Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “AUTOMATION”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41Linked to original sources
PubMed1999

Automated one-step supercritical fluid extraction and clean-up system for the analysis of pesticide residues in fatty matrices.

An automated supercritical fluid extraction and in-line clean-up system has been developed for organochlorine and organophosphate pesticide residues contained in fats. This procedure utilizes supercritical carbon dioxide modified with 3% acetonitrile at 27.58 MPa and 60 degrees C to extract and separate the pesticide residues from the fat on a C1 bonded phase preparative column at 95 degrees C. The automated C1 system recovers 86 of 117 nonpolar to moderately polar organochlorine and organophosphate pesticides from fats. Ten of the 31 pesticides not recovered through the system are not recovered through the conventional clean-up sorbent, Florisil. Pesticide residues can be separated from 0.68 g of butter fat and 0.67 g corn oil, resulting in 2.9 mg of butterfat and 2.1 mg corn oil residue co-eluting into the pesticide fraction. Also, this integrated method can extract and clean-up a 5 g sample of fatty foods containing < 18% fat and 70% moisture. The automated C1 system is reproducible and the amount of co-extracted sample residue in the pesticide fraction yields results comparable to the current methodology, which uses organic solvent extraction and gel permeation chromatography, along with a final Florisil column clean-up step. This automated C1 system simplifies the extraction and clean-up step while reducing solvent usage and hazardous waste.

2-Propanol↗
PubMed2000

Automated data acquisition by confocal laser scanning microscopy and image analysis of triple stained immunofluorescent leukocytes in tissue.

The aim of the study was to develop a novel system permitting automated analysis of multicolor immunofluorescence-staining of cells in solid tissues which would be comparable to the analytical capacity of flow cytometry. In the user friendly automated data acquisition and image processing system which was established, the software includes a set of pre-defined processing steps for improved object identification and can be either interactive or fully automatic. As with multi color flow cytometry, stained cells can be analyzed in a fully automated manner regardless of tissue type. The software organizes computerized sample movement, autofocus, laser readjustment, data capture and storage as well as calculation. Data are presented as histograms indicating the staining intensity and frequency of each antigen, and in dotplots with each channel plotted against the other. The calculated statistics give information about how many of the cells are single-, double- or triple-reactive and how intensely they react with the respective antibodies. Comparison of data generated by this automated fluorescence confocal laser scanning microscopy (AF-CLSM) with flow cytometry using triple stained peripheral blood lymphocytes revealed a highly significant correlation between the methods (P<0.001). A correlation was also observed when sections triple stained for anti-CD45, -CD3 and -CD8 were analyzed by AF-CLSM and the data were compared to visual/manual cell counting (P<0.01). The AF-CLSM system permits for the first time, fast (online) and reproducible analysis of immunofluorescence staining of an unlimited number of cells in tissue sections. The software, including a manual, is available for a small fee to cover the costs of printing and postage.

CD3 Complex↗
PubMed2002

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra. CANDID uses an iterative approach with multiple cycles of NOE cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm, so that the result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE cross-peak assignments in all available spectra and a three-dimensional protein structure represented by a bundle of conformers. The input for the first CANDID cycle consists of the amino acid sequence, the chemical shift list from the sequence-specific resonance assignment, and listings of the cross-peak positions and volumes in one or several two, three or four-dimensional NOESY spectra. The input for the second and subsequent CANDID cycles contains the three-dimensional protein structure from the previous cycle, in addition to the complete input used for the first cycle. CANDID includes two new elements that make it robust with respect to the presence of artifacts in the input data, i.e. network-anchoring and constraint-combination, which have a key role in de novo protein structure determinations for the successful generation of the correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use of the fact that any network of correct NOE cross-peak assignments forms a self-consistent set; the initial, chemical shift-based assignments for each individual NOE cross-peak are therefore weighted by the extent to which they can be embedded into the network formed by all other NOE cross-peak assignments. Constraint-combination reduces the deleterious impact of artifact NOE upper distance constraints in the input for a protein structure calculation by combining the assignments for two or several peaks into a single upper limit distance constraint, which lowers the probability that the presence of an artifact peak will influence the outcome of the structure calculation. CANDID test calculations were performed with NMR data sets of four proteins for which high-quality structures had previously been solved by interactive protocols, and they yielded comparable results to these reference structure determinations with regard to both the residual constraint violations, and the precision and accuracy of the atomic coordinates. The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins. The experience gained in these calculations shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDID approach results in greatly enhanced efficiency of the NOESY spectral analysis. The fact that the correct fold is obtained in cycle 1 of a de novo structure calculation is the single most important advance achieved with CANDID, when compared with previously proposed automated NOESY assignment methods that do not use network-anchoring and constraint-combination.

Algorithms↗
PubMed2001

Optimum criteria for short-wavelength automated perimetry.

OBJECTIVE: To determine the optimum perimetric criteria for short-wavelength automated perimetry on the basis of probabilistic maps that best discriminate between normal and glaucoma. DESIGN: Comparative cross-sectional study. PARTICIPANTS: Ninety-five glaucomatous eyes and 128 normal eyes were included in the study. INTERVENTIONS: The subjects underwent retinal nerve fiber layer photographic evaluation and short-wavelength automated perimetry. MAIN OUTCOME MEASURES: A probabilistic map of differential points for short-wavelength automated perimetry was elaborated, and the number of altered points was calculated for each visual field and level of significance (95%, 98%, 99%, and 99.5%). RESULTS: The presence of a cluster of four or more points outside 95% normal probability limit showed a good combination of sensitivity and specificity. At deeper levels, P: < 1% and P: < 0.5%, the best combination is achieved with three points outside the normal probability limits. CONCLUSIONS: The optimum criterion to define glaucomatous abnormalities in short-wavelength automated perimetry is the presence of a cluster of four points lower than P: < 5% or a cluster of three points lower than P: < 1%.

Adult↗
PubMed2002

Short wavelength automated perimetry, frequency doubling technology perimetry, and pattern electroretinography for prediction of progressive glaucomatous standard visual field defects.

PURPOSE: To evaluate the clinical use of a test battery of short wavelength automated perimetry (SWAP), frequency doubling technology perimetry (FDT), and pattern electroretinography (PERG) in predicting progressive glaucomatous visual field defects on standard automated perimetry (SAP). STUDY DESIGN: A prospective, longitudinal, observational case series. PARTICIPANTS: One hundred and fifty-two patients with primary open-angle glaucoma (POAG) with bilateral glaucomatous visual field defects on SAP were followed at 6-month intervals over a period of 30 months. MAIN OUTCOME MEASURES: Short wavelength automated perimetry, FDT, and PERG results were compared between POAG eyes with and without progressive field loss on SAP. These two groups were used to evaluate whether PERG, SWAP, and/or FDT is predictive of future progression of field loss on SAP. RESULTS: Using the criteria of progressive field loss on SAP defined by the Collaborative Normal Tension Glaucoma Study, 54 eyes (study group) of 54 POAG patients showed progressive defects, whereas 84 eyes (control group) of 84 POAG patients showed no progression. Only 11.1% (6 of 54) of the eyes with a progression of field loss on SAP showed no increase of deficits on the three functional tests before progression. Short wavelength automated perimetry detected early progressive defects on SAP in 43 of the 54 eyes (79.6%). Of these 54 POAG eyes, FDT showed progressive deficits in 40 eyes (74.1%), whereas PERG amplitude P1N2 showed progressive deficits in 35 eyes (64.8%) before progression of field loss on SAP. A test battery consisting of SWAP and PERG P1N2-amplitude was able to detect 88.9% of eyes before a prediction of field loss on SAP. When comparing the results of the two functional tests, SWAP and FDT in the 84 eyes without progression of field loss on SAP between baseline and at 30 months, SWAP and FDT showed progressive deficits in 34.5% and 35.7%, respectively. CONCLUSIONS: All three tests (SWAP, FDT, and PERG) have been successful in detecting glaucoma eyes with a future progression of standard visual field defects. A test battery of SWAP and PERG P1N2-amplitude improved the power to predict these progressive defects on SAP. It remains to be seen whether the long-term follow-up in POAG eyes will improve the false-positive rate of SWAP and FDT.

Disease Progression↗
PubMed2001

Automated immunomagnetic separation and microarray detection of E. coli O157:H7 from poultry carcass rinse.

We describe the development and application of an electromagnetic flow cell and fluidics system for automated immunomagnetic separation (IMS) of Escherichia coli O157:H7 directly from poultry carcass rinse. We further describe the biochemical coupling of automated sample preparation with nucleic acid microarrays. Both the cell concentration system and microarray detection method did not require cell growth or enrichment from the poultry carcass rinse prior to IMS. Highly porous Ni foam was used to enhance the magnetic field gradient within the flow path, providing a mechanism for immobilizing immunomagnetic particles throughout the fluid rather than the tubing wall. A maximum of 32% recovery efficiency of non-pathogenic E. coli was achieved within the automated system with 6 s cell contact times using commercially available antibodies targeted against the O and K antigens. A 15-min protocol (from sample injection though elution) provided a cell recovery efficiency that was statistically similar to > I h batch captures. O157:H7 cells were reproducibly isolated directly from poultry carcass rinse with 39% recovery efficiency at 10(3) CFU ml(-1) inoculum. Direct plating of washed beads showed positive recovery of O157:H7 directly from poultry carcass rinse at an inoculum of 10 CFU ml(-1). Recovered beads were used for direct polymerase chain reaction (PCR) amplification and microarray detection, with a process-level detection limit (automated cell concentration though microarray detection) of < 10(3)CFU ml(-1) in poultry carcass rinse.

Animals↗
PubMed2003

Results of the introduction of an automated external defibrillation programme for non-medical personnel in Galicia.

OBJECTIVES: To describe the plan and development of a programme for the introduction of automated external defibrillation for non medical personnel and to report the results of the first 10 months of activity in a community which is predominently rural, such as Galicia. METHODS: The plan for introduction of the project included aspects of logistics, training and control. We studied cardiac arrests, that were treated in basic life support ambulances (BLS-A) equipped with automated external defibrillators (AEDs), from 1st March to 31st December 2001. RESULTS: Our community benefits from pioneering legislation in Spain. During the 10 months of study, 28 AEDs were in service, mostly in urban areas. In all cases, a thorough control of the quality of the service in which AEDs was used was carried out. 12% of the patients, who were victims of sudden cardiac death (SCD) and were found in ventricular fibrillation (VF), survived and were discharged from hospital. However, the percentage of patients found in VF is only around 26%. This is due to long assistance intervals (from the call to the arrival on site), and an important delay from the moment when circulatory collapse takes place until the emergency service 061 is called, more than 5 min in half the cases. CONCLUSIONS: The programme followed for the introduction of AEDs in Galicia was adapted to the socio-demographic characteristics of the population. The prehospital emergency assistance model was developed, executed and controlled by the Public Emergency Health Foundation of Galicia 061 (PEHF-061). The overall results of our first 10 months experience with the automated external defibrillation programme were as to be expected. In general, they are comparable to other published reports; however, ways of shortening the times from the point of collapse to defibrillation must be found, mainly by training the population and through the extension of automated external defibrillation provision to other first responders.

Adult↗
PubMed2000

Automated contour detection for high-frequency intravascular ultrasound imaging: a technique with blood noise reduction for edge enhancement.

Automated edge detection may standardize measurements among observers, providing for rapid assessment of intravascular ultrasound (IVUS) images. However, with high frequency images, enhanced blood signals make it difficult to define and trace the lumen borders. Accordingly, we evaluated a fully automated contour analysis facilitated with a blood noise reduction algorithm (BNR) for 40-MHz IVUS images in human coronary arteries of 27 patients. This algorithm is based on the principle that blood echo speckles have higher temporal and spatial variations than the arterial wall. A total of 193 paired lumen areas and 78 external elastic membrane (EEM) areas were measured and compared. Automated measurements showed good agreement with manual tracings for lumen and EEM area, with high correlation coefficients (0.945 and 0.950, respectively) and small variability (0.4 +/- 14.4% and 0.6 +/- 9.7%, respectively). This preliminary finding suggests that automated contour detection facilitated with BNR appeared to be a feasible and reliable technique for area measurements in 40-MHz IVUS imaging.

Blood↗
PubMed1985

Automated counting of human tumour colonies in the Courtenay-Mills assay system.

A procedure for using the Omnicon automated image analysis system for counting colonies grown from a human tumour cell line (COLO 205) in the Courtenay-Mills assay is described. This involves the transfer of the agar medium from culture tubes into petri dishes. Comparisons of observer and instrument counts were done on a blinded basis. Run-to-run correlation coefficient was 0.996 for automated counting and the inter-observer correlation coefficient was 0.984. Both assessments showed a linear relationship between the number of cells plated and the number of colonies grown. Automated colony counting is fast, reliable and provides additional information on colony size distribution, not obtainable with manual counting. This automated procedure will greatly facilitate in vitro drug sensitivity evaluation.

Autoanalysis↗
PubMed1989

Automation of liquid chromatographic techniques for biomedical analysis.

The complete automation of liquid chromatographic (LC) techniques increases their work capacity and makes them more acceptable for biomedical applications. The ability to analyse priority specimens is also advantageous. The areas to be considered in a fully automated LC are reviewed in terms of the analytical operations, the types of processing and the various control systems that can be adopted. In particular, sample preparation and liquid handling are described in detail together with techniques and equipment that can be utilised for their automation. Strategies are given for the rational design of a fully automated LC that can analyse raw samples completely unattended.

Autoanalysis↗
PubMed1994

Evaluation of a new automated microneutralization assay for the quantitative detection of neutralizing antibodies against enteroviruses.

An automated microneutralization assay for the quantitative detection of neutralizing antibodies (NA) against polioviruses and non-polio enteroviruses (NPEV) using a pipetting roboter (Tecan RSP 5072) was established and compared to the conventional manually performed test procedure. The qualitative neutralizing antibody detection was not significantly influenced by the assay system (manual or automated assay). Concerning the quantitative antibody detection, two-fold titre differences between the two test systems were observed in only 2.3% of the 260 serum samples investigated. The intra-assay and inter-assay variability of the quantitative detection of neutralizing antibodies using the automated assay proved to be very low. The quantitative detection of neutralizing antibodies using an automated pipetting robot permitted the testing of large numbers of samples within a shorter period and with less labour intensity as compared to the manually performed assay. Therefore it represents a valuable alternative to the conventional microneutralization test, especially for the serodiagnosis of non-polio enterovirus infections in large sample collectives, assessment of immunity to polioviruses and for seroepidemiological surveys.

Animals↗
PubMed2002

Rapid quantitation of cyanide in whole blood by automated headspace gas chromatography.

Cyanide (CN), a chemical asphyxiant, is a rapidly acting and powerful poison. We have developed a sensitive, rapid, simple, and fully automated method for measuring CN in whole blood. The assay is based on the use of gas chromatography (GC) with nitrogen-phosphorus detection and acetonitrile as an internal reference. Following the automated addition of phosphoric acid to the blood sample, the released hydrogen cyanide is analyzed using a fully automated headspace GC system. The assay, validated on human blood samples spiked with potassium cyanide and on clinical samples from fire victims who had smoke inhalation injury, can detect CN at a wide range of concentrations (30-6000 microg/l) in about 17 min (including incubation and GC run time, and <2 min for manual sample preparation). This automated, high-throughput, simple, and sensitive method is suitable for the rapid diagnosis of CN in clinical and forensic specimens.

Calibration↗
PubMed2001

Wavelength Dispersive Spectrometer and Energy Dispersive Spectrometer Automation: Past and Future Development.

As part of the Microbeam Analysis Society (MAS) symposium marking 50 years of electron microprobe analysis, this article reviews the important advances made over the decades to the automation of data collection and computerized analysis of data from the electron microprobe. Out of many innovations that contributed to the advance of microprobe automation, we have chosen to focus on a few developments that the authors feel represent the major trends in advancement of the "state of the art" of this instrumentation. After providing brief summaries of the three generations of advances in the hardware and software of automation systems, several key applications developments are described, followed by our prediction of which current developments may impact the future automation of the microprobe.

Journal Article↗
PubMed1999

Automated face analysis by feature point tracking has high concurrent validity with manual FACS coding.

The face is a rich source of information about human behavior. Available methods for coding facial displays, however, are human-observer dependent, labor intensive, and difficult to standardize. To enable rigorous and efficient quantitative measurement of facial displays, we have developed an automated method of facial display analysis. In this report, we compare the results with this automated system with those of manual FACS (Facial Action Coding System, Ekman & Friesen, 1978a) coding. One hundred university students were videotaped while performing a series of facial displays. The image sequences were coded from videotape by certified FACS coders. Fifteen action units and action unit combinations that occurred a minimum of 25 times were selected for automated analysis. Facial features were automatically tracked in digitized image sequences using a hierarchical algorithm for estimating optical flow. The measurements were normalized for variation in position, orientation, and scale. The image sequences were randomly divided into a training set and a cross-validation set, and discriminant function analyses were conducted on the feature point measurements. In the training set, average agreement with manual FACS coding was 92% or higher for action units in the brow, eye, and mouth regions. In the cross-validation set, average agreement was 91%, 88%, and 81% for action units in the brow, eye, and mouth regions, respectively. Automated face analysis by feature point tracking demonstrated high concurrent validity with manual FACS coding.

Adolescent↗
PubMed2005

Automated microflow NMR: routine analysis of five-microliter samples.

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 microL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 microL of sample per well, as with vials, 5 microL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of approximately 11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in approximately 6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software.

Image Processing, Computer-Assisted↗
PubMed2006

Automated target preparation for microarray-based gene expression analysis.

DNA microarrays have rapidly evolved toward a platform for massively paralleled gene expression analysis. Despite its widespread use, the technology has been criticized to be vulnerable to technical variability. Addressing this issue, recent comparative, interplatform, and interlaboratory studies have revealed that, given defined procedures for "wet lab" experiments and data processing, a satisfactory reproducibility and little experimental variability can be achieved. In view of these advances in standardization, the requirement for uniform sample preparation becomes evident, especially if a microarray platform is used as a facility, i.e., by different users working in the laboratory. While one option to reduce technical variability is to dedicate one laboratory technician to all microarray studies, we have decided to automate the entire RNA sample preparation implementing a liquid handling system coupled to a thermocycler and a microtiter plate reader. Indeed, automated RNA sample preparation prior to chip analysis enables (1) the reduction of experimentally caused result variability, (2) the separation of (important) biological variability from (undesired) experimental variation, and (3) interstudy comparison of gene expression results. Our robotic platform can process up to 24 samples in parallel, using an automated sample preparation method that produces high-quality biotin-labeled cRNA ready to be hybridized on Affymetrix GeneChips. The results show that the technical interexperiment variation is less pronounced than with manually prepared samples. Moreover, experiments using the same starting material showed that the automated process yields a good reproducibility between samples.

Animals↗
PubMed2000

Calibration transfer algorithm for automated qualitative analysis by passive Fourier transform infrared spectrometry

The automated qualitative analysis of passive Fourier transform infrared (FT-IR) remote sensing data is made difficult by the presence in the data of background and instrument-specific variation. For data collected with a single instrument, variation in the data arises from changes in the infrared background radiance, changes in the atmospheric composition within the field-of-view of the spectrometer, and changes in the instrument response function arising from temperature variation in the spectrometer. When more than one spectrometer is used, the variation in detector responses and phase signatures between instruments serves to complicate further the task of implementing an automated processing algorithm for detecting the signature of a target compound. In this work, a combination of signal processing and pattern recognition methodology is applied directly to the interferogram data collected by the FT-IR spectrometer to implement an automated compound detection procedure that is independent of background and instrument-specific variation. The key to this algorithm is the use of highly attenuating digital filters to isolate in the interferogram the frequencies associated with an analyte absorption or emission band while suppressing information at other frequencies. For the test compounds, acetone and sulfur hexafluoride, it is demonstrated that when this digital filtering procedure is coupled with either piecewise linear discriminant analysis or a back-propagation neural network, an automated detection algorithm can be developed with data from a primary instrument and then subsequently used to predict the presence of analyte signatures in data collected with a secondary spectrometer. Correct classification rates in excess of 92% are obtained for both compounds when the algorithm is applied to data collected with the secondary instrument.

Journal Article↗
PubMed2000

Automated high-throughput liquid-liquid extraction for initial purification of combinatorial libraries.

An automated high-throughput liquid-liquid extraction (LLE) methodology has been developed and utilized for the initial purification of the combinatorial library samples containing unreacted amines and other water-soluble byproducts or impurities. Various extraction solvents were evaluated along with different extraction devices. The LLE method was automated using 96-well-format plates and a robotic liquid-handling workstation. In the optimized LLE method, crude combinatorial library samples were dissolved in a water-immiscible organic solvent, butyl acetate, and added to each well in a 96-well-format plate packed with an inert support material coated with hydrochloric acid. Separation occurs based on the partitioning of the compounds between two liquid phases. Product recovery, purity, and amine removal efficiency were determined by HPLC with and without precolumn derivatization. The automated method was successfully applied to the cleanup of some representative combinatorial library samples with greater than 98% amine removal and an average product purity of 90%. The application of the automated high-throughput LLE method should greatly reduce the labor, time, and cost associated with the purification of combinatorial libraries.

Amines↗