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At least 811 records · Page 45Linked to original sources
PubMed2006

A rapid, fully automated, molecular-based assay accurately analyzes sentinel lymph nodes for the presence of metastatic breast cancer.

OBJECTIVE: To develop a fully automated, rapid, molecular-based assay that accurately and objectively evaluates sentinel lymph nodes (SLN) from breast cancer patients. SUMMARY BACKGROUND DATA: Intraoperative analysis for the presence of metastatic cancer in SLNs from breast cancer patients lacks sensitivity. Even with immunohistochemical staining (IHC) and time-consuming review, alarming discordance in the interpretation of SLN has been observed. METHOD: A total of 43 potential markers were evaluated for the ability to accurately characterize lymph node specimens from breast cancer patients as compared with complete histologic analysis including IHC. Selected markers then underwent external validation on 90 independent SLN specimens using rapid, multiplex quantitative reverse transcription-polymerase chain reaction (QRT-PCR) assays. Finally, 18 SLNs were analyzed using a completely automated RNA isolation, reverse transcription, and quantitative PCR instrument (GeneXpert). RESULTS: : Following analysis of potential markers, promising markers were evaluated to establish relative level of expression cutoff values that maximized classification accuracy. A validation set of 90 SLNs from breast cancer patients was prospectively characterized using 4 markers individually or in combinations, and the results compared with histologic analysis. A 2-marker assay was found to be 97.8% accurate (94% sensitive, 100% specific) compared with histologic analysis. The fully automated GeneXpert instrument produced comparable and reproducible results in less than 35 minutes. CONCLUSIONS: A rapid, fully automated QRT-PCR assay definitively characterizes breast cancer SLN with accuracy equal to conventional pathology. This approach is superior to intraoperative SLN analysis and can provide standardized, objective results to assist in pathologic diagnosis.

Biomarkers, Tumor↗
PubMed2007

Cost-effectiveness of automated external defibrillators in public places: con.

PURPOSE OF REVIEW: To discuss the clinical effectiveness, public health impact and cost-effectiveness of public access defibrillation. RECENT FINDINGS: High rates of survival from prehospital ventricular fibrillation have been documented in patients treated by first responders using automated external defibrillators. The recent Public Access Defibrillation trial demonstrated a doubling of cardiac arrest survival in community units where volunteers trained in cardiopulmonary resuscitation were additionally equipped with automated external defibrillators. The cost-effectiveness analysis of the Public Access Defibrillation trial has not yet been published, and previous analyses have lacked full data on cost, outcome, or both. Data from many sources indicate that automated external defibrillator placement at sites with an expected rate of one cardiac arrest per defibrillator per 5 years, as recommended by the American Heart Association, addresses only around 1-2% of prehospital arrests, and will have a minimal impact on population survival. SUMMARY: While highly targeted provision of automated external defibrillators in areas of greatest risk, such as casinos and airports, may be cost-effective, it will have little impact at a population level. Provision of more widespread public access defibrillation to sites with lower incidence of cardiac arrest is unlikely to be cost-effective, and may represent poorer value for money than alternative healthcare interventions in coronary artery disease.

Cost-Benefit Analysis↗
PubMed2004

Automated species identification: why not?

Where possible, automation has been a common response of humankind to many activities that have to be repeated numerous times. The routine identification of specimens of previously described species has many of the characteristics of other activities that have been automated, and poses a major constraint on studies in many areas of both pure and applied biology. In this paper, we consider some of the reasons why automated species identification has not become widely employed, and whether it is a realistic option, addressing the notions that it is too difficult, too threatening, too different or too costly. Although recognizing that there are some very real technical obstacles yet to be overcome, we argue that progress in the development of automated species identification is extremely encouraging that such an approach has the potential to make a valuable contribution to reducing the burden of routine identifications. Vision and enterprise are perhaps more limiting at present than practical constraints on what might possibly be achieved.

Classification↗
PubMed2002

Artificial neural networks for automation of Rutherford backscattering spectroscopy experiments and data analysis.

We present an algorithm based on artificial neural networks able to determine optimized experimental conditions for Rutherford backscattering measurements of Ge-implanted Si. The algorithm can be implemented for any other element implanted into a lighter substrate. It is foreseeable that the method developed in this work can be applied to still many other systems. The algorithm presented is a push-button black box, and does not require any human intervention. It is thus suited for automated control of an experimental setup, given an interface to the relevant hardware. Once the experimental conditions are optimized, the algorithm analyzes the final data obtained, and determines the desired parameters. The method is thus also suited for automated analysis of the data. The algorithm presented can be easily extended to other ion beam analysis techniques. Finally, it is suggested how the artificial neural networks required for automated control and analysis of experiments could be automatically generated. This would be suited for automated generation of the required computer code. Thus could RBS be done without experimentalists, data analysts, or programmers, with only technicians to keep the machines running.

Journal Article↗
PubMed2006

Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

The impetus for the recent development and emergence of automated function prediction methods is an exponentially growing flood of new experimental data, the interpretation of which is hindered by a shortage of reliable annotations for proteins that lack experimental characterization or significant homologs in current databases. Here we introduce PFP, an automated function prediction server that provides the most probable annotations for a query sequence in each of the three branches of the Gene Ontology: biological process, molecular function, and cellular component. Rather than utilizing precise pattern matching to identify functional motifs in the sequences and structures of these proteins, we designed PFP to increase the coverage of function annotation by lowering resolution of predictions when a detailed function is not predictable. To do this we extend a traditional PSI-BLAST search by extracting and scoring annotations (GO terms) individually, including annotations from distantly related sequences, and applying a novel data mining tool, the Function Association Matrix, to score strongly associated pairs of annotations. We show that PFP can correctly assign function using only weakly similar sequences with a significantly better accuracy and coverage than a standard PSI-BLAST search, improving it more than fivefold. The most descriptive annotations predicted by PFP (GO depth > or = 8) can identify a significant subgraph in the GO with > 60% accuracy and approximately 100% coverage for our benchmark set. We also provide examples of the superb performance of PFP in an assessment of automated function prediction servers at the Automated Function Prediction Special Interest Group meeting at ISMB 2005 (AFP-SIG '05).

Algorithms↗
PubMed1993

Laboratory test of an automated cell analysis system for cervical screening.

An automated cell analysis system (Autoplan-MIAC) for the early detection of precancerous lesions of the cervix was tested under semi-routine conditions in a clinical cytology laboratory. A set of 1500 specimens, highly enriched with abnormal cases, was analysed. Cervical scrapings were collected in suspension and processed by cytocentrifugation for microscopy. Two slides were prepared from each sample: one for staining according to Papanicolaou for the visual reference diagnosis and one for Feulgen staining for automated analysis. The specimens were evaluated in two ways: the first one, which is referred to as the automated machine classification system (AMC), classifies the specimens according to the number and ratio of selected objects (alarms) and is a fully automated system. The second system classifies the specimens after visual evaluation of the stored alarms as they are displayed on a TV monitor, and is designated the interactive machine classification system (IMC). The AMC results showed a false positive rate of 16.5% when the cut-off threshold was selected so that all 117 positively diagnosed specimens were classified 'positive' by the system. In that case 87.4% of the CIN I and 96.9% of the CIN II cases were AMC-positive. The IMC results showed a false positive rate of 2.5%, when 86.3% of the CIN I cases, 96.9% of the CIN II cases and all CIN III and invasive carcinoma cases were positively classified.

Cervix Uteri↗
PubMed1991

Comparison of measurements of human sperm motility characteristics by the automated CellSoft system and time-exposure photomicrography.

Human sperm motility characteristics in 28 semen samples with sperm concentrations less than 40 x 10(6) ml-1, as determined by the World Health Organization manual analysis (WHO, 1987), were measured by the automated CellSoft semen analyser (Cryo Resources Ltd, New York, NY, USA) using different system parameter settings (Mortimer & Mortimer, 1988a). The results were compared with those obtained by time-exposure photomicrographic (TEP) analysis. It was found that the settings of the minimum video frame rate and the threshold velocity used to distinguish motile from immotile sperm by the automated CellSoft system had a significant influence on measurements of percentage motility but not on linear velocity. At the five different parameter settings used in the present study, the automated CellSoft system gave significantly lower mean values for percentage motility in comparison with the WHO manual and TEP analyses. Measurements for linear velocity between the automated CellSoft system and TEP analyses were found not to be significantly different in these defined semen samples.

Humans↗
PubMed2006

Characterization of the brewery spoilage bacterium Obesumbacterium proteus by automated ribotyping and development of PCR methods for its biotype 1.

AIMS: To study the ability of automated ribotyping to characterize Obesumbacterium proteus and Hafnia alvei, to design primers and to evaluate standard end-point and real-time PCR for the detection of O. proteus biotype 1 in beer and in brewers's yeast-containing samples. METHODS AND RESULTS: Automated ribotyping was carried out using the standard method with EcoRI and PvuII. The digestions with both enzymes clearly differentiated O. proteus biotypes 1 and 2 and H. alvei. PCR primers were designed according to the 16S rRNA gene sequence of the O. proteus type strain. Two primer sets (Obs137-Obs558 and Obs137-Obs617) detected O. proteus biotype 1 and H. alvei but not O. proteus biotype 2 or other tested beer spoilage bacteria (40 species) in the end-point and real-time PCR, indicating their high specificity. The detection limit for O. proteus was 160-1600 CFU 100 ml(-1) beer in the end-point PCR reactions and < or =160 CFU 100 ml(-1) beer in the real-time PCR reactions. More cells (from 16 to 3200) were needed for detection in the presence of brewer's yeast cells. CONCLUSIONS: Automated ribotyping is a useful tool to characterize and identify O. proteus and H. alvei isolates. The designed primers are suitable for the rapid detection of O. proteus biotype 1 and H. alvei in brewery samples by PCR. SIGNIFICANCE AND IMPACT OF THE STUDY: Automated ribotyping and PCR could improve microbiological quality control in breweries by facilitating the detection, identification and tracing of spoilage bacteria.

Beer↗
PubMed1994

Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures.

The use of fully automated data collection methods for electron tomography allows a substantial reduction in beam dose. The goal has been to develop new protocols for data collection defining optimal approaches for maintaining data self-consistency and maximizing the useful resolution of the reconstruction. The effects of irradiation and post-cure microwaving were examined for a variety of embedding media (Epon, Epox, Lowicryl) in order to quantify beam damage with the goal of identifying the most beam stable embedding medium. Surprisingly, the substantial dose reduction made possible by automated data collection did not result in a significant decrease in specimen shrinkage even for samples stabilized by pre-irradiation. We believe that the accelerated shrinkage is a direct consequence of the stroboscopic illumination patterns inherent to automated data collection. Furthermore neither the choice of embedding resin nor microwave post-curing greatly affected shrinkage. Finally, cryogenic data collection was investigated as a means to minimize the effects of secondary radiation damage. Minimal pre-irradiation coupled with low-temperature automated data collection greatly reduces shrinkage and should result in high-quality data for three-dimensional reconstructions.

Cryopreservation↗
PubMed1985

Automated thermatic condensation of gutta-percha root fillings in teeth with open (immature) apices.

Forty upper human premolar teeth with open (immature) apices were root filled by one of three methods, namely lateral condensation with sealer, automated thermatic condensation with sealer, and automated thermatic condensation without sealer. The completed root fillings were then assessed for apical defects, apical extrusions, radiographic voids, apical seal and surface adaptation. The majority of the results indicate that the automated thermatic technique without sealer produces marginally better root fillings in teeth with open apices than the other two methods. However, it is impossible to say whether this would confer any clinical advantage on the technique. The authors recommend that clinicians who wish to use the automated thermatic technique for condensing gutta-percha become highly proficient before its use on patients.

Bicuspid↗
PubMedDate not supplied

The accuracy of sperm concentration determination by the automated CellSoft semen analyzer before and after discontinuous Percoll gradient centrifugation.

The automated CellSoft semen analyzer identifies human spermatozoa on the basis of user-defined values for cell size and luminosity. Previous studies have shown that the non-sperm particles usually present in seminal plasma would interfere with the computerized determination of sperm concentration by the CellSoft system. Therefore, an effective method to separate the sperm from non-sperm particles would be desirable to obtain accurate determination of sperm concentration. In the present study, sperm concentrations in 72 semen samples before and after discontinuous Percoll gradient centrifugation were determined by the automated CellSoft system and the results compared with those obtained with the routine procedure using the haemocytomer according to the World Health Organization laboratory manual. The computerized measurement caused a significant overestimation when the sperm concentration in semen was less than 80 x 10(6)/ml. Processing of human semen sample by the simple two-layer discontinuous Percoll gradient centrifugation removed the majority of non-sperm particles and the overestimation by the automated CellSoft system became significant only when the sperm concentration in the final Percoll sperm preparation was less than 10 x 10(6)/ml. These findings indicate that the automated CellSoft semen analyzer has to be improved to allow for the correction of non-sperm particles in seminal plasma or processed sperm samples before it can be used to provide sufficiently accurate sperm concentration results for routine laboratory service or research purposes.

Cell Separation↗
PubMed1991

An automated method for determination of total bile acid concentration in canine serum.

The purpose of the study was to evaluate an automated modification of the enzymatic method, Enzabile (Nycomed) for the determination of total bile acid concentration in canine serum. Evaluation of the automated method was accomplished by measuring the within-run and between-day variation, by assessment of accuracy, and by assessment of detectability of the method. The automated method was found to correlate well with the original Enzabile (Nycomed) method. The resulting regression equation was found to be: y = 5.81 + 1.09 x, r = 0.99. Also, the variations and the detection limit of the automated method were smaller, respectively lower, compared to the reference method.

Animals↗
PubMed2006

Semi-automated detection of the foveal avascular zone in fluorescein angiograms in diabetes mellitus.

BACKGROUND: The foveal avascular zone (FAZ) is known to enlarge in diabetic retinopathy. In a preliminary study, the authors applied a region growing algorithm to fluorescein angiograms to detect the FAZ in a semi-automated fashion. METHODS: The FAZ in 44 fluorescein angiograms of 44 eyes of 41 patients with diabetic retinopathy underwent manual outlining, then analysis with the region growing function of the ENVI image analysis software. The same algorithm was applied after median filtering of the images. RESULTS: Correlation coefficient was 0.98 between the first two authors, 0.89 between the first author and semi-automated detection before median filtering and 0.91 after median filtering. Average surface areas however, were smaller with semi-automated detection (1951 pixels before and 2226 pixels after median filtering) than with manual detection (3032 pixels). CONCLUSIONS: Semi-automated detection of the FAZ is possible, but refinements need to be made in angiogram quality and/or image pretreatment to improve results.

Algorithms↗
PubMed2004

Diabetic retinopathy screening using digital non-mydriatic fundus photography and automated image analysis.

PURPOSE: To investigate the use of automated image analysis for the detection of diabetic retinopathy (DR) in fundus photographs captured with and without pharmacological pupil dilation using a digital non-mydriatic camera. METHODS: A total of 83 patients (165 eyes) with type 1 or type 2 diabetes, representing the full spectrum of DR, were photographed with and without pharmacological pupil dilation using a digital non-mydriatic camera. Two sets of five overlapping, non-stereoscopic, 45-degree field images of each eye were obtained. All images were graded in a masked fashion by two readers according to ETDRS standards and disagreements were settled by an independent adjudicator. Automated detection of red lesions as well as image quality control was made: detection of a single red lesion or insufficient image quality was categorized as possible DR. RESULTS: At patient level, the automated red lesion detection and image quality control combined demonstrated a sensitivity of 89.9% and specificity of 85.7% in detecting DR when used on images captured without pupil dilation, and a sensitivity of 97.0% and specificity of 75.0% when used on images captured with pupil dilation. For moderate non-proliferative or more severe DR the sensitivity was 100% for images captured both with and without pupil dilation. CONCLUSION: Our results demonstrate that the described automated image analysis system, which detects the presence or absence of DR, can be used as a first-step screening tool in DR screening with considerable effectiveness.

Area Under Curve↗
PubMed2004

Automated apparatus for quantitation of social approach behaviors in mice.

Mouse models of social dysfunction, designed to investigate the complex genetics of social behaviors, require an objective methodology for scoring social interactions relevant to human disease symptoms. Here we describe an automated, three chambered apparatus designed to monitor social interaction in the mouse. Time spent in each chamber and the number of entries are scored automatically by a system detecting photocell beam breaks. When tested with the automated equipment, juvenile male C57BL/6J mice spent more time in a chamber containing a stranger mouse than in an empty chamber (sociability), similar to results obtained by the observer scored method. In addition, automated scoring detected a preference to spend more time with an unfamiliar stranger than a more familiar conspecific (preference for social novelty), similar to results obtained by the observer scored method. Sniffing directed at the wire cage containing the stranger mouse correlated significantly with time spent in that chamber, indicating that duration in a chamber represents true social approach behavior. Number of entries between chambers did not correlate with duration of time spent in the chambers; entries instead proved a useful control measure of general activity. The most significant social approach behavior took place in the first five minutes of both the sociability and preference for social novelty tests. Application of these methods to C57BL/6J, DBA/2J and FVB/NJ adult males revealed that all three strains displayed tendencies for sociability and preference for social novelty. To evaluate the importance of the strain of the stranger mouse on sociability and preference for social novelty, C57BL/6J subject mice were tested either with A/J strangers or with C57BL/6J strangers. Sociability and preference for social novelty were similar with both stranger strains. The automated equipment provides an accurate and objective approach to measuring social tendencies in mice. Its use may allow higher-throughput scoring of mouse social behaviors in mouse models of social dysfunction.

Animals↗
PubMedDate not supplied

Automation of performance measures reporting.

This article describes efforts to design and automate a balanced performance indicator report to meet the needs of hospital and physician leaders. Indicator measurement reports provide clinical information but often do not provide other administrative data. An automation team developed business rules, standardized definitions, and developed a Web-based electronic application to report quarterly indicators. The efficiency and effectiveness of the automation project were measured and included report production time, data sources, indicators included, and statistical significance of indicator rates. Significant improvement in efficiency of report preparation and a decrease in resources used were demonstrated through this automation project, although variation existed among clinical services. Generic performance measures reports encompassing clinical and administrative data can improve the consistency and quality of reporting to the medical staff. The process provided insight for expanding the prototype.

Data Collection↗
PubMed2003

Automated detection of lung nodules in CT scans: effect of image reconstruction algorithm.

We have investigated the effect of computed tomography (CT) image reconstruction algorithm on the performance of our automated lung nodule detection method. Commercial CT scanners offer a choice of several algorithms for the reconstruction of projection data into transaxial images. Different algorithms produce images with substantially different properties that are apparent not only quantitatively, but also through visual assessment. During some clinical thoracic CT examinations, patient scans are reconstructed with multiple reconstruction algorithms. Thirty-eight such cases were collected to form two databases: one with patient projection data reconstructed with the "standard" reconstruction algorithm and the other with the same patient projection data reconstructed with the "lung" reconstruction algorithm. The automated nodule detection method was applied to both databases. This method is based on gray-level-thresholding techniques to segment the lung regions from each CT section to create a segmented lung volume. Further gray-level-thresholding techniques are applied within the segmented lung volume to identify a set of lung nodule candidates. Rule-based and linear discriminant classifiers are used to differentiate between lung nodule candidates that correspond to actual nodules and those that correspond to non-nodules. The automated method that was applied to both databases was exactly the same, except that the classifiers were calibrated separately for each database. For comparison, the classifier then was trained on one database and tested independently on the other database. When applied to the databases in this manner, the automated method demonstrated overall a similar level of performance, indicating an encouraging degree of robustness.

Adult↗
PubMed2004

An observer study comparing spot imaging regions selected by radiologists and a computer for an automated stereo spot mammography technique.

We are developing an automated stereo spot mammography technique for improved imaging of suspicious dense regions within digital mammograms. The technique entails the acquisition of a full-field digital mammogram, automated detection of a suspicious dense region within that mammogram by a computer aided detection (CAD) program, and acquisition of a stereo pair of images with automated collimation to the suspicious region. The latter stereo spot image is obtained within seconds of the original full-field mammogram, without releasing the compression paddle. The spot image is viewed on a stereo video display. A critical element of this technique is the automated detection of suspicious regions for spot imaging. We performed an observer study to compare the suspicious regions selected by radiologists with those selected by a CAD program developed at the University of Michigan. True regions of interest (TROIs) were separately determined by one of the radiologists who reviewed the original mammograms, biopsy images, and histology results. We compared the radiologist and computer-selected regions of interest (ROIs) to the TROIs. Both the radiologists and the computer were allowed to select up to 3 regions in each of 200 images (mixture of 100 CC and 100 MLO views). We computed overlap indices (the overlap index is defined as the ratio of the area of intersection to the area of interest) to quantify the agreement between the selected regions in each image. The averages of the largest overlap indices per image for the 5 radiologist-to-computer comparisons were directly related to the average number of regions per image traced by the radiologists (about 50% for 1 region/image, 84% for 2 regions/image and 96% for 3 regions/image). The average of the overlap indices with all of the TROIs was 73% for CAD and 76.8% +/- 10.0% for the radiologists. This study indicates that the CAD determined ROIs could potentially be useful for a screening technique that includes stereo spot mammography imaging.

Biophysical Phenomena↗