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At least 685 records · Page 38Linked to original sources
PubMed2006

Automated virtual microscopy of gastric biopsies.

BACKGROUND: Automated virtual microscopy of specimens from gastrointestinal biopsies is based on cytometric parameters of digitized histological sections. To our knowledge, cytometric parameters of gastritis and of adenocarcinoma have yet to be fully characterized. Our objective was to classify gastritis and adenocarcinoma based on cytometric parameters. We hypothesized that automated virtual microscopy using this novel classification can reliably diagnose gastritis and adenocarcinoma. METHODS: Routinely processed hematoxylin-and-eosin-stained histological sections from specimens that showed normal mucosa (14 cases), gastritis (35 cases), and adenocarcinoma (30 cases) diagnosed by conventional optical microscopy were scanned and digitized at high resolution. Thirty-eight cytometric parameters based on density and morphometry were applied to glands and superficial epithelium. Twelve cytometric parameters based on cytologic detail were applied to individual cells. RESULTS: Statistically significant differences in cytometric parameters for normal mucosa, gastritis, and adenocarcinoma were found. The most discriminatory parameter was the ratio of the total number of cells to the number of interstitial cells. These differences correctly classified adenocarcinoma at 100% accuracy and overall correctness was 86%. CONCLUSIONS: We describe a novel method of analyzing gastric mucosal histology based on cytometric parameters. Automated virtual microscopy can be used to classify gastric mucosa as normal, gastritis, or adenocarcinoma with reasonable accuracy. Further research is necessary to determine whether automated virtual microscopy can subclassify gastric mucosal histology in greater detail.

Adenocarcinoma↗
PubMed2001

Automation in genotyping of single nucleotide polymorphisms.

Automation for genotyping of single nucleotide polymorphisms (SNPs) can be split into the automation of the sample preparation and the automation of the analysis technology. SNP genotyping methods are reviewed and solutions for their automation discussed. A panacea for SNP genotyping does not exist. Different scientific questions require adapted solutions. The choice of a technology for SNP genotyping depends on whether few different SNPs are to be genotyped in many individuals, or many different SNPs are to be genotyped in few individuals. The requirements of throughput and the ease of establishing an SNP genotyping operation are important, as well as the degree of integration. The potential and state-of-the-art of different solutions are outlined.

Genotype↗
PubMed1991

Automated comparison of dual-photon absorptiometric studies of the lumbar spine.

An automated image comparison procedure was developed to optimize the precision of bone mineral density measurements by dual-photon absorptiometry. Changed acquisition conditions cause differences between two images to be compared. Alignment of one image with respect to the other is performed by a transformation that involves a rotation, a horizontal or vertical shift, and a correction for the soft tissue level. The best possible transformation is found in a stepwise search, guided by initial estimations of its parameters. After optimum transformation of one image, the region of interest of the other image is applied to both of them. Duplicate measurements of 9 patients and 15 normal subjects were performed; automated analysis yielded improved precision with respect to manual analysis. The coefficient of variation (CV) was also computed. The CV for automated analysis was 2.00% for patients and 1.04% for normal subjects compared to 3.55 and 1.93%, respectively, for manual analysis. For phantoms, the precision was 2.67% for manual analysis and 0.49% for automated analysis.

Absorptiometry, Photon↗
PubMed2007

Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry.

Characterization of recombinant protein purification fractions and final products by liquid chromatography-mass spectrometry (LC/MS) are requested more frequently each year. A protein open-access (OA) LC/MS system was developed in our laboratory to meet this demand. This paper compares the system that we originally implemented in our facilities in 2003 to the one now in use, and discusses, in more detail, recent enhancements that have improved its robustness, reliability, and data reporting capabilities. The system utilizes instruments equipped with reversed-phase chromatography and an orthogonal accelerated time-of-flight mass spectrometer fitted with an electrospray source. Sample analysis requests are accomplished using a simple form on a web-enabled laboratory information management system (LIMS). This distributed form is accessible from any intranet-connected company desktop computer. Automated data acquisition and processing are performed using a combination of in-house (OA-Self Service, OA-Monitor, and OA-Analysis Engine) and vendor-supplied programs (AutoLynx, and OpenLynx) located on acquisition computers and off-line processing workstations. Analysis results are then reported via the same web-based LIMS. Also presented are solutions to problems not addressed on commercially available, small-molecule OA-LC/MS systems. These include automated transforming of mass-to-charge (m/z) spectra to mass spectra and automated data interpretation that considers minor variants to the protein sequence-such as common post-translational modifications (PTMs). Currently, our protein OA-LC/MS platform runs on five LC/MS instruments located in three separate GlaxoSmithKline R&D sites in the US and UK. To date, more than 8000 protein OA-LC/MS samples have been analyzed. With these user friendly and highly automated OA systems in place, mass spectrometry plays a key role in assessing the quality of recombinant proteins, either produced at our facilities or bought from external sources, without dedicating extensive amounts of analyst resource.

Animals↗
PubMed2003

Automated segmentation and analysis of vascular structures in magnetic resonance angiographic images.

The accurate assessment of the presence and extent of vascular disease, and planning of vascular interventions based on MRA requires the determination of vessel dimensions. The current standard is based on measuring vessel diameters on maximum intensity projections (MIPs) using calipers. In order to increase the accuracy and reproducibility of the method, automated analysis of the 3D MR data is required. A novel method for automatically determining the trajectory of the vessel of interest, the luminal boundaries, and subsequent the vessel dimensions is presented. The automated segmentation in 3D uses deformable models, combined with knowledge of the acquisition protocol. The trajectory determination was tested on 20 in vivo studies of the abdomen and legs. In 93% the detected trajectory followed the vessel. The luminal boundary detection was validated on contrast-enhanced (CE) MRA images of five stenotic phantoms. The results from the automated analysis correlated very well with the true diameters of the phantoms used in the in vitro study (r = 0.999, P < 0.001). MRA and x-ray angiography (XA) of the phantoms also correlated well (r = 0.895, P < 0.001). The average unsigned difference between the MRA and XA measurements was 0.08 +/- 0.05 mm. In conclusion, the automated approach allows the accurate assessment of vessel dimensions in MRA images.

Abdomen↗
PubMed1994

Motor unit number estimates based on the automated analysis of F-responses.

An automated technique for estimating the number of motor units based on single motor unit action potentials in the F-response is described. The average surface detected motor unit action potential (S-MUAP) was calculated from the datapoint-by-datapoint average of a sample of S-MUAPs automatically selected from a population of F-responses. The technique was applied to the thenar muscles of young (n = 18, aged 31 +/- 11 years) and older (n = 15, aged 68 +/- 3) subjects. Motor unit number estimates based on the automated selection of S-MUAPs from the F-responses compared well with those derived using a computer-assisted manual method for selecting S-MUAPs from the F-response (automated 245 +/- 105 vs. manual 241 +/- 100, r = 0.93) and were similar to estimates obtained using multiple point stimulation (219 +/- 77). The advantages of the automated technique for collecting S-MUAPs from the F-response include the ready tolerance of the technique by subjects, the minimal amount of operator interaction required, and the additional information relating to the conduction velocities and latencies of single motor axons.

Action Potentials↗
PubMed1992

Automated carboxy-terminal sequence analysis of peptides and proteins using diphenyl phosphoroisothiocyanatidate.

Proteins and peptides can be sequenced from the carboxy-terminus with isothiocyanate reagents to produce amino acid thiohydantoin derivatives. Previous studies in our laboratory have focused on the automation of the thiocyanate chemistry using acetic anhydride and trimethylsilylisothiocyanate (TMS-ITC) to derivatize the C-terminal amino acid to a thiohydantoin and sodium trimethylsilanolate for specific hydrolysis of the derivatized C-terminal amino acid (Bailey, J.M., Shenoy, N.R., Ronk, M., & Shively, J.E., 1992, Protein Sci. 1, 68-80). A major limitation of this approach was the need to activate the C-terminus with acetic anhydride. We now describe the use of a new reagent, diphenyl phosphoroisothiocyanatidate (DPP-ITC) and pyridine, which combines the activation and derivatization steps to produce peptidylthiohydantoins. Previous work by Kenner et al. (Kenner, G.W., Khorana, H.G., & Stedman, R.J., 1953, Chem. Soc. J., 673-678) with this reagent demonstrated slow kinetics. Several days were required for complete reaction. We show here that the inclusion of pyridine was found to promote the formation of C-terminal thiohydantoins by DPP-ITC resulting in complete conversion of the C-terminal amino acid to a thiohydantoin in less than 1 h. Reagents such as imidazole, triazine, and tetrazole were also found to promote the reaction with DPP-ITC as effectively as pyridine. General base catalysts, such as triethylamine, do not promote the reaction, but are required to convert the C-terminal carboxylic acid to a salt prior to the reaction with DPP-ITC and pyridine. By introducing the DPP-ITC reagent and pyridine in separate steps in an automated sequencer, we observed improved sequencing yields for amino acids normally found difficult to derivatize with acetic anhydride/TMS-ITC. This was particularly true for aspartic acid, which now can be sequenced in yields comparable to most of the other amino acids. Automated programs are described for the C-terminal sequencing of peptides covalently attached to carboxylic acid-modified polyethylene and proteins (200 pmol to 5 nmol) noncovalently applied to Zitex (porous Teflon). The generality of our automated C-terminal sequencing methodology was examined by sequencing model peptides containing all 20 of the common amino acids. All of the amino acids tested were found to sequence in good yield except for proline, which was found not to be capable of derivatization. In spite of this limitation, the methodology should be a valuable tool for the C-terminal sequence analysis of peptides and proteins.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1993

Automated docking in crystallography: analysis of the substrates of aconitase.

Automated docking of substrates to proteins of known structure aids the process of crystallographic analysis in two ways. First, automated docking can be used to generate a small number of starting models for substrates using only protein coordinates from an early stage of refinement. Second, automated docking provides a method for exploring aspects of catalysis that are inaccessible to crystallography by postulating binding modes of catalytic intermediates. This paper describes the use of automated docking to explore the binding of substrates to aconitase. The technique starts with a substrate molecule in an arbitrary configuration and position and finds favorable docked configurations in a (static) protein active site based on a molecular mechanics type force field. Using protein coordinates from an early stage of refinement of an aconitase-isocitrate complex, we successfully predicted the binding configuration of isocitrate. Four configurations were found, the energetically most favorable of which fit the observed electron density well and was used as a starting model for further refinement. Two configurations were found in citrate docking experiments, the second of which approximates the mode of substrate binding in an aconitase-nitrocitrate complex. We were also able to propose two binding modes of the catalytic intermediate cis-aconitate. These correspond closely to the isocitrate and the citrate binding modes. The relation of these new results to the proposed reaction mechanism is discussed.

Aconitate Hydratase↗
PubMed2003

Automated analysis of 13C/12C ratios in CO2 and dissolved inorganic carbon for ecological and environmental applications.

Stable carbon isotope ratios (13C/12C) are a valuable tool for studying a wide range of environmental processes, including carbon cycling and subsurface microbial activity. Recent advances in automated analysis provide the opportunity to increase greatly the ease and consistency of isotopic analysis. This study evaluated an automated headspace sampler linked to a commercially available CO2 preconcentration system and continuous flow isotope ratio mass spectrometer. Field sampling and analysis methods are illustrated for delta13C of soil respired CO2, from both tracer and natural abundance experiments, and dissolved inorganic carbon from contaminated groundwater. The automated system demonstrated accuracy, precision, and linearity, with standard errors below 0.1 per thousand for replicate gas standards run at concentrations varying five-fold. It measured 40 samples per 10-hour run, with concentrations ranging from ppb to percentage levels. In the field, gas samples were injected into nitrogen-filled autosampler vials, thereby allowing use of small sample volumes, control of analyte concentration, and direct analysis by the automated system with no further preparation. A significant linear relationship between standard concentrations and peak area allows for accurate estimates of sample CO2 concentration from the mass spectrometric data. The ability to analyze multiple small-volume samples with minimal off-line preparation should enhance the application of isotopes to well-replicated field experiments for process-level studies and spatial and temporal scaling.

Air Pollutants↗
PubMed2004

Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting.

The use of robots has major effects on maximizing the proteomic workflow required in an increasing number of high-throughput projects and on increasing the quality of the data. In peptide mass finger printing (PMF), automation of steps downstream of two-dimensional gel electrophoresis is essential. To achieve this goal, the workflow must be fluid. We have developed tools using macros written in Microsoft Excel and Word to complete the automation of our platform. Additionally, because sample preparation is crucial for identification of proteins by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, we optimized a sandwich method usable by any robot for spotting digests on a MALDI target. This procedure enables further efficient automated washing steps directly on the MALDI target. The success rate of PMF identification was evaluated for the automated sandwich method, and for the dried-droplet method implemented on the robot as recommended by the manufacturer. Of the two methods, the sandwich method achieved the highest identification success rate and sequence coverage of proteins.

Colonic Neoplasms↗
PubMed1998

Automated high-throughput mass spectrometric analysis of synthetic oligonucleotides.

The use of automated sample preparation and data collection coupled with delayed ion extraction matrix-assisted laser desorption ionization with time-of-flight detection mass spectrometry (DE MALDI-TOF MS) enables the rapid mass analysis of oligonucleotide samples. We have incorporated a matrix-diluting and liquid-spotting automated work station and a DE MALDI mass spectrometer to provide high-throughput analysis of synthetic oligonucleotides. Automated sample preparation greatly speeds processing while the spotting function allows for precise sample placement on a 100-well sample plate. The DE MALDI MS typically determines the mass of each sample to within 0.13 +/- 0.10% of the theoretically expected mass. This mass accuracy allows confirmation of identity and detection of low-level impurities present in synthetic oligonucleotide samples with an unprecedented degree of confidence. Using this automation suite, sample preparation, spotting, and analysis of 100 samples ranging from 12 to 70 bases in length can be routinely completed in less than 90 min.

Calibration↗
PubMed1994

Enzyme-linked fluorescent detection for automated multiplex DNA sequencing.

Initiatives to sequence DNA on a large scale have created a need for increased throughput and decreased costs. One scheme for increasing throughput, multiplex sequencing, involves the processing of a mixture of sequencing templates followed by sequential hybridization to reveal the individual sequence ladders on a membrane. Because multiplex sequencing has not been fully automated, and has not seemed automatable, few sequencing efforts have attempted to exploit it. We describe here a scheme for the automation of multiplex sequencing. Probe hybridized to target DNA is detected via spatially localized enzyme-linked fluorescence. Light output is high enough that imaging is possible with simple instrumentation. Direct imaging within an automated hybridization apparatus is made feasible so that the entire process will be automatic once a multiplex membrane is produced. The technique has the potential to increase severalfold the throughput of automated sequencing instruments required for sequencing the human genome.

Base Sequence↗
PubMed1998

Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.

A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automated peak picking for NMR spectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

Algorithms↗
PubMed2001

Automated behavioural analysis in animal pain studies.

The assessment of the effectiveness of analgesics is strongly based on observational data from behavioural tests. These tests are interesting and give a quantification of the effect of the drugs on the whole animal but their use is subject to several difficulties: (i) many results are difficult to analyse as they only correspond to the evaluation of a reflex response; (ii) the tests dealing with more integrated responses are also more difficult to use and closely depend on the experimenter's subjectivity. If automation is widely used in a lot of research fields, this is not the case in behavioural pharmacology. Yet, it can contribute to optimize the tests. The use of signal processing devices allows the automated (and thus objective) measurement of behavioural reactions to nociceptive stimulation (amplitude of a reflex, vocal emission intensity). Mechanical devices based on a computer-driven dynamic force detector allows the recording of some pain behaviours. Video image analysis allows the quantification of more complex behaviours (nociception-induced specific motor behaviours) as well as meaningful information during the same experimentation (exploratory behaviour, total motor activity, feeding behaviour). Moreover, these methods make it possible to obtain a more objective measurement, to reduce animal-experimenter interactions, to ease system use, and to improve effectiveness. The prospects to work in this field are multiple: continuation of the attempts at an automation of the behaviours specifically induced by chronic pain; development of real animal pain monitoring based on analysis of specific and non-specific behavioural modifications induced by pain. In this context, the automation of the behavioural analysis is likely to make possible real ethical progress thanks to an increase in the test's effectiveness and a real taking into account of animal's pain. Nevertheless, there are some limits due to characteristics of the behavioural expression of nociception and technological problems.

Animals↗
PubMed1978

A comparison of human and automated instruction of autistic children.

While it appears reasonable to assume that the autistic child might benefit from the development of programmed instruction and teaching machines to teach imitation, concepts, and receptive vocabulary skills, no systematic research to date has seriously investigated such possibilities. The purpose of this study was to compare the effects of automated versus teacher-controlled instruction in the education of autistic children. Four autistic children, each with extreme deficits in language, social, and self-care behaviors, were trained on a matching-to-sample task under three different instructional situations within an intrasubject replication design and multiple baseline procedure. Analysis of the data showed the following results: (1) The teacher, manually operating the teaching machine, was able to teach and maintain the matching-to-sample task; (2) the same autistic children did not acquire or maintain the task when taught by the machine alone; and (3) the teacher alone (without the machine) was able to teach and maintain the task. The results suggest that automated instruction may, at least, serve as a valuable aid to teachers of autistic children. However, before machines can be used without the participation of a trained teacher, further research appears necessary. Several areas, including the role of motivation in automated instructional settings, the saliency and effectiveness of reinforcers, and the importance of controlling antecedent stimulus conditions and off-task behavior are discussed as areas of primary concern in the development of automated instruction for autistic children.

Adolescent↗
PubMed1991

Improved detection of hypotension by automated noninvasive blood pressure monitoring.

This study was undertaken to determine whether the use of automated noninvasive blood pressure monitoring altered the frequency of detection of intraoperative hypotension. We retrospectively reviewed 1,861 anesthetic records from a period in 1987, when blood pressure was obtained manually by auscultation. We compared the records from 1987 with 1,716 anesthetic records from 1989, when automated blood pressure monitors were used universally. The incidences of hypotension requiring vasopressor therapy were determined during the two periods and compared using Student's two-tailed t test. The data revealed that the incidence of detected hypotension increased from 2.4 to 5.2% with the use of automated blood pressure monitors (P less than 0.00002). We conclude that at our hospital the use of automated noninvasive blood pressure monitors increases the incidence of detection of intraoperative hypotension as compared with the use of manual blood pressure measurement.

Anesthesia↗
PubMed2004

Detection of DNA aneuploidy in exfoliated airway epithelia cells of sputum specimens by the automated image cytometry and its clinical value in the identification of lung cancer.

To evaluate the value of detection of DNA aneuploidy in exfoliated airway epithelia cells of sputum specimens by the automated image cytometry for the identification of lung cancer, 100 patients were divided into patient group (50 patients with lung cancer) and control group (30 patients with tuberculosis and 20 healthy people). Sputum was obtained for the quantitative analysis of DNA content of exfoliated airway epithelial cells with the automated image cytometry, together with the examinations of brush cytology and conventional sputum cytology. Our results showed that DNA aneuploidy (DI>2.5 or 5c) was found in 20 out of 50 sputum samples of lung cancer, 1 out of 30 sputum samples from tuberculosis patients, and none of 20 sputum samples from healthy people. The positive rates of conventional sputum cytology and brush cytology were 16% and 32%, which was lower than that of DNA aneuploidy detection by the automated image cytometry (P<0.01, P>0.05). Our study showed-that automated image cytometry, which uses DNA aneuploidy as a marker for tumor, can detect the malignant cells in sputum samples of lung cancer and it is a sensitive and specific method serving as a complement for the diagnosis of lung cancer.

Adult↗
PubMed2005

Semi-automated digital image analysis of patellofemoral joint space width from lateral knee radiographs.

OBJECTIVE: To design a semi-automated program to measure minimum patellofemoral joint space width (JSW) using standing lateral view radiographs. DESIGN: Lateral patellofemoral knee radiographs were obtained from 35 asymptomatic subjects. The radiographs were analyzed to report both the repeatability of the image analysis program and the reproducibility of JSW measurements within a 2 week period. The results were also compared with manual measurements done by an experienced musculoskeletal radiologist. RESULTS: The image analysis program was shown to have an excellent coefficient of repeatability of 0.18 and 0.23 mm for intra- and inter-observer measurements respectively. The manual method measured a greater minimum JSW than the automated method. Reproducibility between days was comparable to other published results, but was less satisfactory for both manual and semi-automated measurements. The image analysis program had an inter-day coefficient of repeatability of 1.24 mm, which was lower than 1.66 mm for the manual method. CONCLUSIONS: A repeatable semi-automated method for measurement of the patellofemoral JSW from radiographs has been developed. The method is more accurate than manual measurements. However, the between-day reproducibility is higher than the intra-day reproducibility. Further investigation of the protocol for obtaining sequential lateral knee radiographs is needed in order to reduce the between-day variability.

Adult↗