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PubMed1990

Structure detection through automated covariance search.

This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential secondary and tertiary structural interactions, but also provides the covariation evidence that supports the proposed bondings, and any counterevidence that can be detected in the known sequences. A small number of previously unknown higher-order structural features have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. We are systematically studying mitochondrial rRNA, seeking tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. To test hypotheses suggested by an examination of our program's output, our colleagues in biology are sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosomal structure.

Algorithms↗
PubMed1995

Automated contour detection and acoustic quantification.

Echocardiographic left and right ventricular sequences are usually interpreted visually, but current quantitation techniques have been found to be tedious, time-consuming and associated with significant inter- and intra-observer variabilities. In an attempt to eliminate these problems, we have developed the Echocardiographic Analysis System (EAS) which uses robust automated border detection techniques both for single frames as well as for sequences. Comparison of LV cross-sectional area with the semi-automated border detection (AUTO) and those assessed from manual tracings (MAN) yielded a systematic difference (MAN-AUTO) of -6.6% (p < 0.001), and a random difference (standard deviation of paired signed differences) of 11.8%. Current developments are directed towards real-time automated border detection with an Accelerator board, integration of Acoustic Quantification (AQ) data as edge information into EAS, and intravascular echocardiographic applications.

Computers↗
PubMed2000

Automated extraction of 11-nor-delta9-tetrahydrocannabinol carboxylic acid from urine samples using the ASPEC XL solid-phase extraction system.

The analysis of 11-nor-delta9-tetrahydrocannabinol-carboxylic acid (THCCOOH, the major metabolite of cannabis) in urine with gas chromatography and mass spectrometry (GC-MS) and solid-phase extraction (SPE) sample preparation is well documented. Automated SPE sample preparation of THCCOOH in urine, although potentially advantageous, is to our knowledge poorly investigated. The objective of the present study was to develop and validate an automated SPE sample-preparation step using ASPEC XL suited for GC-MS confirmation analysis of THCCOOH in urine drug control. The recoveries showed that it was not possible to transfer the protocol for the manual SPE procedure with the vacuum manifold to the ASPEC XL without loss of recovery. Making the sample more lipophilic by adding 1 mL 2-propanol after hydrolysis to the urine sample in order to overcome the problem of surface adsorption of THCCOOH led to an extraction efficiency (77%) comparable to that reached with the vacuum manifold (84%). The reproducibility of the automated SPE procedure was better (coefficient of variation 5%) than that of the manual procedure (coefficient of variation 12%). The limit of detection was 1 ng/mL, and the limit of quantitation was 4 ng/mL. Precision at the 12.5-ng/mL level was as follows: mean, 12.4 and coefficient of variation, 3.0%. Potential carryover was evaluated, but a carryover effect could not be detected. It was concluded that the proposed method is suited for GC-MS confirmation urinalysis of THCCOOH for prisons and detoxification centers.

Dronabinol↗
PubMedDate not supplied

Automated solid-phase extraction and quantitative analysis of 14 phthalate metabolites in human serum using isotope dilution-high-performance liquid chromatography-tandem mass spectrometry.

Phthalates are industrial chemicals with many commercial applications. Because of their common usage, the general population is exposed to phthalates. A sensitive and selective analytical method is necessary to accurately determine the phthalate levels in serum. We improved our previously developed analytical method to measure nine phthalate metabolites in human serum by automating the solid-phase extraction (SPE) procedure and by including five additional phthalate metabolites: phthalic acid; mono-isobutyl phthalate, a metabolite of di-isobutyl phthalate; mono-(3-carboxypropyl) phthalate, a major oxidative metabolite of di-n-octyl phthalate; and mono-(2-ethyl-5-oxohexyl) phthalate and mono-(2-ethyl-5-hydroxyhexyl) phthalate, two oxidative metabolites of di-(2-ethylhexyl) phthalate. Automation of the SPE eliminated the human variation associated with the manual SPE, thus improving the reproducibility of the measurements. Additional wash steps during SPE produced cleaner extracts and resulted in higher recoveries (80-99%) than the manual SPE method. Furthermore, the automated SPE method allowed for the unattended extraction of samples, with a concomitant increase in sample throughput compared to the manual SPE method. The method is accurate, precise, and sensitive, with limits of detection in the low nanogram-per-milliliter range.

Carbon Isotopes↗
PubMed1989

Specific-primer-directed DNA sequencing using automated fluorescence detection.

Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approach in conjunction with automated fluorescence detection on a commercial instrument (ABI 370A DNA sequencer). This includes procedures for the rapid chemical synthesis and purification of labeled primers, the design of primer sequences that are compatible with the commercial analysis software, and automated DNA sequence analysis using such primers. A set of four fluorophore-labeled primers can be reliably synthesized in a twenty-four hour period, and greater than 300 nucleotides of analyzed new sequence obtained using this set in an additional twenty-four hours. Scale-up of these procedures to take advantage of the full capabilities of the sequencer is, at present, too slow and costly to be suitable for routine sequencing, and therefore the use of specific-primers is best suited to the closure of gaps in extended sequence produced using random cloning and sequencing strategies.

Autoanalysis↗
PubMed2004

PhyloGenie: automated phylome generation and analysis.

Phylogenetic reconstruction is the method of choice to determine the homologous relationships between sequences. Difficulties in producing high-quality alignments, which are the basis of good trees, and in automating the analysis of trees have unfortunately limited the use of phylogenetic reconstruction methods to individual genes or gene families. Due to the large number of sequences involved, phylogenetic analyses of proteomes preclude manual steps and therefore require a high degree of automation in sequence selection, alignment, phylogenetic inference and analysis of the resulting set of trees. We present a set of programs that automates the steps from seed sequence to phylogeny and a utility to extract all phylogenies that match specific topological constraints from a database of trees. Two example applications that show the type of questions that can be answered by phylome analysis are provided. The generation and analysis of the Thermoplasma acidophilum phylome with regard to lateral gene transfer between Thermoplasmata and Sulfolobus, showed best BLAST hits to be far less reliable indicators of lateral transfer than the corresponding protein phylogenies. The generation and analysis of the Danio rerio phylome provided more than twice as many proteins as described previously, supporting the hypothesis of an additional round of genome duplication in the actinopterygian lineage.

Amino Acid Sequence↗
PubMed2005

Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist.

We have developed an automated SELEX (Systematic Evolution of Ligands by EXponential Enrichment) process that allows the execution of in vitro selection cycles without any direct manual intervention steps. The automated selection protocol is designed to provide for high flexibility and versatility in terms of choice of buffers and reagents as well as stringency of selection conditions. Employing the automated SELEX process, we have identified RNA aptamers to the mirror-image configuration (d-peptide) of substance P. The peptide substance P belongs to the tachykinin family and exerts various biologically important functions, such as peripheral vasodilation, smooth muscle contraction and pain transmission. The aptamer that was identified most frequently was truncated to the 44mer SUP-A-004. The mirror-image configuration of SUP-A-004, the so-called Spiegelmer, has been shown to bind to naturally occurring l-substance P displaying a K(d) of 40 nM and to inhibit (IC50 of 45 nM) l-substance P-mediated Ca2+ release in a cell culture assay.

Aptamers, Nucleotide↗
PubMed1997

The role of automated peritoneal dialysis (APD) in an integrated dialysis programme.

While there is no doubt that renal transplantation would be the preferred option for all patients suffering from end stage renal disease, this is sadly an unrealistic aim for many patients in the UK. There is a shortage of donor organs and, with the increasing percentage of elderly patients on dialysis, under 50% of all dialysis patients are on the national transplant waiting list. Of the 12,000 or so patients on dialysis in the UK, approximately half receive haemodialysis and half peritoneal dialysis. In the last few years, there has been a resurgence of interest in automated peritoneal dialysis and just under 20% of the peritoneal dialysis population currently receive this mode of therapy. The advantages of automated peritoneal dialysis include the capacity for an increased dialysis prescription, increased freedom and quality of life and a decreased risk of peritonitis and intra peritoneal pressure related problems. These advantages may offset the increased cost of automated peritoneal dialysis and long-term patient morbidity and mortality may be diminished by its provision in an integrated dialysis programme.

Adolescent↗
PubMed1991

Predictive value of classical and automated sperm analysis for in-vitro fertilization.

The fertilization rates observed in 122 attempts at in-vitro fertilization were examined in relation to sperm characteristics assessed by visual and automated screening. Using linear regression analysis, a significant correlation was found between the fertilization rate and (i) evaluations in fresh semen sperm concentration, percentages of sperm motility, vitality and normal morphology and velocity, (ii) measurements in swim-up preparations of percentages of sperm motility, vitality and morphology, velocity and amplitude of lateral head displacement. No significant correlation was found between the fertilization rate and any of the parameters studied in 24-h-old swim-up suspensions. Analysis by multiple variable stepwise linear regression showed an optimal correlation (R6 = 0.62) between the observed fertilization rate and theoretical calculation obtained from the following predictive function: fertilization rate = -0.3 + (0.008 x swim-up motility) + (0.004 x normal sperm morphology in fresh semen). Introduction of kinematic characteristics studied by automated screening improved the multiple correlation between the calculated and observed fertilization rate in cases of normal or mildly defective semen. Because of the limited availability of motile spermatozoa, automated analysis could not supersede classical sperm analysis in cases of more severe sperm defects.

Autoanalysis↗
PubMed2000

A second-generation blood substitute (Perfluorodichlorooctane emulsion) generates spurious elevations in platelet counts from automated hematology analyzers.

UNLABELLED: Perfluorocarbon emulsions (PFEs) appear as platelets in automated cell counters, which may affect samples from thrombocytopenic patients (less than 100,000/microL). Therefore, we mixed clinically relevant concentrations of perfluorodichlorooctane (Oxyfluor(R); Hemagen, Inc., St. Louis, MO) in vitro with whole blood samples ranging from 0 to 150,000 platelets/microL and compared a new counter that uses optical platelet recognition (Abbott CellDyn 3200; Santa Clara, CA) with conventional electroimpedance-based counters (Abbott CellDyn 3500 and CellDyn 1700). We found that emulsion particles appear as small-sized platelets either in diluent or in blood. The emulsion results in a reproducible overestimate of the platelet counts, of greater importance as PFE concentration increases, and as the actual platelet count of the blood samples decreases. The new optical technology yields smaller overestimates but, even at low PFE concentrations, gives an unacceptable relative error at platelet counts near the transfusion thresholds recommended by the American Society of Anesthesiologists guidelines for blood component therapy. Unexpected interference in the leukocyte and erythrocyte channels is also reported. Experimental limitations preclude extrapolation of these findings to other automated cell counters, because differences in technology or software may affect their capacity to separate PFE particles from platelets. IMPLICATIONS: Perfluorocarbons are being investigated under conditions in which thrombocytopenia is likely to occur. In this in vitro study, we demonstrate significant overestimates in platelet counts from automated cell counters at clinically relevant perfluorocarbon concentrations in thrombocytopenic blood samples.

Blood Substitutes↗
PubMed1980

Time-weighted averaging for nitrous oxide: an automated method.

An automated method of obtaining a time-weighted average of nitrous oxide levels in an operating room was compared with a standard method. The automated method consisted of electronic integration of the voltage output of a nitrous oxide analyzer using a multimeter-microprocessor. The standard method utilized a bag and pump to collect a room air sample, which was subsequently analyzed with a nitrous oxide analyzer. There was a high degree of correlation (r = 0.99) between the two methods. It is concluded that the automated method is an accurate alternative and offers institutions a simple, cost-effective method of monitoring and documenting results of pollution control programs in anesthetizing locations.

Autoanalysis↗
PubMed1997

Evaluation of an automated photometric fibrinogen assay.

A recently-introduced automated method for the determination of plasma fibrinogen is based on the principle of von Clauss, combined with photometric detection: after addition of thrombin, the coagulation time is determined by measuring the change in absorption at 405 nm. This method was evaluated and compared with the original coagulometric Clauss assay and with the prothrombin time (PT)-derived automated method. The inter-assay coefficient of variation of the Clauss-derived assay was lower (14.1, 3.8 and 4.6%) than the PT-derived assay (16.1, 7.5 and 10.5%, respectively) at all three fibrinogen levels tested (1.2, 4.0 and 7.5 g/l). The correlation between the assays was investigated according to the method of Passing and Bablok and could be described as follows: Clauss-derived = 0.79 (PT-derived) + 0.66; Clauss-derived = 1.12 (Clauss) + 0.143. The interference of heparin (< 1.5 U/ml), haemoglobin (< 30 micromol/l), bilirubin (< 200 micromol/l) and triglycerides (< 5.5 mmol/l) in the Clauss-derived assay was negligible. The effects of fibrinogen degradation products on the Clauss-derived assay were comparable with the effects on the Clauss assay, in contrast to the effects on the PT-derived assay. In conclusion, the Clauss-derived assay is a specific and precise automated method to determine fibrinogen concentrations in plasma, which is not liable to interference from different pathophysiological substances.

Autoanalysis↗
PubMed2000

Comparison of the response of saline tonometry and an automated gas tonometry device to a change in CO2.

OBJECTIVE: To examine the speed of response of saline tonometry and an automated gas tonometry system by using standard tonometry catheters. DESIGN: In vitro validation study. SETTING: Experimental research laboratory. INTERVENTIONS: Tonometry catheters were placed in a test chamber designed to simulate the lumen of a hollow viscus and were exposed to a rapid change in CO2 from 0% to 5% or 10%. Measured CO2 over time was fit to a mathematical model to determine the response time constant (the time to reach 63% of the final value) for each system. MEASUREMENTS AND MAIN RESULTS: Response time to a change in CO2 was significantly faster with the automated gas system than with traditional saline tonometry. The mathematical time constant for a 5% change in CO2 in a gas environment was 2.8 mins (95% confidence interval, 2.6-3.0 mins) for the gas and 6.3 mins (95% confidence interval, 5.8-7.3 mins) for the saline technique. These times were longer for the CO2 change in a liquid environment: The time constant was 4.6 mins (95% confidence interval, 4.5-4.7 mins) for the gas system and 7.8 mins (95% confidence interval, 7.15-8.6 mins) for the saline tonometry. There was a significantly lower final equilibration value for the CO2 measurement with saline tonometry. There was essentially no difference in time constants for each system for a 5% change compared with a 10% CO2 change, except for a slightly faster time constant for the gas tonometry system with a 5% change in the gas environment (5%: 2.8 mins vs. 10%: 3.3 mins). CONCLUSIONS: The automated gas tonometry system has a significantly faster response to a change in CO2 than conventional saline tonometry.

Carbon Dioxide↗
PubMedDate not supplied

Survey of automated noninvasive blood pressure monitors.

Automated noninvasive blood pressure (NIBP) monitors, or automated sphygmomanometers, have been increasingly used both inside and outside clinical environments. An extensive survey of such monitors was carried out over the past five years. This survey covers a broad spectrum of monitors including ambulatory monitors, bedside and transport monitors, stress-test monitors, and monitors that are intended for self-measurement. It includes more than 400 models from suppliers in the United States and many other countries. A review of NIBP measurement methods that have been used in automated NIBP monitors is presented in this paper, along with statistical distributions of their use in the surveyed monitors and a list of the suppliers and monitors.

Blood Pressure Determination↗
PubMedDate not supplied

Gradient correction and classification of CT lung images for the automated quantification of mosaic attenuation pattern.

PURPOSE: The detection of density differences, or "mosaic attenuation pattern," on CT images may be difficult when the regional inhomogeneity of the density of the lung parenchyma is subtle. The purpose of this work was to develop a fully automated method for the reproducible quantification of the underattenuated areas of the lung parenchyma. This technique may be useful in increasing the precision of investigation of structure/function relationships. METHOD: Anatomical segmentation was achieved by a structure-filtering operator based on mathematical morphology. To compensate for the density gradient visible on lung CT scans, a model-based iterative deconvolution filter and an adaptive clustering algorithm were developed. Validation was performed with CT images from a lung phantom, 15 patients with constrictive obliterative bronchiolitis, and 8 normal subjects. RESULTS: The accuracy of the estimate of the density gradient on phantom studies was 93.3%. The automated quantification of the areas of decreased attenuation on scans of constrictive obliterative bronchiolitis was within 8.2% from the average scoring of two experienced observers. CONCLUSION: The proposed technique is fully automated and can accurately correct for density gradient and classify areas of decreased attenuation on lung CT images.

Bronchiolitis Obliterans↗
PubMedDate not supplied

Automated knowledge-guided segmentation of colonic walls for computerized detection of polyps in CT colonography.

PURPOSE: We have developed a novel automated technique for segmenting colonic walls for the application of computer-aided polyp detection in CT colonography. In particular, the technique was designed to minimize the presence of extracolonic components, such as small bowel, in the segmented colon. METHODS: The segmentation technique combines an improved version of our previously reported anatomy-oriented colon segmentation technique with a colon-based analysis step that performs self-adjusting volume-growing within the colonic lumen. Extracolonic components are eliminated by intersecting of the resulting two segmentations, so that the colonic walls remain in the intersection. The technique was evaluated on 88 CT colonography datasets. The colon segmentations were evaluated subjectively by four radiologists, as well as objectively by performance of an automated polyp detection on the segmentation. For comparison, the tests were also performed for the anatomy-oriented colon segmentation technique. RESULTS: On average, the technique covered 98% of the visible colonic walls. Approximately 50% of the extracolonic components remaining in the anatomy-oriented segmentation were removed, but 10-15% of the segmentation still contained extracolonic components. The dataset-based false-positive rate of the automated polyp detection was improved by 10% without compromising the 100% case-based sensitivity, and the case-based false-positive rate was improved by 15% over the previous false-positive rate. CONCLUSIONS: The technique segments practically all of the colonic walls in the region of diagnostic quality with a large reduction in the amount of extracolonic components over our previously used technique. The new segmentation improves the specificity of our computer-aided polyp detection scheme significantly without any degradation in detection sensitivity.

Artificial Intelligence↗
PubMed2000

Comparison of cardiac output measured by two automated methods of CO2 rebreathing.

PURPOSE: The aim of the present study was to investigate the reproducibility of the exponential method of CO2 rebreathing with the use of automated curve fitting and to determine whether this method is superior to the equilibrium method in terms of reproducibility and clinical practicability. METHODS: Repeated measurements of cardiac output were performed using the automated equilibrium and exponential methods. These measurements were compared in 12 healthy male subjects at rest and during incremental exercise tests. RESULTS: Estimated cardiac output was not significantly different between duplicate measurements at rest nor at any level of exercise with either method. At rest the exponential method showed a tendency toward larger variability than the equilibrium method. The exponential method produced significantly higher (P < or = 0.001) estimates at rest (averaging up to 9.8 L x min(-1)) compared with the equilibrium method (averaging up to 6.5 L x min(-1)). Reproducibility improved for both methods with increasing workloads, and a second measurement at rest also seemed more reproducible and valid than the first. During exercise, both methods produced comparable values for cardiac output, and highly significant relations between cardiac output and oxygen uptake were observed for both methods (ranging from r2 = 0.79 to r2 = 0.88, P < or = 0.001). The equilibrium method produced unpleasant side effects more frequently (75% vs 21%, P < or = 0.001) compared with the exponential method and lead more subjects to premature interruption of the exercise test because of the rebreathing maneuver (42% vs 17%, P = 0.058). CONCLUSIONS: Automated curve fitting for the exponential method gave reproducible and valid results during submaximal and maximal exercise but not at rest. The equilibrium method on the other hand interfered with exercise. Therefore, the equilibrium method is recommended at rest and at lower levels of exercise and the exponential method at higher intensities.

Adolescent↗
PubMed1978

Automated perimetry.

The history, theory, and practical application of automated perimetry are discussed. Optometrists are urged to consider increasing the efficiency of their examination procedures by using automated field testing--in particular, automated perimetry.

Humans↗