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Sample records for automated analysis method

  1. Automated migration analysis based on cell texture: method & reliability

    Directory of Open Access Journals (Sweden)

    Chittenden Thomas W

    2005-03-01

    Full Text Available Abstract Background In this paper, we present and validate a way to measure automatically the extent of cell migration based on automated examination of a series of digital photographs. It was designed specifically to identify the impact of Second Hand Smoke (SHS on endothelial cell migration but has broader applications. The analysis has two stages: (1 preprocessing of image texture, and (2 migration analysis. Results The output is a graphic overlay that indicates the front lines of cell migration superimposed on each original image, with automated reporting of the distance traversed vs. time. Expert preference compares to manual placement of leading edge shows complete equivalence of automated vs. manual leading edge definition for cell migration measurement. Conclusion Our method is indistinguishable from careful manual determinations of cell front lines, with the advantages of full automation, objectivity, and speed.

  2. A Method of Automated Nonparametric Content Analysis for Social Science

    OpenAIRE

    Hopkins, Daniel J.; King, Gary

    2010-01-01

    The increasing availability of digitized text presents enormous opportunities for social scientists. Yet hand coding many blogs, speeches, government records, newspapers, or other sources of unstructured text is infeasible. Although computer scientists have methods for automated content analysis, most are optimized to classify individual documents, whereas social scientists instead want generalizations about the population of documents, such as the proportion in a given category. Unfortunatel...

  3. Applications of Automation Methods for Nonlinear Fracture Test Analysis

    Science.gov (United States)

    Allen, Phillip A.; Wells, Douglas N.

    2013-01-01

    Using automated and standardized computer tools to calculate the pertinent test result values has several advantages such as: 1. allowing high-fidelity solutions to complex nonlinear phenomena that would be impractical to express in written equation form, 2. eliminating errors associated with the interpretation and programing of analysis procedures from the text of test standards, 3. lessening the need for expertise in the areas of solid mechanics, fracture mechanics, numerical methods, and/or finite element modeling, to achieve sound results, 4. and providing one computer tool and/or one set of solutions for all users for a more "standardized" answer. In summary, this approach allows a non-expert with rudimentary training to get the best practical solution based on the latest understanding with minimum difficulty.Other existing ASTM standards that cover complicated phenomena use standard computer programs: 1. ASTM C1340/C1340M-10- Standard Practice for Estimation of Heat Gain or Loss Through Ceilings Under Attics Containing Radiant Barriers by Use of a Computer Program 2. ASTM F 2815 - Standard Practice for Chemical Permeation through Protective Clothing Materials: Testing Data Analysis by Use of a Computer Program 3. ASTM E2807 - Standard Specification for 3D Imaging Data Exchange, Version 1.0 The verification, validation, and round-robin processes required of a computer tool closely parallel the methods that are used to ensure the solution validity for equations included in test standard. The use of automated analysis tools allows the creation and practical implementation of advanced fracture mechanics test standards that capture the physics of a nonlinear fracture mechanics problem without adding undue burden or expense to the user. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

  4. A novel automated image analysis method for accurate adipocyte quantification

    OpenAIRE

    Osman, Osman S.; Selway, Joanne L; Kępczyńska, Małgorzata A; Stocker, Claire J.; O’Dowd, Jacqueline F; Cawthorne, Michael A.; Arch, Jonathan RS; Jassim, Sabah; Langlands, Kenneth

    2013-01-01

    Increased adipocyte size and number are associated with many of the adverse effects observed in metabolic disease states. While methods to quantify such changes in the adipocyte are of scientific and clinical interest, manual methods to determine adipocyte size are both laborious and intractable to large scale investigations. Moreover, existing computational methods are not fully automated. We, therefore, developed a novel automatic method to provide accurate measurements of the cross-section...

  5. Methods of automated cell analysis and their application in radiation biology

    International Nuclear Information System (INIS)

    The present review is concerned with the methods of automated analysis of biological microobjects and covers two groups into which all the systems of automated analysis can be divided-systems of flow ( flow cytometry) and scanning (image analysis systems) type. Particular emphasis has been placed on their use in radiobiological studies, namely, in the micronucleus test, a cytogenetic assay for monitoring the clastogenic action of ionizing radiation commonly used at present. Examples of suing methods described and actual setups in other biomedical researches are given. Analysis of advantages and disadvantages of the methods of automated cell analysis enables to choose more thoroughly between the systems of flow and scanning type to use them in particular research

  6. Engineering Mathematical Analysis Method for Productivity Rate in Linear Arrangement Serial Structure Automated Flow Assembly Line

    Directory of Open Access Journals (Sweden)

    Tan Chan Sin

    2015-01-01

    Full Text Available Productivity rate (Q or production rate is one of the important indicator criteria for industrial engineer to improve the system and finish good output in production or assembly line. Mathematical and statistical analysis method is required to be applied for productivity rate in industry visual overviews of the failure factors and further improvement within the production line especially for automated flow line since it is complicated. Mathematical model of productivity rate in linear arrangement serial structure automated flow line with different failure rate and bottleneck machining time parameters becomes the basic model for this productivity analysis. This paper presents the engineering mathematical analysis method which is applied in an automotive company which possesses automated flow assembly line in final assembly line to produce motorcycle in Malaysia. DCAS engineering and mathematical analysis method that consists of four stages known as data collection, calculation and comparison, analysis, and sustainable improvement is used to analyze productivity in automated flow assembly line based on particular mathematical model. Variety of failure rate that causes loss of productivity and bottleneck machining time is shown specifically in mathematic figure and presents the sustainable solution for productivity improvement for this final assembly automated flow line.

  7. Tool for automated method design in activation analysis

    International Nuclear Information System (INIS)

    A computational approach to the optimization of the adjustable parameters of nuclear activation analysis has been developed for use in comprehensive method design calculations. An estimate of sample composition is used to predict the gamma-ray spectra to be expected for given sets of values of experimental parameters. These spectra are used to evaluate responses such as detection limits and measurement precision for application to optimization by the simplex method. This technique has been successfully implemented for the simultaneous determination of sample size and irradiation, decay and counting times by the optimization of either detection limit or precision. Both single-element and multielement determinations can be designed with the aid of these calculations. The combination of advance prediction and simplex optimization is both flexible and efficient and produces numerical results suitable for use in further computations

  8. An optimized method for automated analysis of algal pigments by HPLC

    NARCIS (Netherlands)

    van Leeuwe, M. A.; Villerius, L. A.; Roggeveld, J.; Visser, R. J. W.; Stefels, J.

    2006-01-01

    A recent development in algal pigment analysis by high-performance liquid chromatography (HPLC) is the application of automation. An optimization of a complete sampling and analysis protocol applied specifically in automation has not yet been performed. In this paper we show that automation can only

  9. Comparison of semi-automated image analysis and manual methods for tissue quantification in pancreatic carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Sims, A.J. [Regional Medical Physics Department, Freeman Hospital, Newcastle upon Tyne (United Kingdom)]. E-mail: a.j.sims@newcastle.ac.uk; Murray, A. [Regional Medical Physics Department, Freeman Hospital, Newcastle upon Tyne (United Kingdom); Bennett, M.K. [Department of Histopathology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne (United Kingdom)

    2002-04-21

    Objective measurements of tissue area during histological examination of carcinoma can yield valuable prognostic information. However, such measurements are not made routinely because the current manual approach is time consuming and subject to large statistical sampling error. In this paper, a semi-automated image analysis method for measuring tissue area in histological samples is applied to the measurement of stromal tissue, cell cytoplasm and lumen in samples of pancreatic carcinoma and compared with the standard manual point counting method. Histological samples from 26 cases of pancreatic carcinoma were stained using the sirius red, light-green method. Images from each sample were captured using two magnifications. Image segmentation based on colour cluster analysis was used to subdivide each image into representative colours which were classified manually into one of three tissue components. Area measurements made using this technique were compared to corresponding manual measurements and used to establish the comparative accuracy of the semi-automated image analysis technique, with a quality assurance study to measure the repeatability of the new technique. For both magnifications and for each tissue component, the quality assurance study showed that the semi-automated image analysis algorithm had better repeatability than its manual equivalent. No significant bias was detected between the measurement techniques for any of the comparisons made using the 26 cases of pancreatic carcinoma. The ratio of manual to semi-automatic repeatability errors varied from 2.0 to 3.6. Point counting would need to be increased to be between 400 and 1400 points to achieve the same repeatability as for the semi-automated technique. The results demonstrate that semi-automated image analysis is suitable for measuring tissue fractions in histological samples prepared with coloured stains and is a practical alternative to manual point counting. (author)

  10. Comparison of semi-automated image analysis and manual methods for tissue quantification in pancreatic carcinoma

    International Nuclear Information System (INIS)

    Objective measurements of tissue area during histological examination of carcinoma can yield valuable prognostic information. However, such measurements are not made routinely because the current manual approach is time consuming and subject to large statistical sampling error. In this paper, a semi-automated image analysis method for measuring tissue area in histological samples is applied to the measurement of stromal tissue, cell cytoplasm and lumen in samples of pancreatic carcinoma and compared with the standard manual point counting method. Histological samples from 26 cases of pancreatic carcinoma were stained using the sirius red, light-green method. Images from each sample were captured using two magnifications. Image segmentation based on colour cluster analysis was used to subdivide each image into representative colours which were classified manually into one of three tissue components. Area measurements made using this technique were compared to corresponding manual measurements and used to establish the comparative accuracy of the semi-automated image analysis technique, with a quality assurance study to measure the repeatability of the new technique. For both magnifications and for each tissue component, the quality assurance study showed that the semi-automated image analysis algorithm had better repeatability than its manual equivalent. No significant bias was detected between the measurement techniques for any of the comparisons made using the 26 cases of pancreatic carcinoma. The ratio of manual to semi-automatic repeatability errors varied from 2.0 to 3.6. Point counting would need to be increased to be between 400 and 1400 points to achieve the same repeatability as for the semi-automated technique. The results demonstrate that semi-automated image analysis is suitable for measuring tissue fractions in histological samples prepared with coloured stains and is a practical alternative to manual point counting. (author)

  11. Automated fine structure image analysis method for discrimination of diabetic retinopathy stage using conjunctival microvasculature images

    Science.gov (United States)

    Khansari, Maziyar M; O’Neill, William; Penn, Richard; Chau, Felix; Blair, Norman P; Shahidi, Mahnaz

    2016-01-01

    The conjunctiva is a densely vascularized mucus membrane covering the sclera of the eye with a unique advantage of accessibility for direct visualization and non-invasive imaging. The purpose of this study is to apply an automated quantitative method for discrimination of different stages of diabetic retinopathy (DR) using conjunctival microvasculature images. Fine structural analysis of conjunctival microvasculature images was performed by ordinary least square regression and Fisher linear discriminant analysis. Conjunctival images between groups of non-diabetic and diabetic subjects at different stages of DR were discriminated. The automated method’s discriminate rates were higher than those determined by human observers. The method allowed sensitive and rapid discrimination by assessment of conjunctival microvasculature images and can be potentially useful for DR screening and monitoring. PMID:27446692

  12. A new web-based method for automated analysis of muscle histology

    Directory of Open Access Journals (Sweden)

    Pertl Cordula

    2013-01-01

    Full Text Available Abstract Background Duchenne Muscular Dystrophy is an inherited degenerative neuromuscular disease characterised by rapidly progressive muscle weakness. Currently, curative treatment is not available. Approaches for new treatments that improve muscle strength and quality of life depend on preclinical testing in animal models. The mdx mouse model is the most frequently used animal model for preclinical studies in muscular dystrophy research. Standardised pathology-relevant parameters of dystrophic muscle in mdx mice for histological analysis have been developed in international, collaborative efforts, but automation has not been accessible to most research groups. A standardised and mainly automated quantitative assessment of histopathological parameters in the mdx mouse model is desirable to allow an objective comparison between laboratories. Methods Immunological and histochemical reactions were used to obtain a double staining for fast and slow myosin. Additionally, fluorescence staining of the myofibre membranes allows defining the minimal Feret’s diameter. The staining of myonuclei with the fluorescence dye bisbenzimide H was utilised to identify nuclei located internally within myofibres. Relevant structures were extracted from the image as single objects and assigned to different object classes using web-based image analysis (MyoScan. Quantitative and morphometric data were analysed, e.g. the number of nuclei per fibre and minimal Feret’s diameter in 6 month old wild-type C57BL/10 mice and mdx mice. Results In the current version of the module “MyoScan”, essential parameters for histologic analysis of muscle sections were implemented including the minimal Feret’s diameter of the myofibres and the automated calculation of the percentage of internally nucleated myofibres. Morphometric data obtained in the present study were in good agreement with previously reported data in the literature and with data obtained from manual

  13. A method for the automated detection phishing websites through both site characteristics and image analysis

    Science.gov (United States)

    White, Joshua S.; Matthews, Jeanna N.; Stacy, John L.

    2012-06-01

    Phishing website analysis is largely still a time-consuming manual process of discovering potential phishing sites, verifying if suspicious sites truly are malicious spoofs and if so, distributing their URLs to the appropriate blacklisting services. Attackers increasingly use sophisticated systems for bringing phishing sites up and down rapidly at new locations, making automated response essential. In this paper, we present a method for rapid, automated detection and analysis of phishing websites. Our method relies on near real-time gathering and analysis of URLs posted on social media sites. We fetch the pages pointed to by each URL and characterize each page with a set of easily computed values such as number of images and links. We also capture a screen-shot of the rendered page image, compute a hash of the image and use the Hamming distance between these image hashes as a form of visual comparison. We provide initial results demonstrate the feasibility of our techniques by comparing legitimate sites to known fraudulent versions from Phishtank.com, by actively introducing a series of minor changes to a phishing toolkit captured in a local honeypot and by performing some initial analysis on a set of over 2.8 million URLs posted to Twitter over a 4 days in August 2011. We discuss the issues encountered during our testing such as resolvability and legitimacy of URL's posted on Twitter, the data sets used, the characteristics of the phishing sites we discovered, and our plans for future work.

  14. Automated Nanofiber Diameter Measurement in SEM Images Using a Robust Image Analysis Method

    Directory of Open Access Journals (Sweden)

    Ertan Öznergiz

    2014-01-01

    Full Text Available Due to the high surface area, porosity, and rigidity, applications of nanofibers and nanosurfaces have developed in recent years. Nanofibers and nanosurfaces are typically produced by electrospinning method. In the production process, determination of average fiber diameter is crucial for quality assessment. Average fiber diameter is determined by manually measuring the diameters of randomly selected fibers on scanning electron microscopy (SEM images. However, as the number of the images increases, manual fiber diameter determination becomes a tedious and time consuming task as well as being sensitive to human errors. Therefore, an automated fiber diameter measurement system is desired. In the literature, this task is achieved by using image analysis algorithms. Typically, these methods first isolate each fiber in the image and measure the diameter of each isolated fiber. Fiber isolation is an error-prone process. In this study, automated calculation of nanofiber diameter is achieved without fiber isolation using image processing and analysis algorithms. Performance of the proposed method was tested on real data. The effectiveness of the proposed method is shown by comparing automatically and manually measured nanofiber diameter values.

  15. Selection of Filtration Methods in the Analysis of Motion of Automated Guided Vehicle

    Science.gov (United States)

    Magdalena, Dobrzańska; Paweł, Dobrzański; Mirosław, Śmieszek; Paweł, Pawlus

    2016-08-01

    In this article the issues related to mapping the route and error correction in automated guided vehicle (AGV) movement have been discussed. The nature and size of disruption have been determined using the registered runs in experimental studies. On the basis of the analysis a number of numerical runs have been generated, which mapped possible to obtain runs in a real movement of the vehicle. The obtained data set has been used for further research. The aim of this paper was to test the selected methods of digital filtering on the same data set and determine their effectiveness. The results of simulation studies have been presented in the article. The effectiveness of various methods has been determined and on this basis the conclusions have been drawn.

  16. A Fully Automated and Robust Method to Incorporate Stamping Data in Crash, NVH and Durability Analysis

    Science.gov (United States)

    Palaniswamy, Hariharasudhan; Kanthadai, Narayan; Roy, Subir; Beauchesne, Erwan

    2011-08-01

    Crash, NVH (Noise, Vibration, Harshness), and durability analysis are commonly deployed in structural CAE analysis for mechanical design of components especially in the automotive industry. Components manufactured by stamping constitute a major portion of the automotive structure. In CAE analysis they are modeled at a nominal state with uniform thickness and no residual stresses and strains. However, in reality the stamped components have non-uniformly distributed thickness and residual stresses and strains resulting from stamping. It is essential to consider the stamping information in CAE analysis to accurately model the behavior of the sheet metal structures under different loading conditions. Especially with the current emphasis on weight reduction by replacing conventional steels with aluminum and advanced high strength steels it is imperative to avoid over design. Considering this growing need in industry, a highly automated and robust method has been integrated within Altair Hyperworks® to initialize sheet metal components in CAE models with stamping data. This paper demonstrates this new feature and the influence of stamping data for a full car frontal crash analysis.

  17. Analysis of Various Automated Structural Computing Methods Inpatient with Early Traumatic Brain Injury

    Directory of Open Access Journals (Sweden)

    Neeraj Upadhyay

    2015-02-01

    Full Text Available Aim: To assess Surface Based Morphometry (SBM and Voxel Based Morphometry (VBM, the automated computation methods to demonstrate volume and thickness changes in brain among early Traumatic Brain Injury (TBI and their correlation with cognitive test scores. Methods: 22 mild to moderate TBI patients and 20 age, gender matched healthy individuals were recruited (mean ± SD, age range: 27.7 ± 6.5 years. MRI scans were acquired in the Siemens 3T Magnetom Skyra Scanner. TheT1-weighted magnetization preparation rapid acquisition gradient echo (MP-RAGE sequence used for morphometric analysis provided excellent gray-white matter contrast. The structural data was processed using SBM and VBM methods with statistical significance of P<0.05 corrected for multiple comparisons. Results: both methods did not show any significant changes in brain measures after correcting for false discovery rate. However, on correlating neuropsychological score with structural changes, SBM demonstrated significant voxels survived in animal naming and Token Test after correcting for multiple comparisons. No significant change was found while using VBM. Conclusion: The study emphasizes the similarities in the results obtained after using different automatedmethods. Our findings suggest that SBM is more sensitive as compared to VBM in detecting structural changes correlated with Neuropsychological scores during early phase of TBI.

  18. Semi-automated method to measure pneumonia severity in mice through computed tomography (CT) scan analysis

    Science.gov (United States)

    Johri, Ansh; Schimel, Daniel; Noguchi, Audrey; Hsu, Lewis L.

    2010-03-01

    Imaging is a crucial clinical tool for diagnosis and assessment of pneumonia, but quantitative methods are lacking. Micro-computed tomography (micro CT), designed for lab animals, provides opportunities for non-invasive radiographic endpoints for pneumonia studies. HYPOTHESIS: In vivo micro CT scans of mice with early bacterial pneumonia can be scored quantitatively by semiautomated imaging methods, with good reproducibility and correlation with bacterial dose inoculated, pneumonia survival outcome, and radiologists' scores. METHODS: Healthy mice had intratracheal inoculation of E. coli bacteria (n=24) or saline control (n=11). In vivo micro CT scans were performed 24 hours later with microCAT II (Siemens). Two independent radiologists scored the extent of airspace abnormality, on a scale of 0 (normal) to 24 (completely abnormal). Using the Amira 5.2 software (Mercury Computer Systems), a histogram distribution of voxel counts between the Hounsfield range of -510 to 0 was created and analyzed, and a segmentation procedure was devised. RESULTS: A t-test was performed to determine whether there was a significant difference in the mean voxel value of each mouse in the three experimental groups: Saline Survivors, Pneumonia Survivors, and Pneumonia Non-survivors. It was found that the voxel count method was able to statistically tell apart the Saline Survivors from the Pneumonia Survivors, the Saline Survivors from the Pneumonia Non-survivors, but not the Pneumonia Survivors vs. Pneumonia Non-survivors. The segmentation method, however, was successfully able to distinguish the two Pneumonia groups. CONCLUSION: We have pilot-tested an evaluation of early pneumonia in mice using micro CT and a semi-automated method for lung segmentation and scoring system. Statistical analysis indicates that the system is reliable and merits further evaluation.

  19. Knee x-ray image analysis method for automated detection of osteoarthritis.

    Science.gov (United States)

    Shamir, Lior; Ling, Shari M; Scott, William W; Bos, Angelo; Orlov, Nikita; Macura, Tomasz J; Eckley, D Mark; Ferrucci, Luigi; Goldberg, Ilya G

    2009-02-01

    We describe a method for automated detection of radiographic osteoarthritis (OA) in knee X-ray images. The detection is based on the Kellgren-Lawrence (KL) classification grades, which correspond to the different stages of OA severity. The classifier was built using manually classified X-rays, representing the first four KL grades (normal, doubtful, minimal, and moderate). Image analysis is performed by first identifying a set of image content descriptors and image transforms that are informative for the detection of OA in the X-rays and assigning weights to these image features using Fisher scores. Then, a simple weighted nearest neighbor rule is used in order to predict the KL grade to which a given test X-ray sample belongs. The dataset used in the experiment contained 350 X-ray images classified manually by their KL grades. Experimental results show that moderate OA (KL grade 3) and minimal OA (KL grade 2) can be differentiated from normal cases with accuracy of 91.5% and 80.4%, respectively. Doubtful OA (KL grade 1) was detected automatically with a much lower accuracy of 57%. The source code developed and used in this study is available for free download at www.openmicroscopy.org. PMID:19342330

  20. An Automated High-Throughput Metabolic Stability Assay Using an Integrated High-Resolution Accurate Mass Method and Automated Data Analysis Software

    Science.gov (United States)

    Shah, Pranav; Kerns, Edward; Nguyen, Dac-Trung; Obach, R. Scott; Wang, Amy Q.; Zakharov, Alexey; McKew, John; Simeonov, Anton; Hop, Cornelis E. C. A.

    2016-01-01

    Advancement of in silico tools would be enabled by the availability of data for metabolic reaction rates and intrinsic clearance (CLint) of a diverse compound structure data set by specific metabolic enzymes. Our goal is to measure CLint for a large set of compounds with each major human cytochrome P450 (P450) isozyme. To achieve our goal, it is of utmost importance to develop an automated, robust, sensitive, high-throughput metabolic stability assay that can efficiently handle a large volume of compound sets. The substrate depletion method [in vitro half-life (t1/2) method] was chosen to determine CLint. The assay (384-well format) consisted of three parts: 1) a robotic system for incubation and sample cleanup; 2) two different integrated, ultraperformance liquid chromatography/mass spectrometry (UPLC/MS) platforms to determine the percent remaining of parent compound, and 3) an automated data analysis system. The CYP3A4 assay was evaluated using two long t1/2 compounds, carbamazepine and antipyrine (t1/2 > 30 minutes); one moderate t1/2 compound, ketoconazole (10 < t1/2 < 30 minutes); and two short t1/2 compounds, loperamide and buspirone (t½ < 10 minutes). Interday and intraday precision and accuracy of the assay were within acceptable range (∼12%) for the linear range observed. Using this assay, CYP3A4 CLint and t1/2 values for more than 3000 compounds were measured. This high-throughput, automated, and robust assay allows for rapid metabolic stability screening of large compound sets and enables advanced computational modeling for individual human P450 isozymes. PMID:27417180

  1. A revised automated proximity and conformity analysis method to compare predicted and observed spatial boundaries of geologic phenomena

    Science.gov (United States)

    Li, Yingkui; Napieralski, Jacob; Harbor, Jon

    2008-12-01

    Quantitative assessment of the level of agreement between model-predicted and field-observed geologic data is crucial to calibrate and validate numerical landscape models. Application of Geographic Information Systems (GIS) provides an opportunity to integrate model and field data and quantify their levels of correspondence. Napieralski et al. [Comparing predicted and observed spatial boundaries of geologic phenomena: Automated Proximity and Conformity Analysis (APCA) applied to ice sheet reconstructions. Computers and Geosciences 32, 124-134] introduced an Automated Proximity and Conformity Analysis (APCA) method to compare model-predicted and field-observed spatial boundaries and used it to quantify the level of correspondence between predicted ice margins from ice sheet models and field observations from end moraines. However, as originally formulated, APCA involves a relatively large amount of user intervention during the analysis and results in an index to quantify the level of correspondence that lacks direct statistical meaning. Here, we propose a revised APCA approach and a more automated and statistically robust way to quantify the level of correspondence between model predictions and field observations. Specifically, the mean and standard deviation of distances between model and field boundaries are used to quantify proximity and conformity, respectively. An illustration of the revised method comparing modeled ice margins of the Fennoscandian Ice Sheet with observed end moraines of the Last Glacial Maximum shows that this approach provides a more automated and statistically robust means to quantify correspondence than the original APCA. The revised approach can be adopted for a wide range of geoscience issues where comparisons of model-predicted and field-observed spatial boundaries are useful, including mass movement and flood extents.

  2. Automated Motivic Analysis

    DEFF Research Database (Denmark)

    Lartillot, Olivier

    2016-01-01

    Motivic analysis provides very detailed understanding of musical composi- tions, but is also particularly difficult to formalize and systematize. A computational automation of the discovery of motivic patterns cannot be reduced to a mere extraction of all possible sequences of descriptions....... The systematic approach inexorably leads to a proliferation of redundant structures that needs to be addressed properly. Global filtering techniques cause a drastic elimination of interesting structures that damages the quality of the analysis. On the other hand, a selection of closed patterns allows...... for lossless compression. The structural complexity resulting from successive repetitions of patterns can be controlled through a simple modelling of cycles. Generally, motivic patterns cannot always be defined solely as sequences of descriptions in a fixed set of dimensions: throughout the descriptions...

  3. Automated methods of corrosion measurement

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov; Bech-Nielsen, Gregers; Reeve, John Ch;

    1997-01-01

    Measurements of corrosion rates and other parameters connected with corrosion processes are important, first as indicators of the corrosion resistance of metallic materials and second because such measurements are based on general and fundamental physical, chemical, and electrochemical relations....... Hence improvements and innovations in methods applied in corrosion research are likeliy to benefit basic disciplines as well. A method for corrosion measurements can only provide reliable data if the beckground of the method is fully understood. Failure of a method to give correct data indicates a need...... to revise assumptions regarding the basis of the method, which sometimes leads to the discovery of as-yet unnoticed phenomena. The present selection of automated methods for corrosion measurements is not motivated simply by the fact that a certain measurement can be performed automatically. Automation...

  4. Development and application of an automated analysis method for individual cerebral perfusion single photon emission tomography images

    CERN Document Server

    Cluckie, A J

    2001-01-01

    Neurological images may be analysed by performing voxel by voxel comparisons with a group of control subject images. An automated, 3D, voxel-based method has been developed for the analysis of individual single photon emission tomography (SPET) scans. Clusters of voxels are identified that represent regions of abnormal radiopharmaceutical uptake. Morphological operators are applied to reduce noise in the clusters, then quantitative estimates of the size and degree of the radiopharmaceutical uptake abnormalities are derived. Statistical inference has been performed using a Monte Carlo method that has not previously been applied to SPET scans, or for the analysis of individual images. This has been validated for group comparisons of SPET scans and for the analysis of an individual image using comparison with a group. Accurate statistical inference was obtained independent of experimental factors such as degrees of freedom, image smoothing and voxel significance level threshold. The analysis method has been eval...

  5. AUTOMATED TEXT CLUSTERING OF NEWSPAPER AND SCIENTIFIC TEXTS IN BRAZILIAN PORTUGUESE: ANALYSIS AND COMPARISON OF METHODS

    Directory of Open Access Journals (Sweden)

    Alexandre Ribeiro Afonso

    2014-10-01

    Full Text Available This article reports the findings of an empirical study about Automated Text Clustering applied to scientific articles and newspaper texts in Brazilian Portuguese, the objective was to find the most effective computational method able to cluster the input of texts in their original groups. The study covered four experiments, each experiment had four procedures: 1. Corpus Selections (a set of texts is selected for clustering, 2. Word Class Selections (Nouns, Verbs and Adjectives are chosen from each text by using specific algorithms, 3. Filtering Algorithms (a set of terms is selected from the results of the preview stage, a semantic weight is also inserted for each term and an index is generated for each text, 4. Clustering Algorithms (the clustering algorithms Simple K-Means, sIB and EM are applied to the indexes. After those procedures, clustering correctness and clustering time statistical results were collected. The sIB clustering algorithm is the best choice for both scientific and newspaper corpus, under the condition that the sIB clustering algorithm asks for the number of clusters as input before running (for the newspaper corpus, 68.9% correctness in 1 minute and for the scientific corpus, 77.8% correctness in 1 minute. The EM clustering algorithm additionally guesses the number of clusters without user intervention, but its best case is less than 53% correctness. Considering the experiments carried out, the results of human text classification and automated clustering are distant; it was also observed that the clustering correctness results vary according to the number of input texts and their topics.

  6. A Robust and Fully-Automated Chromatographic Method for the Quantitative Purification of Ca and Sr for Isotopic Analysis

    Science.gov (United States)

    Smith, H. B.; Kim, H.; Romaniello, S. J.; Field, P.; Anbar, A. D.

    2014-12-01

    High throughput methods for sample purification are required to effectively exploit new opportunities in the study of non-traditional stable isotopes. Many geochemical isotopic studies would benefit from larger data sets, but these are often impractical with manual drip chromatography techniques, which can be time-consuming and demand the attention of skilled laboratory staff. Here we present a new, fully-automated single-column method suitable for the purification of both Ca and Sr for stable and radiogenic isotopic analysis. The method can accommodate a wide variety of sample types, including carbonates, bones, and teeth; silicate rocks and sediments; fresh and marine waters; and biological samples such as blood and urine. Protocols for these isotopic analyses are being developed for use on the new prepFAST-MCTM system from Elemental Scientific (ESI). The system is highly adaptable and processes up to 24-60 samples per day by reusing a single chromatographic column. Efficient column cleaning between samples and an all Teflon flow path ensures that sample carryover is maintained at the level of background laboratory blanks typical for manual drip chromatography. This method is part of a family of new fully-automated chromatographic methods being developed to address many different isotopic systems including B, Ca, Fe, Cu, Zn, Sr, Cd, Pb, and U. These methods are designed to be rugged and transferrable, and to allow the preparation of large, diverse sample sets via a highly repeatable process with minimal effort.

  7. Automated quantitative analysis for pneumoconiosis

    Science.gov (United States)

    Kondo, Hiroshi; Zhao, Bin; Mino, Masako

    1998-09-01

    Automated quantitative analysis for pneumoconiosis is presented. In this paper Japanese standard radiographs of pneumoconiosis are categorized by measuring the area density and the number density of small rounded opacities. And furthermore the classification of the size and shape of the opacities is made from the measuring of the equivalent radiuses of each opacity. The proposed method includes a bi- level unsharp masking filter with a 1D uniform impulse response in order to eliminate the undesired parts such as the images of blood vessels and ribs in the chest x-ray photo. The fuzzy contrast enhancement is also introduced in this method for easy and exact detection of small rounded opacities. Many simulation examples show that the proposed method is more reliable than the former method.

  8. AUTOMATED ANALYSIS OF BREAKERS

    Directory of Open Access Journals (Sweden)

    E. M. Farhadzade

    2014-01-01

    Full Text Available Breakers relate to Electric Power Systems’ equipment, the reliability of which influence, to a great extend, on reliability of Power Plants. In particular, the breakers determine structural reliability of switchgear circuit of Power Stations and network substations. Failure in short-circuit switching off by breaker with further failure of reservation unit or system of long-distance protection lead quite often to system emergency.The problem of breakers’ reliability improvement and the reduction of maintenance expenses is becoming ever more urgent in conditions of systematic increasing of maintenance cost and repair expenses of oil circuit and air-break circuit breakers. The main direction of this problem solution is the improvement of diagnostic control methods and organization of on-condition maintenance. But this demands to use a great amount of statistic information about nameplate data of breakers and their operating conditions, about their failures, testing and repairing, advanced developments (software of computer technologies and specific automated information system (AIS.The new AIS with AISV logo was developed at the department: “Reliability of power equipment” of AzRDSI of Energy. The main features of AISV are:· to provide the security and data base accuracy;· to carry out systematic control of breakers conformity with operating conditions;· to make the estimation of individual  reliability’s value and characteristics of its changing for given combination of characteristics variety;· to provide personnel, who is responsible for technical maintenance of breakers, not only with information but also with methodological support, including recommendations for the given problem solving  and advanced methods for its realization.

  9. NetFCM: A Semi-Automated Web-Based Method for Flow Cytometry Data Analysis

    DEFF Research Database (Denmark)

    Frederiksen, Juliet Wairimu; Buggert, Marcus; Karlsson, Annika C.;

    2014-01-01

    data analysis has become more complex and labor-intensive than previously. We have therefore developed a semi-automatic gating strategy (NetFCM) that uses clustering and principal component analysis (PCA) together with other statistical methods to mimic manual gating approaches. NetFCM is an online...... corresponding to those obtained by manual gating strategies. These data demonstrate that NetFCM has the potential to identify relevant T cell populations by mimicking classical FCM data analysis and reduce the subjectivity and amount of time associated with such analysis. (c) 2014 International Society......Multi-parametric flow cytometry (FCM) represents an invaluable instrument to conduct single cell analysis and has significantly increased our understanding of the immune system. However, due to new techniques allowing us to measure an increased number of phenotypes within the immune system, FCM...

  10. Introducing Powell's Direction Set Method to a Fully Automated Analysis of Eclipsing Binary Stars

    CERN Document Server

    Prsa, A

    2006-01-01

    With recent observational advancements, substantial amounts of photometric and spectroscopic eclipsing binary data have been acquired. As part of an ongoing effort to assemble a reliable pipeline for fully automatic data analysis, we put Powell's direction set method to the test. The method does not depend on numerical derivatives, only on function evaluations, and as such it cannot diverge. Compared to differential corrections (DC) and Nelder & Mead's downhill simplex (NMS) method, Powell's method proves to be more efficient in terms of solution determination and the required number of iterations. However, its application is still not optimal in terms of time cost. Causes for this deficiency are identified and two steps toward the solution are proposed: non-ortogonality of the parameter set should be removed and better initial directions should be determined before the minimization is initiated. Once these setbacks are worked out, Powell's method will probably replace DC and NMS as the default minimizing...

  11. Automated analysis of 3D echocardiography

    NARCIS (Netherlands)

    Stralen, Marijn van

    2009-01-01

    In this thesis we aim at automating the analysis of 3D echocardiography, mainly targeting the functional analysis of the left ventricle. Manual analysis of these data is cumbersome, time-consuming and is associated with inter-observer and inter-institutional variability. Methods for reconstruction o

  12. Statistical colour models: an automated digital image analysis method for quantification of histological biomarkers

    OpenAIRE

    Shu, Jie; Dolman, G. E.; Duan, Jiang; Qiu, Guoping; Ilyas, Mohammad

    2016-01-01

    Background Colour is the most important feature used in quantitative immunohistochemistry (IHC) image analysis; IHC is used to provide information relating to aetiology and to confirm malignancy. Methods Statistical modelling is a technique widely used for colour detection in computer vision. We have developed a statistical model of colour detection applicable to detection of stain colour in digital IHC images. Model was first trained by massive colour pixels collected semi-automatically. To ...

  13. Longitudinal analysis of the temporal evolution of Acinetobacter baumannii strains in Ohio, USA, by using rapid automated typing methods.

    Directory of Open Access Journals (Sweden)

    Brooke K Decker

    Full Text Available Genotyping methods are essential to understand the transmission dynamics of Acinetobacter baumannii. We examined the representative genotypes of A. baumannii at different time periods in select locations in Ohio, using two rapid automated typing methods: PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS, a form of multi-locus sequence typing (MLST, and repetitive-sequence-based-PCR (rep-PCR. Our analysis included 122 isolates from 4 referral hospital systems, in 2 urban areas of Ohio. These isolates were associated with outbreaks at 3 different time periods (1996, 2000 and 2005-2007. Type assignments of PCR/ESI-MS and rep-PCR were compared to each other and to worldwide (WW clone types. The discriminatory power of each method was determined using the Simpson's index of diversity (DI. We observed that PCR/ESI-MS sequence type (ST 14, corresponding to WW clone 3, predominated in 1996, whereas ST 12 and 14 co-existed in the intermediate period (2000 and ST 10 and 12, belonging to WW clone 2, predominated more recently in 2007. The shift from WW clone 3 to WW clone 2 was accompanied by an increase in carbapenem resistance. The DI was approximately 0.74 for PCR/ESI-MS, 0.88 for rep-PCR and 0.90 for the combination of both typing methods. We conclude that combining rapid automated typing methods such as PCR/ESI-MS and rep-PCR serves to optimally characterize the regional molecular epidemiology of A. baumannii. Our data also sheds light on the changing sequence types in an 11 year period in Northeast Ohio.

  14. A method for the automated processing and analysis of images of ULVWF-platelet strings.

    Science.gov (United States)

    Reeve, Scott R; Abbitt, Katherine B; Cruise, Thomas D; Hose, D Rodney; Lawford, Patricia V

    2013-01-01

    We present a method for identifying and analysing unusually large von Willebrand factor (ULVWF)-platelet strings in noisy low-quality images. The method requires relatively inexpensive, non-specialist equipment and allows multiple users to be employed in the capture of images. Images are subsequently enhanced and analysed, using custom-written software to perform the processing tasks. The formation and properties of ULVWF-platelet strings released in in vitro flow-based assays have recently become a popular research area. Endothelial cells are incorporated into a flow chamber, chemically stimulated to induce ULVWF release and perfused with isolated platelets which are able to bind to the ULVWF to form strings. The numbers and lengths of the strings released are related to characteristics of the flow. ULVWF-platelet strings are routinely identified by eye from video recordings captured during experiments and analysed manually using basic NIH image software to determine the number of strings and their lengths. This is a laborious, time-consuming task and a single experiment, often consisting of data from four to six dishes of endothelial cells, can take 2 or more days to analyse. The method described here allows analysis of the strings to provide data such as the number and length of strings, number of platelets per string and the distance between each platelet to be found. The software reduces analysis time, and more importantly removes user subjectivity, producing highly reproducible results with an error of less than 2% when compared with detailed manual analysis.

  15. Development testing of the chemical analysis automation polychlorinated biphenyl standard analysis method during surface soils sampling at the David Witherspoon 1630 site

    International Nuclear Information System (INIS)

    The Chemical Analysis Automation (CAA) project is developing standardized, software-driven, site-deployable robotic laboratory systems with the objective of lowering the per-sample analysis cost, decreasing sample turnaround time, and minimizing human exposure to hazardous and radioactive materials associated with DOE remediation projects. The first integrated system developed by the CAA project is designed to determine polychlorinated biphenyls (PCB) content in soil matrices. A demonstration and development testing of this system was conducted in conjuction with surface soil characterization activities at the David Witherspoon 1630 Site in Knoxville, Tennessee. The PCB system consists of five hardware standard laboratory modules (SLMs), one software SLM, the task sequence controller (TSC), and the human-computer interface (HCI). Four of the hardware SLMs included a four-channel Soxhlet extractor, a high-volume concentrator, a column cleanup, and a gas chromatograph. These SLMs performed the sample preparation and measurement steps within the total analysis protocol. The fifth hardware module was a robot that transports samples between the SLMs and the required consumable supplies to the SLMs. The software SLM is an automated data interpretation module that receives raw data from the gas chromatograph SLM and analyzes the data to yield the analyte information. The TSC is a software system that provides the scheduling, management of system resources, and the coordination of all SLM activities. The HCI is a graphical user interface that presents the automated laboratory to the analyst in terms of the analytical procedures and methods. Human control of the automated laboratory is accomplished via the HCI. Sample information required for processing by the automated laboratory is entered through the HCI. Information related to the sample and the system status is presented to the analyst via graphical icons

  16. Computer-implemented system and method for automated and highly accurate plaque analysis, reporting, and visualization

    Science.gov (United States)

    Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)

    2008-01-01

    A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.

  17. GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Chris Cheadle

    2007-01-01

    Full Text Available Background: Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The assignment of functional information to these complex patterns remains a challenging task in effectively interpreting data and correlating results from across experiments, projects and laboratories. Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently.Results: We have developed (gene set matrix analysis GSMA as a useful method for the rapid testing of group-wise up- or downregulation of gene expression simultaneously for multiple lists of genes (gene sets against entire distributions of gene expression changes (datasets for single or multiple experiments. The utility of GSMA lies in its flexibility to rapidly poll gene sets related by known biological function or as designated solely by the end-user against large numbers of datasets simultaneously.Conclusions: GSMA provides a simple and straightforward method for hypothesis testing in which genes are tested by groups across multiple datasets for patterns of expression enrichment.

  18. An automated method for nonparametric kinetic analysis of clinical DCE-MRI data: application to glioblastoma treated with bevacizumab.

    Science.gov (United States)

    Ferl, Gregory Z; Xu, Lu; Friesenhahn, Michel; Bernstein, Lisa J; Barboriak, Daniel P; Port, Ruediger E

    2010-05-01

    Here, we describe an automated nonparametric method for evaluating gadolinium-diethylene triamine pentaacetic acid (Gd-DTPA) kinetics, based on dynamic contrast-enhanced-MRI scans of glioblastoma patients taken before and after treatment with bevacizumab; no specific model or equation structure is assumed or used. Tumor and venous blood concentration-time profiles are smoothed, using a robust algorithm that removes artifacts due to patient motion, and then deconvolved, yielding an impulse response function. In addition to smoothing, robustness of the deconvolution operation is assured by excluding data that occur prior to the plasma peak; an exhaustive analysis was performed to demonstrate that exclusion of the prepeak plasma data does not significantly affect results. All analysis steps are executed by a single R script that requires blood and tumor curves as the sole input. Statistical moment analysis of the Impulse response function yields the area under the curve (AUC) and mean residence time (MRT). Comparison of deconvolution results to fitted Tofts model parameters suggests that AUCMRT and AUC of the Impulse response function closely approximate fractional clearance from plasma to tissue (K(trans)) and fractional interstitial volume (v(e)). Intervisit variability is shown to be comparable when using the deconvolution method (11% [AUCMRT] and 13%[AUC]) compared to the Tofts model (14%[K(trans)] and 24%[v(e)]). AUC and AUCMRT both exhibit a statistically significant decrease (P < 0.005) 1 day after administration of bevacizumab. PMID:20432307

  19. Automated analysis of protein NMR assignments using methods from artificial intelligence.

    Science.gov (United States)

    Zimmerman, D E; Kulikowski, C A; Huang, Y; Feng, W; Tashiro, M; Shimotakahara, S; Chien, C; Powers, R; Montelione, G T

    1997-06-20

    An expert system for determining resonance assignments from NMR spectra of proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H heteronuclear correlation spectrum and seven to eight three-dimensional triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average of 98% of sequence-specific spin-system assignments with an error rate of less than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for smaller proteins with simple spectra to one to nine minutes for medium size proteins exhibiting numerous extra spin systems attributed to conformational isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods with a domain-specific knowledge base to exploit the logical structure of the sequential assignment problem, the specific features of the various NMR experiments, and the expected chemical shift frequencies of different amino acids. The current implementation specializes in the analysis of data derived from the most sensitive of the currently available triple-resonance experiments. Potential extensions of the system for analysis of additional types of protein NMR data are also discussed.

  20. Triangulation methods for automated docking

    Science.gov (United States)

    Bales, John W.

    1996-01-01

    An automated docking system must have a reliable method for determining range and orientation of the passive (target) vehicle with respect to the active vehicle. This method must also provide accurate information on the rates of change of range to and orientation of the passive vehicle. The method must be accurate within required tolerances and capable of operating in real time. The method being developed at Marshall Space Flight Center employs a single TV camera, a laser illumination system and a target consisting, in its minimal configuration, of three retro-reflectors. Two of the retro-reflectors are mounted flush to the same surface, with the third retro-reflector mounted to a post fixed midway between the other two and jutting at a right angle from the surface. For redundancy, two additional retroreflectors are mounted on the surface on a line at right angles to the line containing the first two retro-reflectors, and equally spaced on either side of the post. The target vehicle will contain a large target for initial acquisition and several smaller targets for close range.

  1. Automated Methods Of Corrosion Measurements

    DEFF Research Database (Denmark)

    Bech-Nielsen, Gregers; Andersen, Jens Enevold Thaulov; Reeve, John Ch;

    1997-01-01

    The chapter describes the following automated measurements: Corrosion Measurements by Titration, Imaging Corrosion by Scanning Probe Microscopy, Critical Pitting Temperature and Application of the Electrochemical Hydrogen Permeation Cell.......The chapter describes the following automated measurements: Corrosion Measurements by Titration, Imaging Corrosion by Scanning Probe Microscopy, Critical Pitting Temperature and Application of the Electrochemical Hydrogen Permeation Cell....

  2. Feasibility Analysis of Crane Automation

    Institute of Scientific and Technical Information of China (English)

    DONG Ming-xiao; MEI Xue-song; JIANG Ge-dong; ZHANG Gui-qing

    2006-01-01

    This paper summarizes the modeling methods, open-loop control and closed-loop control techniques of various forms of cranes, worldwide, and discusses their feasibilities and limitations in engineering. Then the dynamic behaviors of cranes are analyzed. Finally, we propose applied modeling methods and feasible control techniques and demonstrate the feasibilities of crane automation.

  3. Automated activation-analysis system

    International Nuclear Information System (INIS)

    An automated delayed neutron counting and instrumental neutron activation analysis system has been developed at Los Alamos National Laboratory's Omega West Reactor (OWR) to analyze samples for uranium and 31 additional elements with a maximum throughput of 400 samples per day. The system and its mode of operation for a large reconnaissance survey are described

  4. A novel, rapid and automated conductometric method to evaluate surfactant-cells interactions by means of critical micellar concentration analysis.

    Science.gov (United States)

    Tiecco, Matteo; Corte, Laura; Roscini, Luca; Colabella, Claudia; Germani, Raimondo; Cardinali, Gianluigi

    2014-07-25

    Conductometry is widely used to determine critical micellar concentration and micellar aggregates surface properties of amphiphiles. Current conductivity experiments of surfactant solutions are typically carried out by manual pipetting, yielding some tens reading points within a couple of hours. In order to study the properties of surfactant-cells interactions, each amphiphile must be tested in different conditions against several types of cells. This calls for complex experimental designs making the application of current methods seriously time consuming, especially because long experiments risk to determine alterations of cells, independently of the surfactant action. In this paper we present a novel, accurate and rapid automated procedure to obtain conductometric curves with several hundreds reading points within tens of minutes. The method was validated with surfactant solutions alone and in combination with Saccharomyces cerevisiae cells. An easy-to use R script, calculates conductometric parameters and their statistical significance with a graphic interface to visualize data and results. The validations showed that indeed the procedure works in the same manner with surfactant alone or in combination with cells, yielding around 1000 reading points within 20 min and with high accuracy, as determined by the regression analysis.

  5. Automated methods of textual content analysis and description of text structures

    CERN Document Server

    Chýla, Roman

    Universal Semantic Language (USL) is a semi-formalized approach for the description of knowledge (a knowledge representation tool). The idea of USL was introduced by Vladimir Smetacek in the system called SEMAN which was used for keyword extraction tasks in the former Information centre of the Czechoslovak Republic. However due to the dissolution of the centre in early 90's, the system has been lost. This thesis reintroduces the idea of USL in a new context of quantitative content analysis. First we introduce the historical background and the problems of semantics and knowledge representation, semes, semantic fields, semantic primes and universals. The basic methodology of content analysis studies is illustrated on the example of three content analysis tools and we describe the architecture of a new system. The application was built specifically for USL discovery but it can work also in the context of classical content analysis. It contains Natural Language Processing (NLP) components and employs the algorith...

  6. Validation of three viable-cell counting methods: Manual, semi-automated, and automated

    Directory of Open Access Journals (Sweden)

    Daniela Cadena-Herrera

    2015-09-01

    Full Text Available A viable cell count is essential to evaluate the kinetics of cell growth. Since the hemocytometer was first used for counting blood cells, several variants of the methodology have been developed towards reducing the time of analysis and improving accuracy through automation of both sample preparation and counting. The successful implementation of automated techniques relies in the adjustment of cell staining, image display parameters and cell morphology to obtain equivalent precision, accuracy and linearity with respect to the hemocytometer. In this study we conducted the validation of three trypan blue exclusion-based methods: manual, semi-automated, and fully automated; which were used for the estimation of density and viability of cells employed for the biosynthesis and bioassays of recombinant proteins. Our results showed that the evaluated attributes remained within the same range for the automated methods with respect to the manual, providing an efficient alternative for analyzing a huge number of samples.

  7. VID-R and SCAN: Tools and Methods for the Automated Analysis of Visual Records.

    Science.gov (United States)

    Ekman, Paul; And Others

    The VID-R (Visual Information Display and Retrieval) system that enables computer-aided analysis of visual records is composed of a film-to-television chain, two videotape recorders with complete remote control of functions, a video-disc recorder, three high-resolution television monitors, a teletype, a PDP-8, a video and audio interface, three…

  8. Introducing adapted Nelder & Mead's downhill simplex method to a fully automated analysis of eclipsing binaries

    CERN Document Server

    Prsa, A

    2004-01-01

    Eclipsing binaries are extremely attractive objects because absolute physical parameters (masses, luminosities, radii) of both components may be determined from observations. Since most efforts to extract these parameters were based on dedicated observing programs, existing modeling code is based on interactivity. Gaia will make a revolutionary advance in shear number of observed eclipsing binaries and new methods for automatic handling must be introduced and thoroughly tested. This paper focuses on Nelder & Mead's downhill simplex method applied to a synthetically created test binary as it will be observed by Gaia.

  9. Introducing adapted Nelder & Mead's downhill simplex method to a fully automated analysis of eclipsing binaries

    OpenAIRE

    Prsa, A.; Zwitter, T.

    2004-01-01

    Eclipsing binaries are extremely attractive objects because absolute physical parameters (masses, luminosities, radii) of both components may be determined from observations. Since most efforts to extract these parameters were based on dedicated observing programs, existing modeling code is based on interactivity. Gaia will make a revolutionary advance in shear number of observed eclipsing binaries and new methods for automatic handling must be introduced and thoroughly tested. This paper foc...

  10. Automated Analysis Methods for the Assessment of Bicycle Infrastructure and Demand

    OpenAIRE

    Pashkevich, Anton

    2013-01-01

    A first phase of the research activity has been related to the study of the state of art of the infrastructures for cycling, bicycle use and methods for evaluation. In this part, the candidate has studied the "bicycle system" in countries with high bicycle use and in particular in the Netherlands. Has been carried out an evaluation of the questionnaires of the survey conducted within the European project BICY on mobility in general in 13 cities of the participating countries. The questionn...

  11. Integrated Design Engineering Analysis (IDEA) Environment Automated Generation of Structured CFD Grids using Topology Methods

    Science.gov (United States)

    Kamhawi, Hilmi N.

    2012-01-01

    This report documents the work performed from March 2010 to March 2012. The Integrated Design and Engineering Analysis (IDEA) environment is a collaborative environment based on an object-oriented, multidisciplinary, distributed framework using the Adaptive Modeling Language (AML) as a framework and supporting the configuration design and parametric CFD grid generation. This report will focus on describing the work in the area of parametric CFD grid generation using novel concepts for defining the interaction between the mesh topology and the geometry in such a way as to separate the mesh topology from the geometric topology while maintaining the link between the mesh topology and the actual geometry.

  12. A method to quantify movement activity of groups of animals using automated image analysis

    Science.gov (United States)

    Xu, Jianyu; Yu, Haizhen; Liu, Ying

    2009-07-01

    Most physiological and environmental changes are capable of inducing variations in animal behavior. The behavioral parameters have the possibility to be measured continuously in-situ by a non-invasive and non-contact approach, and have the potential to be used in the actual productions to predict stress conditions. Most vertebrates tend to live in groups, herds, flocks, shoals, bands, packs of conspecific individuals. Under culture conditions, the livestock or fish are in groups and interact on each other, so the aggregate behavior of the group should be studied rather than that of individuals. This paper presents a method to calculate the movement speed of a group of animal in a enclosure or a tank denoted by body length speed that correspond to group activity using computer vision technique. Frame sequences captured at special time interval were subtracted in pairs after image segmentation and identification. By labeling components caused by object movement in difference frame, the projected area caused by the movement of every object in the capture interval was calculated; this projected area was divided by the projected area of every object in the later frame to get body length moving distance of each object, and further could obtain the relative body length speed. The average speed of all object can well respond to the activity of the group. The group activity of a tilapia (Oreochromis niloticus) school to high (2.65 mg/L) levels of unionized ammonia (UIA) concentration were quantified based on these methods. High UIA level condition elicited a marked increase in school activity at the first hour (P<0.05) exhibiting an avoidance reaction (trying to flee from high UIA condition), and then decreased gradually.

  13. Automation of the proximate analysis of coals

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    A study is reported of the feasibility of using a multi-jointed general-purpose robot for the automated analysis of moisture, volatile matter, ash and total post-combustion sulfur in coal and coke. The results obtained with an automated system are compared with those of conventional manual methods. The design of the robot hand and the safety measures provided are now both fully satisfactory, and the analytic values obtained exhibit little scatter. It is concluded that the use of this robot system results in a better working environment and in considerable labour saving. Applications to other tasks are under development.

  14. Method development in automated mineralogy

    OpenAIRE

    Sandmann, Dirk

    2015-01-01

    The underlying research that resulted in this doctoral dissertation was performed at the Division of Economic Geology and Petrology of the Department of Mineralogy, TU Bergakademie Freiberg between 2011 and 2014. It was the primary aim of this thesis to develop and test novel applications for the technology of ‘Automated Mineralogy’ in the field of economic geology and geometallurgy. A “Mineral Liberation Analyser” (MLA) instrument of FEI Company was used to conduct most analytical studies. T...

  15. Automation of finite element methods

    CERN Document Server

    Korelc, Jože

    2016-01-01

    New finite elements are needed as well in research as in industry environments for the development of virtual prediction techniques. The design and implementation of novel finite elements for specific purposes is a tedious and time consuming task, especially for nonlinear formulations. The automation of this process can help to speed up this process considerably since the generation of the final computer code can be accelerated by order of several magnitudes. This book provides the reader with the required knowledge needed to employ modern automatic tools like AceGen within solid mechanics in a successful way. It covers the range from the theoretical background, algorithmic treatments to many different applications. The book is written for advanced students in the engineering field and for researchers in educational and industrial environments.

  16. Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions.

    Science.gov (United States)

    Shen, Simon; Syal, Karan; Tao, Nongjian; Wang, Shaopeng

    2015-12-01

    We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion. PMID:26724085

  17. Automated pipelines for spectroscopic analysis

    Science.gov (United States)

    Allende Prieto, C.

    2016-09-01

    The Gaia mission will have a profound impact on our understanding of the structure and dynamics of the Milky Way. Gaia is providing an exhaustive census of stellar parallaxes, proper motions, positions, colors and radial velocities, but also leaves some glaring holes in an otherwise complete data set. The radial velocities measured with the on-board high-resolution spectrograph will only reach some 10 % of the full sample of stars with astrometry and photometry from the mission, and detailed chemical information will be obtained for less than 1 %. Teams all over the world are organizing large-scale projects to provide complementary radial velocities and chemistry, since this can now be done very efficiently from the ground thanks to large and mid-size telescopes with a wide field-of-view and multi-object spectrographs. As a result, automated data processing is taking an ever increasing relevance, and the concept is applying to many more areas, from targeting to analysis. In this paper, I provide a quick overview of recent, ongoing, and upcoming spectroscopic surveys, and the strategies adopted in their automated analysis pipelines.

  18. Reload safety analysis automation tools

    International Nuclear Information System (INIS)

    Performing core physics calculations for the sake of reload safety analysis is a very demanding and time consuming process. This process generally begins with the preparation of libraries for the core physics code using a lattice code. The next step involves creating a very large set of calculations with the core physics code. Lastly, the results of the calculations must be interpreted, correctly applying uncertainties and checking whether applicable limits are satisfied. Such a procedure requires three specialized experts. One must understand the lattice code in order to correctly calculate and interpret its results. The next expert must have a good understanding of the physics code in order to create libraries from the lattice code results and to correctly define all the calculations involved. The third expert must have a deep knowledge of the power plant and the reload safety analysis procedure in order to verify, that all the necessary calculations were performed. Such a procedure involves many steps and is very time consuming. At ÚJV Řež, a.s., we have developed a set of tools which can be used to automate and simplify the whole process of performing reload safety analysis. Our application QUADRIGA automates lattice code calculations for library preparation. It removes user interaction with the lattice code and reduces his task to defining fuel pin types, enrichments, assembly maps and operational parameters all through a very nice and user-friendly GUI. The second part in reload safety analysis calculations is done by CycleKit, a code which is linked with our core physics code ANDREA. Through CycleKit large sets of calculations with complicated interdependencies can be performed using simple and convenient notation. CycleKit automates the interaction with ANDREA, organizes all the calculations, collects the results, performs limit verification and displays the output in clickable html format. Using this set of tools for reload safety analysis simplifies

  19. Exploratory analysis of methods for automated classification of laboratory test orders into syndromic groups in veterinary medicine.

    Directory of Open Access Journals (Sweden)

    Fernanda C Dórea

    Full Text Available BACKGROUND: Recent focus on earlier detection of pathogen introduction in human and animal populations has led to the development of surveillance systems based on automated monitoring of health data. Real- or near real-time monitoring of pre-diagnostic data requires automated classification of records into syndromes--syndromic surveillance--using algorithms that incorporate medical knowledge in a reliable and efficient way, while remaining comprehensible to end users. METHODS: This paper describes the application of two of machine learning (Naïve Bayes and Decision Trees and rule-based methods to extract syndromic information from laboratory test requests submitted to a veterinary diagnostic laboratory. RESULTS: High performance (F1-macro = 0.9995 was achieved through the use of a rule-based syndrome classifier, based on rule induction followed by manual modification during the construction phase, which also resulted in clear interpretability of the resulting classification process. An unmodified rule induction algorithm achieved an F(1-micro score of 0.979 though this fell to 0.677 when performance for individual classes was averaged in an unweighted manner (F(1-macro, due to the fact that the algorithm failed to learn 3 of the 16 classes from the training set. Decision Trees showed equal interpretability to the rule-based approaches, but achieved an F(1-micro score of 0.923 (falling to 0.311 when classes are given equal weight. A Naïve Bayes classifier learned all classes and achieved high performance (F(1-micro= 0.994 and F(1-macro = .955, however the classification process is not transparent to the domain experts. CONCLUSION: The use of a manually customised rule set allowed for the development of a system for classification of laboratory tests into syndromic groups with very high performance, and high interpretability by the domain experts. Further research is required to develop internal validation rules in order to establish

  20. A Systematic, Automated Network Planning Method

    DEFF Research Database (Denmark)

    Holm, Jens Åge; Pedersen, Jens Myrup

    2006-01-01

    This paper describes a case study conducted to evaluate the viability of a systematic, automated network planning method. The motivation for developing the network planning method was that many data networks are planned in an adhoc manner with no assurance of quality of the solution with respect...

  1. Automated image analysis techniques for cardiovascular magnetic resonance imaging

    NARCIS (Netherlands)

    Geest, Robertus Jacobus van der

    2011-01-01

    The introductory chapter provides an overview of various aspects related to quantitative analysis of cardiovascular MR (CMR) imaging studies. Subsequently, the thesis describes several automated methods for quantitative assessment of left ventricular function from CMR imaging studies. Several novel

  2. APSAS; an Automated Particle Size Analysis System

    Science.gov (United States)

    Poppe, Lawrence J.; Eliason, A.H.; Fredericks, J.J.

    1985-01-01

    The Automated Particle Size Analysis System integrates a settling tube and an electroresistance multichannel particle-size analyzer (Coulter Counter) with a Pro-Comp/gg microcomputer and a Hewlett Packard 2100 MX(HP 2100 MX) minicomputer. This system and its associated software digitize the raw sediment grain-size data, combine the coarse- and fine-fraction data into complete grain-size distributions, perform method of moments and inclusive graphics statistics, verbally classify the sediment, generate histogram and cumulative frequency plots, and transfer the results into a data-retrieval system. This system saves time and labor and affords greater reliability, resolution, and reproducibility than conventional methods do.

  3. Automated Methods of Corrosion Measurements

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov

    1997-01-01

    electrochemical measurements as well as elemental analysis look very promising for elucidating corrosion reaction mechanisms. The study of initial surface reactions at the atomic or submicron level is becoming an important field of research in the understanding of corrosion processes. At present, mainly two...... scanning microscope techniques are employed investigating corrosion processes, and usually in situ: in situ scanning tunneling microscopy (in situ STM) and in situ scanning force microscopy (in situ AFM). It is these techniques to which attention is directed here....

  4. Automated liquid chromatography-tandem mass spectrometry method for the analysis of firocoxib in urine and plasma from horse and dog.

    Science.gov (United States)

    Letendre, Laura; Kvaternick, Valerie; Tecle, Berhane; Fischer, James

    2007-06-15

    A rugged, sensitive and efficient liquid chromatography-tandem mass spectrometry method was developed and validated for the quantitative analysis of firocoxib in urine from 5 to 3000 ng/mL and in plasma from 1 to 3000 ng/mL. The method requires 200 microL of either plasma or urine and includes sample preparation in 96-well solid phase extraction (SPE) plates using a BIOMEK 2000 Laboratory Automated Workstation. Chromatographic separation of firocoxib from matrix interferences was achieved using isocratic reversed phase chromatography on a PHENOMENEX LUNA Phenyl-Hexyl column. The mobile phase was 45% acetonitrile and 55% of a 2 mM ammonium formate buffer. The method was accurate (88-107%) and precise (CV93% were achieved and ionization efficiencies (due to matrix effects) were >72%. Extensive stability and ruggedness testing was also performed; therefore, the method can be used for pharmacokinetic studies as well as drug monitoring and screening. The data presented here is the first LC-MS/MS method for the quantitation of firocoxib in plasma (LLOQ of 1 ng/mL), a 25-fold improvement in sensitivity over the HPLC-UV method and the first quantitative method for firocoxib in urine (LLOQ of 5 ng/mL). Additionally the sample preparation process has been automated to improve efficiency. PMID:17459786

  5. Automation for System Safety Analysis

    Science.gov (United States)

    Malin, Jane T.; Fleming, Land; Throop, David; Thronesbery, Carroll; Flores, Joshua; Bennett, Ted; Wennberg, Paul

    2009-01-01

    This presentation describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

  6. Automated method for the direct analysis of 8-oxo-guanosine and 8-oxo-2'-deoxyguanosine in human urine using ultraperformance liquid chromatography and tandem mass spectrometry

    DEFF Research Database (Denmark)

    Hillestrøm, Peter R; Henriksen, Trine; Hillestrøm, Peter René;

    2009-01-01

    . In addition there is a need for assays that can measure more than one product from DNA oxidation. We present a sensitive, precise, and accurate method for quantitative analysis of the oxidized nucleosides 8-oxoGuo and 8-oxodG in human urine. The assay is based on automated sample handling using a BIOMEK 3000......The potential use of oxidative stress-induced DNA and RNA damage products as biomarkers is an important aspect of biomedical research. There is a need for assays with high specificity and sensitivity that also can be used in molecular epidemiology studies with a large number of subjects...

  7. Automated Pipelines for Spectroscopic Analysis

    CERN Document Server

    Prieto, Carlos Allende

    2016-01-01

    The Gaia mission will have a profound impact on our understanding of the structure and dynamics of the Milky Way. Gaia is providing an exhaustive census of stellar parallaxes, proper motions, positions, colors and radial velocities, but also leaves some flaring holes in an otherwise complete data set. The radial velocities measured with the on-board high-resolution spectrograph will only reach some 10% of the full sample of stars with astrometry and photometry from the mission, and detailed chemical information will be obtained for less than 1%. Teams all over the world are organizing large-scale projects to provide complementary radial velocities and chemistry, since this can now be done very efficiently from the ground thanks to large and mid-size telescopes with a wide field-of-view and multi-object spectrographs. As a result, automated data processing is taking an ever increasing relevance, and the concept is applying to many more areas, from targeting to analysis. In this paper, I provide a quick overvie...

  8. NEW TECHNIQUES USED IN AUTOMATED TEXT ANALYSIS

    Directory of Open Access Journals (Sweden)

    M. I strate

    2010-12-01

    Full Text Available Automated analysis of natural language texts is one of the most important knowledge discovery tasks for any organization. According to Gartner Group, almost 90% of knowledge available at an organization today is dispersed throughout piles of documents buried within unstructured text. Analyzing huge volumes of textual information is often involved in making informed and correct business decisions. Traditional analysis methods based on statistics fail to help processing unstructured texts and the society is in search of new technologies for text analysis. There exist a variety of approaches to the analysis of natural language texts, but most of them do not provide results that could be successfully applied in practice. This article concentrates on recent ideas and practical implementations in this area.

  9. A Comparison of Fully Automated Methods of Data Analysis and Computer Assisted Heuristic Methods in an Electrode Kinetic Study of the Pathologically Variable [Fe(CN) 6 ] 3–/4– Process by AC Voltammetry

    KAUST Repository

    Morris, Graham P.

    2013-12-17

    Fully automated and computer assisted heuristic data analysis approaches have been applied to a series of AC voltammetric experiments undertaken on the [Fe(CN)6]3-/4- process at a glassy carbon electrode in 3 M KCl aqueous electrolyte. The recovered parameters in all forms of data analysis encompass E0 (reversible potential), k0 (heterogeneous charge transfer rate constant at E0), α (charge transfer coefficient), Ru (uncompensated resistance), and Cdl (double layer capacitance). The automated method of analysis employed time domain optimization and Bayesian statistics. This and all other methods assumed the Butler-Volmer model applies for electron transfer kinetics, planar diffusion for mass transport, Ohm\\'s Law for Ru, and a potential-independent Cdl model. Heuristic approaches utilize combinations of Fourier Transform filtering, sensitivity analysis, and simplex-based forms of optimization applied to resolved AC harmonics and rely on experimenter experience to assist in experiment-theory comparisons. Remarkable consistency of parameter evaluation was achieved, although the fully automated time domain method provided consistently higher α values than those based on frequency domain data analysis. The origin of this difference is that the implemented fully automated method requires a perfect model for the double layer capacitance. In contrast, the importance of imperfections in the double layer model is minimized when analysis is performed in the frequency domain. Substantial variation in k0 values was found by analysis of the 10 data sets for this highly surface-sensitive pathologically variable [Fe(CN) 6]3-/4- process, but remarkably, all fit the quasi-reversible model satisfactorily. © 2013 American Chemical Society.

  10. Statistical Analysis of Filament Features Based on the Hα Solar Images from 1988 to 2013 by Computer Automated Detection Method

    Science.gov (United States)

    Hao, Q.; Fang, C.; Cao, W.; Chen, P. F.

    2015-12-01

    We improve our filament automated detection method which was proposed in our previous works. It is then applied to process the full disk Hα data mainly obtained by the Big Bear Solar Observatory from 1988 to 2013, spanning nearly three solar cycles. The butterfly diagrams of the filaments, showing the information of the filament area, spine length, tilt angle, and the barb number, are obtained. The variations of these features with the calendar year and the latitude band are analyzed. The drift velocities of the filaments in different latitude bands are calculated and studied. We also investigate the north-south (N-S) asymmetries of the filament numbers in total and in each subclass classified according to the filament area, spine length, and tilt angle. The latitudinal distribution of the filament number is found to be bimodal. About 80% of all the filaments have tilt angles within [0°, 60°]. For the filaments within latitudes lower (higher) than 50°, the northeast (northwest) direction is dominant in the northern hemisphere and the southeast (southwest) direction is dominant in the southern hemisphere. The latitudinal migrations of the filaments experience three stages with declining drift velocities in each of solar cycles 22 and 23, and it seems that the drift velocity is faster in shorter solar cycles. Most filaments in latitudes lower (higher) than 50° migrate toward the equator (polar region). The N-S asymmetry indices indicate that the southern hemisphere is the dominant hemisphere in solar cycle 22 and the northern hemisphere is the dominant one in solar cycle 23.

  11. Distribution system analysis and automation

    CERN Document Server

    Gers, Juan

    2013-01-01

    A comprehensive guide to techniques that allow engineers to simulate, analyse and optimise power distribution systems which combined with automation, underpin the emerging concept of the "smart grid". This book is supported by theoretical concepts with real-world applications and MATLAB exercises.

  12. Computer vision methods applied to semi-automated analysis of inter-individual distances of perching birds

    OpenAIRE

    Kumperščak, Borut

    2010-01-01

    A system for analysis of perchnig bird flocks based on computer vision technologies and OpenCV library. Input data are high resolution photos of perching birds with uniform background. Number of birds, their sizes, and positions is computed out of these images. First, the objects are found that are reasonably assumed to be birds and segmented out of the background by means of computer vision methods. Analitic measurements are made on these objects, and results are saved to a database. Gathere...

  13. Automated macromolecular crystal detection system and method

    Science.gov (United States)

    Christian, Allen T.; Segelke, Brent; Rupp, Bernard; Toppani, Dominique

    2007-06-05

    An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

  14. Optimization-based Method for Automated Road Network Extraction

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, D

    2001-09-18

    Automated road information extraction has significant applicability in transportation. It provides a means for creating, maintaining, and updating transportation network databases that are needed for purposes ranging from traffic management to automated vehicle navigation and guidance. This paper is to review literature on the subject of road extraction and to describe a study of an optimization-based method for automated road network extraction.

  15. Management issues in automated audit analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, K.A.; Hochberg, J.G.; Wilhelmy, S.K.; McClary, J.F.; Christoph, G.G.

    1994-03-01

    This paper discusses management issues associated with the design and implementation of an automated audit analysis system that we use to detect security events. It gives the viewpoint of a team directly responsible for developing and managing such a system. We use Los Alamos National Laboratory`s Network Anomaly Detection and Intrusion Reporter (NADIR) as a case in point. We examine issues encountered at Los Alamos, detail our solutions to them, and where appropriate suggest general solutions. After providing an introduction to NADIR, we explore four general management issues: cost-benefit questions, privacy considerations, legal issues, and system integrity. Our experiences are of general interest both to security professionals and to anyone who may wish to implement a similar system. While NADIR investigates security events, the methods used and the management issues are potentially applicable to a broad range of complex systems. These include those used to audit credit card transactions, medical care payments, and procurement systems.

  16. Analysis of an automated background correction method for cardiovascular MR phase contrast imaging in children and young adults

    Energy Technology Data Exchange (ETDEWEB)

    Rigsby, Cynthia K.; Hilpipre, Nicholas; Boylan, Emma E.; Popescu, Andrada R.; Deng, Jie [Ann and Robert H. Lurie Children' s Hospital of Chicago, Department of Medical Imaging, Chicago, IL (United States); McNeal, Gary R. [Siemens Medical Solutions USA Inc., Customer Solutions Group, Cardiovascular MR R and D, Chicago, IL (United States); Zhang, Gang [Ann and Robert H. Lurie Children' s Hospital of Chicago Research Center, Biostatistics Research Core, Chicago, IL (United States); Choi, Grace [Ann and Robert H. Lurie Children' s Hospital of Chicago, Department of Pediatrics, Chicago, IL (United States); Greiser, Andreas [Siemens AG Healthcare Sector, Erlangen (Germany)

    2014-03-15

    Phase contrast magnetic resonance imaging (MRI) is a powerful tool for evaluating vessel blood flow. Inherent errors in acquisition, such as phase offset, eddy currents and gradient field effects, can cause significant inaccuracies in flow parameters. These errors can be rectified with the use of background correction software. To evaluate the performance of an automated phase contrast MRI background phase correction method in children and young adults undergoing cardiac MR imaging. We conducted a retrospective review of patients undergoing routine clinical cardiac MRI including phase contrast MRI for flow quantification in the aorta (Ao) and main pulmonary artery (MPA). When phase contrast MRI of the right and left pulmonary arteries was also performed, these data were included. We excluded patients with known shunts and metallic implants causing visible MRI artifact and those with more than mild to moderate aortic or pulmonary stenosis. Phase contrast MRI of the Ao, mid MPA, proximal right pulmonary artery (RPA) and left pulmonary artery (LPA) using 2-D gradient echo Fast Low Angle SHot (FLASH) imaging was acquired during normal respiration with retrospective cardiac gating. Standard phase image reconstruction and the automatic spatially dependent background-phase-corrected reconstruction were performed on each phase contrast MRI dataset. Non-background-corrected and background-phase-corrected net flow, forward flow, regurgitant volume, regurgitant fraction, and vessel cardiac output were recorded for each vessel. We compared standard non-background-corrected and background-phase-corrected mean flow values for the Ao and MPA. The ratio of pulmonary to systemic blood flow (Qp:Qs) was calculated for the standard non-background and background-phase-corrected data and these values were compared to each other and for proximity to 1. In a subset of patients who also underwent phase contrast MRI of the MPA, RPA, and LPA a comparison was made between standard non

  17. Cooling method with automated seasonal freeze protection

    Energy Technology Data Exchange (ETDEWEB)

    Cambell, Levi; Chu, Richard; David, Milnes; Ellsworth, Jr, Michael; Iyengar, Madhusudan; Simons, Robert; Singh, Prabjit; Zhang, Jing

    2016-05-31

    An automated multi-fluid cooling method is provided for cooling an electronic component(s). The method includes obtaining a coolant loop, and providing a coolant tank, multiple valves, and a controller. The coolant loop is at least partially exposed to outdoor ambient air temperature(s) during normal operation, and the coolant tank includes first and second reservoirs containing first and second fluids, respectively. The first fluid freezes at a lower temperature than the second, the second fluid has superior cooling properties compared with the first, and the two fluids are soluble. The multiple valves are controllable to selectively couple the first or second fluid into the coolant in the coolant loop, wherein the coolant includes at least the second fluid. The controller automatically controls the valves to vary first fluid concentration level in the coolant loop based on historical, current, or anticipated outdoor air ambient temperature(s) for a time of year.

  18. A semi-automated method for the detection of seismic anisotropy at depth via receiver function analysis

    Science.gov (United States)

    Licciardi, A.; Piana Agostinetti, N.

    2016-06-01

    Information about seismic anisotropy is embedded in the variation of the amplitude of the Ps pulses as a function of the azimuth, on both the Radial and the Transverse components of teleseismic receiver functions (RF). We develop a semi-automatic method to constrain the presence and the depth of anisotropic layers beneath a single seismic broad-band station. An algorithm is specifically designed to avoid trial and error methods and subjective crustal parametrizations in RF inversions, providing a suitable tool for large-size data set analysis. The algorithm couples together information extracted from a 1-D VS profile and from a harmonic decomposition analysis of the RF data set. This information is used to determine the number of anisotropic layers and their approximate position at depth, which, in turn, can be used to, for example, narrow the search boundaries for layer thickness and S-wave velocity in a subsequent parameter space search. Here, the output of the algorithm is used to invert an RF data set by means of the Neighbourhood Algorithm (NA). To test our methodology, we apply the algorithm to both synthetic and observed data. We make use of synthetic RF with correlated Gaussian noise to investigate the resolution power for multiple and thin (1-3 km) anisotropic layers in the crust. The algorithm successfully identifies the number and position of anisotropic layers at depth prior the NA inversion step. In the NA inversion, strength of anisotropy and orientation of the symmetry axis are correctly retrieved. Then, the method is applied to field measurement from station BUDO in the Tibetan Plateau. Two consecutive layers of anisotropy are automatically identified with our method in the first 25-30 km of the crust. The data are then inverted with the retrieved parametrization. The direction of the anisotropic axis in the uppermost layer correlates well with the orientation of the major planar structure in the area. The deeper anisotropic layer is associated with

  19. Proximate analysis by automated thermogravimetry

    Energy Technology Data Exchange (ETDEWEB)

    Elder, J.P.

    1983-05-01

    A study has been made of the use of the Perkin-Elmer thermogravimetric instrument TGS-2, under the control of the System 4 microprocessor for the automatic proximate analysis of solid fossil fuels and related matter. The programs developed are simple to operate, and do not require detailed temperature calibration of the instrumental system. They have been tested with coals of varying rank, biomass samples and Devonian oil shales all of which were of special importance to the State of Kentucky. Precise, accurate data conforming to ASTM specifications were obtained. The simplicity of the technique suggests that it may complement the classical ASTM method and could be used when this latter procedure cannot be employed. However, its adoption as a standardized method must await the development of statistical data resulting from interlaboratory testing on a variety of fossil fuels. (9 refs.)

  20. Automated Technology for Verificiation and Analysis

    DEFF Research Database (Denmark)

    This volume contains the papers presented at the 7th International Symposium on Automated Technology for Verification and Analysis held during October 13-16 in Macao SAR, China. The primary objective of the ATVA conferences remains the same: to exchange and promote the latest advances of state-of-the-art...... research on theoretical and practical aspects of automated analysis, verification, and synthesis. Among 74 research papers and 10 tool papers submitted to ATVA 2009, the Program Committee accepted 23 as regular papers and 3 as tool papers. In all, 33 experts from 17 countries worked hard to make sure...

  1. An Automated Method for Ozonesonde Calibration: New Insights

    Science.gov (United States)

    Schmidlin, F. J.; Hoegger, Bruno A.; Levrat, Gilbert; Baldwin, Tony

    2008-01-01

    An automated method for preparation of the electrochemical concentration cell (ECC) ozonesonde is presented. Development of a computer-controlled system for preparation and calibration of the ECC is an improvement over the manual preparation method, and reduces subjectivity considerably. Preparation measurements in digital form aids analysis of the ECC before release and enhances post-flight data certification. Calibration of ozonesondes over a range of ozone concentrations between 0 mPA and 30 mPA is discussed. This presentation describes the automatic system, gives examples of calibrations. The automated system enables comparison of varying potassium iodide (KI) concentrations that should allow adjustment of earlier ozonesonde data obtained with different KT concentrations used since 1970, i.e., 2, 1.5, 1, and 0.5 percent. Preliminary results indicate ECC accuracy has a strong dependence on the electrolyte concentration and should not be considered linear with altitude.

  2. An automated nudged elastic band method

    Science.gov (United States)

    Kolsbjerg, Esben L.; Groves, Michael N.; Hammer, Bjørk

    2016-09-01

    A robust, efficient, dynamic, and automated nudged elastic band (AutoNEB) algorithm to effectively locate transition states is presented. The strength of the algorithm is its ability to use fewer resources than the nudged elastic band (NEB) method by focusing first on converging a rough path before improving upon the resolution around the transition state. To demonstrate its efficiency, it has been benchmarked using a simple diffusion problem and a dehydrogenation reaction. In both cases, the total number of force evaluations used by the AutoNEB method is significantly less than the NEB method. Furthermore, it is shown that for a fast and robust relaxation to the transition state, a climbing image elastic band method where the full spring force, rather than only the component parallel to the local tangent to the path, is preferred especially for pathways through energy landscapes with multiple local minima. The resulting corner cutting does not affect the accuracy of the transition state as long as this is located with the climbing image method. Finally, a number of pitfalls often encountered while locating the true transition state of a reaction are discussed in terms of systematically exploring the multidimensional energy landscape of a given process.

  3. An overview of the contaminant analysis automation program

    International Nuclear Information System (INIS)

    The Department of Energy (DOE) has significant amounts of radioactive and hazardous wastes stored, buried, and still being generated at many sites within the United States. These wastes must be characterized to determine the elemental, isotopic, and compound content before remediation can begin. In this paper, the authors project that sampling requirements will necessitate generating more than 10 million samples by 1995, which will far exceed the capabilities of our current manual chemical analysis laboratories. The Contaminant Analysis Automation effort (CAA), with Los Alamos National Laboratory (LANL) as to the coordinating Laboratory, is designing and fabricating robotic systems that will standardize and automate both the hardware and the software of the most common environmental chemical methods. This will be accomplished by designing and producing several unique analysis systems called Standard Analysis Methods (SAM). Each SAM will automate a specific chemical method, including sample preparation, the analytical analysis, and the data interpretation, by using a building block known as the Standard Laboratory Module (SLM). This concept allows the chemist to assemble an automated environmental method using standardized SLMs easily and without the worry of hardware compatibility or the necessity of generating complicated control programs

  4. CRITICAL ASSESSMENT OF AUTOMATED FLOW CYTOMETRY DATA ANALYSIS TECHNIQUES

    Science.gov (United States)

    Aghaeepour, Nima; Finak, Greg; Hoos, Holger; Mosmann, Tim R.; Gottardo, Raphael; Brinkman, Ryan; Scheuermann, Richard H.

    2013-01-01

    Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks – mammalian cell population identification to determine if automated algorithms can reproduce expert manual gating, and sample classification to determine if analysis pipelines can identify characteristics that correlate with external variables (e.g., clinical outcome). This analysis presents the results of the first of these challenges. Several methods performed well compared to manual gating or external variables using statistical performance measures, suggesting that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis. PMID:23396282

  5. An approach to automated chromosome analysis

    International Nuclear Information System (INIS)

    The methods of approach developed with a view to automatic processing of the different stages of chromosome analysis are described in this study divided into three parts. Part 1 relates the study of automated selection of metaphase spreads, which operates a decision process in order to reject ail the non-pertinent images and keep the good ones. This approach has been achieved by Computing a simulation program that has allowed to establish the proper selection algorithms in order to design a kit of electronic logical units. Part 2 deals with the automatic processing of the morphological study of the chromosome complements in a metaphase: the metaphase photographs are processed by an optical-to-digital converter which extracts the image information and writes it out as a digital data set on a magnetic tape. For one metaphase image this data set includes some 200 000 grey values, encoded according to a 16, 32 or 64 grey-level scale, and is processed by a pattern recognition program isolating the chromosomes and investigating their characteristic features (arm tips, centromere areas), in order to get measurements equivalent to the lengths of the four arms. Part 3 studies a program of automated karyotyping by optimized pairing of human chromosomes. The data are derived from direct digitizing of the arm lengths by means of a BENSON digital reader. The program supplies' 1/ a list of the pairs, 2/ a graphic representation of the pairs so constituted according to their respective lengths and centromeric indexes, and 3/ another BENSON graphic drawing according to the author's own representation of the chromosomes, i.e. crosses with orthogonal arms, each branch being the accurate measurement of the corresponding chromosome arm. This conventionalized karyotype indicates on the last line the really abnormal or non-standard images unpaired by the program, which are of special interest for the biologist. (author)

  6. Automated Loads Analysis System (ATLAS)

    Science.gov (United States)

    Gardner, Stephen; Frere, Scot; O’Reilly, Patrick

    2013-01-01

    ATLAS is a generalized solution that can be used for launch vehicles. ATLAS is used to produce modal transient analysis and quasi-static analysis results (i.e., accelerations, displacements, and forces) for the payload math models on a specific Shuttle Transport System (STS) flight using the shuttle math model and associated forcing functions. This innovation solves the problem of coupling of payload math models into a shuttle math model. It performs a transient loads analysis simulating liftoff, landing, and all flight events between liftoff and landing. ATLAS utilizes efficient and numerically stable algorithms available in MSC/NASTRAN.

  7. Automated procedure for performing computer security risk analysis

    International Nuclear Information System (INIS)

    Computers, the invisible backbone of nuclear safeguards, monitor and control plant operations and support many materials accounting systems. Our automated procedure to assess computer security effectiveness differs from traditional risk analysis methods. The system is modeled as an interactive questionnaire, fully automated on a portable microcomputer. A set of modular event trees links the questionnaire to the risk assessment. Qualitative scores are obtained for target vulnerability, and qualitative impact measures are evaluated for a spectrum of threat-target pairs. These are then combined by a linguistic algebra to provide an accurate and meaningful risk measure. 12 references, 7 figures

  8. Rapid, automated online SPE-LC-QTRAP-MS/MS method for the simultaneous analysis of 14 phthalate metabolites and 5 bisphenol analogues in human urine.

    Science.gov (United States)

    Heffernan, A L; Thompson, K; Eaglesham, G; Vijayasarathy, S; Mueller, J F; Sly, P D; Gomez, M J

    2016-05-01

    Phthalates and bisphenol A (BPA) have received special attention in recent years due to their frequent use in consumer products and potential for adverse effects on human health. BPA is being replaced with a number of alternatives, including bisphenol S, bisphenol B, bisphenol F and bisphenol AF. These bisphenol analogues have similar potential for adverse health effects, but studies on human exposure are limited. Accurate measurement of multiple contaminants is important for estimating exposure. This paper describes a sensitive and automated method for the simultaneous determination of 14 phthalate metabolites, BPA and four bisphenol analogues in urine using online solid phase extraction coupled with high-performance liquid chromatography/tandem mass spectrometry using a hybrid triple-quadrupole linear ion trap mass spectrometer (LC-QTRAP-MS/MS), requiring very little sample volume (50µL). Quantification was performed under selected reaction monitoring (SRM) mode with negative electrospray ionization. The use of SRM combined with an enhanced product ion scan within the same analysis was examined. Unequivocal identification was provided by the acquisition of three SRM transitions per compound and isotope dilution. The analytical performance of the method was evaluated in synthetic and human urine. Linearity of response over three orders of magnitude was demonstrated for all of the compounds (R(2)>0.99), with method detection limits of 0.01-0.5ng/mL and limits of reporting of 0.07-3.1ng/mL. Accuracy ranged from 93% to 113% and inter- and intra-day precision were bisphenol S) to 18.5ng/mL (monoethyl phthalate).

  9. Techniques for Automated Performance Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Marcus, Ryan C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-09-02

    The performance of a particular HPC code depends on a multitude of variables, including compiler selection, optimization flags, OpenMP pool size, file system load, memory usage, MPI configuration, etc. As a result of this complexity, current predictive models have limited applicability, especially at scale. We present a formulation of scientific codes, nodes, and clusters that reduces complex performance analysis to well-known mathematical techniques. Building accurate predictive models and enhancing our understanding of scientific codes at scale is an important step towards exascale computing.

  10. ENHANCEMENT OF METHODICAL BACKGROUND FOR AUTOMATION WITH ENTERPRISE SPECIFICATION

    OpenAIRE

    Pisarchuk, O.; Uvarova, V.

    2010-01-01

    The article gets over the key methodical approaches to building up automated accounting information system with enterprise specification, by the example of program product «1C:Accounting». Shows the advantages and disadvantages of each key methodical approaches.

  11. Computer automated movement detection for the analysis of behavior

    OpenAIRE

    Ramazani, Roseanna B.; Harish R Krishnan; BERGESON, SUSAN E.; Atkinson, Nigel S.

    2007-01-01

    Currently, measuring ethanol behaviors in flies depends on expensive image analysis software or time intensive experimenter observation. We have designed an automated system for the collection and analysis of locomotor behavior data, using the IEEE 1394 acquisition program dvgrab, the image toolkit ImageMagick and the programming language Perl. In the proposed method, flies are placed in a clear container and a computer-controlled camera takes pictures at regular intervals. Digital subtractio...

  12. A Method for Automated Planning of FTTH Access Network Infrastructures

    DEFF Research Database (Denmark)

    Riaz, Muhammad Tahir; Pedersen, Jens Myrup; Madsen, Ole Brun

    2005-01-01

    In this paper a method for automated planning of Fiber to the Home (FTTH) access networks is proposed. We introduced a systematic approach for planning access network infrastructure. The GIS data and a set of algorithms were employed to make the planning process more automatic. The method explains...... method. The method, however, does not fully automate the planning but make the planning process significantly fast. The results and discussion are presented and conclusion is given in the end....

  13. Flux-P: Automating Metabolic Flux Analysis

    Directory of Open Access Journals (Sweden)

    Birgitta E. Ebert

    2012-11-01

    Full Text Available Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.

  14. Fully automated TV-image analysis of the cell-cycle: comparison of the PLM method with determinations of the percentage and the DNA content of labelled cells.

    Science.gov (United States)

    Wachsmuth, E D; van Golitschek, M; Macht, F; Maurer-Schultze, B

    1988-01-01

    A cell-cycle analysis based on a fully automated TV-image scanning system is proposed to replace the laborious PLM method. To compare the efficiency of the two procedures, cell-cycle parameters were assessed in Ehrlich (diploid and hyperdiploid), L-1210, and JB-1 mouse ascites tumours and in rat jejunal crypts. The percentages of labelled mitoses (PLM) were counted visually on Feulgen-stained autoradiographs obtained at various times after a single 3H-thymidine pulse. The fraction of labelled cells (P) and the DNA ratio of labelled and unlabelled cells were measured by TV-image analysis in the same slides and plotted against time. Within practical limits, TV-image analysis using the P-curve gives the same results as the PLM method. Using the P-curve has the important advantage that its first part, beginning at the time of 3H-thymidine injection and ending at the first maximum, furnishes more information about the cell cycle than the corresponding part of the PLM curve. It can be used to compute tG2M tS and the ratio of the growth faction index to the cell-cycle time (IP/tC) whereas the first part of the PLM-curve reveals only the length of the S-phase (tS). The IP/tC ratio is a readily accessible measure of growth and increases when the cells divide more frequently. Cell death rates may be neglected since the ratio is determined within less than the duration of one cell cycle. Moreover, the data from the first part of the P curve indicate whether there is a large non-growth fraction. If the non-growth fraction is small, i.e. if IP approximately 1, the P curve need only be measured until the first maximum is reached so that fewer samples and animals are required. If the non-growth fraction is large or unknown, the cell-cycle parameters are calculated by reference to the position and size not only of the first minimum and the first maximum, but also of the second minimum of the P curve.

  15. US Environmental Protection Agency Method 314.1, an automated sample preconcentration/matrix elimination suppressed conductivity method for the analysis of trace levels (0.50 microg/L) of perchlorate in drinking water.

    Science.gov (United States)

    Wagner, Herbert P; Pepich, B V; Pohl, C; Later, D; Joyce, R; Srinivasan, K; Thomas, D; Woodruff, A; Deborba, B; Munch, D J

    2006-06-16

    Since 1997 there has been increasing interest in the development of analytical methods for the analysis of perchlorate. The US Environmental Protection Agency (EPA) Method 314.0, which was used during the first Unregulated Contaminant Monitoring Regulation (UCMR) cycle, supports a method reporting limit (MRL) of 4.0 microg/L. The non-selective nature of conductivity detection, combined with very high ionic strength matrices, can create conditions that make the determination of perchlorate difficult. The objective of this work was to develop an automated, suppressed conductivity method with improved sensitivity for use in the second UCMR cycle. The new method, EPA Method 314.1, uses a 35 mm x 4 mm cryptand concentrator column in the sample loop position to concentrate perchlorate from a 2 mL sample volume, which is subsequently rinsed with 10 mM NaOH to remove interfering anions. The cryptand concentrator column is combined with a primary AS16 analytical column and a confirmation AS20 analytical column. Unique characteristics of the cryptand column allow perchlorate to be desorbed from the cryptand trap and refocused on the head of the guard column for subsequent separation and analysis. EPA Method 314.1 has a perchlorate lowest concentration minimum reporting level (LCMRL) of 0.13 microg/L in both drinking water and laboratory synthetic sample matrices (LSSM) containing up to 1,000 microg/L each of chloride, bicarbonate and sulfate.

  16. Automated Cache Performance Analysis And Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-12-23

    While there is no lack of performance counter tools for coarse-grained measurement of cache activity, there is a critical lack of tools for relating data layout to cache behavior to application performance. Generally, any nontrivial optimizations are either not done at all, or are done ”by hand” requiring significant time and expertise. To the best of our knowledge no tool available to users measures the latency of memory reference instructions for partic- ular addresses and makes this information available to users in an easy-to-use and intuitive way. In this project, we worked to enable the Open|SpeedShop performance analysis tool to gather memory reference latency information for specific instructions and memory ad- dresses, and to gather and display this information in an easy-to-use and intuitive way to aid performance analysts in identifying problematic data structures in their codes. This tool was primarily designed for use in the supercomputer domain as well as grid, cluster, cloud-based parallel e-commerce, and engineering systems and middleware. Ultimately, we envision a tool to automate optimization of application cache layout and utilization in the Open|SpeedShop performance analysis tool. To commercialize this soft- ware, we worked to develop core capabilities for gathering enhanced memory usage per- formance data from applications and create and apply novel methods for automatic data structure layout optimizations, tailoring the overall approach to support existing supercom- puter and cluster programming models and constraints. In this Phase I project, we focused on infrastructure necessary to gather performance data and present it in an intuitive way to users. With the advent of enhanced Precise Event-Based Sampling (PEBS) counters on recent Intel processor architectures and equivalent technology on AMD processors, we are now in a position to access memory reference information for particular addresses. Prior to the introduction of PEBS counters

  17. Streamlining and automation of radioanalytical methods at a commercial laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, J.T.; Dillard, J.W. [IT Corp., Knoxville, TN (United States)

    1993-12-31

    Through the careful planning and design of laboratory facilities and incorporation of modern instrumentation and robotics systems, properly trained and competent laboratory associates can efficiently and safely handle radioactive and mixed waste samples. This paper addresses the potential improvements radiochemistry and mixed waste laboratories can achieve utilizing robotics for automated sample analysis. Several examples of automated systems for sample preparation and analysis will be discussed.

  18. Automating Risk Analysis of Software Design Models

    Directory of Open Access Journals (Sweden)

    Maxime Frydman

    2014-01-01

    Full Text Available The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance.

  19. A Novel Automated Method for Analyzing Cylindrical Computed Tomography Data

    Science.gov (United States)

    Roth, D. J.; Burke, E. R.; Rauser, R. W.; Martin, R. E.

    2011-01-01

    A novel software method is presented that is applicable for analyzing cylindrical and partially cylindrical objects inspected using computed tomography. This method involves unwrapping and re-slicing data so that the CT data from the cylindrical object can be viewed as a series of 2-D sheets in the vertical direction in addition to volume rendering and normal plane views provided by traditional CT software. The method is based on interior and exterior surface edge detection and under proper conditions, is FULLY AUTOMATED and requires no input from the user except the correct voxel dimension from the CT scan. The software is available from NASA in 32- and 64-bit versions that can be applied to gigabyte-sized data sets, processing data either in random access memory or primarily on the computer hard drive. Please inquire with the presenting author if further interested. This software differentiates itself in total from other possible re-slicing software solutions due to complete automation and advanced processing and analysis capabilities.

  20. Comparison of Manual Versus Automated Data Collection Method for an Evidence-Based Nursing Practice Study

    Science.gov (United States)

    Byrne, M.D.; Jordan, T.R.; Welle, T.

    2013-01-01

    Objective The objective of this study was to investigate and improve the use of automated data collection procedures for nursing research and quality assurance. Methods A descriptive, correlational study analyzed 44 orthopedic surgical patients who were part of an evidence-based practice (EBP) project examining post-operative oxygen therapy at a Midwestern hospital. The automation work attempted to replicate a manually-collected data set from the EBP project. Results Automation was successful in replicating data collection for study data elements that were available in the clinical data repository. The automation procedures identified 32 “false negative” patients who met the inclusion criteria described in the EBP project but were not selected during the manual data collection. Automating data collection for certain data elements, such as oxygen saturation, proved challenging because of workflow and practice variations and the reliance on disparate sources for data abstraction. Automation also revealed instances of human error including computational and transcription errors as well as incomplete selection of eligible patients. Conclusion Automated data collection for analysis of nursing-specific phenomenon is potentially superior to manual data collection methods. Creation of automated reports and analysis may require initial up-front investment with collaboration between clinicians, researchers and information technology specialists who can manage the ambiguities and challenges of research and quality assurance work in healthcare. PMID:23650488

  1. Automated Parameter Studies Using a Cartesian Method

    Science.gov (United States)

    Murman, Scott M.; Aftosimis, Michael J.; Nemec, Marian

    2004-01-01

    Computational Fluid Dynamics (CFD) is now routinely used to analyze isolated points in a design space by performing steady-state computations at fixed flight conditions (Mach number, angle of attack, sideslip), for a fixed geometric configuration of interest. This "point analysis" provides detailed information about the flowfield, which aides an engineer in understanding, or correcting, a design. A point analysis is typically performed using high fidelity methods at a handful of critical design points, e.g. a cruise or landing configuration, or a sample of points along a flight trajectory.

  2. Automated Methods in Chiral Perturbation Theory on the Lattice

    CERN Document Server

    Borasoy, B; Krebs, H; Lewis, R; Borasoy, Bugra; Hippel, Georg M. von; Krebs, Hermann; Lewis, Randy

    2005-01-01

    We present a method to automatically derive the Feynman rules for mesonic chiral perturbation theory with a lattice regulator. The Feynman rules can be output both in a human-readable format and in a form suitable for an automated numerical evaluation of lattice Feynman diagrams. The automated method significantly simplifies working with improved or extended actions. Some applications to the study of finite-volume effects will be presented.

  3. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  4. Automated Radiochemical Separation, Analysis, and Sensing

    International Nuclear Information System (INIS)

    Chapter 14 for the 2nd edition of the Handbook of Radioactivity Analysis. The techniques and examples described in this chapter demonstrate that modern fluidic techniques and instrumentation can be used to develop automated radiochemical separation workstations. In many applications, these can be mechanically simple and key parameters can be controlled from software. If desired, many of the fluidic components and solution can be located remotely from the radioactive samples and other hot sample processing zones. There are many issues to address in developing automated radiochemical separation that perform reliably time after time in unattended operation. These are associated primarily with the separation and analytical chemistry aspects of the process. The relevant issues include the selectivity of the separation, decontamination factors, matrix effects, and recoveries from the separation column. In addition, flow rate effects, column lifetimes, carryover from one sample to another, and sample throughput must be considered. Nevertheless, successful approaches for addressing these issues have been developed. Radiochemical analysis is required not only for processing nuclear waste samples in the laboratory, but also for at-site or in situ applications. Monitors for nuclear waste processing operations represent an at-site application where continuous unattended monitoring is required to assure effective process radiochemical separations that produce waste streams that qualify for conversion to stable waste forms. Radionuclide sensors for water monitoring and long term stewardship represent an application where at-site or in situ measurements will be most effective. Automated radiochemical analyzers and sensors have been developed that demonstrate that radiochemical analysis beyond the analytical laboratory is both possible and practical

  5. Automated analysis of Xe-133 pulmonary ventilation (AAPV) in children

    Science.gov (United States)

    Cao, Xinhua; Treves, S. Ted

    2011-03-01

    In this study, an automated analysis of pulmonary ventilation (AAPV) was developed to visualize the ventilation in pediatric lungs using dynamic Xe-133 scintigraphy. AAPV is a software algorithm that converts a dynamic series of Xe- 133 images into four functional images: equilibrium, washout halftime, residual, and clearance rate by analyzing pixelbased activity. Compared to conventional methods of calculating global or regional ventilation parameters, AAPV provides a visual representation of pulmonary ventilation functions.

  6. Multispectral tissue analysis and classification towards enabling automated robotic surgery

    Science.gov (United States)

    Triana, Brian; Cha, Jaepyeong; Shademan, Azad; Krieger, Axel; Kang, Jin U.; Kim, Peter C. W.

    2014-02-01

    Accurate optical characterization of different tissue types is an important tool for potentially guiding surgeons and enabling automated robotic surgery. Multispectral imaging and analysis have been used in the literature to detect spectral variations in tissue reflectance that may be visible to the naked eye. Using this technique, hidden structures can be visualized and analyzed for effective tissue classification. Here, we investigated the feasibility of automated tissue classification using multispectral tissue analysis. Broadband reflectance spectra (200-1050 nm) were collected from nine different ex vivo porcine tissues types using an optical fiber-probe based spectrometer system. We created a mathematical model to train and distinguish different tissue types based upon analysis of the observed spectra using total principal component regression (TPCR). Compared to other reported methods, our technique is computationally inexpensive and suitable for real-time implementation. Each of the 92 spectra was cross-referenced against the nine tissue types. Preliminary results show a mean detection rate of 91.3%, with detection rates of 100% and 70.0% (inner and outer kidney), 100% and 100% (inner and outer liver), 100% (outer stomach), and 90.9%, 100%, 70.0%, 85.7% (four different inner stomach areas, respectively). We conclude that automated tissue differentiation using our multispectral tissue analysis method is feasible in multiple ex vivo tissue specimens. Although measurements were performed using ex vivo tissues, these results suggest that real-time, in vivo tissue identification during surgery may be possible.

  7. Automated Analysis of Security in Networking Systems

    DEFF Research Database (Denmark)

    Buchholtz, Mikael

    2004-01-01

    It has for a long time been a challenge to built secure networking systems. One way to counter this problem is to provide developers of software applications for networking systems with easy-to-use tools that can check security properties before the applications ever reach the marked. These tools...... will both help raise the general level of awareness of the problems and prevent the most basic flaws from occurring. This thesis contributes to the development of such tools. Networking systems typically try to attain secure communication by applying standard cryptographic techniques. In this thesis...... such networking systems are modelled in the process calculus LySa. On top of this programming language based formalism an analysis is developed, which relies on techniques from data and control ow analysis. These are techniques that can be fully automated, which make them an ideal basis for tools targeted at non...

  8. Automated Analysis, Classification, and Display of Waveforms

    Science.gov (United States)

    Kwan, Chiman; Xu, Roger; Mayhew, David; Zhang, Frank; Zide, Alan; Bonggren, Jeff

    2004-01-01

    A computer program partly automates the analysis, classification, and display of waveforms represented by digital samples. In the original application for which the program was developed, the raw waveform data to be analyzed by the program are acquired from space-shuttle auxiliary power units (APUs) at a sampling rate of 100 Hz. The program could also be modified for application to other waveforms -- for example, electrocardiograms. The program begins by performing principal-component analysis (PCA) of 50 normal-mode APU waveforms. Each waveform is segmented. A covariance matrix is formed by use of the segmented waveforms. Three eigenvectors corresponding to three principal components are calculated. To generate features, each waveform is then projected onto the eigenvectors. These features are displayed on a three-dimensional diagram, facilitating the visualization of the trend of APU operations.

  9. Automated quantification of budding Saccharomyces cerevisiae using a novel image cytometry method.

    Science.gov (United States)

    Laverty, Daniel J; Kury, Alexandria L; Kuksin, Dmitry; Pirani, Alnoor; Flanagan, Kevin; Chan, Leo Li-Ying

    2013-06-01

    The measurements of concentration, viability, and budding percentages of Saccharomyces cerevisiae are performed on a routine basis in the brewing and biofuel industries. Generation of these parameters is of great importance in a manufacturing setting, where they can aid in the estimation of product quality, quantity, and fermentation time of the manufacturing process. Specifically, budding percentages can be used to estimate the reproduction rate of yeast populations, which directly correlates with metabolism of polysaccharides and bioethanol production, and can be monitored to maximize production of bioethanol during fermentation. The traditional method involves manual counting using a hemacytometer, but this is time-consuming and prone to human error. In this study, we developed a novel automated method for the quantification of yeast budding percentages using Cellometer image cytometry. The automated method utilizes a dual-fluorescent nucleic acid dye to specifically stain live cells for imaging analysis of unique morphological characteristics of budding yeast. In addition, cell cycle analysis is performed as an alternative method for budding analysis. We were able to show comparable yeast budding percentages between manual and automated counting, as well as cell cycle analysis. The automated image cytometry method is used to analyze and characterize corn mash samples directly from fermenters during standard fermentation. Since concentration, viability, and budding percentages can be obtained simultaneously, the automated method can be integrated into the fermentation quality assurance protocol, which may improve the quality and efficiency of beer and bioethanol production processes.

  10. Automated Cache Performance Analysis And Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-12-23

    While there is no lack of performance counter tools for coarse-grained measurement of cache activity, there is a critical lack of tools for relating data layout to cache behavior to application performance. Generally, any nontrivial optimizations are either not done at all, or are done ”by hand” requiring significant time and expertise. To the best of our knowledge no tool available to users measures the latency of memory reference instructions for partic- ular addresses and makes this information available to users in an easy-to-use and intuitive way. In this project, we worked to enable the Open|SpeedShop performance analysis tool to gather memory reference latency information for specific instructions and memory ad- dresses, and to gather and display this information in an easy-to-use and intuitive way to aid performance analysts in identifying problematic data structures in their codes. This tool was primarily designed for use in the supercomputer domain as well as grid, cluster, cloud-based parallel e-commerce, and engineering systems and middleware. Ultimately, we envision a tool to automate optimization of application cache layout and utilization in the Open|SpeedShop performance analysis tool. To commercialize this soft- ware, we worked to develop core capabilities for gathering enhanced memory usage per- formance data from applications and create and apply novel methods for automatic data structure layout optimizations, tailoring the overall approach to support existing supercom- puter and cluster programming models and constraints. In this Phase I project, we focused on infrastructure necessary to gather performance data and present it in an intuitive way to users. With the advent of enhanced Precise Event-Based Sampling (PEBS) counters on recent Intel processor architectures and equivalent technology on AMD processors, we are now in a position to access memory reference information for particular addresses. Prior to the introduction of PEBS counters

  11. ASteCA - Automated Stellar Cluster Analysis

    CERN Document Server

    Perren, Gabriel I; Piatti, Andrés E

    2014-01-01

    We present ASteCA (Automated Stellar Cluster Analysis), a suit of tools designed to fully automatize the standard tests applied on stellar clusters to determine their basic parameters. The set of functions included in the code make use of positional and photometric data to obtain precise and objective values for a given cluster's center coordinates, radius, luminosity function and integrated color magnitude, as well as characterizing through a statistical estimator its probability of being a true physical cluster rather than a random overdensity of field stars. ASteCA incorporates a Bayesian field star decontamination algorithm capable of assigning membership probabilities using photometric data alone. An isochrone fitting process based on the generation of synthetic clusters from theoretical isochrones and selection of the best fit through a genetic algorithm is also present, which allows ASteCA to provide accurate estimates for a cluster's metallicity, age, extinction and distance values along with its unce...

  12. Automation of Large-scale Computer Cluster Monitoring Information Analysis

    Science.gov (United States)

    Magradze, Erekle; Nadal, Jordi; Quadt, Arnulf; Kawamura, Gen; Musheghyan, Haykuhi

    2015-12-01

    High-throughput computing platforms consist of a complex infrastructure and provide a number of services apt to failures. To mitigate the impact of failures on the quality of the provided services, a constant monitoring and in time reaction is required, which is impossible without automation of the system administration processes. This paper introduces a way of automation of the process of monitoring information analysis to provide the long and short term predictions of the service response time (SRT) for a mass storage and batch systems and to identify the status of a service at a given time. The approach for the SRT predictions is based on Adaptive Neuro Fuzzy Inference System (ANFIS). An evaluation of the approaches is performed on real monitoring data from the WLCG Tier 2 center GoeGrid. Ten fold cross validation results demonstrate high efficiency of both approaches in comparison to known methods.

  13. Prevalence of discordant microscopic changes with automated CBC analysis

    Directory of Open Access Journals (Sweden)

    Fabiano de Jesus Santos

    2014-12-01

    Full Text Available Introduction:The most common cause of diagnostic error is related to errors in laboratory tests as well as errors of results interpretation. In order to reduce them, the laboratory currently has modern equipment which provides accurate and reliable results. The development of automation has revolutionized the laboratory procedures in Brazil and worldwide.Objective:To determine the prevalence of microscopic changes present in blood slides concordant and discordant with results obtained using fully automated procedures.Materials and method:From January to July 2013, 1,000 hematological parameters slides were analyzed. Automated analysis was performed on last generation equipment, which methodology is based on electrical impedance, and is able to quantify all the figurative elements of the blood in a universe of 22 parameters. The microscopy was performed by two experts in microscopy simultaneously.Results:The data showed that only 42.70% were concordant, comparing with 57.30% discordant. The main findings among discordant were: Changes in red blood cells 43.70% (n = 250, white blood cells 38.46% (n = 220, and number of platelet 17.80% (n = 102.Discussion:The data show that some results are not consistent with clinical or physiological state of an individual, and cannot be explained because they have not been investigated, which may compromise the final diagnosis.Conclusion:It was observed that it is of fundamental importance that the microscopy qualitative analysis must be performed in parallel with automated analysis in order to obtain reliable results, causing a positive impact on the prevention, diagnosis, prognosis, and therapeutic follow-up.

  14. ASteCA: Automated Stellar Cluster Analysis

    Science.gov (United States)

    Perren, G. I.; Vázquez, R. A.; Piatti, A. E.

    2015-04-01

    We present the Automated Stellar Cluster Analysis package (ASteCA), a suit of tools designed to fully automate the standard tests applied on stellar clusters to determine their basic parameters. The set of functions included in the code make use of positional and photometric data to obtain precise and objective values for a given cluster's center coordinates, radius, luminosity function and integrated color magnitude, as well as characterizing through a statistical estimator its probability of being a true physical cluster rather than a random overdensity of field stars. ASteCA incorporates a Bayesian field star decontamination algorithm capable of assigning membership probabilities using photometric data alone. An isochrone fitting process based on the generation of synthetic clusters from theoretical isochrones and selection of the best fit through a genetic algorithm is also present, which allows ASteCA to provide accurate estimates for a cluster's metallicity, age, extinction and distance values along with its uncertainties. To validate the code we applied it on a large set of over 400 synthetic MASSCLEAN clusters with varying degrees of field star contamination as well as a smaller set of 20 observed Milky Way open clusters (Berkeley 7, Bochum 11, Czernik 26, Czernik 30, Haffner 11, Haffner 19, NGC 133, NGC 2236, NGC 2264, NGC 2324, NGC 2421, NGC 2627, NGC 6231, NGC 6383, NGC 6705, Ruprecht 1, Tombaugh 1, Trumpler 1, Trumpler 5 and Trumpler 14) studied in the literature. The results show that ASteCA is able to recover cluster parameters with an acceptable precision even for those clusters affected by substantial field star contamination. ASteCA is written in Python and is made available as an open source code which can be downloaded ready to be used from its official site.

  15. Automating Object-Oriented Software Development Methods

    OpenAIRE

    Tekinerdogan, Bedir; SAEKI, Motoshi; Sunyé, Gerson; Broek, van den, E.; Hruby, Pavel; Frohner, A´ kos

    2002-01-01

    Current software projects have generally to deal with producing and managing large and complex software products. It is generally believed that applying software development methods are useful in coping with this complexity and for supporting quality. As such numerous object-oriented software development methods have been defined. Nevertheless, methods often provide a complexity by their own due to their large number of artifacts, method rules and their complicated processes. We think that au...

  16. Automating Object-Oriented Software Development Methods

    OpenAIRE

    Tekinerdogan, Bedir; SAEKI, Motoshi; Sunyé, Gerson; Broek, van den, E.; Hruby, Pavel

    2001-01-01

    Current software projects have generally to deal with producing and managing large and complex software products. It is generally believed that applying software development methods are useful in coping with this complexity and for supporting quality. As such numerous object-oriented software development methods have been defined. Nevertheless, methods often provide a complexity by their own due to their large number of artifacts, method rules and their complicated processes. We think that au...

  17. An automated method for the layup of fiberglass fabric

    Science.gov (United States)

    Zhu, Siqi

    This dissertation presents an automated composite fabric layup solution based on a new method to deform fiberglass fabric referred to as shifting. A layup system was designed and implemented using a large robotic gantry and custom end-effector for shifting. Layup tests proved that the system can deposit fabric onto two-dimensional and three-dimensional tooling surfaces accurately and repeatedly while avoiding out-of-plane deformation. A process planning method was developed to generate tool paths for the layup system based on a geometric model of the tooling surface. The approach is analogous to Computer Numerical Controlled (CNC) machining, where Numerical Control (NC) code from a Computer-Aided Design (CAD) model is generated to drive the milling machine. Layup experiments utilizing the proposed method were conducted to validate the performance. The results show that the process planning software requires minimal time or human intervention and can generate tool paths leading to accurate composite fabric layups. Fiberglass fabric samples processed with shifting deformation were observed for meso-scale deformation. Tow thinning, bending and spacing was observed and measured. Overall, shifting did not create flaws in amounts that would disqualify the method from use in industry. This suggests that shifting is a viable method for use in automated manufacturing. The work of this dissertation provides a new method for the automated layup of broad width composite fabric that is not possible with any available composite automation systems to date.

  18. Ecological Automation Design, Extending Work Domain Analysis

    NARCIS (Netherlands)

    Amelink, M.H.J.

    2010-01-01

    In high–risk domains like aviation, medicine and nuclear power plant control, automation has enabled new capabilities, increased the economy of operation and has greatly contributed to safety. However, automation increases the number of couplings in a system, which can inadvertently lead to more com

  19. Automated seismic event location by waveform coherence analysis

    OpenAIRE

    Grigoli, Francesco

    2014-01-01

    Automated location of seismic events is a very important task in microseismic monitoring operations as well for local and regional seismic monitoring. Since microseismic records are generally characterised by low signal-to-noise ratio, such methods are requested to be noise robust and sufficiently accurate. Most of the standard automated location routines are based on the automated picking, identification and association of the first arrivals of P and S waves and on the minimization of the re...

  20. Automation literature: A brief review and analysis

    Science.gov (United States)

    Smith, D.; Dieterly, D. L.

    1980-01-01

    Current thought and research positions which may allow for an improved capability to understand the impact of introducing automation to an existing system are established. The orientation was toward the type of studies which may provide some general insight into automation; specifically, the impact of automation in human performance and the resulting system performance. While an extensive number of articles were reviewed, only those that addressed the issue of automation and human performance were selected to be discussed. The literature is organized along two dimensions: time, Pre-1970, Post-1970; and type of approach, Engineering or Behavioral Science. The conclusions reached are not definitive, but do provide the initial stepping stones in an attempt to begin to bridge the concept of automation in a systematic progression.

  1. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  2. Grasping devices and methods in automated production processes

    DEFF Research Database (Denmark)

    Fantoni, Gualtiero; Santochi, Marco; Dini, Gino;

    2014-01-01

    In automated production processes grasping devices and methods play a crucial role in the handling of many parts, components and products. This keynote paper starts with a classification of grasping phases, describes how different principles are adopted at different scales in different applications...... assembly to disassembly, from aerospace to food industry, from textile to logistics) are discussed. Finally, the most recent research is reviewed in order to introduce the new trends in grasping. They provide an outlook on the future of both grippers and robotic hands in automated production processes. (C...

  3. Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; determination of the total phosphorus by a Kjeldahl digestion method and an automated colorimetric finish that includes dialysis

    Science.gov (United States)

    Patton, Charles J.; Truitt, Earl P.

    1992-01-01

    A method to determine total phosphorus (TP) in the same digests prepared for total Kjeldahl nitrogen (TKN) determinations is desribed. The batch, high-temperature (block digester), HG(II)-catalyzed digestion step is similar to U.S. Geological Survey methods I-2552-85/I-4552-85 and U.S. Environmental Protection Agency method 365.4 except that sample and reagent volumes are halved. Prepared digests are desolvated at 220 degrees Celsius and digested at 370 degrees Celsius in separate block digesters set at these temperatures, rather than in a single, temperature-programmed block digester. This approach is used in the method escribed here, which permits 40 calibrants, reference waters, and smaples to be digested and resolvated in about an hour. Orthophosphate ions originally present in samples, along with those released during the digestion step, are determined colorimetrically at a rate of 90 tests per hour by an automated version of the phosphoantimonylmolybdenum blue procedure. About 100 microliters of digest are required per determination. The upper concentration limit is 2 milligrams per liter (mg/L) with a method detection limt of 0.01 mg/L. Repeatability for a sample containing approximately 1.6 mg/L of TP in a high suspended-solids matrix is 0.7 percent. Between-day precision for the same sample is 5.0 percent. A dialyzer in the air-segmented continuous flow analyzer provides on-line digest cleanup, eliminated particulates that otherwise would interfere in the colorimetric finish. An single-channel analyzer can process the resolvated digests from two pairs of block digesters each hour. Paired t-test analysis of TP concentrations for approximately 1,600 samples determined by the new method (U.S. Geologial Survey methods I-2610-91 and I-4610-91) and the old method (U.S. Geological Survey methods I-2600-85 and I-4600-85) revealed positive bias in the former of 0.02 to 0.04 mg/L for surface-water samples in agreement with previous studies. Concentrations of total

  4. Automated Model Fit Method for Diesel Engine Control Development

    NARCIS (Netherlands)

    Seykens, X.; Willems, F.P.T.; Kuijpers, B.; Rietjens, C.

    2014-01-01

    This paper presents an automated fit for a control-oriented physics-based diesel engine combustion model. This method is based on the combination of a dedicated measurement procedure and structured approach to fit the required combustion model parameters. Only a data set is required that is consider

  5. Statistical Analysis of Filament Features Based on the H{\\alpha} Solar Images from 1988 to 2013 by Computer Automated Detection Method

    CERN Document Server

    Hao, Q; Cao, W; Chen, P F

    2015-01-01

    We improve our filament automated detection method which was proposed in our previous works. It is then applied to process the full disk H$\\alpha$ data mainly obtained by Big Bear Solar Observatory (BBSO) from 1988 to 2013, spanning nearly 3 solar cycles. The butterfly diagrams of the filaments, showing the information of the filament area, spine length, tilt angle, and the barb number, are obtained. The variations of these features with the calendar year and the latitude band are analyzed. The drift velocities of the filaments in different latitude bands are calculated and studied. We also investigate the north-south (N-S) asymmetries of the filament numbers in total and in each subclass classified according to the filament area, spine length, and tilt angle. The latitudinal distribution of the filament number is found to be bimodal. About 80% of all the filaments have tilt angles within [0{\\deg}, 60{\\deg}]. For the filaments within latitudes lower (higher) than 50{\\deg} the northeast (northwest) direction i...

  6. Automating Object-Oriented Software Development Methods

    NARCIS (Netherlands)

    Tekinerdogan, Bedir; Saeki, Motoshi; Sunyé, Gerson; Broek, van den Pim; Hruby, Pavel

    2001-01-01

    Current software projects have generally to deal with producing and managing large and complex software products. It is generally believed that applying software development methods are useful in coping with this complexity and for supporting quality. As such numerous object-oriented software devel

  7. Automating Object-Oriented Software Development Methods

    NARCIS (Netherlands)

    Tekinerdogan, Bedir; Saeki, Motoshi; Sunyé, Gerson; Broek, van den Pim; Hruby, Pavel; Frohner, A´ kos

    2002-01-01

    Current software projects have generally to deal with producing and managing large and complex software products. It is generally believed that applying software development methods are useful in coping with this complexity and for supporting quality. As such numerous object-oriented software develo

  8. Automated Traffic Management System and Method

    Science.gov (United States)

    Glass, Brian J. (Inventor); Spirkovska, Liljana (Inventor); McDermott, William J. (Inventor); Reisman, Ronald J. (Inventor); Gibson, James (Inventor); Iverson, David L. (Inventor)

    2000-01-01

    A data management system and method that enables acquisition, integration, and management of real-time data generated at different rates, by multiple heterogeneous incompatible data sources. The system achieves this functionality by using an expert system to fuse data from a variety of airline, airport operations, ramp control, and air traffic control tower sources, to establish and update reference data values for every aircraft surface operation. The system may be configured as a real-time airport surface traffic management system (TMS) that electronically interconnects air traffic control, airline data, and airport operations data to facilitate information sharing and improve taxi queuing. In the TMS operational mode, empirical data shows substantial benefits in ramp operations for airlines, reducing departure taxi times by about one minute per aircraft in operational use, translating as $12 to $15 million per year savings to airlines at the Atlanta, Georgia airport. The data management system and method may also be used for scheduling the movement of multiple vehicles in other applications, such as marine vessels in harbors and ports, trucks or railroad cars in ports or shipping yards, and railroad cars in switching yards. Finally, the data management system and method may be used for managing containers at a shipping dock, stock on a factory floor or in a warehouse, or as a training tool for improving situational awareness of FAA tower controllers, ramp and airport operators, or commercial airline personnel in airfield surface operations.

  9. ECG Artifact Removal from Surface EMG Signal Using an Automated Method Based on Wavelet-ICA.

    Science.gov (United States)

    Abbaspour, Sara; Lindén, Maria; Gholamhosseini, Hamid

    2015-01-01

    This study aims at proposing an efficient method for automated electrocardiography (ECG) artifact removal from surface electromyography (EMG) signals recorded from upper trunk muscles. Wavelet transform is applied to the simulated data set of corrupted surface EMG signals to create multidimensional signal. Afterward, independent component analysis (ICA) is used to separate ECG artifact components from the original EMG signal. Components that correspond to the ECG artifact are then identified by an automated detection algorithm and are subsequently removed using a conventional high pass filter. Finally, the results of the proposed method are compared with wavelet transform, ICA, adaptive filter and empirical mode decomposition-ICA methods. The automated artifact removal method proposed in this study successfully removes the ECG artifacts from EMG signals with a signal to noise ratio value of 9.38 while keeping the distortion of original EMG to a minimum. PMID:25980853

  10. Testing an Automated Accuracy Assessment Method on Bibliographic Data

    Directory of Open Access Journals (Sweden)

    Marlies Olensky

    2014-12-01

    Full Text Available This study investigates automated data accuracy assessment as described in data quality literature for its suitability to assess bibliographic data. The data samples comprise the publications of two Nobel Prize winners in the field of Chemistry for a 10-year-publication period retrieved from the two bibliometric data sources, Web of Science and Scopus. The bibliographic records are assessed against the original publication (gold standard and an automatic assessment method is compared to a manual one. The results show that the manual assessment method reflects truer accuracy scores. The automated assessment method would need to be extended by additional rules that reflect specific characteristics of bibliographic data. Both data sources had higher accuracy scores per field than accumulated per record. This study contributes to the research on finding a standardized assessment method of bibliographic data accuracy as well as defining the impact of data accuracy on the citation matching process.

  11. Automated drawing of network plots in network meta-analysis.

    Science.gov (United States)

    Rücker, Gerta; Schwarzer, Guido

    2016-03-01

    In systematic reviews based on network meta-analysis, the network structure should be visualized. Network plots often have been drawn by hand using generic graphical software. A typical way of drawing networks, also implemented in statistical software for network meta-analysis, is a circular representation, often with many crossing lines. We use methods from graph theory in order to generate network plots in an automated way. We give a number of requirements for graph drawing and present an algorithm that fits prespecified ideal distances between the nodes representing the treatments. The method was implemented in the function netgraph of the R package netmeta and applied to a number of networks from the literature. We show that graph representations with a small number of crossing lines are often preferable to circular representations. PMID:26060934

  12. Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: An analysis of ATP-induced ribonucleotide reductase R1 hexamerization data

    Directory of Open Access Journals (Sweden)

    Radivoyevitch Tomas

    2009-12-01

    /30 > 508/2088 with p -15. Finally, 99 of the 2088 models did not have any terms with ATP/R1 ratios >1.5, but of the top 30, there were 14 such models (14/30 > 99/2088 with p -16, i.e. the existence of R1 hexamers with >3 a-sites occupied by ATP is also not supported by this dataset. Conclusion The analysis presented suggests that three a-sites may not be occupied by ATP in R1 hexamers under the conditions of the data analyzed. If a-sites fill before h-sites, this implies that the dataset analyzed can be explained without the existence of an h-site. Reviewers This article was reviewed by Ossama Kashlan (nominated by Philip Hahnfeldt, Bin Hu (nominated by William Hlavacek and Rainer Sachs.

  13. An automated confirmatory system for analysis of mammograms.

    Science.gov (United States)

    Peng, W; Mayorga, R V; Hussein, E M A

    2016-03-01

    This paper presents an integrated system for the automatic analysis of mammograms to assist radiologists in confirming their diagnosis in mammography screening. The proposed automated confirmatory system (ACS) can process a digitalized mammogram online, and generates a high quality filtered segmentation of an image for biological interpretation and a texture-feature based diagnosis. We use a serial of image pre-processing and segmentation techniques, including 2D median filtering, seeded region growing (SRG) algorithm, image contrast enhancement, to remove noise, delete radiopaque artifacts and eliminate the projection of the pectoral muscle from a digitalized mammogram. We also develop an entire-image texture-feature based classification method, by combining a Rough-set approach to extract five fundamental texture features from images, and then an Artificial Neural Network technique to classify a mammogram as: normal; indicating the presence of a benign lump; or representing a malignant tumor. Here, 222 random images from the Mammographic Image Analysis Society (MIAS) database are used for the offline ACS training. Once the system is tuned and trained, it is ready for the automated use for the analysis and diagnosis of new mammograms. To test the trained system, a separate set of 100 random images from the MIAS and another set of 100 random images from the independent BancoWeb database are selected. The proposed ACS is shown to be successful in confirming diagnosis of mammograms from the two independent databases. PMID:26742491

  14. Quantifying biodiversity using digital cameras and automated image analysis.

    Science.gov (United States)

    Roadknight, C. M.; Rose, R. J.; Barber, M. L.; Price, M. C.; Marshall, I. W.

    2009-04-01

    Monitoring the effects on biodiversity of extensive grazing in complex semi-natural habitats is labour intensive. There are also concerns about the standardization of semi-quantitative data collection. We have chosen to focus initially on automating the most time consuming aspect - the image analysis. The advent of cheaper and more sophisticated digital camera technology has lead to a sudden increase in the number of habitat monitoring images and information that is being collected. We report on the use of automated trail cameras (designed for the game hunting market) to continuously capture images of grazer activity in a variety of habitats at Moor House National Nature Reserve, which is situated in the North of England at an average altitude of over 600m. Rainfall is high, and in most areas the soil consists of deep peat (1m to 3m), populated by a mix of heather, mosses and sedges. The cameras have been continuously in operation over a 6 month period, daylight images are in full colour and night images (IR flash) are black and white. We have developed artificial intelligence based methods to assist in the analysis of the large number of images collected, generating alert states for new or unusual image conditions. This paper describes the data collection techniques, outlines the quantitative and qualitative data collected and proposes online and offline systems that can reduce the manpower overheads and increase focus on important subsets in the collected data. By converting digital image data into statistical composite data it can be handled in a similar way to other biodiversity statistics thus improving the scalability of monitoring experiments. Unsupervised feature detection methods and supervised neural methods were tested and offered solutions to simplifying the process. Accurate (85 to 95%) categorization of faunal content can be obtained, requiring human intervention for only those images containing rare animals or unusual (undecidable) conditions, and

  15. Comparison of manual and automated quantification methods of {sup 123}I-ADAM

    Energy Technology Data Exchange (ETDEWEB)

    Kauppinen, T. [Helsinki Univ. Central Hospital (Finland). HUS Helsinki Medical Imaging Center; Helsinki Univ. Central Hospital (Finland). Division of Nuclear Medicine; Koskela, A.; Ahonen, A. [Helsinki Univ. Central Hospital (Finland). Division of Nuclear Medicine; Diemling, M. [Hermes Medical Solutions, Stockholm (Sweden); Keski-Rahkonen, A.; Sihvola, E. [Helsinki Univ. (Finland). Dept. of Public Health; Helsinki Univ. Central Hospital (Finland). Dept. of Psychiatry

    2005-07-01

    {sup 123}I-ADAM is a novel radioligand for imaging of the brain serotonin transporters (SERTs). Traditionally, the analysis of brain receptor studies has been based on observer-dependent manual region of interest definitions and visual interpretation. Our aim was to create a template for automated image registrations and volume of interest (VOI) quantification and to show that an automated quantification method of {sup 123}I-ADAM is more repeatable than the manual method. Patients, methods: A template and a predefined VOI map was created from {sup 123}I-ADAM scans done for healthy volunteers (n=15). Scans of another group of healthy persons (HS, n=12) and patients with bulimia nervosa (BN, n=10) were automatically fitted to the template and specific binding ratios (SBRs) were calculated by using the VOI map. Manual VOI definitions were done for the HS and BN groups by both one and two observers. The repeatability of the automated method was evaluated by using the BN group. Results: For the manual method, the interobserver coefficient of repeatability was 0.61 for the HS group and 1.00 for the BN group. The intra-observer coefficient of repeatability for the BN group was 0.70. For the automated method, the coefficient of repeatability was 0.13 for SBRs in midbrain. Conclusion: An automated quantification gives valuable information in addition to visual interpretation decreasing also the total image handling time and giving clear advantages for research work. An automated method for analysing {sup 123}I-ADAM binding to the brain SERT gives repeatable results for fitting the studies to the template and for calculating SBRs, and could therefore replace manual methods. (orig.)

  16. α-Automated Reasoning Method Based on Lattice-Valued Propositional Logic LP(X)

    Institute of Scientific and Technical Information of China (English)

    王伟; 徐扬; 王学芳

    2002-01-01

    This paper is focused on automated reasoning based on classical propositional logic and lattice-valued propositional logic LP(X). A new method of automated reasoning is given, and the soundness and completeness theorems of this method are proved.

  17. Trends in biomedical informatics: automated topic analysis of JAMIA articles.

    Science.gov (United States)

    Han, Dong; Wang, Shuang; Jiang, Chao; Jiang, Xiaoqian; Kim, Hyeon-Eui; Sun, Jimeng; Ohno-Machado, Lucila

    2015-11-01

    Biomedical Informatics is a growing interdisciplinary field in which research topics and citation trends have been evolving rapidly in recent years. To analyze these data in a fast, reproducible manner, automation of certain processes is needed. JAMIA is a "generalist" journal for biomedical informatics. Its articles reflect the wide range of topics in informatics. In this study, we retrieved Medical Subject Headings (MeSH) terms and citations of JAMIA articles published between 2009 and 2014. We use tensors (i.e., multidimensional arrays) to represent the interaction among topics, time and citations, and applied tensor decomposition to automate the analysis. The trends represented by tensors were then carefully interpreted and the results were compared with previous findings based on manual topic analysis. A list of most cited JAMIA articles, their topics, and publication trends over recent years is presented. The analyses confirmed previous studies and showed that, from 2012 to 2014, the number of articles related to MeSH terms Methods, Organization & Administration, and Algorithms increased significantly both in number of publications and citations. Citation trends varied widely by topic, with Natural Language Processing having a large number of citations in particular years, and Medical Record Systems, Computerized remaining a very popular topic in all years.

  18. Automated Steel Cleanliness Analysis Tool (ASCAT)

    International Nuclear Information System (INIS)

    The objective of this study was to develop the Automated Steel Cleanliness Analysis Tool (ASCATTM) to permit steelmakers to evaluate the quality of the steel through the analysis of individual inclusions. By characterizing individual inclusions, determinations can be made as to the cleanliness of the steel. Understanding the complicating effects of inclusions in the steelmaking process and on the resulting properties of steel allows the steel producer to increase throughput, better control the process, reduce remelts, and improve the quality of the product. The ASCAT (Figure 1) is a steel-smart inclusion analysis tool developed around a customized next-generation computer controlled scanning electron microscopy (NG-CCSEM) hardware platform that permits acquisition of inclusion size and composition data at a rate never before possible in SEM-based instruments. With built-in customized ''intelligent'' software, the inclusion data is automatically sorted into clusters representing different inclusion types to define the characteristics of a particular heat (Figure 2). The ASCAT represents an innovative new tool for the collection of statistically meaningful data on inclusions, and provides a means of understanding the complicated effects of inclusions in the steel making process and on the resulting properties of steel. Research conducted by RJLG with AISI (American Iron and Steel Institute) and SMA (Steel Manufactures of America) members indicates that the ASCAT has application in high-grade bar, sheet, plate, tin products, pipes, SBQ, tire cord, welding rod, and specialty steels and alloys where control of inclusions, whether natural or engineered, are crucial to their specification for a given end-use. Example applications include castability of calcium treated steel; interstitial free (IF) degasser grade slag conditioning practice; tundish clogging and erosion minimization; degasser circulation and optimization; quality assessment/steel cleanliness; slab, billet

  19. Automated Steel Cleanliness Analysis Tool (ASCAT)

    Energy Technology Data Exchange (ETDEWEB)

    Gary Casuccio (RJ Lee Group); Michael Potter (RJ Lee Group); Fred Schwerer (RJ Lee Group); Dr. Richard J. Fruehan (Carnegie Mellon University); Dr. Scott Story (US Steel)

    2005-12-30

    The objective of this study was to develop the Automated Steel Cleanliness Analysis Tool (ASCATTM) to permit steelmakers to evaluate the quality of the steel through the analysis of individual inclusions. By characterizing individual inclusions, determinations can be made as to the cleanliness of the steel. Understanding the complicating effects of inclusions in the steelmaking process and on the resulting properties of steel allows the steel producer to increase throughput, better control the process, reduce remelts, and improve the quality of the product. The ASCAT (Figure 1) is a steel-smart inclusion analysis tool developed around a customized next-generation computer controlled scanning electron microscopy (NG-CCSEM) hardware platform that permits acquisition of inclusion size and composition data at a rate never before possible in SEM-based instruments. With built-in customized ''intelligent'' software, the inclusion data is automatically sorted into clusters representing different inclusion types to define the characteristics of a particular heat (Figure 2). The ASCAT represents an innovative new tool for the collection of statistically meaningful data on inclusions, and provides a means of understanding the complicated effects of inclusions in the steel making process and on the resulting properties of steel. Research conducted by RJLG with AISI (American Iron and Steel Institute) and SMA (Steel Manufactures of America) members indicates that the ASCAT has application in high-grade bar, sheet, plate, tin products, pipes, SBQ, tire cord, welding rod, and specialty steels and alloys where control of inclusions, whether natural or engineered, are crucial to their specification for a given end-use. Example applications include castability of calcium treated steel; interstitial free (IF) degasser grade slag conditioning practice; tundish clogging and erosion minimization; degasser circulation and optimization; quality assessment

  20. A Simple Method for Automated Equilibration Detection in Molecular Simulations.

    Science.gov (United States)

    Chodera, John D

    2016-04-12

    Molecular simulations intended to compute equilibrium properties are often initiated from configurations that are highly atypical of equilibrium samples, a practice which can generate a distinct initial transient in mechanical observables computed from the simulation trajectory. Traditional practice in simulation data analysis recommends this initial portion be discarded to equilibration, but no simple, general, and automated procedure for this process exists. Here, we suggest a conceptually simple automated procedure that does not make strict assumptions about the distribution of the observable of interest in which the equilibration time is chosen to maximize the number of effectively uncorrelated samples in the production timespan used to compute equilibrium averages. We present a simple Python reference implementation of this procedure and demonstrate its utility on typical molecular simulation data. PMID:26771390

  1. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods.

    Science.gov (United States)

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D

    2016-02-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  2. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods.

    Science.gov (United States)

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D

    2016-02-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  3. Automated haematology analysis to diagnose malaria

    Directory of Open Access Journals (Sweden)

    Grobusch Martin P

    2010-11-01

    Full Text Available Abstract For more than a decade, flow cytometry-based automated haematology analysers have been studied for malaria diagnosis. Although current haematology analysers are not specifically designed to detect malaria-related abnormalities, most studies have found sensitivities that comply with WHO malaria-diagnostic guidelines, i.e. ≥ 95% in samples with > 100 parasites/μl. Establishing a correct and early malaria diagnosis is a prerequisite for an adequate treatment and to minimizing adverse outcomes. Expert light microscopy remains the 'gold standard' for malaria diagnosis in most clinical settings. However, it requires an explicit request from clinicians and has variable accuracy. Malaria diagnosis with flow cytometry-based haematology analysers could become an important adjuvant diagnostic tool in the routine laboratory work-up of febrile patients in or returning from malaria-endemic regions. Haematology analysers so far studied for malaria diagnosis are the Cell-Dyn®, Coulter® GEN·S and LH 750, and the Sysmex XE-2100® analysers. For Cell-Dyn analysers, abnormal depolarization events mainly in the lobularity/granularity and other scatter-plots, and various reticulocyte abnormalities have shown overall sensitivities and specificities of 49% to 97% and 61% to 100%, respectively. For the Coulter analysers, a 'malaria factor' using the monocyte and lymphocyte size standard deviations obtained by impedance detection has shown overall sensitivities and specificities of 82% to 98% and 72% to 94%, respectively. For the XE-2100, abnormal patterns in the DIFF, WBC/BASO, and RET-EXT scatter-plots, and pseudoeosinophilia and other abnormal haematological variables have been described, and multivariate diagnostic models have been designed with overall sensitivities and specificities of 86% to 97% and 81% to 98%, respectively. The accuracy for malaria diagnosis may vary according to species, parasite load, immunity and clinical context where the

  4. A screened automated structural search with semiempirical methods

    Science.gov (United States)

    Ota, Yukihiro; Ruiz-Barragan, Sergi; Machida, Masahiko; Shiga, Motoyuki

    2016-03-01

    We developed an interface program between a program suite for an automated search of chemical reaction pathways, GRRM, and a program package of semiempirical methods, MOPAC. A two-step structural search is proposed as an application of this interface program. A screening test is first performed by semiempirical calculations. Subsequently, a reoptimization procedure is done by ab initio or density functional calculations. We apply this approach to ion adsorption on cellulose. The computational efficiency is also shown for a GRRM search. The interface program is suitable for the structural search of large molecular systems for which semiempirical methods are applicable.

  5. A screened automated structural search with semiempirical methods

    CERN Document Server

    Ota, Yukihiro; Machida, Masahiko; Shiga, Motoyuki

    2016-01-01

    We developed an interface program between a program suite for an automated search of chemical reaction pathways, GRRM, and a program package of semiempirical methods, MOPAC. A two-step structural search is proposed as an application of this interface program. A screening test is first performed by semiempirical calculations. Subsequently, a reoptimization procedure is done by ab initio or density functional calculations. We apply this approach to ion adsorption on cellulose. The computational efficiency is also shown for a GRRM search. The interface program is suitable for the structural search of large molecular systems for which semiempirical methods are applicable.

  6. A new automated method of e-learner's satisfaction measurement

    Directory of Open Access Journals (Sweden)

    Armands Strazds

    2007-06-01

    Full Text Available This paper presents a new method of measuring learner’s satisfaction while using electronic learning materials (e-courses, edutainment games, etc. in virtual non-linear environments. Method is based on a relation of Discovering and Learning probability distribution curves obtained by collecting and evaluating the human-computer interaction data. While being near real-time, this measurement is considered highly unobtrusive and cost-effective because of its automated approach. The first working prototype EDUSA 1.0 was developed and successfully tested by the Distance Education Studies Centre of Riga Technical University.

  7. Individual flexor tendon identification within the carpal tunnel: A semi-automated analysis method for serial cross-section magnetic resonance images

    Directory of Open Access Journals (Sweden)

    Nicole M Kunze

    2009-12-01

    Full Text Available Nicole M Kunze1, Jessica E Goetz2, Daniel R Thedens3, Thomas E Baer2, Ericka A Lawler2, Thomas D Brown21Department of Biomedical Engineering, 2Department of Orthopaedics and Rehabilitation, 3Department of Radiology, University of Iowa, Iowa City, IA, USAAbstract: Carpal tunnel syndrome is commonly viewed as resulting from chronic mechanical insult of the median nerve by adjacent anatomical structures. Both the median nerve and its surrounding soft tissue structures are well visualized on magnetic resonance (MR images of the wrist and hand. Addressing nerve damage from impingement of flexor digitorum tendons co-occupying the tunnel is attractive, but to date has been restricted by a lack of means for making individual identifications of the respective tendons. In this image analysis work, we have developed a region-growing method to positively identify each individual digital flexor tendon within the carpal tunnel by tracking it from a more distal MR section where the respective tendon identities are unambiguous. Illustratively, the new method was applied to MRI scans from four different subjects in a variety of hand poses. Conventional shape measures yielded less discriminatory information than did evaluations of individual tendon location and arrangement. This new method of rapid identification of individual tendons will facilitate analysis of tendon/nerve interactions within the tunnel, thereby providing better information about mechanical insult of the median nerve.Keywords: carpal tunnel syndrome, magnetic resonance imaging, region growing, digital flexor tendons

  8. Fully automated diabetic retinopathy screening using morphological component analysis.

    Science.gov (United States)

    Imani, Elaheh; Pourreza, Hamid-Reza; Banaee, Touka

    2015-07-01

    Diabetic retinopathy is the major cause of blindness in the world. It has been shown that early diagnosis can play a major role in prevention of visual loss and blindness. This diagnosis can be made through regular screening and timely treatment. Besides, automation of this process can significantly reduce the work of ophthalmologists and alleviate inter and intra observer variability. This paper provides a fully automated diabetic retinopathy screening system with the ability of retinal image quality assessment. The novelty of the proposed method lies in the use of Morphological Component Analysis (MCA) algorithm to discriminate between normal and pathological retinal structures. To this end, first a pre-screening algorithm is used to assess the quality of retinal images. If the quality of the image is not satisfactory, it is examined by an ophthalmologist and must be recaptured if necessary. Otherwise, the image is processed for diabetic retinopathy detection. In this stage, normal and pathological structures of the retinal image are separated by MCA algorithm. Finally, the normal and abnormal retinal images are distinguished by statistical features of the retinal lesions. Our proposed system achieved 92.01% sensitivity and 95.45% specificity on the Messidor dataset which is a remarkable result in comparison with previous work. PMID:25863517

  9. Tank Farm Operations Surveillance Automation Analysis

    Energy Technology Data Exchange (ETDEWEB)

    MARQUEZ, D.L.

    2000-12-21

    The Nuclear Operations Project Services identified the need to improve manual tank farm surveillance data collection, review, distribution and storage practices often referred to as Operator Rounds. This document provides the analysis in terms of feasibility to improve the manual data collection methods by using handheld computer units, barcode technology, a database for storage and acquisitions, associated software, and operational procedures to increase the efficiency of Operator Rounds associated with surveillance activities.

  10. Tank Farm Operations Surveillance Automation Analysis

    International Nuclear Information System (INIS)

    The Nuclear Operations Project Services identified the need to improve manual tank farm surveillance data collection, review, distribution and storage practices often referred to as Operator Rounds. This document provides the analysis in terms of feasibility to improve the manual data collection methods by using handheld computer units, barcode technology, a database for storage and acquisitions, associated software, and operational procedures to increase the efficiency of Operator Rounds associated with surveillance activities

  11. Automating sensitivity analysis of computer models using computer calculus

    International Nuclear Information System (INIS)

    An automated procedure for performing sensitivity analysis has been developed. The procedure uses a new FORTRAN compiler with computer calculus capabilities to generate the derivatives needed to set up sensitivity equations. The new compiler is called GRESS - Gradient Enhanced Software System. Application of the automated procedure with direct and adjoint sensitivity theory for the analysis of non-linear, iterative systems of equations is discussed. Calculational efficiency consideration and techniques for adjoint sensitivity analysis are emphasized. The new approach is found to preserve the traditional advantages of adjoint theory while removing the tedious human effort previously needed to apply this theoretical methodology. Conclusions are drawn about the applicability of the automated procedure in numerical analysis and large-scale modelling sensitivity studies

  12. Feasibility studies of safety assessment methods for programmable automation systems. Final report of the AVV project

    International Nuclear Information System (INIS)

    Feasibility studies of two different groups of methodologies for safety assessment of programmable automation systems has been executed at the Technical Research Centre of Finland (VTT). The studies concerned the dynamic testing methods and the fault tree (FT) and failure mode and effects analysis (FMEA) methods. In order to get real experience in the application of these methods, an experimental testing of two realistic pilot systems were executed and a FT/FMEA analysis of a programmable safety function accomplished. The purpose of the studies was not to assess the object systems, but to get experience in the application of methods and assess their potentials and development needs. (46 refs., 21 figs.)

  13. Automated SEM Modal Analysis Applied to the Diogenites

    Science.gov (United States)

    Bowman, L. E.; Spilde, M. N.; Papike, James J.

    1996-01-01

    Analysis of volume proportions of minerals, or modal analysis, is routinely accomplished by point counting on an optical microscope, but the process, particularly on brecciated samples such as the diogenite meteorites, is tedious and prone to error by misidentification of very small fragments, which may make up a significant volume of the sample. Precise volume percentage data can be gathered on a scanning electron microscope (SEM) utilizing digital imaging and an energy dispersive spectrometer (EDS). This form of automated phase analysis reduces error, and at the same time provides more information than could be gathered using simple point counting alone, such as particle morphology statistics and chemical analyses. We have previously studied major, minor, and trace-element chemistry of orthopyroxene from a suite of diogenites. This abstract describes the method applied to determine the modes on this same suite of meteorites and the results of that research. The modal abundances thus determined add additional information on the petrogenesis of the diogenites. In addition, low-abundance phases such as spinels were located for further analysis by this method.

  14. Comparison of Particulate Mercury Measured with Manual and Automated Methods

    Directory of Open Access Journals (Sweden)

    Rachel Russo

    2011-01-01

    Full Text Available A study was conducted to compare measuring particulate mercury (HgP with the manual filter method and the automated Tekran system. Simultaneous measurements were conducted with the Tekran and Teflon filter methodologies in the marine and coastal continental atmospheres. Overall, the filter HgP values were on the average 21% higher than the Tekran HgP, and >85% of the data were outside of ±25% region surrounding the 1:1 line. In some cases the filter values were as much as 3-fold greater, with

  15. Method and apparatus for automated, modular, biomass power generation

    Science.gov (United States)

    Diebold, James P.; Lilley, Arthur; Browne, Kingsbury III; Walt, Robb Ray; Duncan, Dustin; Walker, Michael; Steele, John; Fields, Michael; Smith, Trevor

    2011-03-22

    Method and apparatus for generating a low tar, renewable fuel gas from biomass and using it in other energy conversion devices, many of which were designed for use with gaseous and liquid fossil fuels. An automated, downdraft gasifier incorporates extensive air injection into the char bed to maintain the conditions that promote the destruction of residual tars. The resulting fuel gas and entrained char and ash are cooled in a special heat exchanger, and then continuously cleaned in a filter prior to usage in standalone as well as networked power systems.

  16. Method and automated apparatus for detecting coliform organisms

    Science.gov (United States)

    Dill, W. P.; Taylor, R. E.; Jeffers, E. L. (Inventor)

    1980-01-01

    Method and automated apparatus are disclosed for determining the time of detection of metabolically produced hydrogen by coliform bacteria cultured in an electroanalytical cell from the time the cell is inoculated with the bacteria. The detection time data provides bacteria concentration values. The apparatus is sequenced and controlled by a digital computer to discharge a spent sample, clean and sterilize the culture cell, provide a bacteria nutrient into the cell, control the temperature of the nutrient, inoculate the nutrient with a bacteria sample, measures the electrical potential difference produced by the cell, and measures the time of detection from inoculation.

  17. Automated quantitative gait analysis in animal models of movement disorders

    Directory of Open Access Journals (Sweden)

    Vandeputte Caroline

    2010-08-01

    Full Text Available Abstract Background Accurate and reproducible behavioral tests in animal models are of major importance in the development and evaluation of new therapies for central nervous system disease. In this study we investigated for the first time gait parameters of rat models for Parkinson's disease (PD, Huntington's disease (HD and stroke using the Catwalk method, a novel automated gait analysis test. Static and dynamic gait parameters were measured in all animal models, and these data were compared to readouts of established behavioral tests, such as the cylinder test in the PD and stroke rats and the rotarod tests for the HD group. Results Hemiparkinsonian rats were generated by unilateral injection of the neurotoxin 6-hydroxydopamine in the striatum or in the medial forebrain bundle. For Huntington's disease, a transgenic rat model expressing a truncated huntingtin fragment with multiple CAG repeats was used. Thirdly, a stroke model was generated by a photothrombotic induced infarct in the right sensorimotor cortex. We found that multiple gait parameters were significantly altered in all three disease models compared to their respective controls. Behavioural deficits could be efficiently measured using the cylinder test in the PD and stroke animals, and in the case of the PD model, the deficits in gait essentially confirmed results obtained by the cylinder test. However, in the HD model and the stroke model the Catwalk analysis proved more sensitive than the rotarod test and also added new and more detailed information on specific gait parameters. Conclusion The automated quantitative gait analysis test may be a useful tool to study both motor impairment and recovery associated with various neurological motor disorders.

  18. Analysis of Trinity Power Metrics for Automated Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Michalenko, Ashley Christine [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-07-28

    This is a presentation from Los Alamos National Laboraotyr (LANL) about the analysis of trinity power metrics for automated monitoring. The following topics are covered: current monitoring efforts, motivation for analysis, tools used, the methodology, work performed during the summer, and future work planned.

  19. On Automating and Standardising Corpus Callosum Analysis in Brain MRI

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille; Skoglund, Karl

    2005-01-01

    Corpus callosum analysis is influenced by many factors. The effort in controlling these has previously been incomplete and scattered. This paper sketches a complete pipeline for automated corpus callosum analysis from magnetic resonance images, with focus on measurement standardisation. The prese...

  20. Image analysis and platform development for automated phenotyping in cytomics

    NARCIS (Netherlands)

    Yan, Kuan

    2013-01-01

    This thesis is dedicated to the empirical study of image analysis in HT/HC screen study. Often a HT/HC screening produces extensive amounts that cannot be manually analyzed. Thus, an automated image analysis solution is prior to an objective understanding of the raw image data. Compared to general a

  1. Automating sensitivity analysis of computer models using computer calculus

    International Nuclear Information System (INIS)

    An automated procedure for performing sensitivity analyses has been developed. The procedure uses a new FORTRAN compiler with computer calculus capabilities to generate the derivatives needed to set up sensitivity equations. The new compiler is called GRESS - Gradient Enhanced Software System. Application of the automated procedure with ''direct'' and ''adjoint'' sensitivity theory for the analysis of non-linear, iterative systems of equations is discussed. Calculational efficiency consideration and techniques for adjoint sensitivity analysis are emphasized. The new approach is found to preserve the traditional advantages of adjoint theory while removing the tedious human effort previously needed to apply this theoretical methodology. Conclusions are drawn about the applicability of the automated procedure in numerical analysis and large-scale modelling sensitivity studies. 24 refs., 2 figs

  2. Malaria: the value of the automated depolarization analysis.

    Science.gov (United States)

    Josephine, F P; Nissapatorn, V

    2005-01-01

    This retrospective and descriptive study was carried out in the University of Malaya Medical Center (UMMC) from January to September, 2004. This study aimed to evaluate the diagnostic utility of the Cell-Dyn 4000 hematology analyzer's depolarization analysis and to determine the sensitivity and specificity of this technique in the context of malaria diagnosis. A total of 889 cases presenting with pyrexia of unknown origin or clinically suspected of malaria were examined. Sixteen of these blood samples were found to be positive; 12 for P. vivax, 3 for P. malariae, and 1 for P. falciparum by peripheral blood smear as the standard technique for parasite detection and species identification. Demographic characteristics showed that the majority of patients were in the age range of 20-57 with a mean of 35.9 (+/- SD) 11.4 years, and male foreign workers. Of these, 16 positive blood samples were also processed by Cell-Dyne 4000 analyzer in the normal complete blood count (CBC) operational mode. Malaria parasites produce hemozoin, which depolarizes light and this allows the automated detection of malaria during routine complete blood count analysis with the Abbot Cell-Dyn CD4000 instrument. The white blood cell (WBC) differential plots of all malaria positive samples showed abnormal depolarization events in the NEU-EOS and EOS I plots. This was not seen in the negative samples. In 12 patients with P. vivax infection, a cluster pattern in the Neu-EOS and EOS I plots was observed, and appeared color-coded green or black. In 3 patients with P. malariae infection, few random depolarization events in the NEU-EOS and EOS I plots were seen, and appeared color-coded green, black or blue. While in the patient with P. falciparum infection, the sample was color-coded green with a few random purple depolarizing events in the NEU-EOS and EOS I plots. This study confirms that automated depolarization analysis is a highly sensitive and specific method to diagnose whether or not a patient

  3. An automated method for identifying artifact in ICA of resting-state fMRI

    Directory of Open Access Journals (Sweden)

    Kaushik eBhaganagarapu

    2013-07-01

    Full Text Available An enduring issue with data-driven analysis and filtering methods is the interpretation of results. To assist, we present an automatic method for identifaction of artifact in independent components (ICs derived from functional MRI (fMRI. The method was designed with the following features: Does not require temporal information about an fMRI paradigm; Does not require the user to train the algorithm; Requires only the fMRI images (additional acquisition of anatomical imaging not required; Is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin; Can be applied to resting-state fMRI; Is automated, requiring minimal or no human intervention.We applied the method to a MELODIC probabilistic ICA of resting-state functional connectivity data acquired in 50 healthy control subjects, and compared the results to a blinded expert manual classification. The method identified between 26% and 72% of the components as artifact (mean 55%. 0.3% of components identified as artifact were discordant with the manual classification; retrospective examination of these ICs suggested the automated method had correctly identified these as artifact.We have developed an effective automated method which removes a substantial number of unwanted noisy components in ICA analyses of resting-state fMRI data. Source code of our implementation of the method is available.

  4. Extending and automating a Systems-Theoretic hazard analysis for requirements generation and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, John (Massachusetts Institute of Technology)

    2012-05-01

    Systems Theoretic Process Analysis (STPA) is a powerful new hazard analysis method designed to go beyond traditional safety techniques - such as Fault Tree Analysis (FTA) - that overlook important causes of accidents like flawed requirements, dysfunctional component interactions, and software errors. While proving to be very effective on real systems, no formal structure has been defined for STPA and its application has been ad-hoc with no rigorous procedures or model-based design tools. This report defines a formal mathematical structure underlying STPA and describes a procedure for systematically performing an STPA analysis based on that structure. A method for using the results of the hazard analysis to generate formal safety-critical, model-based system and software requirements is also presented. Techniques to automate both the analysis and the requirements generation are introduced, as well as a method to detect conflicts between the safety and other functional model-based requirements during early development of the system.

  5. A survey of automated methods for sensemaking support

    Science.gov (United States)

    Llinas, James

    2014-05-01

    Complex, dynamic problems in general present a challenge for the design of analysis support systems and tools largely because there is limited reliable a priori procedural knowledge descriptive of the dynamic processes in the environment. Problem domains that are non-cooperative or adversarial impute added difficulties involving suboptimal observational data and/or data containing the effects of deception or covertness. The fundamental nature of analysis in these environments is based on composite approaches involving mining or foraging over the evidence, discovery and learning processes, and the synthesis of fragmented hypotheses; together, these can be labeled as sensemaking procedures. This paper reviews and analyzes the features, benefits, and limitations of a variety of automated techniques that offer possible support to sensemaking processes in these problem domains.

  6. ORIGAMI Automator Primer. Automated ORIGEN Source Terms and Spent Fuel Storage Pool Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wieselquist, William A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Thompson, Adam B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bowman, Stephen M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Peterson, Joshua L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-04-01

    Source terms and spent nuclear fuel (SNF) storage pool decay heat load analyses for operating nuclear power plants require a large number of Oak Ridge Isotope Generation and Depletion (ORIGEN) calculations. SNF source term calculations also require a significant amount of bookkeeping to track quantities such as core and assembly operating histories, spent fuel pool (SFP) residence times, heavy metal masses, and enrichments. The ORIGEN Assembly Isotopics (ORIGAMI) module in the SCALE code system provides a simple scheme for entering these data. However, given the large scope of the analysis, extensive scripting is necessary to convert formats and process data to create thousands of ORIGAMI input files (one per assembly) and to process the results into formats readily usable by follow-on analysis tools. This primer describes a project within the SCALE Fulcrum graphical user interface (GUI) called ORIGAMI Automator that was developed to automate the scripting and bookkeeping in large-scale source term analyses. The ORIGAMI Automator enables the analyst to (1) easily create, view, and edit the reactor site and assembly information, (2) automatically create and run ORIGAMI inputs, and (3) analyze the results from ORIGAMI. ORIGAMI Automator uses the standard ORIGEN binary concentrations files produced by ORIGAMI, with concentrations available at all time points in each assembly’s life. The GUI plots results such as mass, concentration, activity, and decay heat using a powerful new ORIGEN Post-Processing Utility for SCALE (OPUS) GUI component. This document includes a description and user guide for the GUI, a step-by-step tutorial for a simplified scenario, and appendices that document the file structures used.

  7. Formal Methods for Automated Diagnosis of Autosub 6000

    Science.gov (United States)

    Ernits, Juhan; Dearden, Richard; Pebody, Miles

    2009-01-01

    This is a progress report on applying formal methods in the context of building an automated diagnosis and recovery system for Autosub 6000, an Autonomous Underwater Vehicle (AUV). The diagnosis task involves building abstract models of the control system of the AUV. The diagnosis engine is based on Livingstone 2, a model-based diagnoser originally built for aerospace applications. Large parts of the diagnosis model can be built without concrete knowledge about each mission, but actual mission scripts and configuration parameters that carry important information for diagnosis are changed for every mission. Thus we use formal methods for generating the mission control part of the diagnosis model automatically from the mission script and perform a number of invariant checks to validate the configuration. After the diagnosis model is augmented with the generated mission control component model, it needs to be validated using verification techniques.

  8. Improving automated 3D reconstruction methods via vision metrology

    Science.gov (United States)

    Toschi, Isabella; Nocerino, Erica; Hess, Mona; Menna, Fabio; Sargeant, Ben; MacDonald, Lindsay; Remondino, Fabio; Robson, Stuart

    2015-05-01

    This paper aims to provide a procedure for improving automated 3D reconstruction methods via vision metrology. The 3D reconstruction problem is generally addressed using two different approaches. On the one hand, vision metrology (VM) systems try to accurately derive 3D coordinates of few sparse object points for industrial measurement and inspection applications; on the other, recent dense image matching (DIM) algorithms are designed to produce dense point clouds for surface representations and analyses. This paper strives to demonstrate a step towards narrowing the gap between traditional VM and DIM approaches. Efforts are therefore intended to (i) test the metric performance of the automated photogrammetric 3D reconstruction procedure, (ii) enhance the accuracy of the final results and (iii) obtain statistical indicators of the quality achieved in the orientation step. VM tools are exploited to integrate their main functionalities (centroid measurement, photogrammetric network adjustment, precision assessment, etc.) into the pipeline of 3D dense reconstruction. Finally, geometric analyses and accuracy evaluations are performed on the raw output of the matching (i.e. the point clouds) by adopting a metrological approach. The latter is based on the use of known geometric shapes and quality parameters derived from VDI/VDE guidelines. Tests are carried out by imaging the calibrated Portable Metric Test Object, designed and built at University College London (UCL), UK. It allows assessment of the performance of the image orientation and matching procedures within a typical industrial scenario, characterised by poor texture and known 3D/2D shapes.

  9. CRITICAL ASSESSMENT OF AUTOMATED FLOW CYTOMETRY DATA ANALYSIS TECHNIQUES

    OpenAIRE

    Aghaeepour, Nima; Finak, Greg; ,; Hoos, Holger; Mosmann, Tim R; Gottardo, Raphael; Brinkman, Ryan; Scheuermann, Richard H.

    2013-01-01

    Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks – mammalian cell population identification to determine if automated algorithms can reproduce expert manu...

  10. An Automated Data Analysis Tool for Livestock Market Data

    Science.gov (United States)

    Williams, Galen S.; Raper, Kellie Curry

    2011-01-01

    This article describes an automated data analysis tool that allows Oklahoma Cooperative Extension Service educators to disseminate results in a timely manner. Primary data collected at Oklahoma Quality Beef Network (OQBN) certified calf auctions across the state results in a large amount of data per sale site. Sale summaries for an individual sale…

  11. Automated image analysis in the study of collagenous colitis

    DEFF Research Database (Denmark)

    Fiehn, Anne-Marie Kanstrup; Kristensson, Martin; Engel, Ulla;

    2016-01-01

    PURPOSE: The aim of this study was to develop an automated image analysis software to measure the thickness of the subepithelial collagenous band in colon biopsies with collagenous colitis (CC) and incomplete CC (CCi). The software measures the thickness of the collagenous band on microscopic...

  12. Automated SEM-EDS GSR Analysis for Turkish Ammunitions

    International Nuclear Information System (INIS)

    In this work, Automated Scanning Electron Microscopy with Energy Dispersive X-ray Spectrometry (SEM-EDS) was used to characterize 7.65 and 9mm cartridges Turkish ammunition. All samples were analyzed in a SEM Jeol JSM-5600LV equipped BSE detector and a Link ISIS 300 (EDS). A working distance of 20mm, an accelerating voltage of 20 keV and gunshot residue software was used in all analysis. Automated search resulted in a high number of particles analyzed containing gunshot residues (GSR) unique elements (PbBaSb). The obtained data about the definition of characteristic GSR particles was concordant with other studies on this topic

  13. Automated analysis for scintigraphic evaluation of gastric emptying using invariant moments.

    Science.gov (United States)

    Abutaleb, A; Delalic, Z J; Ech, R; Siegel, J A

    1989-01-01

    This study introduces a method for automated analysis of the standard solid-meal gastric emptying test. The purpose was to develop a diagnostic tool to characterize more reproducibly abnormalities of solid-phase gastric emptying. The processing of gastric emptying is automated using geometrical moments that are invariant to scaling, rotation, and shift. Twenty subjects were studied. The first step was to obtain images of the stomach using a nuclear gamma camera immediately after the subject had eaten a radio-labeled meal. The second step was to process and analyze the images by a recently developed automated gastric emptying analysis (AGEA) method, which determines the gastric contour and the geometrical properties include such parameters as area, centroid, orientation, and moments of inertia. Statistical tests showed that some of the moments were sensitive to the patient's gastric status (normal versus abnormal). The difference between the normal and abnormal patients became noticeable approximately 1 h after meal ingestion. PMID:18230536

  14. Granulometric profiling of aeolian dust deposits by automated image analysis

    Science.gov (United States)

    Varga, György; Újvári, Gábor; Kovács, János; Jakab, Gergely; Kiss, Klaudia; Szalai, Zoltán

    2016-04-01

    Determination of granulometric parameters is of growing interest in the Earth sciences. Particle size data of sedimentary deposits provide insights into the physicochemical environment of transport, accumulation and post-depositional alterations of sedimentary particles, and are important proxies applied in paleoclimatic reconstructions. It is especially true for aeolian dust deposits with a fairly narrow grain size range as a consequence of the extremely selective nature of wind sediment transport. Therefore, various aspects of aeolian sedimentation (wind strength, distance to source(s), possible secondary source regions and modes of sedimentation and transport) can be reconstructed only from precise grain size data. As terrestrial wind-blown deposits are among the most important archives of past environmental changes, proper explanation of the proxy data is a mandatory issue. Automated imaging provides a unique technique to gather direct information on granulometric characteristics of sedimentary particles. Granulometric data obtained from automatic image analysis of Malvern Morphologi G3-ID is a rarely applied new technique for particle size and shape analyses in sedimentary geology. Size and shape data of several hundred thousand (or even million) individual particles were automatically recorded in this study from 15 loess and paleosoil samples from the captured high-resolution images. Several size (e.g. circle-equivalent diameter, major axis, length, width, area) and shape parameters (e.g. elongation, circularity, convexity) were calculated by the instrument software. At the same time, the mean light intensity after transmission through each particle is automatically collected by the system as a proxy of optical properties of the material. Intensity values are dependent on chemical composition and/or thickness of the particles. The results of the automated imaging were compared to particle size data determined by three different laser diffraction instruments

  15. Volumetric measurements of pulmonary nodules: variability in automated analysis tools

    Science.gov (United States)

    Juluru, Krishna; Kim, Woojin; Boonn, William; King, Tara; Siddiqui, Khan; Siegel, Eliot

    2007-03-01

    Over the past decade, several computerized tools have been developed for detection of lung nodules and for providing volumetric analysis. Incidentally detected lung nodules have traditionally been followed over time by measurements of their axial dimensions on CT scans to ensure stability or document progression. A recently published article by the Fleischner Society offers guidelines on the management of incidentally detected nodules based on size criteria. For this reason, differences in measurements obtained by automated tools from various vendors may have significant implications on management, yet the degree of variability in these measurements is not well understood. The goal of this study is to quantify the differences in nodule maximum diameter and volume among different automated analysis software. Using a dataset of lung scans obtained with both "ultra-low" and conventional doses, we identified a subset of nodules in each of five size-based categories. Using automated analysis tools provided by three different vendors, we obtained size and volumetric measurements on these nodules, and compared these data using descriptive as well as ANOVA and t-test analysis. Results showed significant differences in nodule maximum diameter measurements among the various automated lung nodule analysis tools but no significant differences in nodule volume measurements. These data suggest that when using automated commercial software, volume measurements may be a more reliable marker of tumor progression than maximum diameter. The data also suggest that volumetric nodule measurements may be relatively reproducible among various commercial workstations, in contrast to the variability documented when performing human mark-ups, as is seen in the LIDC (lung imaging database consortium) study.

  16. On Automating and Standardising Corpus Callosum Analysis in Brain MRI

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille; Skoglund, Karl

    2005-01-01

    Corpus callosum analysis is influenced by many factors. The effort in controlling these has previously been incomplete and scattered. This paper sketches a complete pipeline for automated corpus callosum analysis from magnetic resonance images, with focus on measurement standardisation. The...... presented pipeline deals with i) estimation of the mid-sagittal plane, ii) localisation and registration of the corpus callosum, iii) parameterisation and representation of its contour, and iv) means of standardising the traditional reference area measurements....

  17. Fully automated apparatus for the proximate analysis of coals

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, K.; Ishibashi, Y.; Ishii, T.; Maeda, K.; Ogawa, A.; Gotoh, K.

    1985-01-01

    The authors report the development of fully-automated equipment for the proximate analysis of coals, a development undertaken with the twin aims of labour-saving and developing robot applications technology. This system comprises a balance, electric furnaces, a sulfur analyzer, etc., arranged concentrically around a multi-jointed robot which automatically performs all the necessary operations, such as sampling and weighing the materials for analysis, and inserting and removing them from the furnaces. 2 references.

  18. Automated analysis for detecting beams in laser wakefield simulations

    Energy Technology Data Exchange (ETDEWEB)

    Ushizima, Daniela M.; Rubel, Oliver; Prabhat, Mr.; Weber, Gunther H.; Bethel, E. Wes; Aragon, Cecilia R.; Geddes, Cameron G.R.; Cormier-Michel, Estelle; Hamann, Bernd; Messmer, Peter; Hagen, Hans

    2008-07-03

    Laser wakefield particle accelerators have shown the potential to generate electric fields thousands of times higher than those of conventional accelerators. The resulting extremely short particle acceleration distance could yield a potential new compact source of energetic electrons and radiation, with wide applications from medicine to physics. Physicists investigate laser-plasma internal dynamics by running particle-in-cell simulations; however, this generates a large dataset that requires time-consuming, manual inspection by experts in order to detect key features such as beam formation. This paper describes a framework to automate the data analysis and classification of simulation data. First, we propose a new method to identify locations with high density of particles in the space-time domain, based on maximum extremum point detection on the particle distribution. We analyze high density electron regions using a lifetime diagram by organizing and pruning the maximum extrema as nodes in a minimum spanning tree. Second, we partition the multivariate data using fuzzy clustering to detect time steps in a experiment that may contain a high quality electron beam. Finally, we combine results from fuzzy clustering and bunch lifetime analysis to estimate spatially confined beams. We demonstrate our algorithms successfully on four different simulation datasets.

  19. Automated Method for Monitoring Water Quality Using Landsat Imagery

    Directory of Open Access Journals (Sweden)

    D. Clay Barrett

    2016-06-01

    Full Text Available Regular monitoring of water quality is increasingly necessary to keep pace with rapid environmental change and protect human health and well-being. Remote sensing has been suggested as a potential solution for monitoring certain water quality parameters without the need for in situ sampling, but universal methods and tools are lacking. While many studies have developed predictive relationships between remotely sensed surface reflectance and water parameters, these relationships are often unique to a particular geographic region and have little applicability in other areas. In order to remotely monitor water quality, these relationships must be developed on a region by region basis. This paper presents an automated method for processing remotely sensed images from Landsat Thematic Mapper (TM and Enhanced Thematic Mapper Plus (ETM+ and extracting corrected reflectance measurements around known sample locations to allow rapid development of predictive water quality relationships to improve remote monitoring. Using open Python scripting, this study (1 provides an openly accessible and simple method for processing publicly available remote sensing data; and (2 allows determination of relationships between sampled water quality parameters and reflectance values to ultimately allow predictive monitoring. The method is demonstrated through a case study of the Ozark/Ouchita-Appalachian ecoregion in eastern Oklahoma using data collected for the Beneficial Use Monitoring Program (BUMP.

  20. Towards Automated Design, Analysis and Optimization of Declarative Curation Workflows

    Directory of Open Access Journals (Sweden)

    Tianhong Song

    2014-10-01

    Full Text Available Data curation is increasingly important. Our previous work on a Kepler curation package has demonstrated advantages that come from automating data curation pipelines by using workflow systems. However, manually designed curation workflows can be error-prone and inefficient due to a lack of user understanding of the workflow system, misuse of actors, or human error. Correcting problematic workflows is often very time-consuming. A more proactive workflow system can help users avoid such pitfalls. For example, static analysis before execution can be used to detect the potential problems in a workflow and help the user to improve workflow design. In this paper, we propose a declarative workflow approach that supports semi-automated workflow design, analysis and optimization. We show how the workflow design engine helps users to construct data curation workflows, how the workflow analysis engine detects different design problems of workflows and how workflows can be optimized by exploiting parallelism.

  1. Automating with ROBOCOM. An expert system for complex engineering analysis

    International Nuclear Information System (INIS)

    Nuclear engineering analysis is automated with the help of preprocessors and postprocessors. All the analysis and processing steps are recorded in a form that is reportable and replayable. These recordings serve both as documentations and as robots, for they are capable of performing the analyses they document. Since the processors and robots in ROBOCOM interface the users in a way independent of the analysis program being used, it is now possible to unify input modeling for programs with similar functionality. ROBOCOM will eventually evolve into an encyclopedia of how every nuclear engineering analysis is performed

  2. The automation of analysis of technological process effectiveness

    Directory of Open Access Journals (Sweden)

    B. Krupińska

    2007-10-01

    Full Text Available Purpose: Improvement of technological processes by the use of technological efficiency analysis can create basis of their optimization. Informatization and computerization of wider and wider scope of activity is one of the most important current development trends of an enterprise.Design/methodology/approach: Indicators appointment makes it possible to evaluate the process efficiency, which can constitute an optimization basis of particular operation. Model of technological efficiency analysis is based on particular efficiency indicators that characterize operation, taking into account following criteria: operation – material, operation – machine, operation – human, operation – technological parameters.Findings: From the qualitative and correctness of choose of technology point of view comprehensive technological processes assessment makes up the basis of technological efficiency analysis. Results of technological efficiency analysis of technological process of prove that the chosen model of technological efficiency analysis makes it possible to improve the process continuously by the technological analysis, and application of computer assistance makes it possible to automate the process of efficiency analysis, and finally controlled improvement of technological processes.Practical implications: For the sake of complexity of technological efficiency analysis one has created an AEPT computer analysis from which result: operation efficiency indicators with distinguished indicators with minimal acceptable values, values of efficiency of the applied samples, value of technological process efficiency.Originality/value: The created computer analysis of ef technological process efficiency (AEPT makes it possible to automate the process of analysis and optimization.

  3. Method and system for assigning a confidence metric for automated determination of optic disc location

    Science.gov (United States)

    Karnowski, Thomas P.; Tobin, Jr., Kenneth W.; Muthusamy Govindasamy, Vijaya Priya; Chaum, Edward

    2012-07-10

    A method for assigning a confidence metric for automated determination of optic disc location that includes analyzing a retinal image and determining at least two sets of coordinates locating an optic disc in the retinal image. The sets of coordinates can be determined using first and second image analysis techniques that are different from one another. An accuracy parameter can be calculated and compared to a primary risk cut-off value. A high confidence level can be assigned to the retinal image if the accuracy parameter is less than the primary risk cut-off value and a low confidence level can be assigned to the retinal image if the accuracy parameter is greater than the primary risk cut-off value. The primary risk cut-off value being selected to represent an acceptable risk of misdiagnosis of a disease having retinal manifestations by the automated technique.

  4. Automated SIMS Isotopic Analysis Of Small Dust Particles

    Science.gov (United States)

    Nittler, L.; Alexander, C.; Gyngard, F.; Morgand, A.; Zinner, E. K.

    2009-12-01

    The isotopic compositions of sub-μm to μm sized dust grains are of increasing interest in cosmochemistry, nuclear forensics and terrestrial aerosol research. Because of its high sensitivity and spatial resolution, Secondary Ion Mass Spectrometry (SIMS) is the tool of choice for measuring isotopes in such small samples. Indeed, SIMS has enabled an entirely new sub-field of astronomy: presolar grains in meteorites. In recent years, the development of the Cameca NanoSIMS ion probe has extended the reach of isotopic measurements to particles as small as 100 nm in diameter, a regime where isotopic precision is strongly limited by the total number of atoms in the sample. Many applications require obtaining isotopic data on large numbers of particles, necessitating the development of automated techniques. One such method is isotopic imaging, wherein images of multiple isotopes are acquired, each containing multiple dispersed particles, and image processing is used to determine isotopic ratios for individual particles. This method is powerful, but relatively inefficient for raster-based imaging on the NanoSIMS. Modern computerized control of instrumentation has allowed for another approach, analogous to commercial automated SEM-EDS particle analysis systems, in which images are used solely to locate particles followed by fully automated grain-by-grain analysis. The first such system was developed on the Carnegie Institution’s Cameca ims-6f, and was used to generate large databases of presolar grains. We have recently developed a similar system for the NanoSIMS, whose high sensitivity allows for smaller grains to be analyzed with less sample consumption than is possible with the 6f system. The 6f and NanoSIMS systems are functionally identical: an image of dispersed grains is obtained with sufficient statistical precision for an algorithm to identify the positions of individual particles, the primary ion beam is deflected to each particle in turn and rastered in a small

  5. Micro photometer's automation for quantitative spectrograph analysis

    International Nuclear Information System (INIS)

    A Microphotometer is used to increase the sharpness of dark spectral lines. Analyzing these lines one sample content and its concentration could be determined and the analysis is known as Quantitative Spectrographic Analysis. The Quantitative Spectrographic Analysis is carried out in 3 steps, as follows. 1. Emulsion calibration. This consists of gauging a photographic emulsion, to determine the intensity variations in terms of the incident radiation. For the procedure of emulsion calibration an adjustment with square minimum to the data obtained is applied to obtain a graph. It is possible to determine the density of dark spectral line against the incident light intensity shown by the microphotometer. 2. Working curves. The values of known concentration of an element against incident light intensity are plotted. Since the sample contains several elements, it is necessary to find a work curve for each one of them. 3. Analytical results. The calibration curve and working curves are compared and the concentration of the studied element is determined. The automatic data acquisition, calculation and obtaining of resulting, is done by means of a computer (PC) and a computer program. The conditioning signal circuits have the function of delivering TTL levels (Transistor Transistor Logic) to make the communication between the microphotometer and the computer possible. Data calculation is done using a computer programm

  6. Automated Asteroseismic Analysis of Solar-type Stars

    DEFF Research Database (Denmark)

    Karoff, Christoffer; Campante, T.L.; Chaplin, W.J.

    2010-01-01

    , radius, luminosity, effective temperature, surface gravity and age based on grid modeling. All the tools take into account the window function of the observations which means that they work equally well for space-based photometry observations from e.g. the NASA Kepler satellite and ground-based velocity......The rapidly increasing volume of asteroseismic observations on solar-type stars has revealed a need for automated analysis tools. The reason for this is not only that individual analyses of single stars are rather time consuming, but more importantly that these large volumes of observations open...... are calculated in a consistent way. Here we present a set of automated asterosesimic analysis tools. The main engine of these set of tools is an algorithm for modelling the autocovariance spectra of the stellar acoustic spectra allowing us to measure not only the frequency of maximum power and the large...

  7. Development of methods for DSM and distribution automation planning

    Energy Technology Data Exchange (ETDEWEB)

    Kaerkkaeinen, S.; Kekkonen, V. [VTT Energy, Espoo (Finland); Rissanen, P. [Tietosavo Oy (Finland)

    1998-08-01

    Demand-Side Management (DSM) is usually an utility (or sometimes governmental) activity designed to influence energy demand of customers (both level and load variation). It includes basic options like strategic conservation or load growth, peak clipping. Load shifting and fuel switching. Typical ways to realize DSM are direct load control, innovative tariffs, different types of campaign etc. Restructuring of utility in Finland and increased competition in electricity market have had dramatic influence on the DSM. Traditional ways are impossible due to the conflicting interests of generation, network and supply business and increased competition between different actors in the market. Costs and benefits of DSM are divided to different companies, and different type of utilities are interested only in those activities which are beneficial to them. On the other hand, due to the increased competition the suppliers are diversifying to different types of products and increasing number of customer services partly based on DSM are available. The aim of this project was to develop and assess methods for DSM and distribution automation planning from the utility point of view. The methods were also applied to case studies at utilities

  8. RFI detection by automated feature extraction and statistical analysis

    OpenAIRE

    Winkel, Benjamin; Kerp, Juergen; Stanko, Stephan

    2006-01-01

    In this paper we present an interference detection toolbox consisting of a high dynamic range Digital Fast-Fourier-Transform spectrometer (DFFT, based on FPGA-technology) and data analysis software for automated radio frequency interference (RFI) detection. The DFFT spectrometer allows high speed data storage of spectra on time scales of less than a second. The high dynamic range of the device assures constant calibration even during extremely powerful RFI events. The software uses an algorit...

  9. Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images

    Directory of Open Access Journals (Sweden)

    Jianfang Cao

    2015-01-01

    Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.

  10. An automated 3D reconstruction method of UAV images

    Science.gov (United States)

    Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

    2015-10-01

    In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

  11. Analysis of Defense Language Institute automated student questionnaire data

    OpenAIRE

    Strycharz, Theodore M.

    1996-01-01

    This thesis explores the dimensionality of the Defense Language Institute's (DLI) primary student feed back tool - the Automated Student Questionnaire (ASQ). In addition a data set from ASQ 2.0 (the newest version) is analyzed for trends in student satisfaction across the sub-scales of sex, pay grade, and Defense Language Proficiency Test (DLPT) results. The method of principal components is used to derive initial factors. Although an interpretation of those factors seems plausible, these are...

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

    Science.gov (United States)

    Cohn, J F; Zlochower, A J; Lien, J; Kanade, T

    1999-01-01

    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.

  13. An automated image analysis system to measure and count organisms in laboratory microcosms.

    Science.gov (United States)

    Mallard, François; Le Bourlot, Vincent; Tully, Thomas

    2013-01-01

    1. Because of recent technological improvements in the way computer and digital camera perform, the potential use of imaging for contributing to the study of communities, populations or individuals in laboratory microcosms has risen enormously. However its limited use is due to difficulties in the automation of image analysis. 2. We present an accurate and flexible method of image analysis for detecting, counting and measuring moving particles on a fixed but heterogeneous substrate. This method has been specifically designed to follow individuals, or entire populations, in experimental laboratory microcosms. It can be used in other applications. 3. The method consists in comparing multiple pictures of the same experimental microcosm in order to generate an image of the fixed background. This background is then used to extract, measure and count the moving organisms, leaving out the fixed background and the motionless or dead individuals. 4. We provide different examples (springtails, ants, nematodes, daphnia) to show that this non intrusive method is efficient at detecting organisms under a wide variety of conditions even on faintly contrasted and heterogeneous substrates. 5. The repeatability and reliability of this method has been assessed using experimental populations of the Collembola Folsomia candida. 6. We present an ImageJ plugin to automate the analysis of digital pictures of laboratory microcosms. The plugin automates the successive steps of the analysis and recursively analyses multiple sets of images, rapidly producing measurements from a large number of replicated microcosms. PMID:23734199

  14. An automated image analysis system to measure and count organisms in laboratory microcosms.

    Directory of Open Access Journals (Sweden)

    François Mallard

    Full Text Available 1. Because of recent technological improvements in the way computer and digital camera perform, the potential use of imaging for contributing to the study of communities, populations or individuals in laboratory microcosms has risen enormously. However its limited use is due to difficulties in the automation of image analysis. 2. We present an accurate and flexible method of image analysis for detecting, counting and measuring moving particles on a fixed but heterogeneous substrate. This method has been specifically designed to follow individuals, or entire populations, in experimental laboratory microcosms. It can be used in other applications. 3. The method consists in comparing multiple pictures of the same experimental microcosm in order to generate an image of the fixed background. This background is then used to extract, measure and count the moving organisms, leaving out the fixed background and the motionless or dead individuals. 4. We provide different examples (springtails, ants, nematodes, daphnia to show that this non intrusive method is efficient at detecting organisms under a wide variety of conditions even on faintly contrasted and heterogeneous substrates. 5. The repeatability and reliability of this method has been assessed using experimental populations of the Collembola Folsomia candida. 6. We present an ImageJ plugin to automate the analysis of digital pictures of laboratory microcosms. The plugin automates the successive steps of the analysis and recursively analyses multiple sets of images, rapidly producing measurements from a large number of replicated microcosms.

  15. Implicit media frames: Automated analysis of public debate on artificial sweeteners

    CERN Document Server

    Hellsten, Iina; Leydesdorff, Loet

    2010-01-01

    The framing of issues in the mass media plays a crucial role in the public understanding of science and technology. This article contributes to research concerned with diachronic analysis of media frames by making an analytical distinction between implicit and explicit media frames, and by introducing an automated method for analysing diachronic changes of implicit frames. In particular, we apply a semantic maps method to a case study on the newspaper debate about artificial sweeteners, published in The New York Times (NYT) between 1980 and 2006. Our results show that the analysis of semantic changes enables us to filter out the dynamics of implicit frames, and to detect emerging metaphors in public debates. Theoretically, we discuss the relation between implicit frames in public debates and codification of information in scientific discourses, and suggest further avenues for research interested in the automated analysis of frame changes and trends in public debates.

  16. Detailed interrogation of trypanosome cell biology via differential organelle staining and automated image analysis

    Directory of Open Access Journals (Sweden)

    Wheeler Richard J

    2012-01-01

    Full Text Available Abstract Background Many trypanosomatid protozoa are important human or animal pathogens. The well defined morphology and precisely choreographed division of trypanosomatid cells makes morphological analysis a powerful tool for analyzing the effect of mutations, chemical insults and changes between lifecycle stages. High-throughput image analysis of micrographs has the potential to accelerate collection of quantitative morphological data. Trypanosomatid cells have two large DNA-containing organelles, the kinetoplast (mitochondrial DNA and nucleus, which provide useful markers for morphometric analysis; however they need to be accurately identified and often lie in close proximity. This presents a technical challenge. Accurate identification and quantitation of the DNA content of these organelles is a central requirement of any automated analysis method. Results We have developed a technique based on double staining of the DNA with a minor groove binding (4'', 6-diamidino-2-phenylindole (DAPI and a base pair intercalating (propidium iodide (PI or SYBR green fluorescent stain and color deconvolution. This allows the identification of kinetoplast and nuclear DNA in the micrograph based on whether the organelle has DNA with a more A-T or G-C rich composition. Following unambiguous identification of the kinetoplasts and nuclei the resulting images are amenable to quantitative automated analysis of kinetoplast and nucleus number and DNA content. On this foundation we have developed a demonstrative analysis tool capable of measuring kinetoplast and nucleus DNA content, size and position and cell body shape, length and width automatically. Conclusions Our approach to DNA staining and automated quantitative analysis of trypanosomatid morphology accelerated analysis of trypanosomatid protozoa. We have validated this approach using Leishmania mexicana, Crithidia fasciculata and wild-type and mutant Trypanosoma brucei. Automated analysis of T. brucei

  17. Monitoring method for automated CD-SEM recipes

    Science.gov (United States)

    Maeda, Tatsuya; Iwama, Satoru; Nishihara, Makoto; Berger, Daniel; Berger, Andrew; Ueda, Kazuhiro; Kenichi, Takenouchi; Iizumi, Takashi

    2005-05-01

    A prototype of a digital video storage system (CD-watcher) has been developed and attached to a Hitachi S-9380 CD-SEM. The storage system has several modes that are selectable depending on the phenomenon of interest. The system can store video images of duration from a few seconds to a few weeks depending on resolution, sampling rate, and hard disc drive capacity. The system was used to analyze apparent focusing problems that occurred during the execution of automated recipes. Intermittent focusing problems had been an issue on a particular tool for a period of approximately three months. By reviewing saved images, the original diagnosis of the problem appeared to be auto focus. Two days after installation, the CD-watcher system was able to record the errors making it possible to determine the root cause by checking the stored video files. After analysis of the stored video files, it was apparent that the problem consisted of three types of errors. The ability to record and store video files reduced the time to isolate the problem and prevented incorrect diagnosis. The system was also used to explain a complex phenomenon that occurred during the observation a particular layer. Because it is sometimes difficult to accurately describe, and to have others easily understand, certain phenomena in a written report, the video storage system can be used in place of manual annotation. In this report, we describe the CD-watcher system, test results after installing the system on a Hitachi S9380 CD-SEM, and potential applications of the system.

  18. Using historical wafermap data for automated yield analysis

    International Nuclear Information System (INIS)

    To be productive and profitable in a modern semiconductor fabrication environment, large amounts of manufacturing data must be collected, analyzed, and maintained. This includes data collected from in- and off-line wafer inspection systems and from the process equipment itself. This data is increasingly being used to design new processes, control and maintain tools, and to provide the information needed for rapid yield learning and prediction. Because of increasing device complexity, the amount of data being generated is outstripping the yield engineer close-quote s ability to effectively monitor and correct unexpected trends and excursions. The 1997 SIA National Technology Roadmap for Semiconductors highlights a need to address these issues through open-quotes automated data reduction algorithms to source defects from multiple data sources and to reduce defect sourcing time.close quotes SEMATECH and the Oak Ridge National Laboratory have been developing new strategies and technologies for providing the yield engineer with higher levels of assisted data reduction for the purpose of automated yield analysis. In this article, we will discuss the current state of the art and trends in yield management automation. copyright 1999 American Vacuum Society

  19. Cost Analysis of an Automated and Manual Cataloging and Book Processing System.

    Science.gov (United States)

    Druschel, Joselyn

    1981-01-01

    Cost analysis of an automated network system and a manual system of cataloging and book processing indicates a 20 percent savings using automation. Per unit costs based on the average monthly automation rate are used for comparison. Higher manual system costs are attributed to staff costs. (RAA)

  20. Colorimetric determination of nitrate plus nitrite in water by enzymatic reduction, automated discrete analyzer methods

    Science.gov (United States)

    Patton, Charles J.; Kryskalla, Jennifer R.

    2011-01-01

    This report documents work at the U.S. Geological Survey (USGS) National Water Quality Laboratory (NWQL) to validate enzymatic reduction, colorimetric determinative methods for nitrate + nitrite in filtered water by automated discrete analysis. In these standard- and low-level methods (USGS I-2547-11 and I-2548-11), nitrate is reduced to nitrite with nontoxic, soluble nitrate reductase rather than toxic, granular, copperized cadmium used in the longstanding USGS automated continuous-flow analyzer methods I-2545-90 (NWQL laboratory code 1975) and I-2546-91 (NWQL laboratory code 1979). Colorimetric reagents used to determine resulting nitrite in aforementioned enzymatic- and cadmium-reduction methods are identical. The enzyme used in these discrete analyzer methods, designated AtNaR2 by its manufacturer, is produced by recombinant expression of the nitrate reductase gene from wall cress (Arabidopsis thaliana) in the yeast Pichia pastoris. Unlike other commercially available nitrate reductases we evaluated, AtNaR2 maintains high activity at 37°C and is not inhibited by high-phenolic-content humic acids at reaction temperatures in the range of 20°C to 37°C. These previously unrecognized AtNaR2 characteristics are essential for successful performance of discrete analyzer nitrate + nitrite assays (henceforth, DA-AtNaR2) described here.

  1. AMDA: an R package for the automated microarray data analysis

    Directory of Open Access Journals (Sweden)

    Foti Maria

    2006-07-01

    Full Text Available Abstract Background Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. Results To address these problems we have developed an automated microarray data analysis (AMDA software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. Conclusion AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopolis http://www.genopolis.it/

  2. Semi-automated analysis of EEG spikes in the preterm fetal sheep using wavelet analysis

    International Nuclear Information System (INIS)

    Full text: Presentation Preference Oral Presentation Perinatal hypoxia plays a key role in the cause of brain injury in premature infants. Cerebral hypothermia commenced in the latent phase of evolving injury (first 6-8 h post hypoxic-ischemic insult) is the lead candidate for treatment however currently there is no means to identify which infants can benefit from treatment. Recent studies suggest that epileptiform transients in latent phase are predictive of neural outcome. To quantify this, an automated means of EEG analysis is required as EEG monitoring produces vast amounts of data which is timely to analyse manually. We have developed a semi-automated EEG spike detection method which employs a discretized version of the continuous wavelet transform (CWT). EEG data was obtained from a fetal sheep at approximately 0.7 of gestation. Fetal asphyxia was maintained for 25 min and the EEG recorded for 8 h before and after asphyxia. The CWT was calculated followed by the power of the wavelet transform coefficients. Areas of high power corresponded to spike waves so thresholding was employed to identify the spikes. The performance of the method was found have a good sensitivity and selectivity, thus demonstrating that this method is a simple, robust and potentially effective spike detection algorithm.

  3. Comparison of a quantitative microtiter method, a quantitative automated method, and the plate-count method for determining microbial complement resistance.

    Science.gov (United States)

    Lee, M D; Wooley, R E; Brown, J; Spears, K R; Nolan, L K; Shotts, E B

    1991-01-01

    A quantitative microtiter method for determining the degree of complement resistance or sensitivity of microorganisms is described. The microtiter method is compared with a quantitative automated system and the standard plate-count technique. Data were accumulated from 30 avian Escherichia coli isolates incubated at 35 C with either chicken plasma or heat-inactivated chicken plasma. Analysis of data generated by the automated system and plate-count techniques resulted in a classification of the microorganisms into three groups: those sensitive to the action of complement; those of intermediate sensitivity to the action of complement; and those resistant to the action of complement. Although the three methods studied did not agree absolutely, there were statistically significant correlations among them.

  4. Analysis and simulation of a torque assist automated manual transmission

    Science.gov (United States)

    Galvagno, E.; Velardocchia, M.; Vigliani, A.

    2011-08-01

    The paper presents the kinematic and dynamic analysis of a power-shift automated manual transmission (AMT) characterised by a wet clutch, called assist clutch (ACL), replacing the fifth gear synchroniser. This torque assist mechanism becomes a torque transfer path during gearshifts, in order to overcome a typical dynamic problem of the AMTs, that is the driving force interruption. The mean power contributions during gearshifts are computed for different engine and ACL interventions, thus allowing to draw considerations useful for developing the control algorithms. The simulation results prove the advantages in terms of gearshift quality and ride comfort of the analysed transmission.

  5. SCHUBOT: Machine Learning Tools for the Automated Analysis of Schubert’s Lieder

    OpenAIRE

    Nagler, Dylan Jeremy

    2014-01-01

    This paper compares various methods for automated musical analysis, applying machine learning techniques to gain insight about the Lieder (art songs) of com- poser Franz Schubert (1797-1828). Known as a rule-breaking, individualistic, and adventurous composer, Schubert produced hundreds of emotionally-charged songs that have challenged music theorists to this day. The algorithms presented in this paper analyze the harmonies, melodies, and texts of these songs. This paper begins with an explor...

  6. Method for semi-automated microscopy of filtration-enriched circulating tumor cells

    OpenAIRE

    Pailler, Emma; Oulhen, Marianne; Billiot, Fanny; Galland, Alexandre; Auger, Nathalie; Faugeroux, Vincent; Laplace-Builhé, Corinne; Besse, Benjamin; Loriot, Yohann; Ngo-Camus, Maud; Hemanda, Merouan; Colin R. Lindsay; Soria, Jean-Charles; Vielh, Philippe; Farace, Françoise

    2016-01-01

    Background Circulating tumor cell (CTC)-filtration methods capture high numbers of CTCs in non-small-cell lung cancer (NSCLC) and metastatic prostate cancer (mPCa) patients, and hold promise as a non-invasive technique for treatment selection and disease monitoring. However filters have drawbacks that make the automation of microscopy challenging. We report the semi-automated microscopy method we developed to analyze filtration-enriched CTCs from NSCLC and mPCa patients. Methods Spiked cell l...

  7. Semi-automated potentiometric titration method for uranium characterization.

    Science.gov (United States)

    Cristiano, B F G; Delgado, J U; da Silva, J W S; de Barros, P D; de Araújo, R M S; Lopes, R T

    2012-07-01

    The manual version of the potentiometric titration method has been used for certification and characterization of uranium compounds. In order to reduce the analysis time and the influence of the analyst, a semi-automatic version of the method was developed in the Brazilian Nuclear Energy Commission. The method was applied with traceability assured by using a potassium dichromate primary standard. The combined standard uncertainty in determining the total concentration of uranium was around 0.01%, which is suitable for uranium characterization. PMID:22154105

  8. Automated Live Forensics Analysis for Volatile Data Acquisition

    Directory of Open Access Journals (Sweden)

    Bharath B,

    2015-03-01

    Full Text Available The increase in sophisticated attack on computers needs the assistance of Live forensics to uncover the evidence since traditional forensics methods doesn’t collect volatile data. The volatile data can ease the difficulty towards investigation in fact it can provide investigator with rich information towards solving a case. Here we are trying to eliminate the complexity involved in normal process by automating the process of acquisition and analyzing at the same time providing integrity towards evidence data through python scripting.

  9. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  10. Automated quantitative analysis of ventilation-perfusion lung scintigrams

    International Nuclear Information System (INIS)

    An automated computer analysis of ventilation (Kr-81m) and perfusion (Tc-99m) lung images has been devised that produces a graphical image of the distribution of ventilation and perfusion, and of ventilation-perfusion ratios. The analysis has overcome the following problems: the identification of the midline between two lungs and the lung boundaries, the exclusion of extrapulmonary radioactivity, the superimposition of lung images of different sizes, and the format for presentation of the data. Therefore, lung images of different sizes and shapes may be compared with each other. The analysis has been used to develop normal ranges from 55 volunteers. Comparison of younger and older age groups of men and women show small but significant differences in the distribution of ventilation and perfusion, but no differences in ventilation-perfusion ratios

  11. Analysis of automated highway system risks and uncertainties. Volume 5

    Energy Technology Data Exchange (ETDEWEB)

    Sicherman, A.

    1994-10-01

    This volume describes a risk analysis performed to help identify important Automated Highway System (AHS) deployment uncertainties and quantify their effect on costs and benefits for a range of AHS deployment scenarios. The analysis identified a suite of key factors affecting vehicle and roadway costs, capacities and market penetrations for alternative AHS deployment scenarios. A systematic protocol was utilized for obtaining expert judgments of key factor uncertainties in the form of subjective probability percentile assessments. Based on these assessments, probability distributions on vehicle and roadway costs, capacity and market penetration were developed for the different scenarios. The cost/benefit risk methodology and analysis provide insights by showing how uncertainties in key factors translate into uncertainties in summary cost/benefit indices.

  12. Reproducibility of In Vivo Corneal Confocal Microscopy Using an Automated Analysis Program for Detection of Diabetic Sensorimotor Polyneuropathy.

    Directory of Open Access Journals (Sweden)

    Ilia Ostrovski

    Full Text Available In vivo Corneal Confocal Microscopy (IVCCM is a validated, non-invasive test for diabetic sensorimotor polyneuropathy (DSP detection, but its utility is limited by the image analysis time and expertise required. We aimed to determine the inter- and intra-observer reproducibility of a novel automated analysis program compared to manual analysis.In a cross-sectional diagnostic study, 20 non-diabetes controls (mean age 41.4±17.3y, HbA1c 5.5±0.4% and 26 participants with type 1 diabetes (42.8±16.9y, 8.0±1.9% underwent two separate IVCCM examinations by one observer and a third by an independent observer. Along with nerve density and branch density, corneal nerve fibre length (CNFL was obtained by manual analysis (CNFLMANUAL, a protocol in which images were manually selected for automated analysis (CNFLSEMI-AUTOMATED, and one in which selection and analysis were performed electronically (CNFLFULLY-AUTOMATED. Reproducibility of each protocol was determined using intraclass correlation coefficients (ICC and, as a secondary objective, the method of Bland and Altman was used to explore agreement between protocols.Mean CNFLManual was 16.7±4.0, 13.9±4.2 mm/mm2 for non-diabetes controls and diabetes participants, while CNFLSemi-Automated was 10.2±3.3, 8.6±3.0 mm/mm2 and CNFLFully-Automated was 12.5±2.8, 10.9 ± 2.9 mm/mm2. Inter-observer ICC and 95% confidence intervals (95%CI were 0.73(0.56, 0.84, 0.75(0.59, 0.85, and 0.78(0.63, 0.87, respectively (p = NS for all comparisons. Intra-observer ICC and 95%CI were 0.72(0.55, 0.83, 0.74(0.57, 0.85, and 0.84(0.73, 0.91, respectively (p<0.05 for CNFLFully-Automated compared to others. The other IVCCM parameters had substantially lower ICC compared to those for CNFL. CNFLSemi-Automated and CNFLFully-Automated underestimated CNFLManual by mean and 95%CI of 35.1(-4.5, 67.5% and 21.0(-21.6, 46.1%, respectively.Despite an apparent measurement (underestimation bias in comparison to the manual strategy of image

  13. An Automated Method to Quantify Radiation Damage in Human Blood Cells

    Energy Technology Data Exchange (ETDEWEB)

    Gordon K. Livingston, Mark S. Jenkins and Akio A. Awa

    2006-07-10

    Cytogenetic analysis of blood lymphocytes is a well established method to assess the absorbed dose in persons exposed to ionizing radiation. Because mature lymphocytes circulate throughout the body, the dose to these cells is believed to represent the average whole body exposure. Cytogenetic methods measure the incidence of structural aberrations in chromosomes as a means to quantify DNA damage which occurs when ionizing radiation interacts with human tissue. Methods to quantify DNA damage at the chromosomal level vary in complexity and tend to be laborious and time consuming. In a mass casualty scenario involving radiological/nuclear materials, the ability to rapidly triage individuals according to radiation dose is critically important. For high-throughput screening for dicentric chromosomes, many of the data collection steps can be optimized with motorized microscopes coupled to automated slide scanning platforms.

  14. Development of design automation codes using software engineering methods

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.J. II

    1976-10-31

    The Electrical Engineering Department of the Lawrence Livermore Laboratory (LLL) has recently formed a Design Automation (DA) Group responsible for development of new DA capabilities at the Laboratory. This paper briefly discusses the environment in which the software is being produced, and methodologies employed by the development team. The discussion of software engineering approaches should be of interest to small groups producing relatively large complex software systems. (auth)

  15. Automating Flood Hazard Mapping Methods for Near Real-time Storm Surge Inundation and Vulnerability Assessment

    Science.gov (United States)

    Weigel, A. M.; Griffin, R.; Gallagher, D.

    2015-12-01

    Storm surge has enough destructive power to damage buildings and infrastructure, erode beaches, and threaten human life across large geographic areas, hence posing the greatest threat of all the hurricane hazards. The United States Gulf of Mexico has proven vulnerable to hurricanes as it has been hit by some of the most destructive hurricanes on record. With projected rises in sea level and increases in hurricane activity, there is a need to better understand the associated risks for disaster mitigation, preparedness, and response. GIS has become a critical tool in enhancing disaster planning, risk assessment, and emergency response by communicating spatial information through a multi-layer approach. However, there is a need for a near real-time method of identifying areas with a high risk of being impacted by storm surge. Research was conducted alongside Baron, a private industry weather enterprise, to facilitate automated modeling and visualization of storm surge inundation and vulnerability on a near real-time basis. This research successfully automated current flood hazard mapping techniques using a GIS framework written in a Python programming environment, and displayed resulting data through an Application Program Interface (API). Data used for this methodology included high resolution topography, NOAA Probabilistic Surge model outputs parsed from Rich Site Summary (RSS) feeds, and the NOAA Census tract level Social Vulnerability Index (SoVI). The development process required extensive data processing and management to provide high resolution visualizations of potential flooding and population vulnerability in a timely manner. The accuracy of the developed methodology was assessed using Hurricane Isaac as a case study, which through a USGS and NOAA partnership, contained ample data for statistical analysis. This research successfully created a fully automated, near real-time method for mapping high resolution storm surge inundation and vulnerability for the

  16. Development of automated preparation system for isotopocule analysis of N2O in various air samples

    Science.gov (United States)

    Toyoda, Sakae; Yoshida, Naohiro

    2016-05-01

    Nitrous oxide (N2O), an increasingly abundant greenhouse gas in the atmosphere, is the most important stratospheric ozone-depleting gas of this century. Natural abundance ratios of isotopocules of N2O, NNO molecules substituted with stable isotopes of nitrogen and oxygen, are a promising index of various sources or production pathways of N2O and of its sink or decomposition pathways. Several automated methods have been reported to improve the analytical precision for the isotopocule ratio of atmospheric N2O and to reduce the labor necessary for complicated sample preparation procedures related to mass spectrometric analysis. However, no method accommodates flask samples with limited volume or pressure. Here we present an automated preconcentration system which offers flexibility with respect to the available gas volume, pressure, and N2O concentration. The shortest processing time for a single analysis of typical atmospheric sample is 40 min. Precision values of isotopocule ratio analysis are < 0.1 ‰ for δ15Nbulk (average abundances of 14N15N16O and 15N14N16O relative to 14N14N16O), < 0.2 ‰ for δ18O (relative abundance of 14N14N18O), and < 0.5 ‰ for site preference (SP; difference between relative abundance of 14N15N16O and 15N14N16O). This precision is comparable to that of other automated systems, but better than that of our previously reported manual measurement system.

  17. Automated IR determination of petroleum products in water based on sequential injection analysis.

    Science.gov (United States)

    Falkova, Marina; Vakh, Christina; Shishov, Andrey; Zubakina, Ekaterina; Moskvin, Aleksey; Moskvin, Leonid; Bulatov, Andrey

    2016-02-01

    The simple and easy performed automated method for the IR determination of petroleum products (PP) in water using extraction-chromatographic cartridges has been developed. The method assumes two stages: on-site extraction of PP during a sampling by using extraction-chromatographic cartridges and subsequent determination of the extracted PP using sequential injection analysis (SIA) with IR detection. The appropriate experimental conditions for extraction of the dissolved in water PP and for automated SIA procedure were investigated. The calibration plot constructed using the developed procedure was linear in the range of 3-200 μg L(-1). The limit of detection (LOD), calculated from a blank test based on 3σ was 1 µg L(-1). The sample volume was 1L. The system throughput was found to be 12 h(-1). PMID:26653498

  18. Automated cell colony counting and analysis using the circular Hough image transform algorithm (CHiTA)

    Energy Technology Data Exchange (ETDEWEB)

    Bewes, J M; Suchowerska, N; McKenzie, D R [School of Physics, University of Sydney, Sydney, NSW (Australia)], E-mail: jbewes@physics.usyd.edu.au

    2008-11-07

    We present an automated cell colony counting method that is flexible, robust and capable of providing more in-depth clonogenic analysis than existing manual and automated approaches. The full form of the Hough transform without approximation has been implemented, for the first time. Improvements in computing speed have facilitated this approach. Colony identification was achieved by pre-processing the raw images of the colonies in situ in the flask, including images of the flask edges, by erosion, dilation and Gaussian smoothing processes. Colony edges were then identified by intensity gradient field discrimination. Our technique eliminates the need for specialized hardware for image capture and enables the use of a standard desktop scanner for distortion-free image acquisition. Additional parameters evaluated included regional colony counts, average colony area, nearest neighbour distances and radial distribution. This spatial and qualitative information extends the utility of the clonogenic assay, allowing analysis of spatially-variant cytotoxic effects. To test the automated system, two flask types and three cell lines with different morphology, cell size and plating density were examined. A novel Monte Carlo method of simulating cell colony images, as well as manual counting, were used to quantify algorithm accuracy. The method was able to identify colonies with unusual morphology, to successfully resolve merged colonies and to correctly count colonies adjacent to flask edges.

  19. Automated cell colony counting and analysis using the circular Hough image transform algorithm (CHiTA)

    Science.gov (United States)

    Bewes, J. M.; Suchowerska, N.; McKenzie, D. R.

    2008-11-01

    We present an automated cell colony counting method that is flexible, robust and capable of providing more in-depth clonogenic analysis than existing manual and automated approaches. The full form of the Hough transform without approximation has been implemented, for the first time. Improvements in computing speed have facilitated this approach. Colony identification was achieved by pre-processing the raw images of the colonies in situ in the flask, including images of the flask edges, by erosion, dilation and Gaussian smoothing processes. Colony edges were then identified by intensity gradient field discrimination. Our technique eliminates the need for specialized hardware for image capture and enables the use of a standard desktop scanner for distortion-free image acquisition. Additional parameters evaluated included regional colony counts, average colony area, nearest neighbour distances and radial distribution. This spatial and qualitative information extends the utility of the clonogenic assay, allowing analysis of spatially-variant cytotoxic effects. To test the automated system, two flask types and three cell lines with different morphology, cell size and plating density were examined. A novel Monte Carlo method of simulating cell colony images, as well as manual counting, were used to quantify algorithm accuracy. The method was able to identify colonies with unusual morphology, to successfully resolve merged colonies and to correctly count colonies adjacent to flask edges.

  20. Automated image analysis for quantification of filamentous bacteria

    DEFF Research Database (Denmark)

    Fredborg, Marlene; Rosenvinge, Flemming Schønning; Spillum, Erik;

    2015-01-01

    Background Antibiotics of the β-lactam group are able to alter the shape of the bacterial cell wall, e.g. filamentation or a spheroplast formation. Early determination of antimicrobial susceptibility may be complicated by filamentation of bacteria as this can be falsely interpreted as growth...... in systems relying on colorimetry or turbidometry (such as Vitek-2, Phoenix, MicroScan WalkAway). The objective was to examine an automated image analysis algorithm for quantification of filamentous bacteria using the 3D digital microscopy imaging system, oCelloScope. Results Three E. coli strains displaying...... different resistant profiles and differences in filamentation kinetics were used to study a novel image analysis algorithm to quantify length of bacteria and bacterial filamentation. A total of 12 β-lactam antibiotics or β-lactam–β-lactamase inhibitor combinations were analyzed for their ability to induce...

  1. Automated measurement of estrogen receptor in breast cancer: a comparison of fluorescent and chromogenic methods of measurement.

    Science.gov (United States)

    Zarrella, Elizabeth R; Coulter, Madeline; Welsh, Allison W; Carvajal, Daniel E; Schalper, Kurt A; Harigopal, Malini; L Rimm, David; M Neumeister, Veronique

    2016-09-01

    Whereas FDA-approved methods of assessment of estrogen receptor (ER) are 'fit for purpose', they represent a 30-year-old technology. New quantitative methods, both chromogenic and fluorescent, have been developed and studies have shown that these methods increase the accuracy of assessment of ER. Here, we compare three methods of ER detection and assessment on two retrospective tissue microarray (TMA) cohorts of breast cancer patients: estimates of percent nuclei positive by pathologists and by Aperio's nuclear algorithm (standard chromogenic immunostaining), and immunofluorescence as quantified with the automated quantitative analysis (AQUA) method of quantitative immunofluorescence (QIF). Reproducibility was excellent (R(2)>0.95) between users for both automated analysis methods, and the Aperio and QIF scoring results were also highly correlated, despite the different detection systems. The subjective readings show lower levels of reproducibility and a discontinuous, bimodal distribution of scores not seen by either mechanized method. Kaplan-Meier analysis of 10-year disease-free survival was significant for each method (Pathologist, P=0.0019; Aperio, P=0.0053, AQUA, P=0.0026); however, there were discrepancies in patient classification in 19 out of 233 cases analyzed. Out of these, 11 were visually positive by both chromogenic and fluorescent detection. In 10 cases, the Aperio nuclear algorithm labeled the nuclei as negative; in 1 case, the AQUA score was just under the cutoff for positivity (determined by an Index TMA). In contrast, 8 out of 19 discrepant cases had clear nuclear positivity by fluorescence that was unable to be visualized by chromogenic detection, perhaps because of low positivity masked by the hematoxylin counterstain. These results demonstrate that automated systems enable objective, precise quantification of ER. Furthermore, immunofluorescence detection offers the additional advantage of a signal that cannot be masked by a counterstaining

  2. Toward an automated method for optical coherence tomography characterization

    Science.gov (United States)

    Strupler, Mathias; Beckley, Amber M.; Benboujja, Fouzi; Dubois, Sylvain; Noiseux, Isabelle; Mermut, Ozzy; Bouchard, Jean-Pierre; Boudoux, Caroline

    2015-12-01

    With the increasing use of optical coherence tomography (OCT) in biomedical applications, robust yet simple methods for calibrating and benchmarking a system are needed. We present here a procedure based on a calibration object complemented with an algorithm that analyzes three-dimensional OCT datasets to retrieve key characteristics of an OCT system. The calibration object combines state-of-the-art tissue phantom material with a diamond-turned aluminum multisegment mirror. This method is capable of determining rapidly volumetric field-of-view, axial resolution, and image curvature. Moreover, as the phantom material mimics biological tissue, the system's signal and noise levels can be evaluated in conditions close to biological experiments. We believe this method could improve OCT quantitative data analysis and help OCT data comparison for longitudinal or multicenter studies.

  3. Semi-automated potentiometric titration method for uranium characterization

    Energy Technology Data Exchange (ETDEWEB)

    Cristiano, B.F.G., E-mail: barbara@ird.gov.br [Comissao Nacional de Energia Nuclear (CNEN), Instituto de Radioprotecao e Dosimetria (IRD), Avenida Salvador Allende s/n Recreio dos Bandeirantes, PO Box 37750, Rio de Janeiro, 22780-160 RJ (Brazil); Delgado, J.U.; Silva, J.W.S. da; Barros, P.D. de; Araujo, R.M.S. de [Comissao Nacional de Energia Nuclear (CNEN), Instituto de Radioprotecao e Dosimetria (IRD), Avenida Salvador Allende s/n Recreio dos Bandeirantes, PO Box 37750, Rio de Janeiro, 22780-160 RJ (Brazil); Lopes, R.T. [Programa de Engenharia Nuclear (PEN/COPPE), Universidade Federal do Rio de Janeiro (UFRJ), Ilha do Fundao, PO Box 68509, Rio de Janeiro, 21945-970 RJ (Brazil)

    2012-07-15

    The manual version of the potentiometric titration method has been used for certification and characterization of uranium compounds. In order to reduce the analysis time and the influence of the analyst, a semi-automatic version of the method was developed in the Brazilian Nuclear Energy Commission. The method was applied with traceability assured by using a potassium dichromate primary standard. The combined standard uncertainty in determining the total concentration of uranium was around 0.01%, which is suitable for uranium characterization. - Highlights: Black-Right-Pointing-Pointer We developed a semi-automatic version of potentiometric titration method. Black-Right-Pointing-Pointer The method is used for certification and characterization of uranium compounds. Black-Right-Pointing-Pointer The traceability of the method was assured by a K{sub 2}Cr{sub 2}O{sub 7} primary standard. Black-Right-Pointing-Pointer The results of U{sub 3}O{sub 8} reference material analyzed was consistent with certified value. Black-Right-Pointing-Pointer The uncertainty obtained, near 0.01%, is useful for characterization purposes.

  4. AutoGate: automating analysis of flow cytometry data.

    Science.gov (United States)

    Meehan, Stephen; Walther, Guenther; Moore, Wayne; Orlova, Darya; Meehan, Connor; Parks, David; Ghosn, Eliver; Philips, Megan; Mitsunaga, Erin; Waters, Jeffrey; Kantor, Aaron; Okamura, Ross; Owumi, Solomon; Yang, Yang; Herzenberg, Leonard A; Herzenberg, Leonore A

    2014-05-01

    Nowadays, one can hardly imagine biology and medicine without flow cytometry to measure CD4 T cell counts in HIV, follow bone marrow transplant patients, characterize leukemias, etc. Similarly, without flow cytometry, there would be a bleak future for stem cell deployment, HIV drug development and full characterization of the cells and cell interactions in the immune system. But while flow instruments have improved markedly, the development of automated tools for processing and analyzing flow data has lagged sorely behind. To address this deficit, we have developed automated flow analysis software technology, provisionally named AutoComp and AutoGate. AutoComp acquires sample and reagent labels from users or flow data files, and uses this information to complete the flow data compensation task. AutoGate replaces the manual subsetting capabilities provided by current analysis packages with newly defined statistical algorithms that automatically and accurately detect, display and delineate subsets in well-labeled and well-recognized formats (histograms, contour and dot plots). Users guide analyses by successively specifying axes (flow parameters) for data subset displays and selecting statistically defined subsets to be used for the next analysis round. Ultimately, this process generates analysis "trees" that can be applied to automatically guide analyses for similar samples. The first AutoComp/AutoGate version is currently in the hands of a small group of users at Stanford, Emory and NIH. When this "early adopter" phase is complete, the authors expect to distribute the software free of charge to .edu, .org and .gov users.

  5. Automated retinal image analysis for diabetic retinopathy in telemedicine.

    Science.gov (United States)

    Sim, Dawn A; Keane, Pearse A; Tufail, Adnan; Egan, Catherine A; Aiello, Lloyd Paul; Silva, Paolo S

    2015-03-01

    There will be an estimated 552 million persons with diabetes globally by the year 2030. Over half of these individuals will develop diabetic retinopathy, representing a nearly insurmountable burden for providing diabetes eye care. Telemedicine programmes have the capability to distribute quality eye care to virtually any location and address the lack of access to ophthalmic services. In most programmes, there is currently a heavy reliance on specially trained retinal image graders, a resource in short supply worldwide. These factors necessitate an image grading automation process to increase the speed of retinal image evaluation while maintaining accuracy and cost effectiveness. Several automatic retinal image analysis systems designed for use in telemedicine have recently become commercially available. Such systems have the potential to substantially improve the manner by which diabetes eye care is delivered by providing automated real-time evaluation to expedite diagnosis and referral if required. Furthermore, integration with electronic medical records may allow a more accurate prognostication for individual patients and may provide predictive modelling of medical risk factors based on broad population data. PMID:25697773

  6. Software fault tree analysis of an automated control system device written in Ada

    OpenAIRE

    Winter, Mathias William.

    1995-01-01

    Software Fault Tree Analysis (SFTA) is a technique used to analyze software for faults that could lead to hazardous conditions in systems which contain software components. Previous thesis works have developed three Ada-based, semi-automated software analysis tools, the Automated Code Translation Tool (ACm) an Ada statement template generator, the Fault Tree Editor (Fm) a graphical fault tree editor, and the Fault Isolator (Fl) an automated software fault tree isolator. These previous works d...

  7. An automated system for whole microscopic image acquisition and analysis.

    Science.gov (United States)

    Bueno, Gloria; Déniz, Oscar; Fernández-Carrobles, María Del Milagro; Vállez, Noelia; Salido, Jesús

    2014-09-01

    The field of anatomic pathology has experienced major changes over the last decade. Virtual microscopy (VM) systems have allowed experts in pathology and other biomedical areas to work in a safer and more collaborative way. VMs are automated systems capable of digitizing microscopic samples that were traditionally examined one by one. The possibility of having digital copies reduces the risk of damaging original samples, and also makes it easier to distribute copies among other pathologists. This article describes the development of an automated high-resolution whole slide imaging (WSI) system tailored to the needs and problems encountered in digital imaging for pathology, from hardware control to the full digitization of samples. The system has been built with an additional digital monochromatic camera together with the color camera by default and LED transmitted illumination (RGB). Monochrome cameras are the preferred method of acquisition for fluorescence microscopy. The system is able to digitize correctly and form large high resolution microscope images for both brightfield and fluorescence. The quality of the digital images has been quantified using three metrics based on sharpness, contrast and focus. It has been proved on 150 tissue samples of brain autopsies, prostate biopsies and lung cytologies, at five magnifications: 2.5×, 10×, 20×, 40×, and 63×. The article is focused on the hardware set-up and the acquisition software, although results of the implemented image processing techniques included in the software and applied to the different tissue samples are also presented.

  8. Automated methods for accurate determination of the critical velocity of packed bed chromatography.

    Science.gov (United States)

    Chang, Yu-Chih; Gerontas, Spyridon; Titchener-Hooker, Nigel J

    2012-01-01

    Knowing the critical velocity (ucrit) of a chromatography column is an important part of process development as it allows the optimization of chromatographic flow conditions. The conventional flow step method for determining ucrit is prone to error as it depends heavily on human judgment. In this study, two automated methods for determining ucrit have been developed: the automatic flow step (AFS) method and the automatic pressure step (APS) method. In the AFS method, the column pressure drop is monitored upon application of automated incremental increases in flow velocity, whereas in the APS method the flow velocity is monitored upon application of automated incremental increases in pressure drop. The APS method emerged as the one with the higher levels of accuracy, efficiency and ease of application having the greater potential to assist defining the best operational parameters of a chromatography column.

  9. Methods for Automated and Continuous Commissioning of Building Systems

    Energy Technology Data Exchange (ETDEWEB)

    Larry Luskay; Michael Brambley; Srinivas Katipamula

    2003-04-30

    Avoidance of poorly installed HVAC systems is best accomplished at the close of construction by having a building and its systems put ''through their paces'' with a well conducted commissioning process. This research project focused on developing key components to enable the development of tools that will automatically detect and correct equipment operating problems, thus providing continuous and automatic commissioning of the HVAC systems throughout the life of a facility. A study of pervasive operating problems reveled the following would most benefit from an automated and continuous commissioning process: (1) faulty economizer operation; (2) malfunctioning sensors; (3) malfunctioning valves and dampers, and (4) access to project design data. Methodologies for detecting system operation faults in these areas were developed and validated in ''bare-bones'' forms within standard software such as spreadsheets, databases, statistical or mathematical packages. Demonstrations included flow diagrams and simplified mock-up applications. Techniques to manage data were demonstrated by illustrating how test forms could be populated with original design information and the recommended sequence of operation for equipment systems. Proposed tools would use measured data, design data, and equipment operating parameters to diagnosis system problems. Steps for future research are suggested to help more toward practical application of automated commissioning and its high potential to improve equipment availability, increase occupant comfort, and extend the life of system equipment.

  10. Automated alignment method for coherence-controlled holographic microscope

    Science.gov (United States)

    Dostal, Zbynek; Slaby, Tomas; Kvasnica, Lukas; Lostak, Martin; Krizova, Aneta; Chmelik, Radim

    2015-11-01

    A coherence-controlled holographic microscope (CCHM) was developed particularly for quantitative phase imaging and measurement of live cell dynamics, which is the proper subject of digital holographic microscopy (DHM). CCHM in low-coherence mode extends DHM in the study of living cells. However, this advantage is compensated by sensitivity of the system to easily become misaligned, which is a serious hindrance to wanted performance. Therefore, it became clear that introduction of a self-correcting system is inevitable. Accordingly, we had to devise a theory of a suitable control and design an automated alignment system for CCHM. The modulus of the reconstructed holographic signal was identified as a significant variable for guiding the alignment procedures. From this, we derived the original basic realignment three-dimensional algorithm, which encompasses a unique set of procedures for automated alignment that contains processes for initial and advanced alignment as well as long-term maintenance of microscope tuning. All of these procedures were applied to a functioning microscope and the tested processes were successfully validated. Finally, in such a way, CCHM is enabled to substantially contribute to study of biology, particularly of cancer cells in vitro.

  11. Towards the Procedure Automation of Full Stochastic Spectral Based Fatigue Analysis

    Directory of Open Access Journals (Sweden)

    Khurram Shehzad

    2013-05-01

    Full Text Available Fatigue is one of the most significant failure modes for marine structures such as ships and offshore platforms. Among numerous methods for fatigue life estimation, spectral method is considered as the most reliable one due to its ability to cater different sea states as well as their probabilities of occurrence. However, spectral based simulation procedure itself is quite complex and numerically intensive owing to various critical technical details. Present research study is focused on the application and automation of spectral based fatigue analysis procedure for ship structure using ANSYS software with 3D liner sea keeping code AQWA. Ansys Parametric Design Language (APDL macros are created and subsequently implemented to automate the workflow of simulation process by reducing the time spent on non-value added repetitive activity. A MATLAB program based on direct calculation procedure of spectral fatigue is developed to calculate total fatigue damage. The automation procedure is employed to predict the fatigue life of a ship structural detail using wave scatter data of North Atlantic and Worldwide trade. The current work will provide a system for efficient implementation of stochastic spectral fatigue analysis procedure for ship structures.

  12. RootGraph: a graphic optimization tool for automated image analysis of plant roots.

    Science.gov (United States)

    Cai, Jinhai; Zeng, Zhanghui; Connor, Jason N; Huang, Chun Yuan; Melino, Vanessa; Kumar, Pankaj; Miklavcic, Stanley J

    2015-11-01

    This paper outlines a numerical scheme for accurate, detailed, and high-throughput image analysis of plant roots. In contrast to existing root image analysis tools that focus on root system-average traits, a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process is presented. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits for each identified primary and lateral root. Thirdly, it associates lateral roots and their properties with the specific primary root from which the laterals emerge. The performance of this approach was evaluated through comparisons with other automated and semi-automated software solutions as well as against results based on manual measurements. The comparisons and subsequent application of the algorithm to an array of experimental data demonstrate that this method outperforms existing methods in terms of accuracy, robustness, and the ability to process root images under high-throughput conditions.

  13. Automated generation of burnup chain for reactor analysis applications

    International Nuclear Information System (INIS)

    This paper presents the development of an automated generation of a new burnup chain for reactor analysis applications. The JENDL FP Decay Data File 2011 and Fission Yields Data File 2011 were used as the data sources. The nuclides in the new chain are determined by restrictions of the half-life and cumulative yield of fission products or from a given list. Then, decay modes, branching ratios and fission yields are recalculated taking into account intermediate reactions. The new burnup chain is output according to the format for the SRAC code system. Verification was performed to evaluate the accuracy of the new burnup chain. The results show that the new burnup chain reproduces well the results of a reference one with 193 fission products used in SRAC. Further development and applications are being planned with the burnup chain code. (author)

  14. Automated Large-Scale Shoreline Variability Analysis From Video

    Science.gov (United States)

    Pearre, N. S.

    2006-12-01

    Land-based video has been used to quantify changes in nearshore conditions for over twenty years. By combining the ability to track rapid, short-term shoreline change and changes associated with longer term or seasonal processes, video has proved to be a cost effective and versatile tool for coastal science. Previous video-based studies of shoreline change have typically examined the position of the shoreline along a small number of cross-shore lines as a proxy for the continuous coast. The goal of this study is twofold: (1) to further develop automated shoreline extraction algorithms for continuous shorelines, and (2) to track the evolution of a nourishment project at Rehoboth Beach, DE that was concluded in June 2005. Seven cameras are situated approximately 30 meters above mean sea level and 70 meters from the shoreline. Time exposure and variance images are captured hourly during daylight and transferred to a local processing computer. After correcting for lens distortion and geo-rectifying to a shore-normal coordinate system, the images are merged to form a composite planform image of 6 km of coast. Automated extraction algorithms establish shoreline and breaker positions throughout a tidal cycle on a daily basis. Short and long term variability in the daily shoreline will be characterized using empirical orthogonal function (EOF) analysis. Periodic sediment volume information will be extracted by incorporating the results of monthly ground-based LIDAR surveys and by correlating the hourly shorelines to the corresponding tide level under conditions with minimal wave activity. The Delaware coast in the area downdrift of the nourishment site is intermittently interrupted by short groins. An Even/Odd analysis of the shoreline response around these groins will be performed. The impact of groins on the sediment volume transport along the coast during periods of accretive and erosive conditions will be discussed. [This work is being supported by DNREC and the

  15. galaxieEST: addressing EST identity through automated phylogenetic analysis

    Directory of Open Access Journals (Sweden)

    Larsson Karl-Henrik

    2004-07-01

    Full Text Available Abstract Background Research involving expressed sequence tags (ESTs is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. Results galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. Conclusions By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches

  16. Automation of block assignment planning using a diagram-based scenario modeling method

    Directory of Open Access Journals (Sweden)

    Hwang In Hyuck

    2014-03-01

    Full Text Available Most shipbuilding scheduling research so far has focused on the load level on the dock plan. This is be¬cause the dock is the least extendable resource in shipyards, and its overloading is difficult to resolve. However, once dock scheduling is completed, making a plan that makes the best use of the rest of the resources in the shipyard to minimize any additional cost is also important. Block assignment planning is one of the midterm planning tasks; it assigns a block to the facility (factory/shop or surface plate that will actually manufacture the block according to the block characteristics and current situation of the facility. It is one of the most heavily loaded midterm planning tasks and is carried out manu¬ally by experienced workers. In this study, a method of representing the block assignment rules using a diagram was su¬ggested through analysis of the existing manual process. A block allocation program was developed which automated the block assignment process according to the rules represented by the diagram. The planning scenario was validated through a case study that compared the manual assignment and two automated block assignment results.

  17. 14 CFR 1261.413 - Analysis of costs; automation; prevention of overpayments, delinquencies, or defaults.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Analysis of costs; automation; prevention of overpayments, delinquencies, or defaults. 1261.413 Section 1261.413 Aeronautics and Space NATIONAL...) § 1261.413 Analysis of costs; automation; prevention of overpayments, delinquencies, or defaults....

  18. Automated DNA extraction of single dog hairs without roots for mitochondrial DNA analysis.

    Science.gov (United States)

    Bekaert, Bram; Larmuseau, Maarten H D; Vanhove, Maarten P M; Opdekamp, Anouschka; Decorte, Ronny

    2012-03-01

    Dogs are intensely integrated in human social life and their shed hairs can play a major role in forensic investigations. The overall aim of this study was to validate a semi-automated extraction method for mitochondrial DNA analysis of telogenic dog hairs. Extracted DNA was amplified with a 95% success rate from 43 samples using two new experimental designs in which the mitochondrial control region was amplified as a single large (± 1260 bp) amplicon or as two individual amplicons (HV1 and HV2; ± 650 and 350 bp) with tailed-primers. The results prove that the extraction of dog hair mitochondrial DNA can easily be automated to provide sufficient DNA yield for the amplification of a forensically useful long mitochondrial DNA fragment or alternatively two short fragments with minimal loss of sequence in case of degraded samples.

  19. Automated Bifurcation Analysis for Nonlinear Elliptic Partial Difference Equations on Graphs

    CERN Document Server

    Neuberger, John M; Swift, James W

    2010-01-01

    We seek solutions $u\\in\\R^n$ to the semilinear elliptic partial difference equation $-Lu + f_s(u) = 0$, where $L$ is the matrix corresponding to the Laplacian operator on a graph $G$ and $f_s$ is a one-parameter family of nonlinear functions. This article combines the ideas introduced by the authors in two papers: a) {\\it Nonlinear Elliptic Partial Difference Equations on Graphs} (J. Experimental Mathematics, 2006), which introduces analytical and numerical techniques for solving such equations, and b) {\\it Symmetry and Automated Branch Following for a Semilinear Elliptic PDE on a Fractal Region} wherein we present some of our recent advances concerning symmetry, bifurcation, and automation fo We apply the symmetry analysis found in the SIAM paper to arbitrary graphs in order to obtain better initial guesses for Newton's method, create informative graphics, and be in the underlying variational structure. We use two modified implementations of the gradient Newton-Galerkin algorithm (GNGA, Neuberger and Swift) ...

  20. Research Prototype: Automated Analysis of Scientific and Engineering Semantics

    Science.gov (United States)

    Stewart, Mark E. M.; Follen, Greg (Technical Monitor)

    2001-01-01

    Physical and mathematical formulae and concepts are fundamental elements of scientific and engineering software. These classical equations and methods are time tested, universally accepted, and relatively unambiguous. The existence of this classical ontology suggests an ideal problem for automated comprehension. This problem is further motivated by the pervasive use of scientific code and high code development costs. To investigate code comprehension in this classical knowledge domain, a research prototype has been developed. The prototype incorporates scientific domain knowledge to recognize code properties (including units, physical, and mathematical quantity). Also, the procedure implements programming language semantics to propagate these properties through the code. This prototype's ability to elucidate code and detect errors will be demonstrated with state of the art scientific codes.

  1. Conventional Versus Automated Implantation of Loose Seeds in Prostate Brachytherapy: Analysis of Dosimetric and Clinical Results

    Energy Technology Data Exchange (ETDEWEB)

    Genebes, Caroline, E-mail: genebes.caroline@claudiusregaud.fr [Radiation Oncology Department, Institut Claudius Regaud, Toulouse (France); Filleron, Thomas; Graff, Pierre [Radiation Oncology Department, Institut Claudius Regaud, Toulouse (France); Jonca, Frédéric [Department of Urology, Clinique Ambroise Paré, Toulouse (France); Huyghe, Eric; Thoulouzan, Matthieu; Soulie, Michel; Malavaud, Bernard [Department of Urology and Andrology, CHU Rangueil, Toulouse (France); Aziza, Richard; Brun, Thomas; Delannes, Martine; Bachaud, Jean-Marc [Radiation Oncology Department, Institut Claudius Regaud, Toulouse (France)

    2013-11-15

    Purpose: To review the clinical outcome of I-125 permanent prostate brachytherapy (PPB) for low-risk and intermediate-risk prostate cancer and to compare 2 techniques of loose-seed implantation. Methods and Materials: 574 consecutive patients underwent I-125 PPB for low-risk and intermediate-risk prostate cancer between 2000 and 2008. Two successive techniques were used: conventional implantation from 2000 to 2004 and automated implantation (Nucletron, FIRST system) from 2004 to 2008. Dosimetric and biochemical recurrence-free (bNED) survival results were reported and compared for the 2 techniques. Univariate and multivariate analysis researched independent predictors for bNED survival. Results: 419 (73%) and 155 (27%) patients with low-risk and intermediate-risk disease, respectively, were treated (median follow-up time, 69.3 months). The 60-month bNED survival rates were 95.2% and 85.7%, respectively, for patients with low-risk and intermediate-risk disease (P=.04). In univariate analysis, patients treated with automated implantation had worse bNED survival rates than did those treated with conventional implantation (P<.0001). By day 30, patients treated with automated implantation showed lower values of dose delivered to 90% of prostate volume (D90) and volume of prostate receiving 100% of prescribed dose (V100). In multivariate analysis, implantation technique, Gleason score, and V100 on day 30 were independent predictors of recurrence-free status. Grade 3 urethritis and urinary incontinence were observed in 2.6% and 1.6% of the cohort, respectively, with no significant differences between the 2 techniques. No grade 3 proctitis was observed. Conclusion: Satisfactory 60-month bNED survival rates (93.1%) and acceptable toxicity (grade 3 urethritis <3%) were achieved by loose-seed implantation. Automated implantation was associated with worse dosimetric and bNED survival outcomes.

  2. Development of automated high throughput single molecular microfluidic detection platform for signal transduction analysis

    Science.gov (United States)

    Huang, Po-Jung; Baghbani Kordmahale, Sina; Chou, Chao-Kai; Yamaguchi, Hirohito; Hung, Mien-Chie; Kameoka, Jun

    2016-03-01

    Signal transductions including multiple protein post-translational modifications (PTM), protein-protein interactions (PPI), and protein-nucleic acid interaction (PNI) play critical roles for cell proliferation and differentiation that are directly related to the cancer biology. Traditional methods, like mass spectrometry, immunoprecipitation, fluorescence resonance energy transfer, and fluorescence correlation spectroscopy require a large amount of sample and long processing time. "microchannel for multiple-parameter analysis of proteins in single-complex (mMAPS)"we proposed can reduce the process time and sample volume because this system is composed by microfluidic channels, fluorescence microscopy, and computerized data analysis. In this paper, we will present an automated mMAPS including integrated microfluidic device, automated stage and electrical relay for high-throughput clinical screening. Based on this result, we estimated that this automated detection system will be able to screen approximately 150 patient samples in a 24-hour period, providing a practical application to analyze tissue samples in a clinical setting.

  3. Comparison of automated method and improved AOAC Kjeldahl method for determination of protein in meat and meat products.

    Science.gov (United States)

    McGill, D L

    1981-01-01

    The Kjel-Foss automated method for protein determination meat and meat products was compared with the improved AOAC Kjeldahl method. Meat samples were separated into 3 categories based on fat content and analyzed in duplicate by both methods. No significant difference was found in a paired comparison of the 2 methods in each of the 3 meat categories, using Student's t-test at the 99% confidence level. A number of additional meat samples analyzed 6-9 times by the automated method showed an overall average range of 0.55% protein and average standard deviation of 0.20. The Kjel-Foss automated method was applicable for total protein determination in a wide variety of meat and meat products.

  4. A time-series method for automated measurement of changes in mitotic and interphase duration from time-lapse movies.

    Directory of Open Access Journals (Sweden)

    Frederic D Sigoillot

    Full Text Available BACKGROUND: Automated time-lapse microscopy can visualize proliferation of large numbers of individual cells, enabling accurate measurement of the frequency of cell division and the duration of interphase and mitosis. However, extraction of quantitative information by manual inspection of time-lapse movies is too time-consuming to be useful for analysis of large experiments. METHODOLOGY/PRINCIPAL FINDINGS: Here we present an automated time-series approach that can measure changes in the duration of mitosis and interphase in individual cells expressing fluorescent histone 2B. The approach requires analysis of only 2 features, nuclear area and average intensity. Compared to supervised learning approaches, this method reduces processing time and does not require generation of training data sets. We demonstrate that this method is as sensitive as manual analysis in identifying small changes in interphase or mitotic duration induced by drug or siRNA treatment. CONCLUSIONS/SIGNIFICANCE: This approach should facilitate automated analysis of high-throughput time-lapse data sets to identify small molecules or gene products that influence timing of cell division.

  5. A Semi-Automated Functional Test Data Analysis Tool

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Peng; Haves, Philip; Kim, Moosung

    2005-05-01

    The growing interest in commissioning is creating a demand that will increasingly be met by mechanical contractors and less experienced commissioning agents. They will need tools to help them perform commissioning effectively and efficiently. The widespread availability of standardized procedures, accessible in the field, will allow commissioning to be specified with greater certainty as to what will be delivered, enhancing the acceptance and credibility of commissioning. In response, a functional test data analysis tool is being developed to analyze the data collected during functional tests for air-handling units. The functional test data analysis tool is designed to analyze test data, assess performance of the unit under test and identify the likely causes of the failure. The tool has a convenient user interface to facilitate manual entry of measurements made during a test. A graphical display shows the measured performance versus the expected performance, highlighting significant differences that indicate the unit is not able to pass the test. The tool is described as semiautomated because the measured data need to be entered manually, instead of being passed from the building control system automatically. However, the data analysis and visualization are fully automated. The tool is designed to be used by commissioning providers conducting functional tests as part of either new building commissioning or retro-commissioning, as well as building owners and operators interested in conducting routine tests periodically to check the performance of their HVAC systems.

  6. Intelligent Control in Automation Based on Wireless Traffic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kurt Derr; Milos Manic

    2007-08-01

    Wireless technology is a central component of many factory automation infrastructures in both the commercial and government sectors, providing connectivity among various components in industrial realms (distributed sensors, machines, mobile process controllers). However wireless technologies provide more threats to computer security than wired environments. The advantageous features of Bluetooth technology resulted in Bluetooth units shipments climbing to five million per week at the end of 2005 [1, 2]. This is why the real-time interpretation and understanding of Bluetooth traffic behavior is critical in both maintaining the integrity of computer systems and increasing the efficient use of this technology in control type applications. Although neuro-fuzzy approaches have been applied to wireless 802.11 behavior analysis in the past, a significantly different Bluetooth protocol framework has not been extensively explored using this technology. This paper presents a new neurofuzzy traffic analysis algorithm of this still new territory of Bluetooth traffic. Further enhancements of this algorithm are presented along with the comparison against the traditional, numerical approach. Through test examples, interesting Bluetooth traffic behavior characteristics were captured, and the comparative elegance of this computationally inexpensive approach was demonstrated. This analysis can be used to provide directions for future development and use of this prevailing technology in various control type applications, as well as making the use of it more secure.

  7. Intelligent Control in Automation Based on Wireless Traffic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kurt Derr; Milos Manic

    2007-09-01

    Wireless technology is a central component of many factory automation infrastructures in both the commercial and government sectors, providing connectivity among various components in industrial realms (distributed sensors, machines, mobile process controllers). However wireless technologies provide more threats to computer security than wired environments. The advantageous features of Bluetooth technology resulted in Bluetooth units shipments climbing to five million per week at the end of 2005 [1, 2]. This is why the real-time interpretation and understanding of Bluetooth traffic behavior is critical in both maintaining the integrity of computer systems and increasing the efficient use of this technology in control type applications. Although neuro-fuzzy approaches have been applied to wireless 802.11 behavior analysis in the past, a significantly different Bluetooth protocol framework has not been extensively explored using this technology. This paper presents a new neurofuzzy traffic analysis algorithm of this still new territory of Bluetooth traffic. Further enhancements of this algorithm are presented along with the comparison against the traditional, numerical approach. Through test examples, interesting Bluetooth traffic behavior characteristics were captured, and the comparative elegance of this computationally inexpensive approach was demonstrated. This analysis can be used to provide directions for future development and use of this prevailing technology in various control type applications, as well as making the use of it more secure.

  8. Automated Quantification of Optic Nerve Axons in Primate Glaucomatous and Normal Eyes—Method and Comparison to Semi-Automated Manual Quantification

    OpenAIRE

    Reynaud, Juan; Cull, Grant; Lin WANG; Fortune, Brad; Gardiner, Stuart; Burgoyne, Claude F.; Cioffi, George A.

    2012-01-01

    An algorithm and software application for counting 100% of the axons in nonhuman primate optic nerve cross sections (normal through end-stage experimental glaucoma) is presented and validated against a semi-automated manual method.

  9. Automated microscopical method for the characterization of pyrite in coal

    Energy Technology Data Exchange (ETDEWEB)

    Kuehn, K. W.; Davis, A.

    1979-08-01

    The Rapid Scan system of automated reflectance microscopy is a line scanning device capable of characterizing the pyrite content of a coal. The system combines a sophisticated software base with standard hardware components to provide flexibility in analytical format. As a prepared coal sample is moved automatically beneath the microscope objective, reflectance values from adjacent 2 ..mu..m squares are sampled by the photomultiplier tube. These values are stored in computer memory for subsequent calculation of the volumetric proportion of pyrite in the sample. Simultaneously, the Rapid Scan also accumulates a distribution of pyrite chord lengths. In a modification of the Rosiwal linear scanning technique, the number of consecutive readings on a pyrite particle are recorded and stored independently in computer memory. In order to determine the precision of pyrite volume estimates, a suite of coals with varying pyrite content was analyzed at several sample-point densities. The level of precision achieved was found to be a function of sample density and was always superior to the precision of the conventional, visual point counting technique. From these data, sampling plans to achieve a desired level of analytical precision were designed. The ability of the Rapid Scan system to quickly characterize many samples of a feed coal in this manner, makes it a potentially effective tool in helping to optimize preparation facility operation for the removal of pyrite.

  10. Automated calibration methods for robotic multisensor landmine detection

    Science.gov (United States)

    Keranen, Joe G.; Miller, Jonathan; Schultz, Gregory; Topolosky, Zeke

    2007-04-01

    Both force protection and humanitarian demining missions require efficient and reliable detection and discrimination of buried anti-tank and anti-personnel landmines. Widely varying surface and subsurface conditions, mine types and placement, as well as environmental regimes challenge the robustness of the automatic target recognition process. In this paper we present applications created for the U.S. Army Nemesis detection platform. Nemesis is an unmanned rubber-tracked vehicle-based system designed to eradicate a wide variety of anti-tank and anti-personnel landmines for humanitarian demining missions. The detection system integrates advanced ground penetrating synthetic aperture radar (GPSAR) and electromagnetic induction (EMI) arrays, highly accurate global and local positioning, and on-board target detection/classification software on the front loader of a semi-autonomous UGV. An automated procedure is developed to estimate the soil's dielectric constant using surface reflections from the ground penetrating radar. The results have implications not only for calibration of system data acquisition parameters, but also for user awareness and tuning of automatic target recognition detection and discrimination algorithms.

  11. Twelve automated thresholding methods for segmentation of PET images: a phantom study

    Science.gov (United States)

    Prieto, Elena; Lecumberri, Pablo; Pagola, Miguel; Gómez, Marisol; Bilbao, Izaskun; Ecay, Margarita; Peñuelas, Iván; Martí-Climent, Josep M.

    2012-06-01

    Tumor volume delineation over positron emission tomography (PET) images is of great interest for proper diagnosis and therapy planning. However, standard segmentation techniques (manual or semi-automated) are operator dependent and time consuming while fully automated procedures are cumbersome or require complex mathematical development. The aim of this study was to segment PET images in a fully automated way by implementing a set of 12 automated thresholding algorithms, classical in the fields of optical character recognition, tissue engineering or non-destructive testing images in high-tech structures. Automated thresholding algorithms select a specific threshold for each image without any a priori spatial information of the segmented object or any special calibration of the tomograph, as opposed to usual thresholding methods for PET. Spherical 18F-filled objects of different volumes were acquired on clinical PET/CT and on a small animal PET scanner, with three different signal-to-background ratios. Images were segmented with 12 automatic thresholding algorithms and results were compared with the standard segmentation reference, a threshold at 42% of the maximum uptake. Ridler and Ramesh thresholding algorithms based on clustering and histogram-shape information, respectively, provided better results that the classical 42%-based threshold (p < 0.05). We have herein demonstrated that fully automated thresholding algorithms can provide better results than classical PET segmentation tools.

  12. Twelve automated thresholding methods for segmentation of PET images: a phantom study

    International Nuclear Information System (INIS)

    Tumor volume delineation over positron emission tomography (PET) images is of great interest for proper diagnosis and therapy planning. However, standard segmentation techniques (manual or semi-automated) are operator dependent and time consuming while fully automated procedures are cumbersome or require complex mathematical development. The aim of this study was to segment PET images in a fully automated way by implementing a set of 12 automated thresholding algorithms, classical in the fields of optical character recognition, tissue engineering or non-destructive testing images in high-tech structures. Automated thresholding algorithms select a specific threshold for each image without any a priori spatial information of the segmented object or any special calibration of the tomograph, as opposed to usual thresholding methods for PET. Spherical 18F-filled objects of different volumes were acquired on clinical PET/CT and on a small animal PET scanner, with three different signal-to-background ratios. Images were segmented with 12 automatic thresholding algorithms and results were compared with the standard segmentation reference, a threshold at 42% of the maximum uptake. Ridler and Ramesh thresholding algorithms based on clustering and histogram-shape information, respectively, provided better results that the classical 42%-based threshold (p < 0.05). We have herein demonstrated that fully automated thresholding algorithms can provide better results than classical PET segmentation tools. (paper)

  13. OpenComet: An automated tool for comet assay image analysis

    Directory of Open Access Journals (Sweden)

    Benjamin M. Gyori

    2014-01-01

    Full Text Available Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

  14. Development of an Automated Technique for Failure Modes and Effect Analysis

    DEFF Research Database (Denmark)

    Blanke, M.; Borch, Ole; Allasia, G.;

    1999-01-01

    Advances in automation have provided integration of monitoring and control functions to enhance the operator's overview and ability to take remedy actions when faults occur. Automation in plant supervision is technically possible with integrated automation systems as platforms, but new design...... implementing an automated technique for Failure Modes and Effects Analysis (FMEA). This technique is based on the matrix formulation of FMEA for the investigation of failure propagation through a system. As main result, this technique will provide the design engineer with decision tables for fault handling...

  15. Development of an automated technique for failure modes and effect analysis

    DEFF Research Database (Denmark)

    Blanke, M.; Borch, Ole; Bagnoli, F.;

    Advances in automation have provided integration of monitoring and control functions to enhance the operator's overview and ability to take remedy actions when faults occur. Automation in plant supervision is technically possible with integrated automation systems as platforms, but new design...... implementing an automated technique for Failure Modes and Effects Analysis (FMEA). This technique is based on the matrix formulation of FMEA for the investigation of failure propagation through a system. As main result, this technique will provide the design engineer with decision tables for fault handling...

  16. a Psycholinguistic Model for Simultaneous Translation, and Proficiency Assessment by Automated Acoustic Analysis of Discourse.

    Science.gov (United States)

    Yaghi, Hussein M.

    Two separate but related issues are addressed: how simultaneous translation (ST) works on a cognitive level and how such translation can be objectively assessed. Both of these issues are discussed in the light of qualitative and quantitative analyses of a large corpus of recordings of ST and shadowing. The proposed ST model utilises knowledge derived from a discourse analysis of the data, many accepted facts in the psychology tradition, and evidence from controlled experiments that are carried out here. This model has three advantages: (i) it is based on analyses of extended spontaneous speech rather than word-, syllable-, or clause -bound stimuli; (ii) it draws equally on linguistic and psychological knowledge; and (iii) it adopts a non-traditional view of language called 'the linguistic construction of reality'. The discourse-based knowledge is also used to develop three computerised systems for the assessment of simultaneous translation: one is a semi-automated system that treats the content of the translation; and two are fully automated, one of which is based on the time structure of the acoustic signals whilst the other is based on their cross-correlation. For each system, several parameters of performance are identified, and they are correlated with assessments rendered by the traditional, subjective, qualitative method. Using signal processing techniques, the acoustic analysis of discourse leads to the conclusion that quality in simultaneous translation can be assessed quantitatively with varying degrees of automation. It identifies as measures of performance (i) three content-based standards; (ii) four time management parameters that reflect the influence of the source on the target language time structure; and (iii) two types of acoustical signal coherence. Proficiency in ST is shown to be directly related to coherence and speech rate but inversely related to omission and delay. High proficiency is associated with a high degree of simultaneity and

  17. An automated method to quantify microglia morphology and application to monitor activation state longitudinally in vivo.

    Directory of Open Access Journals (Sweden)

    Cleopatra Kozlowski

    Full Text Available Microglia are specialized immune cells of the brain. Upon insult, microglia initiate a cascade of cellular responses including a characteristic change in cell morphology. To study the dynamics of microglia immune response in situ, we developed an automated image analysis method that enables the quantitative assessment of microglia activation state within tissue based solely on cell morphology. Per cell morphometric analysis of fluorescently labeled microglia is achieved through local iterative threshold segmentation, which reduces errors caused by signal-to-noise variation across large volumes. We demonstrate, utilizing systemic application of lipopolysaccharide as a model of immune challenge, that several morphological parameters, including cell perimeter length, cell roundness and soma size, quantitatively distinguish resting versus activated populations of microglia within tissue comparable to traditional immunohistochemistry methods. Furthermore, we provide proof-of-concept data that monitoring soma size enables the longitudinal assessment of microglia activation in the mouse neocortex imaged via 2-photon in vivo microscopy. The ability to quantify microglia activation automatically by shape alone allows unbiased and rapid analysis of both fixed and in vivo central nervous system tissue.

  18. 40 CFR 13.19 - Analysis of costs; automation; prevention of overpayments, delinquencies or defaults.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Analysis of costs; automation; prevention of overpayments, delinquencies or defaults. 13.19 Section 13.19 Protection of Environment...; automation; prevention of overpayments, delinquencies or defaults. (a) The Administrator may...

  19. AUTOMATION METHODS FOR FORMING AND RECTIFYING STIFFENED PARTS WITH ROLLING MACHINES

    Directory of Open Access Journals (Sweden)

    A.Ye. Pashkov

    2015-12-01

    Full Text Available To improve the capabilities of forming and rectifying stiffened parts, rolling as one of the implemented methods of local plastic deformation has been examined. The tools for edge and sheet rolling have been described. The methods of process automation have been developed.

  20. The BoneXpert method for automated determination of skeletal maturity

    DEFF Research Database (Denmark)

    Thodberg, Hans Henrik; Kreiborg, Sven; Juul, Anders;

    2009-01-01

    Bone age rating is associated with a considerable variability from the human interpretation, and this is the motivation for presenting a new method for automated determination of bone age (skeletal maturity). The method, called BoneXpert, reconstructs, from radiographs of the hand, the borders of...

  1. Fully automated quantitative analysis of breast cancer risk in DCE-MR images

    Science.gov (United States)

    Jiang, Luan; Hu, Xiaoxin; Gu, Yajia; Li, Qiang

    2015-03-01

    Amount of fibroglandular tissue (FGT) and background parenchymal enhancement (BPE) in dynamic contrast enhanced magnetic resonance (DCE-MR) images are two important indices for breast cancer risk assessment in the clinical practice. The purpose of this study is to develop and evaluate a fully automated scheme for quantitative analysis of FGT and BPE in DCE-MR images. Our fully automated method consists of three steps, i.e., segmentation of whole breast, fibroglandular tissues, and enhanced fibroglandular tissues. Based on the volume of interest extracted automatically, dynamic programming method was applied in each 2-D slice of a 3-D MR scan to delineate the chest wall and breast skin line for segmenting the whole breast. This step took advantages of the continuity of chest wall and breast skin line across adjacent slices. We then further used fuzzy c-means clustering method with automatic selection of cluster number for segmenting the fibroglandular tissues within the segmented whole breast area. Finally, a statistical method was used to set a threshold based on the estimated noise level for segmenting the enhanced fibroglandular tissues in the subtraction images of pre- and post-contrast MR scans. Based on the segmented whole breast, fibroglandular tissues, and enhanced fibroglandular tissues, FGT and BPE were automatically computed. Preliminary results of technical evaluation and clinical validation showed that our fully automated scheme could obtain good segmentation of the whole breast, fibroglandular tissues, and enhanced fibroglandular tissues to achieve accurate assessment of FGT and BPE for quantitative analysis of breast cancer risk.

  2. A METHOD OF TASK ALLOCATION AND AUTOMATED NEGOTIATION FOR MULTI ROBOTS

    Institute of Scientific and Technical Information of China (English)

    Ke Wende; Peng Zhiping; Yuan Quande; Hong Bingrong; Chen Ke; Cai Zesu

    2012-01-01

    A method of task allocation and automated negotiation for multi robots was proposed.Firstly,the principles of task allocation were described based on the real capability of robot.Secondly,the model of automated negotiation was constructed,in which Least-Squares Support Vector Regression (LSSVR) was improved to estimate the opponent's negotiation utility and the robust controller of H∞ output feedback was employed to optimize the utility performance indicators.Thirdly,the protocol of negotiation and reallocation was proposed to improve the real-time capability and task allocation.Finally,the validity of method was proved through experiments.

  3. Parameter Studies, time-dependent simulations and design with automated Cartesian methods

    Science.gov (United States)

    Aftosmis, Michael

    2005-01-01

    Over the past decade, NASA has made a substantial investment in developing adaptive Cartesian grid methods for aerodynamic simulation. Cartesian-based methods played a key role in both the Space Shuttle Accident Investigation and in NASA's return to flight activities. The talk will provide an overview of recent technological developments focusing on the generation of large-scale aerodynamic databases, automated CAD-based design, and time-dependent simulations with of bodies in relative motion. Automation, scalability and robustness underly all of these applications and research in each of these topics will be presented.

  4. Models, methods and software for distributed knowledge acquisition for the automated construction of integrated expert systems knowledge bases

    International Nuclear Information System (INIS)

    Based on an analysis of existing models, methods and means of acquiring knowledge, a base method of automated knowledge acquisition has been chosen. On the base of this method, a new approach to integrate information acquired from knowledge sources of different typologies has been proposed, and the concept of a distributed knowledge acquisition with the aim of computerized formation of the most complete and consistent models of problem areas has been introduced. An original algorithm for distributed knowledge acquisition from databases, based on the construction of binary decision trees has been developed

  5. Automated Reasoning and Equation Solving with the Characteristic Set Method

    Institute of Scientific and Technical Information of China (English)

    Wen-Tsun Wu; Xiao-Shan Gao

    2006-01-01

    A brief introduction to the characteristic set method is given for solving algebraic equation systems and then the method is extended to algebraic difference systems. The method can be used to decompose the zero set for a difference polynomial set in general form to the union of difference polynomial sets in triangular form. Based on the characteristic set method, a decision procedure for the first order theory over an algebraically closed field and a procedure to prove certain difference identities are proposed.

  6. Synchronous Control Method and Realization of Automated Pharmacy Elevator

    Science.gov (United States)

    Liu, Xiang-Quan

    Firstly, the control method of elevator's synchronous motion is provided, the synchronous control structure of double servo motor based on PMAC is accomplished. Secondly, synchronous control program of elevator is implemented by using PMAC linear interpolation motion model and position error compensation method. Finally, the PID parameters of servo motor were adjusted. The experiment proves the control method has high stability and reliability.

  7. Application of automated image analysis to coal petrography

    Science.gov (United States)

    Chao, E.C.T.; Minkin, J.A.; Thompson, C.L.

    1982-01-01

    The coal petrologist seeks to determine the petrographic characteristics of organic and inorganic coal constituents and their lateral and vertical variations within a single coal bed or different coal beds of a particular coal field. Definitive descriptions of coal characteristics and coal facies provide the basis for interpretation of depositional environments, diagenetic changes, and burial history and determination of the degree of coalification or metamorphism. Numerous coal core or columnar samples must be studied in detail in order to adequately describe and define coal microlithotypes, lithotypes, and lithologic facies and their variations. The large amount of petrographic information required can be obtained rapidly and quantitatively by use of an automated image-analysis system (AIAS). An AIAS can be used to generate quantitative megascopic and microscopic modal analyses for the lithologic units of an entire columnar section of a coal bed. In our scheme for megascopic analysis, distinctive bands 2 mm or more thick are first demarcated by visual inspection. These bands consist of either nearly pure microlithotypes or lithotypes such as vitrite/vitrain or fusite/fusain, or assemblages of microlithotypes. Megascopic analysis with the aid of the AIAS is next performed to determine volume percentages of vitrite, inertite, minerals, and microlithotype mixtures in bands 0.5 to 2 mm thick. The microlithotype mixtures are analyzed microscopically by use of the AIAS to determine their modal composition in terms of maceral and optically observable mineral components. Megascopic and microscopic data are combined to describe the coal unit quantitatively in terms of (V) for vitrite, (E) for liptite, (I) for inertite or fusite, (M) for mineral components other than iron sulfide, (S) for iron sulfide, and (VEIM) for the composition of the mixed phases (Xi) i = 1,2, etc. in terms of the maceral groups vitrinite V, exinite E, inertinite I, and optically observable mineral

  8. Rapid Quantification of Myocardial Fibrosis: A New Macro-Based Automated Analysis

    Directory of Open Access Journals (Sweden)

    Awal M. Hadi

    2010-01-01

    Full Text Available Background: Fibrosis is associated with various cardiac pathologies and dysfunction. Current quantification methods are time-consuming and laborious. We describe a semi-automated quantification technique for myocardial fibrosis and validated this using traditional methods.

  9. Automated absolute activation analysis with californium-252 sources

    Energy Technology Data Exchange (ETDEWEB)

    MacMurdo, K.W.; Bowman, W.W.

    1978-09-01

    A 100-mg /sup 252/Cf neutron activation analysis facility is used routinely at the Savannah River Laboratory for multielement analysis of many solid and liquid samples. An absolute analysis technique converts counting data directly to elemental concentration without the use of classical comparative standards and flux monitors. With the totally automated pneumatic sample transfer system, cyclic irradiation-decay-count regimes can be pre-selected for up to 40 samples, and samples can be analyzed with the facility unattended. An automatic data control system starts and stops a high-resolution gamma-ray spectrometer and/or a delayed-neutron detector; the system also stores data and controls output modes. Gamma ray data are reduced by three main programs in the IBM 360/195 computer: the 4096-channel spectrum and pertinent experimental timing, counting, and sample data are stored on magnetic tape; the spectrum is then reduced to a list of significant photopeak energies, integrated areas, and their associated statistical errors; and the third program assigns gamma ray photopeaks to the appropriate neutron activation product(s) by comparing photopeak energies to tabulated gamma ray energies. Photopeak areas are then converted to elemental concentration by using experimental timing and sample data, calculated elemental neutron capture rates, absolute detector efficiencies, and absolute spectroscopic decay data. Calculational procedures have been developed so that fissile material can be analyzed by cyclic neutron activation and delayed-neutron counting procedures. These calculations are based on a 6 half-life group model of delayed neutron emission; calculations include corrections for delayed neutron interference from /sup 17/O. Detection sensitivities of < or = 400 ppB for natural uranium and 8 ppB (< or = 0.5 (nCi/g)) for /sup 239/Pu were demonstrated with 15-g samples at a throughput of up to 140 per day. Over 40 elements can be detected at the sub-ppM level.

  10. Automated preparation of Kepler time series of planet hosts for asteroseismic analysis

    CERN Document Server

    Handberg, R

    2014-01-01

    One of the tasks of the Kepler Asteroseismic Science Operations Center (KASOC) is to provide asteroseismic analyses on Kepler Objects of Interest (KOIs). However, asteroseismic analysis of planetary host stars presents some unique complications with respect to data preprocessing, compared to pure asteroseismic targets. If not accounted for, the presence of planetary transits in the photometric time series often greatly complicates or even hinders these asteroseismic analyses. This drives the need for specialised methods of preprocessing data to make them suitable for asteroseismic analysis. In this paper we present the KASOC Filter, which is used to automatically prepare data from the Kepler/K2 mission for asteroseismic analyses of solar-like planet host stars. The methods are very effective at removing unwanted signals of both instrumental and planetary origins and produce significantly cleaner photometric time series than the original data. The methods are automated and can therefore easily be applied to a ...

  11. Comparison of Dimension Reduction Methods for Automated Essay Grading

    Science.gov (United States)

    Kakkonen, Tuomo; Myller, Niko; Sutinen, Erkki; Timonen, Jari

    2008-01-01

    Automatic Essay Assessor (AEA) is a system that utilizes information retrieval techniques such as Latent Semantic Analysis (LSA), Probabilistic Latent Semantic Analysis (PLSA), and Latent Dirichlet Allocation (LDA) for automatic essay grading. The system uses learning materials and relatively few teacher-graded essays for calibrating the scoring…

  12. MORPHY, a program for an automated "atoms in molecules" analysis

    Science.gov (United States)

    Popelier, Paul L. A.

    1996-02-01

    The operating manual for a structured FORTAN 77 program called MORPHY is presented. This code performs an automated topological analysis of a molecular electron density and its Laplacian. The program is written in a stylistically homogeneous, transparant and modular manner. The input is compact but flexible and allows for multiple jobs in one deck. The output is detailed and has an attractive lay-out. Critical points in the charge density and its Laplacian can be located in a robust and economic way and are displayed via an external on-line visualisation package. The gradient vector field of the charge density can be traced with great accuracy, planar contour, relief and one-dimensional line plots of many scalar properties can be generated. Non-bonded radii are calculated and analytical expressions for interatomic surfaces are computed (with error estimates) and plotted. MORPHY is interfaced with the AIMPAC suite of programs. The capabilities of the program are illustrated with two test runs and five selected figures.

  13. Hybrid digital signal processing and neural networks for automated diagnostics using NDE methods

    Energy Technology Data Exchange (ETDEWEB)

    Upadhyaya, B.R.; Yan, W. [Tennessee Univ., Knoxville, TN (United States). Dept. of Nuclear Engineering

    1993-11-01

    The primary purpose of the current research was to develop an integrated approach by combining information compression methods and artificial neural networks for the monitoring of plant components using nondestructive examination data. Specifically, data from eddy current inspection of heat exchanger tubing were utilized to evaluate this technology. The focus of the research was to develop and test various data compression methods (for eddy current data) and the performance of different neural network paradigms for defect classification and defect parameter estimation. Feedforward, fully-connected neural networks, that use the back-propagation algorithm for network training, were implemented for defect classification and defect parameter estimation using a modular network architecture. A large eddy current tube inspection database was acquired from the Metals and Ceramics Division of ORNL. These data were used to study the performance of artificial neural networks for defect type classification and for estimating defect parameters. A PC-based data preprocessing and display program was also developed as part of an expert system for data management and decision making. The results of the analysis showed that for effective (low-error) defect classification and estimation of parameters, it is necessary to identify proper feature vectors using different data representation methods. The integration of data compression and artificial neural networks for information processing was established as an effective technique for automation of diagnostics using nondestructive examination methods.

  14. Evaluation of a content-based retrieval system for blood cell images with automated methods.

    Science.gov (United States)

    Seng, Woo Chaw; Mirisaee, Seyed Hadi

    2011-08-01

    Content-based image retrieval techniques have been extensively studied for the past few years. With the growth of digital medical image databases, the demand for content-based analysis and retrieval tools has been increasing remarkably. Blood cell image is a key diagnostic tool for hematologists. An automated system that can retrieved relevant blood cell images correctly and efficiently would save the effort and time of hematologists. The purpose of this work is to develop such a content-based image retrieval system. Global color histogram and wavelet-based methods are used in the prototype. The system allows users to search by providing a query image and select one of four implemented methods. The obtained results demonstrate the proposed extended query refinement has the potential to capture a user's high level query and perception subjectivity by dynamically giving better query combinations. Color-based methods performed better than wavelet-based methods with regard to precision, recall rate and retrieval time. Shape and density of blood cells are suggested as measurements for future improvement. The system developed is useful for undergraduate education. PMID:20703533

  15. Automated Counting of Airborne Asbestos Fibers by a High-Throughput Microscopy (HTM Method

    Directory of Open Access Journals (Sweden)

    Hwataik Han

    2011-07-01

    Full Text Available Inhalation of airborne asbestos causes serious health problems such as lung cancer and malignant mesothelioma. The phase-contrast microscopy (PCM method has been widely used for estimating airborne asbestos concentrations because it does not require complicated processes or high-priced equipment. However, the PCM method is time-consuming and laborious as it is manually performed off-site by an expert. We have developed a high-throughput microscopy (HTM method that can detect fibers distinguishable from other spherical particles in a sample slide by image processing both automatically and quantitatively. A set of parameters for processing and analysis of asbestos fiber images was adjusted for standard asbestos samples with known concentrations. We analyzed sample slides containing airborne asbestos fibers collected at 11 different workplaces following PCM and HTM methods, and found a reasonably good agreement in the asbestos concentration. Image acquisition synchronized with the movement of the robotic sample stages followed by an automated batch processing of a stack of sample images enabled us to count asbestos fibers with greatly reduced time and labors. HTM should be a potential alternative to conventional PCM, moving a step closer to realization of on-site monitoring of asbestos fibers in air.

  16. Hybrid digital signal processing and neural networks for automated diagnostics using NDE methods

    International Nuclear Information System (INIS)

    The primary purpose of the current research was to develop an integrated approach by combining information compression methods and artificial neural networks for the monitoring of plant components using nondestructive examination data. Specifically, data from eddy current inspection of heat exchanger tubing were utilized to evaluate this technology. The focus of the research was to develop and test various data compression methods (for eddy current data) and the performance of different neural network paradigms for defect classification and defect parameter estimation. Feedforward, fully-connected neural networks, that use the back-propagation algorithm for network training, were implemented for defect classification and defect parameter estimation using a modular network architecture. A large eddy current tube inspection database was acquired from the Metals and Ceramics Division of ORNL. These data were used to study the performance of artificial neural networks for defect type classification and for estimating defect parameters. A PC-based data preprocessing and display program was also developed as part of an expert system for data management and decision making. The results of the analysis showed that for effective (low-error) defect classification and estimation of parameters, it is necessary to identify proper feature vectors using different data representation methods. The integration of data compression and artificial neural networks for information processing was established as an effective technique for automation of diagnostics using nondestructive examination methods

  17. Automated static image analysis as a novel tool in describing the physical properties of dietary fiber

    Directory of Open Access Journals (Sweden)

    Marcin Andrzej KUREK

    2015-01-01

    Full Text Available Abstract The growing interest in the usage of dietary fiber in food has caused the need to provide precise tools for describing its physical properties. This research examined two dietary fibers from oats and beets, respectively, in variable particle sizes. The application of automated static image analysis for describing the hydration properties and particle size distribution of dietary fiber was analyzed. Conventional tests for water holding capacity (WHC were conducted. The particles were measured at two points: dry and after water soaking. The most significant water holding capacity (7.00 g water/g solid was achieved by the smaller sized oat fiber. Conversely, the water holding capacity was highest (4.20 g water/g solid in larger sized beet fiber. There was evidence for water absorption increasing with a decrease in particle size in regards to the same fiber source. Very strong correlations were drawn between particle shape parameters, such as fiber length, straightness, width and hydration properties measured conventionally. The regression analysis provided the opportunity to estimate whether the automated static image analysis method could be an efficient tool in describing the hydration properties of dietary fiber. The application of the method was validated using mathematical model which was verified in comparison to conventional WHC measurement results.

  18. Push-through direct injection NMR: an optimized automation method applied to metabolomics

    Science.gov (United States)

    There is a pressing need to increase the throughput of NMR analysis in fields such as metabolomics and drug discovery. Direct injection (DI) NMR automation is recognized to have the potential to meet this need due to its suitability for integration with the 96-well plate format. ...

  19. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    Energy Technology Data Exchange (ETDEWEB)

    Ruebel, Oliver [Technical Univ. of Darmstadt (Germany)

    2009-11-20

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  20. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    Energy Technology Data Exchange (ETDEWEB)

    Ruebel, Oliver

    2009-12-01

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  1. Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-Energy Physics

    International Nuclear Information System (INIS)

    Knowledge discovery from large and complex collections of today's scientific datasets is a challenging task. With the ability to measure and simulate more processes at increasingly finer spatial and temporal scales, the increasing number of data dimensions and data objects is presenting tremendous challenges for data analysis and effective data exploration methods and tools. Researchers are overwhelmed with data and standard tools are often insufficient to enable effective data analysis and knowledge discovery. The main objective of this thesis is to provide important new capabilities to accelerate scientific knowledge discovery form large, complex, and multivariate scientific data. The research covered in this thesis addresses these scientific challenges using a combination of scientific visualization, information visualization, automated data analysis, and other enabling technologies, such as efficient data management. The effectiveness of the proposed analysis methods is demonstrated via applications in two distinct scientific research fields, namely developmental biology and high-energy physics.Advances in microscopy, image analysis, and embryo registration enable for the first time measurement of gene expression at cellular resolution for entire organisms. Analysis of high-dimensional spatial gene expression datasets is a challenging task. By integrating data clustering and visualization, analysis of complex, time-varying, spatial gene expression patterns and their formation becomes possible. The analysis framework MATLAB and the visualization have been integrated, making advanced analysis tools accessible to biologist and enabling bioinformatic researchers to directly integrate their analysis with the visualization. Laser wakefield particle accelerators (LWFAs) promise to be a new compact source of high-energy particles and radiation, with wide applications ranging from medicine to physics. To gain insight into the complex physical processes of particle

  2. Research into the automation of the proximate analysis of coal (II): the establishment of a method for the rapid determination of ash in coal, and combustion residues in coal ash

    Energy Technology Data Exchange (ETDEWEB)

    Hase, Y.

    1986-01-01

    The JIS method for coal ash analysis requires 2.5-3 hours for ashing and a total of 3-3.5 hours for the complete determination. The author reports a new method in which ashing time is reduced to about 3 minutes and overall analysis time to approximately 30 minutes. The former is achieved by employing oxygen and using a new type of ashing vessel, while the latter time reduction is due to the introduction of cooling. Measurement precision with the new method is adequate for all practical purposes, apart from in the case of Miike coal, which has a particularly high sulfur content. 2 references, 4 figures, 17 tables.

  3. Automated Chemical Analysis of Internally Mixed Aerosol Particles Using X-ray Spectromicroscopy at the Carbon K-Edge

    Energy Technology Data Exchange (ETDEWEB)

    Gilles, Mary K; Moffet, R.C.; Henn, T.; Laskin, A.

    2011-01-20

    We have developed an automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure spectroscopy (STXM/NEXAFS). This method is applied to complex internally mixed submicrometer particles containing organic and inorganic material. Several algorithms were developed to exploit NEXAFS spectral features in the energy range from 278 to 320 eV for quantitative mapping of the spatial distribution of elemental carbon, organic carbon, potassium, and noncarbonaceous elements in particles of mixed composition. This energy range encompasses the carbon K-edge and potassium L2 and L3 edges. STXM/NEXAFS maps of different chemical components were complemented with a subsequent analysis using elemental maps obtained by scanning electron microscopy coupled with energy dispersive X-ray analysis (SEM/EDX). We demonstrate the application of the automated mapping algorithms for data analysis and the statistical classification of particles.

  4. Interobserver and Intraobserver Variability in pH-Impedance Analysis between 10 Experts and Automated Analysis

    DEFF Research Database (Denmark)

    Loots, Clara M; van Wijk, Michiel P; Blondeau, Kathleen;

    2011-01-01

    OBJECTIVE: To determine interobserver and intraobserver variability in pH-impedance interpretation between experts and accuracy of automated analysis (AA). STUDY DESIGN: Ten pediatric 24-hour pH-impedance tracings were analyzed by 10 observers from 7 world groups and with AA. Detection of gastroe......OBJECTIVE: To determine interobserver and intraobserver variability in pH-impedance interpretation between experts and accuracy of automated analysis (AA). STUDY DESIGN: Ten pediatric 24-hour pH-impedance tracings were analyzed by 10 observers from 7 world groups and with AA. Detection....... CONCLUSION: Interobserver agreement in combined pH-multichannel intraluminal impedance analysis in experts is moderate; only 42% of GER episodes were detected by the majority of observers. Detection of total GER numbers is more consistent. Considering these poor outcomes, AA seems favorable compared...

  5. Evaluating E-Learning Accessibility by Automated and Student-Centered Methods

    Science.gov (United States)

    Kumar, Kari L.; Owston, Ron

    2016-01-01

    The use of learning technologies is becoming ubiquitous in higher education. As a result, there is a pressing need to develop methods to evaluate their accessibility to ensure that students do not encounter barriers to accessibility while engaging in e-learning. In this study, sample online units were evaluated for accessibility by automated tools…

  6. Automation of a center pivot using the temperature-time-threshold method of irriation scheduling

    Science.gov (United States)

    A center pivot was completely automated using the temperature-time-threshold (TTT) method of irrigation scheduling. An array of infrared thermometers was mounted on the center pivot and these were used to remotely determine the crop leaf temperature as an indicator of crop water stress. We describ...

  7. The Ocular Redness Index: A Novel Automated Method for Measuring Ocular Injection

    OpenAIRE

    Amparo, Francisco; Wang, Haobing; Emami-Naeini, Parisa; Karimian, Parisa; Dana, Reza

    2013-01-01

    In this study, we present and validate an automated method to assess ocular redness in clinical images. This system is based on a continuous, centesimal scale, and employs a computer algorithm that objectively scores redness without need for a trained physician.

  8. A simple method for validation and verification of pipettes mounted on automated liquid handlers

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Hansen, Anders Johannes; Frøslev, Tobias Guldberg;

     We have implemented a simple method for validation and verification of the performance of pipettes mounted on automated liquid handlers as necessary for laboratories accredited under ISO 17025. An 8-step serial dilution of Orange G was prepared in quadruplicates in a flat bottom 96-well microtiter...

  9. Automation of the method gamma of comparison dosimetry images

    International Nuclear Information System (INIS)

    The objective of this work was the development of JJGAMMA application analysis software, which enables this task systematically, minimizing intervention specialist and therefore the variability due to the observer. Both benefits, allow comparison of images is done in practice with the required frequency and objectivity. (Author)

  10. Analysis methods of neutrons induced resonances in the transmission experiments by time-of-flight and automation of these methods on IBM 7094 II computer; Methode d'analyse des resonances induites par les neutrons dans les experiences de transmission par temps-de-vol et automatisation de ces methodes sur ordinateur IBM-7094 II

    Energy Technology Data Exchange (ETDEWEB)

    Corge, C

    1967-07-01

    The neutron induced resonances analysis aims to determine the neutrons characteristics, leading to the excitation energies, de-excitation probabilities by gamma radiation emission, by neutron emission or by fission, their spin, their parity... This document describes the methods developed, or adapted, the calculation schemes and the algorithms implemented to realize such analysis on a computer, from data obtained during time-of-flight experiments on the linear accelerator of Saclay. (A.L.B.)

  11. Automated Design and Analysis Tool for CEV Structural and TPS Components Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation of the proposed effort is a unique automated process for the analysis, design, and sizing of CEV structures and TPS. This developed process will...

  12. Automated Design and Analysis Tool for CLV/CEV Composite and Metallic Structural Components Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation of the proposed effort is a unique automated process for the analysis, design, and sizing of CLV/CEV composite and metallic structures. This...

  13. Wine analysis to check quality and authenticity by fully-automated 1H-NMR

    Directory of Open Access Journals (Sweden)

    Spraul Manfred

    2015-01-01

    Full Text Available Fully-automated high resolution 1H-NMR spectroscopy offers unique screening capabilities for food quality and safety by combining non-targeted and targeted screening in one analysis (15–20 min from acquisition to report. The advantage of high resolution 1H-NMR is its absolute reproducibility and transferability from laboratory to laboratory, which is not equaled by any other method currently used in food analysis. NMR reproducibility allows statistical investigations e.g. for detection of variety, geographical origin and adulterations, where smallest changes of many ingredients at the same time must be recorded. Reproducibility and transferability of the solutions shown are user-, instrument- and laboratory-independent. Sample prepara- tion, measurement and processing are based on strict standard operation procedures which are substantial for this fully automated solution. The non-targeted approach to the data allows detecting even unknown deviations, if they are visible in the 1H-NMR spectra of e.g. fruit juice, wine or honey. The same data acquired in high-throughput mode are also subjected to quantification of multiple compounds. This 1H-NMR methodology will shortly be introduced, then results on wine will be presented and the advantages of the solutions shown. The method has been proven on juice, honey and wine, where so far unknown frauds could be detected, while at the same time generating targeted parameters are obtained.

  14. Evaluation of automated and manual DNA purification methods for detecting Ricinus communis DNA during ricin investigations.

    Science.gov (United States)

    Hutchins, Anne S; Astwood, Michael J; Saah, J Royden; Michel, Pierre A; Newton, Bruce R; Dauphin, Leslie A

    2014-03-01

    In April of 2013, letters addressed to the President of United States and other government officials were intercepted and found to be contaminated with ricin, heightening awareness about the need to evaluate laboratory methods for detecting ricin. This study evaluated commercial DNA purification methods for isolating Ricinus communis DNA as measured by real-time polymerase chain reaction (PCR). Four commercially available DNA purification methods (two automated, MagNA Pure compact and MagNA Pure LC, and two manual, MasterPure complete DNA and RNA purification kit and QIAamp DNA blood mini kit) were evaluated. We compared their ability to purify detectable levels of R. communis DNA from four different sample types, including crude preparations of ricin that could be used for biological crimes or acts of bioterrorism. Castor beans, spiked swabs, and spiked powders were included to simulate sample types typically tested during criminal and public health investigations. Real-time PCR analysis indicated that the QIAamp kit resulted in the greatest sensitivity for ricin preparations; the MasterPure kit performed best with spiked powders. The four methods detected equivalent levels by real-time PCR when castor beans and spiked swabs were used. All four methods yielded DNA free of PCR inhibitors as determined by the use of a PCR inhibition control assay. This study demonstrated that DNA purification methods differ in their ability to purify R. communis DNA; therefore, the purification method used for a given sample type can influence the sensitivity of real-time PCR assays for R. communis.

  15. Automated ''float'' method for determination of densities of molten salts

    DEFF Research Database (Denmark)

    Andreasen, Helge A.; Bjerrum, Niels; Foverskov, Carl Erik

    1977-01-01

    wound with platinum wire, an amplifier, a digital voltmeter, an interface, a paper tape punch, and a recorder. The advantages of the system are its ease of operation compared to other ''float'' methods, and the possibility of looking at highly colored melts and also melts having a high vapor pressure....... Review of Scientific Instruments is copyrighted by The American Institute of Physics....

  16. Automated Production Flow Line Failure Rate Mathematical Analysis with Probability Theory

    Directory of Open Access Journals (Sweden)

    Tan Chan Sin

    2014-12-01

    Full Text Available Automated lines have been widely used in the industries especially for mass production and to customize product. Productivity of automated line is a crucial indicator to show the output and performance of the production. Failure or breakdown of station or mechanisms is commonly occurs in the automated line in real condition due to the technological and technical problem which is highly affect the productivity. The failure rates of automated line are not express or analyse in terms of mathematic form. This paper presents the mathematic analysis by using probability theory towards the failure condition in automated line. The mathematic express for failure rates can produce and forecast the output of productivity accurately

  17. Automated analysis of eclipsing binary lightcurves. I. EBAS -- a new Eclipsing Binary Automated Solver with EBOP

    CERN Document Server

    Tamuz, O; North, P; Mazeh, Tsevi; North, Pierre; Tamuz, Omer

    2006-01-01

    We present a new algorithm -- Eclipsing Binary Automated Solver (EBAS), to analyse lightcurves of eclipsing binaries. The algorithm is designed to analyse large numbers of lightcurves, and is therefore based on the relatively fast EBOP code. To facilitate the search for the best solution, EBAS uses two parameter transformations. Instead of the radii of the two stellar components, EBAS uses the sum of radii and their ratio, while the inclination is transformed into the impact parameter. To replace human visual assessment, we introduce a new 'alarm' goodness-of-fit statistic that takes into account correlation between neighbouring residuals. We perform extensive tests and simulations that show that our algorithm converges well, finds a good set of parameters and provides reasonable error estimation.

  18. Automated patient and medication payment method for clinical trials

    Directory of Open Access Journals (Sweden)

    Yawn BP

    2013-01-01

    Full Text Available Barbara P Yawn,1 Suzanne Madison,1 Susan Bertram,1 Wilson D Pace,2 Anne Fuhlbrigge,3 Elliot Israel,3 Dawn Littlefield,1 Margary Kurland,1 Michael E Wechsler41Olmsted Medical Center, Department of Research, Rochester, MN, 2UCDHSC, Department of Family Medicine, University of Colorado Health Science Centre, Aurora, CO, 3Brigham and Women's Hospital, Pulmonary and Critical Care Division, Boston, MA, 4National Jewish Medical Center, Division of Pulmonology, Denver, CO, USABackground: Published reports and studies related to patient compensation for clinical trials focus primarily on the ethical issues related to appropriate amounts to reimburse for patient's time and risk burden. Little has been published regarding the method of payment for patient participation. As clinical trials move into widely dispersed community practices and more complex designs, the method of payment also becomes more complex. Here we review the decision process and payment method selected for a primary care-based randomized clinical trial of asthma management in Black Americans.Methods: The method selected is a credit card system designed specifically for clinical trials that allows both fixed and variable real-time payments. We operationalized the study design by providing each patient with two cards, one for reimbursement for study visits and one for payment of medication costs directly to the pharmacies.Results: Of the 1015 patients enrolled, only two refused use of the ClinCard, requesting cash payments for visits and only rarely a weekend or fill-in pharmacist refused to use the card system for payment directly to the pharmacy. Overall, the system has been well accepted by patients and local study teams. The ClinCard administrative system facilitates the fiscal accounting and medication adherence record-keeping by the central teams. Monthly fees are modest, and all 12 study institutional review boards approved use of the system without concern for patient

  19. Interferences in automated phenol red method for determination of bromide in water

    Science.gov (United States)

    Basel, C.L.; Defreese, J.D.; Whittemore, D.O.

    1982-01-01

    The phenol red method for the determination of bromide in water has been automated by segmented flow analysis. Samples can be analyzed at a rate of 20 samples/h with a method detection limit, defined, as the concentration giving a signal about three times the standard deviation of replicate anaiyte determinations in reagent water, of 10 ??g/L. Samples studied include oil-field brines, halite solution brines, ground-waters contaminated with these brines, and fresh groundwaters. Chloride and bicarbonate cause significant positive interferences at levels as low as 100 mg/L and 50 mg/L, respectively. Ammonia gives a negative interference that is important at levels as low as 0.05 mg/L. An ionic strength buffer is used to suppress a positive ionic strength interference, correction curves are used to compensate for the chloride interference, the bicarbonate interference is minimized by acidification, and the ammonia interference is eliminated by its removal by ion exchange. Reaction product studies are used to suggest a plausible mode of chloride interference. ?? 1982 American Chemical Society.

  20. A weld inspection method including an automated dye penetration process

    International Nuclear Information System (INIS)

    An inspection and crack detection method for weldments on a nuclear reactor vessel cover, is presented; it involves spraying a developer product onto the welded surface to be controlled, through a nozzle mounted on a pressure gun; the dye penetration test is driven by a computer which controls the injection pressure, the nozzle travelling speed and the motion of a shutter which role is to prevent that developer product is sprayed during the nozzle opening and shutting transients in order to achieve a perfectly homogenous developer layer on the weldment surface

  1. Image cytometer method for automated assessment of human spermatozoa concentration

    DEFF Research Database (Denmark)

    Egeberg, D L; Kjaerulff, S; Hansen, C;

    2013-01-01

    In the basic clinical work-up of infertile couples, a semen analysis is mandatory and the sperm concentration is one of the most essential variables to be determined. Sperm concentration is usually assessed by manual counting using a haemocytometer and is hence labour intensive and may be subjected...... to investigator bias. Here we show that image cytometry can be used to accurately measure the sperm concentration of human semen samples with great ease and reproducibility. The impact of several factors (pipetting, mixing, round cell content, sperm concentration), which can influence the read-out as well....... Moreover, by evaluation of repeated measurements it appeared that image cytometry produced more consistent and accurate measurements than manual counting of human spermatozoa concentration. In conclusion, image cytometry provides an appealing substitute of manual counting by providing reliable, robust...

  2. Automated turbidimetric method for total sulfur in plant tissue and sulfate sulfur in soils

    Energy Technology Data Exchange (ETDEWEB)

    Wall, L.L.; Gehrke, C.W.; Suzuki, J.

    1980-01-01

    An automated turbidimetric method has been developed for the rapid and accurate determination of sulfate. The method is practical and useful for accurately measuring total sulfur in plant tissues, and extractable sulfate in soils. The principle of intermittent reagent addition is used which eliminates drift and sensitivity changes caused by coating of BaSO/sub 4/ on tubing and cell walls. The sensitivity of the method is excellent with a working range of 0 to 15 ppM sulfur for soils. For plant digests the sample solutions are diluted to 0 to 35 ppM S. The automated turbidimetric method for sulfate has excellent precision and sensitivity in plant tissue and soil analyses where gravimetric BaSO/sub 4/ assays are not practical.

  3. Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study

    Science.gov (United States)

    Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith GM; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

    2015-01-01

    Background Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. Objective This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. Methods We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher’s tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). Results An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Conclusions Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis

  4. Automated retinofugal visual pathway reconstruction with multi-shell HARDI and FOD-based analysis.

    Science.gov (United States)

    Kammen, Alexandra; Law, Meng; Tjan, Bosco S; Toga, Arthur W; Shi, Yonggang

    2016-01-15

    Diffusion MRI tractography provides a non-invasive modality to examine the human retinofugal projection, which consists of the optic nerves, optic chiasm, optic tracts, the lateral geniculate nuclei (LGN) and the optic radiations. However, the pathway has several anatomic features that make it particularly challenging to study with tractography, including its location near blood vessels and bone-air interface at the base of the cerebrum, crossing fibers at the chiasm, somewhat-tortuous course around the temporal horn via Meyer's Loop, and multiple closely neighboring fiber bundles. To date, these unique complexities of the visual pathway have impeded the development of a robust and automated reconstruction method using tractography. To overcome these challenges, we develop a novel, fully automated system to reconstruct the retinofugal visual pathway from high-resolution diffusion imaging data. Using multi-shell, high angular resolution diffusion imaging (HARDI) data, we reconstruct precise fiber orientation distributions (FODs) with high order spherical harmonics (SPHARM) to resolve fiber crossings, which allows the tractography algorithm to successfully navigate the complicated anatomy surrounding the retinofugal pathway. We also develop automated algorithms for the identification of ROIs used for fiber bundle reconstruction. In particular, we develop a novel approach to extract the LGN region of interest (ROI) based on intrinsic shape analysis of a fiber bundle computed from a seed region at the optic chiasm to a target at the primary visual cortex. By combining automatically identified ROIs and FOD-based tractography, we obtain a fully automated system to compute the main components of the retinofugal pathway, including the optic tract and the optic radiation. We apply our method to the multi-shell HARDI data of 215 subjects from the Human Connectome Project (HCP). Through comparisons with post-mortem dissection measurements, we demonstrate the retinotopic

  5. Prototype Software for Automated Structural Analysis of Systems

    DEFF Research Database (Denmark)

    Jørgensen, A.; Izadi-Zamanabadi, Roozbeh; Kristensen, M.

    2004-01-01

    In this paper we present a prototype software tool that is developed to analyse the structural model of automated systems in order to identify redundant information that is hence utilized for Fault detection and Isolation (FDI) purposes. The dedicated algorithms in this software tool use a tri...

  6. Orbit transfer rocket engine technology program: Automated preflight methods concept definition

    Science.gov (United States)

    Erickson, C. M.; Hertzberg, D. W.

    1991-01-01

    The possibility of automating preflight engine checkouts on orbit transfer engines is discussed. The minimum requirements in terms of information and processing necessary to assess the engine'e integrity and readiness to perform its mission were first defined. A variety of ways for remotely obtaining that information were generated. The sophistication of these approaches varied from a simple preliminary power up, where the engine is fired up for the first time, to the most advanced approach where the sensor and operational history data system alone indicates engine integrity. The critical issues and benefits of these methods were identified, outlined, and prioritized. The technology readiness of each of these automated preflight methods were then rated on a NASA Office of Exploration scale used for comparing technology options for future mission choices. Finally, estimates were made of the remaining cost to advance the technology for each method to a level where the system validation models have been demonstrated in a simulated environment.

  7. Redevelopment and reliability study of simultaneously uranium and thorium analysis automation control system

    International Nuclear Information System (INIS)

    Full-text: This project is to refurbish the Instrumental Delayed Neutron Activation Analysis System for Simultaneously Determination of Uranium and Thorium namely PAUTS. PAUTS use nuclear techniques for the quantitative determination of Uranium-235 (U-235) and Thorium-232 (Th-232)radionuclides contents in the samples. It consists of three main automation procedures namely Control sample handling, Data Acquisition for neutron counting, and data handling and analysis program. The automation control technology for this project is based on a personal computer (PC), Ethernet communication support, programmable automation control (PAC) module CFP 2220, infrared photo sensors and LabVIEW software package. The analysis samples capsule was placed in transfers containers or rabbit and will be transfer using fast pneumatic sample handling for activation by irradiate it to neutron in the reactor core. Both radionuclides as a fission product will decay and emit the delayed neutron which are count using the nuclear counting electronics module. Studies on the reliability of fast pneumatic sample handling using the statistical method shows that 95 % confidence level had been reach. Results shows the mean transfer time of the sample from the loader to the reactor core is 3251 ± 210 ms, while the mean transfer time of the samples from the core to the counter chamber is 3264 ± 407 ms. The overall system reliability has been verified using analysis of calibration standard material with known quantity of uranium and thorium IAEA-S17, the IAEA-ThO2 and the IAEA-S14 method. At the moment nuclear counting electronic based on 4 units neutron detector and the results were in line with the previous experiment. Results shows that the content of U and Th is in the average of 19:35 ppm and 432.25 ppm respectively compared with the known quantity of the sample is 29.0 ppm and 460 ppm. Studies on the effects pneumatic sample handling to the irradiation time parameter indicated that the previous

  8. RoboSCell: An automated single cell arraying and analysis instrument

    KAUST Repository

    Sakaki, Kelly

    2009-09-09

    Single cell research has the potential to revolutionize experimental methods in biomedical sciences and contribute to clinical practices. Recent studies suggest analysis of single cells reveals novel features of intracellular processes, cell-to-cell interactions and cell structure. The methods of single cell analysis require mechanical resolution and accuracy that is not possible using conventional techniques. Robotic instruments and novel microdevices can achieve higher throughput and repeatability; however, the development of such instrumentation is a formidable task. A void exists in the state-of-the-art for automated analysis of single cells. With the increase in interest in single cell analyses in stem cell and cancer research the ability to facilitate higher throughput and repeatable procedures is necessary. In this paper, a high-throughput, single cell microarray-based robotic instrument, called the RoboSCell, is described. The proposed instrument employs a partially transparent single cell microarray (SCM) integrated with a robotic biomanipulator for in vitro analyses of live single cells trapped at the array sites. Cells, labeled with immunomagnetic particles, are captured at the array sites by channeling magnetic fields through encapsulated permalloy channels in the SCM. The RoboSCell is capable of systematically scanning the captured cells temporarily immobilized at the array sites and using optical methods to repeatedly measure extracellular and intracellular characteristics over time. The instrument\\'s capabilities are demonstrated by arraying human T lymphocytes and measuring the uptake dynamics of calcein acetoxymethylester-all in a fully automated fashion. © 2009 Springer Science+Business Media, LLC.

  9. The CAIRN method: automated, reproducible calculation of catchment-averaged denudation rates from cosmogenic nuclide concentrations

    Science.gov (United States)

    Marius Mudd, Simon; Harel, Marie-Alice; Hurst, Martin D.; Grieve, Stuart W. D.; Marrero, Shasta M.

    2016-08-01

    We report a new program for calculating catchment-averaged denudation rates from cosmogenic nuclide concentrations. The method (Catchment-Averaged denudatIon Rates from cosmogenic Nuclides: CAIRN) bundles previously reported production scaling and topographic shielding algorithms. In addition, it calculates production and shielding on a pixel-by-pixel basis. We explore the effect of sampling frequency across both azimuth (Δθ) and altitude (Δϕ) angles for topographic shielding and show that in high relief terrain a relatively high sampling frequency is required, with a good balance achieved between accuracy and computational expense at Δθ = 8° and Δϕ = 5°. CAIRN includes both internal and external uncertainty analysis, and is packaged in freely available software in order to facilitate easily reproducible denudation rate estimates. CAIRN calculates denudation rates but also automates catchment averaging of shielding and production, and thus can be used to provide reproducible input parameters for the CRONUS family of online calculators.

  10. Kinetics analysis and automated online screening of aminocarbonylation of aryl halides in flow

    OpenAIRE

    Moore, Jason S.; Smith, Christopher D; Jensen, Klavs F.

    2016-01-01

    Temperature, pressure, gas stoichiometry, and residence time were varied to control the yield and product distribution of the palladium-catalyzed aminocarbonylation of aromatic bromides in both a silicon microreactor and a packed-bed tubular reactor. Automation of the system set points and product sampling enabled facile and repeatable reaction analysis with minimal operator supervision. It was observed that the reaction was divided into two temperature regimes. An automated system was used t...

  11. Automated red blood cell analysis compared with routine red blood cell morphology by smear review

    OpenAIRE

    Dr.Poonam Radadiya; Dr.Nandita Mehta; Dr.Hansa Goswami; Dr.R.N.Gonsai

    2015-01-01

    The RBC histogram is an integral part of automated haematology analysis and is now routinely available on all automated cell counters. This histogram and other associated complete blood count (CBC) parameters have been found abnormal in various haematological conditions and may provide major clues in the diagnosis and management of significant red cell disorders. Performing manual blood smears is important to ensure the quality of blood count results an...

  12. The BUME method: a novel automated chloroform-free 96-well total lipid extraction method for blood plasma[S

    OpenAIRE

    Löfgren, Lars; Ståhlman, Marcus; Forsberg, Gun-Britt; Saarinen, Sinikka; Nilsson, Ralf; Göran I Hansson

    2012-01-01

    Lipid extraction from biological samples is a critical and often tedious preanalytical step in lipid research. Primarily on the basis of automation criteria, we have developed the BUME method, a novel chloroform-free total lipid extraction method for blood plasma compatible with standard 96-well robots. In only 60 min, 96 samples can be automatically extracted with lipid profiles of commonly analyzed lipid classes almost identically and with absolute recoveries similar or better to what is ob...

  13. Quantification of Eosinophilic Granule Protein Deposition in Biopsies of Inflammatory Skin Diseases by Automated Image Analysis of Highly Sensitive Immunostaining

    Directory of Open Access Journals (Sweden)

    Peter Kiehl

    1999-01-01

    Full Text Available Eosinophilic granulocytes are major effector cells in inflammation. Extracellular deposition of toxic eosinophilic granule proteins (EGPs, but not the presence of intact eosinophils, is crucial for their functional effect in situ. As even recent morphometric approaches to quantify the involvement of eosinophils in inflammation have been only based on cell counting, we developed a new method for the cell‐independent quantification of EGPs by image analysis of immunostaining. Highly sensitive, automated immunohistochemistry was done on paraffin sections of inflammatory skin diseases with 4 different primary antibodies against EGPs. Image analysis of immunostaining was performed by colour translation, linear combination and automated thresholding. Using strictly standardized protocols, the assay was proven to be specific and accurate concerning segmentation in 8916 fields of 520 sections, well reproducible in repeated measurements and reliable over 16 weeks observation time. The method may be valuable for the cell‐independent segmentation of immunostaining in other applications as well.

  14. Long-term live cell imaging and automated 4D analysis of drosophila neuroblast lineages.

    Directory of Open Access Journals (Sweden)

    Catarina C F Homem

    Full Text Available The developing Drosophila brain is a well-studied model system for neurogenesis and stem cell biology. In the Drosophila central brain, around 200 neural stem cells called neuroblasts undergo repeated rounds of asymmetric cell division. These divisions typically generate a larger self-renewing neuroblast and a smaller ganglion mother cell that undergoes one terminal division to create two differentiating neurons. Although single mitotic divisions of neuroblasts can easily be imaged in real time, the lack of long term imaging procedures has limited the use of neuroblast live imaging for lineage analysis. Here we describe a method that allows live imaging of cultured Drosophila neuroblasts over multiple cell cycles for up to 24 hours. We describe a 4D image analysis protocol that can be used to extract cell cycle times and growth rates from the resulting movies in an automated manner. We use it to perform lineage analysis in type II neuroblasts where clonal analysis has indicated the presence of a transit-amplifying population that potentiates the number of neurons. Indeed, our experiments verify type II lineages and provide quantitative parameters for all cell types in those lineages. As defects in type II neuroblast lineages can result in brain tumor formation, our lineage analysis method will allow more detailed and quantitative analysis of tumorigenesis and asymmetric cell division in the Drosophila brain.

  15. A method to establish seismic noise baselines for automated station assessment

    Science.gov (United States)

    McNamara, D.E.; Hutt, C.R.; Gee, L.S.; Benz, H.M.; Buland, R.P.

    2009-01-01

    We present a method for quantifying station noise baselines and characterizing the spectral shape of out-of-nominal noise sources. Our intent is to automate this method in order to ensure that only the highest-quality data are used in rapid earthquake products at NEIC. In addition, the station noise baselines provide a valuable tool to support the quality control of GSN and ANSS backbone data and metadata. The procedures addressed here are currently in development at the NEIC, and work is underway to understand how quickly changes from nominal can be observed and used within the NEIC processing framework. The spectral methods and software used to compute station baselines and described herein (PQLX) can be useful to both permanent and portable seismic stations operators. Applications include: general seismic station and data quality control (QC), evaluation of instrument responses, assessment of near real-time communication system performance, characterization of site cultural noise conditions, and evaluation of sensor vault design, as well as assessment of gross network capabilities (McNamara et al. 2005). Future PQLX development plans include incorporating station baselines for automated QC methods and automating station status report generation and notification based on user-defined QC parameters. The PQLX software is available through the USGS (http://earthquake. usgs.gov/research/software/pqlx.php) and IRIS (http://www.iris.edu/software/ pqlx/).

  16. Quantization of polyphenolic compounds in histological sections of grape berries by automated color image analysis

    Science.gov (United States)

    Clement, Alain; Vigouroux, Bertnand

    2003-04-01

    We present new results in applied color image analysis that put in evidence the significant influence of soil on localization and appearance of polyphenols in grapes. These results have been obtained with a new unsupervised classification algorithm founded on hierarchical analysis of color histograms. The process is automated thanks to a software platform we developed specifically for color image analysis and it's applications.

  17. Alert management for home healthcare based on home automation analysis.

    Science.gov (United States)

    Truong, T T; de Lamotte, F; Diguet, J-Ph; Said-Hocine, F

    2010-01-01

    Rising healthcare for elder and disabled people can be controlled by offering people autonomy at home by means of information technology. In this paper, we present an original and sensorless alert management solution which performs multimedia and home automation service discrimination and extracts highly regular home activities as sensors for alert management. The results of simulation data, based on real context, allow us to evaluate our approach before application to real data.

  18. Object Type Recognition for Automated Analysis of Protein Subcellular Location

    OpenAIRE

    Zhao, Ting; Velliste, Meel; Boland, Michael V.; Murphy, Robert F.

    2005-01-01

    The new field of location proteomics seeks to provide a comprehensive, objective characterization of the subcellular locations of all proteins expressed in a given cell type. Previous work has demonstrated that automated classifiers can recognize the patterns of all major subcellular organelles and structures in fluorescence microscope images with high accuracy. However, since some proteins may be present in more than one organelle, this paper addresses a more difficult task: recognizing a pa...

  19. Automated analysis of damages for radiation in plastics surfaces; Analisis automatizado de danos por radiacion en superficies plasticas

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, C.; Camacho M, E.; Tavera, L.; Balcazar, M. [ININ, 52045 Ocoyoacac, Estado de Mexico (Mexico)

    1990-02-15

    Analysis of damages done by the radiation in a polymer characterized by optic properties of polished surfaces, of uniformity and chemical resistance that the acrylic; resistant until the 150 centigrade grades of temperature, and with an approximate weight of half of the glass. An objective of this work is the development of a method that analyze in automated form the superficial damages induced by radiation in plastic materials means an images analyst. (Author)

  20. Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods

    OpenAIRE

    Suleimanov, Yury V.; Green, William H.

    2015-01-01

    We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not on...

  1. Assessment of paclitaxel induced sensory polyneuropathy with "Catwalk" automated gait analysis in mice.

    Directory of Open Access Journals (Sweden)

    Petra Huehnchen

    Full Text Available Neuropathic pain as a symptom of sensory nerve damage is a frequent side effect of chemotherapy. The most common behavioral observation in animal models of chemotherapy induced polyneuropathy is the development of mechanical allodynia, which is quantified with von Frey filaments. The data from one study, however, cannot be easily compared with other studies owing to influences of environmental factors, inter-rater variability and differences in test paradigms. To overcome these limitations, automated quantitative gait analysis was proposed as an alternative, but its usefulness for assessing animals suffering from polyneuropathy has remained unclear. In the present study, we used a novel mouse model of paclitaxel induced polyneuropathy to compare results from electrophysiology and the von Frey method to gait alterations measured with the Catwalk test. To mimic recently improved clinical treatment strategies of gynecological malignancies, we established a mouse model of dose-dense paclitaxel therapy on the common C57Bl/6 background. In this model paclitaxel treated animals developed mechanical allodynia as well as reduced caudal sensory nerve action potential amplitudes indicative of a sensory polyneuropathy. Gait analysis with the Catwalk method detected distinct alterations of gait parameters in animals suffering from sensory neuropathy, revealing a minimized contact of the hind paws with the floor. Treatment of mechanical allodynia with gabapentin improved altered dynamic gait parameters. This study establishes a novel mouse model for investigating the side effects of dose-dense paclitaxel therapy and underlines the usefulness of automated gait analysis as an additional easy-to-use objective test for evaluating painful sensory polyneuropathy.

  2. Automated extraction of DNA from biological stains on fabric from crime cases. A comparison of a manual and three automated methods

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Hjort, Benjamin B; Hansen, Thomas N;

    2013-01-01

    that may be co-extracted with the DNA. Using 120 forensic trace evidence samples consisting of various types of fabric, we compared three automated DNA extraction methods based on magnetic beads (PrepFiler Express Forensic DNA Extraction Kit on an AutoMate Express, QIAsyphony DNA Investigator kit either......The presence of PCR inhibitors in extracted DNA may interfere with the subsequent quantification and short tandem repeat (STR) reactions used in forensic genetic DNA typing. DNA extraction from fabric for forensic genetic purposes may be challenging due to the occasional presence of PCR inhibitors...

  3. Use of automated video analysis for the evaluation of bicycle movement and interaction

    Science.gov (United States)

    Twaddle, Heather; Schendzielorz, Tobias; Fakler, Oliver; Amini, Sasan

    2014-03-01

    With the purpose of developing valid models of microscopic bicycle behavior, a large quantity of video data is collected at three busy urban intersections in Munich, Germany. Due to the volume of data, the manual processing of this data is infeasible and an automated or semi-automated analysis method must be implemented. An open source software, "Traffic Intelligence", is used and extended to analyze the collected video data with regard to research questions concerning the tactical behavior of bicyclists. In a first step, the feature detection parameters, the tracking parameters and the object grouping parameters are calibrated, making it possible to accurately track and group the objects at intersections used by large volumes of motor vehicles, bicycles and pedestrians. The resulting parameters for the three intersections are presented. A methodology for the classification of road users as cars, bicycles or pedestrians is presented and evaluated. This is achieved by making hypotheses about which features belong to cars, or bicycles and pedestrians, and using grouping parameters specified for that road user group to cluster the features into objects. These objects are then classified based on their dynamic characteristics. A classification structure for the maneuvers of different road users is presented and future applications are discussed.

  4. Comparison of Automated Continuous Flow Method With Shake- Flask Method in Determining Partition Coefficients of Bidentate Hydroxypyridinone Ligands

    Directory of Open Access Journals (Sweden)

    Lotfollah Saghaie

    2003-08-01

    Full Text Available The partition coefficients (Kpart , in octanol/water system of a range of bidentate ligands containing the 3-hydroxypyridin-4-one moiety were determined using shake flask and automated continuous flow methods (filter probe method. The shake flask method was used for extremely hydrophilic or hydrophobic compounds with a Kpart values greater than 100 and less than 0.01. For other ligands which possess moderate lipophilicity (Kpart values between 0.01-100 the filter probe method was used. Also the partition coefficient of four ligands with moderate lipophilicity was determined by shake flask method in order to check comparability of these two methods. While the shake flask method was able to determine either extremely hydrophilic or hydrophobic compounds efficiently, the filter probe method was unable to measure such Kpart values. Although, determination of the Kpart values of all compounds is possible with the classical shake-flask method, the procedure is time consuming. In contrast, the filter probe method offers many advantages over the traditional shake-flask method in terms of speed, efficiency of separation and degree of automation. The shake-flask method is the method of choice for determination of partition coefficients of extremely hydrophilic and hydrophobic ligands.

  5. A method for the automated, reliable retrieval of publication-citation records.

    Directory of Open Access Journals (Sweden)

    Derek Ruths

    Full Text Available BACKGROUND: Publication records and citation indices often are used to evaluate academic performance. For this reason, obtaining or computing them accurately is important. This can be difficult, largely due to a lack of complete knowledge of an individual's publication list and/or lack of time available to manually obtain or construct the publication-citation record. While online publication search engines have somewhat addressed these problems, using raw search results can yield inaccurate estimates of publication-citation records and citation indices. METHODOLOGY: In this paper, we present a new, automated method that produces estimates of an individual's publication-citation record from an individual's name and a set of domain-specific vocabulary that may occur in the individual's publication titles. Because this vocabulary can be harvested directly from a research web page or online (partial publication list, our method delivers an easy way to obtain estimates of a publication-citation record and the relevant citation indices. Our method works by applying a series of stringent name and content filters to the raw publication search results returned by an online publication search engine. In this paper, our method is run using Google Scholar, but the underlying filters can be easily applied to any existing publication search engine. When compared against a manually constructed data set of individuals and their publication-citation records, our method provides significant improvements over raw search results. The estimated publication-citation records returned by our method have an average sensitivity of 98% and specificity of 72% (in contrast to raw search result specificity of less than 10%. When citation indices are computed using these records, the estimated indices are within of the true value 10%, compared to raw search results which have overestimates of, on average, 75%. CONCLUSIONS: These results confirm that our method provides

  6. Rapid Automated Dissolution and Analysis Techniques for Radionuclides in Recycle Process Streams

    Energy Technology Data Exchange (ETDEWEB)

    Sudowe, Ralf [Univ. of Nevada, Las Vegas, NV (United States). Radiochemistry Program and Health Physics Dept.; Roman, Audrey [Univ. of Nevada, Las Vegas, NV (United States). Radiochemistry Program; Dailey, Ashlee [Univ. of Nevada, Las Vegas, NV (United States). Radiochemistry Program; Go, Elaine [Univ. of Nevada, Las Vegas, NV (United States). Radiochemistry Program

    2013-07-18

    The analysis of process samples for radionuclide content is an important part of current procedures for material balance and accountancy in the different process streams of a recycling plant. The destructive sample analysis techniques currently available necessitate a significant amount of time. It is therefore desirable to develop new sample analysis procedures that allow for a quick turnaround time and increased sample throughput with a minimum of deviation between samples. In particular, new capabilities for rapid sample dissolution and radiochemical separation are required. Most of the radioanalytical techniques currently employed for sample analysis are based on manual laboratory procedures. Such procedures are time- and labor-intensive, and not well suited for situations in which a rapid sample analysis is required and/or large number of samples need to be analyzed. To address this issue we are currently investigating radiochemical separation methods based on extraction chromatography that have been specifically optimized for the analysis of process stream samples. The influence of potential interferences present in the process samples as well as mass loading, flow rate and resin performance is being studied. In addition, the potential to automate these procedures utilizing a robotic platform is evaluated. Initial studies have been carried out using the commercially available DGA resin. This resin shows an affinity for Am, Pu, U, and Th and is also exhibiting signs of a possible synergistic effects in the presence of iron.

  7. Mass asymmetry and tricyclic wobble motion assessment using automated launch video analysis

    Institute of Scientific and Technical Information of China (English)

    Ryan DECKER; Joseph DONINI; William GARDNER; Jobin JOHN; Walter KOENIG

    2016-01-01

    This paper describes an approach to identify epicyclic and tricyclic motion during projectile flight caused by mass asymmetries in spin-stabilized projectiles. Flight video was captured following projectile launch of several M110A2E1 155 mm artillery projectiles. These videos were then analyzed using the automated flight video analysis method to attain their initial position and orientation histories. Examination of the pitch and yaw histories clearly indicates that in addition to epicyclic motion’s nutation and precession oscillations, an even faster wobble amplitude is present during each spin revolution, even though some of the amplitudes of the oscillation are smaller than 0.02 degree. The results are compared to a sequence of shots where little appreciable mass asymmetries were present, and only nutation and precession frequencies are predominantly apparent in the motion history results. Magnitudes of the wobble motion are estimated and compared to product of inertia measurements of the asymmetric projectiles.

  8. Results of Automated Retinal Image Analysis for Detection of Diabetic Retinopathy from the Nakuru Study, Kenya

    DEFF Research Database (Denmark)

    Juul Bøgelund Hansen, Morten; Abramoff, M. D.; Folk, J. C.;

    2015-01-01

    Objective Digital retinal imaging is an established method of screening for diabetic retinopathy (DR). It has been established that currently about 1% of the world's blind or visually impaired is due to DR. However, the increasing prevalence of diabetes mellitus and DR is creating an increased...... workload on those with expertise in grading retinal images. Safe and reliable automated analysis of retinal images may support screening services worldwide. This study aimed to compare the Iowa Detection Program (IDP) ability to detect diabetic eye diseases (DED) to human grading carried out at Moorfields...... gave an AUC of 0.878 (95% CI 0.850-0.905). It showed a negative predictive value of 98%. The IDP missed no vision threatening retinopathy in any patients and none of the false negative cases met criteria for treatment. Conclusions In this epidemiological sample, the IDP's grading was comparable...

  9. Automation of C-terminal sequence analysis of 2D-PAGE separated proteins

    Directory of Open Access Journals (Sweden)

    P.P. Moerman

    2014-06-01

    Full Text Available Experimental assignment of the protein termini remains essential to define the functional protein structure. Here, we report on the improvement of a proteomic C-terminal sequence analysis method. The approach aims to discriminate the C-terminal peptide in a CNBr-digest where Met-Xxx peptide bonds are cleaved in internal peptides ending at a homoserine lactone (hsl-derivative. pH-dependent partial opening of the lactone ring results in the formation of doublets for all internal peptides. C-terminal peptides are distinguished as singlet peaks by MALDI-TOF MS and MS/MS is then used for their identification. We present a fully automated protocol established on a robotic liquid-handling station.

  10. Automated Dissolution for Enteric-Coated Aspirin Tablets: A Case Study for Method Transfer to a RoboDis II.

    Science.gov (United States)

    Ibrahim, Sarah A; Martini, Luigi

    2014-08-01

    Dissolution method transfer is a complicated yet common process in the pharmaceutical industry. With increased pharmaceutical product manufacturing and dissolution acceptance requirements, dissolution testing has become one of the most labor-intensive quality control testing methods. There is an increased trend for automation in dissolution testing, particularly for large pharmaceutical companies to reduce variability and increase personnel efficiency. There is no official guideline for dissolution testing method transfer from a manual, semi-automated, to automated dissolution tester. In this study, a manual multipoint dissolution testing procedure for an enteric-coated aspirin tablet was transferred effectively and reproducibly to a fully automated dissolution testing device, RoboDis II. Enteric-coated aspirin samples were used as a model formulation to assess the feasibility and accuracy of media pH change during continuous automated dissolution testing. Several RoboDis II parameters were evaluated to ensure the integrity and equivalency of dissolution method transfer from a manual dissolution tester. This current study provides a systematic outline for the transfer of the manual dissolution testing protocol to an automated dissolution tester. This study further supports that automated dissolution testers compliant with regulatory requirements and similar to manual dissolution testers facilitate method transfer.

  11. An automated method of quantifying ferrite microstructures using electron backscatter diffraction (EBSD) data

    Energy Technology Data Exchange (ETDEWEB)

    Shrestha, Sachin L., E-mail: sachin.shrestha@sydney.edu.au [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006 (Australia); Breen, Andrew J.; Trimby, Patrick [Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia); Proust, Gwénaëlle [School of Civil Engineering, The University of Sydney, NSW 2006 (Australia); Ringer, Simon P.; Cairney, Julie M. [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006 (Australia); Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia)

    2014-02-01

    The identification and quantification of the different ferrite microconstituents in steels has long been a major challenge for metallurgists. Manual point counting from images obtained by optical and scanning electron microscopy (SEM) is commonly used for this purpose. While classification systems exist, the complexity of steel microstructures means that identifying and quantifying these phases is still a great challenge. Moreover, point counting is extremely tedious, time consuming, and subject to operator bias. This paper presents a new automated identification and quantification technique for the characterisation of complex ferrite microstructures by electron backscatter diffraction (EBSD). This technique takes advantage of the fact that different classes of ferrite exhibit preferential grain boundary misorientations, aspect ratios and mean misorientation, all of which can be detected using current EBSD software. These characteristics are set as criteria for identification and linked to grain size to determine the area fractions. The results of this method were evaluated by comparing the new automated technique with point counting results. The technique could easily be applied to a range of other steel microstructures. - Highlights: • New automated method to identify and quantify ferrite microconstituents in HSLA steels is presented. • Unique characteristics of the ferrite microconstituents are investigated using EBSD. • Characteristics of ferrite microconstituents are exploited to identify the type of ferrite grains within the steel's microstructures. • The identified ferrite grains are linked to their associated grain's size for area fraction calculations.

  12. Automated quality control methods for sensor data: a novel observatory approach

    Directory of Open Access Journals (Sweden)

    J. R. Taylor

    2012-12-01

    Full Text Available National and international networks and observatories of terrestrial-based sensors are emerging rapidly. As such, there is demand for a standardized approach to data quality control, as well as interoperability of data among sensor networks. The National Ecological Observatory Network (NEON has begun constructing their first terrestrial observing sites with 60 locations expected to be distributed across the US by 2017. This will result in over 14 000 automated sensors recording more than > 100 Tb of data per year. These data are then used to create other datasets and subsequent "higher-level" data products. In anticipation of this challenge, an overall data quality assurance plan has been developed and the first suite of data quality control measures defined. This data-driven approach focuses on automated methods for defining a suite of plausibility test parameter thresholds. Specifically, these plausibility tests scrutinize data range, persistence, and stochasticity on each measurement type by employing a suite of binary checks. The statistical basis for each of these tests is developed and the methods for calculating test parameter thresholds are explored here. While these tests have been used elsewhere, we apply them in a novel approach by calculating their relevant test parameter thresholds. Finally, implementing automated quality control is demonstrated with preliminary data from a NEON prototype site.

  13. Automated quality control methods for sensor data: a novel observatory approach

    Directory of Open Access Journals (Sweden)

    J. R. Taylor

    2013-07-01

    Full Text Available National and international networks and observatories of terrestrial-based sensors are emerging rapidly. As such, there is demand for a standardized approach to data quality control, as well as interoperability of data among sensor networks. The National Ecological Observatory Network (NEON has begun constructing their first terrestrial observing sites, with 60 locations expected to be distributed across the US by 2017. This will result in over 14 000 automated sensors recording more than > 100 Tb of data per year. These data are then used to create other datasets and subsequent "higher-level" data products. In anticipation of this challenge, an overall data quality assurance plan has been developed and the first suite of data quality control measures defined. This data-driven approach focuses on automated methods for defining a suite of plausibility test parameter thresholds. Specifically, these plausibility tests scrutinize the data range and variance of each measurement type by employing a suite of binary checks. The statistical basis for each of these tests is developed, and the methods for calculating test parameter thresholds are explored here. While these tests have been used elsewhere, we apply them in a novel approach by calculating their relevant test parameter thresholds. Finally, implementing automated quality control is demonstrated with preliminary data from a NEON prototype site.

  14. Method and System for Protection of Automated Control Systems for “Smart Buildings”

    Directory of Open Access Journals (Sweden)

    Dmitry Mikhaylov

    2013-07-01

    Full Text Available The paper is related to system and method for protection of an automated control system (ACS against un-authorized devices connected to the ACS via wired or wireless channels that substantially obviates the disadvantages of the related art. The protection system monitors the signals spreading in the network analyzing the performance of the network for malicious code or hidden connections of attacker. The system is developed specifically for this purpose and it can protect the industrial control systems more effectively than standard anti-virus programs. Specific anti-virus software installed on a central server of the automated control system protects it from software-based attacks both from internal and external offenders. The system comprises a plurality of bus protection devices of different types, including any of a twisted-pair protection device, a power lines protection device, On-Board Diagnostics signal protocol protection device, and a wireless protection device.

  15. Automated analysis of image mammogram for breast cancer diagnosis

    Science.gov (United States)

    Nurhasanah, Sampurno, Joko; Faryuni, Irfana Diah; Ivansyah, Okto

    2016-03-01

    Medical imaging help doctors in diagnosing and detecting diseases that attack the inside of the body without surgery. Mammogram image is a medical image of the inner breast imaging. Diagnosis of breast cancer needs to be done in detail and as soon as possible for determination of next medical treatment. The aim of this work is to increase the objectivity of clinical diagnostic by using fractal analysis. This study applies fractal method based on 2D Fourier analysis to determine the density of normal and abnormal and applying the segmentation technique based on K-Means clustering algorithm to image abnormal for determine the boundary of the organ and calculate the area of organ segmentation results. The results show fractal method based on 2D Fourier analysis can be used to distinguish between the normal and abnormal breast and segmentation techniques with K-Means Clustering algorithm is able to generate the boundaries of normal and abnormal tissue organs, so area of the abnormal tissue can be determined.

  16. Application of quantum dots as analytical tools in automated chemical analysis: A review

    Energy Technology Data Exchange (ETDEWEB)

    Frigerio, Christian; Ribeiro, David S.M.; Rodrigues, S. Sofia M.; Abreu, Vera L.R.G.; Barbosa, Joao A.C.; Prior, Joao A.V.; Marques, Karine L. [REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of Porto University, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Santos, Joao L.M., E-mail: joaolms@ff.up.pt [REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of Porto University, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal)

    2012-07-20

    Highlights: Black-Right-Pointing-Pointer Review on quantum dots application in automated chemical analysis. Black-Right-Pointing-Pointer Automation by using flow-based techniques. Black-Right-Pointing-Pointer Quantum dots in liquid chromatography and capillary electrophoresis. Black-Right-Pointing-Pointer Detection by fluorescence and chemiluminescence. Black-Right-Pointing-Pointer Electrochemiluminescence and radical generation. - Abstract: Colloidal semiconductor nanocrystals or quantum dots (QDs) are one of the most relevant developments in the fast-growing world of nanotechnology. Initially proposed as luminescent biological labels, they are finding new important fields of application in analytical chemistry, where their photoluminescent properties have been exploited in environmental monitoring, pharmaceutical and clinical analysis and food quality control. Despite the enormous variety of applications that have been developed, the automation of QDs-based analytical methodologies by resorting to automation tools such as continuous flow analysis and related techniques, which would allow to take advantage of particular features of the nanocrystals such as the versatile surface chemistry and ligand binding ability, the aptitude to generate reactive species, the possibility of encapsulation in different materials while retaining native luminescence providing the means for the implementation of renewable chemosensors or even the utilisation of more drastic and even stability impairing reaction conditions, is hitherto very limited. In this review, we provide insights into the analytical potential of quantum dots focusing on prospects of their utilisation in automated flow-based and flow-related approaches and the future outlook of QDs applications in chemical analysis.

  17. Comparison of Automated Image-Based Grain Sizing to Standard Pebble Count Methods

    Science.gov (United States)

    Strom, K. B.

    2009-12-01

    This study explores the use of an automated, image-based method for characterizing grain-size distributions (GSDs) of exposed, open-framework gravel beds. This was done by comparing the GSDs measured with an image-based method to distributions obtained with two pebble-count methods. Selection of grains for the two pebble-count methods was carried out using a gridded sampling frame and the heel-to-toe Wolman walk method at six field sites. At each site, 500-partcle pebble-count samples were collected with each of the two pebble-count methods and digital images were systematically collected over the same sampling area. For the methods used, the pebble counts collected with the gridded sampling frame were assumed to be the most accurate representations of the true grain-size population, and results from the image-based method were compared to the grid derived GSDs for accuracy estimates; comparisons between the grid and Wolman walk methods were conducted to give an indication of possible variation between commonly used methods for each particular field site. Comparison of grain sizes were made at two spatial scales. At the larger scale, results from the image-based method were integrated over the sampling area required to collect the 500-particle pebble-count samples. At the smaller sampling scale, the image derived GSDs were compared to those from 100-particle, pebble-count samples obtained with the gridded sampling frame. The comparisons show that the image-based method performed reasonably well on five of the six study sites. For those five sites, the image-based method slightly underestimate all grain-size percentiles relative to the pebble counts collected with the gridded sampling frame. The average bias for Ψ5, Ψ50, and Ψ95 between the image and grid count methods at the larger sampling scale was 0.07Ψ, 0.04Ψ, and 0.19Ψ respectively; at the smaller sampling scale the average bias was 0.004Ψ, 0.03Ψ, and 0.18Ψ respectively. The average bias between the

  18. Methods of Multivariate Analysis

    CERN Document Server

    Rencher, Alvin C

    2012-01-01

    Praise for the Second Edition "This book is a systematic, well-written, well-organized text on multivariate analysis packed with intuition and insight . . . There is much practical wisdom in this book that is hard to find elsewhere."-IIE Transactions Filled with new and timely content, Methods of Multivariate Analysis, Third Edition provides examples and exercises based on more than sixty real data sets from a wide variety of scientific fields. It takes a "methods" approach to the subject, placing an emphasis on how students and practitioners can employ multivariate analysis in real-life sit

  19. Sleep-spindle detection: crowdsourcing and evaluating performance of experts, non-experts and automated methods

    DEFF Research Database (Denmark)

    Warby, Simon C.; Wendt, Sabrina Lyngbye; Welinder, Peter;

    2014-01-01

    to crowdsource spindle identification by human experts and non-experts, and we compared their performance with that of automated detection algorithms in data from middle- to older-aged subjects from the general population. We also refined methods for forming group consensus and evaluating the performance...... that crowdsourcing the scoring of sleep data is an efficient method to collect large data sets, even for difficult tasks such as spindle identification. Further refinements to spindle detection algorithms are needed for middle- to older-aged subjects....

  20. A New Automated Design Method Based on Machine Learning for CMOS Analog Circuits

    Science.gov (United States)

    Moradi, Behzad; Mirzaei, Abdolreza

    2016-11-01

    A new simulation based automated CMOS analog circuit design method which applies a multi-objective non-Darwinian-type evolutionary algorithm based on Learnable Evolution Model (LEM) is proposed in this article. The multi-objective property of this automated design of CMOS analog circuits is governed by a modified Strength Pareto Evolutionary Algorithm (SPEA) incorporated in the LEM algorithm presented here. LEM includes a machine learning method such as the decision trees that makes a distinction between high- and low-fitness areas in the design space. The learning process can detect the right directions of the evolution and lead to high steps in the evolution of the individuals. The learning phase shortens the evolution process and makes remarkable reduction in the number of individual evaluations. The expert designer's knowledge on circuit is applied in the design process in order to reduce the design space as well as the design time. The circuit evaluation is made by HSPICE simulator. In order to improve the design accuracy, bsim3v3 CMOS transistor model is adopted in this proposed design method. This proposed design method is tested on three different operational amplifier circuits. The performance of this proposed design method is verified by comparing it with the evolutionary strategy algorithm and other similar methods.

  1. Object-oriented database design for the contaminant analysis automation project

    International Nuclear Information System (INIS)

    The Contaminant Analysis Automation project's automated soil analysis laboratory uses an Object-Oriented database for storage of runtime and archive information. Data which is generated by the processing of a sample, and is relevant for verification of the specifics of that process, is retained in the database. The database also contains intermediate results which are generated by one step of the process and used for decision making by later steps. The description of this database reveals design considerations of the objects used to model the behavior of the chemical laboratory and its components

  2. Adverse drug events with hyperkalaemia during inpatient stays: evaluation of an automated method for retrospective detection in hospital databases

    OpenAIRE

    Ficheur, Grégoire; Chazard, Emmanuel; Beuscart, Jean-Baptiste; Merlin, Béatrice; Luyckx, Michel; Beuscart, Régis

    2014-01-01

    Background Adverse drug reactions and adverse drug events (ADEs) are major public health issues. Many different prospective tools for the automated detection of ADEs in hospital databases have been developed and evaluated. The objective of the present study was to evaluate an automated method for the retrospective detection of ADEs with hyperkalaemia during inpatient stays. Methods We used a set of complex detection rules to take account of the patient’s clinical and biological context and th...

  3. The length of the glaciers in the world – a straightforward method for the automated calculation of glacier center lines

    OpenAIRE

    Machguth, H.; M. Huss

    2014-01-01

    Glacier length is an important measure of glacier geometry but global glacier inventories are mostly lacking length data. Only recently semi-automated approaches to measure glacier length have been developed and applied regionally. Here we present a first global assessment of glacier length using a fully automated method based on glacier surface slope, distance to the glacier margins and a set of trade-off functions. The method is developed for East Greenlan...

  4. Automated analysis of pumping tests; Analise automatizada de testes de bombeamento

    Energy Technology Data Exchange (ETDEWEB)

    Sugahara, Luiz Alberto Nozaki

    1996-01-01

    An automated procedure for analysis of pumping test data performed in groundwater wells is described. A computer software was developed to be used under the Windows operational system. The software allows the choice of 3 mathematical models for representing the aquifer behavior, which are: Confined aquifer (Theis model); Leaky aquifer (Hantush model); unconfined aquifer (Boulton model). The analysis of pumping test data using the proper aquifer model, allows for the determination of the model parameters such as transmissivity, storage coefficient, leakage coefficient and delay index. The computer program can be used for the analysis of data obtained from both pumping tests, with one or more pumping rates, and recovery tests. In the multiple rate case, a de superposition procedure has been implemented in order to obtain the equivalent aquifer response for the first flow rate, which is used in obtaining an initial estimate of the model parameters. Such initial estimate is required in the non-linear regression analysis method. The solutions to the partial differential equations describing the aquifer behavior were obtained in Laplace space, followed by numerical inversion of the transformed solution using the Stehfest algorithm. The data analysis procedure is based on a non-linear regression method by matching the field data to the theoretical response of a selected aquifer model, for a given type of test. A least squared regression analysis method was implemented using either Gauss-Newton or Levenberg-Marquardt procedures for minimization of a objective function. The computer software can also be applied to multiple rate test data in order to determine the non-linear well coefficient, allowing for the computation of the well inflow performance curve. (author)

  5. Automated Image Processing for the Analysis of DNA Repair Dynamics

    CERN Document Server

    Riess, Thorsten; Tomas, Martin; Ferrando-May, Elisa; Merhof, Dorit

    2011-01-01

    The efficient repair of cellular DNA is essential for the maintenance and inheritance of genomic information. In order to cope with the high frequency of spontaneous and induced DNA damage, a multitude of repair mechanisms have evolved. These are enabled by a wide range of protein factors specifically recognizing different types of lesions and finally restoring the normal DNA sequence. This work focuses on the repair factor XPC (xeroderma pigmentosum complementation group C), which identifies bulky DNA lesions and initiates their removal via the nucleotide excision repair pathway. The binding of XPC to damaged DNA can be visualized in living cells by following the accumulation of a fluorescent XPC fusion at lesions induced by laser microirradiation in a fluorescence microscope. In this work, an automated image processing pipeline is presented which allows to identify and quantify the accumulation reaction without any user interaction. The image processing pipeline comprises a preprocessing stage where the ima...

  6. 3D Assembly Group Analysis for Cognitive Automation

    Directory of Open Access Journals (Sweden)

    Christian Brecher

    2012-01-01

    Full Text Available A concept that allows the cognitive automation of robotic assembly processes is introduced. An assembly cell comprised of two robots was designed to verify the concept. For the purpose of validation a customer-defined part group consisting of Hubelino bricks is assembled. One of the key aspects for this process is the verification of the assembly group. Hence a software component was designed that utilizes the Microsoft Kinect to perceive both depth and color data in the assembly area. This information is used to determine the current state of the assembly group and is compared to a CAD model for validation purposes. In order to efficiently resolve erroneous situations, the results are interactively accessible to a human expert. The implications for an industrial application are demonstrated by transferring the developed concepts to an assembly scenario for switch-cabinet systems.

  7. AUTOMATION OF MORPHOMETRIC MEASUREMENTS FOR PLANETARY SURFACE ANALYSIS AND CARTOGRAPHY

    Directory of Open Access Journals (Sweden)

    A. A. Kokhanov

    2016-06-01

    Full Text Available For automation of measurements of morphometric parameters of surface relief various tools were developed and integrated into GIS. We have created a tool, which calculates statistical characteristics of the surface: interquartile range of heights, and slopes, as well as second derivatives of height fields as measures of topographic roughness. Other tools were created for morphological studies of craters. One of them allows automatic placing of topographic profiles through the geometric center of a crater. Another tool was developed for calculation of small crater depths and shape estimation, using C++ programming language. Additionally, we have prepared tool for calculating volumes of relief features from DTM rasters. The created software modules and models will be available in a new developed web-GIS system, operating in distributed cloud environment.

  8. Automation of Morphometric Measurements for Planetary Surface Analysis and Cartography

    Science.gov (United States)

    Kokhanov, A. A.; Bystrov, A. Y.; Kreslavsky, M. A.; Matveev, E. V.; Karachevtseva, I. P.

    2016-06-01

    For automation of measurements of morphometric parameters of surface relief various tools were developed and integrated into GIS. We have created a tool, which calculates statistical characteristics of the surface: interquartile range of heights, and slopes, as well as second derivatives of height fields as measures of topographic roughness. Other tools were created for morphological studies of craters. One of them allows automatic placing of topographic profiles through the geometric center of a crater. Another tool was developed for calculation of small crater depths and shape estimation, using C++ programming language. Additionally, we have prepared tool for calculating volumes of relief features from DTM rasters. The created software modules and models will be available in a new developed web-GIS system, operating in distributed cloud environment.

  9. Automated Multivariate Optimization Tool for Energy Analysis: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, P. G.; Griffith, B. T.; Long, N.; Torcellini, P. A.; Crawley, D.

    2006-07-01

    Building energy simulations are often used for trial-and-error evaluation of ''what-if'' options in building design--a limited search for an optimal solution, or ''optimization''. Computerized searching has the potential to automate the input and output, evaluate many options, and perform enough simulations to account for the complex interactions among combinations of options. This paper describes ongoing efforts to develop such a tool. The optimization tool employs multiple modules, including a graphical user interface, a database, a preprocessor, the EnergyPlus simulation engine, an optimization engine, and a simulation run manager. Each module is described and the overall application architecture is summarized.

  10. Automated quantification and analysis of facial asymmetry in children with arthritis in the temporomandibular joint

    DEFF Research Database (Denmark)

    Darvann, Tron A.; Hermann, Nuno V.; Demant, Sune;

    2011-01-01

    We present an automated method of spatially detailed 3D asymmetry quantification of face surfaces obtained in a stereophotogrammetric system, and the method was applied to a population of children with juvenile idiopathic arthritis (JIA) who have involvement of one temporomandibular joint (TMJ...

  11. Toward designing for trust in database automation

    International Nuclear Information System (INIS)

    . The connection between an AH for an automated tool and a list of information elements at the three levels of attributional abstraction is then direct, providing a method for satisfying information requirements for appropriate trust in automation. In this paper, we will present our method for developing specific information requirements for an automated tool, based on a formal analysis of that tool and the models presented by Lee and See. We will show an example of the application of the AH to automation, in the domain of relational database automation, and the resulting set of specific information elements for appropriate trust in the automated tool. Finally, we will comment on the applicability of this approach to the domain of nuclear plant instrumentation. (authors)

  12. Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease.

    Science.gov (United States)

    Yang, Zhen; Ye, Chuyang; Bogovic, John A; Carass, Aaron; Jedynak, Bruno M; Ying, Sarah H; Prince, Jerry L

    2016-02-15

    The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes shows distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes. PMID:26408861

  13. Microbleed detection using automated segmentation (MIDAS: a new method applicable to standard clinical MR images.

    Directory of Open Access Journals (Sweden)

    Mohamed L Seghier

    Full Text Available BACKGROUND: Cerebral microbleeds, visible on gradient-recalled echo (GRE T2* MRI, have generated increasing interest as an imaging marker of small vessel diseases, with relevance for intracerebral bleeding risk or brain dysfunction. METHODOLOGY/PRINCIPAL FINDINGS: Manual rating methods have limited reliability and are time-consuming. We developed a new method for microbleed detection using automated segmentation (MIDAS and compared it with a validated visual rating system. In thirty consecutive stroke service patients, standard GRE T2* images were acquired and manually rated for microbleeds by a trained observer. After spatially normalizing each patient's GRE T2* images into a standard stereotaxic space, the automated microbleed detection algorithm (MIDAS identified cerebral microbleeds by explicitly incorporating an "extra" tissue class for abnormal voxels within a unified segmentation-normalization model. The agreement between manual and automated methods was assessed using the intraclass correlation coefficient (ICC and Kappa statistic. We found that MIDAS had generally moderate to good agreement with the manual reference method for the presence of lobar microbleeds (Kappa = 0.43, improved to 0.65 after manual exclusion of obvious artefacts. Agreement for the number of microbleeds was very good for lobar regions: (ICC = 0.71, improved to ICC = 0.87. MIDAS successfully detected all patients with multiple (≥2 lobar microbleeds. CONCLUSIONS/SIGNIFICANCE: MIDAS can identify microbleeds on standard MR datasets, and with an additional rapid editing step shows good agreement with a validated visual rating system. MIDAS may be useful in screening for multiple lobar microbleeds.

  14. Widely applicable MATLAB routines for automated analysis of saccadic reaction times.

    Science.gov (United States)

    Leppänen, Jukka M; Forssman, Linda; Kaatiala, Jussi; Yrttiaho, Santeri; Wass, Sam

    2015-06-01

    Saccadic reaction time (SRT) is a widely used dependent variable in eye-tracking studies of human cognition and its disorders. SRTs are also frequently measured in studies with special populations, such as infants and young children, who are limited in their ability to follow verbal instructions and remain in a stable position over time. In this article, we describe a library of MATLAB routines (Mathworks, Natick, MA) that are designed to (1) enable completely automated implementation of SRT analysis for multiple data sets and (2) cope with the unique challenges of analyzing SRTs from eye-tracking data collected from poorly cooperating participants. The library includes preprocessing and SRT analysis routines. The preprocessing routines (i.e., moving median filter and interpolation) are designed to remove technical artifacts and missing samples from raw eye-tracking data. The SRTs are detected by a simple algorithm that identifies the last point of gaze in the area of interest, but, critically, the extracted SRTs are further subjected to a number of postanalysis verification checks to exclude values contaminated by artifacts. Example analyses of data from 5- to 11-month-old infants demonstrated that SRTs extracted with the proposed routines were in high agreement with SRTs obtained manually from video records, robust against potential sources of artifact, and exhibited moderate to high test-retest stability. We propose that the present library has wide utility in standardizing and automating SRT-based cognitive testing in various populations. The MATLAB routines are open source and can be downloaded from http://www.uta.fi/med/icl/methods.html .

  15. Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures

    Science.gov (United States)

    Gambin, Anna; Dutkowski, Janusz; Karczmarski, Jakub; Kluge, Boguslaw; Kowalczyk, Krzysztof; Ostrowski, Jerzy; Poznanski, Jaroslaw; Tiuryn, Jerzy; Bakun, Magda; Dadlez, Michal

    2007-01-01

    Here we develop a fully automated procedure for the analysis of liquid chromatography-mass spectrometry (LC-MS) datasets collected during the analysis of complex peptide mixtures. We present the underlying algorithm and outcomes of several experiments justifying its applicability. The novelty of our approach is to exploit the multidimensional character of the datasets. It is common knowledge that highly complex peptide mixtures can be analyzed by liquid chromatography coupled with mass spectrometry, but we are not aware of any existing automated MS spectra interpretation procedure designed to take into account the multidimensional character of the data. Our work fills this gap by providing an effective algorithm for this task, allowing for automated conversion of raw data to the list of masses of peptides.

  16. Comparison between manual and automated analysis for the quantification of carotid wall by using sonography. A validation study with CT

    International Nuclear Information System (INIS)

    Purpose: The purpose of this paper was to compare manual and automated analysis for the quantification of carotid wall obtained with sonography by using the computed tomography as validation technique. Material and methods: 21 consecutive patients underwent MDCTA and ultrasound analysis of carotid arteries (mean age 68 years; age range 59–81 years). The intima–media-thickness (IMT) of the 42 carotids was measured with novel and dedicated automated software analysis (called AtheroEdge™, Biomedical Technologies, Denver, CO, USA) and by four observers that manually calculated the IMT. The carotid artery wall thickness (CAWT) was also quantified in the CT datasets. Bland–Altman statistics was employed to measure the agreement between methods. A Student's t-test was used to test the differences between the IMT values of AtheroEdge™. The study obtained the IRB approval. Results: The correlation between automated AtheroEdge™ measurements and those of the human experts were equal to 95.5%, 73.5%, 88.9%, and 81.7%. The IMT coefficient of variation of the human experts was equal to 11.9%. By using a Student's t-test, the differences between the IMT values of AtheroEdge™ and those of the human experts were not found statistically significant (p value = 0.02). On comparing AtheroEdge™ (using Ultrasound) with CAWT (using CT), the results suggested a very good concordance of 84.96%. Conclusions: Data of this preliminary study indicate that automated software AtheroEdge™ can analyze with precision the IMT of carotid arteries and that the concordance with CT is optimal.

  17. Automation of Axisymmetric Drop Shape Analysis Using Digital Image Processing

    Science.gov (United States)

    Cheng, Philip Wing Ping

    The Axisymmetric Drop Shape Analysis - Profile (ADSA-P) technique, as initiated by Rotenberg, is a user -oriented scheme to determine liquid-fluid interfacial tensions and contact angles from the shape of axisymmetric menisci, i.e., from sessile as well as pendant drops. The ADSA -P program requires as input several coordinate points along the drop profile, the value of the density difference between the bulk phases, and gravity. The solution yields interfacial tension and contact angle. Although the ADSA-P technique was in principle complete, it was found that it was of very limited practical use. The major difficulty with the method is the need for very precise coordinate points along the drop profile, which, up to now, could not be obtained readily. In the past, the coordinate points along the drop profile were obtained by manual digitization of photographs or negatives. From manual digitization data, the surface tension values obtained had an average error of +/-5% when compared with literature values. Another problem with the ADSA-P technique was that the computer program failed to converge for the case of very elongated pendant drops. To acquire the drop profile coordinates automatically, a technique which utilizes recent developments in digital image acquisition and analysis was developed. In order to determine the drop profile coordinates as precisely as possible, the errors due to optical distortions were eliminated. In addition, determination of drop profile coordinates to pixel and sub-pixel resolution was developed. It was found that high precision could be obtained through the use of sub-pixel resolution and a spline fitting method. The results obtained using the automatic digitization technique in conjunction with ADSA-P not only compared well with the conventional methods, but also outstripped the precision of conventional methods considerably. To solve the convergence problem of very elongated pendant drops, it was found that the reason for the

  18. Automated combustion accelerator mass spectrometry for the analysis of biomedical samples in the low attomole range.

    Science.gov (United States)

    van Duijn, Esther; Sandman, Hugo; Grossouw, Dimitri; Mocking, Johannes A J; Coulier, Leon; Vaes, Wouter H J

    2014-08-01

    The increasing role of accelerator mass spectrometry (AMS) in biomedical research necessitates modernization of the traditional sample handling process. AMS was originally developed and used for carbon dating, therefore focusing on a very high precision but with a comparably low sample throughput. Here, we describe the combination of automated sample combustion with an elemental analyzer (EA) online coupled to an AMS via a dedicated interface. This setup allows direct radiocarbon measurements for over 70 samples daily by AMS. No sample processing is required apart from the pipetting of the sample into a tin foil cup, which is placed in the carousel of the EA. In our system, up to 200 AMS analyses are performed automatically without the need for manual interventions. We present results on the direct total (14)C count measurements in <2 μL human plasma samples. The method shows linearity over a range of 0.65-821 mBq/mL, with a lower limit of quantification of 0.65 mBq/mL (corresponding to 0.67 amol for acetaminophen). At these extremely low levels of activity, it becomes important to quantify plasma specific carbon percentages. This carbon percentage is automatically generated upon combustion of a sample on the EA. Apparent advantages of the present approach include complete omission of sample preparation (reduced hands-on time) and fully automated sample analysis. These improvements clearly stimulate the standard incorporation of microtracer research in the drug development process. In combination with the particularly low sample volumes required and extreme sensitivity, AMS strongly improves its position as a bioanalysis method. PMID:25033319

  19. An automated classification system for the differentiation of obstructive lung diseases based on the textural analysis of HRCT images

    Energy Technology Data Exchange (ETDEWEB)

    Park, Seong Hoon; Seo, Joon Beom; Kim, Nam Kug; Lee, Young Kyung; Kim, Song Soo; Chae, Eun Jin [University of Ulsan, College of Medicine, Asan Medical Center, Seoul (Korea, Republic of); Lee, June Goo [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    2007-07-15

    To develop an automated classification system for the differentiation of obstructive lung diseases based on the textural analysis of HRCT images, and to evaluate the accuracy and usefulness of the system. For textural analysis, histogram features, gradient features, run length encoding, and a co-occurrence matrix were employed. A Bayesian classifier was used for automated classification. The images (image number n = 256) were selected from the HRCT images obtained from 17 healthy subjects (n = 67), 26 patients with bronchiolitis obliterans (n = 70), 28 patients with mild centrilobular emphysema (n = 65), and 21 patients with panlobular emphysema or severe centrilobular emphysema (n = 63). An five-fold cross-validation method was used to assess the performance of the system. Class-specific sensitivities were analyzed and the overall accuracy of the system was assessed with kappa statistics. The sensitivity of the system for each class was as follows: normal lung 84.9%, bronchiolitis obliterans 83.8%, mild centrilobular emphysema 77.0%, and panlobular emphysema or severe centrilobular emphysema 95.8%. The overall performance for differentiating each disease and the normal lung was satisfactory with a kappa value of 0.779. An automated classification system for the differentiation between obstructive lung diseases based on the textural analysis of HRCT images was developed. The proposed system discriminates well between the various obstructive lung diseases and the normal lung.

  20. Functional MRI Preprocessing in Lesioned Brains: Manual Versus Automated Region of Interest Analysis.

    Science.gov (United States)

    Garrison, Kathleen A; Rogalsky, Corianne; Sheng, Tong; Liu, Brent; Damasio, Hanna; Winstein, Carolee J; Aziz-Zadeh, Lisa S

    2015-01-01

    Functional magnetic resonance imaging (fMRI) has significant potential in the study and treatment of neurological disorders and stroke. Region of interest (ROI) analysis in such studies allows for testing of strong a priori clinical hypotheses with improved statistical power. A commonly used automated approach to ROI analysis is to spatially normalize each participant's structural brain image to a template brain image and define ROIs using an atlas. However, in studies of individuals with structural brain lesions, such as stroke, the gold standard approach may be to manually hand-draw ROIs on each participant's non-normalized structural brain image. Automated approaches to ROI analysis are faster and more standardized, yet are susceptible to preprocessing error (e.g., normalization error) that can be greater in lesioned brains. The manual approach to ROI analysis has high demand for time and expertise, but may provide a more accurate estimate of brain response. In this study, commonly used automated and manual approaches to ROI analysis were directly compared by reanalyzing data from a previously published hypothesis-driven cognitive fMRI study, involving individuals with stroke. The ROI evaluated is the pars opercularis of the inferior frontal gyrus. Significant differences were identified in task-related effect size and percent-activated voxels in this ROI between the automated and manual approaches to ROI analysis. Task interactions, however, were consistent across ROI analysis approaches. These findings support the use of automated approaches to ROI analysis in studies of lesioned brains, provided they employ a task interaction design.

  1. Instrumental neutron activation analysis - a routine method

    International Nuclear Information System (INIS)

    This thesis describes the way in which at IRI instrumental neutron activation analysis (INAA) has been developed into an automated system for routine analysis. The basis of this work are 20 publications describing the development of INAA since 1968. (Auth.)

  2. Archaeological field survey automation: concurrent multisensor site mapping and automated analysis

    Science.gov (United States)

    Józefowicz, Mateusz; Sokolov, Oleksandr; Meszyński, Sebastian; Siemińska, Dominika; Kołosowski, Przemysław

    2016-04-01

    control the platform from a remote location via satellite, with only servicing person on the site and the survey team operating from their office, globally. The method is under development. The team contributing to the project includes also: Oleksii Sokolov, Michał Koepke, Krzysztof Rydel, Michał Stypczyński, Maciej Ślęk, Łukasz Zapała, Michał Dąbrowski.

  3. Automated analysis of small animal PET studies through deformable registration to an atlas

    International Nuclear Information System (INIS)

    This work aims to develop a methodology for automated atlas-guided analysis of small animal positron emission tomography (PET) data through deformable registration to an anatomical mouse model. A non-rigid registration technique is used to put into correspondence relevant anatomical regions of rodent CT images from combined PET/CT studies to corresponding CT images of the Digimouse anatomical mouse model. The latter provides a pre-segmented atlas consisting of 21 anatomical regions suitable for automated quantitative analysis. Image registration is performed using a package based on the Insight Toolkit allowing the implementation of various image registration algorithms. The optimal parameters obtained for deformable registration were applied to simulated and experimental mouse PET/CT studies. The accuracy of the image registration procedure was assessed by segmenting mouse CT images into seven regions: brain, lungs, heart, kidneys, bladder, skeleton and the rest of the body. This was accomplished prior to image registration using a semi-automated algorithm. Each mouse segmentation was transformed using the parameters obtained during CT to CT image registration. The resulting segmentation was compared with the original Digimouse atlas to quantify image registration accuracy using established metrics such as the Dice coefficient and Hausdorff distance. PET images were then transformed using the same technique and automated quantitative analysis of tracer uptake performed. The Dice coefficient and Hausdorff distance show fair to excellent agreement and a mean registration mismatch distance of about 6 mm. The results demonstrate good quantification accuracy in most of the regions, especially the brain, but not in the bladder, as expected. Normalized mean activity estimates were preserved between the reference and automated quantification techniques with relative errors below 10 % in most of the organs considered. The proposed automated quantification technique is

  4. Automated analysis of small animal PET studies through deformable registration to an atlas

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez, Daniel F. [Geneva University Hospital, Division of Nuclear Medicine and Molecular Imaging, Geneva 4 (Switzerland); Zaidi, Habib [Geneva University Hospital, Division of Nuclear Medicine and Molecular Imaging, Geneva 4 (Switzerland); Geneva University, Geneva Neuroscience Center, Geneva (Switzerland); University of Groningen, Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, Groningen (Netherlands)

    2012-11-15

    This work aims to develop a methodology for automated atlas-guided analysis of small animal positron emission tomography (PET) data through deformable registration to an anatomical mouse model. A non-rigid registration technique is used to put into correspondence relevant anatomical regions of rodent CT images from combined PET/CT studies to corresponding CT images of the Digimouse anatomical mouse model. The latter provides a pre-segmented atlas consisting of 21 anatomical regions suitable for automated quantitative analysis. Image registration is performed using a package based on the Insight Toolkit allowing the implementation of various image registration algorithms. The optimal parameters obtained for deformable registration were applied to simulated and experimental mouse PET/CT studies. The accuracy of the image registration procedure was assessed by segmenting mouse CT images into seven regions: brain, lungs, heart, kidneys, bladder, skeleton and the rest of the body. This was accomplished prior to image registration using a semi-automated algorithm. Each mouse segmentation was transformed using the parameters obtained during CT to CT image registration. The resulting segmentation was compared with the original Digimouse atlas to quantify image registration accuracy using established metrics such as the Dice coefficient and Hausdorff distance. PET images were then transformed using the same technique and automated quantitative analysis of tracer uptake performed. The Dice coefficient and Hausdorff distance show fair to excellent agreement and a mean registration mismatch distance of about 6 mm. The results demonstrate good quantification accuracy in most of the regions, especially the brain, but not in the bladder, as expected. Normalized mean activity estimates were preserved between the reference and automated quantification techniques with relative errors below 10 % in most of the organs considered. The proposed automated quantification technique is

  5. Analysis of numerical methods

    CERN Document Server

    Isaacson, Eugene

    1994-01-01

    This excellent text for advanced undergraduates and graduate students covers norms, numerical solution of linear systems and matrix factoring, iterative solutions of nonlinear equations, eigenvalues and eigenvectors, polynomial approximation, and other topics. It offers a careful analysis and stresses techniques for developing new methods, plus many examples and problems. 1966 edition.

  6. Automation of statistical analysis in the WIPP hazardous waste facility permit for analytical results from characterization

    International Nuclear Information System (INIS)

    One goal of characterizing, processing, and shipping waste to the Waste Isolation Pilot Plant (WIPP) is to make all activities as efficient as possible. Data management and repetitive calculations are a critical part of the process that can be automated, thereby increasing the accuracy and rate at which work is completed and reducing costs. This paper presents the tools developed to automate statistical analysis and other calculations required by the WIPP Hazardous Waste Facility Permit (HWFP). Statistical analyses are performed on the analytical results on gas samples from the headspace of waste containers and solid samples from the core of the waste container. The calculations include determining the number of samples, test for the shape of the distribution of the analytical results, mean, standard deviation, upper 90-percent confidence limit of the mean, and the minimum required Waste Acceptance Plan (WAP) sample size. The input data for these calculations are from the batch data reports for headspace gas analytical results and solids analysis, which must also be obtained and collated for proper use. The most challenging component of the statistical analysis, if performed manually, is the determination of the distribution shape; therefore, the distribution testing is typically performed using a certified software tool. All other calculations can be completed manually, with a spreadsheet, custom developed software, and/or certified software tool. Out of the options available, manually performing the calculations or using a spreadsheet are the least desirable. These methods rely heavily on the availability of an expert, such as a statistician, to perform the calculation. These methods are also more open to human error such as transcription or 'cut and paste' errors. A SAS program is in the process of being developed to perform the calculations. Due to the potential size of the data input files and the need to archive the data in an accessible format, the SAS

  7. A Novel Method for the Separation of Overlapping Pollen Species for Automated Detection and Classification.

    Science.gov (United States)

    Tello-Mijares, Santiago; Flores, Francisco

    2016-01-01

    The identification of pollen in an automated way will accelerate different tasks and applications of palynology to aid in, among others, climate change studies, medical allergies calendar, and forensic science. The aim of this paper is to develop a system that automatically captures a hundred microscopic images of pollen and classifies them into the 12 different species from Lagunera Region, Mexico. Many times, the pollen is overlapping on the microscopic images, which increases the difficulty for its automated identification and classification. This paper focuses on a method to segment the overlapping pollen. First, the proposed method segments the overlapping pollen. Second, the method separates the pollen based on the mean shift process (100% segmentation) and erosion by H-minima based on the Fibonacci series. Thus, pollen is characterized by its shape, color, and texture for training and evaluating the performance of three classification techniques: random tree forest, multilayer perceptron, and Bayes net. Using the newly developed system, we obtained segmentation results of 100% and classification on top of 96.2% and 96.1% in recall and precision using multilayer perceptron in twofold cross validation. PMID:27034710

  8. Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis

    Science.gov (United States)

    Stirling, Julian; Woolley, Richard A. J.; Moriarty, Philip

    2013-11-01

    We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure.

  9. Chapter 2: Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis

    NARCIS (Netherlands)

    Nistor, Nicolae; Dascalu, Mihai; Stavarache, Lucia; Tarnai, Christian; Trausan-Matu, Stefan

    2016-01-01

    Nistor, N., Dascalu, M., Stavarache, L.L., Tarnai, C., & Trausan-Matu, S. (2015). Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis. In Y. Li, M. Chang, M. Kravcik, E. Popescu, R. Huang, Kinshuk & N.-S. Chen (Eds.), State-of-the-Art and Future Directions of

  10. Miniaturized Mass-Spectrometry-Based Analysis System for Fully Automated Examination of Conditioned Cell Culture Media

    NARCIS (Netherlands)

    Weber, E.; Pinkse, M.W.H.; Bener-Aksam, E.; Vellekoop, M.J.; Verhaert, P.D.E.M.

    2012-01-01

    We present a fully automated setup for performing in-line mass spectrometry (MS) analysis of conditioned media in cell cultures, in particular focusing on the peptides therein. The goal is to assess peptides secreted by cells in different culture conditions. The developed system is compatible with M

  11. Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

    DEFF Research Database (Denmark)

    Schwarz, G.; Herz, M.; Huang, X.Q.;

    2000-01-01

    of semi-automated codominant analysis for hemizygous AFLP markers in an F-2 population was too low, proposing the use of dominant allele-typing defaults. Nevertheless, the efficiency of genetic mapping, especially of complex plant genomes, will be accelerated by combining the presented genotyping...

  12. Development of a novel and automated fluorescent immunoassay for the analysis of beta-lactam antibiotics

    NARCIS (Netherlands)

    Benito-Pena, E.; Moreno-Bondi, M.C.; Orellana, G.; Maquieira, K.; Amerongen, van A.

    2005-01-01

    An automated immunosensor for the rapid and sensitive analysis of penicillin type -lactam antibiotics has been developed and optimized. An immunogen was prepared by coupling the common structure of the penicillanic -lactam antibiotics, i.e., 6-aminopenicillanic acid to keyhole limpet hemocyanin. Pol

  13. Chemical composition dispersion in bi-metallic nanoparticles: semi-automated analysis using HAADF-STEM

    Energy Technology Data Exchange (ETDEWEB)

    Epicier, T., E-mail: thierry.epicier@insa-lyon.fr [INSA-Lyon, MATEIS CNRS UMR5510, Bat. Blaise Pascal (France); Sato, K. [Institute for Materials Research, Tohoku University, Material Processing and Characterization Division (Japan); Tournus, F. [Universite Lyon 1, LPMCN, UMR 5586 CNRS and Universite de Lyon (France); Konno, T. [Institute for Materials Research, Tohoku University, Material Processing and Characterization Division (Japan)

    2012-09-15

    We present a method using high-angle annular dark field scanning transmission electron microscopy (HAADF-STEM) to determine the chemical composition of bi-metallic nanoparticles. This method, which can be applied in a semi-automated way, allows large scale analysis with a statistical number of particles (several hundreds) in a short time. Once a calibration curve has been obtained, e.g., using energy-dispersive X-ray spectroscopy (EDX) measurements on a few particles, the HAADF integrated intensity of each particle can indeed be directly related to its chemical composition. After a theoretical description, this approach is applied to the case of iron-palladium nanoparticles (expected to be nearly stoichiometric) with a mean size of 8.3 nm. It will be shown that an accurate chemical composition histogram is obtained, i.e., the Fe content has been determined to be 49.0 at.% with a dispersion of 10.4 %. HAADF-STEM analysis represents a powerful alternative to fastidious single particle EDX measurements, for the compositional dispersion in alloy nanoparticles.

  14. Comparison of automated pre-column and post-column analysis of amino acid oligomers

    Science.gov (United States)

    Chow, J.; Orenberg, J. B.; Nugent, K. D.

    1987-01-01

    It has been shown that various amino acids will polymerize under plausible prebiotic conditions on mineral surfaces, such as clays and soluble salts, to form varying amounts of oligomers (n = 2-6). The investigations of these surface reactions required a quantitative method for the separation and detection of these amino acid oligomers at the picomole level in the presence of nanomole levels of the parent amino acid. In initial high-performance liquid chromatography (HPLC) studies using a classical postcolumn o-phthalaldehyde (OPA) derivatization ion-exchange HPLC procedure with fluorescence detection, problems encountered included lengthy analysis time, inadequate separation and large relative differences in sensitivity for the separated species, expressed as a variable fluorescent yield, which contributed to poor quantitation. We have compared a simple, automated, pre-column OPA derivatization and reversed-phase HPLC method with the classical post-column OPA derivatization and ion-exchange HPLC procedure. A comparison of UV and fluorescent detection of the amino acid oligomers is also presented. The conclusion reached is that the pre-column OPA derivatization, reversed-phase HPLC and UV detection produces enhanced separation, improved sensitivity and faster analysis than post-column OPA derivatization, ion-exchange HPLC and fluorescence detection.

  15. Automated data acquisition and analysis system for inventory verification

    International Nuclear Information System (INIS)

    A real-time system is proposed which would allow CLO Safeguards Branch to conduct a meaningful inventory verification using a variety of NDA instruments. The overall system would include the NDA instruments, automated data handling equipment, and a vehicle to house and transport the instruments and equipment. For the purpose of the preliminary cost estimate a specific data handling system and vehicle were required. A Tracor Northern TN-11 data handling system including a PDP-11 minicomputer and a measurement vehicle similar to the Commission's Regulatory Region I van were used. The basic system is currently estimated to cost about $100,000, and future add-ons which would expand the systems' capabilities are estimated to cost about $40,000. The concept of using a vehicle in order to permanently rack mount the data handling equipmentoffers a number of benefits such as control of equipment environment and allowance for improvements, expansion, and flexibility in the system. Justification is also presented for local design and assembly of the overall system. A summary of the demonstration system which illustrates the advantages and feasibility of the overall system is included in this discussion. Two ideas are discussed which are not considered to be viable alternatives to the proposed system: addition of the data handling capabilities to the semiportable ''cart'' and use of a telephone link to a large computer center

  16. An Analysis of Intelligent Automation Demands in Taiwanese Firms

    Directory of Open Access Journals (Sweden)

    Ying-Mei Tai

    2016-03-01

    Full Text Available To accurately elucidate the production deployment, process intelligent automation (IA, and production bottlenecks of Taiwanese companies, as well as the IA application status, this research conducted a structured questionnaire survey on the participants of the IA promotion activities arranged by the Industrial Development Bureau, Ministry of Economic Affairs. A total of 35 valid questionnaires were recovered. Research findings indicated that the majority of participants were large-scale enterprises. These enterprises anticipated adding production bases in Taiwan and China to transit and upgrade their operations or strengthen influence in the domestic market. The degrees of various process IA and production bottlenecks were relatively low, which was associated with the tendency to small amount of diversified products. The majority of sub-categories of hardware equipment and simulation technologies have reached maturity, and the effective application of these technologies can enhance production efficiency. Technologies of intelligent software remain immature and need further development and application. More importantly, they can meet customer values and create new business models, so as to satisfy the purpose of sustainable development.

  17. Fully automated fluorescent in situ hybridization (FISH staining and digital analysis of HER2 in breast cancer: a validation study.

    Directory of Open Access Journals (Sweden)

    Elise M J van der Logt

    Full Text Available HER2 assessment is routinely used to select patients with invasive breast cancer that might benefit from HER2-targeted therapy. The aim of this study was to validate a fully automated in situ hybridization (ISH procedure that combines the automated Leica HER2 fluorescent ISH system for Bond with supervised automated analysis with the Visia imaging D-Sight digital imaging platform. HER2 assessment was performed on 328 formalin-fixed/paraffin-embedded invasive breast cancer tumors on tissue microarrays (TMA and 100 (50 selected IHC 2+ and 50 random IHC scores full-sized slides of resections/biopsies obtained for diagnostic purposes previously. For digital analysis slides were pre-screened at 20x and 100x magnification for all fluorescent signals and supervised-automated scoring was performed on at least two pictures (in total at least 20 nuclei were counted with the D-Sight HER2 FISH analysis module by two observers independently. Results were compared to data obtained previously with the manual Abbott FISH test. The overall agreement with Abbott FISH data among TMA samples and 50 selected IHC 2+ cases was 98.8% (κ = 0.94 and 93.8% (κ = 0.88, respectively. The results of 50 additionally tested unselected IHC cases were concordant with previously obtained IHC and/or FISH data. The combination of the Leica FISH system with the D-Sight digital imaging platform is a feasible method for HER2 assessment in routine clinical practice for patients with invasive breast cancer.

  18. The iFly Tracking System for an Automated Locomotor and Behavioural Analysis of Drosophila melanogaster

    Science.gov (United States)

    Kohlhoff, Kai J.; Jahn, Thomas R.; Lomas, David A.; Dobson, Christopher M.; Crowther, Damian C.; Vendruscolo, Michele

    2016-01-01

    The use of animal models in medical research provides insights into molecular and cellular mechanisms of human disease, and helps identify and test novel therapeutic strategies. Drosophila melanogaster – the common fruit fly – is one of the most established model organisms, as its study can be performed more readily and with far less expense than for other model animal systems, such as mice, fish, or indeed primates. In the case of fruit flies, standard assays are based on the analysis of longevity and basic locomotor functions. Here we present the iFly tracking system, which enables to increase the amount of quantitative information that can be extracted from these studies, and to reduce significantly the duration and costs associated with them. The iFly system uses a single camera to simultaneously track the trajectories of up to 20 individual flies with about 100μm spatial and 33ms temporal resolution. The statistical analysis of fly movements recorded with such accuracy makes it possible to perform a rapid and fully automated quantitative analysis of locomotor changes in response to a range of different stimuli. We anticipate that the iFly method will reduce very considerably the costs and the duration of the testing of genetic and pharmacological interventions in Drosophila models, including an earlier detection of behavioural changes and a large increase in throughput compared to current longevity and locomotor assays. PMID:21698336

  19. Automated red blood cell analysis compared with routine red blood cell morphology by smear review

    Directory of Open Access Journals (Sweden)

    Dr.Poonam Radadiya

    2015-01-01

    Full Text Available The RBC histogram is an integral part of automated haematology analysis and is now routinely available on all automated cell counters. This histogram and other associated complete blood count (CBC parameters have been found abnormal in various haematological conditions and may provide major clues in the diagnosis and management of significant red cell disorders. Performing manual blood smears is important to ensure the quality of blood count results and to make presumptive diagnosis. In this article we have taken 100 samples for comparative study between RBC histograms obtained by automated haematology analyzer with peripheral blood smear. This article discusses some morphological features of dimorphism and the ensuing characteristic changes in their RBC histograms.

  20. Trend Analysis on the Automation of the Notebook PC Production Process

    Directory of Open Access Journals (Sweden)

    Chin-Ching Yeh

    2012-09-01

    Full Text Available Notebook PCs are among the Taiwanese electronic products that generate the highest production value and market share. According to the ITRI IEK statistics, the domestic Notebook PC - production value in 2011 was about NT $2.3 trillion. Of about 200 million notebook PCs in global markets in 2011, Taiwan’s notebook PC output accounts for more than 90% of them, meaning that nine out of every ten notebook PCs in the world are manufactured by Taiwanese companies. For such a large industry with its output value and quantity, the degree of automation in production processes is not high. This means that there is still a great room for the automation of the notebook PC production process, or that the degree of automation of the production process of the laptops cannot be enhanced. This paper presents an analysis of the situation.

  1. Automated longitudinal intra-subject analysis (ALISA) for diffusion MRI tractography

    DEFF Research Database (Denmark)

    Aarnink, Saskia H; Vos, Sjoerd B; Leemans, Alexander;

    2014-01-01

    . The major disadvantage of manual FT segmentations, unfortunately, is that placing regions-of-interest for tract selection can be very labor-intensive and time-consuming. Although there are several methods that can identify specific WM fiber bundles in an automated way, manual FT segmentations across...... multiple subjects performed by a trained rater with neuroanatomical expertise are generally assumed to be more accurate. However, for longitudinal DTI analyses it may still be beneficial to automate the FT segmentation across multiple time points, but then for each individual subject separately. Both...

  2. Automating case reports for the analysis of digital evidence

    OpenAIRE

    Cassidy, Regis H. Friend

    2005-01-01

    The reporting process during computer analysis is critical in the practice of digital forensics. Case reports are used to review the process and results of an investigation and serve multiple purposes. The investigator may refer to these reports to monitor the progress of his analysis throughout the investigation. When acting as an expert witness, the investigator will refer to organized documentation to recall past analysis. A lot of time can elapse between the analysis and the actual testim...

  3. A Novel Vision Localization Method of Automated Micro-Polishing Robot

    Institute of Scientific and Technical Information of China (English)

    Zhao-jun Yang; Fei Chen; Ji Zhao; Xiao-jie Wu

    2009-01-01

    Based on photograrnmetry technology, a novel localization method of micro-polishing robot, which is restricted within certain working space, is presented in this paper. On the basis of pinhole camera model, a new mathematical model of vision localization of automated polishing robot is established. The vision localization is based on the distance-constraints of feature points. The method to solve the mathematical model is discussed. According to the characteristics of gray image, an adaptive method of automatic threshold selection based on connected components is presented. The center coordinate of the feature image point is resolved by bilinear interpolation gray square weighted algorithm. Finally, the mathematical model of testing system is verified by global localization test. The experimental results show that the vision localization system in working space has high precision.

  4. Measurement of the total antioxidant potential in chronic obstructive pulmonary diseases with a novel automated method

    International Nuclear Information System (INIS)

    To determine the oxidative and antioxidative status of plasma of patients with chronic obstructive pulmonary disease (COPD) and to compare these values with healthy smokers and healthy non-smokers control subjects using a more recently developed automated measurement method. This study involved 40 COPD patients, 25 healthy smokers, and 25 non-healthy smokers who attended the Chest Disease Outpatient Clinic in Harran University Research Hospital, Turkey between the period March 2006 and June 2006. We calculated the total antioxidant potential (TAOP) to determine the antioxidative status of plasma and we measured the total peroxide levels to determine the oxidative status of plasma. The TAOP of plasma was significantly lower in patients with COPD than in healthy smokers and healthy non-smokers (p< 0.001). In contrast, the mean total peroxide level of plasma was significantly higher in COPD patients than in healthy smokers and healthy non-smokers (p<0.001). We found a decreased in TAOP COPD patients using a simple, rapid and reliably automated colorimetric assay, which may suitable for use in routine clinical biochemistry laboratory and considerably facilitates the assessment of this useful clinical parameter. We suggest that this novel method may be used as a routine test to evaluate and follow-up the levels of oxidative stress in COPD. (author)

  5. A rapid and automated low resolution NMR method to analyze oil quality in intact oilseeds

    International Nuclear Information System (INIS)

    Oilseeds with modified fatty acid profiles have been the genetic alternative for high quality vegetable oil for food and biodiesel applications. They can provide stable, functional oils for the food industry, without the hydrogenation process that produces trans-fatty acid, which has been linked to cardiovascular disease. High yield and high quality oilseeds are also necessary for the success of biodiesel programs, as polyunsatured or saturated fatty acid oil produces biofuel with undesirable properties. In this paper, a rapid and automated low resolution NMR method to select intact oilseeds with a modified fatty acid profile is introduced, based on 1H transverse relaxation time (T 2). The T 2 weighted NMR signal, obtained by a CPMG pulse sequence and processed by chemometric methods was able to determine the oil quality in intact seeds by its fatty composition, cetane number, iodine value and kinematic viscosity with a correlation coefficient r > 0.9. The automated system has the potential to analyze more than 1000 samples per hour and is a powerful tool to speed up the selection of high quality oilseeds for food and biodiesel applications

  6. Automated image analysis for space debris identification and astrometric measurements

    Science.gov (United States)

    Piattoni, Jacopo; Ceruti, Alessandro; Piergentili, Fabrizio

    2014-10-01

    The space debris is a challenging problem for the human activity in the space. Observation campaigns are conducted around the globe to detect and track uncontrolled space objects. One of the main problems in optical observation is obtaining useful information about the debris dynamical state by the images collected. For orbit determination, the most relevant information embedded in optical observation is the precise angular position, which can be evaluated by astrometry procedures, comparing the stars inside the image with star catalogs. This is typically a time consuming process, if done by a human operator, which makes this task impractical when dealing with large amounts of data, in the order of thousands images per night, generated by routinely conducted observations. An automated procedure is investigated in this paper that is capable to recognize the debris track inside a picture, calculate the celestial coordinates of the image's center and use these information to compute the debris angular position in the sky. This procedure has been implemented in a software code, that does not require human interaction and works without any supplemental information besides the image itself, detecting space objects and solving for their angular position without a priori information. The algorithm for object detection was developed inside the research team. For the star field computation, the software code astrometry.net was used and released under GPL v2 license. The complete procedure was validated by an extensive testing, using the images obtained in the observation campaign performed in a joint project between the Italian Space Agency (ASI) and the University of Bologna at the Broglio Space center, Kenya.

  7. A microchip electrophoresis-mass spectrometric platform with double cell lysis nano-electrodes for automated single cell analysis.

    Science.gov (United States)

    Li, Xiangtang; Zhao, Shulin; Hu, Hankun; Liu, Yi-Ming

    2016-06-17

    Capillary electrophoresis-based single cell analysis has become an essential approach in researches at the cellular level. However, automation of single cell analysis has been a challenge due to the difficulty to control the number of cells injected and the irreproducibility associated with cell aggregation. Herein we report the development of a new microfluidic platform deploying the double nano-electrode cell lysis technique for automated analysis of single cells with mass spectrometric detection. The proposed microfluidic chip features integration of a cell-sized high voltage zone for quick single cell lysis, a microfluidic channel for electrophoretic separation, and a nanoelectrospray emitter for ionization in MS detection. Built upon this platform, a microchip electrophoresis-mass spectrometric method (MCE-MS) has been developed for automated single cell analysis. In the method, cell introduction, cell lysis, and MCE-MS separation are computer controlled and integrated as a cycle into consecutive assays. Analysis of large numbers of individual PC-12 neuronal cells (both intact and exposed to 25mM KCl) was carried out to determine intracellular levels of dopamine (DA) and glutamic acid (Glu). It was found that DA content in PC-12 cells was higher than Glu content, and both varied from cell to cell. The ratio of intracellular DA to Glu was 4.20±0.8 (n=150). Interestingly, the ratio drastically decreased to 0.38±0.20 (n=150) after the cells are exposed to 25mM KCl for 8min, suggesting the cells released DA promptly and heavily while they released Glu at a much slower pace in response to KCl-induced depolarization. These results indicate that the proposed MCE-MS analytical platform may have a great potential in researches at the cellular level. PMID:27207575

  8. Automated local bright feature image analysis of nuclear proteindistribution identifies changes in tissue phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-02-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues.

  9. Automated Student Model Improvement

    Science.gov (United States)

    Koedinger, Kenneth R.; McLaughlin, Elizabeth A.; Stamper, John C.

    2012-01-01

    Student modeling plays a critical role in developing and improving instruction and instructional technologies. We present a technique for automated improvement of student models that leverages the DataShop repository, crowd sourcing, and a version of the Learning Factors Analysis algorithm. We demonstrate this method on eleven educational…

  10. Automating methods to improve precision in Monte-Carlo event generation for particle colliders

    Energy Technology Data Exchange (ETDEWEB)

    Gleisberg, Tanju

    2008-07-01

    The subject of this thesis was the development of tools for the automated calculation of exact matrix elements, which are a key for the systematic improvement of precision and confidence for theoretical predictions. Part I of this thesis concentrates on the calculations of cross sections at tree level. A number of extensions have been implemented in the matrix element generator AMEGIC++, namely new interaction models such as effective loop-induced couplings of the Higgs boson with massless gauge bosons, required for a number of channels for the Higgs boson search at LHC and anomalous gauge couplings, parameterizing a number of models beyond th SM. Further a special treatment to deal with complicated decay chains of heavy particles has been constructed. A significant effort went into the implementation of methods to push the limits on particle multiplicities. Two recursive methods have been implemented, the Cachazo-Svrcek-Witten recursion and the colour dressed Berends-Giele recursion. For the latter the new module COMIX has been added to the SHERPA framework. The Monte-Carlo phase space integration techniques have been completely revised, which led to significantly reduced statistical error estimates when calculating cross sections and a greatly improved unweighting efficiency for the event generation. Special integration methods have been developed to cope with the newly accessible final states. The event generation framework SHERPA directly benefits from those new developments, improving the precision and the efficiency. Part II was addressed to the automation of QCD calculations at next-to-leading order. A code has been developed, that, for the first time fully automates the real correction part of a NLO calculation. To calculate the correction for a m-parton process obeying the Catani-Seymour dipole subtraction method the following components are provided: 1. the corresponding m+1-parton tree level matrix elements, 2. a number dipole subtraction terms to remove

  11. Experimental saltwater intrusion in coastal aquifers using automated image analysis: Applications to homogeneous aquifers

    Science.gov (United States)

    Robinson, G.; Ahmed, Ashraf A.; Hamill, G. A.

    2016-07-01

    This paper presents the applications of a novel methodology to quantify saltwater intrusion parameters in laboratory-scale experiments. The methodology uses an automated image analysis procedure, minimising manual inputs and the subsequent systematic errors that can be introduced. This allowed the quantification of the width of the mixing zone which is difficult to measure in experimental methods that are based on visual observations. Glass beads of different grain sizes were tested for both steady-state and transient conditions. The transient results showed good correlation between experimental and numerical intrusion rates. The experimental intrusion rates revealed that the saltwater wedge reached a steady state condition sooner while receding than advancing. The hydrodynamics of the experimental mixing zone exhibited similar traits; a greater increase in the width of the mixing zone was observed in the receding saltwater wedge, which indicates faster fluid velocities and higher dispersion. The angle of intrusion analysis revealed the formation of a volume of diluted saltwater at the toe position when the saltwater wedge is prompted to recede. In addition, results of different physical repeats of the experiment produced an average coefficient of variation less than 0.18 of the measured toe length and width of the mixing zone.

  12. Automated acquisition and analysis of small angle X-ray scattering data

    International Nuclear Information System (INIS)

    Small Angle X-ray Scattering (SAXS) is a powerful tool in the study of biological macromolecules providing information about the shape, conformation, assembly and folding states in solution. Recent advances in robotic fluid handling make it possible to perform automated high throughput experiments including fast screening of solution conditions, measurement of structural responses to ligand binding, changes in temperature or chemical modifications. Here, an approach to full automation of SAXS data acquisition and data analysis is presented, which advances automated experiments to the level of a routine tool suitable for large scale structural studies. The approach links automated sample loading, primary data reduction and further processing, facilitating queuing of multiple samples for subsequent measurement and analysis and providing means of remote experiment control. The system was implemented and comprehensively tested in user operation at the BioSAXS beamlines X33 and P12 of EMBL at the DORIS and PETRA storage rings of DESY, Hamburg, respectively, but is also easily applicable to other SAXS stations due to its modular design.

  13. Fully Automated Sample Preparation for Ultrafast N-Glycosylation Analysis of Antibody Therapeutics.

    Science.gov (United States)

    Szigeti, Marton; Lew, Clarence; Roby, Keith; Guttman, Andras

    2016-04-01

    There is a growing demand in the biopharmaceutical industry for high-throughput, large-scale N-glycosylation profiling of therapeutic antibodies in all phases of product development, but especially during clone selection when hundreds of samples should be analyzed in a short period of time to assure their glycosylation-based biological activity. Our group has recently developed a magnetic bead-based protocol for N-glycosylation analysis of glycoproteins to alleviate the hard-to-automate centrifugation and vacuum-centrifugation steps of the currently used protocols. Glycan release, fluorophore labeling, and cleanup were all optimized, resulting in a automating all steps of the optimized magnetic bead-based protocol from endoglycosidase digestion, through fluorophore labeling and cleanup with high-throughput sample processing in 96-well plate format, using an automated laboratory workstation. Capillary electrophoresis analysis of the fluorophore-labeled glycans was also optimized for rapid (automated sample preparation workflow. Ultrafast N-glycosylation analyses of several commercially relevant antibody therapeutics are also shown and compared to their biosimilar counterparts, addressing the biological significance of the differences.

  14. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.

    OpenAIRE

    Greg Finak; Jacob Frelinger; Wenxin Jiang; Newell, Evan W.; John Ramey; Davis, Mark M.; Kalams, Spyros A.; De Rosa, Stephen C.; Raphael Gottardo

    2014-01-01

    Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis fra...

  15. OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

    OpenAIRE

    Greg Finak; Jacob Frelinger; Wenxin Jiang; Newell, Evan W; John Ramey; Davis, Mark M.; Kalams, Spyros A.; De Rosa, Stephen C.; Raphael Gottardo

    2014-01-01

    Flow cytometry is used increasingly in clinical research for cancer, immunology and vaccines. Technological advances in cytometry instrumentation are increasing the size and dimensionality of data sets, posing a challenge for traditional data management and analysis. Automated analysis methods, despite a general consensus of their importance to the future of the field, have been slow to gain widespread adoption. Here we present OpenCyto, a new BioConductor infrastructure and data analysis fra...

  16. An automated data processing method dedicated to 3D ultrasonic non destructive testing of composite pieces

    International Nuclear Information System (INIS)

    State-of the art Non Destructive Testing using ultrasound is based on evaluation of C-scan images, which is done mainly visually. The development of the new Sampling Phased Array technique SPA by IZFP Fraunhofer provides a fast three-dimensional reconstruction of inner object structures. This new inspection technique is to be complemented with fully or semi-automated evaluation of ultrasonic data, providing maximum support to the operator. We present in this contribution a processing method for SPA ultrasonic data, where the main focus of this paper will be on speckle noise reduction. The evaluation method is applied on carbon fibre composite where it demonstrates robust and successful performance in recognition of defects.

  17. Automated ion-selective electrode method for determining fluoride in natural waters

    Science.gov (United States)

    Erdmann, D.E.

    1975-01-01

    An automated fluoride method which uses AutoAnalyzer modules in conjunction with a fluoride ion-selective electrode was evaluated. The results obtained on 38 natural water samples are in excellent agreement with those determined by a similar manual method (average difference = 0.026 mg/l). An average fluoride concentration of 0.496 mg/l was found when several natural water samples were spiked with 0.50 mg/l fluoride. Aluminum is the only significant interfering substance, and it can be easily tolerated if its concentration does not exceed 2 mg/l. Thirty samples were analyzed per hour over a concentration range of 0-2 mg/l.

  18. Automated segmentation of muscle and adipose tissue on CT images for human body composition analysis

    Science.gov (United States)

    Chung, Howard; Cobzas, Dana; Birdsell, Laura; Lieffers, Jessica; Baracos, Vickie

    2009-02-01

    The ability to compute body composition in cancer patients lends itself to determining the specific clinical outcomes associated with fat and lean tissue stores. For example, a wasting syndrome of advanced disease associates with shortened survival. Moreover, certain tissue compartments represent sites for drug distribution and are likely determinants of chemotherapy efficacy and toxicity. CT images are abundant, but these cannot be fully exploited unless there exist practical and fast approaches for tissue quantification. Here we propose a fully automated method for segmenting muscle, visceral and subcutaneous adipose tissues, taking the approach of shape modeling for the analysis of skeletal muscle. Muscle shape is represented using PCA encoded Free Form Deformations with respect to a mean shape. The shape model is learned from manually segmented images and used in conjunction with a tissue appearance prior. VAT and SAT are segmented based on the final deformed muscle shape. In comparing the automatic and manual methods, coefficients of variation (COV) (1 - 2%), were similar to or smaller than inter- and intra-observer COVs reported for manual segmentation.

  19. An Automated High Throughput Proteolysis and Desalting Platform for Quantitative Proteomic Analysis

    Directory of Open Access Journals (Sweden)

    Albert-Baskar Arul

    2013-06-01

    Full Text Available Proteomics for biomarker validation needs high throughput instrumentation to analyze huge set of clinical samples for quantitative and reproducible analysis at a minimum time without manual experimental errors. Sample preparation, a vital step in proteomics plays a major role in identification and quantification of proteins from biological samples. Tryptic digestion a major check point in sample preparation for mass spectrometry based proteomics needs to be more accurate with rapid processing time. The present study focuses on establishing a high throughput automated online system for proteolytic digestion and desalting of proteins from biological samples quantitatively and qualitatively in a reproducible manner. The present study compares online protein digestion and desalting of BSA with conventional off-line (in-solution method and validated for real time sample for reproducibility. Proteins were identified using SEQUEST data base search engine and the data were quantified using IDEALQ software. The present study shows that the online system capable of handling high throughput samples in 96 well formats carries out protein digestion and peptide desalting efficiently in a reproducible and quantitative manner. Label free quantification showed clear increase of peptide quantities with increase in concentration with much linearity compared to off line method. Hence we would like to suggest that inclusion of this online system in proteomic pipeline will be effective in quantification of proteins in comparative proteomics were the quantification is really very crucial.

  20. Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

    Directory of Open Access Journals (Sweden)

    Tözeren Aydin

    2007-03-01

    Full Text Available Abstract Background Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. Methods This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B, percentage occupied by stroma-like regions (P, and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. Results Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. Conclusion These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists as hundreds of tumors that are used to develop an array have typically been evaluated

  1. Evaporation from weighing precipitation gauges: impacts on automated gauge measurements and quality assurance methods

    Directory of Open Access Journals (Sweden)

    R. D. Leeper

    2014-12-01

    Full Text Available The effects of evaporation on precipitation measurements have been understood to bias total precipitation lower. For automated weighing-bucket gauges, the World Meteorological Organization (WMO suggests the use of evaporative suppressants with frequent observations. However, the use of evaporation suppressants is not always feasible due to environmental hazards and the added cost of maintenance, transport, and disposal of the gauge additive. In addition, research has suggested that evaporation prior to precipitation may affect precipitation measurements from auto-recording gauges operating at sub-hourly frequencies. For further evaluation, a field campaign was conducted to monitor evaporation and its impacts on the quality of precipitation measurements from gauges used at US Climate Reference Network (USCRN stations. Collocated Geonor gauges with (nonEvap and without (evap an evaporative suppressant were compared to evaluate evaporative losses and evaporation biases on precipitation measurements. From June to August, evaporative losses from the evap gauge exceeded accumulated precipitation, with an average loss of 0.12 mm h−1. However, the impact of evaporation on precipitation measurements was sensitive to calculation methods. In general, methods that utilized a longer time series to smooth out sensor noise were more sensitive to gauge (−4.6% bias with respect to control evaporation than methods computing depth change without smoothing (< +1% bias. These results indicate that while climate and gauge design affect gauge evaporation rates computational methods can influence the magnitude of evaporation bias on precipitation measurements. It is hoped this study will advance QA techniques that mitigate the impact of evaporation biases on precipitation measurements from other automated networks.

  2. GenePublisher: automated analysis of DNA microarray data

    DEFF Research Database (Denmark)

    Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, T.;

    2003-01-01

    GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with aspecification of the data. The server performs normalization......, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user....

  3. Analysis of the thoracic aorta using a semi-automated post processing tool

    Energy Technology Data Exchange (ETDEWEB)

    Entezari, Pegah, E-mail: p-entezari@northwestern.edu [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Kino, Aya, E-mail: ayakino@gmail.com [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Honarmand, Amir R., E-mail: arhonarmand@yahoo.com [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Galizia, Mauricio S., E-mail: maugalizia@yahoo.com.br [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Yang, Yan, E-mail: yyang@vitalimages.com [Vital images Inc, Minnetonka, MN (United States); Collins, Jeremy, E-mail: collins@fsm.northwestern.edu [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Yaghmai, Vahid, E-mail: vyaghmai@northwestern.edu [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States); Carr, James C., E-mail: jcarr@northwestern.edu [Department of Radiology, Cardiovascular Imaging, Northwestern University, Chicago, IL (United States)

    2013-09-15

    Objective: To evaluates a semi-automated method for Thoracic Aortic Aneurysm (TAA) measurement using ECG-gated Dual Source CT Angiogram (DSCTA). Methods: This retrospective HIPAA compliant study was approved by our IRB. Transaxial maximum diameters of outer wall to outer wall were studied in fifty patients at seven anatomic locations of the thoracic aorta: annulus, sinus, sinotubular junction (STJ), mid ascending aorta (MAA) at the level of right pulmonary artery, proximal aortic arch (PROX) immediately proximal to innominate artery, distal aortic arch (DIST) immediately distal to left subclavian artery, and descending aorta (DESC) at the level of diaphragm. Measurements were performed using a manual method and semi-automated software. All readers repeated their measurements. Inter-method, intra-observer and inter-observer agreements were evaluated according to intraclass correlation coefficient (ICC) and Bland–Altman plot. The number of cases with manual contouring or center line adjustment for the semi-automated method and also the post-processing time for each method were recorded. Results: The mean difference between semi-automated and manual methods was less than 1.3 mm at all seven points. Strong inter-method, inter-observer and intra-observer agreement was recorded at all levels (ICC ≥ 0.9). The maximum rate of manual adjustment of center line and contour was at the level of annulus. The average time for manual post-processing of the aorta was 19 ± 0.3 min, while it took 8.26 ± 2.1 min to do the measurements with the semi-automated tool (Vitrea version 6.0.0.1 software). The center line was edited manually at all levels, with most corrections at the level of annulus (60%), while the contour was adjusted at all levels with highest and lowest number of corrections at the levels of annulus and DESC (75% and 0.07% of the cases), respectively. Conclusion: Compared to the commonly used manual method, semi-automated measurement of vessel dimensions is

  4. Infrascope: Full-Spectrum Phonocardiography with Automated Signal Analysis Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Using digital signal analysis tools, we will generate a repeatable output from the infrascope and compare it to the output of a traditional electrocardiogram, and...

  5. Automation of Safety Analysis with SysML Models Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This project was a small proof-of-concept case study, generating SysML model information as a side effect of safety analysis. A prototype FMEA Assistant was...

  6. Semi-automated competitive protein binding analysis of serum thyroxine on reusable Sephadex columns and its advantages over radioimmunoassay.

    Science.gov (United States)

    Alexander, N M

    1976-06-01

    Competitive protein-binding analysis of serum thyroxine on small, reusable, Sephadex columns has been further studied and improved. The improved, semi-automated procedure results in reduced working time and costs. It has also been established that triiodothyronine crossreacts only 1/6 to 1/9 as well as thyroxine, and can be ignored because it represents only about 1/80 of the total serum iodothyronine content. The economic and methodological advantages of the improved method over radioammunoassay and other displacement assays are discussed.

  7. Photogrammetry-Based Automated Measurements for Tooth Shape and Occlusion Analysis

    Science.gov (United States)

    Knyaz, V. A.; Gaboutchian, A. V.

    2016-06-01

    Tooth measurements (odontometry) are performed for various scientific and practical applications, including dentistry. Present-day techniques are being increasingly based on 3D model use that provides wider prospects in comparison to measurements on real objects: teeth or their plaster copies. The main advantages emerge through application of new measurement methods which provide the needed degree of non-invasiveness, precision, convenience and details. Tooth measurements have been always regarded as a time-consuming research, even more so with use of new methods due to their wider opportunities. This is where automation becomes essential for further development and implication of measurement techniques. In our research automation in obtaining 3D models and automation of measurements provided essential data that was analysed to suggest recommendations for tooth preparation - one of the most responsible clinical procedures in prosthetic dentistry - within a comparatively short period of time. The original photogrammetric 3D reconstruction system allows to generate 3D models of dental arches, reproduce their closure, or occlusion, and to perform a set of standard measurement in automated mode.

  8. RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry

    Science.gov (United States)

    Zhang, Jing

    2016-01-01

    Background Statistical analysis and data visualization are two crucial aspects in molecular biology and biology. For analyses that compare one dependent variable between standard (e.g., control) and one or multiple independent variables, a comprehensive yet highly streamlined solution is valuable. The computer programming language R is a popular platform for researchers to develop tools that are tailored specifically for their research needs. Here we present an R package RBioplot that takes raw input data for automated statistical analysis and plotting, highly compatible with various molecular biology and biochemistry lab techniques, such as, but not limited to, western blotting, PCR, and enzyme activity assays. Method The package is built based on workflows operating on a simple raw data layout, with minimum user input or data manipulation required. The package is distributed through GitHub, which can be easily installed through one single-line R command. A detailed installation guide is available at http://kenstoreylab.com/?page_id=2448. Users can also download demo datasets from the same website. Results and Discussion By integrating selected functions from existing statistical and data visualization packages with extensive customization, RBioplot features both statistical analysis and data visualization functionalities. Key properties of RBioplot include: -Fully automated and comprehensive statistical analysis, including normality test, equal variance test, Student’s t-test and ANOVA (with post-hoc tests);-Fully automated histogram, heatmap and joint-point curve plotting modules;-Detailed output files for statistical analysis, data manipulation and high quality graphs;-Axis range finding and user customizable tick settings;-High user-customizability. PMID:27703842

  9. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    While increasing evidence appoints diverse types of RNA as key players in the regulatory networks underlying cellular differentiation and metabolism, the potential functions of thousands of conserved RNA structures encoded in mammalian genomes remain to be determined. Since the functions of most...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA......-protein pulldown combined with mass spectrometry analysis is applied for in vivo as well as in vitro identification of RNA-binding proteins, the latter succeeding in verifying known RNA-protein interactions. Secondly, acknowledging the significance of flexible promoter usage for the diversification...

  10. Automative Multi Classifier Framework for Medical Image Analysis

    Directory of Open Access Journals (Sweden)

    R. Edbert Rajan

    2015-04-01

    Full Text Available Medical image processing is the technique used to create images of the human body for medical purposes. Nowadays, medical image processing plays a major role and a challenging solution for the critical stage in the medical line. Several researches have done in this area to enhance the techniques for medical image processing. However, due to some demerits met by some advanced technologies, there are still many aspects that need further development. Existing study evaluate the efficacy of the medical image analysis with the level-set shape along with fractal texture and intensity features to discriminate PF (Posterior Fossa tumor from other tissues in the brain image. To develop the medical image analysis and disease diagnosis, to devise an automotive subjective optimality model for segmentation of images based on different sets of selected features from the unsupervised learning model of extracted features. After segmentation, classification of images is done. The classification is processed by adapting the multiple classifier frameworks in the previous work based on the mutual information coefficient of the selected features underwent for image segmentation procedures. In this study, to enhance the classification strategy, we plan to implement enhanced multi classifier framework for the analysis of medical images and disease diagnosis. The performance parameter used for the analysis of the proposed enhanced multi classifier framework for medical image analysis is Multiple Class intensity, image quality, time consumption.

  11. A Method to Identify and Analyze Biological Programs through Automated Reasoning

    Science.gov (United States)

    Kugler, Hillel; Smith, Austin; Martello, Graziano; Emmott, Stephen

    2016-01-01

    Predictive biology is elusive because rigorous, data-constrained, mechanistic models of complex biological systems are difficult to derive and validate. Current approaches tend to construct and examine static interaction network models, which are descriptively rich but often lack explanatory and predictive power, or dynamic models that can be simulated to reproduce known behavior. However, in such approaches implicit assumptions are introduced as typically only one mechanism is considered, and exhaustively investigating all scenarios is impractical using simulation. To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations. We test hypotheses against all candidate models, and remove the need for simulation by characterizing and simultaneously analyzing all mechanistic explanations of observed behavior. Our methodology transforms knowledge of complex biological processes from sets of possible interactions and experimental observations to precise, predictive biological programs governing cell function. PMID:27668090

  12. Fully Automated Laser Ablation Liquid Capture Sample Analysis using NanoElectrospray Ionization Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Lorenz, Matthias [ORNL; Ovchinnikova, Olga S [ORNL; Van Berkel, Gary J [ORNL

    2014-01-01

    RATIONALE: Laser ablation provides for the possibility of sampling a large variety of surfaces with high spatial resolution. This type of sampling when employed in conjunction with liquid capture followed by nanoelectrospray ionization provides the opportunity for sensitive and prolonged interrogation of samples by mass spectrometry as well as the ability to analyze surfaces not amenable to direct liquid extraction. METHODS: A fully automated, reflection geometry, laser ablation liquid capture spot sampling system was achieved by incorporating appropriate laser fiber optics and a focusing lens into a commercially available, liquid extraction surface analysis (LESA ) ready Advion TriVersa NanoMate system. RESULTS: Under optimized conditions about 10% of laser ablated material could be captured in a droplet positioned vertically over the ablation region using the NanoMate robot controlled pipette. The sampling spot size area with this laser ablation liquid capture surface analysis (LA/LCSA) mode of operation (typically about 120 m x 160 m) was approximately 50 times smaller than that achievable by direct liquid extraction using LESA (ca. 1 mm diameter liquid extraction spot). The set-up was successfully applied for the analysis of ink on glass and paper as well as the endogenous components in Alstroemeria Yellow King flower petals. In a second mode of operation with a comparable sampling spot size, termed laser ablation/LESA , the laser system was used to drill through, penetrate, or otherwise expose material beneath a solvent resistant surface. Once drilled, LESA was effective in sampling soluble material exposed at that location on the surface. CONCLUSIONS: Incorporating the capability for different laser ablation liquid capture spot sampling modes of operation into a LESA ready Advion TriVersa NanoMate enhanced the spot sampling spatial resolution of this device and broadened the surface types amenable to analysis to include absorbent and solvent resistant

  13. AMAB: Automated measurement and analysis of body motion

    NARCIS (Netherlands)

    Poppe, Ronald; Zee, van der Sophie; Heylen, Dirk K.J.; Taylor, Paul J.

    2014-01-01

    Technologies that measure human nonverbal behavior have existed for some time, and their use in the analysis of social behavior has become more popular following the development of sensor technologies that record full-body movement. However, a standardized methodology to efficiently represent and an

  14. Automated analysis of security requirements through risk-based argumentation

    NARCIS (Netherlands)

    Yu, Yijun; Franqueira, Virginia N.L.; Tun, Thein Tan; Wieringa, Roel J.; Nuseibeh, Bashar

    2015-01-01

    Computer-based systems are increasingly being exposed to evolving security threats, which often reveal new vulnerabilities. A formal analysis of the evolving threats is difficult due to a number of practical considerations such as incomplete knowledge about the design, limited information about atta

  15. Automated analysis of three-dimensional stress echocardiography

    NARCIS (Netherlands)

    K.Y.E. Leung (Esther); M. van Stralen (Marijn); M.G. Danilouchkine (Mikhail); G. van Burken (Gerard); M.L. Geleijnse (Marcel); J.H.C. Reiber (Johan); N. de Jong (Nico); A.F.W. van der Steen (Ton); J.G. Bosch (Johan)

    2011-01-01

    textabstractReal-time three-dimensional (3D) ultrasound imaging has been proposed as an alternative for two-dimensional stress echocardiography for assessing myocardial dysfunction and underlying coronary artery disease. Analysis of 3D stress echocardiography is no simple task and requires considera

  16. Analysis of the automated systems of planning of spatial constructions

    Directory of Open Access Journals (Sweden)

    М.С. Барабаш

    2004-04-01

    Full Text Available  The article is devoted to the questions of analysis of existing SAPR and questions of development of new information technologies of planning on the basis of integration of programmatic complexes with the use of united informatively-logical model of object.

  17. Automation determining of thermal economical efficiency of the K-500-60/1500 turbine plant by the reverse balance method

    International Nuclear Information System (INIS)

    Application experience of the automated system of operating control at the Novovoronezh-5 by the reverse balance method of steam turbine efficiency is described. The method is based on measuring amount of heat removed from the turbine plant circuit (mainly, with cooling condenser water)

  18. Immunohistochemical Ki-67/KL1 double stains increase accuracy of Ki-67 indices in breast cancer and simplify automated image analysis

    DEFF Research Database (Denmark)

    Nielsen, Patricia S; Bentzer, Nina K; Jensen, Vibeke;

    2014-01-01

    by digital image analysis. This study aims to detect the difference in accuracy and precision between manual indices of single and double stains, to develop an automated quantification of double stains, and to explore the relation between automated indices and tumor characteristics when quantified...... in different regions: hot spots, global tumor areas, and invasive fronts. MATERIALS AND METHODS: Paraffin-embedded, formalin-fixed tissue from 100 consecutive patients with invasive breast cancer was immunohistochemically stained for Ki-67 and Ki-67/KL1. Ki-67 was manually scored in different regions by 2...

  19. Automated four color CD4/CD8 analysis of leukocytes by scanning fluorescence microscopy using Quantum dots

    Science.gov (United States)

    Bocsi, Jozsef; Mittag, Anja; Varga, Viktor S.; Molnar, Bela; Tulassay, Zsolt; Sack, Ulrich; Lenz, Dominik; Tarnok, Attila

    2006-02-01

    Scanning Fluorescence Microscope (SFM) is a new technique for automated motorized microscopes to measure multiple fluorochrome labeled cells (Bocsi et al. Cytometry 2004, 61A:1). The ratio of CD4+/CD8+ cells is an important in immune diagnostics in immunodeficiency and HIV. Therefor a four-color staining protocol (DNA, CD3, CD4 and CD8) for automated SFM analysis of lymphocytes was developed. EDTA uncoagulated blood was stained with organic and inorganic (Quantum dots) fluorochromes in different combinations. Aliquots of samples were measured by Flow Cytometry (FCM) and SFM. By SFM specimens were scanned and digitized using four fluorescence filter sets. Automated cell detection (based on Hoechst 33342 fluorescence), CD3, CD4 and CD8 detection were performed, CD4/CD8 ratio was calculated. Fluorescence signals were well separable on SFM and FCM. Passing and Bablok regression of all CD4/CD8 ratios obtained by FCM and SFM (F(X)=0.0577+0.9378x) are in the 95% confidence interval. Cusum test did not show significant deviation from linearity (P>0.10). This comparison indicates that there is no systemic bias between the two different methods. In SFM analyses the inorganic Quantum dot staining was very stable in PBS in contrast to the organic fluorescent dyes, but bleached shortly after mounting with antioxidant and free radical scavenger mounting media. This shows the difficulty of combinations of organic dyes and Quantum dots. Slide based multi-fluorescence labeling system and automated SFM are applicable tools for the CD4/CD8 ratio determination in peripheral blood samples. Quantum Dots are stable inorganic fluorescence labels that may be used as reliable high resolution dyes for cell labeling.

  20. A method for automating calibration and records management for instrumentation and dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    O`Brien, J.M. Jr.; Rushton, R.O.; Burns, R.E. Jr. [Atlan-Tech, Inc., Roswell, GA (United States)

    1993-12-31

    Current industry requirements are becoming more stringent on quality assurance records and documentation for calibration of instruments and dosimetry. A novel method is presented here that will allow a progressive automation scheme to be used in pursuit of that goal. This concept is based on computer-controlled irradiators that can act as stand-alone devices or be interfaced to other components via a computer local area network. In this way, complete systems can be built with modules to create a records management system to meet the needs of small laboratories or large multi-building calibration groups. Different database engines or formats can be used simply by replacing a module. Modules for temperature and pressure monitoring or shipping and receiving can be added, as well as equipment modules for direct IEEE-488 interface to electrometers and other instrumentation.

  1. Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

    Science.gov (United States)

    Suleimanov, Yury V; Green, William H

    2015-09-01

    We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes. PMID:26575920

  2. Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods

    CERN Document Server

    Suleimanov, Yury V

    2015-01-01

    We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation single- and double-ended transition-state optimization algorithms - the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the possibility of discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

  3. Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

    Science.gov (United States)

    Suleimanov, Yury V; Green, William H

    2015-09-01

    We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

  4. Automated Performance Monitoring Data Analysis and Reporting within the Open Source R Environment

    Science.gov (United States)

    Kennel, J.; Tonkin, M. J.; Faught, W.; Lee, A.; Biebesheimer, F.

    2013-12-01

    Environmental scientists encounter quantities of data at a rate that in many cases outpaces our ability to appropriately store, visualize and convey the information. The free software environment, R, provides a framework for efficiently processing, analyzing, depicting and reporting on data from a multitude of formats in the form of traceable and quality-assured data summary reports. Automated data summary reporting leverages document markup languages such as markdown, HTML, or LaTeX using R-scripts capable of completing a variety of simple or sophisticated data processing, analysis and visualization tasks. Automated data summary reports seamlessly integrate analysis into report production with calculation outputs - such as plots, maps and statistics - included alongside report text. Once a site-specific template is set up, including data types, geographic base data and reporting requirements, reports can be (re-)generated trivially as the data evolve. The automated data summary report can be a stand-alone report, or it can be incorporated as an attachment to an interpretive report prepared by a subject-matter expert, thereby providing the technical basis to report on and efficiently evaluate large volumes of data resulting in a concise interpretive report. Hence, the data summary report does not replace the scientist, but relieves them of repetitive data processing tasks, facilitating a greater level of analysis. This is demonstrated using an implementation developed for monthly groundwater data reporting for a multi-constituent contaminated site, highlighting selected analysis techniques that can be easily incorporated in a data summary report.

  5. Automated detection and analysis of particle beams in laser-plasma accelerator simulations

    Energy Technology Data Exchange (ETDEWEB)

    Ushizima, Daniela Mayumi; Geddes, C.G.; Cormier-Michel, E.; Bethel, E. Wes; Jacobsen, J.; Prabhat, ,; R.ubel, O.; Weber, G,; Hamann, B.

    2010-05-21

    scientific data mining is increasingly considered. In plasma simulations, Bagherjeiran et al. presented a comprehensive report on applying graph-based techniques for orbit classification. They used the KAM classifier to label points and components in single and multiple orbits. Love et al. conducted an image space analysis of coherent structures in plasma simulations. They used a number of segmentation and region-growing techniques to isolate regions of interest in orbit plots. Both approaches analyzed particle accelerator data, targeting the system dynamics in terms of particle orbits. However, they did not address particle dynamics as a function of time or inspected the behavior of bunches of particles. Ruebel et al. addressed the visual analysis of massive laser wakefield acceleration (LWFA) simulation data using interactive procedures to query the data. Sophisticated visualization tools were provided to inspect the data manually. Ruebel et al. have integrated these tools to the visualization and analysis system VisIt, in addition to utilizing efficient data management based on HDF5, H5Part, and the index/query tool FastBit. In Ruebel et al. proposed automatic beam path analysis using a suite of methods to classify particles in simulation data and to analyze their temporal evolution. To enable researchers to accurately define particle beams, the method computes a set of measures based on the path of particles relative to the distance of the particles to a beam. To achieve good performance, this framework uses an analysis pipeline designed to quickly reduce the amount of data that needs to be considered in the actual path distance computation. As part of this process, region-growing methods are utilized to detect particle bunches at single time steps. Efficient data reduction is essential to enable automated analysis of large data sets as described in the next section, where data reduction methods are steered to the particular requirements of our clustering analysis

  6. Modelling application for cognitive reliability and error analysis method

    Directory of Open Access Journals (Sweden)

    Fabio De Felice

    2013-10-01

    Full Text Available The automation of production systems has delegated to machines the execution of highly repetitive and standardized tasks. In the last decade, however, the failure of the automatic factory model has led to partially automated configurations of production systems. Therefore, in this scenario, centrality and responsibility of the role entrusted to the human operators are exalted because it requires problem solving and decision making ability. Thus, human operator is the core of a cognitive process that leads to decisions, influencing the safety of the whole system in function of their reliability. The aim of this paper is to propose a modelling application for cognitive reliability and error analysis method.

  7. A method for automated control of belt velocity changes with an instrumented treadmill.

    Science.gov (United States)

    Hinkel-Lipsker, Jacob W; Hahn, Michael E

    2016-01-01

    Increased practice difficulty during asymmetrical split-belt treadmill rehabilitation has been shown to improve gait outcomes during retention and transfer tests. However, research in this area has been limited by manual treadmill operation. In the case of variable practice, which requires stride-by-stride changes to treadmill belt velocities, the treadmill control must be automated. This paper presents a method for automation of asymmetrical split-belt treadmill walking, and evaluates how well this method performs with regards to timing of gait events. One participant walked asymmetrically for 100 strides, where the non-dominant limb was driven at their self-selected walking speed, while the other limb was driven randomly on a stride-by-stride basis. In the control loop, the key factors to insure that the treadmill belt had accelerated to its new velocity safely during the swing phase were the sampling rate of the A/D converter, processing time within the controller software, and acceleration of the treadmill belt. The combination of these three factors resulted in a total control loop time during each swing phase that satisfied these requirements with a factor of safety that was greater than 4. Further, a polynomial fit indicated that belt acceleration was the largest contributor to changes in this total time. This approach appears to be safe and reliable for stride-by-stride adjustment of treadmill belt speed, making it suitable for future asymmetrical split-belt walking studies. Further, it can be incorporated into virtual reality rehabilitation paradigms that utilize split-belt treadmill walking. PMID:26654110

  8. BitTorrent Swarm Analysis through Automation and Enhanced Logging

    OpenAIRE

    R˘azvan Deaconescu; Marius Sandu-Popa; Adriana Dr˘aghici; Nicolae T˘apus

    2011-01-01

    Peer-to-Peer protocols currently form the most heavily used protocol class in the Internet, with BitTorrent, the most popular protocol for content distribution, as its flagship. A high number of studies and investigations have been undertaken to measure, analyse and improve the inner workings of the BitTorrent protocol. Approaches such as tracker message analysis, network probing and packet sniffing have been deployed to understand and enhance BitTorrent's internal behaviour. In this paper we...

  9. Automated analysis of protein subcellular location in time series images

    OpenAIRE

    Hu, Yanhua; Osuna-Highley, Elvira; Hua, Juchang; Nowicki, Theodore Scott; Stolz, Robert; McKayle, Camille; Murphy, Robert F.

    2010-01-01

    Motivation: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve...

  10. BitTorrent Swarm Analysis through Automation and Enhanced Logging

    CERN Document Server

    Deaconescu, Răzvan; Drăghici, Adriana; Tăpus, Nicolae

    2011-01-01

    Peer-to-Peer protocols currently form the most heavily used protocol class in the Internet, with BitTorrent, the most popular protocol for content distribution, as its flagship. A high number of studies and investigations have been undertaken to measure, analyse and improve the inner workings of the BitTorrent protocol. Approaches such as tracker message analysis, network probing and packet sniffing have been deployed to understand and enhance BitTorrent's internal behaviour. In this paper we present a novel approach that aims to collect, process and analyse large amounts of local peer information in BitTorrent swarms. We classify the information as periodic status information able to be monitored in real time and as verbose logging information to be used for subsequent analysis. We have designed and implemented a retrieval, storage and presentation infrastructure that enables easy analysis of BitTorrent protocol internals. Our approach can be employed both as a comparison tool, as well as a measurement syste...

  11. Automated condition classification of a reciprocating compressor using time frequency analysis and an artificial neural network

    Science.gov (United States)

    Lin, Yih-Hwang; Wu, Hsien-Chang; Wu, Chung-Yung

    2006-12-01

    The purpose of this study is to develop an automated system for condition classification of a reciprocating compressor. Various time-frequency analysis techniques will be examined for decomposition of the vibration signals. Because a time-frequency distribution is a 3D data map, data reduction is indispensable for subsequent analysis. The extraction of the system characteristics using three indices, namely the time index, frequency index, and amplitude index, will be presented and examined for their applicability. The probability neural network is applied for automated condition classification using a combination of the three indices. The study reveals that a proper choice of the index combination and the time-frequency band can provide excellent classification accuracy for the machinery conditions examined in this work.

  12. An Empirical Study on the Impact of Automation on the Requirements Analysis Process

    Institute of Scientific and Technical Information of China (English)

    Giuseppe Lami; Robert W. Ferguson

    2007-01-01

    Requirements analysis is an important phase in a software project. The analysis is often performed in aninformal way by specialists who review documents looking for ambiguities, technical inconsistencies and incomplete parts.Automation is still far from being applied in requirements analyses, above all since natural languages are informal andthus difficult to treat automatically. There are only a few tools that can analyse texts. One of them, called QuARS, wasdeveloped by the Istituto di Scienza e Tecnologie dell'Informazione and can analyse texts in terms of ambiguity. This paperdescribes how QuARS was used in a formal empirical experiment to assess the impact in terms of effectiveness and efficacyof the automation in the requirements review process of a software company.

  13. Application of automated mass spectrometry deconvolution and identification software for pesticide analysis in surface waters.

    Science.gov (United States)

    Furtula, Vesna; Derksen, George; Colodey, Alan

    2006-01-01

    A new approach to surface water analysis has been investigated in order to enhance the detection of different organic contaminants in Nathan Creek, British Columbia. Water samples from Nathan Creek were prepared by liquid/liquid extraction using dichloromethane (DCM) as an extraction solvent and analyzed by gas chromatography mass spectrometry method in scan mode (GC-MS scan). To increase sensitivity for pesticides detection, acquired scan data were further analyzed by Automated Mass Spectrometry Deconvolution and Identification Software (AMDIS) incorporated into the Agilent Deconvolution Reporting Software (DRS), which also includes mass spectral libraries for 567 pesticides. Extracts were reanalyzed by gas chromatography mass spectrometry single ion monitoring (GC-MS-SIM) to confirm and quantitate detected pesticides. Pesticides: atrazine, dimethoate, diazinone, metalaxyl, myclobutanil, napropamide, oxadiazon, propazine and simazine were detected at three sampling sites on the mainstream of the Nathan Creek. Results of the study are further discussed in terms of detectivity and identification level for each pesticide found. The proposed approach of monitoring pesticides in surface waters enables their detection and identification at trace levels. PMID:17090491

  14. Is interactional dissynchrony a clue to deception? Insights from automated analysis of nonverbal visual cues.

    Science.gov (United States)

    Yu, Xiang; Zhang, Shaoting; Yan, Zhennan; Yang, Fei; Huang, Junzhou; Dunbar, Norah E; Jensen, Matthew L; Burgoon, Judee K; Metaxas, Dimitris N

    2015-03-01

    Detecting deception in interpersonal dialog is challenging since deceivers take advantage of the give-and-take of interaction to adapt to any sign of skepticism in an interlocutor's verbal and nonverbal feedback. Human detection accuracy is poor, often with no better than chance performance. In this investigation, we consider whether automated methods can produce better results and if emphasizing the possible disruption in interactional synchrony can signal whether an interactant is truthful or deceptive. We propose a data-driven and unobtrusive framework using visual cues that consists of face tracking, head movement detection, facial expression recognition, and interactional synchrony estimation. Analysis were conducted on 242 video samples from an experiment in which deceivers and truth-tellers interacted with professional interviewers either face-to-face or through computer mediation. Results revealed that the framework is able to automatically track head movements and expressions of both interlocutors to extract normalized meaningful synchrony features and to learn classification models for deception recognition. Further experiments show that these features reliably capture interactional synchrony and efficiently discriminate deception from truth. PMID:24988600

  15. Automated analysis for microcalcifications in high resolution digital mammograms

    Energy Technology Data Exchange (ETDEWEB)

    Mascio, L.N.

    1996-12-17

    A method is disclosed for automatically locating microcalcifications indicating breast cancer. The invention assists mammographers in finding very subtle microcalcifications and in recognizing the pattern formed by all the microcalcifications. It also draws attention to microcalcifications that might be overlooked because a more prominent feature draws attention away from an important object. A new filter has been designed to weed out false positives in one of the steps of the method. Previously, iterative selection threshold was used to separate microcalcifications from the spurious signals resulting from texture or other background. A Selective Erosion or Enhancement (SEE) Filter has been invented to improve this step. Since the algorithm detects areas containing potential calcifications on the mammogram, it can be used to determine which areas need be stored at the highest resolution available, while, in addition, the full mammogram can be reduced to an appropriate resolution for the remaining cancer signs. 8 figs.

  16. Automated analysis for microcalcifications in high resolution digital mammograms

    Science.gov (United States)

    Mascio, Laura N.

    1996-01-01

    A method for automatically locating microcalcifications indicating breast cancer. The invention assists mammographers in finding very subtle microcalcifications and in recognizing the pattern formed by all the microcalcifications. It also draws attention to microcalcifications that might be overlooked because a more prominent feature draws attention away from an important object. A new filter has been designed to weed out false positives in one of the steps of the method. Previously, iterative selection threshold was used to separate microcalcifications from the spurious signals resulting from texture or other background. A Selective Erosion or Enhancement (SEE) Filter has been invented to improve this step. Since the algorithm detects areas containing potential calcifications on the mammogram, it can be used to determine which areas need be stored at the highest resolution available, while, in addition, the full mammogram can be reduced to an appropriate resolution for the remaining cancer signs.

  17. A Multi-Wavelength Analysis of Active Regions and Sunspots by Comparison of Automated Detection Algorithms

    OpenAIRE

    Verbeeck, Cis; Higgins, Paul A.; Colak, Tufan; Watson, Fraser T.; Delouille, Veronique; Mampaey, Benjamin; Qahwaji, Rami

    2011-01-01

    Since the Solar Dynamics Observatory (SDO) began recording ~ 1 TB of data per day, there has been an increased need to automatically extract features and events for further analysis. Here we compare the overall detection performance, correlations between extracted properties, and usability for feature tracking of four solar feature-detection algorithms: the Solar Monitor Active Region Tracker (SMART) detects active regions in line-of-sight magnetograms; the Automated Solar Activity Prediction...

  18. Pharmacokinetic analysis of topical tobramycin in equine tears by automated immunoassay

    OpenAIRE

    Czerwinski Sarah L; Lyon Andrew W; Skorobohach Brian; Léguillette Renaud

    2012-01-01

    Abstract Background Ophthalmic antibiotic therapy in large animals is often used empirically because of the lack of pharmacokinetics studies. The purpose of the study was to determine the pharmacokinetics of topical tobramycin 0.3% ophthalmic solution in the tears of normal horses using an automated immunoassay analysis. Results The mean tobramycin concentrations in the tears at 5, 10, 15, 30 minutes and 1, 2, 4, 6 hours after administration were 759 (±414), 489 (±237), 346 (±227), 147 (±264)...

  19. Spectral analysis for automated exploration and sample acquisition

    Science.gov (United States)

    Eberlein, Susan; Yates, Gigi

    1992-05-01

    Future space exploration missions will rely heavily on the use of complex instrument data for determining the geologic, chemical, and elemental character of planetary surfaces. One important instrument is the imaging spectrometer, which collects complete images in multiple discrete wavelengths in the visible and infrared regions of the spectrum. Extensive computational effort is required to extract information from such high-dimensional data. A hierarchical classification scheme allows multispectral data to be analyzed for purposes of mineral classification while limiting the overall computational requirements. The hierarchical classifier exploits the tunability of a new type of imaging spectrometer which is based on an acousto-optic tunable filter. This spectrometer collects a complete image in each wavelength passband without spatial scanning. It may be programmed to scan through a range of wavelengths or to collect only specific bands for data analysis. Spectral classification activities employ artificial neural networks, trained to recognize a number of mineral classes. Analysis of the trained networks has proven useful in determining which subsets of spectral bands should be employed at each step of the hierarchical classifier. The network classifiers are capable of recognizing all mineral types which were included in the training set. In addition, the major components of many mineral mixtures can also be recognized. This capability may prove useful for a system designed to evaluate data in a strange environment where details of the mineral composition are not known in advance.

  20. Bittorrent Swarm Analysis Through Automation and Enhanced Logging

    Directory of Open Access Journals (Sweden)

    R˘azvan Deaconescu

    2011-01-01

    Full Text Available Peer-to-Peer protocols currently form the most heavily used protocol class in the Internet,with BitTorrent, the most popular protocol for content distribution, as its flagship.A high number ofstudies and investigations have been undertaken to measure, analyse and improve the inner workings ofthe BitTorrent protocol. Approaches such as tracker message analysis, network probing and packetsniffing have been deployed to understand and enhance BitTorrent’s internal behaviour. In this paper wepresent a novel approach that aims to collect, process and analyse large amounts of local peerinformation in BitTorrent swarms. We classify the information as periodic status information able to bemonitored in real time and as verbose logging information to be used for subsequent analysis. We havedesigned and implemented a retrieval, storage and presentation infrastructure that enables easy analysisof BitTorrent protocol internals. Our approach can be employed both as a comparison tool, as well as ameasurement system of how network characteristics and protocol implementation influence the overallBitTorrent swarm performance.We base our approach on a framework that allows easy swarm creationand control for different BitTorrent clients.With the help of a virtualized infrastructure and a client-serversoftware layer we are able to create, command and manage large sized BitTorrent swarms. Theframework allows a user to run, schedule, start, stop clients within a swarm and collect informationregarding their behavior.

  1. Wireless Controlled Methods via Voice and Internet (e-mail for Home Automation System

    Directory of Open Access Journals (Sweden)

    R.A.Ramlee

    2013-08-01

    Full Text Available This paper presents a wireless Home Automation System (HAS that mainly performed by computer. The system is designed with several control methods in order to control the target electrical appliances. This various control methods implemented to fulfill the needs of users at home even at outside. The computer application is designed in Microsoft Windows OS that integrated with speech recognition voice control by using Microsoft Speech Application Programming Interface (SAPI. The voice control method provides more convenience especially to the blind and paralyzed users at home. This system is designed to perform short distance control by using wireless Bluetooth technology and long distance control by using Simple Mail Transfer Protocol (SMTP email control method. The short distance control is considered as the control that performed inside the house. Moreover, the long distance control can be performed at everywhere by devices that installed with browser or email application, and also with the internet access. The system intended to control electrical appliances at home with relatively low cost design, user-friendly interface and ease of installation.

  2. Automated MALDI matrix deposition method with inkjet printing for imaging mass spectrometry.

    Science.gov (United States)

    Baluya, Dodge L; Garrett, Timothy J; Yost, Richard A

    2007-09-01

    Careful matrix deposition on tissue samples for matrix-assisted laser desorption/ionization (MALDI) is critical for producing reproducible analyte ion signals. Traditional methods for matrix deposition are often considered an art rather than a science, with significant sample-to-sample variability. Here we report an automated method for matrix deposition, employing a desktop inkjet printer (printer tray, designed to hold CDs and DVDs, was modified to hold microscope slides. Empty ink cartridges were filled with MALDI matrix solutions, including DHB in methanol/water (70:30) at concentrations up to 40 mg/mL. Various samples (including rat brain tissue sections and standards of small drug molecules) were prepared using three deposition methods (electrospray, airbrush, inkjet). A linear ion trap equipped with an intermediate-pressure MALDI source was used for analyses. Optical microscopic examination showed that matrix crystals were formed evenly across the sample. There was minimal background signal after storing the matrix in the cartridges over a 6-month period. Overall, the mass spectral images gathered from inkjet-printed tissue specimens were of better quality and more reproducible than from specimens prepared by the electrospray and airbrush methods.

  3. Knowledge Support and Automation for Performance Analysis with PerfExplorer 2.0

    Directory of Open Access Journals (Sweden)

    Kevin A. Huck

    2008-01-01

    Full Text Available The integration of scalable performance analysis in parallel development tools is difficult. The potential size of data sets and the need to compare results from multiple experiments presents a challenge to manage and process the information. Simply to characterize the performance of parallel applications running on potentially hundreds of thousands of processor cores requires new scalable analysis techniques. Furthermore, many exploratory analysis processes are repeatable and could be automated, but are now implemented as manual procedures. In this paper, we will discuss the current version of PerfExplorer, a performance analysis framework which provides dimension reduction, clustering and correlation analysis of individual trails of large dimensions, and can perform relative performance analysis between multiple application executions. PerfExplorer analysis processes can be captured in the form of Python scripts, automating what would otherwise be time-consuming tasks. We will give examples of large-scale analysis results, and discuss the future development of the framework, including the encoding and processing of expert performance rules, and the increasing use of performance metadata.

  4. Comparing Rough Set Theory with Multiple Regression Analysis as Automated Valuation Methodologies

    OpenAIRE

    Maurizio d’Amato

    2007-01-01

    This paper focuses on the problem of applying rough set theory to mass appraisal. This methodology was first introduced by a Polish mathematician, and has been applied recently as an automated valuation methodology by the author. The method allows the appraiser to estimate a property without defining econometric modeling, although it does not give any quantitative estimation of marginal prices. In a previous paper by the author, data were organized into classes prior to the valuation process,...

  5. Automated Source Code Changes Classification for Effective Code Review and Analysis

    OpenAIRE

    Evgeny, G.

    2008-01-01

    Software development process is a complex sequence of actions having source code of working system as a result. All project participants should track changes in source code during work process to know what’s happening. However to make «manual» code review everyone should have corresponding technical skills and a lot of time to spend. This work describes usage of automated source code changes classification aimed to control source code evolution. The method bases on statistical clusterization ...

  6. ADGEN: a system for automated sensitivity analysis of predictive models

    International Nuclear Information System (INIS)

    A system that can automatically enhance computer codes with a sensitivity calculation capability is presented. With this new system, named ADGEN, rapid and cost-effective calculation of sensitivities can be performed in any FORTRAN code for all input data or parameters. The resulting sensitivities can be used in performance assessment studies related to licensing or interactions with the public to systematically and quantitatively prove the relative importance of each of the system parameters in calculating the final performance results. A general procedure calling for the systematic use of sensitivities in assessment studies is presented. The procedure can be used in modelling and model validation studies to avoid ''over modelling,'' in site characterization planning to avoid ''over collection of data,'' and in performance assessment to determine the uncertainties on the final calculated results. The added capability to formally perform the inverse problem, i.e., to determine the input data or parameters on which to focus additional research or analysis effort in order to improve the uncertainty of the final results, is also discussed

  7. Determination of thymol in human plasma by automated headspace solid-phase microextraction-gas chromatographic analysis.

    Science.gov (United States)

    Kohlert, Claudia; Abel, Gudrun; Schmid, Eleonora; Veit, Markus

    2002-02-01

    A reliable and sensitive method was developed for determination of thymol in human plasma by automated headspace solid-phase microextraction (SPME). After enzymatic cleavage of thymol sulfate thymol was extracted by a 65 microm polydimethylsiloxane-divinylbenzene crimped fiber (Supelco) after addition of sodium chloride and phosphoric acid (85%). Desorption of the fiber was performed in the injection port of a gas chromatograph at 220 degrees C (HP 5890; 50 m x 0.2 mm I.D., 0.2 microm HP Innowax capillary column; flame ionization detection). Fibers were used repeatedly up to 40 analysis. The recovery was 5% after 35 min of extraction. The calibration curve was linear in the range of 8.1-203.5 ng ml(-1) with a limit of quantitation (LOQ) of 8.1 ng ml(-1). The within-day and between-day precision and accuracy were thymol-containing herbal extract only thymol sulfate, no free thymol, could be detected in human plasma, thus analysis of thymol was after enzymatic cleavage of thymol sulfate. It is concluded that the newly developed automated method can be used in clinical trials on bioavailability and pharmacokinetics of thymol-containing herbal medicinal products. PMID:11863281

  8. Automated segmentation and dose-volume analysis with DICOMautomaton

    Science.gov (United States)

    Clark, H.; Thomas, S.; Moiseenko, V.; Lee, R.; Gill, B.; Duzenli, C.; Wu, J.

    2014-03-01

    Purpose: Exploration of historical data for regional organ dose sensitivity is limited by the effort needed to (sub-)segment large numbers of contours. A system has been developed which can rapidly perform autonomous contour sub-segmentation and generic dose-volume computations, substantially reducing the effort required for exploratory analyses. Methods: A contour-centric approach is taken which enables lossless, reversible segmentation and dramatically reduces computation time compared with voxel-centric approaches. Segmentation can be specified on a per-contour, per-organ, or per-patient basis, and can be performed along either an embedded plane or in terms of the contour's bounds (e.g., split organ into fractional-volume/dose pieces along any 3D unit vector). More complex segmentation techniques are available. Anonymized data from 60 head-and-neck cancer patients were used to compare dose-volume computations with Varian's EclipseTM (Varian Medical Systems, Inc.). Results: Mean doses and Dose-volume-histograms computed agree strongly with Varian's EclipseTM. Contours which have been segmented can be injected back into patient data permanently and in a Digital Imaging and Communication in Medicine (DICOM)-conforming manner. Lossless segmentation persists across such injection, and remains fully reversible. Conclusions: DICOMautomaton allows researchers to rapidly, accurately, and autonomously segment large amounts of data into intricate structures suitable for analyses of regional organ dose sensitivity.

  9. Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples.

    Science.gov (United States)

    Witt, Sebastian; Neumann, Jan; Zierdt, Holger; Gébel, Gabriella; Röscheisen, Christiane

    2012-09-01

    Automated systems have been increasingly utilized for DNA extraction by many forensic laboratories to handle growing numbers of forensic casework samples while minimizing the risk of human errors and assuring high reproducibility. The step towards automation however is not easy: The automated extraction method has to be very versatile to reliably prepare high yields of pure genomic DNA from a broad variety of sample types on different carrier materials. To prevent possible cross-contamination of samples or the loss of DNA, the components of the kit have to be designed in a way that allows for the automated handling of the samples with no manual intervention necessary. DNA extraction using paramagnetic particles coated with a DNA-binding surface is predestined for an automated approach. For this study, we tested different DNA extraction kits using DNA-binding paramagnetic particles with regard to DNA yield and handling by a Freedom EVO(®)150 extraction robot (Tecan) equipped with a Te-MagS magnetic separator. Among others, the extraction kits tested were the ChargeSwitch(®)Forensic DNA Purification Kit (Invitrogen), the PrepFiler™Automated Forensic DNA Extraction Kit (Applied Biosystems) and NucleoMag™96 Trace (Macherey-Nagel). After an extensive test phase, we established a novel magnetic bead extraction method based upon the NucleoMag™ extraction kit (Macherey-Nagel). The new method is readily automatable and produces high yields of DNA from different sample types (blood, saliva, sperm, contact stains) on various substrates (filter paper, swabs, cigarette butts) with no evidence of a loss of magnetic beads or sample cross-contamination.

  10. Arsenic fractionation in agricultural soil using an automated three-step sequential extraction method coupled to hydride generation-atomic fluorescence spectrometry

    International Nuclear Information System (INIS)

    Highlights: • A fully automated flow-based modified-BCR extraction method was developed to evaluate the extractable As of soil. • The MSFIA–HG-AFS system included an UV photo-oxidation step for organic species degradation. • The accuracy and precision of the proposed method were found satisfactory. • The time analysis can be reduced up to eight times by using the proposed flow-based BCR method. • The labile As (F1 + F2) was <50% of total As in soil samples from As-contaminated-mining zones. - Abstract: A fully automated modified three-step BCR flow-through sequential extraction method was developed for the fractionation of the arsenic (As) content from agricultural soil based on a multi-syringe flow injection analysis (MSFIA) system coupled to hydride generation-atomic fluorescence spectrometry (HG-AFS). Critical parameters that affect the performance of the automated system were optimized by exploiting a multivariate approach using a Doehlert design. The validation of the flow-based modified-BCR method was carried out by comparison with the conventional BCR method. Thus, the total As content was determined in the following three fractions: fraction 1 (F1), the acid-soluble or interchangeable fraction; fraction 2 (F2), the reducible fraction; and fraction 3 (F3), the oxidizable fraction. The limits of detection (LOD) were 4.0, 3.4, and 23.6 μg L−1 for F1, F2, and F3, respectively. A wide working concentration range was obtained for the analysis of each fraction, i.e., 0.013–0.800, 0.011–0.900 and 0.079–1.400 mg L−1 for F1, F2, and F3, respectively. The precision of the automated MSFIA–HG-AFS system, expressed as the relative standard deviation (RSD), was evaluated for a 200 μg L−1 As standard solution, and RSD values between 5 and 8% were achieved for the three BCR fractions. The new modified three-step BCR flow-based sequential extraction method was satisfactorily applied for arsenic fractionation in real agricultural soil samples from

  11. Arsenic fractionation in agricultural soil using an automated three-step sequential extraction method coupled to hydride generation-atomic fluorescence spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Rosas-Castor, J.M. [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico); Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Portugal, L.; Ferrer, L. [Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Guzmán-Mar, J.L.; Hernández-Ramírez, A. [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico); Cerdà, V. [Group of Analytical Chemistry, Automation and Environment, University of Balearic Islands, Cra. Valldemossa km 7.5, 07122 Palma de Mallorca (Spain); Hinojosa-Reyes, L., E-mail: laura.hinojosary@uanl.edu.mx [Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, C.P. 66451 Nuevo León (Mexico)

    2015-05-18

    Highlights: • A fully automated flow-based modified-BCR extraction method was developed to evaluate the extractable As of soil. • The MSFIA–HG-AFS system included an UV photo-oxidation step for organic species degradation. • The accuracy and precision of the proposed method were found satisfactory. • The time analysis can be reduced up to eight times by using the proposed flow-based BCR method. • The labile As (F1 + F2) was <50% of total As in soil samples from As-contaminated-mining zones. - Abstract: A fully automated modified three-step BCR flow-through sequential extraction method was developed for the fractionation of the arsenic (As) content from agricultural soil based on a multi-syringe flow injection analysis (MSFIA) system coupled to hydride generation-atomic fluorescence spectrometry (HG-AFS). Critical parameters that affect the performance of the automated system were optimized by exploiting a multivariate approach using a Doehlert design. The validation of the flow-based modified-BCR method was carried out by comparison with the conventional BCR method. Thus, the total As content was determined in the following three fractions: fraction 1 (F1), the acid-soluble or interchangeable fraction; fraction 2 (F2), the reducible fraction; and fraction 3 (F3), the oxidizable fraction. The limits of detection (LOD) were 4.0, 3.4, and 23.6 μg L{sup −1} for F1, F2, and F3, respectively. A wide working concentration range was obtained for the analysis of each fraction, i.e., 0.013–0.800, 0.011–0.900 and 0.079–1.400 mg L{sup −1} for F1, F2, and F3, respectively. The precision of the automated MSFIA–HG-AFS system, expressed as the relative standard deviation (RSD), was evaluated for a 200 μg L{sup −1} As standard solution, and RSD values between 5 and 8% were achieved for the three BCR fractions. The new modified three-step BCR flow-based sequential extraction method was satisfactorily applied for arsenic fractionation in real agricultural

  12. Automated validation of patient safety clinical incident classification: macro analysis.

    Science.gov (United States)

    Gupta, Jaiprakash; Patrick, Jon

    2013-01-01

    Patient safety is the buzz word in healthcare. Incident Information Management System (IIMS) is electronic software that stores clinical mishaps narratives in places where patients are treated. It is estimated that in one state alone over one million electronic text documents are available in IIMS. In this paper we investigate the data density available in the fields entered to notify an incident and the validity of the built in classification used by clinician to categories the incidents. Waikato Environment for Knowledge Analysis (WEKA) software was used to test the classes. Four statistical classifier based on J48, Naïve Bayes (NB), Naïve Bayes Multinominal (NBM) and Support Vector Machine using radial basis function (SVM_RBF) algorithms were used to validate the classes. The data pool was 10,000 clinical incidents drawn from 7 hospitals in one state in Australia. In first part of the study 1000 clinical incidents were selected to determine type and number of fields worth investigating and in the second part another 5448 clinical incidents were randomly selected to validate 13 clinical incident types. Result shows 74.6% of the cells were empty and only 23 fields had content over 70% of the time. The percentage correctly classified classes on four algorithms using categorical dataset ranged from 42 to 49%, using free-text datasets from 65% to 77% and using both datasets from 72% to 79%. Kappa statistic ranged from 0.36 to 0.4. for categorical data, from 0.61 to 0.74. for free-text and from 0.67 to 0.77 for both datasets. Similar increases in performance in the 3 experiments was noted on true positive rate, precision, F-measure and area under curve (AUC) of receiver operating characteristics (ROC) scores. The study demonstrates only 14 of 73 fields in IIMS have data that is usable for machine learning experiments. Irrespective of the type of algorithms used when all datasets are used performance was better. Classifier NBM showed best performance. We think the

  13. An automated method for assessing routine radiographs of patients with total hip replacements.

    Science.gov (United States)

    Redhead, A L; Kotcheff, A C; Taylor, C J; Porter, M L; Hukins, D W

    1997-01-01

    This paper describes a new, fully automated method of locating objects on radiographs of patients with total joint replacements (TJRs). A statistical computer model, known as an active shape model, was trained to identify the position of the femur, pelvis, stem and cup marker wire on radiographs of patients with Charnley total hip prostheses. Once trained, the model was able to locate these objects through a process of automatic image searching, despite their appearance depending on the orientation and anatomy of the patient. Experiments were carried out to test the accuracy with which the model was able to fit to previously unseen data and with which reference points could be calculated from the model points. The model was able to locate the femur and stem with a mean error of approximately 0.8 mm and a 95 per cent confidence limit of 1.7 mm. Once the model had successfully located these objects, the midpoint of the stem head could be calculated with a mean error of approximately 0.2 mm. Although the model has been trained on Charnley total hip replacements, the method is generic and so can be applied to radiographs of patients with any TJR. This paper shows that computer models can form the basis of a quick, automatic method of taking measurements from standard clinical radiographs.

  14. Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman's Sleep at Home.

    Science.gov (United States)

    Nishihara, Kyoko; Ohki, Noboru; Kamata, Hideo; Ryo, Eiji; Horiuchi, Shigeko

    2015-01-01

    Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I). We will also demonstrate an appropriate way to use the system (Experiment II). In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK) including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy.

  15. Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman's Sleep at Home.

    Directory of Open Access Journals (Sweden)

    Kyoko Nishihara

    Full Text Available Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I. We will also demonstrate an appropriate way to use the system (Experiment II. In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy.

  16. Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and considerations for experimental design.

    Science.gov (United States)

    Zeidler-Erdely, Patti C; Antonini, James M; Meighan, Terence G; Young, Shih-Houng; Eye, Tracy J; Hammer, Mary Ann; Erdely, Aaron

    2016-08-01

    Pulmonary toxicity studies often use bronchoalveolar lavage (BAL) to investigate potential adverse lung responses to a particulate exposure. The BAL cellular fraction is counted, using automated (i.e. Coulter Counter®), flow cytometry or manual (i.e. hemocytometer) methods, to determine inflammatory cell influx. The goal of the study was to compare the different counting methods to determine which is optimal for examining BAL cell influx after exposure by inhalation or intratracheal instillation (ITI) to different particles with varying inherent pulmonary toxicities in both rat and mouse models. General findings indicate that total BAL cell counts using the automated and manual methods tended to agree after inhalation or ITI exposure to particle samples that are relatively nontoxic or at later time points after exposure to a pneumotoxic particle when the response resolves. However, when the initial lung inflammation and cytotoxicity was high after exposure to a pneumotoxic particle, significant differences were observed when comparing cell counts from the automated, flow cytometry and manual methods. When using total BAL cell count for differential calculations from the automated method, depending on the cell diameter size range cutoff, the data suggest that the number of lung polymorphonuclear leukocytes (PMN) varies. Importantly, the automated counts, regardless of the size cutoff, still indicated a greater number of total lung PMN when compared with the manual method, which agreed more closely with flow cytometry. The results suggest that either the manual method or flow cytometry would be better suited for BAL studies where cytotoxicity is an unknown variable. PMID:27251196

  17. Optimization of RNA Purification and Analysis for Automated, Pre-Symptomatic Disease Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Vaidya, A; Nasarabadi, S; Milanovich, F

    2005-06-28

    When diagnosing disease, time is often a more formidable enemy than the pathogen itself. Current detection methods rely primarily on post-symptomatic protein production (i.e. antibodies), which does not occur in noticeable levels until several weeks after infection. As such, a major goal among researchers today is to expedite pre-symptomatic disease recognition and treatment. Since most pathogens are known to leave a unique signature on the genetic expression of the host, one potential diagnostic tool is host mRNA. In my experiments, I examined several methods of isolating RNA and reading its genetic sequence. I first used two types of reverse transcriptase polymerase chain reactions (using commercial RNA) and examined the resultant complementary DNA through gel electrophoresis. I then proceeded to isolate and purify whole RNA from actual human monocytes and THP-1 cells using several published methods, and examined gene expression on the RNA itself. I compared the two RT-PCR methods and concluded that a double step RT-PCR is superior to the single step method. I also compared the various techniques of RNA isolation by examining the yield and purity of the resultant RNA. Finally, I studied the level of cellular IL-8 and IL-1 gene expression, two genes involved in the human immune response, which can serve as a baseline for future genetic comparison with LPS-exposed cells. Based on the results, I have determined which conditions and procedures are optimal for RNA isolation, RT-PCR, and RNA yield assessment. The overall goal of my research is to develop a flow-through system of RNA analysis, whereby blood samples can be collected and analyzed for disease prior to the onset of symptoms. The Pathomics group hopes to automate this process by removing the human labor factor, thereby decreasing the procedure's cost and increasing its availability to the general population. Eventually, our aim is to have an autonomous diagnostic system based on RNA analysis that would

  18. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image.

  19. Automated Image Analysis for the Detection of Benthic Crustaceans and Bacterial Mat Coverage Using the VENUS Undersea Cabled Network

    Directory of Open Access Journals (Sweden)

    Jacopo Aguzzi

    2011-11-01

    Coverage and Fractal Dimension. A constant Region of Interest (ROI was defined and background extraction by a Gaussian Blurring Filter was performed. Image subtraction within ROI was followed by the sum of the RGB channels matrices. Percent Coverage was calculated on the resulting image. Fractal Dimension was estimated using the box-counting method. The images were then resized to a dimension in pixels equal to a power of 2, allowing subdivision into sub-multiple quadrants. In comparisons of manual and automated Percent Coverage and Fractal Dimension estimates, the former showed an overestimation tendency for both parameters. The primary limitations on the automatic analysis of benthic images were habitat variations in sediment texture and water column turbidity. The application of filters for background corrections is a required preliminary step for the efficient recognition of animals and bacterial mat patches.

  20. Methods for semi-automated indexing for high precision information retrieval

    Science.gov (United States)

    Berrios, Daniel C.; Cucina, Russell J.; Fagan, Lawrence M.

    2002-01-01

    OBJECTIVE: To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. DESIGN: Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. PARTICIPANTS: Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. MEASUREMENTS: Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. RESULTS: Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). SUMMARY: Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

  1. Method 349.0 Determination of Ammonia in Estuarine and Coastal Waters by Gas Segmented Continuous Flow Colorimetric Analysis

    Science.gov (United States)

    This method provides a procedure for the determination of ammonia in estuarine and coastal waters. The method is based upon the indophenol reaction,1-5 here adapted to automated gas-segmented continuous flow analysis.

  2. SU-E-J-252: Reproducibility of Radiogenomic Image Features: Comparison of Two Semi-Automated Segmentation Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lee, M; Woo, B; Kim, J [Seoul National University, Seoul (Korea, Republic of); Jamshidi, N; Kuo, M [UCLA School of Medicine, Los Angeles, CA (United States)

    2015-06-15

    Purpose: Objective and reliable quantification of imaging phenotype is an essential part of radiogenomic studies. We compared the reproducibility of two semi-automatic segmentation methods for quantitative image phenotyping in magnetic resonance imaging (MRI) of glioblastoma multiforme (GBM). Methods: MRI examinations with T1 post-gadolinium and FLAIR sequences of 10 GBM patients were downloaded from the Cancer Image Archive site. Two semi-automatic segmentation tools with different algorithms (deformable model and grow cut method) were used to segment contrast enhancement, necrosis and edema regions by two independent observers. A total of 21 imaging features consisting of area and edge groups were extracted automatically from the segmented tumor. The inter-observer variability and coefficient of variation (COV) were calculated to evaluate the reproducibility. Results: Inter-observer correlations and coefficient of variation of imaging features with the deformable model ranged from 0.953 to 0.999 and 2.1% to 9.2%, respectively, and the grow cut method ranged from 0.799 to 0.976 and 3.5% to 26.6%, respectively. Coefficient of variation for especially important features which were previously reported as predictive of patient survival were: 3.4% with deformable model and 7.4% with grow cut method for the proportion of contrast enhanced tumor region; 5.5% with deformable model and 25.7% with grow cut method for the proportion of necrosis; and 2.1% with deformable model and 4.4% with grow cut method for edge sharpness of tumor on CE-T1W1. Conclusion: Comparison of two semi-automated tumor segmentation techniques shows reliable image feature extraction for radiogenomic analysis of GBM patients with multiparametric Brain MRI.

  3. AGAPE (Automated Genome Analysis PipelinE for pan-genome analysis of Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Giltae Song

    Full Text Available The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

  4. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

    Science.gov (United States)

    Song, Giltae; Dickins, Benjamin J A; Demeter, Janos; Engel, Stacia; Gallagher, Jennifer; Choe, Kisurb; Dunn, Barbara; Snyder, Michael; Cherry, J Michael

    2015-01-01

    The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.

  5. Analysis of Complexity Evolution Management and Human Performance Issues in Commercial Aircraft Automation Systems

    Science.gov (United States)

    Vakil, Sanjay S.; Hansman, R. John

    2000-01-01

    Autoflight systems in the current generation of aircraft have been implicated in several recent incidents and accidents. A contributory aspect to these incidents may be the manner in which aircraft transition between differing behaviours or 'modes.' The current state of aircraft automation was investigated and the incremental development of the autoflight system was tracked through a set of aircraft to gain insight into how these systems developed. This process appears to have resulted in a system without a consistent global representation. In order to evaluate and examine autoflight systems, a 'Hybrid Automation Representation' (HAR) was developed. This representation was used to examine several specific problems known to exist in aircraft systems. Cyclomatic complexity is an analysis tool from computer science which counts the number of linearly independent paths through a program graph. This approach was extended to examine autoflight mode transitions modelled with the HAR. A survey was conducted of pilots to identify those autoflight mode transitions which airline pilots find difficult. The transitions identified in this survey were analyzed using cyclomatic complexity to gain insight into the apparent complexity of the autoflight system from the perspective of the pilot. Mode transitions which had been identified as complex by pilots were found to have a high cyclomatic complexity. Further examination was made into a set of specific problems identified in aircraft: the lack of a consistent representation of automation, concern regarding appropriate feedback from the automation, and the implications of physical limitations on the autoflight systems. Mode transitions involved in changing to and leveling at a new altitude were identified across multiple aircraft by numerous pilots. Where possible, evaluation and verification of the behaviour of these autoflight mode transitions was investigated via aircraft-specific high fidelity simulators. Three solution

  6. A simple and robust method for automated photometric classification of supernovae using neural networks

    CERN Document Server

    Karpenka, N V; Hobson, M P

    2012-01-01

    A method is presented for automated photometric classification of supernovae (SNe) as Type-Ia or non-Ia. A two-step approach is adopted in which: (i) the SN lightcurve flux measurements in each observing filter are fitted separately; and (ii) the fitted function parameters and their associated uncertainties, along with the number of flux measurements, the maximum-likelihood value of the fit and Bayesian evidence for the model, are used as the input feature vector to a classification neural network (NN) that outputs the probability that the SN under consideration is of Type-Ia. The method is trained and tested using data released following the SuperNova Photometric Classification Challenge (SNPCC). We consider several random divisions of the data into training and testing sets: for instance, for our sample D_1 (D_4), a total of 10% (40%) of the data are involved in training the algorithm and the remainder used for blind testing of the resulting classifier; we make no selection cuts. Assigning a canonical thres...

  7. Fully automated objective-based method for master recession curve separation.

    Science.gov (United States)

    Posavec, Kristijan; Parlov, Jelena; Nakić, Zoran

    2010-01-01

    The fully automated objective-based method for master recession curve (MRC) separation was developed by using Microsoft Excel spreadsheet and Visual Basic for Applications (VBA) code. The core of the program code is used to construct an MRC by using the adapted matching strip method (Posavec et al. 2006). Criteria for separating the MRC into two or three segments are determined from the flow-duration curve and are represented as the probable range of percent of flow rate duration. Successive separations are performed automatically on two and three MRCs using sets of percent of flow rate duration from selected ranges and an optimal separation model scenario, having the highest average coefficient of determination R(2), is selected as the most appropriate one. The resulting separated master recession curves are presented graphically, whereas the statistics are presented numerically, all in separate sheets. Examples of field data obtained from two springs in Istria, Croatia, are used to illustrate its application. The freely available Excel spreadsheet and VBA program ensures the ease of use and applicability for larger data sets. PMID:20100291

  8. Predicting the Evolution of CO2 Emissions in Bahrain with Automated Forecasting Methods

    Directory of Open Access Journals (Sweden)

    Cristiana Tudor

    2016-09-01

    Full Text Available The 2012 Doha meeting established the continuation of the Kyoto protocol, the legally-binding global agreement under which signatory countries had agreed to reduce their carbon emissions. Contrary to this assumed obligation, all G20 countries with the exception of France and the UK saw significant increases in their CO2 emissions over the last 25 years, surpassing 300% in the case of China. This paper attempts to forecast the evolution of carbon dioxide emissions in Bahrain over the 2012–2021 decade by employing seven Automated Forecasting Methods, including the exponential smoothing state space model (ETS, the Holt–Winters Model, the BATS/TBATS model, ARIMA, the structural time series model (STS, the naive model, and the neural network time series forecasting method (NNAR. Results indicate a reversal of the current decreasing trend of pollution in the country, with a point estimate of 2309 metric tons per capita at the end of 2020 and 2317 at the end of 2021, as compared to the 1934 level achieved in 2010. The country’s baseline level corresponding to year 1990 (as specified by the Doha amendment of the Kyoto protocol is approximately 25.54 metric tons per capita, which implies a maximum level of 20.96 metric tons per capita for the year 2020 (corresponding to a decrease of 18% relative to the baseline level in order for Bahrain to comply with the protocol. Our results therefore suggest that Bahrain cannot meet its assumed target.

  9. Automating the Purple Crow Lidar

    Science.gov (United States)

    Hicks, Shannon; Sica, R. J.; Argall, P. S.

    2016-06-01

    The Purple Crow LiDAR (PCL) was built to measure short and long term coupling between the lower, middle, and upper atmosphere. The initial component of my MSc. project is to automate two key elements of the PCL: the rotating liquid mercury mirror and the Zaber alignment mirror. In addition to the automation of the Zaber alignment mirror, it is also necessary to describe the mirror's movement and positioning errors. Its properties will then be added into the alignment software. Once the alignment software has been completed, we will compare the new alignment method with the previous manual procedure. This is the first among several projects that will culminate in a fully-automated lidar. Eventually, we will be able to work remotely, thereby increasing the amount of data we collect. This paper will describe the motivation for automation, the methods we propose, preliminary results for the Zaber alignment error analysis, and future work.

  10. Semi-automated calibration method for modelling of mountain permafrost evolution in Switzerland

    Science.gov (United States)

    Marmy, A.; Rajczak, J.; Delaloye, R.; Hilbich, C.; Hoelzle, M.; Kotlarski, S.; Lambiel, C.; Noetzli, J.; Phillips, M.; Salzmann, N.; Staub, B.; Hauck, C.

    2015-09-01

    Permafrost is a widespread phenomenon in the European Alps. Many important topics such as the future evolution of permafrost related to climate change and the detection of permafrost related to potential natural hazards sites are of major concern to our society. Numerical permafrost models are the only tools which facilitate the projection of the future evolution of permafrost. Due to the complexity of the processes involved and the heterogeneity of Alpine terrain, models must be carefully calibrated and results should be compared with observations at the site (borehole) scale. However, a large number of local point data are necessary to obtain a broad overview of the thermal evolution of mountain permafrost over a larger area, such as the Swiss Alps, and the site-specific model calibration of each point would be time-consuming. To face this issue, this paper presents a semi-automated calibration method using the Generalized Likelihood Uncertainty Estimation (GLUE) as implemented in a 1-D soil model (CoupModel) and applies it to six permafrost sites in the Swiss Alps prior to long-term permafrost evolution simulations. We show that this automated calibration method is able to accurately reproduce the main thermal condition characteristics with some limitations at sites with unique conditions such as 3-D air or water circulation, which have to be calibrated manually. The calibration obtained was used for RCM-based long-term simulations under the A1B climate scenario specifically downscaled at each borehole site. The projection shows general permafrost degradation with thawing at 10 m, even partially reaching 20 m depths until the end of the century, but with different timing among the sites. The degradation is more rapid at bedrock sites whereas ice-rich sites with a blocky surface cover showed a reduced sensitivity to climate change. The snow cover duration is expected to be reduced drastically (between -20 to -37 %) impacting the ground thermal regime. However

  11. Development of a System and Method for Automated Isolation of Stromal Vascular Fraction from Adipose Tissue Lipoaspirate

    Directory of Open Access Journals (Sweden)

    Swathi SundarRaj

    2015-01-01

    Full Text Available Autologous fat grafting for soft tissue reconstruction is challenged by unpredictable long-term graft survival. Fat derived stromal vascular fraction (SVF is gaining popularity in tissue reconstruction as SVF-enriched fat grafts demonstrate improved engraftment. SVF also has potential in regenerative medicine for remodeling of ischemic tissues by promoting angiogenesis. Since SVF cells do not require culture expansion, attempts are being made to develop automated devices to isolate SVF at the point of care. We report development of a closed, automated system to process up to 500 mL lipoaspirate using cell size-dependent filtration technology. The yield of SVF obtained by automated tissue digestion and filtration (1.17 ± 0.5 × 105 cells/gram was equivalent to that obtained by manual isolation (1.15 ± 0.3 × 105; p = 0.8, and the viability of the cells isolated by both methods was greater than 90%. Cell composition included CD34+CD31− adipose stromal cells, CD34+CD31+ endothelial progenitor cells, and CD34−CD31+ endothelial cells, and their relative percentages were equivalent to SVF isolated by the manual method. CFU-F capacity and expression of angiogenic factors were also comparable with the manual method, establishing proof-of-concept for fully automated SVF isolation, suitable for use in reconstructive surgeries and regenerative medicine applications.

  12. Object-based Dune Analysis: Automated dune mapping and pattern characterization for Ganges Chasma and Gale crater, Mars

    Science.gov (United States)

    Vaz, David A.; Sarmento, Pedro T. K.; Barata, Maria T.; Fenton, Lori K.; Michaels, Timothy I.

    2015-12-01

    A method that enables the automated mapping and characterization of dune fields on Mars is described. Using CTX image mosaics, the introduced Object-based Dune Analysis (OBDA) technique produces an objective and reproducible mapping of dune morphologies over extensive areas. The data set thus obtained integrates a large variety of data, allowing a simple cross-analysis of dune patterns, spectral and morphometric information, and mesoscale wind models. Two dune fields, located in Gale crater and Ganges Chasma, were used to test and validate the methodology. The segmentation of dune-related morphologies is highly efficient, reaching overall accuracies of 95%. In addition, we show that the automated segmentation of slipface traces is also possible with expected accuracies of 85-90%. A qualitative and quantitative comparison of the final outputs with photointerpretations is performed, and the precision of the directional characterization of the dune patterns is evaluated. We demonstrate a good agreement between the OBDA outputs and the photointerpreted dune morphologies, with local trend deviations below 45° for 80-95% of the mapped areas. Because the developed algorithm is tuned for the recognition of linear features from the imagery, the slipfaces of small barchans can be preferentially overlooked owing to their small extent at the spatial resolution of the CTX mosaics. Dune types composed of longer linear morphologies are much better represented, including correct mapping of secondary structures. Having proved the effectiveness and accuracy of the mapping procedure, we discuss its future applications for the improvement of dune catalogs on Mars.

  13. Automated kidney morphology measurements from ultrasound images using texture and edge analysis

    Science.gov (United States)

    Ravishankar, Hariharan; Annangi, Pavan; Washburn, Michael; Lanning, Justin

    2016-04-01

    In a typical ultrasound scan, a sonographer measures Kidney morphology to assess renal abnormalities. Kidney morphology can also help to discriminate between chronic and acute kidney failure. The caliper placements and volume measurements are often time consuming and an automated solution will help to improve accuracy, repeatability and throughput. In this work, we developed an automated Kidney morphology measurement solution from long axis Ultrasound scans. Automated kidney segmentation is challenging due to wide variability in kidney shape, size, weak contrast of the kidney boundaries and presence of strong edges like diaphragm, fat layers. To address the challenges and be able to accurately localize and detect kidney regions, we present a two-step algorithm that makes use of edge and texture information in combination with anatomical cues. First, we use an edge analysis technique to localize kidney region by matching the edge map with predefined templates. To accurately estimate the kidney morphology, we use textural information in a machine learning algorithm framework using Haar features and Gradient boosting classifier. We have tested the algorithm on 45 unseen cases and the performance against ground truth is measured by computing Dice overlap, % error in major and minor axis of kidney. The algorithm shows successful performance on 80% cases.

  14. An architecture and model for cognitive engineering simulation analysis - Application to advanced aviation automation

    Science.gov (United States)

    Corker, Kevin M.; Smith, Barry R.

    1993-01-01

    The process of designing crew stations for large-scale, complex automated systems is made difficult because of the flexibility of roles that the crew can assume, and by the rapid rate at which system designs become fixed. Modern cockpit automation frequently involves multiple layers of control and display technology in which human operators must exercise equipment in augmented, supervisory, and fully automated control modes. In this context, we maintain that effective human-centered design is dependent on adequate models of human/system performance in which representations of the equipment, the human operator(s), and the mission tasks are available to designers for manipulation and modification. The joint Army-NASA Aircrew/Aircraft Integration (A3I) Program, with its attendant Man-machine Integration Design and Analysis System (MIDAS), was initiated to meet this challenge. MIDAS provides designers with a test bed for analyzing human-system integration in an environment in which both cognitive human function and 'intelligent' machine function are described in similar terms. This distributed object-oriented simulation system, its architecture and assumptions, and our experiences from its application in advanced aviation crew stations are described.

  15. Automated High-Throughput Permethylation for Glycosylation Analysis of Biologics Using MALDI-TOF-MS.

    Science.gov (United States)

    Shubhakar, Archana; Kozak, Radoslaw P; Reiding, Karli R; Royle, Louise; Spencer, Daniel I R; Fernandes, Daryl L; Wuhrer, Manfred

    2016-09-01

    Monitoring glycoprotein therapeutics for changes in glycosylation throughout the drug's life cycle is vital, as glycans significantly modulate the stability, biological activity, serum half-life, safety, and immunogenicity. Biopharma companies are increasingly adopting Quality by Design (QbD) frameworks for measuring, optimizing, and controlling drug glycosylation. Permethylation of glycans prior to analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is a valuable tool for glycan characterization and for screening of large numbers of samples in QbD drug realization. However, the existing protocols for manual permethylation and liquid-liquid extraction (LLE) steps are labor intensive and are thus not practical for high-throughput (HT) studies. Here we present a glycan permethylation protocol, based on 96-well microplates, that has been developed into a kit suitable for HT work. The workflow is largely automated using a liquid handling robot and includes N-glycan release, enrichment of N-glycans, permethylation, and LLE. The kit has been validated according to industry analytical performance guidelines and applied to characterize biopharmaceutical samples, including IgG4 monoclonal antibodies (mAbs) and recombinant human erythropoietin (rhEPO). The HT permethylation enabled glycan characterization and relative quantitation with minimal side reactions: the MALDI-TOF-MS profiles obtained were in good agreement with hydrophilic liquid interaction chromatography (HILIC) and ultrahigh performance liquid chromatography (UHPLC) data. Automated permethylation and extraction of 96 glycan samples was achieved in less than 5 h and automated data acquisition on MALDI-TOF-MS took on average less than 1 min per sample. This automated and HT glycan preparation and permethylation showed to be convenient, fast, and reliable and can be applied for drug glycan profiling and clinical glycan biomarker studies. PMID:27479043

  16. Hyper-Cam automated calibration method for continuous hyperspectral imaging measurements

    Science.gov (United States)

    Gagnon, Jean-Philippe; Habte, Zewdu; George, Jacks; Farley, Vincent; Tremblay, Pierre; Chamberland, Martin; Romano, Joao; Rosario, Dalton

    2010-04-01

    The midwave and longwave infrared regions of the electromagnetic spectrum contain rich information which can be captured by hyperspectral sensors thus enabling enhanced detection of targets of interest. A continuous hyperspectral imaging measurement capability operated 24/7 over varying seasons and weather conditions permits the evaluation of hyperspectral imaging for detection of different types of targets in real world environments. Such a measurement site was built at Picatinny Arsenal under the Spectral and Polarimetric Imagery Collection Experiment (SPICE), where two Hyper-Cam hyperspectral imagers are installed at the Precision Armament Laboratory (PAL) and are operated autonomously since Fall of 2009. The Hyper-Cam are currently collecting a complete hyperspectral database that contains the MWIR and LWIR hyperspectral measurements of several targets under day, night, sunny, cloudy, foggy, rainy and snowy conditions. The Telops Hyper-Cam sensor is an imaging spectrometer that enables the spatial and spectral analysis capabilities using a single sensor. It is based on the Fourier-transform technology yielding high spectral resolution and enabling high accuracy radiometric calibration. It provides datacubes of up to 320x256 pixels at spectral resolutions of up to 0.25 cm-1. The MWIR version covers the 3 to 5 μm spectral range and the LWIR version covers the 8 to 12 μm spectral range. This paper describes the automated operation of the two Hyper-Cam sensors being used in the SPICE data collection. The Reveal Automation Control Software (RACS) developed collaboratively between Telops, ARDEC, and ARL enables flexible operating parameters and autonomous calibration. Under the RACS software, the Hyper-Cam sensors can autonomously calibrate itself using their internal blackbody targets, and the calibration events are initiated by user defined time intervals and on internal beamsplitter temperature monitoring. The RACS software is the first software developed for

  17. Automated quantification and analysis of facial asymmetry in children with arthritis in the temporomandibular joint

    DEFF Research Database (Denmark)

    Darvann, Tron A.; Hermann, Nuno V.; Demant, Sune;

    2011-01-01

    We present an automated method of spatially detailed 3D asymmetry quantification of face surfaces obtained in a stereophotogrammetric system, and the method was applied to a population of children with juvenile idiopathic arthritis (JIA) who have involvement of one temporomandibular joint (TMJ......). Non-rigid registration of a patient face surface to a mirrored version of the same face surface provided a spatially dense map of left-right point correspondences that were used in the asymmetry calculation. For inter-patient comparison and modeling, detailed point correspondence was obtained by non...

  18. Automated analysis of short responses in an interactive synthetic tutoring system for introductory physics

    Science.gov (United States)

    Nakamura, Christopher M.; Murphy, Sytil K.; Christel, Michael G.; Stevens, Scott M.; Zollman, Dean A.

    2016-06-01

    Computer-automated assessment of students' text responses to short-answer questions represents an important enabling technology for online learning environments. We have investigated the use of machine learning to train computer models capable of automatically classifying short-answer responses and assessed the results. Our investigations are part of a project to develop and test an interactive learning environment designed to help students learn introductory physics concepts. The system is designed around an interactive video tutoring interface. We have analyzed 9 with about 150 responses or less. We observe for 4 of the 9 automated assessment with interrater agreement of 70% or better with the human rater. This level of agreement may represent a baseline for practical utility in instruction and indicates that the method warrants further investigation for use in this type of application. Our results also suggest strategies that may be useful for writing activities and questions that are more appropriate for automated assessment. These strategies include building activities that have relatively few conceptually distinct ways of perceiving the physical behavior of relatively few physical objects. Further success in this direction may allow us to promote interactivity and better provide feedback in online learning systems. These capabilities could enable our system to function more like a real tutor.

  19. Automated multi-plug filtration cleanup for liquid chromatographic-tandem mass spectrometric pesticide multi-residue analysis in representative crop commodities.

    Science.gov (United States)

    Qin, Yuhong; Zhang, Jingru; Zhang, Yuan; Li, Fangbing; Han, Yongtao; Zou, Nan; Xu, Haowei; Qian, Meiyuan; Pan, Canping

    2016-09-01

    An automated multi-plug filtration cleanup (m-PFC) method on modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) extracts was developed. The automatic device was aimed to reduce labor-consuming manual operation workload in the cleanup steps. It could control the volume and the speed of pulling and pushing cycles accurately. In this work, m-PFC was based on multi-walled carbon nanotubes (MWCNTs) mixed with other sorbents and anhydrous magnesium sulfate (MgSO4) in a packed tip for analysis of pesticide multi-residues in crop commodities followed by liquid chromatography with tandem mass spectrometric (LC-MS/MS) detection. It was validated by analyzing 25 pesticides in six representative matrices spiked at two concentration levels of 10 and 100μg/kg. Salts, sorbents, m-PFC procedure, automated pulling and pushing volume, automated pulling speed, and pushing speed for each matrix were optimized. After optimization, two general automated m-PFC methods were introduced to relatively simple (apple, citrus fruit, peanut) and relatively complex (spinach, leek, green tea) matrices. Spike recoveries were within 83 and 108% and 1-14% RSD for most analytes in the tested matrices. Matrix-matched calibrations were performed with the coefficients of determination >0.997 between concentration levels of 10 and 1000μg/kg. The developed method was successfully applied to the determination of pesticide residues in market samples.

  20. Computer-automated multi-disciplinary analysis and design optimization of internally cooled turbine blades

    Science.gov (United States)

    Martin, Thomas Joseph

    This dissertation presents the theoretical methodology, organizational strategy, conceptual demonstration and validation of a fully automated computer program for the multi-disciplinary analysis, inverse design and optimization of convectively cooled axial gas turbine blades and vanes. Parametric computer models of the three-dimensional cooled turbine blades and vanes were developed, including the automatic generation of discretized computational grids. Several new analysis programs were written and incorporated with existing computational tools to provide computer models of the engine cycle, aero-thermodynamics, heat conduction and thermofluid physics of the internally cooled turbine blades and vanes. A generalized information transfer protocol was developed to provide the automatic mapping of geometric and boundary condition data between the parametric design tool and the numerical analysis programs. A constrained hybrid optimization algorithm controlled the overall operation of the system and guided the multi-disciplinary internal turbine cooling design process towards the objectives and constraints of engine cycle performance, aerodynamic efficiency, cooling effectiveness and turbine blade and vane durability. Several boundary element computer programs were written to solve the steady-state non-linear heat conduction equation inside the internally cooled and thermal barrier-coated turbine blades and vanes. The boundary element method (BEM) did not require grid generation inside the internally cooled turbine blades and vanes, so the parametric model was very robust. Implicit differentiations of the BEM thermal and thereto-elastic analyses were done to compute design sensitivity derivatives faster and more accurately than via explicit finite differencing. A factor of three savings of computer processing time was realized for two-dimensional thermal optimization problems, and a factor of twenty was obtained for three-dimensional thermal optimization problems

  1. A new automated NaCl based robust method for routine production of gallium-68 labeled peptides

    International Nuclear Information System (INIS)

    A new NaCl based method for preparation of gallium-68 labeled radiopharmaceuticals has been adapted for use with an automated gallium-68 generator system. The method was evaluated based on 56 preparations of [68Ga]DOTATOC and compared to a similar acetone-based approach. Advantages of the new NaCl approach include reduced preparation time (97%), and specific activity (>40 MBq nmole−1 [68Ga]DOTATOC) and is well-suited for clinical production of radiopharmaceuticals. - Highlights: ► A NaCl based automated production of Ga-68-radiopharmaceuticals is described. ► Using 5 M NaCl for pre-purification of 68Ga eliminates the need for organic solvents. ► The method provides for high efficiency, specific activity, and radiochemical purity. ► The new method eliminates the need for the quality control by gas chromatography

  2. A semi-automated method for measuring thickness and white matter integrity of the corpus callosum

    Directory of Open Access Journals (Sweden)

    S Andronikou

    2012-12-01

    Full Text Available Aim. Diseases affecting cerebral white matter may lead to left-right asymmetries and atrophy of interhemispheric connections, i.e. the corpus callosum (CC. Our aim was to describe and test a semi-automated system that divides the midline CC into a number of segments and determines thickness at each, then performs fibre tracking from these segments. Methods. Six normal female volunteers (average age 25.8 ±6.7 years and a female patient with diagnosed multiple sclerosis (age 26 years were scanned on a 3T MRI. We performed diffusion-weighted imaging in 12 directions, and calculated diffusion tensors and fractional anisotropy (FA maps from this pre-processed data. Fibre tracking from a region-of-interest encompassing the entire CC was done. This fibre data, together with FA maps and the unweighted diffusion tensor imaging (DTI image (b = 0 s/mm2, were imported into a custom tool written in MATLAB. The midline sagittal position was carefully defined by selecting multiple midline points in coronal and axial views and rotating the image volume and fibre co-ordinates accordingly. Using the customised tool, dorsal and ventral CC contours were manually drawn on the mid-sagittal FA image, initiating automated calculation of a contour midway between these manually drawn lines. The programme was designed to then divide the midline contour into a pre-selected number of segments; from each segment border, perpendicular spokes were projected until they intersected with the dorsal and ventral contours. This technique divided the CC into a pre-set amount of segments, the number of which was limited by the spatial resolution. It was decided to set the number at 40 to ensure that each segment depicted a contiguous strip of voxels across the CC from the dorsal to the ventral contour. The system allows these segments to then be used as seeds for separate fibre tracking in each cerebral hemisphere, and various parameters are automatically plotted as a function of

  3. Comparison between automated system and PCR-based method for identification and antimicrobial susceptibility profile of clinical Enterococcus spp.

    Science.gov (United States)

    Furlaneto-Maia, Luciana; Rocha, Kátia Real; Siqueira, Vera Lúcia Dias; Furlaneto, Márcia Cristina

    2014-01-01

    Enterococci are increasingly responsible for nosocomial infections worldwide. This study was undertaken to compare the identification and susceptibility profile using an automated MicrosScan system, PCR-based assay and disk diffusion assay of Enterococcus spp. We evaluated 30 clinical isolates of Enterococcus spp. Isolates were identified by MicrosScan system and PCR-based assay. The detection of antibiotic resistance genes (vancomycin, gentamicin, tetracycline and erythromycin) was also determined by PCR. Antimicrobial susceptibilities to vancomycin (30 µg), gentamicin (120 µg), tetracycline (30 µg) and erythromycin (15 µg) were tested by the automated system and disk diffusion method, and were interpreted according to the criteria recommended in CLSI guidelines. Concerning Enterococcus identification the general agreement between data obtained by the PCR method and by the automatic system was 90.0% (27/30). For all isolates of E. faecium and E. faecalis we observed 100% agreement. Resistance frequencies were higher in E. faecium than E. faecalis. The resistance rates obtained were higher for erythromycin (86.7%), vancomycin (80.0%), tetracycline (43.35) and gentamicin (33.3%). The correlation between disk diffusion and automation revealed an agreement for the majority of the antibiotics with category agreement rates of > 80%. The PCR-based assay, the van(A) gene was detected in 100% of vancomycin resistant enterococci. This assay is simple to conduct and reliable in the identification of clinically relevant enterococci. The data obtained reinforced the need for an improvement of the automated system to identify some enterococci.

  4. An automated method for generating analogic signals that embody the Markov kinetics of model ionic channels.

    Science.gov (United States)

    Luchian, Tudor

    2005-08-30

    In this work we present an automated method for generating electrical signals which reflect the kinetics of ionic channels that have custom-tailored intermediate sub-states and intermediate reaction constants. The concept of our virtual single-channel waveform generator makes use of two software platforms, one for the numerical generation of single channel traces stemming from a pre-defined model and another for the digital-to-analog conversion of such numerical generated single channel traces. This technique of continuous generation and recording of the activity of a model ionic channel provides an efficient protocol to teach neophytes in the field of single-channel electrophysiology about its major phenomenological facets. Random analogic signals generated by using our technique can be successfully employed in a number of applications, such us: assisted learning of the single-molecule kinetic investigation via electrical recordings, impedance spectroscopy, the evaluation of linear frequency response of neurons and the study of stochastic resonance of ion channels. PMID:16054511

  5. Automated methods of predicting the function of biological sequences using GO and BLAST

    Directory of Open Access Journals (Sweden)

    Baumann Ute

    2005-11-01

    Full Text Available Abstract Background With the exponential increase in genomic sequence data there is a need to develop automated approaches to deducing the biological functions of novel sequences with high accuracy. Our aim is to demonstrate how accuracy benchmarking can be used in a decision-making process evaluating competing designs of biological function predictors. We utilise the Gene Ontology, GO, a directed acyclic graph of functional terms, to annotate sequences with functional information describing their biological context. Initially we examine the effect on accuracy scores of increasing the allowed distance between predicted and a test set of curator assigned terms. Next we evaluate several annotator methods using accuracy benchmarking. Given an unannotated sequence we use the Basic Local Alignment Search Tool, BLAST, to find similar sequences that have already been assigned GO terms by curators. A number of methods were developed that utilise terms associated with the best five matching sequences. These methods were compared against a benchmark method of simply using terms associated with the best BLAST-matched sequence (best BLAST approach. Results The precision and recall of estimates increases rapidly as the amount of distance permitted between a predicted term and a correct term assignment increases. Accuracy benchmarking allows a comparison of annotation methods. A covering graph approach performs poorly, except where the term assignment rate is high. A term distance concordance approach has a similar accuracy to the best BLAST approach, demonstrating lower precision but higher recall. However, a discriminant function method has higher precision and recall than the best BLAST approach and other methods shown here. Conclusion Allowing term predictions to be counted correct if closely related to a correct term decreases the reliability of the accuracy score. As such we recommend using accuracy measures that require exact matching of predicted

  6. Computerized method for automated measurement of thickness of cerebral cortex for 3-D MR images

    Science.gov (United States)

    Arimura, Hidetaka; Yoshiura, Takashi; Kumazawa, Seiji; Koga, Hiroshi; Sakai, Shuji; Mihara, Futoshi; Honda, Hiroshi; Ohki, Masafumi; Toyofuku, Fukai; Higashida, Yoshiharu

    2006-03-01

    Alzheimer's disease (AD) is associated with the degeneration of cerebral cortex, which results in focal volume change or thinning in the cerebral cortex in magnetic resonance imaging (MRI). Therefore, the measurement of the cortical thickness is important for detection of the atrophy related to AD. Our purpose was to develop a computerized method for automated measurement of the cortical thickness for three-dimensional (3-D) MRI. The cortical thickness was measured with normal vectors from white matter surface to cortical gray matter surface on a voxel-by-voxel basis. First, a head region was segmented by use of an automatic thresholding technique, and then the head region was separated into the cranium region and brain region by means of a multiple gray level thresholding with monitoring the ratio of the first maximum volume to the second one. Next, a fine white matter region was determined based on a level set method as a seed region of the rough white matter region extracted from the brain region. Finally, the cortical thickness was measured by extending normal vectors from the white matter surface to gray matter surface (brain surface) on a voxel-by-voxel basis. We applied the computerized method to high-resolution 3-D T1-weighted images of the whole brains from 7 clinically diagnosed AD patients and 8 healthy subjects. The average cortical thicknesses in the upper slices for AD patients were thinner than those for non-AD subjects, whereas the average cortical thicknesses in the lower slices for most AD patients were slightly thinner. Our preliminary results suggest that the MRI-based computerized measurement of gray matter atrophy is promising for detecting AD.

  7. A rapid and automated relocation method of an AFM probe for high-resolution imaging

    Science.gov (United States)

    Zhou, Peilin; Yu, Haibo; Shi, Jialin; Jiao, Niandong; Wang, Zhidong; Wang, Yuechao; Liu, Lianqing

    2016-09-01

    The atomic force microscope (AFM) is one of the most powerful tools for high-resolution imaging and high-precision positioning for nanomanipulation. The selection of the scanning area of the AFM depends on the use of the optical microscope. However, the resolution of an optical microscope is generally no larger than 200 nm owing to wavelength limitations of visible light. Taking into consideration the two determinants of relocation—relative angular rotation and positional offset between the AFM probe and nano target—it is therefore extremely challenging to precisely relocate the AFM probe to the initial scan/manipulation area for the same nano target after the AFM probe has been replaced, or after the sample has been moved. In this paper, we investigate a rapid automated relocation method for the nano target of an AFM using a coordinate transformation. The relocation process is both simple and rapid; moreover, multiple nano targets can be relocated by only identifying a pair of reference points. It possesses a centimeter-scale location range and nano-scale precision. The main advantages of this method are that it overcomes the limitations associated with the resolution of optical microscopes, and that it is label-free on the target areas, which means that it does not require the use of special artificial markers on the target sample areas. Relocation experiments using nanospheres, DNA, SWCNTs, and nano patterns amply demonstrate the practicality and efficiency of the proposed method, which provides technical support for mass nanomanipulation and detection based on AFM for multiple nano targets that are widely distributed in a large area.

  8. Development and Applications of a Prototypic SCALE Control Module for Automated Burnup Credit Analysis

    International Nuclear Information System (INIS)

    Consideration of the depletion phenomena and isotopic uncertainties in burnup-credit criticality analysis places an increasing reliance on computational tools and significantly increases the overall complexity of the calculations. An automated analysis and data management capability is essential for practical implementation of large-scale burnup credit analyses that can be performed in a reasonable amount of time. STARBUCS is a new prototypic analysis sequence being developed for the SCALE code system to perform automated criticality calculations of spent fuel systems employing burnup credit. STARBUCS is designed to help analyze the dominant burnup credit phenomena including spatial burnup gradients and isotopic uncertainties. A search capability also allows STARBUCS to iterate to determine the spent fuel parameters (e.g., enrichment and burnup combinations) that result in a desired keff for a storage configuration. Although STARBUCS was developed to address the analysis needs for spent fuel transport and storage systems, it provides sufficient flexibility to allow virtually any configuration of spent fuel to be analyzed, such as storage pools and reprocessing operations. STARBUCS has been used extensively at Oak Ridge National Laboratory (ORNL) to study burnup credit phenomena in support of the NRC Research program

  9. Integrating automated structured analysis and design with Ada programming support environments

    Science.gov (United States)

    Hecht, Alan; Simmons, Andy

    1986-01-01

    Ada Programming Support Environments (APSE) include many powerful tools that address the implementation of Ada code. These tools do not address the entire software development process. Structured analysis is a methodology that addresses the creation of complete and accurate system specifications. Structured design takes a specification and derives a plan to decompose the system subcomponents, and provides heuristics to optimize the software design to minimize errors and maintenance. It can also produce the creation of useable modules. Studies have shown that most software errors result from poor system specifications, and that these errors also become more expensive to fix as the development process continues. Structured analysis and design help to uncover error in the early stages of development. The APSE tools help to insure that the code produced is correct, and aid in finding obscure coding errors. However, they do not have the capability to detect errors in specifications or to detect poor designs. An automated system for structured analysis and design TEAMWORK, which can be integrated with an APSE to support software systems development from specification through implementation is described. These tools completement each other to help developers improve quality and productivity, as well as to reduce development and maintenance costs. Complete system documentation and reusable code also resultss from the use of these tools. Integrating an APSE with automated tools for structured analysis and design provide capabilities and advantages beyond those realized with any of these systems used by themselves.

  10. Evaluation of Automated and Manual Commercial DNA Extraction Methods for Recovery of Brucella DNA from Suspensions and Spiked Swabs ▿

    OpenAIRE

    Dauphin, Leslie A.; Hutchins, Rebecca J.; Bost, Liberty A.; Bowen, Michael D.

    2009-01-01

    This study evaluated automated and manual commercial DNA extraction methods for their ability to recover DNA from Brucella species in phosphate-buffered saline (PBS) suspension and from spiked swab specimens. Six extraction methods, representing several of the methodologies which are commercially available for DNA extraction, as well as representing various throughput capacities, were evaluated: the MagNA Pure Compact and the MagNA Pure LC instruments, the IT 1-2-3 DNA sample purification kit...

  11. Two Methods for High-Throughput NGS Template Preparation for Small and Degraded Clinical Samples Without Automation

    OpenAIRE

    Kamberov, E.; Tesmer, T.; Mastronardi, M.; Langmore, John

    2012-01-01

    Clinical samples are difficult to prepare for NGS, because of the small amounts or degraded states of formalin-fixed tissue, plasma, urine, and single-cell DNA. Conventional whole genome amplification methods are too biased for NGS applications, and the existing NGS preparation kits require intermediate purifications and excessive time to prepare hundreds of samples in a day without expensive automation. We have tested two 96-well manual methods to make NGS templates from FFPE tissue, plasma,...

  12. CT导向下经皮肺胸膜外定位法自动切割活检并发症的相关因素分析%The factor analysis of the incidence of complication in CT-guided lung automated cutting needle biopsy with extrapleural locating method

    Institute of Scientific and Technical Information of China (English)

    廖美焱; 周云峰; 田志雄; 罗锐; 屈艳娟; 徐丽莹

    2010-01-01

    目的 统计CT导向下经皮肺胸膜外定位法(EPL)自动切割活检(ACNB)并发症,分析影响因素.方法 回顾性总结武汉大学中南医院2005年3月至2009年9月480例EPL法ACNB结果,对气胸、出血及咯血的相关因素行多因素非条件 Logistic 回归分析.结果 ACNB准确率95.0%,每例时间(16±2)min,活检针肺内停留时间10 mm及>20mm、伴有肺气肿及穿刺次数多出血率高,穿刺深度>20 mm咯血率高.%Objective To evaluate the complication rate and analyze its impact of multiple facts of CT-guided percutaneous lung automated cutting needle biopsies (ACNB) with extrapleural locating method (EPL).Methods Retrospective study where information was obtained from the department of medical imaging,the sign of complication after 480 cases CT-guided ACNB with EPL was observed and its relationship with multiple factors were analyzed by multiple logistic regression model.Results The diagnostic accuracy was made in 456 cages (95.0%).The length of the biopsy procedures was 16±2 min and the time of the biopsy needle in pulmonary parenchyma was 10 mm or 20 mm.emphysema and number of pleural needle passes had higher hemorrhage rates.The multivariate logistic regression analysis showed that depth of intrapulmonal biopsy path and emphysema were sole effective factors (OR=1.077,and 0.578,respectively) of hemoptysis.Lesions with depth >20 mm had higher hemoptysis rate.One cage with pulmonary Cryptococcus presented pleural reaction,and three cases had the insistent pain.The total number of severe complications was 15 (3.1%) cases.Conclusion ACNB with EPL was a accurate method for diagnosing pulmonary lesions.ACNB can be safely performed,which reduces the rate of pneumothorax and hemorrhage.Pneumothorax rate was influenced by emphysema,depth of intrapulmonal biopsy path and lesion size ≤10 mm. Hemorrhage was related with depth > 10 mm or 20 mm,emphysema and number of pleural needle passes.Hemoptysis was related with depth of

  13. A feasibility assessment of automated FISH image and signal analysis to assist cervical cancer detection

    Science.gov (United States)

    Wang, Xingwei; Li, Yuhua; Liu, Hong; Li, Shibo; Zhang, Roy R.; Zheng, Bin

    2012-02-01

    Fluorescence in situ hybridization (FISH) technology provides a promising molecular imaging tool to detect cervical cancer. Since manual FISH analysis is difficult, time-consuming, and inconsistent, the automated FISH image scanning systems have been developed. Due to limited focal depth of scanned microscopic image, a FISH-probed specimen needs to be scanned in multiple layers that generate huge image data. To improve diagnostic efficiency of using automated FISH image analysis, we developed a computer-aided detection (CAD) scheme. In this experiment, four pap-smear specimen slides were scanned by a dual-detector fluorescence image scanning system that acquired two spectrum images simultaneously, which represent images of interphase cells and FISH-probed chromosome X. During image scanning, once detecting a cell signal, system captured nine image slides by automatically adjusting optical focus. Based on the sharpness index and maximum intensity measurement, cells and FISH signals distributed in 3-D space were projected into a 2-D con-focal image. CAD scheme was applied to each con-focal image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm and detect FISH-probed signals using a top-hat transform. The ratio of abnormal cells was calculated to detect positive cases. In four scanned specimen slides, CAD generated 1676 con-focal images that depicted analyzable cells. FISH-probed signals were independently detected by our CAD algorithm and an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots. The study demonstrated the feasibility of applying automated FISH image and signal analysis to assist cyto-geneticists in detecting cervical cancers.

  14. An Automated Video Object Extraction System Based on Spatiotemporal Independent Component Analysis and Multiscale Segmentation

    Directory of Open Access Journals (Sweden)

    Zhang Xiao-Ping

    2006-01-01

    Full Text Available Video content analysis is essential for efficient and intelligent utilizations of vast multimedia databases over the Internet. In video sequences, object-based extraction techniques are important for content-based video processing in many applications. In this paper, a novel technique is developed to extract objects from video sequences based on spatiotemporal independent component analysis (stICA and multiscale analysis. The stICA is used to extract the preliminary source images containing moving objects in video sequences. The source image data obtained after stICA analysis are further processed using wavelet-based multiscale image segmentation and region detection techniques to improve the accuracy of the extracted object. An automated video object extraction system is developed based on these new techniques. Preliminary results demonstrate great potential for the new stICA and multiscale-segmentation-based object extraction system in content-based video processing applications.

  15. Computer-aided method for automated selection of optimal imaging plane for measurement of total cerebral blood flow by MRI

    Science.gov (United States)

    Teng, Pang-yu; Bagci, Ahmet Murat; Alperin, Noam

    2009-02-01

    A computer-aided method for finding an optimal imaging plane for simultaneous measurement of the arterial blood inflow through the 4 vessels leading blood to the brain by phase contrast magnetic resonance imaging is presented. The method performance is compared with manual selection by two observers. The skeletons of the 4 vessels for which centerlines are generated are first extracted. Then, a global direction of the relatively less curved internal carotid arteries is calculated to determine the main flow direction. This is then used as a reference direction to identify segments of the vertebral arteries that strongly deviates from the main flow direction. These segments are then used to identify anatomical landmarks for improved consistency of the imaging plane selection. An optimal imaging plane is then identified by finding a plane with the smallest error value, which is defined as the sum of the angles between the plane's normal and the vessel centerline's direction at the location of the intersections. Error values obtained using the automated and the manual methods were then compared using 9 magnetic resonance angiography (MRA) data sets. The automated method considerably outperformed the manual selection. The mean error value with the automated method was significantly lower than the manual method, 0.09+/-0.07 vs. 0.53+/-0.45, respectively (p<.0001, Student's t-test). Reproducibility of repeated measurements was analyzed using Bland and Altman's test, the mean 95% limits of agreements for the automated and manual method were 0.01~0.02 and 0.43~0.55 respectively.

  16. Bacterial growth on surfaces: Automated image analysis for quantification of growth rate-related parameters

    DEFF Research Database (Denmark)

    Møller, S.; Sternberg, Claus; Poulsen, L. K.;

    1995-01-01

    species-specific hybridizations with fluorescence-labelled ribosomal probes to estimate the single-cell concentration of RNA. By automated analysis of digitized images of stained cells, we determined four independent growth rate-related parameters: cellular RNA and DNA contents, cell volume......, and the frequency of dividing cells in a cell population. These parameters were used to compare physiological states of liquid-suspended and surfacegrowing Pseudomonas putida KT2442 in chemostat cultures. The major finding is that the correlation between substrate availability and cellular growth rate found...

  17. Analysis of Automated Modern Web Crawling and Testing Tools and Their Possible Employment for Information Extraction

    Directory of Open Access Journals (Sweden)

    Tomas Grigalis

    2012-04-01

    Full Text Available World Wide Web has become an enormously big repository of data. Extracting, integrating and reusing this kind of data has a wide range of applications, including meta-searching, comparison shopping, business intelligence tools and security analysis of information in websites. However, reaching information in modern WEB 2.0 web pages, where HTML tree is often dynamically modified by various JavaScript codes, new data are added by asynchronous requests to the web server and elements are positioned with the help of cascading style sheets, is a difficult task. The article reviews automated web testing tools for information extraction tasks.Article in Lithuanian

  18. Automated Static Culture System Cell Module Mixing Protocol and Computational Fluid Dynamics Analysis

    Science.gov (United States)

    Kleis, Stanley J.; Truong, Tuan; Goodwin, Thomas J,

    2004-01-01

    This report is a documentation of a fluid dynamic analysis of the proposed Automated Static Culture System (ASCS) cell module mixing protocol. The report consists of a review of some basic fluid dynamics principles appropriate for the mixing of a patch of high oxygen content media into the surrounding media which is initially depleted of oxygen, followed by a computational fluid dynamics (CFD) study of this process for the proposed protocol over a range of the governing parameters. The time histories of oxygen concentration distributions and mechanical shear levels generated are used to characterize the mixing process for different parameter values.

  19. Software Tool for Automated Failure Modes and Effects Analysis (FMEA) of Hydraulic Systems

    DEFF Research Database (Denmark)

    Stecki, J. S.; Conrad, Finn; Oh, B.

    2002-01-01

    management techniques and a vast array of computer aided techniques are applied during design and testing stages. The paper present and discusses the research and development of a software tool for automated failure mode and effects analysis - FMEA - of hydraulic systems. The paper explains the underlying......Offshore, marine,aircraft and other complex engineering systems operate in harsh environmental and operational conditions and must meet stringent requirements of reliability, safety and maintability. To reduce the hight costs of development of new systems in these fields improved the design...

  20. Failure mode and effect analysis oriented to risk-reduction interventions in intraoperative electron radiation therapy: The specific impact of patient transportation, automation, and treatment planning availability

    International Nuclear Information System (INIS)

    Background and purpose: Industrial companies use failure mode and effect analysis (FMEA) to improve quality. Our objective was to describe an FMEA and subsequent interventions for an automated intraoperative electron radiotherapy (IOERT) procedure with computed tomography simulation, pre-planning, and a fixed conventional linear accelerator. Material and methods: A process map, an FMEA, and a fault tree analysis are reported. The equipment considered was the radiance treatment planning system (TPS), the Elekta Precise linac, and TN-502RDM-H metal–oxide-semiconductor-field-effect transistor in vivo dosimeters. Computerized order-entry and treatment-automation were also analyzed. Results: Fifty-seven potential modes and effects were identified and classified into ‘treatment cancellation’ and ‘delivering an unintended dose’. They were graded from ‘inconvenience’ or ‘suboptimal treatment’ to ‘total cancellation’ or ‘potentially wrong’ or ‘very wrong administered dose’, although these latter effects were never experienced. Risk priority numbers (RPNs) ranged from 3 to 324 and totaled 4804. After interventions such as double checking, interlocking, automation, and structural changes the final total RPN was reduced to 1320. Conclusions: FMEA is crucial for prioritizing risk-reduction interventions. In a semi-surgical procedure like IOERT double checking has the potential to reduce risk and improve quality. Interlocks and automation should also be implemented to increase the safety of the procedure