating in CASP5 actually performed worse even though they had full access to all automatic predictions. Pmodeller is based on Pcons (Lundström et al., Protein Sci 2001; 10(11):2354-2365) the first "consensus" predictor that uses predictions from many other servers. Therefore, the success of Pmodeller and other consensus servers should be seen as a tribute to the collective of all developers of fold recognition servers. Furthermore we show that the inclusion of another novel method, ProQ2, to evaluate the quality of the protein models improves the predictions.

Algorithms↗
PubMed2001

Software (MSPECTRA) for automatic interpretation of triacylglycerol molecular mass distribution spectra and collision induced dissociation product ion spectra obtained by ammonia negative ion chemical ionization mass spectrometry.

Rapid analysis of molecular mass distributions of triacylglycerol (TAG) mixtures and regioisomeric structures of selected molecular mass species is possible using ammonia negative ion chemical ionization mass spectrometry utilizing sample introduction by direct exposure probe. However, interpretation of spectra and calculation of results is time consuming, thus lengthening the total analysis time. To facilitate result calculation a software package (MSPECTRA 1.3) was developed and applied to automatic processing of triacylglycerol molecular mass distribution spectra and collision induced dissociation (CID) product ion spectra. The program is capable of identifying triacylglycerol molecular mass species possessing different ACN:DB (acyl carbon number:number of double bonds) ratios on the basis of m/z values of [M - H](-) ions. In addition to such identification the program also corrects spectra for abundances of naturally occurring (13)C isotopes and calculates relative proportions of triacylglycerol molecular species in the analyzed samples. If several replicate spectra are processed simultaneously the program automatically calculates an average and standard deviation of relative proportions of molecular species. In the case of CID spectra the program identifies fatty acid fragment ions [RCO(2)](-) and the corresponding [M - H - RCO(2)H - 100](-) ions, and calculates the relative proportions of ions in both groups. These proportions are then used automatically to calculate the fatty acid combinations comprising the parent triacylglycerol molecule and the regiospecific positions of fatty acids. Processing of several replicate product ion spectra simultaneously produces averaged proportions of regioisomers comprising the parent triacylglycerol molecular species and the standard deviation of the analysis. The performance of the program was tested by analyzing triacylglycerol samples of human milk, human milk substitutes, human chylomicron and cocoa butter, and by comparing results obtained by automated processing of the data with manually calculated results.

Ammonia↗
PubMed1993

Neural network model: application to automatic analysis of human sleep.

We describe an approach to automatic all-night sleep analysis based on neural network models and simulated on a digital computer. First, automatic sleep stage scoring was performed using a multilayer feedforward network. Second, supervision of the automatic decision was achieved using ambiguity rejection and artifact rejection. Then, numerical analysis of sleep was carried out using all-night spectral analysis for the background activity of the EEG and sleep pattern detectors for the transient activity. Computerized analysis of sleep recordings may be considered as an essential tool to describe the sleep process and to reflect the dynamical organization of human sleep.

Computer Simulation↗