Science.gov

Sample records for automated sampling assessment

  1. Reference values for performance on the Automated Neuropsychological Assessment Metrics V3.0 in an active duty military sample.

    PubMed

    Reeves, Dennis L; Bleiberg, Joseph; Roebuck-Spencer, Tresa; Cernich, Alison N; Schwab, Karen; Ivins, Brian; Salazar, Andres M; Harvey, Sally C; Brown, Fred H; Warden, Deborah

    2006-10-01

    The Automated Neuropsychological Assessment Metrics (ANAM) is a computerized measure of processing speed, cognitive efficiency, and memory. This study describes performance and psychometric properties of ANAM in an active duty, healthy military sample (N = 2,371) composed primarily of young (18-46 years) adult males. Rarely have neuropsychological reference values for use with individuals in the military been derived from a large, active duty military population, and this is the first computerized neuropsychological test battery with military-specific reference values. Although these results do not provide demographically corrected, formal normative data, they provide reference points for neuropsychologists and other health care providers who are using ANAM data in research or clinical settings, with patients of comparable demographics to the present sample.

  2. AUTOMATING GROUNDWATER SAMPLING AT HANFORD

    SciTech Connect

    CONNELL CW; HILDEBRAND RD; CONLEY SF; CUNNINGHAM DE

    2009-01-16

    Until this past October, Fluor Hanford managed Hanford's integrated groundwater program for the U.S. Department of Energy (DOE). With the new contract awards at the Site, however, the CH2M HILL Plateau Remediation Company (CHPRC) has assumed responsibility for the groundwater-monitoring programs at the 586-square-mile reservation in southeastern Washington State. These programs are regulated by the Resource Conservation and Recovery Act (RCRA) and the Comprehensive Environmental Response Compensation and Liability Act (CERCLA). The purpose of monitoring is to track existing groundwater contamination from past practices, as well as other potential contamination that might originate from RCRA treatment, storage, and disposal (TSD) facilities. An integral part of the groundwater-monitoring program involves taking samples of the groundwater and measuring the water levels in wells scattered across the site. More than 1,200 wells are sampled each year. Historically, field personnel or 'samplers' have been issued pre-printed forms that have information about the well(s) for a particular sampling evolution. This information is taken from the Hanford Well Information System (HWIS) and the Hanford Environmental Information System (HEIS)--official electronic databases. The samplers used these hardcopy forms to document the groundwater samples and well water-levels. After recording the entries in the field, the samplers turned the forms in at the end of the day and the collected information was posted onto a spreadsheet that was then printed and included in a log book. The log book was then used to make manual entries of the new information into the software application(s) for the HEIS and HWIS databases. This is a pilot project for automating this tedious process by providing an electronic tool for automating water-level measurements and groundwater field-sampling activities. The automation will eliminate the manual forms and associated data entry, improve the accuracy of the

  3. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT ...

    EPA Pesticide Factsheets

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execution of the Soil Water Assessment Tool (SWAT) and KINEmatic Runoff and EROSion (KINEROS2) hydrologic models. The application of these two models allows AGWA to conduct hydrologic modeling and watershed assessments at multiple temporal and spatial scales. AGWA’s current outputs are runoff (volumes and peaks) and sediment yield, plus nitrogen and phosphorus with the SWAT model. AGWA uses commonly available GIS data layers to fully parameterize, execute, and visualize results from both models. Through an intuitive interface the user selects an outlet from which AGWA delineates and discretizes the watershed using a Digital Elevation Model (DEM) based on the individual model requirements. The watershed model elements are then intersected with soils and land cover data layers to derive the requisite model input parameters. The chosen model is then executed, and the results are imported back into AGWA for visualization. This allows managers to identify potential problem areas where additional monitoring can be undertaken or mitigation activities can be focused. AGWA also has tools to apply an array of best management practices. There are currently two versions of AGWA available; AGWA 1.5 for

  4. Water-quality assessment of south-central Texas : comparison of water quality in surface-water samples collected manually and by automated samplers

    USGS Publications Warehouse

    Ging, Patricia B.

    1999-01-01

    Surface-water sampling protocols of the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program specify samples for most properties and constituents to be collected manually in equal-width increments across a stream channel and composited for analysis. Single-point sampling with an automated sampler (autosampler) during storms was proposed in the upper part of the South-Central Texas NAWQA study unit, raising the question of whether property and constituent concentrations from automatically collected samples differ significantly from those in samples collected manually. Statistical (Wilcoxon signed-rank test) analyses of 3 to 16 paired concentrations for each of 26 properties and constituents from water samples collected using both methods at eight sites in the upper part of the study unit indicated that there were no significant differences in concentrations for dissolved constituents, other than calcium and organic carbon.

  5. Continuous Monitoring, Automated Analyses, and Sampling Procedures.

    ERIC Educational Resources Information Center

    Hensley, C. P.; And Others

    1978-01-01

    Presents water analysis literature, covering publications of 1976-77. This series covers: (1) monitoring strategies and sampling protocols; (2) continuous monitoring applications; (3) biological monitoring systems; and (4) automated analysis. A list of 57 references is also presented. (HM)

  6. Automated microorganism Sample Collection Module

    NASA Technical Reports Server (NTRS)

    Gall, L. S.; Graham, M. D.; Umbreit, W.

    1969-01-01

    Modified Gelman Sampler obtains representative sample of microorganism population. Proposed Sample Collection Module is based on direct inoculation of selected solid growth media encased in a cartridge at all times except during inoculation. Cartridge can be handled with no danger of contamination to sample or operator.

  7. Automated Chromosome Breakage Assessment

    NASA Technical Reports Server (NTRS)

    Castleman, Kenneth

    1985-01-01

    An automated karyotyping machine was built at JPL in 1972. It does computerized karyotyping, but it has some hardware limitations. The image processing hardware that was available at a reasonable price in 1972 was marginal, at best, for this job. In the meantime, NASA has developed an interest in longer term spaceflights and an interest in using chromosome breakage studies as a dosimeter for radiation or perhaps other damage that might occur to the tissues. This uses circulating lymphocytes as a physiological dosimeter looking for chromosome breakage on long-term spaceflights. For that reason, we have reactivated the automated karyotyping work at JPL. An update on that work, and a description of where it appears to be headed is presented.

  8. Automated Chromosome Breakage Assessment

    NASA Technical Reports Server (NTRS)

    Castleman, Kenneth

    1985-01-01

    An automated karyotyping machine was built at JPL in 1972. It does computerized karyotyping, but it has some hardware limitations. The image processing hardware that was available at a reasonable price in 1972 was marginal, at best, for this job. In the meantime, NASA has developed an interest in longer term spaceflights and an interest in using chromosome breakage studies as a dosimeter for radiation or perhaps other damage that might occur to the tissues. This uses circulating lymphocytes as a physiological dosimeter looking for chromosome breakage on long-term spaceflights. For that reason, we have reactivated the automated karyotyping work at JPL. An update on that work, and a description of where it appears to be headed is presented.

  9. Technology modernization assessment flexible automation

    SciTech Connect

    Bennett, D.W.; Boyd, D.R.; Hansen, N.H.; Hansen, M.A.; Yount, J.A.

    1990-12-01

    The objectives of this report are: to present technology assessment guidelines to be considered in conjunction with defense regulations before an automation project is developed to give examples showing how assessment guidelines may be applied to a current project to present several potential areas where automation might be applied successfully in the depot system. Depots perform primarily repair and remanufacturing operations, with limited small batch manufacturing runs. While certain activities (such as Management Information Systems and warehousing) are directly applicable to either environment, the majority of applications will require combining existing and emerging technologies in different ways, with the special needs of depot remanufacturing environment. Industry generally enjoys the ability to make revisions to its product lines seasonally, followed by batch runs of thousands or more. Depot batch runs are in the tens, at best the hundreds, of parts with a potential for large variation in product mix; reconfiguration may be required on a week-to-week basis. This need for a higher degree of flexibility suggests a higher level of operator interaction, and, in turn, control systems that go beyond the state of the art for less flexible automation and industry in general. This report investigates the benefits and barriers to automation and concludes that, while significant benefits do exist for automation, depots must be prepared to carefully investigate the technical feasibility of each opportunity and the life-cycle costs associated with implementation. Implementation is suggested in two ways: (1) develop an implementation plan for automation technologies based on results of small demonstration automation projects; (2) use phased implementation for both these and later stage automation projects to allow major technical and administrative risk issues to be addressed. 10 refs., 2 figs., 2 tabs. (JF)

  10. Automated sample preparation for CE-SDS.

    PubMed

    Le, M Eleanor; Vizel, Alona; Hutterer, Katariina M

    2013-05-01

    Traditionally, CE with SDS (CE-SDS) places many restrictions on sample composition. Requirements include low salt content, known initial sample concentration, and a narrow window of final sample concentration. As these restrictions require buffer exchange for many sample types, sample preparation is often tedious and yields poor sample recoveries. To improve capacity and streamline sample preparation, an automated robotic platform was developed using the PhyNexus Micro-Extractor Automated Instrument (MEA) for both the reduced and nonreduced CE-SDS assays. This automated sample preparation normalizes sample concentration, removes salts and other contaminants, and adds the required CE-SDS reagents, essentially eliminating manual steps during sample preparation. Fc-fusion proteins and monoclonal antibodies were used in this work to demonstrate benefits of this approach when compared to the manual method. With optimized conditions, this application has demonstrated decreased analyst "hands on" time and reduced total assay time. Sample recovery greater than 90% can be achieved, regardless of initial composition and concentration of analyte.

  11. Automated storm water sampling on small watersheds

    USGS Publications Warehouse

    Harmel, R.D.; King, K.W.; Slade, R.M.

    2003-01-01

    Few guidelines are currently available to assist in designing appropriate automated storm water sampling strategies for small watersheds. Therefore, guidance is needed to develop strategies that achieve an appropriate balance between accurate characterization of storm water quality and loads and limitations of budget, equipment, and personnel. In this article, we explore the important sampling strategy components (minimum flow threshold, sampling interval, and discrete versus composite sampling) and project-specific considerations (sampling goal, sampling and analysis resources, and watershed characteristics) based on personal experiences and pertinent field and analytical studies. These components and considerations are important in achieving the balance between sampling goals and limitations because they determine how and when samples are taken and the potential sampling error. Several general recommendations are made, including: setting low minimum flow thresholds, using flow-interval or variable time-interval sampling, and using composite sampling to limit the number of samples collected. Guidelines are presented to aid in selection of an appropriate sampling strategy based on user's project-specific considerations. Our experiences suggest these recommendations should allow implementation of a successful sampling strategy for most small watershed sampling projects with common sampling goals.

  12. Automated Sample Deoxygenation for Improved Luminescence Measurements.

    DTIC Science & Technology

    1986-11-25

    fET-AY4 732 AUTOMATED SAMPLE DEOXYGENATION FOR IMPROVED LUMINESCENCE MEASUREMENTS U) EMORY UNIV RTLANTA GA DEPT OF CHEMISTRY M E ROLLIE ET AL 25 NOV... Deoxygenation for Improved Luminescence Measurements 12 PERSONAL AUTHOR(S) | ,Rollie, M.E.; Patonay, Gabor; and Warner, Isiah M. A .3a. TYPE OF REPORT...GROUP ISU*GRO P ,,,uminescence Spectroscopy; Fluorescence Analysis,* Room *f Temperature Phosphorescence; Deoxygenation ; Quenching ISTRACT (Continue on

  13. Black tea volatiles fingerprinting by comprehensive two-dimensional gas chromatography - Mass spectrometry combined with high concentration capacity sample preparation techniques: Toward a fully automated sensomic assessment.

    PubMed

    Magagna, Federico; Cordero, Chiara; Cagliero, Cecilia; Liberto, Erica; Rubiolo, Patrizia; Sgorbini, Barbara; Bicchi, Carlo

    2017-06-15

    Tea prepared by infusion of dried leaves of Camellia sinensis (L.) Kuntze, is the second world's most popular beverage, after water. Its consumption is associated with its chemical composition: it influences its sensory and nutritional quality addressing consumer preferences, and potential health benefits. This study aims to obtain an informative chemical signature of the volatile fraction of black tea samples from Ceylon by applying the principles of sensomics. In particular, several high concentration capacity (HCC) sample preparation techniques were tested in combination with GC×GC-MS to investigate chemical signatures of black tea volatiles. This platform, using headspace solid phase microextraction (HS-SPME) with multicomponent fiber as sampling technique, recovers 95% of the key-odorants in a fully automated work-flow. A group 123 components, including key-odorants, technological and botanical tracers, were mapped. The resulting 2D fingerprints were interpreted by pattern recognition tools (i.e. template matching fingerprinting and scripting) providing highly informative chemical signatures for quality assessment.

  14. Automated Assessment in Massive Open Online Courses

    ERIC Educational Resources Information Center

    Ivaniushin, Dmitrii A.; Shtennikov, Dmitrii G.; Efimchick, Eugene A.; Lyamin, Andrey V.

    2016-01-01

    This paper describes an approach to use automated assessments in online courses. Open edX platform is used as the online courses platform. The new assessment type uses Scilab as learning and solution validation tool. This approach allows to use automated individual variant generation and automated solution checks without involving the course…

  15. Precise and automated microfluidic sample preparation.

    SciTech Connect

    Crocker, Robert W.; Patel, Kamlesh D.; Mosier, Bruce P.; Harnett, Cindy K.

    2004-07-01

    Autonomous bio-chemical agent detectors require sample preparation involving multiplex fluid control. We have developed a portable microfluidic pump array for metering sub-microliter volumes at flowrates of 1-100 {micro}L/min. Each pump is composed of an electrokinetic (EK) pump and high-voltage power supply with 15-Hz feedback from flow sensors. The combination of high pump fluid impedance and active control results in precise fluid metering with nanoliter accuracy. Automated sample preparation will be demonstrated by labeling proteins with fluorescamine and subsequent injection to a capillary gel electrophoresis (CGE) chip.

  16. National Sample Assessment Protocols

    ERIC Educational Resources Information Center

    Ministerial Council on Education, Employment, Training and Youth Affairs (NJ1), 2012

    2012-01-01

    These protocols represent a working guide for planning and implementing national sample assessments in connection with the national Key Performance Measures (KPMs). The protocols are intended for agencies involved in planning or conducting national sample assessments and personnel responsible for administering associated tenders or contracts,…

  17. Automated Assessment in a Programming Tools Course

    ERIC Educational Resources Information Center

    Fernandez Aleman, J. L.

    2011-01-01

    Automated assessment systems can be useful for both students and instructors. Ranking and immediate feedback can have a strongly positive effect on student learning. This paper presents an experience using automatic assessment in a programming tools course. The proposal aims at extending the traditional use of an online judging system with a…

  18. Automated Assessment in a Programming Tools Course

    ERIC Educational Resources Information Center

    Fernandez Aleman, J. L.

    2011-01-01

    Automated assessment systems can be useful for both students and instructors. Ranking and immediate feedback can have a strongly positive effect on student learning. This paper presents an experience using automatic assessment in a programming tools course. The proposal aims at extending the traditional use of an online judging system with a…

  19. Optimized Heart Sampling and Systematic Evaluation of Cardiac Therapies in Mouse Models of Ischemic Injury: Assessment of Cardiac Remodeling and Semi-Automated Quantification of Myocardial Infarct Size.

    PubMed

    Valente, Mariana; Araújo, Ana; Esteves, Tiago; Laundos, Tiago L; Freire, Ana G; Quelhas, Pedro; Pinto-do-Ó, Perpétua; Nascimento, Diana S

    2015-12-02

    Cardiac therapies are commonly tested preclinically in small-animal models of myocardial infarction. Following functional evaluation, post-mortem histological analysis is essential to assess morphological and molecular alterations underlying the effectiveness of treatment. However, non-methodical and inadequate sampling of the left ventricle often leads to misinterpretations and variability, making direct study comparisons unreliable. Protocols are provided for representative sampling of the ischemic mouse heart followed by morphometric analysis of the left ventricle. Extending the use of this sampling to other types of in situ analysis is also illustrated through the assessment of neovascularization and cellular engraftment in a cell-based therapy setting. This is of interest to the general cardiovascular research community as it details methods for standardization and simplification of histo-morphometric evaluation of emergent heart therapies. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.

  20. Automated Geospatial Watershed Assessment Tool (AGWA)

    USDA-ARS?s Scientific Manuscript database

    The Automated Geospatial Watershed Assessment tool (AGWA, see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University ...

  1. AGWA: The Automated Geospatial Watershed Assessment Tool

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Tool (AGWA, see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface jointly developed by the USDA-Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona...

  2. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  3. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  4. AGWA: The Automated Geospatial Watershed Assessment Tool

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Tool (AGWA, see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface jointly developed by the USDA-Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona...

  5. Automated collection and processing of environmental samples

    DOEpatents

    Troyer, Gary L.; McNeece, Susan G.; Brayton, Darryl D.; Panesar, Amardip K.

    1997-01-01

    For monitoring an environmental parameter such as the level of nuclear radiation, at distributed sites, bar coded sample collectors are deployed and their codes are read using a portable data entry unit that also records the time of deployment. The time and collector identity are cross referenced in memory in the portable unit. Similarly, when later recovering the collector for testing, the code is again read and the time of collection is stored as indexed to the sample collector, or to a further bar code, for example as provided on a container for the sample. The identity of the operator can also be encoded and stored. After deploying and/or recovering the sample collectors, the data is transmitted to a base processor. The samples are tested, preferably using a test unit coupled to the base processor, and again the time is recorded. The base processor computes the level of radiation at the site during exposure of the sample collector, using the detected radiation level of the sample, the delay between recovery and testing, the duration of exposure and the half life of the isotopes collected. In one embodiment, an identity code and a site code are optically read by an image grabber coupled to the portable data entry unit.

  6. Automated bone age assessment: motivation, taxonomies, and challenges.

    PubMed

    Mansourvar, Marjan; Ismail, Maizatul Akmar; Herawan, Tutut; Raj, Ram Gopal; Kareem, Sameem Abdul; Nasaruddin, Fariza Hanum

    2013-01-01

    Bone age assessment (BAA) of unknown people is one of the most important topics in clinical procedure for evaluation of biological maturity of children. BAA is performed usually by comparing an X-ray of left hand wrist with an atlas of known sample bones. Recently, BAA has gained remarkable ground from academia and medicine. Manual methods of BAA are time-consuming and prone to observer variability. This is a motivation for developing automated methods of BAA. However, there is considerable research on the automated assessment, much of which are still in the experimental stage. This survey provides taxonomy of automated BAA approaches and discusses the challenges. Finally, we present suggestions for future research.

  7. Automated Bone Age Assessment: Motivation, Taxonomies, and Challenges

    PubMed Central

    Ismail, Maizatul Akmar; Herawan, Tutut; Gopal Raj, Ram; Abdul Kareem, Sameem; Nasaruddin, Fariza Hanum

    2013-01-01

    Bone age assessment (BAA) of unknown people is one of the most important topics in clinical procedure for evaluation of biological maturity of children. BAA is performed usually by comparing an X-ray of left hand wrist with an atlas of known sample bones. Recently, BAA has gained remarkable ground from academia and medicine. Manual methods of BAA are time-consuming and prone to observer variability. This is a motivation for developing automated methods of BAA. However, there is considerable research on the automated assessment, much of which are still in the experimental stage. This survey provides taxonomy of automated BAA approaches and discusses the challenges. Finally, we present suggestions for future research. PMID:24454534

  8. Rapid Automated Sample Preparation for Biological Assays

    SciTech Connect

    Shusteff, M

    2011-03-04

    Our technology utilizes acoustic, thermal, and electric fields to separate out contaminants such as debris or pollen from environmental samples, lyse open cells, and extract the DNA from the lysate. The objective of the project is to optimize the system described for a forensic sample, and demonstrate its performance for integration with downstream assay platforms (e.g. MIT-LL's ANDE). We intend to increase the quantity of DNA recovered from the sample beyond the current {approx}80% achieved using solid phase extraction methods. Task 1: Develop and test an acoustic filter for cell extraction. Task 2: Develop and test lysis chip. Task 3: Develop and test DNA extraction chip. All chips have been fabricated based on the designs laid out in last month's report.

  9. Automation of motor dexterity assessment.

    PubMed

    Heyer, Patrick; Castrejon, Luis R; Orihuela-Espina, Felipe; Sucar, Luis Enrique

    2017-07-01

    Motor dexterity assessment is regularly performed in rehabilitation wards to establish patient status and automatization for such routinary task is sought. A system for automatizing the assessment of motor dexterity based on the Fugl-Meyer scale and with loose restrictions on sensing technologies is presented. The system consists of two main elements: 1) A data representation that abstracts the low level information obtained from a variety of sensors, into a highly separable low dimensionality encoding employing t-distributed Stochastic Neighbourhood Embedding, and, 2) central to this communication, a multi-label classifier that boosts classification rates by exploiting the fact that the classes corresponding to the individual exercises are naturally organized as a network. Depending on the targeted therapeutic movement class labels i.e. exercises scores, are highly correlated-patients who perform well in one, tends to perform well in related exercises-; and critically no node can be used as proxy of others - an exercise does not encode the information of other exercises. Over data from a cohort of 20 patients, the novel classifier outperforms classical Naive Bayes, random forest and variants of support vector machines (ANOVA: p < 0.001). The novel multi-label classification strategy fulfills an automatic system for motor dexterity assessment, with implications for lessening therapist's workloads, reducing healthcare costs and providing support for home-based virtual rehabilitation and telerehabilitation alternatives.

  10. Automated Sample collection and Analysis unit

    SciTech Connect

    Latner, Norman; Sanderson, Colin G.; Negro, Vincent C.

    1999-03-31

    Autoramp is an atmospheric radionuclide collection and analysis unit designed for unattended operation. A large volume of air passes through one of 31 filter cartridges which is then moved from a sampling chamber and past a bar code reader, to a shielded enclosure. The collected dust-borne radionuclides are counted with a high resolution germanium gamma-ray detector. An analysis is made and the results are transmitted to a central station that can also remotely control the unit.

  11. Automated biowaste sampling system feces monitoring system

    NASA Technical Reports Server (NTRS)

    Hunt, S. R.; Glanfield, E. J.

    1979-01-01

    The Feces Monitoring System (FMS) Program designed, fabricated, assembled and tested an engineering model waste collector system (WCS) to be used in support of life science and medical experiments related to Shuttle missions. The FMS design was patterned closely after the Shuttle WCS, including: interface provisions; mounting; configuration; and operating procedures. These similarities make it possible to eventually substitute an FMS for the Shuttle WCS of Orbiter. In addition, several advanced waste collection features, including the capability of real-time inertial fecal separation and fecal mass measurement and sampling were incorporated into the FMS design.

  12. Non-Contact Conductivity Measurement for Automated Sample Processing Systems

    NASA Technical Reports Server (NTRS)

    Beegle, Luther W.; Kirby, James P.

    2012-01-01

    A new method has been developed for monitoring and control of automated sample processing and preparation especially focusing on desalting of samples before analytical analysis (described in more detail in Automated Desalting Apparatus, (NPO-45428), NASA Tech Briefs, Vol. 34, No. 8 (August 2010), page 44). The use of non-contact conductivity probes, one at the inlet and one at the outlet of the solid phase sample preparation media, allows monitoring of the process, and acts as a trigger for the start of the next step in the sequence (see figure). At each step of the muti-step process, the system is flushed with low-conductivity water, which sets the system back to an overall low-conductivity state. This measurement then triggers the next stage of sample processing protocols, and greatly minimizes use of consumables. In the case of amino acid sample preparation for desalting, the conductivity measurement will define three key conditions for the sample preparation process. First, when the system is neutralized (low conductivity, by washing with excess de-ionized water); second, when the system is acidified, by washing with a strong acid (high conductivity); and third, when the system is at a basic condition of high pH (high conductivity). Taken together, this non-contact conductivity measurement for monitoring sample preparation will not only facilitate automation of the sample preparation and processing, but will also act as a way to optimize the operational time and use of consumables

  13. Automated Data Quality Assessment of Marine Sensors

    PubMed Central

    Timms, Greg P.; de Souza, Paulo A.; Reznik, Leon; Smith, Daniel V.

    2011-01-01

    The automated collection of data (e.g., through sensor networks) has led to a massive increase in the quantity of environmental and other data available. The sheer quantity of data and growing need for real-time ingestion of sensor data (e.g., alerts and forecasts from physical models) means that automated Quality Assurance/Quality Control (QA/QC) is necessary to ensure that the data collected is fit for purpose. Current automated QA/QC approaches provide assessments based upon hard classifications of the gathered data; often as a binary decision of good or bad data that fails to quantify our confidence in the data for use in different applications. We propose a novel framework for automated data quality assessments that uses Fuzzy Logic to provide a continuous scale of data quality. This continuous quality scale is then used to compute error bars upon the data, which quantify the data uncertainty and provide a more meaningful measure of the data’s fitness for purpose in a particular application compared with hard quality classifications. The design principles of the framework are presented and enable both data statistics and expert knowledge to be incorporated into the uncertainty assessment. We have implemented and tested the framework upon a real time platform of temperature and conductivity sensors that have been deployed to monitor the Derwent Estuary in Hobart, Australia. Results indicate that the error bars generated from the Fuzzy QA/QC implementation are in good agreement with the error bars manually encoded by a domain expert. PMID:22163714

  14. Investigating Factors Affecting the Uptake of Automated Assessment Technology

    ERIC Educational Resources Information Center

    Dreher, Carl; Reiners, Torsten; Dreher, Heinz

    2011-01-01

    Automated assessment is an emerging innovation in educational praxis, however its pedagogical potential is not fully utilised in Australia, particularly regarding automated essay grading. The rationale for this research is that the usage of automated assessment currently lags behind the capacity that the technology provides, thus restricting the…

  15. Investigating Factors Affecting the Uptake of Automated Assessment Technology

    ERIC Educational Resources Information Center

    Dreher, Carl; Reiners, Torsten; Dreher, Heinz

    2011-01-01

    Automated assessment is an emerging innovation in educational praxis, however its pedagogical potential is not fully utilised in Australia, particularly regarding automated essay grading. The rationale for this research is that the usage of automated assessment currently lags behind the capacity that the technology provides, thus restricting the…

  16. Automated Power Assessment for Helicopter Turboshaft Engines

    NASA Technical Reports Server (NTRS)

    Simon, Donald L.; Litt, Jonathan S.

    2008-01-01

    An accurate indication of available power is required for helicopter mission planning purposes. Available power is currently estimated on U.S. Army Blackhawk helicopters by performing a Maximum Power Check (MPC), a manual procedure performed by maintenance pilots on a periodic basis. The MPC establishes Engine Torque Factor (ETF), an indication of available power. It is desirable to replace the current manual MPC procedure with an automated approach that will enable continuous real-time assessment of available power utilizing normal mission data. This report presents an automated power assessment approach which processes data currently collected within helicopter Health and Usage Monitoring System (HUMS) units. The overall approach consists of: 1) a steady-state data filter which identifies and extracts steady-state operating points within HUMS data sets; 2) engine performance curve trend monitoring and updating; and 3) automated ETF calculation. The algorithm is coded in MATLAB (The MathWorks, Inc.) and currently runs on a PC. Results from the application of this technique to HUMS mission data collected from UH-60L aircraft equipped with T700-GE-701C engines are presented and compared to manually calculated ETF values. Potential future enhancements are discussed.

  17. BriteStep: Automation in IT Assessment

    NASA Astrophysics Data System (ADS)

    Petropoulakis, Lykourgos; Khan, Taha; Steedman, Linda

    This focuses on an assessment system which permits the automated creation of tests and the evaluation of output from IT trainees. The existing prototype differs radically from other approaches in that it does not require any specific software platform to operate. Instead, it integrates seamlessly with standard existing business software such as Microsoft Word, PowerPoint or Excel. To achieve its objectives the system monitors and records user activity and through an intelligent inference engine it either creates test templates or it automatically assesses submitted tests. The present prototype operates on Windows XP and Vista and minimizes the effort of tutors to set and evaluate tests.

  18. Modular Automated Processing System (MAPS) for analysis of biological samples.

    SciTech Connect

    Gil, Geun-Cheol; Chirica, Gabriela S.; Fruetel, Julia A.; VanderNoot, Victoria A.; Branda, Steven S.; Schoeniger, Joseph S.; Throckmorton, Daniel J.; Brennan, James S.; Renzi, Ronald F.

    2010-10-01

    We have developed a novel modular automated processing system (MAPS) that enables reliable, high-throughput analysis as well as sample-customized processing. This system is comprised of a set of independent modules that carry out individual sample processing functions: cell lysis, protein concentration (based on hydrophobic, ion-exchange and affinity interactions), interferent depletion, buffer exchange, and enzymatic digestion of proteins of interest. Taking advantage of its unique capacity for enclosed processing of intact bioparticulates (viruses, spores) and complex serum samples, we have used MAPS for analysis of BSL1 and BSL2 samples to identify specific protein markers through integration with the portable microChemLab{trademark} and MALDI.

  19. Automated utility assessment of global health.

    PubMed

    Nease, R F; Tsai, R; Hynes, L M; Littenberg, B

    1996-02-01

    The objective of this study was to characterize the performance of an automated utility assessment instrument for measuring preferences for overall health. The study population consisted of 83 subjects recruited from the cafeteria of a large tertiary care hospital. We assessed utilities for current health relative to perfect health and death using the rating scale, time tradeoff and standard gamble metrics. To validate the instrument, we compared utilities with the General Health subscale of the SF-36 Health Survey instrument, satisfaction with current health, and degree of bother due to current health. We evaluated interview failure rate based on irrational orderings of two practice assessments (monocular and binocular blindness) or inability to complete the interview. As expected, utility for overall health was statistically significantly associated with the General Health subscale score and measures of satisfaction with current health and degree of bother. There is substantial variation in utilities among patients with similarly severe overall health, and substantial overlap in utilities among subjects with different levels of overall health. The failure rate in the study was acceptable (9.6%). Automated assessment of utility for overall health provides a feasible means for estimating individual preferences.

  20. Automated Levodopa-induced dyskinesia assessment.

    PubMed

    Tsipouras, Markos G; Tzallas, Alexandros T; Rigas, Georgios; Bougia, Panagiota; Fotiadis, Dimitrios I; Konitsiotis, Spyridon

    2010-01-01

    An automated methodology for Levodopa-induced dyskinesia (LID) assessment is presented in this paper. The methodology is based on the analysis of the signals recorded from accelerometers and gyroscopes, which are placed on certain positions on the subject's body. The obtained signals are analyzed and several features are extracted. Based on these features a classification technique is used for LID detection and classification of its severity. The method has been evaluated using a group of 10 subjects. Results are presented related to each individual sensor as well as for various sensor combinations. The obtained results indicate high classification ability (93.73% classification accuracy).

  1. Automated assessment of postural stability system.

    PubMed

    Napoli, Alessandro; Ward, Christian R; Glass, Stephen M; Tucker, Carole; Obeid, Iyad

    2016-08-01

    The Balance Error Scoring System (BESS) is one of the most commonly used clinical tests to evaluate static postural stability deficits resulting from traumatic brain events and musculoskeletal injury. This test requires a trained operator to visually assess balance and give the subject a performance score based on the number of balance "errors" they committed. Despite being regularly used in several real-world situations, the BESS test is scored by clinician observation and is therefore (a) potentially susceptible to biased and inaccurate test scores and (b) cannot be administered in the absence of a trained provider. The purpose of this research is to develop, calibrate and field test a computerized version of the BESS test using low-cost commodity motion tracking technology. This `Automated Assessment of Postural Stability' (AAPS) system will quantify balance control in field conditions. This research goal is to overcome the main limitations of both the commercially available motion capture systems and the standard BESS test. The AAPS system has been designed to be operated by a minimally trained user and it requires little set-up time with no sensor calibration necessary. These features make the proposed automated system a valuable balance assessment tool to be utilized in the field.

  2. An Automated Home Made Low Cost Vibrating Sample Magnetometer

    NASA Astrophysics Data System (ADS)

    Kundu, S.; Nath, T. K.

    2011-07-01

    The design and operation of a homemade low cost vibrating sample magnetometer is described here. The sensitivity of this instrument is better than 10-2 emu and found to be very efficient for the measurement of magnetization of most of the ferromagnetic and other magnetic materials as a function of temperature down to 77 K and magnetic field upto 800 Oe. Both M(H) and M(T) data acquisition are fully automated employing computer and Labview software.

  3. Automated DNA extraction for large numbers of plant samples.

    PubMed

    Mehle, Nataša; Nikolić, Petra; Rupar, Matevž; Boben, Jana; Ravnikar, Maja; Dermastia, Marina

    2013-01-01

    The method described here is a rapid, total DNA extraction procedure applicable to a large number of plant samples requiring pathogen detection. The procedure combines a simple and quick homogenization step of crude extracts with DNA extraction based upon the binding of DNA to magnetic beads. DNA is purified in an automated process in which the magnetic beads are transferred through a series of washing buffers. The eluted DNA is suitable for efficient amplification in PCR reactions.

  4. Statistical and Economical Efficiency in Assessment of Liver Regeneration Using Defined Sample Size and Selection in Combination With a Fully Automated Image Analysis System

    PubMed Central

    Deng, Meihong; Kleinert, Robert; Huang, Hai; He, Qing; Madrahimova, Fotima; Dirsch, Olaf; Dahmen, Uta

    2009-01-01

    Quantification of liver regeneration is frequently based on determining the 5-bromo-2-deoxyuridine labeling index (BrdU-LI). The quantitative result is influenced by preanalytical, analytical, and postanalytical variables such as the region of interest (ROI). We aimed to present our newly developed and validated automatic computer-based image analysis system (AnalySIS-Macro), and to standardize the selection and sample size of ROIs. Images from BrdU-labeled and immunohistochemically stained liver sections were analyzed conventionally and with the newly developed AnalySIS-Macro and used for validation of the system. Automatic quantification correlated well with the manual counting result (r=0.9976). Validation of our AnalySIS-Macro revealed its high sensitivity (>90%) and specificity. The BrdU-LI ranged from 11% to 57% within the same liver (32.96 ± 11.94%), reflecting the highly variable spatial distribution of hepatocyte proliferation. At least 2000 hepatocytes (10 images at 200× magnification) per lobe were required as sample size for achieving a representative BrdU-LI. Furthermore, the number of pericentral areas should be equal to that of periportal areas. The combination of our AnalySIS-Macro with rules for the selection and size of ROIs represents an accurate, sensitive, specific, and efficient diagnostic tool for the determination of the BrdU-LI and the spatial distribution of proliferating hepatocytes. (J Histochem Cytochem 57:1075–1085, 2009) PMID:19620322

  5. Automated sample area definition for high-throughput microscopy.

    PubMed

    Zeder, M; Ellrott, A; Amann, R

    2011-04-01

    High-throughput screening platforms based on epifluorescence microscopy are powerful tools in a variety of scientific fields. Although some applications are based on imaging geometrically defined samples such as microtiter plates, multiwell slides, or spotted gene arrays, others need to cope with inhomogeneously located samples on glass slides. The analysis of microbial communities in aquatic systems by sample filtration on membrane filters followed by multiple fluorescent staining, or the investigation of tissue sections are examples. Therefore, we developed a strategy for flexible and fast definition of sample locations by the acquisition of whole slide overview images and automated sample recognition by image analysis. Our approach was tested on different microscopes and the computer programs are freely available (http://www.technobiology.ch). Copyright © 2011 International Society for Advancement of Cytometry.

  6. High-throughput sample processing and sample management; the functional evolution of classical cytogenetic assay towards automation.

    PubMed

    Ramakumar, Adarsh; Subramanian, Uma; Prasanna, Pataje G S

    2015-11-01

    High-throughput individual diagnostic dose assessment is essential for medical management of radiation-exposed subjects after a mass casualty. Cytogenetic assays such as the Dicentric Chromosome Assay (DCA) are recognized as the gold standard by international regulatory authorities. DCA is a multi-step and multi-day bioassay. DCA, as described in the IAEA manual, can be used to assess dose up to 4-6 weeks post-exposure quite accurately but throughput is still a major issue and automation is very essential. The throughput is limited, both in terms of sample preparation as well as analysis of chromosome aberrations. Thus, there is a need to design and develop novel solutions that could utilize extensive laboratory automation for sample preparation, and bioinformatics approaches for chromosome-aberration analysis to overcome throughput issues. We have transitioned the bench-based cytogenetic DCA to a coherent process performing high-throughput automated biodosimetry for individual dose assessment ensuring quality control (QC) and quality assurance (QA) aspects in accordance with international harmonized protocols. A Laboratory Information Management System (LIMS) is designed, implemented and adapted to manage increased sample processing capacity, develop and maintain standard operating procedures (SOP) for robotic instruments, avoid data transcription errors during processing, and automate analysis of chromosome-aberrations using an image analysis platform. Our efforts described in this paper intend to bridge the current technological gaps and enhance the potential application of DCA for a dose-based stratification of subjects following a mass casualty. This paper describes one such potential integrated automated laboratory system and functional evolution of the classical DCA towards increasing critically needed throughput.

  7. AUTOMATING GROUNDWATER SAMPLING AT HANFORD THE NEXT STEP

    SciTech Connect

    CONNELL CW; CONLEY SF; HILDEBRAND RD; CUNNINGHAM DE; R_D_Doug_Hildebrand@rl.gov; DeVon_E_Cunningham@rl.gov

    2010-01-21

    Historically, the groundwater monitoring activities at the Department of Energy's Hanford Site in southeastern Washington State have been very "people intensive." Approximately 1500 wells are sampled each year by field personnel or "samplers." These individuals have been issued pre-printed forms showing information about the well(s) for a particular sampling evolution. This information is taken from 2 official electronic databases: the Hanford Well information System (HWIS) and the Hanford Environmental Information System (HEIS). The samplers used these hardcopy forms to document the groundwater samples and well water-levels. After recording the entries in the field, the samplers turned the forms in at the end of the day and other personnel posted the collected information onto a spreadsheet that was then printed and included in a log book. The log book was then used to make manual entries of the new information into the software application(s) for the HEIS and HWIS databases. A pilot project for automating this extremely tedious process was lauched in 2008. Initially, the automation was focused on water-level measurements. Now, the effort is being extended to automate the meta-data associated with collecting groundwater samples. The project allowed electronic forms produced in the field by samplers to be used in a work flow process where the data is transferred to the database and electronic form is filed in managed records - thus eliminating manually completed forms. Elimating the manual forms and streamlining the data entry not only improved the accuracy of the information recorded, but also enhanced the efficiency and sampling capacity of field office personnel.

  8. Experiences of Using Automated Assessment in Computer Science Courses

    ERIC Educational Resources Information Center

    English, John; English, Tammy

    2015-01-01

    In this paper we discuss the use of automated assessment in a variety of computer science courses that have been taught at Israel Academic College by the authors. The course assignments were assessed entirely automatically using Checkpoint, a web-based automated assessment framework. The assignments all used free-text questions (where the students…

  9. Experiences of Using Automated Assessment in Computer Science Courses

    ERIC Educational Resources Information Center

    English, John; English, Tammy

    2015-01-01

    In this paper we discuss the use of automated assessment in a variety of computer science courses that have been taught at Israel Academic College by the authors. The course assignments were assessed entirely automatically using Checkpoint, a web-based automated assessment framework. The assignments all used free-text questions (where the students…

  10. Critical assessment of automated flow cytometry data analysis techniques.

    PubMed

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

    2013-03-01

    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: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.

  11. CRITICAL ASSESSMENT OF AUTOMATED FLOW CYTOMETRY DATA ANALYSIS TECHNIQUES

    PubMed Central

    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

  12. Drug discovery from Nature: automated high-quality sample preparation

    PubMed Central

    Thiericke, Ralf

    2000-01-01

    Secondary metabolites from plants, animals and microorganisms have been proven to be an outstanding source for new and innovative drugs and show a striking structural diversity that supplements chemically synthesized compounds or libraries in drug discovery programs. Unfortunately, extracts from natural sources are usually complex mixtures of compounds:: often generated in time consuming and for the most part manual processes. As quality and quantity of the provided samples play a pivotal role in the success of high-throughput screening programs this poses serious problems. In order to make samples of natural origin competitive with synthetic compound libraries, we devised a novel, automated sample preparation procedure based on solid-phase extraction (SPE). By making use of a modified Zymark RapidTrace® SPE workstation an easy-to-handle and effective fractionation method has been developed which allows the generation of highquality samples from natural origin, fulfilling the requirements of an integration into high-throughput screening programs. PMID:18924703

  13. Components for automated microfluidics sample preparation and analysis

    NASA Astrophysics Data System (ADS)

    Archer, M.; Erickson, J. S.; Hilliard, L. R.; Howell, P. B., Jr.; Stenger, D. A.; Ligler, F. S.; Lin, B.

    2008-02-01

    The increasing demand for portable devices to detect and identify pathogens represents an interdisciplinary effort between engineering, materials science, and molecular biology. Automation of both sample preparation and analysis is critical for performing multiplexed analyses on real world samples. This paper selects two possible components for such automated portable analyzers: modified silicon structures for use in the isolation of nucleic acids and a sheath flow system suitable for automated microflow cytometry. Any detection platform that relies on the genetic content (RNA and DNA) present in complex matrices requires careful extraction and isolation of the nucleic acids in order to ensure their integrity throughout the process. This sample pre-treatment step is commonly performed using commercially available solid phases along with various molecular biology techniques that require multiple manual steps and dedicated laboratory space. Regardless of the detection scheme, a major challenge in the integration of total analysis systems is the development of platforms compatible with current isolation techniques that will ensure the same quality of nucleic acids. Silicon is an ideal candidate for solid phase separations since it can be tailored structurally and chemically to mimic the conditions used in the laboratory. For analytical purposes, we have developed passive structures that can be used to fully ensheath one flow stream with another. As opposed to traditional flow focusing methods, our sheath flow profile is truly two dimensional, making it an ideal candidate for integration into a microfluidic flow cytometer. Such a microflow cytometer could be used to measure targets captured on either antibody- or DNA-coated beads.

  14. Digital microfluidic hub for automated nucleic acid sample preparation.

    SciTech Connect

    He, Jim; Bartsch, Michael S.; Patel, Kamlesh D.; Kittlaus, Eric A.; Remillared, Erin M.; Pezzola, Genevieve L.; Renzi, Ronald F.; Kim, Hanyoup

    2010-07-01

    We have designed, fabricated, and characterized a digital microfluidic (DMF) platform to function as a central hub for interfacing multiple lab-on-a-chip sample processing modules towards automating the preparation of clinically-derived DNA samples for ultrahigh throughput sequencing (UHTS). The platform enables plug-and-play installation of a two-plate DMF device with consistent spacing, offers flexible connectivity for transferring samples between modules, and uses an intuitive programmable interface to control droplet/electrode actuations. Additionally, the hub platform uses transparent indium-tin oxide (ITO) electrodes to allow complete top and bottom optical access to the droplets on the DMF array, providing additional flexibility for various detection schemes.

  15. Automated Formative Feedback and Summative Assessment Using Individualised Spreadsheet Assignments

    ERIC Educational Resources Information Center

    Blayney, Paul; Freeman, Mark

    2004-01-01

    This paper reports on the effects of automating formative feedback at the student's discretion and automating summative assessment with individualised spreadsheet assignments. Quality learning outcomes are achieved when students adopt deep approaches to learning (Ramsden, 2003). Learning environments designed to align assessment to learning…

  16. Automated Formative Feedback and Summative Assessment Using Individualised Spreadsheet Assignments

    ERIC Educational Resources Information Center

    Blayney, Paul; Freeman, Mark

    2004-01-01

    This paper reports on the effects of automating formative feedback at the student's discretion and automating summative assessment with individualised spreadsheet assignments. Quality learning outcomes are achieved when students adopt deep approaches to learning (Ramsden, 2003). Learning environments designed to align assessment to learning…

  17. Sample Tracking in an Automated Cytogenetic Biodosimetry Laboratory for Radiation Mass Casualties.

    PubMed

    Martin, P R; Berdychevski, R E; Subramanian, U; Blakely, W F; Prasanna, P G S

    2007-07-01

    Chromosome aberration-based dicentric assay is expected to be used after mass casualty life-threatening radiation exposures to assess radiation dose to individuals. This will require processing of a large number of samples for individual dose assessment and clinical triage to aid treatment decisions. We have established an automated, high-throughput, cytogenetic biodosimetry laboratory to process a large number of samples for conducting the dicentric assay using peripheral blood from exposed individuals according to internationally accepted laboratory protocols (i.e., within days following radiation exposures). The components of an automated cytogenetic biodosimetry laboratory include blood collection kits for sample shipment, a cell viability analyzer, a robotic liquid handler, an automated metaphase harvester, a metaphase spreader, high-throughput slide stainer and coverslipper, a high-throughput metaphase finder, multiple satellite chromosome-aberration analysis systems, and a computerized sample tracking system. Laboratory automation using commercially available, off-the-shelf technologies, customized technology integration, and implementation of a laboratory information management system (LIMS) for cytogenetic analysis will significantly increase throughput.This paper focuses on our efforts to eliminate data transcription errors, increase efficiency, and maintain samples' positive chain-of-custody by sample tracking during sample processing and data analysis. This sample tracking system represents a "beta" version, which can be modeled elsewhere in a cytogenetic biodosimetry laboratory, and includes a customized LIMS with a central server, personal computer workstations, barcode printers, fixed station and wireless hand-held devices to scan barcodes at various critical steps, and data transmission over a private intra-laboratory computer network. Our studies will improve diagnostic biodosimetry response, aid confirmation of clinical triage, and medical

  18. Automated acoustic matrix deposition for MALDI sample preparation.

    PubMed

    Aerni, Hans-Rudolf; Cornett, Dale S; Caprioli, Richard M

    2006-02-01

    Novel high-throughput sample preparation strategies for MALDI imaging mass spectrometry (IMS) and profiling are presented. An acoustic reagent multispotter was developed to provide improved reproducibility for depositing matrix onto a sample surface, for example, such as a tissue section. The unique design of the acoustic droplet ejector and its optimization for depositing matrix solution are discussed. Since it does not contain a capillary or nozzle for fluid ejection, issues with clogging of these orifices are avoided. Automated matrix deposition provides better control of conditions affecting protein extraction and matrix crystallization with the ability to deposit matrix accurately onto small surface features. For tissue sections, matrix spots of 180-200 microm in diameter were obtained and a procedure is described for generating coordinate files readable by a mass spectrometer to permit automated profile acquisition. Mass spectral quality and reproducibility was found to be better than that obtained with manual pipet spotting. The instrument can also deposit matrix spots in a dense array pattern so that, after analysis in a mass spectrometer, two-dimensional ion images may be constructed. Example ion images from a mouse brain are presented.

  19. Sample Tracking in an Automated Cytogenetic Biodosimetry Laboratory for Radiation Mass Casualties

    PubMed Central

    Martin, P.R.; Berdychevski, R.E.; Subramanian, U.; Blakely, W.F.; Prasanna, P.G.S.

    2007-01-01

    Chromosome aberration-based dicentric assay is expected to be used after mass casualty life-threatening radiation exposures to assess radiation dose to individuals. This will require processing of a large number of samples for individual dose assessment and clinical triage to aid treatment decisions. We have established an automated, high-throughput, cytogenetic biodosimetry laboratory to process a large number of samples for conducting the dicentric assay using peripheral blood from exposed individuals according to internationally accepted laboratory protocols (i.e., within days following radiation exposures). The components of an automated cytogenetic biodosimetry laboratory include blood collection kits for sample shipment, a cell viability analyzer, a robotic liquid handler, an automated metaphase harvester, a metaphase spreader, high-throughput slide stainer and coverslipper, a high-throughput metaphase finder, multiple satellite chromosome-aberration analysis systems, and a computerized sample tracking system. Laboratory automation using commercially available, off-the-shelf technologies, customized technology integration, and implementation of a laboratory information management system (LIMS) for cytogenetic analysis will significantly increase throughput. This paper focuses on our efforts to eliminate data transcription errors, increase efficiency, and maintain samples’ positive chain-of-custody by sample tracking during sample processing and data analysis. This sample tracking system represents a “beta” version, which can be modeled elsewhere in a cytogenetic biodosimetry laboratory, and includes a customized LIMS with a central server, personal computer workstations, barcode printers, fixed station and wireless hand-held devices to scan barcodes at various critical steps, and data transmission over a private intra-laboratory computer network. Our studies will improve diagnostic biodosimetry response, aid confirmation of clinical triage, and medical

  20. Improved helium exchange gas cryostat and sample tube designs for automated gas sampling and cryopumping

    NASA Astrophysics Data System (ADS)

    Buerki, P. R.; Jackson, Brian C.; Schilling, Tim; Rufer, Terry; Severinghaus, Jeffrey P.

    2006-10-01

    In order to eliminate the use of liquid helium for the extraction of atmospheric gases from polar ice cores, two units of a redesigned top load helium exchange gas cryostat were built and tested. The cryostats feature the shortest and largest diameter sample wells built to date, a base temperature below 7 Kelvin, and a sample well without baffles. The cryostats allowed shortening the length and thus increasing the gas pressure inside our sample tubes by 58% and increasing the amount of sample ending up in the mass spectrometer by 4.4%. The cryostats can either be used as mobile stand-alone units for manual gas processing lines or integrated into a fully automated vacuum extraction and gas analysis line. For the latter application the cryostat was equipped with a custom-designed automated changeover system.

  1. Automated, differentially pumped, mass-spectrometer sampling system

    NASA Astrophysics Data System (ADS)

    Little, Jon C.; Gordon, Lloyd B.

    1991-02-01

    The design, construction, and testing of an automated gas sampling system for a quadrupole mass spectrometer on a process chamber with a wide pressure range is described. A set of two parallel stepper-activated vacuum valves are used to vary the amount of gas admitted into the mass spectrometer chamber. The computer-controlled sampling system automatically adjusts the position of the valves to provide the proper leak rate so that the mass spectrometer can continuously monitor a process chamber with a time varying pressure between 760 and 0.00002 torr. This provides a constant pressure at the mass spectrometer sensing head, despite the varying process chamber pressure. No commercially-available mass spectrometer system was found which was able to automatically monitor the gas composition in a proces chamber with such time varying pressures. The principles of operation are presented along with calculations of the gas flow and the control equations.

  2. Validation of Automated Scoring of Science Assessments

    ERIC Educational Resources Information Center

    Liu, Ou Lydia; Rios, Joseph A.; Heilman, Michael; Gerard, Libby; Linn, Marcia C.

    2016-01-01

    Constructed response items can both measure the coherence of student ideas and serve as reflective experiences to strengthen instruction. We report on new automated scoring technologies that can reduce the cost and complexity of scoring constructed-response items. This study explored the accuracy of c-rater-ML, an automated scoring engine…

  3. Validation of Automated Scoring of Science Assessments

    ERIC Educational Resources Information Center

    Liu, Ou Lydia; Rios, Joseph A.; Heilman, Michael; Gerard, Libby; Linn, Marcia C.

    2016-01-01

    Constructed response items can both measure the coherence of student ideas and serve as reflective experiences to strengthen instruction. We report on new automated scoring technologies that can reduce the cost and complexity of scoring constructed-response items. This study explored the accuracy of c-rater-ML, an automated scoring engine…

  4. The Development of the Missouri Automated Reinforcer Assessment (MARA).

    ERIC Educational Resources Information Center

    Vatterott, Madeleine

    A knowledge of an individual's preferences is essential to create an effective reward or reinforcer program for individuals who have either a need to reduce maladaptive behaviors or to increase adaptive behaviors. The goal of the Missouri Automated Reinforcer Assessment (MARA) project is to develop an efficient yet thorough automated reinforcer…

  5. The ECLSS Advanced Automation Project Evolution and Technology Assessment

    NASA Technical Reports Server (NTRS)

    Dewberry, Brandon S.; Carnes, James R.; Lukefahr, Brenda D.; Rogers, John S.; Rochowiak, Daniel M.; Mckee, James W.; Benson, Brian L.

    1990-01-01

    Viewgraphs on Environmental Control and Life Support System (ECLSS) advanced automation project evolution and technology assessment are presented. Topics covered include: the ECLSS advanced automation project; automatic fault diagnosis of ECLSS subsystems descriptions; in-line, real-time chemical and microbial fluid analysis; and object-oriented, distributed chemical and microbial modeling of regenerative environmental control systems description.

  6. An Office Automation Needs Assessment Model

    DTIC Science & Technology

    1985-08-01

    21 Translation of Business Strategy to I/S Strategy . . . 31 Top-down Analysis with Bottom-Up Implementation . . . 31 ISP Process...perceived demand, without regard for an office automation needs analysis or an overall MTF automation strategy . What resulted was user... strategy prior to the procure- ment of the NCR equipment, and had committed an error common to the TAMC and Midland hospitals. The lesson learned

  7. Comparison of manual and automated nucleic acid extraction from whole-blood samples.

    PubMed

    Riemann, Kathrin; Adamzik, Michael; Frauenrath, Stefan; Egensperger, Rupert; Schmid, Kurt W; Brockmeyer, Norbert H; Siffert, Winfried

    2007-01-01

    Nucleic acid extraction and purification from whole blood is a routine application in many laboratories. Automation of this procedure promises standardized sample treatment, a low error rate, and avoidance of contamination. The performance of the BioRobot M48 (Qiagen) and the manual QIAmp DNA Blood Mini Kit (Qiagen) was compared for the extraction of DNA from whole blood. The concentration and purity of the extracted DNAs were determined by spectrophotometry. Analytical sensitivity was assessed by common PCR and genotyping techniques. The quantity and quality of the generated DNAs were slightly higher using the manual extraction method. The results of downstream applications were comparable to each other. Amplification of high-molecular-weight PCR fragments, genotyping by restriction digest, and pyrosequencing were successful for all samples. No cross-contamination could be detected. While automated DNA extraction requires significantly less hands-on time, it is slightly more expensive than the manual extraction method.

  8. Current advances and strategies towards fully automated sample preparation for regulated LC-MS/MS bioanalysis.

    PubMed

    Zheng, Naiyu; Jiang, Hao; Zeng, Jianing

    2014-09-01

    Robotic liquid handlers (RLHs) have been widely used in automated sample preparation for liquid chromatography-tandem mass spectrometry (LC-MS/MS) bioanalysis. Automated sample preparation for regulated bioanalysis offers significantly higher assay efficiency, better data quality and potential bioanalytical cost-savings. For RLHs that are used for regulated bioanalysis, there are additional requirements, including 21 CFR Part 11 compliance, software validation, system qualification, calibration verification and proper maintenance. This article reviews recent advances in automated sample preparation for regulated bioanalysis in the last 5 years. Specifically, it covers the following aspects: regulated bioanalysis requirements, recent advances in automation hardware and software development, sample extraction workflow simplification, strategies towards fully automated sample extraction, and best practices in automated sample preparation for regulated bioanalysis.

  9. Automated Intelligibility Assessment of Pathological Speech Using Phonological Features

    NASA Astrophysics Data System (ADS)

    Middag, Catherine; Martens, Jean-Pierre; Van Nuffelen, Gwen; De Bodt, Marc

    2009-12-01

    It is commonly acknowledged that word or phoneme intelligibility is an important criterion in the assessment of the communication efficiency of a pathological speaker. People have therefore put a lot of effort in the design of perceptual intelligibility rating tests. These tests usually have the drawback that they employ unnatural speech material (e.g., nonsense words) and that they cannot fully exclude errors due to listener bias. Therefore, there is a growing interest in the application of objective automatic speech recognition technology to automate the intelligibility assessment. Current research is headed towards the design of automated methods which can be shown to produce ratings that correspond well with those emerging from a well-designed and well-performed perceptual test. In this paper, a novel methodology that is built on previous work (Middag et al., 2008) is presented. It utilizes phonological features, automatic speech alignment based on acoustic models that were trained on normal speech, context-dependent speaker feature extraction, and intelligibility prediction based on a small model that can be trained on pathological speech samples. The experimental evaluation of the new system reveals that the root mean squared error of the discrepancies between perceived and computed intelligibilities can be as low as 8 on a scale of 0 to 100.

  10. The Automation of Nowcast Model Assessment Processes

    DTIC Science & Technology

    of forecasts produced by US Army Research Laboratory’s nowcast model, Weather Running Estimate-Nowcast (WRE- N ). This report documents the design and...implementation of the automated process of generating domain-level error statistics that can be used by modelers to improve the accuracy of WRE- N model

  11. Automation bias: empirical results assessing influencing factors.

    PubMed

    Goddard, Kate; Roudsari, Abdul; Wyatt, Jeremy C

    2014-05-01

    To investigate the rate of automation bias - the propensity of people to over rely on automated advice and the factors associated with it. Tested factors were attitudinal - trust and confidence, non-attitudinal - decision support experience and clinical experience, and environmental - task difficulty. The paradigm of simulated decision support advice within a prescribing context was used. The study employed within participant before-after design, whereby 26 UK NHS General Practitioners were shown 20 hypothetical prescribing scenarios with prevalidated correct and incorrect answers - advice was incorrect in 6 scenarios. They were asked to prescribe for each case, followed by being shown simulated advice. Participants were then asked whether they wished to change their prescription, and the post-advice prescription was recorded. Rate of overall decision switching was captured. Automation bias was measured by negative consultations - correct to incorrect prescription switching. Participants changed prescriptions in 22.5% of scenarios. The pre-advice accuracy rate of the clinicians was 50.38%, which improved to 58.27% post-advice. The CDSS improved the decision accuracy in 13.1% of prescribing cases. The rate of automation bias, as measured by decision switches from correct pre-advice, to incorrect post-advice was 5.2% of all cases - a net improvement of 8%. More immediate factors such as trust in the specific CDSS, decision confidence, and task difficulty influenced rate of decision switching. Lower clinical experience was associated with more decision switching. Age, DSS experience and trust in CDSS generally were not significantly associated with decision switching. This study adds to the literature surrounding automation bias in terms of its potential frequency and influencing factors. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  12. Automated Assessment of Postural Stability (AAPS)

    DTIC Science & Technology

    2016-10-01

    has been to develop a mobile motion capture system that is capable of quantifying a person’s sense of balance , which can in turn be used as a proxy for...motion tracker, (2) a graphical user interface, and (3) algorithms of automated balance scoring. Furthermore, we have begun the process of testing...performance against that of human experts and determined that our system is in general more reliable. 15. SUBJECT TERMS motion tracking, balance

  13. Automated Assessment of Cognitive Health Using Smart Home Technologies

    PubMed Central

    Dawadi, Prafulla N.; Cook, Diane J.; Schmitter-Edgecombe, Maureen; Parsey, Carolyn

    2014-01-01

    BACKGROUND The goal of this work is to develop intelligent systems to monitor the well being of individuals in their home environments. OBJECTIVE This paper introduces a machine learning-based method to automatically predict activity quality in smart homes and automatically assess cognitive health based on activity quality. METHODS This paper describes an automated framework to extract set of features from smart home sensors data that reflects the activity performance or ability of an individual to complete an activity which can be input to machine learning algorithms. Output from learning algorithms including principal component analysis, support vector machine, and logistic regression algorithms are used to quantify activity quality for a complex set of smart home activities and predict cognitive health of participants. RESULTS Smart home activity data was gathered from volunteer participants (n=263) who performed a complex set of activities in our smart home testbed. We compare our automated activity quality prediction and cognitive health prediction with direct observation scores and health assessment obtained from neuropsychologists. With all samples included, we obtained statistically significant correlation (r=0.54) between direct observation scores and predicted activity quality. Similarly, using a support vector machine classifier, we obtained reasonable classification accuracy (area under the ROC curve = 0.80, g-mean = 0.73) in classifying participants into two different cognitive classes, dementia and cognitive healthy. CONCLUSIONS The results suggest that it is possible to automatically quantify the task quality of smart home activities and perform limited assessment of the cognitive health of individual if smart home activities are properly chosen and learning algorithms are appropriately trained. PMID:23949177

  14. Automated assessment of cognitive health using smart home technologies.

    PubMed

    Dawadi, Prafulla N; Cook, Diane J; Schmitter-Edgecombe, Maureen; Parsey, Carolyn

    2013-01-01

    The goal of this work is to develop intelligent systems to monitor the wellbeing of individuals in their home environments. This paper introduces a machine learning-based method to automatically predict activity quality in smart homes and automatically assess cognitive health based on activity quality. This paper describes an automated framework to extract set of features from smart home sensors data that reflects the activity performance or ability of an individual to complete an activity which can be input to machine learning algorithms. Output from learning algorithms including principal component analysis, support vector machine, and logistic regression algorithms are used to quantify activity quality for a complex set of smart home activities and predict cognitive health of participants. Smart home activity data was gathered from volunteer participants (n=263) who performed a complex set of activities in our smart home testbed. We compare our automated activity quality prediction and cognitive health prediction with direct observation scores and health assessment obtained from neuropsychologists. With all samples included, we obtained statistically significant correlation (r=0.54) between direct observation scores and predicted activity quality. Similarly, using a support vector machine classifier, we obtained reasonable classification accuracy (area under the ROC curve=0.80, g-mean=0.73) in classifying participants into two different cognitive classes, dementia and cognitive healthy. The results suggest that it is possible to automatically quantify the task quality of smart home activities and perform limited assessment of the cognitive health of individual if smart home activities are properly chosen and learning algorithms are appropriately trained.

  15. Automated Force Volume Image Processing for Biological Samples

    PubMed Central

    Duan, Junbo; Duval, Jérôme F. L.; Brie, David; Francius, Grégory

    2011-01-01

    Atomic force microscopy (AFM) has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature) which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image. PMID:21559483

  16. Manual versus automated blood sampling: impact of repeated blood sampling on stress parameters and behavior in male NMRI mice.

    PubMed

    Teilmann, A C; Kalliokoski, Otto; Sørensen, Dorte B; Hau, Jann; Abelson, Klas S P

    2014-10-01

    Facial vein (cheek blood) and caudal vein (tail blood) phlebotomy are two commonly used techniques for obtaining blood samples from laboratory mice, while automated blood sampling through a permanent catheter is a relatively new technique in mice. The present study compared physiological parameters, glucocorticoid dynamics as well as the behavior of mice sampled repeatedly for 24 h by cheek blood, tail blood or automated blood sampling from the carotid artery. Mice subjected to cheek blood sampling lost significantly more body weight, had elevated levels of plasma corticosterone, excreted more fecal corticosterone metabolites, and expressed more anxious behavior than did the mice of the other groups. Plasma corticosterone levels of mice subjected to tail blood sampling were also elevated, although less significantly. Mice subjected to automated blood sampling were less affected with regard to the parameters measured, and expressed less anxious behavior. We conclude that repeated blood sampling by automated blood sampling and from the tail vein is less stressful than cheek blood sampling. The choice between automated blood sampling and tail blood sampling should be based on the study requirements, the resources of the laboratory and skills of the staff. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  17. Manual versus automated blood sampling: impact of repeated blood sampling on stress parameters and behavior in male NMRI mice

    PubMed Central

    Kalliokoski, Otto; Sørensen, Dorte B; Hau, Jann; Abelson, Klas S P

    2014-01-01

    Facial vein (cheek blood) and caudal vein (tail blood) phlebotomy are two commonly used techniques for obtaining blood samples from laboratory mice, while automated blood sampling through a permanent catheter is a relatively new technique in mice. The present study compared physiological parameters, glucocorticoid dynamics as well as the behavior of mice sampled repeatedly for 24 h by cheek blood, tail blood or automated blood sampling from the carotid artery. Mice subjected to cheek blood sampling lost significantly more body weight, had elevated levels of plasma corticosterone, excreted more fecal corticosterone metabolites, and expressed more anxious behavior than did the mice of the other groups. Plasma corticosterone levels of mice subjected to tail blood sampling were also elevated, although less significantly. Mice subjected to automated blood sampling were less affected with regard to the parameters measured, and expressed less anxious behavior. We conclude that repeated blood sampling by automated blood sampling and from the tail vein is less stressful than cheek blood sampling. The choice between automated blood sampling and tail blood sampling should be based on the study requirements, the resources of the laboratory and skills of the staff. PMID:24958546

  18. Automated 3-D Printed Arrays to Evaluate Genotoxic Chemistry: E-Cigarettes and Water Samples.

    PubMed

    Kadimisetty, Karteek; Malla, Spundana; Rusling, James F

    2017-05-26

    A novel, automated, low cost, three-dimensional (3-D) printed microfluidic array was developed to detect DNA damage from metabolites of chemicals in environmental samples. The electrochemiluminescent (ECL) detection platform incorporates layer-by-layer (LbL) assembled films of microsomal enzymes, DNA and an ECL-emitting ruthenium metallopolymer in ∼10 nm deep microwells. Liquid samples are introduced into the array, metabolized by the human enzymes, products react with DNA if possible, and DNA damage is detected by ECL with a camera. Measurements of relative DNA damage by the array assess the genotoxic potential of the samples. The array analyzes three samples simultaneously in 5 min. Measurement of cigarette and e-cigarette smoke extracts and polluted water samples was used to establish proof of concept. Potentially genotoxic reactions from e-cigarette vapor similar to smoke from conventional cigarettes were demonstrated. Untreated wastewater showed a high genotoxic potential compared to negligible values for treated wastewater from a pollution control treatment plant. Reactivity of chemicals known to produce high rates of metabolite-related DNA damage were measured, and array results for environmental samples were expressed in terms of equivalent responses from these standards to assess severity of possible DNA damage. Genotoxic assessment of wastewater samples during processing also highlighted future on-site monitoring applications.

  19. Ability-Training-Oriented Automated Assessment in Introductory Programming Course

    ERIC Educational Resources Information Center

    Wang, Tiantian; Su, Xiaohong; Ma, Peijun; Wang, Yuying; Wang, Kuanquan

    2011-01-01

    Learning to program is a difficult process for novice programmers. AutoLEP, an automated learning and assessment system, was developed by us, to aid novice programmers to obtain programming skills. AutoLEP is ability-training-oriented. It adopts a novel assessment mechanism, which combines static analysis with dynamic testing to analyze student…

  20. Evaluating the Validity of the Automated Working Memory Assessment

    ERIC Educational Resources Information Center

    Alloway, Tracy; Gathercole, Susan E.; Kirkwood, Hannah; Elliott, Julian

    2008-01-01

    The aim of the present study was to investigate the construct stability and diagnostic validity of a standardised computerised tool for assessing working memory: the Automated Working Memory Assessment (AWMA). The purpose of the AWMA is to provide educators with a quick and effective tool to screen for and support those with memory impairments.…

  1. Evaluating the Validity of the Automated Working Memory Assessment

    ERIC Educational Resources Information Center

    Alloway, Tracy; Gathercole, Susan E.; Kirkwood, Hannah; Elliott, Julian

    2008-01-01

    The aim of the present study was to investigate the construct stability and diagnostic validity of a standardised computerised tool for assessing working memory: the Automated Working Memory Assessment (AWMA). The purpose of the AWMA is to provide educators with a quick and effective tool to screen for and support those with memory impairments.…

  2. Ability-Training-Oriented Automated Assessment in Introductory Programming Course

    ERIC Educational Resources Information Center

    Wang, Tiantian; Su, Xiaohong; Ma, Peijun; Wang, Yuying; Wang, Kuanquan

    2011-01-01

    Learning to program is a difficult process for novice programmers. AutoLEP, an automated learning and assessment system, was developed by us, to aid novice programmers to obtain programming skills. AutoLEP is ability-training-oriented. It adopts a novel assessment mechanism, which combines static analysis with dynamic testing to analyze student…

  3. Automated biowaste sampling system improved feces collection, mass measurement and sampling. [by use of a breadboard model

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.; Mangialardi, J. K.; Young, R.

    1974-01-01

    The capability of the basic automated Biowaste Sampling System (ABSS) hardware was extended and improved through the design, fabrication and test of breadboard hardware. A preliminary system design effort established the feasibility of integrating the breadboard concepts into the ABSS.

  4. Hearing assessment-reliability, accuracy, and efficiency of automated audiometry.

    PubMed

    Swanepoel, De Wet; Mngemane, Shadrack; Molemong, Silindile; Mkwanazi, Hilda; Tutshini, Sizwe

    2010-06-01

    This study investigated the reliability, accuracy, and time efficiency of automated hearing assessment using a computer-based telemedicine-compliant audiometer. Thirty normal-hearing subjects and eight hearing-impaired subjects were tested with pure-tone air conduction audiometry (125-8,000 Hz) in a manual and automated configuration in a counterbalanced manner. For the normal-hearing group each test was repeated to determine test-retest reliability and recording time, and preference for threshold-seeking method (manual vs. automated) was documented. Test-retest thresholds were not significantly different for manual and automated testing. Manual audiometry test-retest correspondence was 5 dB or less in 88% of thresholds compared to 91% for automated audiometry. Thresholds for automated audiometry did not differ significantly from manual audiometry with 87% of thresholds in the normal-hearing group and 97% in the hearing-impaired group, corresponding within 5 dB or less of each other. The largest overall average absolute difference across frequencies was 3.6 +/- 3.9 dB for the normal-hearing group and 3.3 +/- 2.4 for the hearing-impaired group. Both techniques were equally time efficient in the normal-hearing population, and 63% of subjects preferred the automated threshold-seeking method. Automated audiometry provides reliable, accurate, and time-efficient hearing assessments for normal-hearing and hearing-impaired adults. Combined with an asynchronous telehealth model it holds significant potential for reaching underserved areas where hearing health professionals are unavailable.

  5. Automated Aqueous Sample Concentration Methods for in situ Astrobiological Instrumentation

    NASA Astrophysics Data System (ADS)

    Aubrey, A. D.; Grunthaner, F. J.

    2009-12-01

    The era of wet chemical experiments for in situ planetary science investigations is upon us, as evidenced by recent results from the surface of Mars by Phoenix’s microscopy, electrochemistry, and conductivity analyzer, MECA [1]. Studies suggest that traditional thermal volatilization methods for planetary science in situ investigations induce organic degradation during sample processing [2], an effect that is enhanced in the presence of oxidants [3]. Recent developments have trended towards adaptation of non-destructive aqueous extraction and analytical methods for future astrobiological instrumentation. Wet chemical extraction techniques under investigation include subcritical water extraction, SCWE [4], aqueous microwave assisted extraction, MAE, and organic solvent extraction [5]. Similarly, development of miniaturized analytical space flight instruments that require aqueous extracts include microfluidic capillary electrophoresis chips, μCE [6], liquid-chromatography mass-spectrometrometers, LC-MS [7], and life marker chips, LMC [8]. If organics are present on the surface of Mars, they are expected to be present at extremely low concentrations (parts-per-billion), orders of magnitude below the sensitivities of most flight instrument technologies. Therefore, it becomes necessary to develop and integrate concentration mechanisms for in situ sample processing before delivery to analytical flight instrumentation. We present preliminary results of automated solid-phase-extraction (SPE) sample purification and concentration methods for the treatment of highly saline aqueous soil extracts. These methods take advantage of the affinity of low molecular weight organic compounds with natural and synthetic scavenger materials. These interactions allow for the separation of target organic analytes from unfavorable background species (i.e. salts) during inline treatment, and a clever method for selective desorption is utilized to obtain concentrated solutions on the order

  6. Automated Mars surface sample return mission concepts for achievement of essential scientific objectives

    NASA Technical Reports Server (NTRS)

    Weaver, W. L.; Norton, H. N.; Darnell, W. L.

    1975-01-01

    Mission concepts were investigated for automated return to Earth of a Mars surface sample adequate for detailed analyses in scientific laboratories. The minimum sample mass sufficient to meet scientific requirements was determined. Types of materials and supporting measurements for essential analyses are reported. A baseline trajectory profile was selected for its low energy requirements and relatively simple implementation, and trajectory profile design data were developed for 1979 and 1981 launch opportunities. Efficient spacecraft systems were conceived by utilizing existing technology where possible. Systems concepts emphasized the 1979 launch opportunity, and the applicability of results to other opportunities was assessed. It was shown that the baseline missions (return through Mars parking orbit) and some comparison missions (return after sample transfer in Mars orbit) can be accomplished by using a single Titan III E/Centaur as the launch vehicle. All missions investigated can be accomplished by use of Space Shuttle/Centaur vehicles.

  7. Automated Cough Assessment on a Mobile Platform.

    PubMed

    Sterling, Mark; Rhee, Hyekyun; Bocko, Mark

    2014-01-01

    The development of an Automated System for Asthma Monitoring (ADAM) is described. This consists of a consumer electronics mobile platform running a custom application. The application acquires an audio signal from an external user-worn microphone connected to the device analog-to-digital converter (microphone input). This signal is processed to determine the presence or absence of cough sounds. Symptom tallies and raw audio waveforms are recorded and made easily accessible for later review by a healthcare provider. The symptom detection algorithm is based upon standard speech recognition and machine learning paradigms and consists of an audio feature extraction step followed by a Hidden Markov Model based Viterbi decoder that has been trained on a large database of audio examples from a variety of subjects. Multiple Hidden Markov Model topologies and orders are studied. Performance of the recognizer is presented in terms of the sensitivity and the rate of false alarm as determined in a cross-validation test.

  8. Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

    PubMed

    Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

    2006-12-20

    Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the

  9. A modular approach for automated sample preparation and chemical analysis

    NASA Technical Reports Server (NTRS)

    Clark, Michael L.; Turner, Terry D.; Klingler, Kerry M.; Pacetti, Randolph

    1994-01-01

    Changes in international relations, especially within the past several years, have dramatically affected the programmatic thrusts of the U.S. Department of Energy (DOE). The DOE now is addressing the environmental cleanup required as a result of 50 years of nuclear arms research and production. One major obstacle in the remediation of these areas is the chemical determination of potentially contaminated material using currently acceptable practices. Process bottlenecks and exposure to hazardous conditions pose problems for the DOE. One proposed solution is the application of modular automated chemistry using Standard Laboratory Modules (SLM) to perform Standard Analysis Methods (SAM). The Contaminant Analysis Automation (CAA) Program has developed standards and prototype equipment that will accelerate the development of modular chemistry technology and is transferring this technology to private industry.

  10. Estimates of Radionuclide Loading to Cochiti Lake from Los Alamos Canyon Using Manual and Automated Sampling

    SciTech Connect

    McLean, Christopher T.

    2000-07-01

    Los Alamos National Laboratory has a long-standing program of sampling storm water runoff inside the Laboratory boundaries. In 1995, the Laboratory started collecting the samples using automated storm water sampling stations; prior to this time the samples were collected manually. The Laboratory has also been periodically collecting sediment samples from Cochiti Lake. This paper presents the data for Pu-238 and Pu-239 bound to the sediments for Los Alamos Canyon storm water runoff and compares the sampling types by mass loading and as a percentage of the sediment deposition to Cochiti Lake. The data for both manual and automated sampling are used to calculate mass loads from Los Alamos Canyon on a yearly basis. The automated samples show mass loading 200- 500 percent greater for Pu-238 and 300-700 percent greater for Pu-239 than the manual samples. Using the mean manual flow volume for mass loading calculations, the automated samples are over 900 percent greater for Pu-238 and over 1800 percent greater for Pu-239. Evaluating the Pu-238 and Pu-239 activities as a percentage of deposition to Cochiti Lake indicates that the automated samples are 700-1300 percent greater for Pu- 238 and 200-500 percent greater for Pu-239. The variance was calculated by two methods. The first method calculates the variance for each sample event. The second method calculates the variances by the total volume of water discharged in Los Alamos Canyon for the year.

  11. Automated Geospatial Watershed Assessment (AGWA) Documentation Version 2.0

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Http://www.epa.gov/nerlesd1/landsci/agwa/introduction.htm and www.tucson.ars.ag.gov/agwa) tool is a GIS interface jointly developed by the U.S. Environmental Protection Agency, USDA-Agricultural Research Service, University of Arizon...

  12. Validity Arguments for Diagnostic Assessment Using Automated Writing Evaluation

    ERIC Educational Resources Information Center

    Chapelle, Carol A.; Cotos, Elena; Lee, Jooyoung

    2015-01-01

    Two examples demonstrate an argument-based approach to validation of diagnostic assessment using automated writing evaluation (AWE). "Criterion"®, was developed by Educational Testing Service to analyze students' papers grammatically, providing sentence-level error feedback. An interpretive argument was developed for its use as part of…

  13. Automated Geospatial Watershed Assessment Tool (AGWA) Poster Presentation

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA, see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface jointly developed by the USDA-Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona...

  14. Automated Geospatial Watershed Assessment (AGWA) Documentation Version 2.0

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Http://www.epa.gov/nerlesd1/landsci/agwa/introduction.htm and www.tucson.ars.ag.gov/agwa) tool is a GIS interface jointly developed by the U.S. Environmental Protection Agency, USDA-Agricultural Research Service, University of Arizon...

  15. Automated Geospatial Watershed Assessment Tool (AGWA) Poster Presentation

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA, see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface jointly developed by the USDA-Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona...

  16. Technology assessment of automation trends in the modular home industry

    Treesearch

    Phil Mitchell; Robert Russell Hurst

    2009-01-01

    This report provides an assessment of technology used in manufacturing modular homes in the United States, and that used in the German prefabricated wooden home industry. It is the first step toward identifying the research needs in automation and manufacturing methods that will facilitate mass customization in the home manufacturing industry. Within the United States...

  17. Automated Geospatial Watershed Assessment (AGWA) 3.0 Software Tool

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment (AGWA) tool has been developed under an interagency research agreement between the U.S. Environmental Protection Agency, Office of Research and Development, and the U.S. Department of Agriculture, Agricultural Research Service. AGWA i...

  18. Validity Arguments for Diagnostic Assessment Using Automated Writing Evaluation

    ERIC Educational Resources Information Center

    Chapelle, Carol A.; Cotos, Elena; Lee, Jooyoung

    2015-01-01

    Two examples demonstrate an argument-based approach to validation of diagnostic assessment using automated writing evaluation (AWE). "Criterion"®, was developed by Educational Testing Service to analyze students' papers grammatically, providing sentence-level error feedback. An interpretive argument was developed for its use as part of…

  19. Automated Geospatial Watershed Assessment (AGWA) 3.0 Software Tool

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment (AGWA) tool has been developed under an interagency research agreement between the U.S. Environmental Protection Agency, Office of Research and Development, and the U.S. Department of Agriculture, Agricultural Research Service. AGWA i...

  20. Human and Automated Assessment of Oral Reading Fluency

    ERIC Educational Resources Information Center

    Bolaños, Daniel; Cole, Ron A.; Ward, Wayne H.; Tindal, Gerald A.; Hasbrouck, Jan; Schwanenflugel, Paula J.

    2013-01-01

    This article describes a comprehensive approach to fully automated assessment of children's oral reading fluency (ORF), one of the most informative and frequently administered measures of children's reading ability. Speech recognition and machine learning techniques are described that model the 3 components of oral reading fluency: word accuracy,…

  1. Needs Assessments for Automated Manufacturing Training Programs.

    ERIC Educational Resources Information Center

    Northampton Community Coll., Bethlehem, PA.

    This document contains needs assessments used by Northampton Community College to develop training courses for a business-industry technology resource center for firms in eastern Pennsylvania. The following needs assessments are included: (1) individual skills survey for workers at Keystone Cement Company; (2) Keystone group skills survey; (3)…

  2. Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples.

    PubMed

    Wallinger, Corinna; Staudacher, Karin; Sint, Daniela; Thalinger, Bettina; Oehm, Johannes; Juen, Anita; Traugott, Michael

    2017-08-01

    Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next-generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high-quality DNA extraction procedures for obtaining the minute quantities of short-fragmented food DNA. Automatic high-throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole-body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high-throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor-intensive, low-throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost-efficient and innovative methodology at low contamination risk also in trophic ecology.

  3. Automated Rendezvous and Capture in Space: A Technology Assessment

    NASA Technical Reports Server (NTRS)

    Polites, Michael E.

    1998-01-01

    This paper presents the results of a study to assess the technology of automated rendezvous and capture (AR&C) in space. The outline of the paper is as follows: First, the history of manual and automated rendezvous and capture and rendezvous and dock is presented. Next, the need for AR&C in space is reviewed. In light of these, AR&C systems are proposed that meet NASA's future needs, but can be developed in a reasonable amount of time with a reasonable amount of money. Technology plans for developing these systems are presented; cost and schedule are included.

  4. Evaluation of the measurement uncertainty in automated long-term sampling of PCDD/PCDFs.

    PubMed

    Vicaretti, M; D'Emilia, G; Mosca, S; Guerriero, E; Rotatori, M

    2013-12-01

    Since the publication of the first version of European standard EN-1948 in 1996, long-term sampling equipment has been improved to a high standard for the sampling and analysis of polychlorodibenzo-p-dioxin (PCDD)/polychlorodibenzofuran (PCDF) emissions from industrial sources. The current automated PCDD/PCDF sampling systems enable to extend the measurement time from 6-8 h to 15-30 days in order to have data values better representative of the real pollutant emission of the plant in the long period. EN-1948:2006 is still the European technical reference standard for the determination of PCDD/PCDF from stationary source emissions. In this paper, a methodology to estimate the measurement uncertainty of long-term automated sampling is presented. The methodology has been tested on a set of high concentration sampling data resulting from a specific experience; it is proposed with the intent that it is to be applied on further similar studies and generalized. A comparison between short-term sampling data resulting from manual and automated parallel measurements has been considered also in order to verify the feasibility and usefulness of automated systems and to establish correlations between results of the two methods to use a manual method for calibration of automatic long-term one. The uncertainty components of the manual method are analyzed, following the requirements of EN-1948-3:2006, allowing to have a preliminary evaluation of the corresponding uncertainty components of the automated system. Then, a comparison between experimental data coming from parallel sampling campaigns carried out in short- and long-term sampling periods is realized. Long-term sampling is more reliable to monitor PCDD/PCDF emissions than occasional short-term sampling. Automated sampling systems can assure very useful emission data both in short and long sampling periods. Despite this, due to the different application of the long-term sampling systems, the automated results could not be

  5. Operator-based metric for nuclear operations automation assessment

    SciTech Connect

    Zacharias, G.L.; Miao, A.X.; Kalkan, A.

    1995-04-01

    Continuing advances in real-time computational capabilities will support enhanced levels of smart automation and AI-based decision-aiding systems in the nuclear power plant (NPP) control room of the future. To support development of these aids, we describe in this paper a research tool, and more specifically, a quantitative metric, to assess the impact of proposed automation/aiding concepts in a manner that can account for a number of interlinked factors in the control room environment. In particular, we describe a cognitive operator/plant model that serves as a framework for integrating the operator`s information-processing capabilities with his procedural knowledge, to provide insight as to how situations are assessed by the operator, decisions made, procedures executed, and communications conducted. Our focus is on the situation assessment (SA) behavior of the operator, the development of a quantitative metric reflecting overall operator awareness, and the use of this metric in evaluating automation/aiding options. We describe the results of a model-based simulation of a selected emergency scenario, and metric-based evaluation of a range of contemplated NPP control room automation/aiding options. The results demonstrate the feasibility of model-based analysis of contemplated control room enhancements, and highlight the need for empirical validation.

  6. Automated Assessment and Experiences of Teaching Programming

    ERIC Educational Resources Information Center

    Higgins, Colin A.; Gray, Geoffrey; Symeonidis, Pavlos; Tsintsifas, Athanasios

    2005-01-01

    This article reports on the design, implementation, and usage of the CourseMarker (formerly known as CourseMaster) courseware Computer Based Assessment (CBA) system at the University of Nottingham. Students use CourseMarker to solve (programming) exercises and to submit their solutions. CourseMarker returns immediate results and feedback to the…

  7. Automated Assessment and Experiences of Teaching Programming

    ERIC Educational Resources Information Center

    Higgins, Colin A.; Gray, Geoffrey; Symeonidis, Pavlos; Tsintsifas, Athanasios

    2005-01-01

    This article reports on the design, implementation, and usage of the CourseMarker (formerly known as CourseMaster) courseware Computer Based Assessment (CBA) system at the University of Nottingham. Students use CourseMarker to solve (programming) exercises and to submit their solutions. CourseMarker returns immediate results and feedback to the…

  8. Automated FMV image quality assessment based on power spectrum statistics

    NASA Astrophysics Data System (ADS)

    Kalukin, Andrew

    2015-05-01

    Factors that degrade image quality in video and other sensor collections, such as noise, blurring, and poor resolution, also affect the spatial power spectrum of imagery. Prior research in human vision and image science from the last few decades has shown that the image power spectrum can be useful for assessing the quality of static images. The research in this article explores the possibility of using the image power spectrum to automatically evaluate full-motion video (FMV) imagery frame by frame. This procedure makes it possible to identify anomalous images and scene changes, and to keep track of gradual changes in quality as collection progresses. This article will describe a method to apply power spectral image quality metrics for images subjected to simulated blurring, blocking, and noise. As a preliminary test on videos from multiple sources, image quality measurements for image frames from 185 videos are compared to analyst ratings based on ground sampling distance. The goal of the research is to develop an automated system for tracking image quality during real-time collection, and to assign ratings to video clips for long-term storage, calibrated to standards such as the National Imagery Interpretability Rating System (NIIRS).

  9. Flightdeck Automation Problems (FLAP) Model for Safety Technology Portfolio Assessment

    NASA Technical Reports Server (NTRS)

    Ancel, Ersin; Shih, Ann T.

    2014-01-01

    NASA's Aviation Safety Program (AvSP) develops and advances methodologies and technologies to improve air transportation safety. The Safety Analysis and Integration Team (SAIT) conducts a safety technology portfolio assessment (PA) to analyze the program content, to examine the benefits and risks of products with respect to program goals, and to support programmatic decision making. The PA process includes systematic identification of current and future safety risks as well as tracking several quantitative and qualitative metrics to ensure the program goals are addressing prominent safety risks accurately and effectively. One of the metrics within the PA process involves using quantitative aviation safety models to gauge the impact of the safety products. This paper demonstrates the role of aviation safety modeling by providing model outputs and evaluating a sample of portfolio elements using the Flightdeck Automation Problems (FLAP) model. The model enables not only ranking of the quantitative relative risk reduction impact of all portfolio elements, but also highlighting the areas with high potential impact via sensitivity and gap analyses in support of the program office. Although the model outputs are preliminary and products are notional, the process shown in this paper is essential to a comprehensive PA of NASA's safety products in the current program and future programs/projects.

  10. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED TOOL FOR WATERSHED ASSESSMENT AND PLANNING

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execu...

  11. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED TOOL FOR WATERSHED ASSESSMENT AND PLANNING

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execu...

  12. Automating risk of bias assessment for clinical trials.

    PubMed

    Marshall, Iain J; Kuiper, Joël; Wallace, Byron C

    2015-07-01

    Systematic reviews, which summarize the entirety of the evidence pertaining to a specific clinical question, have become critical for evidence-based decision making in healthcare. But such reviews have become increasingly onerous to produce due to the exponentially expanding biomedical literature base. This study proposes a step toward mitigating this problem by automating risk of bias assessment in systematic reviews, in which reviewers determine whether study results may be affected by biases (e.g., poor randomization or blinding). Conducting risk of bias assessment is an important but onerous task. We thus describe a machine learning approach to automate this assessment, using the standard Cochrane Risk of Bias Tool which assesses seven common types of bias. Training such a system would typically require a large labeled corpus, which would be prohibitively expensive to collect here. Instead, we use distant supervision, using data from the Cochrane Database of Systematic Reviews (a large repository of systematic reviews), to pseudoannotate a corpus of 2200 clinical trial reports in PDF format. We then develop a joint model which, using the full text of a clinical trial report as input, predicts the risks of bias while simultaneously extracting the text fragments supporting these assessments. This study represents a step toward automating or semiautomating extraction of data necessary for the synthesis of clinical trials.

  13. Automated Assessment of Medical Training Evaluation Text

    PubMed Central

    Zhang, Rui; Pakhomov, Serguei; Gladding, Sophia; Aylward, Michael; Borman-Shoap, Emily; Melton, Genevieve B.

    2012-01-01

    Medical post-graduate residency training and medical student training increasingly utilize electronic systems to evaluate trainee performance based on defined training competencies with quantitative and qualitative data, the later of which typically consists of text comments. Medical education is concomitantly becoming a growing area of clinical research. While electronic systems have proliferated in number, little work has been done to help manage and analyze qualitative data from these evaluations. We explored the use of text-mining techniques to assist medical education researchers in sentiment analysis and topic analysis of residency evaluations with a sample of 812 evaluation statements. While comments were predominantly positive, sentiment analysis improved the ability to discriminate statements with 93% accuracy. Similar to other domains, Latent Dirichlet Analysis and Information Gain revealed groups of core subjects and appear to be useful for identifying topics from this data. PMID:23304426

  14. Automated risk assessment tool for pregnancy care.

    PubMed

    Gorthi, Aparna; Firtion, Celine; Vepa, Jithendra

    2009-01-01

    Clinical decision support systems augment the quality of medical care by aiding healthcare workers in the evaluation and management of complicated cases. Clinical decision support systems are especially instrumental in quickly assessing the criticality of pregnancy as it involves interpreting multiple maternal and fetal parameters. We propose a machine learning approach for early determination of the risk category of pregnancy based on patterns gleaned from profiles of known clinical parameters. In particular, we demonstrate the usefulness of classification and regression trees in solving multivariate problems in obstetric care since the decision making process and the importance of specific parameters are clearly illustrated in the tree. As proof of concept, an application use case has been presented.

  15. A New Automated Method and Sample Data Flow for Analysis of Volatile Nitrosamines in Human Urine*

    PubMed Central

    Hodgson, James A.; Seyler, Tiffany H.; McGahee, Ernest; Arnstein, Stephen; Wang, Lanqing

    2016-01-01

    Volatile nitrosamines (VNAs) are a group of compounds classified as probable (group 2A) and possible (group 2B) carcinogens in humans. Along with certain foods and contaminated drinking water, VNAs are detected at high levels in tobacco products and in both mainstream and sidestream smoke. Our laboratory monitors six urinary VNAs—N-nitrosodimethylamine (NDMA), N-nitrosomethylethylamine (NMEA), N-nitrosodiethylamine (NDEA), N-nitrosopiperidine (NPIP), N-nitrosopyrrolidine (NPYR), and N-nitrosomorpholine (NMOR)—using isotope dilution GC-MS/MS (QQQ) for large population studies such as the National Health and Nutrition Examination Survey (NHANES). In this paper, we report for the first time a new automated sample preparation method to more efficiently quantitate these VNAs. Automation is done using Hamilton STAR™ and Caliper Staccato™ workstations. This new automated method reduces sample preparation time from 4 hours to 2.5 hours while maintaining precision (inter-run CV < 10%) and accuracy (85% - 111%). More importantly this method increases sample throughput while maintaining a low limit of detection (<10 pg/mL) for all analytes. A streamlined sample data flow was created in parallel to the automated method, in which samples can be tracked from receiving to final LIMs output with minimal human intervention, further minimizing human error in the sample preparation process. This new automated method and the sample data flow are currently applied in bio-monitoring of VNAs in the US non-institutionalized population NHANES 2013-2014 cycle. PMID:26949569

  16. Automation of a Surface Sampling Probe/Electrospray Mass Spectrometry System

    SciTech Connect

    Kertesz, Vilmos; Ford, Michael J; Van Berkel, Gary J

    2005-01-01

    An image analysis automation concept and the associated software (HandsFree TLC/MS) were developed to control the surface sampling probe-to-surface distance during operation of a surface sampling electrospray system. This automation system enables both 'hands-free' formation of the liquid microjunction used to sample material from the surface and hands-free reoptimization of the microjunction thickness during a surface scan to achieve a fully automated surface sampling system. The image analysis concept and the practical implementation of the monitoring and automated adjustment of the sampling probe-to-surface distance (i.e., liquid microjunction thickness) are presented. The added capabilities for the preexisting surface sampling electrospray system afforded through this software control are illustrated by an example of automated scanning of multiple development lanes on a reversed-phase C8 TLC plate and by imaging inked lettering on a paper surface. The post data acquisition processing and data display aspects of the software package are also discussed.

  17. An automated sample preparation for detection of 72 doping-related substances.

    PubMed

    Cuervo, Darío; Díaz-Rodríguez, Pablo; Muñoz-Guerra, Jesús

    2014-06-01

    Automation of sample preparation procedures in a doping control laboratory is of great interest due to the large number of samples that have to be analyzed, especially in large events where a high throughput protocol is required to process samples over 24 h. The automation of such protocols requires specific equipment capable of carrying out the diverse mechanical tasks required for accomplishing these analytical methodologies, which include pipetting, shaking, heating, or crimping. An automated sample preparation procedure for the determination of doping-related substances by gas chromatography-mass spectrometry (GC-MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis, including enzymatic hydrolysis, liquid-phase extraction and derivatization steps, was developed by using an automated liquid handling system. This paper presents a description of the equipment, together with the validation data for 72 doping-related compounds including extraction efficiency, evaluation of carry-over, interferences, and robustness. Validation was approached as a comparison between the results obtained using the manual protocol and the transferred automated one. The described methodology can be applied for sample preparation in routine anti-doping analysis with high sample throughput and suitable performance. Copyright © 2013 John Wiley & Sons, Ltd.

  18. Automated versus manual sample inoculations in routine clinical microbiology: a performance evaluation of the fully automated InoqulA instrument.

    PubMed

    Froment, P; Marchandin, H; Vande Perre, P; Lamy, B

    2014-03-01

    The process of plate streaking has been automated to improve the culture readings, isolation quality, and workflow of microbiology laboratories. However, instruments have not been well evaluated under routine conditions. We aimed to evaluate the performance of the fully automated InoqulA instrument (BD Kiestra B.V., The Netherlands) in the automated seeding of liquid specimens and samples collected using swabs with transport medium. We compared manual and automated methods according to the (i) within-run reproducibility using Escherichia coli-calibrated suspensions, (ii) intersample contamination using a series of alternating sterile broths and broths with >10(5) CFU/ml of either E. coli or Proteus mirabilis, (iii) isolation quality with standardized mixed bacterial suspensions of diverse complexity and a 4-category standardized scale (very poor, poor, fair to good, or excellent), and (iv) agreement of the results obtained from 244 clinical specimens. By involving 15 technicians in the latter part of the comparative study, we estimated the variability in the culture quality at the level of the laboratory team. The instrument produced satisfactory reproducibility with no sample cross-contamination, and it performed better than the manual method, with more colony types recovered and isolated (up to 11% and 17%, respectively). Finally, we showed that the instrument did not shorten the seeding time over short periods of work compared to that for the manual method. Altogether, the instrument improved the quality and standardization of the isolation, thereby contributing to a better overall workflow, shortened the time to results, and provided more accurate results for polymicrobial specimens.

  19. Situation Awareness and Levels of Automation: Empirical Assessment of Levels of Automation in the Commercial Cockpit

    NASA Technical Reports Server (NTRS)

    Kaber, David B.; Schutte, Paul C. (Technical Monitor)

    2000-01-01

    This report has been prepared to closeout a NASA grant to Mississippi State University (MSU) for research into situation awareness (SA) and automation in the advanced commercial aircraft cockpit. The grant was divided into two obligations including $60,000 for the period from May 11, 2000 to December 25, 2000. The information presented in this report summarizes work completed through this obligation. It also details work to be completed with the balance of the current obligation and unobligated funds amounting to $50,043, which are to be granted to North Carolina State University for completion of the research project from July 31, 2000 to May 10, 2001. This research was to involve investigation of a broad spectrum of degrees of automation of complex systems on human-machine performance and SA. The work was to empirically assess the effect of theoretical levels of automation (LOAs) described in a taxonomy developed by Endsley & Kaber (1999) on naive and experienced subject performance and SA in simulated flight tasks. The study was to be conducted in the context of a realistic simulation of aircraft flight control. The objective of this work was to identify LOAs that effectively integrate humans and machines under normal operating conditions and failure modes. In general, the work was to provide insight into the design of automation in the commercial aircraft cockpit. Both laboratory and field investigations were to be conducted. At this point in time, a high-fidelity flight simulator of the McDonald Douglas (MD) 11 aircraft has been completed. The simulator integrates a reconfigurable flight simulator developed by the Georgia Institute of Technology and stand-alone simulations of MD-11 autoflight systems developed at MSU. Use of the simulator has been integrated into a study plan for the laboratory research and it is expected that the simulator will also be used in the field study with actual commercial pilots. In addition to the flight simulator, an electronic

  20. Development of an automated data processing method for sample to sample comparison of seized methamphetamines.

    PubMed

    Choe, Sanggil; Lee, Jaesin; Choi, Hyeyoung; Park, Yujin; Lee, Heesang; Pyo, Jaesung; Jo, Jiyeong; Park, Yonghoon; Choi, Hwakyung; Kim, Suncheun

    2012-11-30

    The information about the sources of supply, trafficking routes, distribution patterns and conspiracy links can be obtained from methamphetamine profiling. The precursor and synthetic method for the clandestine manufacture can be estimated from the analysis of minor impurities contained in methamphetamine. Also, the similarity between samples can be evaluated using the peaks that appear in chromatograms. In South Korea, methamphetamine was the most popular drug but the total seized amount of methamphetamine whole through the country was very small. Therefore, it would be more important to find the links between samples than the other uses of methamphetamine profiling. Many Asian countries including Japan and South Korea have been using the method developed by National Research Institute of Police Science of Japan. The method used gas chromatography-flame ionization detector (GC-FID), DB-5 column and four internal standards. It was developed to increase the amount of impurities and minimize the amount of methamphetamine. After GC-FID analysis, the raw data have to be processed. The data processing steps are very complex and require a lot of time and effort. In this study, Microsoft Visual Basic Application (VBA) modules were developed to handle these data processing steps. This module collected the results from the data into an Excel file and then corrected the retention time shift and response deviation generated from the sample preparation and instruments analysis. The developed modules were tested for their performance using 10 samples from 5 different cases. The processed results were analyzed with Pearson correlation coefficient for similarity assessment and the correlation coefficient of the two samples from the same case was more than 0.99. When the modules were applied to 131 seized methamphetamine samples, four samples from two different cases were found to have the common origin and the chromatograms of the four samples were appeared visually identical

  1. Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory

    SciTech Connect

    Hiraki, Masahiko; Watanabe, Shokei; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Gaponov, Yurii; Wakatsuki, Soichi

    2007-01-19

    We are now developing automated sample exchange robots for high-throughput protein crystallographic experiments for onsite use at synchrotron beam lines. It is part of the fully automated robotics systems being developed at the Photon Factory, for the purposes of protein crystallization, monitoring crystal growth, harvesting and freezing crystals, mounting the crystals inside a hutch and for data collection. We have already installed the sample exchange robots based on the SSRL automated mounting system at our insertion device beam lines BL-5A and AR-NW12A at the Photon Factory. In order to reduce the time required for sample exchange further, a prototype of a double-tonged system was developed. As a result of preliminary experiments with double-tonged robots, the sample exchange time was successfully reduced from 70 seconds to 10 seconds with the exception of the time required for pre-cooling and warming up the tongs.

  2. The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

    PubMed Central

    Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; Cohen, Aina E.

    2016-01-01

    The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. Sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade. PMID:27047309

  3. The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

    SciTech Connect

    Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; Cohen, Aina E.

    2016-02-24

    The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. As a result, sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.

  4. The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

    DOE PAGES

    Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; ...

    2016-02-24

    The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. As a result, sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.

  5. Automated biowaste sampling system, solids subsystem operating model, part 2

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.; Mangialardi, J. K.; Stauffer, R. E.

    1973-01-01

    The detail design and fabrication of the Solids Subsystem were implemented. The system's capacity for the collection, storage or sampling of feces and vomitus from six subjects was tested and verified.

  6. An automated atmospheric sampling system operating on 747 airliners

    NASA Technical Reports Server (NTRS)

    Perkins, P.; Gustafsson, U. R. C.

    1975-01-01

    An air sampling system that automatically measures the temporal and spatial distribution of selected particulate and gaseous constituents of the atmosphere has been installed on a number of commercial airliners and is collecting data on commercial air routes covering the world. Measurements of constituents related to aircraft engine emissions and other pollutants are made in the upper troposphere and lower stratosphere (6 to 12 km) in support of the Global Air Sampling Program (GASP). Aircraft operated by different airlines sample air at latitudes from the Arctic to Australia. This system includes specialized instrumentation for measuring carbon monoxide, ozone, water vapor, and particulates, a special air inlet probe for sampling outside air, a computerized automatic control, and a data acquisition system. Air constituents and related flight data are tape recorded in flight for later computer processing on the ground.

  7. Development and Evaluation of a Pilot Prototype Automated Online Sampling System

    SciTech Connect

    Whitaker, M.J.

    2000-07-27

    An automated online sampling system has been developed for the BNFL-Hanford Technetium Monitoring Program. The system was designed to be flexible and allows for the collection and delivery of samples to a variety of detection devices that may be used.

  8. Novel Automated Morphometric and Kinematic Handwriting Assessment: A Validity Study in Children with ASD and ADHD

    ERIC Educational Resources Information Center

    Dirlikov, Benjamin; Younes, Laurent; Nebel, Mary Beth; Martinelli, Mary Katherine; Tiedemann, Alyssa Nicole; Koch, Carolyn A.; Fiorilli, Diana; Bastian, Amy J.; Denckla, Martha Bridge; Miller, Michael I.; Mostofsky, Stewart H.

    2017-01-01

    This study presents construct validity for a novel automated morphometric and kinematic handwriting assessment, including (1) convergent validity, establishing reliability of automated measures with traditional manual-derived Minnesota Handwriting Assessment (MHA), and (2) discriminant validity, establishing that the automated methods distinguish…

  9. An automated behavioral box to assess forelimb function in rats

    PubMed Central

    Wong, Chelsea C.; Ramanathan, Dhakshin S.; Gulati, Tanuj; Won, Seok Joon; Ganguly, Karunesh

    2015-01-01

    Background Rodent forelimb reaching behaviors are commonly assessed using a single-pellet reach-to-grasp task. While the task is widely recognized as a very sensitive measure of distal limb function, it is also known to be very labor-intensive, both for initial training and the daily assessment of function. New Method Using components developed by open-source electronics platforms, we have designed and tested a low-cost automated behavioral box to measure forelimb function in rats. Our apparatus, made primarily of acrylic, was equipped with multiple sensors to control the duration and difficulty of the task, detect reach outcomes, and dispense pellets. Our control software, developed in MATLAB, was also used to control a camera in order to capture and process video during reaches. Importantly, such processing could monitor task performance in near real-time. Results We further demonstrate that the automated apparatus can be used to expedite skill acquisition, thereby increasing throughput as well as facilitating studies of early versus late motor learning. The setup is also readily compatible with chronic electrophysiological monitoring. Comparison with Existing Methods Compared to a previous version of this task, our setup provides a more efficient method to train and test rodents for studies of motor learning and recovery of function after stroke. The unbiased delivery of behavioral cues and outcomes also facilitates electrophysiological studies. Conclusions In summary, our automated behavioral box will allow high-throughput and efficient monitoring of rat forelimb function in both healthy and injured animals. PMID:25769277

  10. Automated Research Impact Assessment: A New Bibliometrics Approach

    PubMed Central

    Drew, Christina H.; Pettibone, Kristianna G.; Finch, Fallis Owen; Giles, Douglas; Jordan, Paul

    2016-01-01

    As federal programs are held more accountable for their research investments, The National Institute of Environmental Health Sciences (NIEHS) has developed a new method to quantify the impact of our funded research on the scientific and broader communities. In this article we review traditional bibliometric analyses, address challenges associated with them, and describe a new bibliometric analysis method, the Automated Research Impact Assessment (ARIA). ARIA taps into a resource that has only rarely been used for bibliometric analyses: references cited in “important” research artifacts, such as policies, regulations, clinical guidelines, and expert panel reports. The approach includes new statistics that science managers can use to benchmark contributions to research by funding source. This new method provides the ability to conduct automated impact analyses of federal research that can be incorporated in program evaluations. We apply this method to several case studies to examine the impact of NIEHS funded research. PMID:26989272

  11. Automated Research Impact Assessment: A New Bibliometrics Approach.

    PubMed

    Drew, Christina H; Pettibone, Kristianna G; Finch, Fallis Owen; Giles, Douglas; Jordan, Paul

    2016-03-01

    As federal programs are held more accountable for their research investments, The National Institute of Environmental Health Sciences (NIEHS) has developed a new method to quantify the impact of our funded research on the scientific and broader communities. In this article we review traditional bibliometric analyses, address challenges associated with them, and describe a new bibliometric analysis method, the Automated Research Impact Assessment (ARIA). ARIA taps into a resource that has only rarely been used for bibliometric analyses: references cited in "important" research artifacts, such as policies, regulations, clinical guidelines, and expert panel reports. The approach includes new statistics that science managers can use to benchmark contributions to research by funding source. This new method provides the ability to conduct automated impact analyses of federal research that can be incorporated in program evaluations. We apply this method to several case studies to examine the impact of NIEHS funded research.

  12. MARS: bringing the automation of small-molecule bioanalytical sample preparations to a new frontier.

    PubMed

    Li, Ming; Chou, Judy; Jing, Jing; Xu, Hui; Costa, Aldo; Caputo, Robin; Mikkilineni, Rajesh; Flannelly-King, Shane; Rohde, Ellen; Gan, Lawrence; Klunk, Lewis; Yang, Liyu

    2012-06-01

    In recent years, there has been a growing interest in automating small-molecule bioanalytical sample preparations specifically using the Hamilton MicroLab(®) STAR liquid-handling platform. In the most extensive work reported thus far, multiple small-molecule sample preparation assay types (protein precipitation extraction, SPE and liquid-liquid extraction) have been integrated into a suite that is composed of graphical user interfaces and Hamilton scripts. Using that suite, bioanalytical scientists have been able to automate various sample preparation methods to a great extent. However, there are still areas that could benefit from further automation, specifically, the full integration of analytical standard and QC sample preparation with study sample extraction in one continuous run, real-time 2D barcode scanning on the Hamilton deck and direct Laboratory Information Management System database connectivity. We developed a new small-molecule sample-preparation automation system that improves in all of the aforementioned areas. The improved system presented herein further streamlines the bioanalytical workflow, simplifies batch run design, reduces analyst intervention and eliminates sample-handling error.

  13. Automated Blood Sample Preparation Unit (ABSPU) for Portable Microfluidic Flow Cytometry.

    PubMed

    Chaturvedi, Akhil; Gorthi, Sai Siva

    2017-02-01

    Portable microfluidic diagnostic devices, including flow cytometers, are being developed for point-of-care settings, especially in conjunction with inexpensive imaging devices such as mobile phone cameras. However, two pervasive drawbacks of these have been the lack of automated sample preparation processes and cells settling out of sample suspensions, leading to inaccurate results. We report an automated blood sample preparation unit (ABSPU) to prevent blood samples from settling in a reservoir during loading of samples in flow cytometers. This apparatus automates the preanalytical steps of dilution and staining of blood cells prior to microfluidic loading. It employs an assembly with a miniature vibration motor to drive turbulence in a sample reservoir. To validate performance of this system, we present experimental evidence demonstrating prevention of blood cell settling, cell integrity, and staining of cells prior to flow cytometric analysis. This setup is further integrated with a microfluidic imaging flow cytometer to investigate cell count variability. With no need for prior sample preparation, a drop of whole blood can be directly introduced to the setup without premixing with buffers manually. Our results show that integration of this assembly with microfluidic analysis provides a competent automation tool for low-cost point-of-care blood-based diagnostics.

  14. Automated biowaste sampling system urine subsystem operating model, part 1

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.; Mangialardi, J. K.; Rosen, F.

    1973-01-01

    The urine subsystem automatically provides for the collection, volume sensing, and sampling of urine from six subjects during space flight. Verification of the subsystem design was a primary objective of the current effort which was accomplished thru the detail design, fabrication, and verification testing of an operating model of the subsystem.

  15. An Automated Sample Divider for Farmers Stock Peanuts

    USDA-ARS?s Scientific Manuscript database

    In-shell peanuts are harvested, loaded into drying trailers, and delivered to a central facility where they are dried to a moisture content safe for long term storage, sampled, graded, then unloaded into bulk storage. Drying trailers have capacities ranging from five to twenty-five tons of dry farme...

  16. An Automated Sample Divider for Farmers Stock Peanuts

    USDA-ARS?s Scientific Manuscript database

    In-shell peanuts are harvested, loaded into drying trailers, and delivered to a central facility where they are dried to a moisture content safe for long term storage, sampled, graded, then unloaded into bulk storage. Drying trailers have capacities ranging from five to twenty-five tons of dry farme...

  17. A Primer on Sampling for Statewide Assessment.

    ERIC Educational Resources Information Center

    Jaeger, Richard M.

    This paper is a primer on sampling procedures for statewide assessment. The careful reader should gain substantial knowledge about the promises and pitfalls of sampling for assessment. The primer has three basic objectives: (1) to define terms and concepts basic to sampling theory and its application, including population, sampling unit, sampling…

  18. The Impact of Sampling Approach on Population Invariance in Automated Scoring of Essays. Research Report. ETS RR-13-18

    ERIC Educational Resources Information Center

    Zhang, Mo

    2013-01-01

    Many testing programs use automated scoring to grade essays. One issue in automated essay scoring that has not been examined adequately is population invariance and its causes. The primary purpose of this study was to investigate the impact of sampling in model calibration on population invariance of automated scores. This study analyzed scores…

  19. An automated method of sample preparation of biofluids using pierceable caps to eliminate the uncapping of the sample tubes during sample transfer.

    PubMed

    Teitz, D S; Khan, S; Powell, M L; Jemal, M

    2000-09-11

    Biological samples are normally collected and stored frozen in capped tubes until analysis. To obtain aliquots of biological samples for analysis, the sample tubes have to be thawed, uncapped, samples removed and then recapped for further storage. In this paper, we report an automated method of sample transfer devised to eliminate the uncapping and recapping process. This sampling method was incorporated into an automated liquid-liquid extraction procedure of plasma samples. Using a robotic system, the plasma samples were transferred directly from pierceable capped tubes into microtubes contained in a 96-position block. The aliquoted samples were extracted with methyl-tert-butyl ether in the same microtubes. The supernatant organic layers were transferred to a 96-well collection plate and evaporated to dryness. The dried extracts were reconstituted and injected from the same plate for analysis by liquid chromatography with tandem mass spectrometry.

  20. Development of an automated sample preparation module for environmental monitoring of biowarfare agents.

    PubMed

    Hindson, Benjamin J; Brown, Steve B; Marshall, Graham D; McBride, Mary T; Makarewicz, Anthony J; Gutierrez, Dora M; Wolcott, Duane K; Metz, Thomas R; Madabhushi, Ramakrishna S; Dzenitis, John M; Colston, Billy W

    2004-07-01

    An automated sample preparation module, based upon sequential injection analysis (SIA), has been developed for use within an autonomous pathogen detection system. The SIA system interfaced aerosol sampling with multiplexed microsphere immunoassay-flow cytometric detection. Metering and sequestering of microspheres using SIA was found to be reproducible and reliable, over 24-h periods of autonomous operation. Four inbuilt immunoassay controls showed excellent immunoassay and system stability over five days of unattended continuous operation. Titration curves for two biological warfare agents, Bacillus anthracis and Yersinia pestis, obtained using the automated SIA procedure were shown to be similar to those generated using a manual microtiter plate procedure.

  1. Double-blind prospective study comparing two automated sperm analyzers versus manual semen assessment.

    PubMed

    Lammers, J; Splingart, C; Barrière, P; Jean, M; Fréour, T

    2014-01-01

    disadvantages of using automated systems are: notably the problem with testing some atypical samples and the inability to perform an assessment of morphology abnormalities. Based on the results of this study, the SQA-V Gold demonstrated better agreement vs. the manual method. In conclusion, automated semen analyzers can be used for routine semen analysis providing rapid clinically acceptable results with higher precision, and positively impacting laboratory standardization.

  2. An Automated Algorithm to Screen Massive Training Samples for a Global Impervious Surface Classification

    NASA Technical Reports Server (NTRS)

    Tan, Bin; Brown de Colstoun, Eric; Wolfe, Robert E.; Tilton, James C.; Huang, Chengquan; Smith, Sarah E.

    2012-01-01

    An algorithm is developed to automatically screen the outliers from massive training samples for Global Land Survey - Imperviousness Mapping Project (GLS-IMP). GLS-IMP is to produce a global 30 m spatial resolution impervious cover data set for years 2000 and 2010 based on the Landsat Global Land Survey (GLS) data set. This unprecedented high resolution impervious cover data set is not only significant to the urbanization studies but also desired by the global carbon, hydrology, and energy balance researches. A supervised classification method, regression tree, is applied in this project. A set of accurate training samples is the key to the supervised classifications. Here we developed the global scale training samples from 1 m or so resolution fine resolution satellite data (Quickbird and Worldview2), and then aggregate the fine resolution impervious cover map to 30 m resolution. In order to improve the classification accuracy, the training samples should be screened before used to train the regression tree. It is impossible to manually screen 30 m resolution training samples collected globally. For example, in Europe only, there are 174 training sites. The size of the sites ranges from 4.5 km by 4.5 km to 8.1 km by 3.6 km. The amount training samples are over six millions. Therefore, we develop this automated statistic based algorithm to screen the training samples in two levels: site and scene level. At the site level, all the training samples are divided to 10 groups according to the percentage of the impervious surface within a sample pixel. The samples following in each 10% forms one group. For each group, both univariate and multivariate outliers are detected and removed. Then the screen process escalates to the scene level. A similar screen process but with a looser threshold is applied on the scene level considering the possible variance due to the site difference. We do not perform the screen process across the scenes because the scenes might vary due to

  3. Automated syringe sampler. [remote sampling of air and water

    NASA Technical Reports Server (NTRS)

    Purgold, G. C. (Inventor)

    1981-01-01

    A number of sampling services are disposed in a rack which slides into a housing. In response to a signal from an antenna, the circutry elements are activated which provide power individually, collectively, or selectively to a servomechanism thereby moving an actuator arm and the attached jawed bracket supporting an evaculated tube towards a stationary needle. One open end of the needle extends through the side wall of a conduit to the interior and the other open end is maintained within the protective sleeve, supported by a bifurcated bracket. A septum in punctured by the end of the needle within the sleeve and a sample of the fluid medium in the conduit flows through the needle and is transferred to a tube. The signal to the servo is then reversed and the actuator arm moves the tube back to its original position permitting the septum to expand and seal the hole made by the needle. The jawed bracket is attached by pivot to the actuator to facilitate tube replacement.

  4. Automated Sample Preparation for Radiogenic and Non-Traditional Metal Isotopes: Removing an Analytical Barrier for High Sample Throughput

    NASA Astrophysics Data System (ADS)

    Field, M. Paul; Romaniello, Stephen; Gordon, Gwyneth W.; Anbar, Ariel D.; Herrmann, Achim; Martinez-Boti, Miguel A.; Anagnostou, Eleni; Foster, Gavin L.

    2014-05-01

    MC-ICP-MS has dramatically improved the analytical throughput for high-precision radiogenic and non-traditional isotope ratio measurements, compared to TIMS. The generation of large data sets, however, remains hampered by tedious manual drip chromatography required for sample purification. A new, automated chromatography system reduces the laboratory bottle neck and expands the utility of high-precision isotope analyses in applications where large data sets are required: geochemistry, forensic anthropology, nuclear forensics, medical research and food authentication. We have developed protocols to automate ion exchange purification for several isotopic systems (B, Ca, Fe, Cu, Zn, Sr, Cd, Pb and U) using the new prepFAST-MC™ (ESI, Nebraska, Omaha). The system is not only inert (all-flouropolymer flow paths), but is also very flexible and can easily facilitate different resins, samples, and reagent types. When programmed, precise and accurate user defined volumes and flow rates are implemented to automatically load samples, wash the column, condition the column and elute fractions. Unattended, the automated, low-pressure ion exchange chromatography system can process up to 60 samples overnight. Excellent reproducibility, reliability, recovery, with low blank and carry over for samples in a variety of different matrices, have been demonstrated to give accurate and precise isotopic ratios within analytical error for several isotopic systems (B, Ca, Fe, Cu, Zn, Sr, Cd, Pb and U). This illustrates the potential of the new prepFAST-MC™ (ESI, Nebraska, Omaha) as a powerful tool in radiogenic and non-traditional isotope research.

  5. Automated Assessment of the Quality of Depression Websites

    PubMed Central

    Tang, Thanh Tin; Hawking, David; Christensen, Helen

    2005-01-01

    Background Since health information on the World Wide Web is of variable quality, methods are needed to assist consumers to identify health websites containing evidence-based information. Manual assessment tools may assist consumers to evaluate the quality of sites. However, these tools are poorly validated and often impractical. There is a need to develop better consumer tools, and in particular to explore the potential of automated procedures for evaluating the quality of health information on the web. Objective This study (1) describes the development of an automated quality assessment procedure (AQA) designed to automatically rank depression websites according to their evidence-based quality; (2) evaluates the validity of the AQA relative to human rated evidence-based quality scores; and (3) compares the validity of Google PageRank and the AQA as indicators of evidence-based quality. Method The AQA was developed using a quality feedback technique and a set of training websites previously rated manually according to their concordance with statements in the Oxford University Centre for Evidence-Based Mental Health’s guidelines for treating depression. The validation phase involved 30 websites compiled from the DMOZ, Yahoo! and LookSmart Depression Directories by randomly selecting six sites from each of the Google PageRank bands of 0, 1-2, 3-4, 5-6 and 7-8. Evidence-based ratings from two independent raters (based on concordance with the Oxford guidelines) were then compared with scores derived from the automated AQA and Google algorithms. There was no overlap in the websites used in the training and validation phases of the study. Results The correlation between the AQA score and the evidence-based ratings was high and significant (r=0.85, P<.001). Addition of a quadratic component improved the fit, the combined linear and quadratic model explaining 82 percent of the variance. The correlation between Google PageRank and the evidence-based score was lower than

  6. Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers

    PubMed Central

    Rossetti, Cecilia; Świtnicka-Plak, Magdalena A.; Grønhaug Halvorsen, Trine; Cormack, Peter A.G.; Sellergren, Börje; Reubsaet, Léon

    2017-01-01

    Robust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting. PMID:28303910

  7. Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers

    NASA Astrophysics Data System (ADS)

    Rossetti, Cecilia; Świtnicka-Plak, Magdalena A.; Grønhaug Halvorsen, Trine; Cormack, Peter A. G.; Sellergren, Börje; Reubsaet, Léon

    2017-03-01

    Robust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting.

  8. An automated integrated platform for rapid and sensitive multiplexed protein profiling using human saliva samples

    PubMed Central

    Nie, Shuai; Henley, W. Hampton; Miller, Scott E.; Zhang, Huaibin; Mayer, Kathryn M.; Dennis, Patty J.; Oblath, Emily A.; Alarie, Jean Pierre; Wu, Yue; Oppenheim, Frank G.; Little, Frédéric F.; Uluer, Ahmet Z.; Wang, Peidong; Ramsey, J. Michael

    2014-01-01

    During the last decade, saliva has emerged as a potentially ideal diagnostic biofluid for noninvasive testing. In this paper, we present an automated, integrated platform useable by minimally trained personnel in the field for the diagnosis of respiratory diseases using human saliva as a sample specimen. In this platform, a saliva sample is loaded onto a disposable microfluidic chip containing all the necessary reagents and components required for saliva analysis. The chip is then inserted into the automated analyzer, the SDReader, where multiple potential protein biomarkers for respiratory diseases are measured simultaneously using a microsphere-based array via fluorescence sandwich immunoassays. The results are read optically, and the images are analyzed by a custom-designed algorithm. The fully automated assay requires as little as 10 μL of saliva sample, and the results are reported in 70 min. The performance of the platform was characterized by testing protein standard solutions, and the results were comparable to those from the 3.5-h lab bench assay that we have previously reported. The device was also deployed in two clinical environments where 273 human saliva samples collected from different subjects were successfully tested, demonstrating the device’s potential to assist clinicians with the diagnosis of respiratory diseases by providing timely protein biomarker profiling information. This platform, which combines non-invasive sample collection and fully automated analysis, can also be utilized in point-of-care diagnostics. PMID:24448498

  9. Fully automated open access platform for rapid, combined serial evaporation and sample reformatting.

    PubMed

    Benali, Otman; Davies, Gary; Deal, Martyn; Farrant, Elizabeth; Guthrie, Duncan; Holden, John; Wheeler, Rob

    2008-01-01

    This paper reports a novel evaporator and its integration with an automated sample handling system to create a high throughput evaporation platform. The Vaportec V-10 evaporator uses a high speed rotation motor ( approximately 6000 rpm) to spin the vial containing a sample, creating a thin film of solvent which can be readily evaporated by the application of heat to the vial, while the consequent centrifugal force prevents "bumping". An intelligent algorithm controls pressure and temperature for optimum solvent removal conditions and end of run detection, critical for automation. The system allows the option of evaporation directly from a sample source vial, or alternatively, integrated liquid handling facilities provide the capability of transferring samples portionwise from a (large) source vial or bottle to a (small) daughter container, enabling efficient sample reformatting, with minimum user intervention. The open access system makes significant advances over current vacuum centrifugal evaporators in terms of evaporation rate and ease of automation. The evaporator's main features, the integration of robotics to provide automation, and examples of evaporation rates of a wide range of solvents from a variety of containers are described.

  10. An automated integrated platform for rapid and sensitive multiplexed protein profiling using human saliva samples.

    PubMed

    Nie, Shuai; Henley, W Hampton; Miller, Scott E; Zhang, Huaibin; Mayer, Kathryn M; Dennis, Patty J; Oblath, Emily A; Alarie, Jean Pierre; Wu, Yue; Oppenheim, Frank G; Little, Frédéric F; Uluer, Ahmet Z; Wang, Peidong; Ramsey, J Michael; Walt, David R

    2014-03-21

    During the last decade, saliva has emerged as a potentially ideal diagnostic biofluid for noninvasive testing. In this paper, we present an automated, integrated platform useable by minimally trained personnel in the field for the diagnosis of respiratory diseases using human saliva as a sample specimen. In this platform, a saliva sample is loaded onto a disposable microfluidic chip containing all the necessary reagents and components required for saliva analysis. The chip is then inserted into the automated analyzer, the SDReader, where multiple potential protein biomarkers for respiratory diseases are measured simultaneously using a microsphere-based array via fluorescence sandwich immunoassays. The results are read optically, and the images are analyzed by a custom-designed algorithm. The fully automated assay requires as little as 10 μL of saliva sample, and the results are reported in 70 min. The performance of the platform was characterized by testing protein standard solutions, and the results were comparable to those from the 3.5 h lab bench assay that we have previously reported. The device was also deployed in two clinical environments where 273 human saliva samples collected from different subjects were successfully tested, demonstrating the device's potential to assist clinicians with the diagnosis of respiratory diseases by providing timely protein biomarker profiling information. This platform, which combines noninvasive sample collection and fully automated analysis, can also be utilized in point-of-care diagnostics.

  11. Automated Portable Test System (APTS) - A performance envelope assessment tool

    NASA Technical Reports Server (NTRS)

    Kennedy, R. S.; Dunlap, W. P.; Jones, M. B.; Wilkes, R. L.; Bittner, A. C., Jr.

    1985-01-01

    The reliability and stability of microcomputer-based psychological tests are evaluated. The hardware, test programs, and system control of the Automated Portable Test System, which assesses human performance and subjective status, are described. Subjects were administered 11 pen-and-pencil and microcomputer-based tests for 10 sessions. The data reveal that nine of the 10 tests stabilized by the third administration; inertial correlations were high and consistent. It is noted that the microcomputer-based tests display good psychometric properties in terms of differential stability and reliability.

  12. Investigation of Automated Sampling Techniques to Measure Total Mercury in Stream- Water During Storm-Events

    NASA Astrophysics Data System (ADS)

    Riscassi, A. L.; Scanlon, T. M.

    2008-12-01

    High-flow events (storms and snowmelt) are a dominant transport mechanism for total mercury (HgT) from the terrestrial to the aqueous environment. High-gradient headwater catchments are a primary source of downstream contamination because they store large pools of Hg in soils and sediments. Consistent, high- frequency event-sampling of headwater streams is rare, however, because of the unpredictability of high flows, remoteness of sites, and the difficulties associated with the ultra-clean sampling procedures. The use of automated sampling techniques with an ISCO® sampler has been demonstrated in several studies for trace metals, but their use for collection of HgT samples has not been systematically evaluated in the literature. Even with clean equipment at deployment, subsequent contamination and loss by evasion are possible considering the bottles, as currently designed, are open to the atmosphere before sampling and until retrieval. Field tests are conducted using an ISCO® sampler retrofitted with pre- cleaned Teflon® sampling lines and glass bottles to determine the relative errors associated with the automated sampling method for a variety of HgT concentrations and preservation techniques. Differences between quality assurance and quality control results for automated and manual sampling are also investigated. Sample containers are filled with known standards of HgT solution and left in the ISCO® containers at the field site and each day (up to 7 days) are capped and returned for analysis. During a storm event, manual samples are taken from the middle of the water column concurrently with the ISCO® at hourly intervals using "clean hands" procedures. Evaluations of results are used to establish quality assurance guidelines for future field campaigns using automated techniques for HgT sampling.

  13. Automated laboratory based X-ray beamline with multi-capillary sample chamber

    SciTech Connect

    Purushothaman, S.; Gauthé, B. L. L. E.; Brooks, N. J.; Templer, R. H.; Ces, O.

    2013-08-15

    An automated laboratory based X-ray beamline with a multi-capillary sample chamber capable of undertaking small angle X-ray scattering measurements on a maximum of 104 samples at a time as a function of temperature between 5 and 85 °C has been developed. The modular format of the system enables the user to simultaneously equilibrate samples at eight different temperatures with an accuracy of ±0.005 °C. This system couples a rotating anode generator and 2D optoelectronic detector with Franks X-ray optics, leading to typical exposure times of less than 5 min for lyotropic liquid crystalline samples. Beamline control including sample exchange and data acquisition has been fully automated via a custom designed LabVIEW framework.

  14. Optimizing HER2 assessment in breast cancer: application of automated image analysis.

    PubMed

    Holten-Rossing, Henrik; Møller Talman, Maj-Lis; Kristensson, Martin; Vainer, Ben

    2015-07-01

    In breast cancer, analysis of HER2 expression is pivotal for treatment decision. This study aimed at comparing digital, automated image analysis with manual reading using the HER2-CONNECT algorithm (Visiopharm) in order to minimize the number of equivocal 2+ scores and the need for reflex fluorescence in situ hybridization (FISH) analysis. Consecutive samples from 462 patients were included. Tissue micro arrays (TMAs) were routinely manufactured including two 2 mm cores from each patient, and each core was assessed in order to ensure the presence of invasive carcinoma. Immunohistochemical staining (IHC) was performed with Roche/Ventana's HER2 ready-to-use kit. TMAs were scanned in a Zeiss Axio Z1 scanner, and one batch analysis of the HER2-CONNECT algorithm including all core samples was run using Visiopharm's cloud-based software. The automated reading was compared to conventional manual assessment of HER2 protein expression, together with FISH analysis of HER2 gene amplification for borderline (2+) protein expression samples. Compared to FISH analysis, manual assessment of the HER2 protein expression demonstrated a sensitivity of 85.8% and a specificity of 86.0% with 14.0% equivocal samples. With HER2-CONNECT, sensitivity increased to 100 % and specificity to 95.5% with less than 4.5% equivocal. Total agreement when comparing HER2-CONNECT with manual IHC assessment supplemented by FISH for borderline (2+) cases was 93.6%. Application of automated image analysis for HER2 protein expression instead of manual assessment decreases the need for supplementary FISH testing by 68%. In the routine diagnostic setting, this would have significant impact on cost reduction and turn-around time.

  15. Automated LSA Assessment of Summaries in Distance Education: Some Variables to Be Considered

    ERIC Educational Resources Information Center

    Jorge-Botana, Guillermo; Luzón, José M.; Gómez-Veiga, Isabel; Martín-Cordero, Jesús I.

    2015-01-01

    A latent semantic analysis-based automated summary assessment is described; this automated system is applied to a real learning from text task in a Distance Education context. We comment on the use of automated content, plagiarism, text coherence measures, and word weights average and their impact on predicting human judges summary scoring. A…

  16. Automated LSA Assessment of Summaries in Distance Education: Some Variables to Be Considered

    ERIC Educational Resources Information Center

    Jorge-Botana, Guillermo; Luzón, José M.; Gómez-Veiga, Isabel; Martín-Cordero, Jesús I.

    2015-01-01

    A latent semantic analysis-based automated summary assessment is described; this automated system is applied to a real learning from text task in a Distance Education context. We comment on the use of automated content, plagiarism, text coherence measures, and word weights average and their impact on predicting human judges summary scoring. A…

  17. An automated system for global atmospheric sampling using B-747 airliners

    NASA Technical Reports Server (NTRS)

    Lew, K. Q.; Gustafsson, U. R. C.; Johnson, R. E.

    1981-01-01

    The global air sampling program utilizes commercial aircrafts in scheduled service to measure atmospheric constituents. A fully automated system designed for the 747 aircraft is described. Airline operational constraints and data and control subsystems are treated. The overall program management, system monitoring, and data retrieval from four aircraft in global service is described.

  18. Automated Geospatial Watershed Assessment Tool (AGWA): Applications for Fire Management and Assessment.

    EPA Science Inventory

    New tools and functionality have been incorporated into the Automated Geospatial Watershed Assessment Tool (AGWA) to assess the impacts of wildland fire on runoff and erosion. AGWA (see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface joi...

  19. Automated Geospatial Watershed Assessment Tool (AGWA): Applications for Fire Management and Assessment.

    EPA Science Inventory

    New tools and functionality have been incorporated into the Automated Geospatial Watershed Assessment Tool (AGWA) to assess the impacts of wildland fire on runoff and erosion. AGWA (see: www.tucson.ars.ag.gov/agwa or http://www.epa.gov/esd/land-sci/agwa/) is a GIS interface joi...

  20. Application of bar codes to the automation of analytical sample data collection

    SciTech Connect

    Jurgensen, H A

    1986-01-01

    The Health Protection Department at the Savannah River Plant collects 500 urine samples per day for tritium analyses. Prior to automation, all sample information was compiled manually. Bar code technology was chosen for automating this program because it provides a more accurate, efficient, and inexpensive method for data entry. The system has three major functions: sample labeling is accomplished at remote bar code label stations composed of an Intermec 8220 (Intermec Corp.) interfaced to an IBM-PC, data collection is done on a central VAX 11/730 (Digital Equipment Corp.). Bar code readers are used to log-in samples to be analyzed on liquid scintillation counters. The VAX 11/730 processes the data and generates reports, data storage is on the VAX 11/730 and backed up on the plant's central computer. A brief description of several other bar code applications at the Savannah River Plant is also presented.

  1. Automated Clinical Assessment from Smart home-based Behavior Data

    PubMed Central

    Dawadi, Prafulla Nath; Cook, Diane Joyce; Schmitter-Edgecombe, Maureen

    2016-01-01

    Smart home technologies offer potential benefits for assisting clinicians by automating health monitoring and well-being assessment. In this paper, we examine the actual benefits of smart home-based analysis by monitoring daily behaviour in the home and predicting standard clinical assessment scores of the residents. To accomplish this goal, we propose a Clinical Assessment using Activity Behavior (CAAB) approach to model a smart home resident’s daily behavior and predict the corresponding standard clinical assessment scores. CAAB uses statistical features that describe characteristics of a resident’s daily activity performance to train machine learning algorithms that predict the clinical assessment scores. We evaluate the performance of CAAB utilizing smart home sensor data collected from 18 smart homes over two years using prediction and classification-based experiments. In the prediction-based experiments, we obtain a statistically significant correlation (r = 0.72) between CAAB-predicted and clinician-provided cognitive assessment scores and a statistically significant correlation (r = 0.45) between CAAB-predicted and clinician-provided mobility scores. Similarly, for the classification-based experiments, we find CAAB has a classification accuracy of 72% while classifying cognitive assessment scores and 76% while classifying mobility scores. These prediction and classification results suggest that it is feasible to predict standard clinical scores using smart home sensor data and learning-based data analysis. PMID:26292348

  2. Automated Video Quality Assessment for Deep-Sea Video

    NASA Astrophysics Data System (ADS)

    Pirenne, B.; Hoeberechts, M.; Kalmbach, A.; Sadhu, T.; Branzan Albu, A.; Glotin, H.; Jeffries, M. A.; Bui, A. O. V.

    2015-12-01

    Video provides a rich source of data for geophysical analysis, often supplying detailed information about the environment when other instruments may not. This is especially true of deep-sea environments, where direct visual observations cannot be made. As computer vision techniques improve and volumes of video data increase, automated video analysis is emerging as a practical alternative to labor-intensive manual analysis. Automated techniques can be much more sensitive to video quality than their manual counterparts, so performing quality assessment before doing full analysis is critical to producing valid results.Ocean Networks Canada (ONC), an initiative of the University of Victoria, operates cabled ocean observatories that supply continuous power and Internet connectivity to a broad suite of subsea instruments from the coast to the deep sea, including video and still cameras. This network of ocean observatories has produced almost 20,000 hours of video (about 38 hours are recorded each day) and an additional 8,000 hours of logs from remotely operated vehicle (ROV) dives. We begin by surveying some ways in which deep-sea video poses challenges for automated analysis, including: 1. Non-uniform lighting: Single, directional, light sources produce uneven luminance distributions and shadows; remotely operated lighting equipment are also susceptible to technical failures. 2. Particulate noise: Turbidity and marine snow are often present in underwater video; particles in the water column can have sharper focus and higher contrast than the objects of interest due to their proximity to the light source and can also influence the camera's autofocus and auto white-balance routines. 3. Color distortion (low contrast): The rate of absorption of light in water varies by wavelength, and is higher overall than in air, altering apparent colors and lowering the contrast of objects at a distance.We also describe measures under development at ONC for detecting and mitigating

  3. Characteristics of a new automated blood sampling system for positron emission tomography

    SciTech Connect

    Eriksson, L.; Ingvar, M.; Rosenqvist, G.; Ekdahl, T.; Kappel, P.

    1995-08-01

    A new commercially available automated blood sampling system (ABSS) for positron emission tomography has been evaluated. The system uses a single BGO crystal and detects with high efficiency the annihilation radiation from tracers, labelled with positron emitting isotopes, in arterial blood. In addition the possibilities to use the ABSS as a detector in the analysis of the plasma samples with liquid chromatography techniques under flow conditions has been explored.

  4. Using sample entropy for automated sign language recognition on sEMG and accelerometer data.

    PubMed

    Kosmidou, Vasiliki E; Hadjileontiadis, Leontios I

    2010-03-01

    Communication using sign language (SL) provides alternative means for information transmission among the deaf. Automated gesture recognition involved in SL, however, could further expand this communication channel to the world of hearers. In this study, data from five-channel surface electromyogram and three-dimensional accelerometer from signers' dominant hand were subjected to a feature extraction process. The latter consisted of sample entropy (SampEn)-based analysis, whereas time-frequency feature (TFF) analysis was also performed as a baseline method for the automated recognition of 60-word lexicon Greek SL (GSL) isolated signs. Experimental results have shown a 66 and 92% mean classification accuracy threshold using TFF and SampEn, respectively. These results justify the superiority of SampEn against conventional methods, such as TFF, to provide with high recognition hit-ratios, combined with feature vector dimension reduction, toward a fast and reliable automated GSL gesture recognition.

  5. Automated Neuropsychological Assessment Metrics, Version 4 (ANAM4): Examination of Select Psychometric Properties and Administration Procedures

    DTIC Science & Technology

    2016-12-01

    1 Award Number: W81XWH-08-1-0021 TITLE: Automated Neuropsychological Assessment Metrics, Version 4 (ANAM4): Examination of Select Psychometric...NUMBER W81XWH-08-1-0021 Automated Neuropsychological Assessment Metrics, Version 4 (ANAM4): Examination of Select Psychometric Properties and...mission and Force 2025 objectives of the United States military. The Automated Neuropsychological Assessment Metrics (ANAM) is a computer assisted tool

  6. Feasibility of automated speech sample collection with stuttering children using interactive voice response (IVR) technology.

    PubMed

    Vogel, Adam P; Block, Susan; Kefalianos, Elaina; Onslow, Mark; Eadie, Patricia; Barth, Ben; Conway, Laura; Mundt, James C; Reilly, Sheena

    2015-04-01

    To investigate the feasibility of adopting automated interactive voice response (IVR) technology for remotely capturing standardized speech samples from stuttering children. Participants were 10 6-year-old stuttering children. Their parents called a toll-free number from their homes and were prompted to elicit speech from their children using a standard protocol involving conversation, picture description and games. The automated IVR system was implemented using an off-the-shelf telephony software program and delivered by a standard desktop computer. The software infrastructure utilizes voice over internet protocol. Speech samples were automatically recorded during the calls. Video recordings were simultaneously acquired in the home at the time of the call to evaluate the fidelity of the telephone collected samples. Key outcome measures included syllables spoken, percentage of syllables stuttered and an overall rating of stuttering severity using a 10-point scale. Data revealed a high level of relative reliability in terms of intra-class correlation between the video and telephone acquired samples on all outcome measures during the conversation task. Findings were less consistent for speech samples during picture description and games. Results suggest that IVR technology can be used successfully to automate remote capture of child speech samples.

  7. Pharmacological profiles of acute myeloid leukemia treatments in patient samples by automated flow cytometry: a bridge to individualized medicine.

    PubMed

    Bennett, Teresa A; Montesinos, Pau; Moscardo, Federico; Martinez-Cuadron, David; Martinez, Joaquin; Sierra, Jorge; García, Raimundo; de Oteyza, Jaime Perez; Fernandez, Pascual; Serrano, Josefina; Fernandez, Angeles; Herrera, Pilar; Gonzalez, Ataulfo; Bethancourt, Concepcion; Rodriguez-Macias, Gabriela; Alonso, Arancha; Vera, Juan A; Navas, Begoña; Lavilla, Esperanza; Lopez, Juan A; Jimenez, Santiago; Simiele, Adriana; Vidriales, Belen; Gonzalez, Bernardo J; Burgaleta, Carmen; Hernandez Rivas, Jose A; Mascuñano, Raul Cordoba; Bautista, Guiomar; Perez Simon, Jose A; Fuente, Adolfo de la; Rayón, Consolación; Troconiz, Iñaki F; Janda, Alvaro; Bosanquet, Andrew G; Hernandez-Campo, Pilar; Primo, Daniel; Lopez, Rocio; Liebana, Belen; Rojas, Jose L; Gorrochategui, Julian; Sanz, Miguel A; Ballesteros, Joan

    2014-08-01

    We have evaluated the ex vivo pharmacology of single drugs and drug combinations in malignant cells of bone marrow samples from 125 patients with acute myeloid leukemia using a novel automated flow cytometry-based platform (ExviTech). We have improved previous ex vivo drug testing with 4 innovations: identifying individual leukemic cells, using intact whole blood during the incubation, using an automated platform that escalates reliably data, and performing analyses pharmacodynamic population models. Samples were sent from 24 hospitals to a central laboratory and incubated for 48 hours in whole blood, after which drug activity was measured in terms of depletion of leukemic cells. The sensitivity of single drugs is assessed for standard efficacy (EMAX) and potency (EC50) variables, ranked as percentiles within the population. The sensitivity of drug-combination treatments is assessed for the synergism achieved in each patient sample. We found a large variability among patient samples in the dose-response curves to a single drug or combination treatment. We hypothesize that the use of the individual patient ex vivo pharmacological profiles may help to guide a personalized treatment selection. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Automated bone age assessment of older children using the radius

    NASA Astrophysics Data System (ADS)

    Tsao, Sinchai; Gertych, Arkadiusz; Zhang, Aifeng; Liu, Brent J.; Huang, Han K.

    2008-03-01

    The Digital Hand Atlas in Assessment of Skeletal Development is a large-scale Computer Aided Diagnosis (CAD) project for automating the process of grading Skeletal Development of children from 0-18 years of age. It includes a complete collection of 1,400 normal hand X-rays of children between the ages of 0-18 years of age. Bone Age Assessment is used as an index of skeletal development for detection of growth pathologies that can be related to endocrine, malnutrition and other disease types. Previous work at the Image Processing and Informatics Lab (IPILab) allowed the bone age CAD algorithm to accurately assess bone age of children from 1 to 16 (male) or 14 (female) years of age using the Phalanges as well as the Carpal Bones. At the older ages (16(male) or 14(female) -19 years of age) the Phalanges as well as the Carpal Bones are fully developed and do not provide well-defined features for accurate bone age assessment. Therefore integration of the Radius Bone as a region of interest (ROI) is greatly needed and will significantly improve the ability to accurately assess the bone age of older children. Preliminary studies show that an integrated Bone Age CAD that utilizes the Phalanges, Carpal Bones and Radius forms a robust method for automatic bone age assessment throughout the entire age range (1-19 years of age).

  9. Evaluation of automated streamwater sampling during storm events for total mercury analysis.

    PubMed

    Riscassi, Ami L; Converse, Amber D; Hokanson, Kelly J; Scanlon, Todd M

    2010-10-06

    Understanding the processes by which mercury is mobilized from soil to stream is currently limited by a lack of observations during high-flow events, when the majority of this transport occurs. An automated technique to collect stream water for unfiltered total mercury (HgT) analysis was systematically evaluated in a series of laboratory experiments. Potential sources of error investigated were 1) carry-over effects associated with sequential sampling, 2) deposition of HgT into empty bottles prior to sampling, and 3) deposition to or evasion from samples prior to retrieval. Contamination from carry-over effects was minimal (<2%) and HgT deposition to open bottles was negligible. Potentially greater errors are associated with evasive losses of HgT from uncapped samples, with higher temperatures leading to greater evasion. These evasive losses were found to take place primarily within the first eight hours. HgT associated with particulate material is much less prone to evasion than HgT in dissolved form. A field test conducted during a high-flow event confirmed unfiltered HgT concentrations sampled with an automated system were comparable to those taken manually, as the mean absolute difference between automated and manual samples (10%) was similar to the mean difference between duplicate grab samples (9%). Results from this study have demonstrated that a standard automated sampler, retrofitted with appropriately cleaned fluoropolymer tubing and glass bottles, can effectively be used for collection of streamwater during high-flow events for low-level mercury analysis.

  10. Automated cellular sample preparation using a Centrifuge-on-a-Chip.

    PubMed

    Mach, Albert J; Kim, Jae Hyun; Arshi, Armin; Hur, Soojung Claire; Di Carlo, Dino

    2011-09-07

    The standard centrifuge is a laboratory instrument widely used by biologists and medical technicians for preparing cell samples. Efforts to automate the operations of concentration, cell separation, and solution exchange that a centrifuge performs in a simpler and smaller platform have had limited success. Here, we present a microfluidic chip that replicates the functions of a centrifuge without moving parts or external forces. The device operates using a purely fluid dynamic phenomenon in which cells selectively enter and are maintained in microscale vortices. Continuous and sequential operation allows enrichment of cancer cells from spiked blood samples at the mL min(-1) scale, followed by fluorescent labeling of intra- and extra-cellular antigens on the cells without the need for manual pipetting and washing steps. A versatile centrifuge-analogue may open opportunities in automated, low-cost and high-throughput sample preparation as an alternative to the standard benchtop centrifuge in standardized clinical diagnostics or resource poor settings.

  11. Automated quality assessment in three-dimensional breast ultrasound images.

    PubMed

    Schwaab, Julia; Diez, Yago; Oliver, Arnau; Martí, Robert; van Zelst, Jan; Gubern-Mérida, Albert; Mourri, Ahmed Bensouda; Gregori, Johannes; Günther, Matthias

    2016-04-01

    Automated three-dimensional breast ultrasound (ABUS) is a valuable adjunct to x-ray mammography for breast cancer screening of women with dense breasts. High image quality is essential for proper diagnostics and computer-aided detection. We propose an automated image quality assessment system for ABUS images that detects artifacts at the time of acquisition. Therefore, we study three aspects that can corrupt ABUS images: the nipple position relative to the rest of the breast, the shadow caused by the nipple, and the shape of the breast contour on the image. Image processing and machine learning algorithms are combined to detect these artifacts based on 368 clinical ABUS images that have been rated manually by two experienced clinicians. At a specificity of 0.99, 55% of the images that were rated as low quality are detected by the proposed algorithms. The areas under the ROC curves of the single classifiers are 0.99 for the nipple position, 0.84 for the nipple shadow, and 0.89 for the breast contour shape. The proposed algorithms work fast and reliably, which makes them adequate for online evaluation of image quality during acquisition. The presented concept may be extended to further image modalities and quality aspects.

  12. Fully Automated Deep Learning System for Bone Age Assessment.

    PubMed

    Lee, Hyunkwang; Tajmir, Shahein; Lee, Jenny; Zissen, Maurice; Yeshiwas, Bethel Ayele; Alkasab, Tarik K; Choy, Garry; Do, Synho

    2017-08-01

    Skeletal maturity progresses through discrete phases, a fact that is used routinely in pediatrics where bone age assessments (BAAs) are compared to chronological age in the evaluation of endocrine and metabolic disorders. While central to many disease evaluations, little has changed to improve the tedious process since its introduction in 1950. In this study, we propose a fully automated deep learning pipeline to segment a region of interest, standardize and preprocess input radiographs, and perform BAA. Our models use an ImageNet pretrained, fine-tuned convolutional neural network (CNN) to achieve 57.32 and 61.40% accuracies for the female and male cohorts on our held-out test images. Female test radiographs were assigned a BAA within 1 year 90.39% and within 2 years 98.11% of the time. Male test radiographs were assigned 94.18% within 1 year and 99.00% within 2 years. Using the input occlusion method, attention maps were created which reveal what features the trained model uses to perform BAA. These correspond to what human experts look at when manually performing BAA. Finally, the fully automated BAA system was deployed in the clinical environment as a decision supporting system for more accurate and efficient BAAs at much faster interpretation time (<2 s) than the conventional method.

  13. Current status and future prospects of an automated sample exchange system PAM for protein crystallography

    NASA Astrophysics Data System (ADS)

    Hiraki, M.; Yamada, Y.; Chavas, L. M. G.; Matsugaki, N.; Igarashi, N.; Wakatsuki, S.

    2013-03-01

    To achieve fully-automated and/or remote data collection in high-throughput X-ray experiments, the Structural Biology Research Centre at the Photon Factory (PF) has installed PF automated mounting system (PAM) for sample exchange robots at PF macromolecular crystallography beamlines BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. We are upgrading the experimental systems, including the PAM for stable and efficient operation. To prevent human error in automated data collection, we installed a two-dimensional barcode reader for identification of the cassettes and sample pins. Because no liquid nitrogen pipeline in the PF experimental hutch is installed, the users commonly add liquid nitrogen using a small Dewar. To address this issue, an automated liquid nitrogen filling system that links a 100-liter tank to the robot Dewar has been installed on the PF macromolecular beamline. Here we describe this new implementation, as well as future prospects.

  14. The Automated Assessment of Postural Stability: Balance Detection Algorithm.

    PubMed

    Napoli, Alessandro; Glass, Stephen M; Tucker, Carole; Obeid, Iyad

    2017-08-30

    Impaired balance is a common indicator of mild traumatic brain injury, concussion and musculoskeletal injury. Given the clinical relevance of such injuries, especially in military settings, it is paramount to develop more accurate and reliable on-field evaluation tools. This work presents the design and implementation of the automated assessment of postural stability (AAPS) system, for on-field evaluations following concussion. The AAPS is a computer system, based on inexpensive off-the-shelf components and custom software, that aims to automatically and reliably evaluate balance deficits, by replicating a known on-field clinical test, namely, the Balance Error Scoring System (BESS). The AAPS main innovation is its balance error detection algorithm that has been designed to acquire data from a Microsoft Kinect(®) sensor and convert them into clinically-relevant BESS scores, using the same detection criteria defined by the original BESS test. In order to assess the AAPS balance evaluation capability, a total of 15 healthy subjects (7 male, 8 female) were required to perform the BESS test, while simultaneously being tracked by a Kinect 2.0 sensor and a professional-grade motion capture system (Qualisys AB, Gothenburg, Sweden). High definition videos with BESS trials were scored off-line by three experienced observers for reference scores. AAPS performance was assessed by comparing the AAPS automated scores to those derived by three experienced observers. Our results show that the AAPS error detection algorithm presented here can accurately and precisely detect balance deficits with performance levels that are comparable to those of experienced medical personnel. Specifically, agreement levels between the AAPS algorithm and the human average BESS scores ranging between 87.9% (single-leg on foam) and 99.8% (double-leg on firm ground) were detected. Moreover, statistically significant differences in balance scores were not detected by an ANOVA test with alpha equal to

  15. Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33.

    PubMed

    Round, A R; Franke, D; Moritz, S; Huchler, R; Fritsche, M; Malthan, D; Klaering, R; Svergun, D I; Roessle, M

    2008-10-01

    There is a rapidly increasing interest in the use of synchrotron small-angle X-ray scattering (SAXS) for large-scale studies of biological macromolecules in solution, and this requires an adequate means of automating the experiment. A prototype has been developed of an automated sample changer for solution SAXS, where the solutions are kept in thermostatically controlled well plates allowing for operation with up to 192 samples. The measuring protocol involves controlled loading of protein solutions and matching buffers, followed by cleaning and drying of the cell between measurements. The system was installed and tested at the X33 beamline of the EMBL, at the storage ring DORIS-III (DESY, Hamburg), where it was used by over 50 external groups during 2007. At X33, a throughput of approximately 12 samples per hour, with a failure rate of sample loading of less than 0.5%, was observed. The feedback from users indicates that the ease of use and reliability of the user operation at the beamline were greatly improved compared with the manual filling mode. The changer is controlled by a client-server-based network protocol, locally and remotely. During the testing phase, the changer was operated in an attended mode to assess its reliability and convenience. Full integration with the beamline control software, allowing for automated data collection of all samples loaded into the machine with remote control from the user, is presently being implemented. The approach reported is not limited to synchrotron-based SAXS but can also be used on laboratory and neutron sources.

  16. A fully automated plasma protein precipitation sample preparation method for LC-MS/MS bioanalysis.

    PubMed

    Ma, Ji; Shi, Jianxia; Le, Hoa; Cho, Robert; Huang, Judy Chi-jou; Miao, Shichang; Wong, Bradley K

    2008-02-01

    This report describes the development and validation of a robust robotic system that fully integrates all peripheral devices needed for the automated preparation of plasma samples by protein precipitation. The liquid handling system consisted of a Tecan Freedom EVO 200 liquid handling platform equipped with an 8-channel liquid handling arm, two robotic plate-handling arms, and two plate shakers. Important additional components integrated into the platform were a robotic temperature-controlled centrifuge, a plate sealer, and a plate seal piercing station. These enabled unattended operation starting from a stock solution of the test compound, a set of test plasma samples and associated reagents. The stock solution of the test compound was used to prepare plasma calibration and quality control samples. Once calibration and quality control samples were prepared, precipitation of plasma proteins was achieved by addition of three volumes of acetonitrile. Integration of the peripheral devices allowed automated sequential completion of the centrifugation, plate sealing, piercing and supernatant transferral steps. The method produced a sealed, injection-ready 96-well plate of plasma extracts. Accuracy and precision of the automated system were satisfactory for the intended use: intra-day and the inter-day precision were excellent (C.V.<5%), while the intra-day and inter-day accuracies were acceptable (relative error<8%). The flexibility of the platform was sufficient to accommodate pharmacokinetic studies of different numbers of animals and time points. To the best of our knowledge, this represents the first complete automation of the protein precipitation method for plasma sample analysis.

  17. Feasibility of home-based automated Parkinson's disease motor assessment.

    PubMed

    Mera, Thomas O; Heldman, Dustin A; Espay, Alberto J; Payne, Megan; Giuffrida, Joseph P

    2012-01-15

    Patients with Parkinson's disease (PD) receive therapies aimed at addressing a diverse range of motor symptoms. Motor complications in the form of symptom fluctuations and dyskinesias that commonly occur with chronic PD medication use may not be effectively captured by Unified Parkinson's Disease Rating Scale (UPDRS) assessments performed in the clinic. Therefore, home monitoring may be a viable adjunct tool to provide insight into PD motor symptom response to treatment. In this pilot study, we sought to evaluate the feasibility of capturing PD motor symptoms at home using a computer-based assessment system. Ten subjects diagnosed with idiopathic PD used the system at home and ten non-PD control subjects used the system in a laboratory. The Kinesia system consists of a wireless finger-worn motion sensor and a laptop computer with software for automated tremor and bradykinesia severity score assessments. Data from control subjects were used to develop compliance algorithms for rejecting motor tasks performed incorrectly. These algorithms were then applied to data collected from the PD subjects who used the Kinesia system at home to complete motor exams 3-6 times per day over 3-6 days. Motor tasks not rejected by the compliance algorithms were further processed for symptom severity. PD subjects successfully completed motor assessments at home, with approximately 97% of all motor task data files (1222/1260) accepted. These findings suggest that objective home monitoring of PD motor fluctuations is feasible. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Automated semiquantitative direct-current-arc spectrographic analysis of eight argonne premium coal ash samples

    USGS Publications Warehouse

    Skeen, C.J.; Libby, B.J.; Crandell, W.B.

    1990-01-01

    The automated semiquantitative direct-current-arc spectre-graphic method was used to analyze 62 elements in eight Argonne Premium Coal Ash samples. All eight coal ash samples were analyzed in triplicate to verify precision and accuracy of the method. The precision for most elements was within ??10%. The accuracy of this method is limited to +50% or -33% because of the nature of the standard curves for each of the elements. Adjustments to the computer program were implemented to account for unique matrix interferences in these particular coal ash samples.

  19. Automated sampling system for the analysis of amino acids using microfluidic capillary electrophoresis.

    PubMed

    Xu, Zhang-Run; Lan, Yue; Fan, Xiao-Feng; Li, Qi

    2009-04-30

    An improved automated continuous sample introduction system for microfluidic capillary electrophoresis (CE) is described. A sample plate was designed into gear-shaped and was fixed onto the shaft of a step motor. Twenty slotted reservoirs for containing samples and working electrolytes were fabricated on the "gear tooth" of the plate. A single 7.5-cm long Teflon AF-coated silica capillary serves as separation channel, sampling probe, as well as liquid-core waveguide (LCW) for light transmission. Platinum layer deposited on the capillary tip serves as the electrode. Automated continuous sample introduction was achieved by scanning the capillary tip through the slots of reservoirs. The sample was introduced into capillary and separated immediately in the capillary with only about 2-nL gross sample consumption. The laser-induced fluorescence (LIF) method with LCW technique was used for detecting fluorescein isothiocyanate (FITC)-labeled amino acids. With electric-field strength of 320 V/cm for injection and separation, and 1.0-s sample injection time, a mixture of FITC-labeled arginine and leucine was separated with a throughput of 60/h and a carryover of 2.7%.

  20. Development of a Miniature Mass Spectrometer and an Automated Detector for Sampling Explosive Materials

    PubMed Central

    Hashimoto, Yuichiro

    2017-01-01

    The development of a robust ionization source using the counter-flow APCI, miniature mass spectrometer, and an automated sampling system for detecting explosives are described. These development efforts using mass spectrometry were made in order to improve the efficiencies of on-site detection in areas such as security, environmental, and industrial applications. A development team, including the author, has struggled for nearly 20 years to enhance the robustness and reduce the size of mass spectrometers to meet the requirements needed for on-site applications. This article focuses on the recent results related to the detection of explosive materials where automated particle sampling using a cyclone concentrator permitted the inspection time to be successfully reduced to 3 s. PMID:28337396

  1. Development of a Miniature Mass Spectrometer and an Automated Detector for Sampling Explosive Materials.

    PubMed

    Hashimoto, Yuichiro

    2017-01-01

    The development of a robust ionization source using the counter-flow APCI, miniature mass spectrometer, and an automated sampling system for detecting explosives are described. These development efforts using mass spectrometry were made in order to improve the efficiencies of on-site detection in areas such as security, environmental, and industrial applications. A development team, including the author, has struggled for nearly 20 years to enhance the robustness and reduce the size of mass spectrometers to meet the requirements needed for on-site applications. This article focuses on the recent results related to the detection of explosive materials where automated particle sampling using a cyclone concentrator permitted the inspection time to be successfully reduced to 3 s.

  2. Non-uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination

    PubMed Central

    Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

    2015-01-01

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [1H,1H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. PMID:26227870

  3. National Assessment Approach to Sampling Error Estimation. Sampling Error Monograph.

    ERIC Educational Resources Information Center

    Folsom, Ralph E., Jr.

    Beginning with the planning stages of the National Assessment of Educational Progress (NAEP), careful attention has been given to the design of efficient probability sampling methods for the selection of class-age respondents and the assignment of test packages. With these methods, it is possible for NAEP researchers to make relatively precise…

  4. Development and evaluation of an automated fall risk assessment system.

    PubMed

    Lee, Ju Young; Jin, Yinji; Piao, Jinshi; Lee, Sun-Mi

    2016-04-01

    Fall risk assessment is the first step toward prevention, and a risk assessment tool with high validity should be used. This study aimed to develop and validate an automated fall risk assessment system (Auto-FallRAS) to assess fall risks based on electronic medical records (EMRs) without additional data collected or entered by nurses. This study was conducted in a 1335-bed university hospital in Seoul, South Korea. The Auto-FallRAS was developed using 4211 fall-related clinical data extracted from EMRs. Participants included fall patients and non-fall patients (868 and 3472 for the development study; 752 and 3008 for the validation study; and 58 and 232 for validation after clinical application, respectively). The system was evaluated for predictive validity and concurrent validity. The final 10 predictors were included in the logistic regression model for the risk-scoring algorithm. The results of the Auto-FallRAS were shown as high/moderate/low risk on the EMR screen. The predictive validity analyzed after clinical application of the Auto-FallRAS was as follows: sensitivity = 0.95, NPV = 0.97 and Youden index = 0.44. The validity of the Morse Fall Scale assessed by nurses was as follows: sensitivity = 0.68, NPV = 0.88 and Youden index = 0.28. This study found that the Auto-FallRAS results were better than were the nurses' predictions. The advantage of the Auto-FallRAS is that it automatically analyzes information and shows patients' fall risk assessment results without requiring additional time from nurses. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. An automated system for assessing cognitive function in any environment

    NASA Astrophysics Data System (ADS)

    Wesnes, Keith A.

    2005-05-01

    The Cognitive Drug Research (CDR) computerized assessment system has been in use in worldwide clinical trials for over 20 years. It is a computer based system which assesses core aspects of human cognitive function including attention, information, working memory and long-term memory. It has been extensively validated and can be performed by a wide range of clinical populations including patients with various types of dementia. It is currently in worldwide use in clinical trials to evaluate new medicines, as well as a variety of programs involving the effects of age, stressors illnesses and trauma upon human cognitive function. Besides being highly sensitive to drugs which will impair or improve function, its utility has been maintained over the last two decades by constantly increasing the number of platforms upon which it can operate. Besides notebook versions, the system can be used on a wrist worn device, PDA, via tht telephone and over the internet. It is the most widely used automated cognitive function assessment system in worldwide clinical research. It has dozens of parallel forms and requires little training to use or administer. The basic development of the system wil be identified, and the huge databases (normative, patient population, drug effects) which have been built up from hundreds of clinical trials will be described. The system is available for use in virtually any environment or type of trial.

  7. An Automated Summarization Assessment Algorithm for Identifying Summarizing Strategies

    PubMed Central

    Abdi, Asad; Idris, Norisma; Alguliyev, Rasim M.; Aliguliyev, Ramiz M.

    2016-01-01

    Background Summarization is a process to select important information from a source text. Summarizing strategies are the core cognitive processes in summarization activity. Since summarization can be important as a tool to improve comprehension, it has attracted interest of teachers for teaching summary writing through direct instruction. To do this, they need to review and assess the students' summaries and these tasks are very time-consuming. Thus, a computer-assisted assessment can be used to help teachers to conduct this task more effectively. Design/Results This paper aims to propose an algorithm based on the combination of semantic relations between words and their syntactic composition to identify summarizing strategies employed by students in summary writing. An innovative aspect of our algorithm lies in its ability to identify summarizing strategies at the syntactic and semantic levels. The efficiency of the algorithm is measured in terms of Precision, Recall and F-measure. We then implemented the algorithm for the automated summarization assessment system that can be used to identify the summarizing strategies used by students in summary writing. PMID:26735139

  8. An instrument for automated purification of nucleic acids from contaminated forensic samples.

    PubMed

    Broemeling, David J; Pel, Joel; Gunn, Dylan C; Mai, Laura; Thompson, Jason D; Poon, Hiron; Marziali, Andre

    2008-02-01

    Forensic crime scene sample analysis, by its nature, often deals with samples in which there are low amounts of nucleic acids, on substrates that often lead to inhibition of subsequent enzymatic reactions such as PCR amplification for STR profiling. Common substrates include denim from blue jeans, which yields indigo dye as a PCR inhibitor, and soil, which yields humic substances as inhibitors. These inhibitors frequently co-extract with nucleic acids in standard column or bead-based preps, leading to frequent failure of STR profiling. We present a novel instrument for DNA purification of forensic samples that is capable of highly effective concentration of nucleic acids from soil particulates, fabric, and other complex samples including solid components. The novel concentration process, known as SCODA, is inherently selective for long charged polymers such as DNA, and therefore is able to effectively reject known contaminants. We present an automated sample preparation instrument based on this process, and preliminary results based on mock forensic samples.

  9. Automated Prediction of Catalytic Mechanism and Rate Law Using Graph-Based Reaction Path Sampling.

    PubMed

    Habershon, Scott

    2016-04-12

    In a recent article [ J. Chem. Phys. 2015 , 143 , 094106 ], we introduced a novel graph-based sampling scheme which can be used to generate chemical reaction paths in many-atom systems in an efficient and highly automated manner. The main goal of this work is to demonstrate how this approach, when combined with direct kinetic modeling, can be used to determine the mechanism and phenomenological rate law of a complex catalytic cycle, namely cobalt-catalyzed hydroformylation of ethene. Our graph-based sampling scheme generates 31 unique chemical products and 32 unique chemical reaction pathways; these sampled structures and reaction paths enable automated construction of a kinetic network model of the catalytic system when combined with density functional theory (DFT) calculations of free energies and resultant transition-state theory rate constants. Direct simulations of this kinetic network across a range of initial reactant concentrations enables determination of both the reaction mechanism and the associated rate law in an automated fashion, without the need for either presupposing a mechanism or making steady-state approximations in kinetic analysis. Most importantly, we find that the reaction mechanism which emerges from these simulations is exactly that originally proposed by Heck and Breslow; furthermore, the simulated rate law is also consistent with previous experimental and computational studies, exhibiting a complex dependence on carbon monoxide pressure. While the inherent errors of using DFT simulations to model chemical reactivity limit the quantitative accuracy of our calculated rates, this work confirms that our automated simulation strategy enables direct analysis of catalytic mechanisms from first principles.

  10. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments

    PubMed Central

    Nurizzo, Didier; Bowler, Matthew W.; Caserotto, Hugo; Dobias, Fabien; Giraud, Thierry; Surr, John; Guichard, Nicolas; Papp, Gergely; Guijarro, Matias; Mueller-Dieckmann, Christoph; Flot, David; McSweeney, Sean; Cipriani, Florent; Theveneau, Pascal; Leonard, Gordon A.

    2016-01-01

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically. PMID:27487827

  11. Electrochemical pesticide detection with AutoDip--a portable platform for automation of crude sample analyses.

    PubMed

    Drechsel, Lisa; Schulz, Martin; von Stetten, Felix; Moldovan, Carmen; Zengerle, Roland; Paust, Nils

    2015-02-07

    Lab-on-a-chip devices hold promise for automation of complex workflows from sample to answer with minimal consumption of reagents in portable devices. However, complex, inhomogeneous samples as they occur in environmental or food analysis may block microchannels and thus often cause malfunction of the system. Here we present the novel AutoDip platform which is based on the movement of a solid phase through the reagents and sample instead of transporting a sequence of reagents through a fixed solid phase. A ball-pen mechanism operated by an external actuator automates unit operations such as incubation and washing by consecutively dipping the solid phase into the corresponding liquids. The platform is applied to electrochemical detection of organophosphorus pesticides in real food samples using an acetylcholinesterase (AChE) biosensor. Minimal sample preparation and an integrated reagent pre-storage module hold promise for easy handling of the assay. Detection of the pesticide chlorpyrifos-oxon (CPO) spiked into apple samples at concentrations of 10(-7) M has been demonstrated. This concentration is below the maximum residue level for chlorpyrifos in apples defined by the European Commission.

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

    PubMed

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

    2014-08-05

    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.

  13. Automated sample preparation and LC-MS for high-throughput ADME quantification.

    PubMed

    O'Connor, Desmond

    2002-01-01

    Bioanalytical groups in the pharmaceutical industry provide quantitative data to support all stages of drug discovery. The increased use of 96-well plates and robotic liquid handling systems, the availability of robust triple quadruple mass spectrometers, and developments in chromatographic and samples preparation techniques, have all increased the rate at which this data can be generated. This review describes currently used methods and emerging technologies for automation of high-throughput quantitative bioanalysis. The focus is on recent applications of sample preparation and chromatography techniques compatible with detection by triple quadruple mass spectrometers.

  14. Automated mango fruit assessment using fuzzy logic approach

    NASA Astrophysics Data System (ADS)

    Hasan, Suzanawati Abu; Kin, Teoh Yeong; Sauddin@Sa'duddin, Suraiya; Aziz, Azlan Abdul; Othman, Mahmod; Mansor, Ab Razak; Parnabas, Vincent

    2014-06-01

    In term of value and volume of production, mango is the third most important fruit product next to pineapple and banana. Accurate size assessment of mango fruits during harvesting is vital to ensure that they are classified to the grade accordingly. However, the current practice in mango industry is grading the mango fruit manually using human graders. This method is inconsistent, inefficient and labor intensive. In this project, a new method of automated mango size and grade assessment is developed using RGB fiber optic sensor and fuzzy logic approach. The calculation of maximum, minimum and mean values based on RGB fiber optic sensor and the decision making development using minimum entropy formulation to analyse the data and make the classification for the mango fruit. This proposed method is capable to differentiate three different grades of mango fruit automatically with 77.78% of overall accuracy compared to human graders sorting. This method was found to be helpful for the application in the current agricultural industry.

  15. Automated assessment of bradykinesia and dyskinesia in Parkinson's disease.

    PubMed

    Griffiths, Robert I; Kotschet, Katya; Arfon, Sian; Xu, Zheng Ming; Johnson, William; Drago, John; Evans, Andrew; Kempster, Peter; Raghav, Sanjay; Horne, Malcolm K

    2012-01-01

    There is a need for objective measures of dyskinesia and bradykinesia of Parkinson's disease (PD) that are continuous throughout the day and related to levodopa dosing. The output of an algorithm that calculates dyskinesia and bradykinesia scores every two minutes over 10 days (PKG: Global Kinetics Corporation) was compared with conventional rating scales for PD in PD subjects. The algorithm recognises bradykinesia as movements made with lower acceleration and amplitude and with longer intervals between movement. Similarly the algorithm recognises dyskinesia as having movements of normal amplitude and acceleration but with shorter periods without movement. The distribution of the bradykinesia and dyskinesia scores from PD subjects differed from that of normal subjects. The algorithm predicted the clinical dyskinesia rating scale AIMS with a 95% margin of error of 3.2 units compared with the inter-rater 95% limits of agreement from 3 neurologists of -3.4 to +4.3 units. Similarly the algorithm predicted the UPDRS III score with a margin of error similar to the inter-rater limits of agreement. Improvement in scores in response to changes in medication could be assessed statistically in individual patients. This algorithm provides objective, continuous and automated assessment of the clinical features of bradykinesia and dyskinesia in PD.

  16. An automated system for performance assessment of airport lighting

    NASA Astrophysics Data System (ADS)

    Niblock, James; Peng, Jian-Xun; McMenemy, Karen; Irwin, George

    2008-02-01

    This paper presents work undertaken into the development of an automated air-based vision system for assessing the performance of an approach lighting system (ALS) installation in accordance with International Civil Aviation Organisation (ICAO) standards. The measuring device consists of an image sensor with associated lens system fitted to the interior of an aircraft. The vision system is capable of capturing sequences of airport lighting images during a normal approach to the airport. These images are then processed to determine the uniformity of the ALS. To assess the uniformity of the ALS the luminaires must first be uniquely identified and tracked through an image sequence. A model-based matching technique is utilised which uses a camera projection system to match a set of template data to the extracted image data. From the matching results the associated position and pose of the camera is estimated. Each luminaire emits an intensity which is dependant on its angular displacement from the camera. As such, it is possible to predict the intensity that each luminaire within the ALS emits during an approach. Luminaires emitting the same intensity are banded together for the uniformity analysis. Uniformity assumes that luminaires in close proximity exhibit similar luminous intensity characteristics. During a typical approach grouping information is obtained for the various sectors of luminaires. This grouping information is used to compare luminaires against one another in terms of their extracted grey level information. The developed software is validated using data acquired during an actual approach to a UK airport.

  17. Using automated continual performance assessment to improve health care.

    PubMed

    Wulff, K R; Westphal, J R; Shray, S L; Hunkeler, E F

    1997-01-01

    Inefficiency in the work of health care providers is evident and contributes to health care costs. In the early 20th century, industrial engineers developed scientific methods for studying work to improve performance (efficiency) by measuring results--i.e., quality, cost, and productivity. In the mid-20th century, business managers developed ways to apply these methods to improve the work process. These scientific methods and management approaches can be applied to improving medical work. Fee-for-service practice has had incentives to maximize productivity, and prepaid practice has had incentives to minimize costs, but no sector of the health care system has systematically pursued the optimization of all performance variables: quality, cost, and productivity. We have reviewed evolving methods for the automation of continual assessment of performance in health care using touch screen and computer telephone, logging and scheduling software, appropriate combinations of generic or disease-specific health status questionnaires, physiologic measurements or laboratory assays from computerized records, and cost and productivity data from computerized registration logs. We propose that the results of outcome assessment be rapidly and continually transmitted to providers, patients, and managers so that health care processes can be progressively improved. The evolving systems we have described are the practical tools that can help us achieve our performance goals.

  18. Accuracy assessment with complex sampling designs

    Treesearch

    Raymond L. Czaplewski

    2010-01-01

    A reliable accuracy assessment of remotely sensed geospatial data requires a sufficiently large probability sample of expensive reference data. Complex sampling designs reduce cost or increase precision, especially with regional, continental and global projects. The General Restriction (GR) Estimator and the Recursive Restriction (RR) Estimator separate a complex...

  19. Automated sample preparation facilitated by PhyNexus MEA purification system for oligosaccharide mapping of glycoproteins.

    PubMed

    Prater, Bradley D; Anumula, Kalyan R; Hutchins, Jeff T

    2007-10-15

    A reproducible high-throughput sample cleanup method for fluorescent oligosaccharide mapping of glycoproteins is described. Oligosaccharides are released from glycoproteins using PNGase F and labeled with 2-aminobenzoic acid (anthranilic acid, AA). A PhyNexus MEA system was adapted for automated isolation of the fluorescently labeled oligosaccharides from the reaction mixture prior to mapping by HPLC. The oligosaccharide purification uses a normal-phase polyamide resin (DPA-6S) in custom-made pipette tips. The resin volume, wash, and elution steps involved were optimized to obtain high recovery of oligosaccharides with the least amount of contaminating free fluorescent dye in the shortest amount of time. The automated protocol for sample cleanup eliminated all manual manipulations with a recycle time of 23 min. We have reduced the amount of excess AA by 150-fold, allowing quantitative oligosaccharide mapping from as little as 500 ng digested recombinant immunoglobulin G (rIgG). This low sample requirement allows early selection of a cell line with desired characteristics (e.g., oligosaccharide profile and high specific productivity) for the production of glycoprotein drugs. In addition, the use of Tecan or another robotic platform in conjunction with this method should allow the cleanup of 96 samples in 23 min, a significant decrease in the amount of time currently required to process such a large number of samples.

  20. Automated liver sampling using a gradient dual-echo Dixon-based technique.

    PubMed

    Bashir, Mustafa R; Dale, Brian M; Merkle, Elmar M; Boll, Daniel T

    2012-05-01

    Magnetic resonance spectroscopy of the liver requires input from a physicist or physician at the time of acquisition to insure proper voxel selection, while in multiecho chemical shift imaging, numerous regions of interest must be manually selected in order to ensure analysis of a representative portion of the liver parenchyma. A fully automated technique could improve workflow by selecting representative portions of the liver prior to human analysis. Complete volumes from three-dimensional gradient dual-echo acquisitions with two-point Dixon reconstruction acquired at 1.5 and 3 T were analyzed in 100 subjects, using an automated liver sampling algorithm, based on ratio pairs calculated from signal intensity image data as fat-only/water-only and log(in-phase/opposed-phase) on a voxel-by-voxel basis. Using different gridding variations of the algorithm, the average correct liver volume samples ranged from 527 to 733 mL. The average percentage of sample located within the liver ranged from 95.4 to 97.1%, whereas the average incorrect volume selected was 16.5-35.4 mL (2.9-4.6%). Average run time was 19.7-79.0 s. The algorithm consistently selected large samples of the hepatic parenchyma with small amounts of erroneous extrahepatic sampling, and run times were feasible for execution on an MRI system console during exam acquisition. Copyright © 2011 Wiley Periodicals, Inc.

  1. Assessment of organic matter resistance to biodegradation in volcanic ash soils assisted by automated interpretation of infrared spectra from humic acid and whole soil samples by using partial least squares

    NASA Astrophysics Data System (ADS)

    Hernández, Zulimar; Pérez Trujillo, Juan Pedro; Hernández-Hernández, Sergio Alexander; Almendros, Gonzalo; Sanz, Jesús

    2014-05-01

    From a practical viewpoint, the most interesting possibilities of applying infrared (IR) spectroscopy to soil studies lie on processing IR spectra of whole soil (WS) samples [1] in order to forecast functional descriptors at high organizational levels of the soil system, such as soil C resilience. Currently, there is a discussion on whether the resistance to biodegradation of soil organic matter (SOM) depends on its molecular composition or on environmental interactions between SOM and mineral components, such could be the case with physical encapsulation of particulate SOM or organo-mineral derivatives, e.g., those formed with amorphous oxides [2]. A set of about 200 dependent variables from WS and isolated, ash free, humic acids (HA) [3] was obtained in 30 volcanic ash soils from Tenerife Island (Spain). Soil biogeochemical properties such as SOM, allophane (Alo + 1 /2 Feo), total mineralization coefficient (TMC) or aggregate stability were determined in WS. In addition, structural information on SOM was obtained from the isolated HA fractions by visible spectroscopy and analytical pyrolysis (Py-GC/MS). Aiming to explore the potential of partial least squares regression (PLS) in forecasting soil dependent variables, exclusively using the information extracted from WS and HA IR spectral profiles, data were processed by using ParLeS [4] and Unscrambler programs. Data pre-treatments should be carefully chosen: the most significant PLS models from IR spectra of HA were obtained after second derivative pre-treatment, which prevented effects of intrinsically broadband spectral profiles typical in macromolecular heterogeneous material such as HA. Conversely, when using IR spectra of WS, the best forecasting models were obtained using linear baseline correction and maximum normalization pre-treatment. With WS spectra, the most successful prediction models were obtained for SOM, magnetite, allophane, aggregate stability, clay and total aromatic compounds, whereas the PLS

  2. Adapting for Scalability: Automating the Video Assessment of Instructional Learning

    ERIC Educational Resources Information Center

    Roberts , Amy M.; LoCasale-Crouch, Jennifer; Hamre, Bridget K.; Buckrop, Jordan M.

    2017-01-01

    Although scalable programs, such as online courses, have the potential to reach broad audiences, they may pose challenges to evaluating learners' knowledge and skills. Automated scoring offers a possible solution. In the current paper, we describe the process of creating and testing an automated means of scoring a validated measure of teachers'…

  3. Ground Truth Sampling and LANDSAT Accuracy Assessment

    NASA Technical Reports Server (NTRS)

    Robinson, J. W.; Gunther, F. J.; Campbell, W. J.

    1982-01-01

    It is noted that the key factor in any accuracy assessment of remote sensing data is the method used for determining the ground truth, independent of the remote sensing data itself. The sampling and accuracy procedures developed for nuclear power plant siting study are described. The purpose of the sampling procedure was to provide data for developing supervised classifications for two study sites and for assessing the accuracy of that and the other procedures used. The purpose of the accuracy assessment was to allow the comparison of the cost and accuracy of various classification procedures as applied to various data types.

  4. Automation of Workplace Lifting Hazard Assessment for Musculoskeletal Injury Prevention

    PubMed Central

    2014-01-01

    posture and temporal elements of tasks such as task frequency in an automated fashion, although these findings should be confirmed in a larger study. Further work is needed to incorporate force assessments and address workplace feasibility challenges. We anticipate that this approach could ultimately be used to perform large-scale musculoskeletal exposure assessment not only for research but also to provide real-time feedback to workers and employers during work method improvement activities and employee training. PMID:24987523

  5. A new automated system for the rapid analysis of atmospheric water vapor samples for stable isotope composition.

    NASA Astrophysics Data System (ADS)

    Strong, M.; Sharp, Z.; Gutzler, D.

    2004-12-01

    An automated technique for measuring the isotopic composition (δ D) of atmospheric water vapor is being developed at the University of New Mexico. Air is sampled using 12 mL glass vials with screw-on caps. Our analytical system flushes the sample vial with He, isolates the water vapor in a cold trap, and then reduces the water with carbon at 1300° C to form H2 and CO. Isotopic ratios are then measured in continuous flow using a Finnigan Delta plus XL mass spectrometer. With Albuquerque-area air, sample size is approximately 100 nanomoles of H2O. Our system is robotic and interfaces with a commercially available autosampler. This enables us to analyze ~100 air samples per day with little supervision. Standards are prepared by sampling water vapor in equilibrium with waters of known isotopic composition within a glovebox. The advantage of such a system is that it will allow us to analyze atmospheric water vapor at temporal and spatial resolutions not practical with more time-consuming traditional techniques. Sample vials are compact, inexpensive, and easy to use, enabling air samples to be acquired with little effort. One potential application for this technique includes problems requiring high temporal resolution (and a high number of samples) such as diurnal cycles of evapotranspiration. Other applications include studies of the three-dimensional spatial distribution of δ D in water vapor to assess water vapor transport pathways.

  6. ALARA ASSESSMENT OF SETTLER SLUDGE SAMPLING METHODS

    SciTech Connect

    NELSEN LA

    2009-01-30

    The purpose of this assessment is to compare underwater and above water settler sludge sampling methods to determine if the added cost for underwater sampling for the sole purpose of worker dose reductions is justified. Initial planning for sludge sampling included container, settler and knock-out-pot (KOP) sampling. Due to the significantly higher dose consequence of KOP sludge, a decision was made to sample KOP underwater to achieve worker dose reductions. Additionally, initial plans were to utilize the underwater sampling apparatus for settler sludge. Since there are no longer plans to sample KOP sludge, the decision for underwater sampling for settler sludge needs to be revisited. The present sampling plan calls for spending an estimated $2,500,000 to design and construct a new underwater sampling system (per A21 C-PL-001 RevOE). This evaluation will compare and contrast the present method of above water sampling to the underwater method that is planned by the Sludge Treatment Project (STP) and determine if settler samples can be taken using the existing sampling cart (with potentially minor modifications) while maintaining doses to workers As Low As Reasonably Achievable (ALARA) and eliminate the need for costly redesigns, testing and personnel retraining.

  7. Automated, Ultra-Sterile Solid Sample Handling and Analysis on a Chip

    NASA Technical Reports Server (NTRS)

    Mora, Maria F.; Stockton, Amanda M.; Willis, Peter A.

    2013-01-01

    There are no existing ultra-sterile lab-on-a-chip systems that can accept solid samples and perform complete chemical analyses without human intervention. The proposed solution is to demonstrate completely automated lab-on-a-chip manipulation of powdered solid samples, followed by on-chip liquid extraction and chemical analysis. This technology utilizes a newly invented glass micro-device for solid manipulation, which mates with existing lab-on-a-chip instrumentation. Devices are fabricated in a Class 10 cleanroom at the JPL MicroDevices Lab, and are plasma-cleaned before and after assembly. Solid samples enter the device through a drilled hole in the top. Existing micro-pumping technology is used to transfer milligrams of powdered sample into an extraction chamber where it is mixed with liquids to extract organic material. Subsequent chemical analysis is performed using portable microchip capillary electrophoresis systems (CE). These instruments have been used for ultra-highly sensitive (parts-per-trillion, pptr) analysis of organic compounds including amines, amino acids, aldehydes, ketones, carboxylic acids, and thiols. Fully autonomous amino acid analyses in liquids were demonstrated; however, to date there have been no reports of completely automated analysis of solid samples on chip. This approach utilizes an existing portable instrument that houses optics, high-voltage power supplies, and solenoids for fully autonomous microfluidic sample processing and CE analysis with laser-induced fluorescence (LIF) detection. Furthermore, the entire system can be sterilized and placed in a cleanroom environment for analyzing samples returned from extraterrestrial targets, if desired. This is an entirely new capability never demonstrated before. The ability to manipulate solid samples, coupled with lab-on-a-chip analysis technology, will enable ultraclean and ultrasensitive end-to-end analysis of samples that is orders of magnitude more sensitive than the ppb goal given

  8. Direct determination of selenium in serum by electrothermal atomic absorption spectrometry using automated ultrasonic slurry sampling

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Kang; Yen, Cheng-Chieh; Wei, Bai-Luh; Hu, Chao-Chin; Yu, Jya-Jyun; Chung, Chien; Kuo, Sheng-Chu

    1998-01-01

    Selenium concentration in body fluids is a good index to establish human selenium status. This work discusses the determination of selenium in serum by ETAAS using longitudinal Zeeman-effect background correction and combining the use of automated slurry sampling. The standard reference materials bovine serum (NIST, SRM 1598) and second-generation biological freeze-dried human serum are analyzed to verify the accuracy and precision of this technique. The direct method proposed in this study is used for the determination of selenium in human serum collected from healthy people of 19-25 years. The average accuracy values of certified reference serum samples and the recovery values of spiked samples indicate this method to be an efficient and rapid technique for determining selenium in biological samples.

  9. Device and method for automated separation of a sample of whole blood into aliquots

    DOEpatents

    Burtis, Carl A.; Johnson, Wayne F.

    1989-01-01

    A device and a method for automated processing and separation of an unmeasured sample of whole blood into multiple aliquots of plasma. Capillaries are radially oriented on a rotor, with the rotor defining a sample chamber, transfer channels, overflow chamber, overflow channel, vent channel, cell chambers, and processing chambers. A sample of whole blood is placed in the sample chamber, and when the rotor is rotated, the blood moves outward through the transfer channels to the processing chambers where the blood is centrifugally separated into a solid cellular component and a liquid plasma component. When the rotor speed is decreased, the plasma component backfills the capillaries resulting in uniform aliquots of plasma which may be used for subsequent analytical procedures.

  10. Application of existing technology to meet increasing demands for automated sample handling.

    PubMed

    Chow, A T; Kegelman, J E; Kohli, C; McCabe, D D; Moore, J F

    1990-09-01

    As the clinical laboratory advances toward total automation, the marketplace is now demanding more-efficient sample-handling systems. These demands have arisen over a relatively short period of time, in part because of heightened concern over laboratory safety and the resulting manpower shortages. Adding sample-handling capabilities to existing instrumentation is often a challenge, because usually mechanical or system constraints are present that interfere. This challenge has been overcome in the DuPont Sample Management System (SMS), a second-generation general chemistry analyzer that incorporates the latest barcode and computer-interfacing technology. The development of the SMS system relies heavily on recent advances in technology, e.g., software modeling and computer-aided design. The SMS system includes a barcode scanner based on "charge-coupled device" technology, a random-access sample wheel, and new software that oversees the various functions.

  11. Rain and aerosol chemical composition obtained with newly developed automated sampling systems

    SciTech Connect

    Stevens, R.K.; Paur, R.J.; Baumgardner, R.E.; Kronmiller, K.; Ellenson, W.

    1986-04-01

    Rain and aerosol samples were collected concurrently for a number of rain events in the Research Triangle Park, NC recently with a newly developed automated rain sampler and an annular denuder system. The rain sampler collects sequential 0.3 mm aliquots of each rain event and simultaneously 1) measures and records the pH, conductivity and 2) stores the balance of the rain sample at sub-ambient conditions (NH/sub 3/ free conditions) for subsequent chemical analysis. Ambient concentrations of SO/sub 2/, HNO/sub 3/, HONO nitrates and sulfates are also collected concurrently over 12-hour intervals with an automated annular denuder method (ADM) recently developed by scientists at CNR and the USEPA. Data collected with the ADM will be correlated with the composition of the rain samples to examine the relationships between the rain chemistry and ambient pollutant concentrations. A previous study performed at the University of Virginia showed a high correlation (r/sup 2/ = 0.67) between the sulfate and acidity in the fine particles and the acidity and sulfate in the rain samples. This paper examines the relationship of HNO/sub 3/, HNO/sub 2/, and SO/sub 2/ in the ambient air to the sulfate and nitrate in the aliquots of rain collected.

  12. Automated Device for Asynchronous Extraction of RNA, DNA, or Protein Biomarkers from Surrogate Patient Samples.

    PubMed

    Bitting, Anna L; Bordelon, Hali; Baglia, Mark L; Davis, Keersten M; Creecy, Amy E; Short, Philip A; Albert, Laura E; Karhade, Aditya V; Wright, David W; Haselton, Frederick R; Adams, Nicholas M

    2016-12-01

    Many biomarker-based diagnostic methods are inhibited by nontarget molecules in patient samples, necessitating biomarker extraction before detection. We have developed a simple device that purifies RNA, DNA, or protein biomarkers from complex biological samples without robotics or fluid pumping. The device design is based on functionalized magnetic beads, which capture biomarkers and remove background biomolecules by magnetically transferring the beads through processing solutions arrayed within small-diameter tubing. The process was automated by wrapping the tubing around a disc-like cassette and rotating it past a magnet using a programmable motor. This device recovered biomarkers at ~80% of the operator-dependent extraction method published previously. The device was validated by extracting biomarkers from a panel of surrogate patient samples containing clinically relevant concentrations of (1) influenza A RNA in nasal swabs, (2) Escherichia coli DNA in urine, (3) Mycobacterium tuberculosis DNA in sputum, and (4) Plasmodium falciparum protein and DNA in blood. The device successfully extracted each biomarker type from samples representing low levels of clinically relevant infectivity (i.e., 7.3 copies/µL of influenza A RNA, 405 copies/µL of E. coli DNA, 0.22 copies/µL of TB DNA, 167 copies/µL of malaria parasite DNA, and 2.7 pM of malaria parasite protein). © 2015 Society for Laboratory Automation and Screening.

  13. Neurodegenerative changes in Alzheimer's disease: a comparative study of manual, semi-automated, and fully automated assessment using MRI

    NASA Astrophysics Data System (ADS)

    Fritzsche, Klaus H.; Giesel, Frederik L.; Heimann, Tobias; Thomann, Philipp A.; Hahn, Horst K.; Pantel, Johannes; Schröder, Johannes; Essig, Marco; Meinzer, Hans-Peter

    2008-03-01

    Objective quantification of disease specific neurodegenerative changes can facilitate diagnosis and therapeutic monitoring in several neuropsychiatric disorders. Reproducibility and easy-to-perform assessment are essential to ensure applicability in clinical environments. Aim of this comparative study is the evaluation of a fully automated approach that assesses atrophic changes in Alzheimer's disease (AD) and Mild Cognitive Impairment (MCI). 21 healthy volunteers (mean age 66.2), 21 patients with MCI (66.6), and 10 patients with AD (65.1) were enrolled. Subjects underwent extensive neuropsychological testing and MRI was conducted on a 1.5 Tesla clinical scanner. Atrophic changes were measured automatically by a series of image processing steps including state of the art brain mapping techniques. Results were compared with two reference approaches: a manual segmentation of the hippocampal formation and a semi-automated estimation of temporal horn volume, which is based upon interactive selection of two to six landmarks in the ventricular system. All approaches separated controls and AD patients significantly (10 -5 < p < 10 -4) and showed a slight but not significant increase of neurodegeneration for subjects with MCI compared to volunteers. The automated approach correlated significantly with the manual (r = -0.65, p < 10 -6) and semi automated (r = -0.83, p < 10 -13) measurements. It proved high accuracy and at the same time maximized observer independency, time reduction and thus usefulness for clinical routine.

  14. How to assess driver's interaction with partially automated driving systems - A framework for early concept assessment.

    PubMed

    van den Beukel, Arie P; van der Voort, Mascha C

    2017-03-01

    The introduction of partially automated driving systems changes the driving task into supervising the automation with an occasional need to intervene. To develop interface solutions that adequately support drivers in this new role, this study proposes and evaluates an assessment framework that allows designers to evaluate driver-support within relevant real-world scenarios. Aspects identified as requiring assessment in terms of driver-support within the proposed framework are Accident Avoidance, gained Situation Awareness (SA) and Concept Acceptance. Measurement techniques selected to operationalise these aspects and the associated framework are pilot-tested with twenty-four participants in a driving simulator experiment. The objective of the test is to determine the reliability of the applied measurements for the assessment of the framework and whether the proposed framework is effective in predicting the level of support offered by the concepts. Based on the congruency between measurement scores produced in the test and scores with predefined differences in concept-support, this study demonstrates the framework's reliability. A remaining concern is the framework's weak sensitivity to small differences in offered support. The article concludes that applying the framework is especially advantageous for evaluating early design phases and can successfully contribute to the efficient development of driver's in-control and safe means of operating partially automated vehicles. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Threshold for diagnosing hypertension by automated office blood pressure using random sample population data.

    PubMed

    Wohlfahrt, Peter; Cífková, Renata; Movsisyan, Narine; Kunzová, Šárka; Lešovský, Jiří; Homolka, Martin; Soška, Vladimír; Bauerová, Hana; Lopez-Jimenez, Francisco; Sochor, Ondřej

    2016-11-01

    Manual office blood pressure (BP) is still recommended for diagnosing hypertension. However, its predictive value is decreased by errors in measurement technique and the white-coat effect. The errors can be eliminated by automated office BP (AOBP) measurement taking multiple readings with the participant resting quietly alone. Therefore, use of AOBP in clinical practice requires a threshold value for hypertension diagnosis. The aim of the present study was to determine an AOBP threshold corresponding to the 140/90 mmHg manual office BP using data from a large random population sample. In 2145 participants (mean age 47.3 ± 11.3 years) randomly selected from a Brno population aged 25-64 years, BP was measured using manual mercury and automated office sphygmomanometers. Manual SBP (mean difference 6.39 ± 9.76 mmHg) and DBP (mean difference 2.50 ± 6.54 mmHg) were higher than the automated BP. According to polynomial regression, automated systole of 131.06 (95% confidence interval 130.43-131.70) and diastole of 85.43 (95% confidence interval 85.03-85.82) corresponded to the manual BP of 140/90 mmHg. Using this cut-off, the white-coat hypertension was present in 24% of participants with elevated manual BP, whereas 10% had masked hypertension and 11% masked uncontrolled hypertension. In individuals with masked uncontrolled hypertension, only AOBP was associated with the urinary albumin-creatinine ratio, whereas there was no association with manual BP. AOBP of 131/85 mmHg corresponds to the manual BP of 140/90 mmHg. This value may be used as a threshold for diagnosing hypertension using AOBP. However, outcome-driven studies are required to confirm this threshold.

  16. Automated aerosol Raman spectrometer for semi-continuous sampling of atmospheric aerosol

    NASA Astrophysics Data System (ADS)

    Doughty, David C.; Hill, Steven C.

    2017-02-01

    Raman spectroscopy (RS) is useful in characterizing atmospheric aerosol. It is not commonly used in studying ambient particles partly because automated instrumentation for aerosol RS has not been available. Battelle (Columbus, Ohio, USA) has developed the Resource Effective Bioidentification System (REBS) for automated detection of airborne bioagents based on RS. We use a version of the REBS that measures Raman spectra of one set of particles while the next set of particles is collected from air, then moves the newly collected particles to the analysis region and repeats. Here we investigate the use of the REBS as the core of a general-purpose automated Aerosol Raman Spectrometer (ARS) for atmospheric applications. This REBS-based ARS can be operated as a line-scanning Raman imaging spectrometer. Spectra measured by this ARS for single particles made of polystyrene, black carbon, and several other materials are clearly distinguishable. Raman spectra from a 15 min ambient sample (approximately 35-50 particles, 158 spectra) were analyzed using a hierarchical clustering method to find that the cluster spectra are consistent with soot, inorganic aerosol, and other organic compounds. The ARS ran unattended, collecting atmospheric aerosol and measuring spectra for a 7 hr period at 15-min intervals. A total of 32,718 spectra were measured; 5892 exceeded a threshold and were clustered during this time. The number of particles exhibiting the D-G bands of amorphous carbon plotted vs time (at 15-min intervals) increases during the morning commute, then decreases. This data illustrates the potential of the ARS to measure thousands of time resolved aerosol Raman spectra in the ambient atmosphere over the course of several hours. The capability of this ARS for automated measurements of Raman spectra should lead to more extensive RS-based studies of atmospheric aerosols.

  17. Automated biphasic morphological assessment of hepatitis B-related liver fibrosis using second harmonic generation microscopy

    NASA Astrophysics Data System (ADS)

    Wang, Tong-Hong; Chen, Tse-Ching; Teng, Xiao; Liang, Kung-Hao; Yeh, Chau-Ting

    2015-08-01

    Liver fibrosis assessment by biopsy and conventional staining scores is based on histopathological criteria. Variations in sample preparation and the use of semi-quantitative histopathological methods commonly result in discrepancies between medical centers. Thus, minor changes in liver fibrosis might be overlooked in multi-center clinical trials, leading to statistically non-significant data. Here, we developed a computer-assisted, fully automated, staining-free method for hepatitis B-related liver fibrosis assessment. In total, 175 liver biopsies were divided into training (n = 105) and verification (n = 70) cohorts. Collagen was observed using second harmonic generation (SHG) microscopy without prior staining, and hepatocyte morphology was recorded using two-photon excitation fluorescence (TPEF) microscopy. The training cohort was utilized to establish a quantification algorithm. Eleven of 19 computer-recognizable SHG/TPEF microscopic morphological features were significantly correlated with the ISHAK fibrosis stages (P < 0.001). A biphasic scoring method was applied, combining support vector machine and multivariate generalized linear models to assess the early and late stages of fibrosis, respectively, based on these parameters. The verification cohort was used to verify the scoring method, and the area under the receiver operating characteristic curve was >0.82 for liver cirrhosis detection. Since no subjective gradings are needed, interobserver discrepancies could be avoided using this fully automated method.

  18. Development and Validation of an Automated Sepsis Risk Assessment System.

    PubMed

    Back, Ji-Sun; Jin, Yinji; Jin, Taixian; Lee, Sun-Mi

    2016-10-01

    Aggressive resuscitation can decrease sepsis mortality, but its success depends on early detection of sepsis. The purpose of this study was to develop and verify an Automated Sepsis Risk Assessment System (Auto-SepRAS), which would automatically assess the sepsis risk of inpatients by applying data mining techniques to electronic health records (EHR) data and provide daily updates. The seven predictors included in the Auto-SepRAS after initial analysis were admission via the emergency department, which had the highest odds ratio; diastolic blood pressure; length of stay; respiratory rate; heart rate; and age. Auto-SepRAS classifies inpatients into three risk levels (high, moderate, and low) based on the predictive values from the sepsis risk-scoring algorithm. The sepsis risk for each patient is presented on the nursing screen of the EHR. The AutoSepRAS was implemented retrospectively in several stages using EHR data and its cut-off scores adjusted. Overall discrimination power was moderate (AUC>.80). The Auto-SepRAS should be verified or updated continuously or intermittently to maintain high predictive performance, but it does not require invasive tests or data input by nurses that would require additional time. Nurses are able to provide patients with nursing care appropriate to their risk levels by using the sepsis risk information provided by the Auto-SepRAS. In particular, with early detection of changes related to sepsis, nurses should be able to help in providing rapid initial resuscitation of high-risk patients. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Real-time Automated Sampling of Electronic Medical Records Predicts Hospital Mortality

    PubMed Central

    Khurana, Hargobind S.; Groves, Robert H.; Simons, Michael P.; Martin, Mary; Stoffer, Brenda; Kou, Sherri; Gerkin, Richard; Reiman, Eric; Parthasarathy, Sairam

    2016-01-01

    Background Real-time automated continuous sampling of electronic medical record data may expeditiously identify patients at risk for death and enable prompt life-saving interventions. We hypothesized that a real-time electronic medical record-based alert could identify hospitalized patients at risk for mortality. Methods An automated alert was developed and implemented to continuously sample electronic medical record data and trigger when at least two of four systemic inflammatory response syndrome criteria plus at least one of 14 acute organ dysfunction parameters was detected. The SIRS/OD alert was applied real-time to 312,214 patients in 24 hospitals and analyzed in two phases: training and validation datasets. Results In the training phase, 29,317 (18.8%) triggered the alert and 5.2% of such patients died whereas only 0.2% without the alert died (unadjusted odds ratio 30.1; 95% confidence interval [95%CI] 26.1, 34.5; P<0.0001). In the validation phase, the sensitivity, specificity, area under curve (AUC), positive and negative likelihood ratios for predicting mortality were 0.86, 0.82, 0.84, 4.9, and 0.16, respectively. Multivariate Cox-proportional hazard regression model revealed greater hospital mortality when the alert was triggered (adjusted Hazards Ratio 4.0; 95%CI 3.3, 4.9; P<0.0001). Triggering the alert was associated with additional hospitalization days (+3.0 days) and ventilator days (+1.6 days; P<0.0001). Conclusion An automated alert system that continuously samples electronic medical record-data can be implemented, has excellent test characteristics, and can assist in the real-time identification of hospitalized patients at risk for death. PMID:27019043

  20. Automated sample exchange and tracking system for neutron research at cryogenic temperatures.

    PubMed

    Rix, J E; Weber, J K R; Santodonato, L J; Hill, B; Walker, L M; McPherson, R; Wenzel, J; Hammons, S E; Hodges, J; Rennich, M; Volin, K J

    2007-01-01

    An automated system for sample exchange and tracking in a cryogenic environment and under remote computer control was developed. Up to 24 sample "cans" per cycle can be inserted and retrieved in a programed sequence. A video camera acquires a unique identification marked on the sample can to provide a record of the sequence. All operations are coordinated via a LABVIEW program that can be operated locally or over a network. The samples are contained in vanadium cans of 6-10 mm in diameter and equipped with a hermetically sealed lid that interfaces with the sample handler. The system uses a closed-cycle refrigerator (CCR) for cooling. The sample was delivered to a precooling location that was at a temperature of approximately 25 K, after several minutes, it was moved onto a "landing pad" at approximately 10 K that locates the sample in the probe beam. After the sample was released onto the landing pad, the sample handler was retracted. Reading the sample identification and the exchange operation takes approximately 2 min. The time to cool the sample from ambient temperature to approximately 10 K was approximately 7 min including precooling time. The cooling time increases to approximately 12 min if precooling is not used. Small differences in cooling rate were observed between sample materials and for different sample can sizes. Filling the sample well and the sample can with low pressure helium is essential to provide heat transfer and to achieve useful cooling rates. A resistive heating coil can be used to offset the refrigeration so that temperatures up to approximately 350 K can be accessed and controlled using a proportional-integral-derivative control loop. The time for the landing pad to cool to approximately 10 K after it has been heated to approximately 240 K was approximately 20 min.

  1. Mechanical Alteration And Contamination Issues In Automated Subsurface Sample Acquisition And Handling

    NASA Astrophysics Data System (ADS)

    Glass, B. J.; Cannon, H.; Bonaccorsi, R.; Zacny, K.

    2006-12-01

    The Drilling Automation for Mars Exploration (DAME) project's purpose is to develop and field-test drilling automation and robotics technologies for projected use in missions in the 2011-15 period. DAME includes control of the drilling hardware, and state estimation of both the hardware and the lithography being drilled and the state of the hole. A sister drill was constructed for the Mars Analog Río Tinto Experiment (MARTE) project and demonstrated automated core handling and string changeout in 2005 drilling tests at Rio Tinto, Spain. DAME focused instead on the problem of drill control while actively drilling while not getting stuck. Together, the DAME and MARTE projects demonstrate a fully automated robotic drilling capability, including hands-off drilling, adjustment to different strata and downhole conditions, recovery from drilling faults (binding, choking, etc.), drill string changeouts, core acquisition and removal, and sample handling and conveyance to in-situ instruments. The 2006 top-level goal of DAME drilling in-situ tests was to verify and demonstrate a capability for hands-off automated drilling, at an Arctic Mars-analog site. There were three sets of 2006 test goals, all of which were exceeded during the July 2006 field season. The first was to demonstrate the recognition, while drilling, of at least three of the six known major fault modes for the DAME planetary-prototype drill, and to employ the correct recovery or safing procedure in response. The second set of 2006 goals was to operate for three or more hours autonomously, hands-off. And the third 2006 goal was to exceed 3m depth into the frozen breccia and permafrost with the DAME drill (it had not gone further than 2.2m previously). Five of six faults were detected and corrected, there were 43 hours of hands-off drilling (including a 4 hour sequence with no human presence nearby), and 3.2m was the total depth. And ground truth drilling used small commercial drilling equipment in parallel in

  2. Automated cell counts on CSF samples: A multicenter performance evaluation of the GloCyte system.

    PubMed

    Hod, E A; Brugnara, C; Pilichowska, M; Sandhaus, L M; Luu, H S; Forest, S K; Netterwald, J C; Reynafarje, G M; Kratz, A

    2017-09-07

    Automated cell counters have replaced manual enumeration of cells in blood and most body fluids. However, due to the unreliability of automated methods at very low cell counts, most laboratories continue to perform labor-intensive manual counts on many or all cerebrospinal fluid (CSF) samples. This multicenter clinical trial investigated if the GloCyte System (Advanced Instruments, Norwood, MA), a recently FDA-approved automated cell counter, which concentrates and enumerates red blood cells (RBCs) and total nucleated cells (TNCs), is sufficiently accurate and precise at very low cell counts to replace all manual CSF counts. The GloCyte System concentrates CSF and stains RBCs with fluorochrome-labeled antibodies and TNCs with nucleic acid dyes. RBCs and TNCs are then counted by digital image analysis. Residual adult and pediatric CSF samples obtained for clinical analysis at five different medical centers were used for the study. Cell counts were performed by the manual hemocytometer method and with the GloCyte System following the same protocol at all sites. The limits of the blank, detection, and quantitation, as well as precision and accuracy of the GloCyte, were determined. The GloCyte detected as few as 1 TNC/μL and 1 RBC/μL, and reliably counted as low as 3 TNCs/μL and 2 RBCs/μL. The total coefficient of variation was less than 20%. Comparison with cell counts obtained with a hemocytometer showed good correlation (>97%) between the GloCyte and the hemocytometer, including at very low cell counts. The GloCyte instrument is a precise, accurate, and stable system to obtain red cell and nucleated cell counts in CSF samples. It allows for the automated enumeration of even very low cell numbers, which is crucial for CSF analysis. These results suggest that GloCyte is an acceptable alternative to the manual method for all CSF samples, including those with normal cell counts. © 2017 John Wiley & Sons Ltd.

  3. SAMPL4 & DOCK3.7: Lessons for automated docking procedures

    PubMed Central

    Coleman, Ryan G.; Sterling, Teague; Weiss, Dahlia R.

    2014-01-01

    The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: 1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, 2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, 3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed. PMID:24515818

  4. Automated processing of forensic casework samples using robotic workstations equipped with nondisposable tips: contamination prevention.

    PubMed

    Frégeau, Chantal J; Lett, C Marc; Elliott, Jim; Yensen, Craig; Fourney, Ron M

    2008-05-01

    An automated process has been developed for the analysis of forensic casework samples using TECAN Genesis RSP 150/8 or Freedom EVO liquid handling workstations equipped exclusively with nondisposable tips. Robot tip cleaning routines have been incorporated strategically within the DNA extraction process as well as at the end of each session. Alternative options were examined for cleaning the tips and different strategies were employed to verify cross-contamination. A 2% sodium hypochlorite wash (1/5th dilution of the 10.8% commercial bleach stock) proved to be the best overall approach for preventing cross-contamination of samples processed using our automated protocol. The bleach wash steps do not adversely impact the short tandem repeat (STR) profiles developed from DNA extracted robotically and allow for major cost savings through the implementation of fixed tips. We have demonstrated that robotic workstations equipped with fixed pipette tips can be used with confidence with properly designed tip washing routines to process casework samples using an adapted magnetic bead extraction protocol.

  5. Accelerating in vitro studies on circadian clock systems using an automated sampling device

    PubMed Central

    Furuike, Yoshihiko; Abe, Jun; Mukaiyama, Atsushi; Akiyama, Shuji

    2016-01-01

    KaiC, a core protein of the cyanobacterial circadian clock, is rhythmically autophosphorylated and autodephosphorylated with a period of approximately 24 h in the presence of two other Kai proteins, KaiA and KaiB. In vitro experiments to investigate the KaiC phosphorylation cycle consume considerable time and effort. To automate the fractionation, quantification, and evaluation steps, we developed a suite consisting of an automated sampling device equipped with an 8-channel temperature controller and accompanying analysis software. Eight sample tables can be controlled independently at different temperatures within a fluctuation of ±0.01°C, enabling investigation of the temperature dependency of clock activities simultaneously in a single experiment. The suite includes an independent software that helps users intuitively conduct a densitometric analysis of gel images in a short time with improved reliability. Multiple lanes on a gel can be detected quasi-automatically through an auto-detection procedure implemented in the software, with or without correction for lane ‘smiling.’ To demonstrate the performance of the suite, robustness of the period against temperature variations was evaluated using 32 datasets of the KaiC phosphorylation cycle. By using the software, the time required for the analysis was reduced by approximately 65% relative to the conventional method, with reasonable reproducibility and quality. The suite is potentially applicable to other clock or clock-related systems in higher organisms, relieving users from having to repeat multiple manual sampling and analytical steps. PMID:27924279

  6. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYRDOLOGIC MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly

    developed by the USDA Agricultural Research Service, the U.S. Environmental Protection

    Agency, the University of Arizona, and the University of Wyoming to automate the

    parame...

  7. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOGIC MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execu...

  8. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOGIC MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execu...

  9. AUTOMATED GEOSPATICAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOICAL MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execut...

  10. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYRDOLOGIC MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly

    developed by the USDA Agricultural Research Service, the U.S. Environmental Protection

    Agency, the University of Arizona, and the University of Wyoming to automate the

    parame...

  11. AUTOMATED GEOSPATICAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOICAL MODELING TOOL FOR WATERSHED ASSESSMENT AND ANALYSIS

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment tool (AGWA) is a GIS interface jointly developed by the USDA Agricultural Research Service, the U.S. Environmental Protection Agency, the University of Arizona, and the University of Wyoming to automate the parameterization and execut...

  12. Design and practices for use of automated drilling and sample handling in MARTE while minimizing terrestrial and cross contamination.

    PubMed

    Miller, David P; Bonaccorsi, Rosalba; Davis, Kiel

    2008-10-01

    Mars Astrobiology Research and Technology Experiment (MARTE) investigators used an automated drill and sample processing hardware to detect and categorize life-forms found in subsurface rock at Río Tinto, Spain. For the science to be successful, it was necessary for the biomass from other sources--whether from previously processed samples (cross contamination) or the terrestrial environment (forward contamination)-to be insignificant. The hardware and practices used in MARTE were designed around this problem. Here, we describe some of the design issues that were faced and classify them into problems that are unique to terrestrial tests versus problems that would also exist for a system that was flown to Mars. Assessment of the biomass at various stages in the sample handling process revealed mixed results; the instrument design seemed to minimize cross contamination, but contamination from the surrounding environment sometimes made its way onto the surface of samples. Techniques used during the MARTE Río Tinto project, such as facing the sample, appear to remove this environmental contamination without introducing significant cross contamination from previous samples.

  13. Surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes

    PubMed Central

    2012-01-01

    Background The instrument channels of gastrointestinal (GI) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (HLD). The British Society of Gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (AERs) for disinfecting endoscopes. In this study, we aimed to assess the effectiveness of decontamination using reprocessors after HLD by comparing the cultured samples obtained from biopsy channels (BCs) of GI endoscopes and the internal surfaces of AERs. Methods We conducted a 5-year prospective study. Every month random consecutive sampling was carried out after a complete reprocessing cycle; 420 rinse and swabs samples were collected from BCs and internal surface of AERs, respectively. Of the 420 rinse samples collected from the BC of the GI endoscopes, 300 were obtained from the BCs of gastroscopes and 120 from BCs of colonoscopes. Samples were collected by flushing the BCs with sterile distilled water, and swabbing the residual water from the AERs after reprocessing. These samples were cultured to detect the presence of aerobic and anaerobic bacteria and mycobacteria. Results The number of culture-positive samples obtained from BCs (13.6%, 57/420) was significantly higher than that obtained from AERs (1.7%, 7/420). In addition, the number of culture-positive samples obtained from the BCs of gastroscopes (10.7%, 32/300) and colonoscopes (20.8%, 25/120) were significantly higher than that obtained from AER reprocess to gastroscopes (2.0%, 6/300) and AER reprocess to colonoscopes (0.8%, 1/120). Conclusions Culturing rinse samples obtained from BCs provides a better indication of the effectiveness of the decontamination of GI endoscopes after HLD than culturing the swab samples obtained from the inner surfaces of AERs as the swab samples only indicate whether the AERs are free from microbial contamination or not. PMID:22943739

  14. Surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes.

    PubMed

    Chiu, King-Wah; Tsai, Ming-Chao; Wu, Keng-Liang; Chiu, Yi-Chun; Lin, Ming-Tzung; Hu, Tsung-Hui

    2012-09-03

    The instrument channels of gastrointestinal (GI) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (HLD). The British Society of Gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (AERs) for disinfecting endoscopes. In this study, we aimed to assess the effectiveness of decontamination using reprocessors after HLD by comparing the cultured samples obtained from biopsy channels (BCs) of GI endoscopes and the internal surfaces of AERs. We conducted a 5-year prospective study. Every month random consecutive sampling was carried out after a complete reprocessing cycle; 420 rinse and swabs samples were collected from BCs and internal surface of AERs, respectively. Of the 420 rinse samples collected from the BC of the GI endoscopes, 300 were obtained from the BCs of gastroscopes and 120 from BCs of colonoscopes. Samples were collected by flushing the BCs with sterile distilled water, and swabbing the residual water from the AERs after reprocessing. These samples were cultured to detect the presence of aerobic and anaerobic bacteria and mycobacteria. The number of culture-positive samples obtained from BCs (13.6%, 57/420) was significantly higher than that obtained from AERs (1.7%, 7/420). In addition, the number of culture-positive samples obtained from the BCs of gastroscopes (10.7%, 32/300) and colonoscopes (20.8%, 25/120) were significantly higher than that obtained from AER reprocess to gastroscopes (2.0%, 6/300) and AER reprocess to colonoscopes (0.8%, 1/120). Culturing rinse samples obtained from BCs provides a better indication of the effectiveness of the decontamination of GI endoscopes after HLD than culturing the swab samples obtained from the inner surfaces of AERs as the swab samples only indicate whether the AERs are free from microbial contamination or not.

  15. A Bayesian Framework for the Automated Online Assessment of Sensor Data Quality

    PubMed Central

    Smith, Daniel; Timms, Greg; De Souza, Paulo; D'Este, Claire

    2012-01-01

    Online automated quality assessment is critical to determine a sensor's fitness for purpose in real-time applications. A Dynamic Bayesian Network (DBN) framework is proposed to produce probabilistic quality assessments and represent the uncertainty of sequentially correlated sensor readings. This is a novel framework to represent the causes, quality state and observed effects of individual sensor errors without imposing any constraints upon the physical deployment or measured phenomenon. It represents the casual relationship between quality tests and combines them in a way to generate uncertainty estimates of samples. The DBN was implemented for a particular marine deployment of temperature and conductivity sensors in Hobart, Australia. The DBN was shown to offer a substantial average improvement (34%) in replicating the error bars that were generated by experts when compared to a fuzzy logic approach. PMID:23012554

  16. A proposed protocol for remote control of automated assessment devices

    SciTech Connect

    Kissock, P.S.

    1996-09-01

    Systems and devices that are controlled remotely are becoming more common in security systems in the US Air Force and other government agencies to provide protection of valuable assets. These systems reduce the number of needed personnel while still providing a high level of protection. However, each remotely controlled device usually has its own communication protocol. This limits the ability to change devices without changing the system that provides the communications control to the device. Sandia is pursuing a standard protocol that can be used to communicate with the different devices currently in use, or may be used in the future, in the US Air Force and other government agencies throughout the security community. Devices to be controlled include intelligent pan/tilt mounts, day/night video cameras., thermal imaging cameras, and remote data processors. Important features of this protocol include the ability to send messages of varying length, identify the sender, and more importantly, control remote data processors. As camera and digital signal processor (DSP) use expands, the DSP will begin to reside in the camera itself. The DSP can be used to provide auto-focus, frame-to- frame image registration, video motion detection (VMD), target detection, tracking, image compression, and many other functions. With the serial data control link, the actual DSP software can be updated or changed as required. Coaxial video cables may become obsolete once a compression algorithm is established in the DSP. This paper describes the proposed public domain protocol, features, and examples of use. The authors hope to elicit comments from security technology developers regarding format and use of remotely controlled automated assessment devices. 2 figs., 1 tab.

  17. Performance verification of the Maxwell 16 Instrument and DNA IQ Reference Sample Kit for automated DNA extraction of known reference samples.

    PubMed

    Krnajski, Z; Geering, S; Steadman, S

    2007-12-01

    Advances in automation have been made for a number of processes conducted in the forensic DNA laboratory. However, because most robotic systems are designed for high-throughput laboratories batching large numbers of samples, smaller laboratories are left with a limited number of cost-effective options for employing automation. The Maxwell 16 Instrument and DNA IQ Reference Sample Kit marketed by Promega are designed for rapid, automated purification of DNA extracts from sample sets consisting of sixteen or fewer samples. Because the system is based on DNA capture by paramagnetic particles with maximum binding capacity, it is designed to generate extracts with yield consistency. The studies herein enabled evaluation of STR profile concordance, consistency of yield, and cross-contamination performance for the Maxwell 16 Instrument. Results indicate that the system performs suitably for streamlining the process of extracting known reference samples generally used for forensic DNA analysis and has many advantages in a small or moderate-sized laboratory environment.

  18. Automation of high-frequency sampling of environmental waters for reactive species

    NASA Astrophysics Data System (ADS)

    Kim, H.; Bishop, J. K.; Wood, T.; Fung, I.; Fong, M.

    2011-12-01

    Trace metals, particularly iron and manganese, play a critical role in some ecosystems as a limiting factor to determine primary productivity, in geochemistry, especially redox chemistry as important electron donors and acceptors, and in aquatic environments as carriers of contaminant transport. Dynamics of trace metals are closely related to various hydrologic events such as rainfall. Storm flow triggers dramatic changes of both dissolved and particulate trace metals concentrations and affects other important environmental parameters linked to trace metal behavior such as dissolved organic carbon (DOC). To improve our understanding of behaviors of trace metals and underlying processes, water chemistry information must be collected for an adequately long period of time at higher frequency than conventional manual sampling (e.g. weekly, biweekly). In this study, we developed an automated sampling system to document the dynamics of trace metals, focusing on Fe and Mn, and DOC for a multiple-year high-frequency geochemistry time series in a small catchment, called Rivendell located at Angelo Coast Range Reserve, California. We are sampling ground and streamwater using the automated sampling system in daily-frequency and the condition of the site is substantially variable from season to season. The ranges of pH of ground and streamwater are pH 5 - 7 and pH 7.8 - 8.3, respectively. DOC is usually sub-ppm, but during rain events, it increases by an order of magnitude. The automated sampling system focuses on two aspects- 1) a modified design of sampler to improve sample integrity for trace metals and DOC and 2) remote controlling system to update sampling volume and timing according to hydrological conditions. To maintain sample integrity, the developed method employed gravity filtering using large volume syringes (140mL) and syringe filters connected to a set of polypropylene bottles and a borosilicate bottle via Teflon tubing. Without filtration, in a few days, the

  19. An automated method for 'clumped-isotope' measurements on small carbonate samples.

    PubMed

    Schmid, Thomas W; Bernasconi, Stefano M

    2010-07-30

    Clumped-isotope geochemistry deals with the state of ordering of rare isotopes in molecules, in particular with their tendency to form bonds with other rare isotopes rather than with the most abundant ones. Among its possible applications, carbonate clumped-isotope thermometry is the one that has gained most attention because of the wide potential of applications in many disciplines of earth sciences. Clumped-isotope thermometry allows reconstructing the temperature of formation of carbonate minerals without knowing the isotopic composition of the water from which they were formed. This feature enables new approaches in paleothermometry. The currently published method is, however, limited by sample weight requirements of 10-15 mg and because measurements are performed manually. In this paper we present a new method using an automated sample preparation device coupled to an isotope ratio mass spectrometer. The method is based on the repeated analysis (n = 6-8) of 200 microg aliquots of sample material and completely automated measurements. In addition, we propose to use precisely calibrated carbonates spanning a wide range in Delta(47) instead of heated gases to correct for isotope effects caused by the source of the mass spectrometer, following the principle of equal treatment of the samples and standards. We present data for international standards (NBS 19 and LSVEC) and different carbonates formed at temperatures exceeding 600 degrees C to show that precisions in the range of 10 to 15 ppm (1 SE) can be reached for repeated analyses of a single sample. Finally, we discuss and validate the correction procedure based on high-temperature carbonates instead of heated gases.

  20. Robowell: An automated process for monitoring ground water quality using established sampling protocols

    USGS Publications Warehouse

    Granato, G.E.; Smith, K.P.

    1999-01-01

    Robowell is an automated process for monitoring selected ground water quality properties and constituents by pumping a well or multilevel sampler. Robowell was developed and tested to provide a cost-effective monitoring system that meets protocols expected for manual sampling. The process uses commercially available electronics, instrumentation, and hardware, so it can be configured to monitor ground water quality using the equipment, purge protocol, and monitoring well design most appropriate for the monitoring site and the contaminants of interest. A Robowell prototype was installed on a sewage treatment plant infiltration bed that overlies a well-studied unconfined sand and gravel aquifer at the Massachusetts Military Reservation, Cape Cod, Massachusetts, during a time when two distinct plumes of constituents were released. The prototype was operated from May 10 to November 13, 1996, and quality-assurance/quality-control measurements demonstrated that the data obtained by the automated method was equivalent to data obtained by manual sampling methods using the same sampling protocols. Water level, specific conductance, pH, water temperature, dissolved oxygen, and dissolved ammonium were monitored by the prototype as the wells were purged according to U.S Geological Survey (USGS) ground water sampling protocols. Remote access to the data record, via phone modem communications, indicated the arrival of each plume over a few days and the subsequent geochemical reactions over the following weeks. Real-time availability of the monitoring record provided the information needed to initiate manual sampling efforts in response to changes in measured ground water quality, which proved the method and characterized the screened portion of the plume in detail through time. The methods and the case study described are presented to document the process for future use.

  1. Screening urine samples for the absence of urinary tract infection using the sediMAX automated microscopy analyser.

    PubMed

    Sterry-Blunt, Rosanne E; S Randall, Karen; J Doughton, Michael; H Aliyu, Sani; Enoch, David A

    2015-06-01

    Urinalysis culminates in a workload skew within the clinical microbiology laboratory. Routine processing involves screening via manual microscopy or biochemical dipstick measurement, followed by culture for each sample. Despite this, as many as 80% of specimens are reported as negative; thus, there is vast wastage of resources and time, as well as delayed turnaround time of results as numerous negative cultures fulfil their required incubation time. Automation provides the potential for streamlining sample screening by efficiently (>30% sample exclusion) and reliably [negative predictive value (NPV) ≥ 95%] ruling out those likely to be negative, whilst also reducing resource usage and hands-on time. The present study explored this idea by using the sediMAX automated microscopy urinalysis platform. We prospectively collected and processed 1411 non-selected samples directly after routine laboratory processing. The results from this study showed multiple optimum cut-off values for microscopy. However, although optimum cut-off values permitted rule-out of 40.1% of specimens, an associated 87.5% NPV was lower than the acceptable limit of 95%. Sensitivity and specificity of leukocytes and bacteria in determining urinary tract infection was assessed by receiver operator characteristic curves with area under the curve values found to be 0.697 [95% confidence interval (CI): 0.665-0.729] and 0.587 (95% CI: 0.551-0.623), respectively. We suggested that the sediMAX was not suitable for use as a rule-out screen prior to culture and further validation work must be carried out before routine use of the analyser.

  2. Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

    PubMed Central

    2012-01-01

    The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources. PMID:23168231

  3. Automated high-throughput in vitro screening of the acetylcholine esterase inhibiting potential of environmental samples, mixtures and single compounds.

    PubMed

    Froment, Jean; Thomas, Kevin V; Tollefsen, Knut Erik

    2016-08-01

    A high-throughput and automated assay for testing the presence of acetylcholine esterase (AChE) inhibiting compounds was developed, validated and applied to screen different types of environmental samples. Automation involved using the assay in 96-well plates and adapting it for the use with an automated workstation. Validation was performed by comparing the results of the automated assay with that of a previously validated and standardised assay for two known AChE inhibitors (paraoxon and dichlorvos). The results show that the assay provides similar concentration-response curves (CRCs) when run according to the manual and automated protocol. Automation of the assay resulted in a reduction in assay run time as well as in intra- and inter-assay variations. High-quality CRCs were obtained for both of the model AChE inhibitors (dichlorvos IC50=120µM and paraoxon IC50=0.56µM) when tested alone. The effect of co-exposure of an equipotent binary mixture of the two chemicals were consistent with predictions of additivity and best described by the concentration addition model for combined toxicity. Extracts of different environmental samples (landfill leachate, wastewater treatment plant effluent, and road tunnel construction run-off) were then screened for AChE inhibiting activity using the automated bioassay, with only landfill leachate shown to contain potential AChE inhibitors. Potential uses and limitations of the assay were discussed based on the present results.

  4. An instrument for automated purification of nucleic acids from contaminated forensic samples

    PubMed Central

    Broemeling, David J; Pel, Joel; Gunn, Dylan C; Mai, Laura; Thompson, Jason D; Poon, Hiron; Marziali, Andre

    2008-01-01

    Forensic crime scene sample analysis, by its nature, often deals with samples in which there are low amounts of nucleic acids, on substrates that often lead to inhibition of subsequent enzymatic reactions such as PCR amplification for STR profiling. Common substrates include denim from blue jeans, which yields indigo dye as a PCR inhibitor, and soil, which yields humic substances as inhibitors. These inhibitors frequently co-extract with nucleic acids in standard column or bead-based preps, leading to frequent failure of STR profiling. We present a novel instrument for DNA purification of forensic samples that is capable of highly effective concentration of nucleic acids from soil particulates, fabric, and other complex samples including solid components. The novel concentration process, known as SCODA, is inherently selective for long charged polymers such as DNA, and therefore is able to effectively reject known contaminants. We present an automated sample preparation instrument based on this process, and preliminary results based on mock forensic samples. PMID:18438455

  5. Automated quantification of epicardial adipose tissue (EAT) in coronary CT angiography; comparison with manual assessment and correlation with coronary artery disease.

    PubMed

    Mihl, Casper; Loeffen, Daan; Versteylen, Mathijs O; Takx, Richard A P; Nelemans, Patricia J; Nijssen, Estelle C; Vega-Higuera, Fernando; Wildberger, Joachim E; Das, Marco

    2014-01-01

    Epicardial adipose tissue (EAT) is emerging as a risk factor for coronary artery disease (CAD). The aim of this study was to determine the applicability and efficiency of automated EAT quantification. EAT volume was assessed both manually and automatically in 157 patients undergoing coronary CT angiography. Manual assessment consisted of a short-axis-based manual measurement, whereas automated assessment on both contrast and non-contrast-enhanced data sets was achieved through novel prototype software. Duration of both quantification methods was recorded, and EAT volumes were compared with paired samples t test. Correlation of volumes was determined with intraclass correlation coefficient; agreement was tested with Bland-Altman analysis. The association between EAT and CAD was estimated with logistic regression. Automated quantification was significantly less time consuming than automated quantification (17 ± 2 seconds vs 280 ± 78 seconds; P < .0001). Although manual EAT volume differed significantly from automated EAT volume (75 ± 33 cm(³) vs 95 ± 45 cm(³); P < .001), a good correlation between both assessments was found (r = 0.76; P < .001). For all methods, EAT volume was positively associated with the presence of CAD. Stronger predictive value for the severity of CAD was achieved through automated quantification on both contrast-enhanced and non-contrast-enhanced data sets. Automated EAT quantification is a quick method to estimate EAT and may serve as a predictor for CAD presence and severity. Copyright © 2014 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  6. HT-COMET: a novel automated approach for high throughput assessment of human sperm chromatin quality

    PubMed Central

    Albert, Océane; Reintsch, Wolfgang E.; Chan, Peter; Robaire, Bernard

    2016-01-01

    -manual analysis software. Using this method, a cross-sectional study on 123 men showed no significant correlation between sperm concentration and sperm DNA damage, confirming the existence of hidden chromatin damage in men with apparently normal semen characteristics, and a significant correlation between percentage DNA in the tail and percentage of progressively motile spermatozoa. Finally, the use of DNA damage profiles helped to distinguish subjects between and within sperm concentration categories, and allowed a determination of the proportion of highly damaged cells. LIMITATIONS, REASONS FOR CAUTION The main limitations of the HT-COMET are the high, yet indispensable, investment in an automated liquid handling system and heating block to ensure accuracy, and the availability of an automated plate reading microscope and analysis software. WIDER IMPLICATIONS OF THE FINDINGS This standardized HT-COMET assay offers many advantages, including higher accuracy and evenness due to automation of sensitive steps, a 14.4-fold increase in sample analysis capacity, and an imaging and scoring time of 1 min/well. Overall, HT-COMET offers a decrease in total experimental time of more than 90%. Hence, this assay constitutes a more efficient option to assess sperm chromatin quality, paves the way to using this assay to screen large cohorts, and holds prognostic value for infertile patients. STUDY FUNDING/COMPETING INTEREST(S) Funded by the CIHR Institute of Human Development, Child and Youth Health (IHDCYH; RHF 100625). O.A. is a fellow supported by the Fonds de la Recherche du Québec - Santé (FRQS) and the CIHR Training Program in Reproduction, Early Development, and the Impact on Health (REDIH). B.R. is a James McGill Professor. The authors declare no conflicts of interest. PMID:26975326

  7. Fully Automated Laser Ablation Liquid Capture Sample Analysis using NanoElectrospray Ionization Mass Spectrometry

    SciTech Connect

    Lorenz, Matthias; Ovchinnikova, Olga S; Van Berkel, Gary J

    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

  8. Microbiological monitoring and automated event sampling at karst springs using LEO-satellites.

    PubMed

    Stadler, H; Skritek, P; Sommer, R; Mach, R L; Zerobin, W; Farnleitner, A H

    2008-01-01

    Data communication via Low-Earth-Orbit (LEO) Satellites between portable hydrometeorological measuring stations is the backbone of our system. This networking allows automated event sampling with short time increments also for E. coli field analysis. All activities of the course of the event-sampling can be observed on an internet platform based on a Linux-Server. Conventionally taken samples compared with the auto-sampling procedure revealed corresponding results and were in agreement with the ISO 9308-1 reference method. E. coli concentrations were individually corrected by event specific inactivation coefficients (0.10-0.14 day(-1)), compensating losses due to sample storage at spring temperature in the auto sampler.Two large summer events in 2005/2006 at an important alpine karst spring (LKAS2) were monitored including detailed analysis of E. coli dynamics (n = 271) together with comprehensive hydrological characterisations. High-resolution time series demonstrated a sudden increase of E. coli concentrations in spring water (approximately 2 log10 units) with a specific time delay after the beginning of the event. Statistical analysis suggested the spectral absorption coefficient measured at 254 nm (SAC254) as an early warning surrogate for real time monitoring of faecal input. Together with the LEO-satellite based system it is a helpful tool for early-warning systems in the field of drinking water protection. Copyright IWA Publishing 2008.

  9. MICROBIOLOGICAL MONITORING AND AUTOMATED EVENT SAMPLING AT KARST SPRINGS USING LEO-SATELLITES

    PubMed Central

    Stadler, Hermann; Skritek, Paul; Sommer, Regina; Mach, Robert L.; Zerobin, Wolfgang; Farnleitner, Andreas H.

    2010-01-01

    Data communication via Low-Earth-Orbit Satellites between portable hydro-meteorological measuring stations is the backbone of our system. This networking allows automated event sampling with short time increments also for E.coli field analysis. All activities of the course of the event-sampling can be observed on an internet platform based on a Linux-Server. Conventionally taken samples by hand compared with the auto-sampling procedure revealed corresponding results and were in agreement to the ISO 9308-1 reference method. E.coli concentrations were individually corrected by event specific die-off rates (0.10–0.14 day−1) compensating losses due to sample storage at spring temperature in the auto sampler. Two large summer events 2005/2006 at a large alpine karst spring (LKAS2) were monitored including detailed analysis of E.coli dynamics (n = 271) together with comprehensive hydrological characterisations. High resolution time series demonstrated a sudden increase of E.coli concentrations in spring water (approx. 2 log10 units) with a specific time delay after the beginning of the event. Statistical analysis suggested the spectral absorbent coefficient measured at 254nm (SAC254) as an early warning surrogate for real time monitoring of faecal input. Together with the LEO-Satellite based system it is a helpful tool for Early-Warning-Systems in the field of drinking water protection. PMID:18776628

  10. Automated MALDI Matrix Coating System for Multiple Tissue Samples for Imaging Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mounfield, William P.; Garrett, Timothy J.

    2012-03-01

    Uniform matrix deposition on tissue samples for matrix-assisted laser desorption/ionization (MALDI) is key for reproducible analyte ion signals. Current methods often result in nonhomogenous matrix deposition, and take time and effort to produce acceptable ion signals. Here we describe a fully-automated method for matrix deposition using an enclosed spray chamber and spray nozzle for matrix solution delivery. A commercial air-atomizing spray nozzle was modified and combined with solenoid controlled valves and a Programmable Logic Controller (PLC) to control and deliver the matrix solution. A spray chamber was employed to contain the nozzle, sample, and atomized matrix solution stream, and to prevent any interference from outside conditions as well as allow complete control of the sample environment. A gravity cup was filled with MALDI matrix solutions, including DHB in chloroform/methanol (50:50) at concentrations up to 60 mg/mL. Various samples (including rat brain tissue sections) were prepared using two deposition methods (spray chamber, inkjet). A linear ion trap equipped with an intermediate-pressure MALDI source was used for analyses. Optical microscopic examination showed a uniform coating of matrix crystals across the sample. Overall, the mass spectral images gathered from tissues coated using the spray chamber system were of better quality and more reproducible than from tissue specimens prepared by the inkjet deposition method.

  11. Automated MALDI matrix coating system for multiple tissue samples for imaging mass spectrometry.

    PubMed

    Mounfield, William P; Garrett, Timothy J

    2012-03-01

    Uniform matrix deposition on tissue samples for matrix-assisted laser desorption/ionization (MALDI) is key for reproducible analyte ion signals. Current methods often result in nonhomogenous matrix deposition, and take time and effort to produce acceptable ion signals. Here we describe a fully-automated method for matrix deposition using an enclosed spray chamber and spray nozzle for matrix solution delivery. A commercial air-atomizing spray nozzle was modified and combined with solenoid controlled valves and a Programmable Logic Controller (PLC) to control and deliver the matrix solution. A spray chamber was employed to contain the nozzle, sample, and atomized matrix solution stream, and to prevent any interference from outside conditions as well as allow complete control of the sample environment. A gravity cup was filled with MALDI matrix solutions, including DHB in chloroform/methanol (50:50) at concentrations up to 60 mg/mL. Various samples (including rat brain tissue sections) were prepared using two deposition methods (spray chamber, inkjet). A linear ion trap equipped with an intermediate-pressure MALDI source was used for analyses. Optical microscopic examination showed a uniform coating of matrix crystals across the sample. Overall, the mass spectral images gathered from tissues coated using the spray chamber system were of better quality and more reproducible than from tissue specimens prepared by the inkjet deposition method.

  12. Artificial Neural Network for Total Laboratory Automation to Improve the Management of Sample Dilution.

    PubMed

    Ialongo, Cristiano; Pieri, Massimo; Bernardini, Sergio

    2017-02-01

    Diluting a sample to obtain a measure within the analytical range is a common task in clinical laboratories. However, for urgent samples, it can cause delays in test reporting, which can put patients' safety at risk. The aim of this work is to show a simple artificial neural network that can be used to make it unnecessary to predilute a sample using the information available through the laboratory information system. Particularly, the Multilayer Perceptron neural network built on a data set of 16,106 cardiac troponin I test records produced a correct inference rate of 100% for samples not requiring predilution and 86.2% for those requiring predilution. With respect to the inference reliability, the most relevant inputs were the presence of a cardiac event or surgery and the result of the previous assay. Therefore, such an artificial neural network can be easily implemented into a total automation framework to sensibly reduce the turnaround time of critical orders delayed by the operation required to retrieve, dilute, and retest the sample.

  13. A modifiable microarray-based universal sensor: providing sample-to-results automation.

    PubMed

    Yasmin, Rubina; Zhu, Hui; Chen, Zongyuan; Montagna, Richard A

    2016-10-01

    A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA "universal" probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined "reporter" probes that are complementary at their 3' termini to one or more of the universal probes and complementary to the target amplicons at their 5' termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.

  14. Automated Scoring in Context: Rapid Assessment for Placed Students

    ERIC Educational Resources Information Center

    Klobucar, Andrew; Elliot, Norbert; Deess, Perry; Rudniy, Oleksandr; Joshi, Kamal

    2013-01-01

    This study investigated the use of automated essay scoring (AES) to identify at-risk students enrolled in a first-year university writing course. An application of AES, the "Criterion"[R] Online Writing Evaluation Service was evaluated through a methodology focusing on construct modelling, response processes, disaggregation, extrapolation,…

  15. Automating the Fireshed Assessment Process with ArcGIS

    Treesearch

    Alan Ager; Klaus Barber

    2006-01-01

    A library of macros was developed to automate the Fireshed process within ArcGIS. The macros link a number of vegetation simulation and wildfire behavior models (FVS, SVS, FARSITE, and FlamMap) with ESRI geodatabases, desktop software (Access, Excel), and ArcGIS. The macros provide for (1) an interactive linkage between digital imagery, vegetation data, FVS-FFE, and...

  16. Automated Scoring in Context: Rapid Assessment for Placed Students

    ERIC Educational Resources Information Center

    Klobucar, Andrew; Elliot, Norbert; Deess, Perry; Rudniy, Oleksandr; Joshi, Kamal

    2013-01-01

    This study investigated the use of automated essay scoring (AES) to identify at-risk students enrolled in a first-year university writing course. An application of AES, the "Criterion"[R] Online Writing Evaluation Service was evaluated through a methodology focusing on construct modelling, response processes, disaggregation, extrapolation,…

  17. Automated Assessment of Speech Fluency for L2 English Learners

    ERIC Educational Resources Information Center

    Yoon, Su-Youn

    2009-01-01

    This dissertation provides an automated scoring method of speech fluency for second language learners of English (L2 learners) based that uses speech recognition technology. Non-standard pronunciation, frequent disfluencies, faulty grammar, and inappropriate lexical choices are crucial characteristics of L2 learners' speech. Due to the ease of…

  18. Automated negotiation in environmental resource management: Review and assessment.

    PubMed

    Eshragh, Faezeh; Pooyandeh, Majeed; Marceau, Danielle J

    2015-10-01

    Negotiation is an integral part of our daily life and plays an important role in resolving conflicts and facilitating human interactions. Automated negotiation, which aims at capturing the human negotiation process using artificial intelligence and machine learning techniques, is well-established in e-commerce, but its application in environmental resource management remains limited. This is due to the inherent uncertainties and complexity of environmental issues, along with the diversity of stakeholders' perspectives when dealing with these issues. The objective of this paper is to describe the main components of automated negotiation, review and compare machine learning techniques in automated negotiation, and provide a guideline for the selection of suitable methods in the particular context of stakeholders' negotiation over environmental resource issues. We advocate that automated negotiation can facilitate the involvement of stakeholders in the exploration of a plurality of solutions in order to reach a mutually satisfying agreement and contribute to informed decisions in environmental management along with the need for further studies to consolidate the potential of this modeling approach.

  19. Automated Generation and Assessment of Autonomous Systems Test Cases

    NASA Technical Reports Server (NTRS)

    Barltrop, Kevin J.; Friberg, Kenneth H.; Horvath, Gregory A.

    2008-01-01

    This slide presentation reviews some of the issues concerning verification and validation testing of autonomous spacecraft routinely culminates in the exploration of anomalous or faulted mission-like scenarios using the work involved during the Dawn mission's tests as examples. Prioritizing which scenarios to develop usually comes down to focusing on the most vulnerable areas and ensuring the best return on investment of test time. Rules-of-thumb strategies often come into play, such as injecting applicable anomalies prior to, during, and after system state changes; or, creating cases that ensure good safety-net algorithm coverage. Although experience and judgment in test selection can lead to high levels of confidence about the majority of a system's autonomy, it's likely that important test cases are overlooked. One method to fill in potential test coverage gaps is to automatically generate and execute test cases using algorithms that ensure desirable properties about the coverage. For example, generate cases for all possible fault monitors, and across all state change boundaries. Of course, the scope of coverage is determined by the test environment capabilities, where a faster-than-real-time, high-fidelity, software-only simulation would allow the broadest coverage. Even real-time systems that can be replicated and run in parallel, and that have reliable set-up and operations features provide an excellent resource for automated testing. Making detailed predictions for the outcome of such tests can be difficult, and when algorithmic means are employed to produce hundreds or even thousands of cases, generating predicts individually is impractical, and generating predicts with tools requires executable models of the design and environment that themselves require a complete test program. Therefore, evaluating the results of large number of mission scenario tests poses special challenges. A good approach to address this problem is to automatically score the results

  20. Toward Automated Computer-Based Visualization and Assessment of Team-Based Performance

    ERIC Educational Resources Information Center

    Ifenthaler, Dirk

    2014-01-01

    A considerable amount of research has been undertaken to provide insights into the valid assessment of team performance. However, in many settings, manual and therefore labor-intensive assessment instruments for team performance have limitations. Therefore, automated assessment instruments enable more flexible and detailed insights into the…

  1. Toward Automated Computer-Based Visualization and Assessment of Team-Based Performance

    ERIC Educational Resources Information Center

    Ifenthaler, Dirk

    2014-01-01

    A considerable amount of research has been undertaken to provide insights into the valid assessment of team performance. However, in many settings, manual and therefore labor-intensive assessment instruments for team performance have limitations. Therefore, automated assessment instruments enable more flexible and detailed insights into the…

  2. Harmonization of automated hemolysis index assessment and use: Is it possible?

    PubMed

    Dolci, Alberto; Panteghini, Mauro

    2014-05-15

    The major source of errors producing unreliable laboratory test results is the pre-analytical phase with hemolysis accounting for approximately half of them and being the leading cause of unsuitable blood specimens. Hemolysis may produce interference in many laboratory tests by a variety of biological and analytical mechanisms. Consequently, laboratories need to systematically detect and reliably quantify hemolysis in every collected sample by means of objective and consistent technical tools that assess sample integrity. This is currently done by automated estimation of hemolysis index (HI), available on almost all clinical chemistry platforms, making the hemolysis detection reliable and reportable patient test results more accurate. Despite these advantages, a degree of variability still affects the HI estimate and more efforts should be placed on harmonization of this index. The harmonization of HI results from different analytical systems should be the immediate goal, but the scope of harmonization should go beyond analytical steps to include other aspects, such as HI decision thresholds, criteria for result interpretation and application in clinical practice as well as report formats. With regard to this, relevant issues to overcome remain the objective definition of a maximum allowable bias for hemolysis interference based on the clinical application of the measurements and the management of unsuitable samples. Particularly, for the latter a recommended harmonized approach is required when not reporting numerical results of unsuitable samples with significantly increased HI and replacing the test result with a specific comment highlighting hemolysis of the sample. © 2013.

  3. Automated suppression of sample-related artifacts in Fluorescence Correlation Spectroscopy.

    PubMed

    Ries, Jonas; Bayer, Mathias; Csúcs, Gábor; Dirkx, Ronald; Solimena, Michele; Ewers, Helge; Schwille, Petra

    2010-05-24

    Fluorescence Correlation Spectroscopy (FCS) in cells often suffers from artifacts caused by bright aggregates or vesicles, depletion of fluorophores or bleaching of a fluorescent background. The common practice of manually discarding distorted curves is time consuming and subjective. Here we demonstrate the feasibility of automated FCS data analysis with efficient rejection of corrupted parts of the signal. As test systems we use a solution of fluorescent molecules, contaminated with bright fluorescent beads, as well as cells expressing a fluorescent protein (ICA512-EGFP), which partitions into bright secretory granules. This approach improves the accuracy of FCS measurements in biological samples, extends its applicability to especially challenging systems and greatly simplifies and accelerates the data analysis.

  4. Automated Three-Dimensional Microbial Sensing and Recognition Using Digital Holography and Statistical Sampling

    PubMed Central

    Moon, Inkyu; Yi, Faliu; Javidi, Bahram

    2010-01-01

    We overview an approach to providing automated three-dimensional (3D) sensing and recognition of biological micro/nanoorganisms integrating Gabor digital holographic microscopy and statistical sampling methods. For 3D data acquisition of biological specimens, a coherent beam propagates through the specimen and its transversely and longitudinally magnified diffraction pattern observed by the microscope objective is optically recorded with an image sensor array interfaced with a computer. 3D visualization of the biological specimen from the magnified diffraction pattern is accomplished by using the computational Fresnel propagation algorithm. For 3D recognition of the biological specimen, a watershed image segmentation algorithm is applied to automatically remove the unnecessary background parts in the reconstructed holographic image. Statistical estimation and inference algorithms are developed to the automatically segmented holographic image. Overviews of preliminary experimental results illustrate how the holographic image reconstructed from the Gabor digital hologram of biological specimen contains important information for microbial recognition. PMID:22163664

  5. Automated three-dimensional microbial sensing and recognition using digital holography and statistical sampling.

    PubMed

    Moon, Inkyu; Yi, Faliu; Javidi, Bahram

    2010-01-01

    We overview an approach to providing automated three-dimensional (3D) sensing and recognition of biological micro/nanoorganisms integrating Gabor digital holographic microscopy and statistical sampling methods. For 3D data acquisition of biological specimens, a coherent beam propagates through the specimen and its transversely and longitudinally magnified diffraction pattern observed by the microscope objective is optically recorded with an image sensor array interfaced with a computer. 3D visualization of the biological specimen from the magnified diffraction pattern is accomplished by using the computational Fresnel propagation algorithm. For 3D recognition of the biological specimen, a watershed image segmentation algorithm is applied to automatically remove the unnecessary background parts in the reconstructed holographic image. Statistical estimation and inference algorithms are developed to the automatically segmented holographic image. Overviews of preliminary experimental results illustrate how the holographic image reconstructed from the Gabor digital hologram of biological specimen contains important information for microbial recognition.

  6. Application of automated bioacoustic identification in environmental education and assessment.

    PubMed

    Oba, Teruyo

    2004-06-01

    Developments in electronics and computer science have led to the introduction of an automated bioacoustic identification device used to resolve commonly encountered problems in the identification of animal species in the field. This technology aids our auditory observations, and also improves the quality of biological surveys and environmental monitoring. In this paper the future roles and possibilities of bioacoustics are discussed, providing some examples from the realm of environmental education and monitoring that focus on the use of nature sounds.

  7. Design and Development of a Robot-Based Automation System for Cryogenic Crystal Sample Mounting at the Advanced Photon Source

    SciTech Connect

    Shu, D.; Preissner, C.; Nocher, D.; Han, Y.; Barraza, J.; Lee, P.; Lee, W.-K.; Cai, Z.; Ginell, S.; Alkire, R.; Lazarski, K.; Schuessler, R.; Joachimiak, A.

    2004-05-12

    X-ray crystallography is the primary method to determine the 3D structures of complex macromolecules at high resolution. In the years to come, the Advanced Photon Source (APS) and similar 3rd-generation synchrotron sources elsewhere will become the most powerful tools for studying atomic structures of biological molecules. One of the major bottlenecks in the x-ray data collection process is the constant need to change and realign the crystal sample. This is a very time- and manpower-consuming task. An automated sample mounting system will help to solve this bottleneck problem. We have developed a novel robot-based automation system for cryogenic crystal sample mounting at the APS. Design of the robot-based automation system, as well as its on-line test results at the Argonne Structural Biology Center (SBC) 19-BM experimental station, are presented in this paper.

  8. Assessment selection in human-automation interaction studies: The Failure-GAM(2)E and review of assessment methods for highly automated driving.

    PubMed

    Grane, Camilla

    2017-08-30

    Highly automated driving will change driver's behavioural patterns. Traditional methods used for assessing manual driving will only be applicable for the parts of human-automation interaction where the driver intervenes such as in hand-over and take-over situations. Therefore, driver behaviour assessment will need to adapt to the new driving scenarios. This paper aims at simplifying the process of selecting appropriate assessment methods. Thirty-five papers were reviewed to examine potential and relevant methods. The review showed that many studies still relies on traditional driving assessment methods. A new method, the Failure-GAM(2)E model, with purpose to aid assessment selection when planning a study, is proposed and exemplified in the paper. Failure-GAM(2)E includes a systematic step-by-step procedure defining the situation, failures (Failure), goals (G), actions (A), subjective methods (M), objective methods (M) and equipment (E). The use of Failure-GAM(2)E in a study example resulted in a well-reasoned assessment plan, a new way of measuring trust through feet movements and a proposed Optimal Risk Management Model. Failure-GAM(2)E and the Optimal Risk Management Model are believed to support the planning process for research studies in the field of human-automation interaction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization.

    PubMed

    Nassar, Ala F; Wisnewski, Adam V; Raddassi, Khadir

    2017-03-01

    Analysis of multiplexed assays is highly important for clinical diagnostics and other analytical applications. Mass cytometry enables multi-dimensional, single-cell analysis of cell type and state. In mass cytometry, the rare earth metals used as reporters on antibodies allow determination of marker expression in individual cells. Barcode-based bioassays for CyTOF are able to encode and decode for different experimental conditions or samples within the same experiment, facilitating progress in producing straightforward and consistent results. Herein, an integrated protocol for automated sample preparation for barcoding used in conjunction with mass cytometry for clinical bioanalysis samples is described; we offer results of our work with barcoding protocol optimization. In addition, we present some points to be considered in order to minimize the variability of quantitative mass cytometry measurements. For example, we discuss the importance of having multiple populations during titration of the antibodies and effect of storage and shipping of labelled samples on the stability of staining for purposes of CyTOF analysis. Data quality is not affected when labelled samples are stored either frozen or at 4 °C and used within 10 days; we observed that cell loss is greater if cells are washed with deionized water prior to shipment or are shipped in lower concentration. Once the labelled samples for CyTOF are suspended in deionized water, the analysis should be performed expeditiously, preferably within the first hour. Damage can be minimized if the cells are resuspended in phosphate-buffered saline (PBS) rather than deionized water while waiting for data acquisition.

  10. Quality assessment of saliva bank samples.

    PubMed

    Janardhanam, Srihari B; Zunt, Susan L; Srinivasan, Mythily

    2012-06-01

    Biospecimens, such as urine, blood, saliva, tissue, cells, DNA, RNA, and protein, are biological material to be stored in a biorepository. They constitute critical resources of molecular data for basic and translational research integrated with diagnostic, therapeutics, and prevention of human diseases. The reliability of the molecular data is dependent on the quality and the consistency of the biospecimen being analyzed. The potential of human saliva as a valuable diagnostic fluid for oral and systemic conditions is being increasingly recognized. The aim of this study is to determine the molecular quality of unstimulated whole saliva (UWS) samples stored over a period of 1 to 5 years. UWS samples collected between 2006 and 2010 (20/year) and stored at -80°C were assessed for molecular integrity. The study was approved by the institutional review board of the Indiana University Purdue University at Indianapolis. Qualitative and quantitative measurements of salivary proteins were determined by gel electrophoresis and spectrophotometry. The salivary nucleic acid content was determined by the Nanodrop method and genetic analysis. The nature of the cellular sediment in the UWS was determined by amplification of specific gene. No significant differences were observed in the amount of proteins, nucleic acid, or in the number of viable cells in the UWS samples stored for 1 to 5 years. Archived UWS samples could function as excellent biospecimen resources for measurement of protein, DNA, and RNA analytes, and act as an efficient source for human epithelial cells.

  11. Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples.

    PubMed

    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. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  12. An automated method for fibrin clot permeability assessment.

    PubMed

    Ząbczyk, Michał; Piłat, Adam; Awsiuk, Magdalena; Undas, Anetta

    2015-01-01

    The fibrin clot permeability coefficient (Ks) is a useful measure of porosity of the fibrin network, which is determined by a number of genetic and environmental factors. Currently available methods to evaluate Ks are time-consuming, require constant supervision and provide only one parameter. We present an automated method in which drops are weighed individually, buffer is dosed by the pump and well defined clot washing is controlled by the software. The presence of a straight association between drop mass and their dripping time allows to shorten the measurement time twice. In 40 healthy individuals, Ks, the number of drops required to reach the plateau (DTP), the time to achieve the plateau (TTP) and the DTP/TTP ratio (DTR) were calculated. There was a positive association between Ks (r = 0.69, P < 0.0001) evaluated by using the manual [median of 4.17 (3.60-5.18) ·10⁻⁹ cm²) and the automated method [median of 4.35 (3.74-5.38) ·10⁻⁹ cm²]. The correlation was stronger (r = 0.85, P < 0.001) in clots with DTP of 7 or less (n = 12). DTP was associated with total homocysteine (tHcy) (r = 0.35, P < 0.05) and activated partial thromboplastin time (APTT) (r = -0.34, P < 0.05), TTP with Ks (r = -0.55, P < 0.01 for the manual method and r = -0.44, P < 0.01 for the automated method) and DTP (r = 0.75, P < 0.0001), and DTR with Ks (r = 0.70, P < 0.0001 for the manual method and r = 0.76, P < 0.0001 for the automated method), fibrinogen (r = -0.58, P < 0.0001) and C-reactive protein (CRP) (r = -0.47, P < 0.01). The automated method might be a suitable tool for research and clinical use and may offer more additional parameters describing fibrin clot structure.

  13. Drug Discovery Testing Compounds in Patient Samples by Automated Flow Cytometry

    PubMed Central

    Hernández, Pilar; Gorrochategui, Julián; Primo, Daniel; Robles, Alicia; Rojas, José Luis; Espinosa, Ana Belén; Gómez, Cristina; Martínez-López, Joaquín; Bennett, Teresa A.; Ballesteros, Joan

    2017-01-01

    Functional ex vivo assays that predict a patient’s clinical response to anticancer drugs for guiding cancer treatment have long been a goal, but few have yet proved to be reliable. To address this, we have developed an automated flow cytometry platform for drug screening that evaluates multiple endpoints with a robust data analysis system that can capture the complex mechanisms of action across different compounds. This system, called PharmaFlow, is used to test peripheral blood or bone marrow samples from patients diagnosed with hematological malignancies. Functional assays that use the whole sample, retaining all the microenvironmental components contained in the sample, offer an approach to ex vivo testing that may give results that are clinically relevant. This new approach can help to predict the patients’ response to existing treatments or to drugs under development, for hematological malignancies or other tumors. In addition, relevant biomarkers can be identified that determine the patient’s sensitivity, resistance, or toxicity to a given treatment. We propose that this approach, which better recapitulates the human microenvironment, constitutes a more predictive assay for personalized medicine and preclinical drug discovery. PMID:28340541

  14. Drug Discovery Testing Compounds in Patient Samples by Automated Flow Cytometry.

    PubMed

    Hernández, Pilar; Gorrochategui, Julián; Primo, Daniel; Robles, Alicia; Rojas, José Luis; Espinosa, Ana Belén; Gómez, Cristina; Martínez-López, Joaquín; Bennett, Teresa A; Ballesteros, Joan

    2017-06-01

    Functional ex vivo assays that predict a patient's clinical response to anticancer drugs for guiding cancer treatment have long been a goal, but few have yet proved to be reliable. To address this, we have developed an automated flow cytometry platform for drug screening that evaluates multiple endpoints with a robust data analysis system that can capture the complex mechanisms of action across different compounds. This system, called PharmaFlow, is used to test peripheral blood or bone marrow samples from patients diagnosed with hematological malignancies. Functional assays that use the whole sample, retaining all the microenvironmental components contained in the sample, offer an approach to ex vivo testing that may give results that are clinically relevant. This new approach can help to predict the patients' response to existing treatments or to drugs under development, for hematological malignancies or other tumors. In addition, relevant biomarkers can be identified that determine the patient's sensitivity, resistance, or toxicity to a given treatment. We propose that this approach, which better recapitulates the human microenvironment, constitutes a more predictive assay for personalized medicine and preclinical drug discovery.

  15. Automated measurement and quantification of heterotrophic bacteria in water samples based on the MPN method.

    PubMed

    Fuchsluger, C; Preims, M; Fritz, I

    2011-01-01

    Quantification of heterotrophic bacteria is a widely used measure for water analysis. Especially in terms of drinking water analysis, testing for microorganisms is strictly regulated by the European Drinking Water Directive, including quality criteria and detection limits. The quantification procedure presented in this study is based on the most probable number (MPN) method, which was adapted to comply with the need for a quick and easy screening tool for different kinds of water samples as well as varying microbial loads. Replacing tubes with 24-well titer plates for cultivation of bacteria drastically reduces the amount of culture media and also simplifies incubation. Automated photometric measurement of turbidity instead of visual evaluation of bacterial growth avoids misinterpretation by operators. Definition of a threshold ensures definite and user-independent determination of microbial growth. Calculation of the MPN itself is done using a program provided by the US Food and Drug Administration (FDA). For evaluation of the method, real water samples of different origins as well as pure cultures of bacteria were analyzed in parallel with the conventional plating methods. Thus, the procedure described requires less preparation time, reduces costs and ensures both stable and reliable results for water samples.

  16. From Sample Changer to the Robotic Rheometer: Automation and High Throughput Screening in Rotational Rheometry

    NASA Astrophysics Data System (ADS)

    Läuger, Jörg; Krenn, Michael

    2008-07-01

    A fully automated, robotically operated rheometer was developed. The full functionality, modularity and accuracy of the rotational rheometer are available, which means the modern principles of high-throughput screening are brought to full function on the rheometer. The basic rheometer setup remains as modular as before including the ability to run all test modes the rheometer offers with the difference that the high-throughput rheometer now performs all measuring steps automatically. In addition, the standard and proven environmental chambers of the rheometer are available. The rheometer itself runs by the standard rheometer software and the measurement data and analysis results can be transferred to a monitoring database. The sample loading and the cleaning of the geometries is assisted by a sample preparation unit and a cleaning station, respectively. The sample throughput is further maximized by the use of multiple geometries allowing the simultaneous rheological measurement by the rheometer and the cleaning of the geometries at the cleaning station by the robot. The High-Throughput Rheometer (HTR) and its special adaptation to different applications like dispersions and polymer melts are described.

  17. Automated system for sampling, counting, and biological analysis of rotifer populations.

    PubMed

    Stelzer, Claus-Peter

    2009-12-01

    Zooplankton organisms with short generation times, such as rotifers, are ideal models to study general ecological and evolutionary questions on the population level, because meaningful experiments can often be completed within a couple of weeks. Yet biological analysis of such populations is often extremely time consuming, owing to abundance estimation by counting, measuring body size, or determining the investment into sexual versus asexual reproduction. An automated system for sampling and analyzing experimental rotifer populations is described. It relies on image analysis of digital photographs taken from subsamples of the culture. The system works completely autonomously for up to several weeks and can sample up to 12 cultures at time intervals down to a few hours. It allows quantitative analysis of female population density at a precision equivalent to that of conventional methods (i.e., manual counts of samples fixed in Lugol solution), and it can also recognize males, which allows detecting temporal variation of sexual reproduction in such cultures. Another parameter that can be automatically measured with the image analysis system is female body size. This feature may be useful for studies of population productivity and/or in competition experiments with clones of different body size. In this article, I describe the basic setup of the system and tests on the efficiency of data collection, and show some example data sets on the population dynamics of different strains of the rotifer Brachionus calyciflorus.

  18. Automated system for sampling, counting, and biological analysis of rotifer populations

    PubMed Central

    Stelzer, Claus-Peter

    2010-01-01

    Zooplankton organisms with short generation times, such as rotifers, are ideal models to study general ecological and evolutionary questions on the population level, because meaningful experiments can often be completed within a couple of weeks. Yet biological analysis of such populations is often extremely time consuming, owing to abundance estimation by counting, measuring body size, or determining the investment into sexual versus asexual reproduction. An automated system for sampling and analyzing experimental rotifer populations is described. It relies on image analysis of digital photographs taken from subsamples of the culture. The system works completely autonomously for up to several weeks and can sample up to 12 cultures at time intervals down to a few hours. It allows quantitative analysis of female population density at a precision equivalent to that of conventional methods (i.e., manual counts of samples fixed in Lugol solution), and it can also recognize males, which allows detecting temporal variation of sexual reproduction in such cultures. Another parameter that can be automatically measured with the image analysis system is female body size. This feature may be useful for studies of population productivity and/or in competition experiments with clones of different body size. In this article, I describe the basic setup of the system and tests on the efficiency of data collection, and show some example data sets on the population dynamics of different strains of the rotifer Brachionus calyciflorus. PMID:21151824

  19. Design and Implementation of an Automated Illuminating, Culturing, and Sampling System for Microbial Optogenetic Applications.

    PubMed

    Stewart, Cameron J; McClean, Megan N

    2017-02-19

    Optogenetic systems utilize genetically-encoded proteins that change conformation in response to specific wavelengths of light to alter cellular processes. There is a need for culturing and measuring systems that incorporate programmed illumination and stimulation of optogenetic systems. We present a protocol for building and using a continuous culturing apparatus to illuminate microbial cells with programmed doses of light, and automatically acquire and analyze images of cells in the effluent. The operation of this apparatus as a chemostat allows the growth rate and the cellular environment to be tightly controlled. The effluent of the continuous cell culture is regularly sampled and the cells are imaged by multi-channel microscopy. The culturing, sampling, imaging, and image analysis are fully automated so that dynamic responses in the fluorescence intensity and cellular morphology of cells sampled from the culture effluent are measured over multiple days without user input. We demonstrate the utility of this culturing apparatus by dynamically inducing protein production in a strain of Saccharomyces cerevisiae engineered with an optogenetic system that activates transcription.

  20. In vivo hippocampal measurement and memory: a comparison of manual tracing and automated segmentation in a large community-based sample.

    PubMed

    Cherbuin, Nicolas; Anstey, Kaarin J; Réglade-Meslin, Chantal; Sachdev, Perminder S

    2009-01-01

    While manual tracing is the method of choice in measuring hippocampal volume, its time intensive nature and proneness to human error make automated methods attractive, especially when applied to large samples. Few studies have systematically compared the performance of the two techniques. In this study, we measured hippocampal volumes in a large (N = 403) population-based sample of individuals aged 44-48 years using manual tracing by a trained researcher and automated procedure using Freesurfer (http://surfer.nmr.mgh.harvard.edu) imaging suite. Results showed that absolute hippocampal volumes assessed with these methods were significantly different, with automated measures using the Freesurfer software suite being significantly larger, by 23% for the left and 29% for the right hippocampus. The correlation between the two methods varied from 0.61 to 0.80, with lower correlations for hippocampi with visible abnormalities. Inspection of 2D and 3D models suggested that this difference was largely due to greater inclusion of boundary voxels by the automated method and variations in subiculum/entorhinal segmentation. The correlation between left and right hippocampal volumes was very similar by the two methods. The relationship of hippocampal volumes to selected sociodemographic and cognitive variables was not affected by the measurement method, with each measure showing an association with memory performance and suggesting that both were equally valid for this purpose. This study supports the use of automated measures, based on Freesurfer in this instance, as being sufficiently reliable and valid particularly in the context of larger sample sizes when the research question does not rely on 'true' hippocampal volumes.

  1. Assessing bat detectability and occupancy with multiple automated echolocation detectors

    USGS Publications Warehouse

    Gorresen, P.M.; Miles, A.C.; Todd, C.M.; Bonaccorso, F.J.; Weller, T.J.

    2008-01-01

    Occupancy analysis and its ability to account for differential detection probabilities is important for studies in which detecting echolocation calls is used as a measure of bat occurrence and activity. We examined the feasibility of remotely acquiring bat encounter histories to estimate detection probability and occupancy. We used echolocation detectors coupled to digital recorders operating at a series of proximate sites on consecutive nights in 2 trial surveys for the Hawaiian hoary bat (Lasiurus cinereus semotus). Our results confirmed that the technique is readily amenable for use in occupancy analysis. We also conducted a simulation exercise to assess the effects of sampling effort on parameter estimation. The results indicated that the precision and bias of parameter estimation were often more influenced by the number of sites sampled than number of visits. Acceptable accuracy often was not attained until at least 15 sites or 15 visits were used to estimate detection probability and occupancy. The method has significant potential for use in monitoring trends in bat activity and in comparative studies of habitat use. ?? 2008 American Society of Mammalogists.

  2. Development of an Automated Security Risk Assessment Methodology Tool for Critical Infrastructures.

    SciTech Connect

    Jaeger, Calvin Dell; Roehrig, Nathaniel S.; Torres, Teresa M.

    2008-12-01

    This document presents the security automated Risk Assessment Methodology (RAM) prototype tool developed by Sandia National Laboratories (SNL). This work leverages SNL's capabilities and skills in security risk analysis and the development of vulnerability assessment/risk assessment methodologies to develop an automated prototype security RAM tool for critical infrastructures (RAM-CITM). The prototype automated RAM tool provides a user-friendly, systematic, and comprehensive risk-based tool to assist CI sector and security professionals in assessing and managing security risk from malevolent threats. The current tool is structured on the basic RAM framework developed by SNL. It is envisioned that this prototype tool will be adapted to meet the requirements of different CI sectors and thereby provide additional capabilities.

  3. Erratum to: Automated Sample Preparation Method for Suspension Arrays using Renewable Surface Separations with Multiplexed Flow Cytometry Fluorescence Detection

    SciTech Connect

    Grate, Jay W.; Bruckner-Lea, Cindy J.; Jarrell, Ann E.; Chandler, Darrell P.

    2003-04-10

    In this paper we describe a new method of automated sample preparation for multiplexed biological analysis systems that use flow cytometry fluorescence detection. In this approach, color-encoded microspheres derivatized to capture particular biomolecules are temporarily trapped in a renewable surface separation column to enable perfusion with sample and reagents prior to delivery to the detector. This method provides for separation of the biomolecules of interest from other sample matrix components as well as from labeling solutions.

  4. Invention and validation of an automated camera system that uses optical character recognition to identify patient name mislabeled samples.

    PubMed

    Hawker, Charles D; McCarthy, William; Cleveland, David; Messinger, Bonnie L

    2014-03-01

    Mislabeled samples are a serious problem in most clinical laboratories. Published error rates range from 0.39/1000 to as high as 1.12%. Standardization of bar codes and label formats has not yet achieved the needed improvement. The mislabel rate in our laboratory, although low compared with published rates, prompted us to seek a solution to achieve zero errors. To reduce or eliminate our mislabeled samples, we invented an automated device using 4 cameras to photograph the outside of a sample tube. The system uses optical character recognition (OCR) to look for discrepancies between the patient name in our laboratory information system (LIS) vs the patient name on the customer label. All discrepancies detected by the system's software then require human inspection. The system was installed on our automated track and validated with production samples. We obtained 1 009 830 images during the validation period, and every image was reviewed. OCR passed approximately 75% of the samples, and no mislabeled samples were passed. The 25% failed by the system included 121 samples actually mislabeled by patient name and 148 samples with spelling discrepancies between the patient name on the customer label and the patient name in our LIS. Only 71 of the 121 mislabeled samples detected by OCR were found through our normal quality assurance process. We have invented an automated camera system that uses OCR technology to identify potential mislabeled samples. We have validated this system using samples transported on our automated track. Full implementation of this technology offers the possibility of zero mislabeled samples in the preanalytic stage.

  5. To the development of an automated system of assessment of radiological images of joints

    NASA Astrophysics Data System (ADS)

    Grechikhin, A. I.; Grunina, E. A.; Karetnikova, I. R.

    2008-03-01

    An algorithm developed for the adaptive automated computer processing of radiological images of hands and feet in order to assess the degree of bone and cartilage destruction in rheumatoid arthritis is described. A set of new numeral signs was proposed in order to assess a degree of arthritis radiological progression.

  6. Automated Formative Assessment as a Tool to Scaffold Student Documentary Writing

    ERIC Educational Resources Information Center

    Ferster, Bill; Hammond, Thomas C.; Alexander, R. Curby; Lyman, Hunt

    2012-01-01

    The hurried pace of the modern classroom does not permit formative feedback on writing assignments at the frequency or quality recommended by the research literature. One solution for increasing individual feedback to students is to incorporate some form of computer-generated assessment. This study explores the use of automated assessment of…

  7. Automated Multiple-Choice Testing for Summative Assessment: What Do Students Think?

    ERIC Educational Resources Information Center

    Bridge, Pete; Appleyard, Rob; Wilson, Rob

    2007-01-01

    This paper reports undergraduate student feedback contrasting conventional "Long-answer" examinations with automated multiple-choice question (MCQ) assessment. Feedback was gathered after students had undertaken formative MCQ assessments as a revision aid. Feedback was generally supportive of MCQ summative tests, with 74% expressing a…

  8. Designing an Automated Assessment of Public Speaking Skills Using Multimodal Cues

    ERIC Educational Resources Information Center

    Chen, Lei; Feng, Gary; Leong, Chee Wee; Joe, Jilliam; Kitchen, Christopher; Lee, Chong Min

    2016-01-01

    Traditional assessments of public speaking skills rely on human scoring. We report an initial study on the development of an automated scoring model for public speaking performances using multimodal technologies. Task design, rubric development, and human rating were conducted according to standards in educational assessment. An initial corpus of…

  9. ADDING GLOBAL SOILS DATA TO THE AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT TOOL (AGWA)

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Tool (AGWA) is a GIS-based hydrologic modeling tool that is available as an extension for ArcView 3.x from the USDA-ARS Southwest Watershed Research Center (www.tucson.ars.ag.gov/agwa). AGWA is designed to facilitate the assessment of...

  10. Automated Formative Assessment as a Tool to Scaffold Student Documentary Writing

    ERIC Educational Resources Information Center

    Ferster, Bill; Hammond, Thomas C.; Alexander, R. Curby; Lyman, Hunt

    2012-01-01

    The hurried pace of the modern classroom does not permit formative feedback on writing assignments at the frequency or quality recommended by the research literature. One solution for increasing individual feedback to students is to incorporate some form of computer-generated assessment. This study explores the use of automated assessment of…

  11. ADDING GLOBAL SOILS DATA TO THE AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT TOOL (AGWA)

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment Tool (AGWA) is a GIS-based hydrologic modeling tool that is available as an extension for ArcView 3.x from the USDA-ARS Southwest Watershed Research Center (www.tucson.ars.ag.gov/agwa). AGWA is designed to facilitate the assessment of...

  12. Comparison of manual and automated DNA purification for measuring TREC in dried blood spot (DBS) samples with qPCR.

    PubMed

    Lang, Pierre-Olivier; Govind, Sheila; Dramé, Moustapha; Aspinall, Richard

    2012-10-31

    Automated nucleic acid extractions from dried blood spot (DBS) samples promises standardized sample treatment, low error rates, avoidance of contamination and requirement of less hands-on time. In the present study, non-automated and automated column based extraction processes using the QIAamp Investigator procedure were compared for the extraction of DNA from DBS samples. The concentration and the purity of DNA generated were determined by optical density readings. Furthermore qPCR downstream applications using the nucleic acids extracted with the two processes and albumin and T-cell receptor excision circles (TREC) copy numbers were measured and compared. The influence of the time of storage was also investigated by analyzing samples freshly dried and stored up to 11weeks at -20°C from the same individual. Finally, we provide arguments of preferentially choosing the automated procedure for extracting DNAs from DBS samples when downstream qPCR applications are required. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Automation and integration of multiplexed on-line sample preparation with capillary electrophoresis for DNA sequencing

    SciTech Connect

    Tan, H.

    1999-03-31

    The purpose of this research is to develop a multiplexed sample processing system in conjunction with multiplexed capillary electrophoresis for high-throughput DNA sequencing. The concept from DNA template to called bases was first demonstrated with a manually operated single capillary system. Later, an automated microfluidic system with 8 channels based on the same principle was successfully constructed. The instrument automatically processes 8 templates through reaction, purification, denaturation, pre-concentration, injection, separation and detection in a parallel fashion. A multiplexed freeze/thaw switching principle and a distribution network were implemented to manage flow direction and sample transportation. Dye-labeled terminator cycle-sequencing reactions are performed in an 8-capillary array in a hot air thermal cycler. Subsequently, the sequencing ladders are directly loaded into a corresponding size-exclusion chromatographic column operated at {approximately} 60 C for purification. On-line denaturation and stacking injection for capillary electrophoresis is simultaneously accomplished at a cross assembly set at {approximately} 70 C. Not only the separation capillary array but also the reaction capillary array and purification columns can be regenerated after every run. DNA sequencing data from this system allow base calling up to 460 bases with accuracy of 98%.

  14. Analysis of zearalenone in cereal and Swine feed samples using an automated flow-through immunosensor.

    PubMed

    Urraca, Javier L; Benito-Peña, Elena; Pérez-Conde, Concepción; Moreno-Bondi, María C; Pestka, James J

    2005-05-04

    The development of a sensitive flow-though immunosensor for the analysis of the mycotoxin zearalenone in cereal samples is described. The sensor was completely automated and was based on a direct competitive immunosorbent assay and fluorescence detection. The mycotoxin competes with a horseradish-peroxidase-labeled derivative for the binding sites of a rabbit polyclonal antibody. Control pore glass covalently bound to Prot A was used for the oriented immobilization of the antibody-antigen immunocomplexes. The immunosensor shows an IC(50) value of 0.087 ng mL(-1) (RSD = 2.8%, n = 6) and a dynamic range from 0.019 to 0.422 ng mL(-1). The limit of detection (90% of blank signal) of 0.007 ng mL(-1) (RSD = 3.9%, n = 3) is lower than previously published methods. Corn, wheat, and swine feed samples have been analyzed with the device after extraction of the analyte using accelerated solvent extraction (ASE). The immunosensor has been validated using a corn certificate reference material and HPLC with fluorescence detection.

  15. Measurement of airborne carbonyls using an automated sampling and analysis system.

    PubMed

    Aiello, Mauro; McLaren, Robert

    2009-12-01

    Based upon the well established method of derivitization with 2,4-dinitrophenylhydrazine, an instrument was developed for ambient measurement of carbonyls with significantly improved temporal resolution and detection limits through automation, direct injection, and continuous use of a single microsilica DNPH cartridge. Kinetic experiments indicate that the derivitization reaction on the cartridge is fast enough for continuous measurements with 50 min air sampling. Reaction efficiencies measured on the cartridge were 100% for the carbonyls tested, including formaldehyde, acetaldehyde, propanal, acetone, and benzaldehyde. Transmission of the carbonyls through an ozone scrubber (KI) were in the range of 97-101%. Blank levels and detection limits were lower than those obtainable with conventional DNPH methods by an order of magnitude or greater. Mixing ratio detection limits of carbonyls in ambient air were 38-73 ppt for a 50 min air sample (2.5 L). The instrument made continuous measurements of carbonyls on a 2 h cycle over a period of 10 days during a field study in southwestern Ontario. Median mixing ratios were 0.58 ppb formaldehyde; 0.29 ppb acetaldehyde; 1.14 ppb acetone; and 0.45 ppb glyoxal. Glyoxal shows a significant correlation with ozone and zero intercept, consistent with a secondary source and minor direct source to the atmosphere. The method should easily be extendable to the detection of other low molecular weight carbonyls that have been previously reported using the DNPH technique.

  16. A user-friendly robotic sample preparation program for fully automated biological sample pipetting and dilution to benefit the regulated bioanalysis.

    PubMed

    Jiang, Hao; Ouyang, Zheng; Zeng, Jianing; Yuan, Long; Zheng, Naiyu; Jemal, Mohammed; Arnold, Mark E

    2012-06-01

    Biological sample dilution is a rate-limiting step in bioanalytical sample preparation when the concentrations of samples are beyond standard curve ranges, especially when multiple dilution factors are needed in an analytical run. We have developed and validated a Microsoft Excel-based robotic sample preparation program (RSPP) that automatically transforms Watson worklist sample information (identification, sequence and dilution factor) to comma-separated value (CSV) files. The Freedom EVO liquid handler software imports and transforms the CSV files to executable worklists (.gwl files), allowing the robot to perform sample dilutions at variable dilution factors. The dynamic dilution range is 1- to 1000-fold and divided into three dilution steps: 1- to 10-, 11- to 100-, and 101- to 1000-fold. The whole process, including pipetting samples, diluting samples, and adding internal standard(s), is accomplished within 1 h for two racks of samples (96 samples/rack). This platform also supports online sample extraction (liquid-liquid extraction, solid-phase extraction, protein precipitation, etc.) using 96 multichannel arms. This fully automated and validated sample dilution and preparation process has been applied to several drug development programs. The results demonstrate that application of the RSPP for fully automated sample processing is efficient and rugged. The RSPP not only saved more than 50% of the time in sample pipetting and dilution but also reduced human errors. The generated bioanalytical data are accurate and precise; therefore, this application can be used in regulated bioanalysis.

  17. Development of computer automated decision support system for surface water quality assessment

    NASA Astrophysics Data System (ADS)

    Sharma, Asheesh; Naidu, Madhuri; Sargaonkar, Aabha

    2013-02-01

    The Overall Index of Pollution (OIP) is a single number that expresses the overall water quality by integrating measurements of 14 different physicochemical, toxicological, and bacteriological water quality parameters. It provides a simple and concise method for water quality classification as, 'Excellent', 'Acceptable', 'Slightly Polluted', 'Polluted', and 'Heavily Polluted'. OIP values range from 0 to 16. A high OIP value signals poor water quality, while a low value signals good water quality based on the classification scheme developed for India. In this paper, we present a computer-automated, user-friendly, and standalone Surface Water Quality Assessment Tool (SWQAT), which calculates OIP values and displays it on Google map. The software is developed in VB.Net and SQL database. The software application is demonstrated through water quality assessment of two rivers of India, namely Cauvery and Tungabhadra. OIP values are estimated at 10 sampling stations on the river Cauvery and at eight sampling stations on the river Tungabhadra. The Cauvery river OIP scores in the range 0.85-7.91 while for Tungabhadra river, it is in range 2.08 to 8.97. The results are useful to analyze the variations in the water quality of different sites at different times. SWQAT improves understanding of general water quality issues, communicates water quality status, and draws the need for and effectiveness of protection measures.

  18. Strategies for automated sample preparation, nucleic acid purification, and concentration of low-target-number nucleic acids in environmental and food processing samples

    NASA Astrophysics Data System (ADS)

    Bruckner-Lea, Cynthia J.; Holman, David A.; Schuck, Beatrice L.; Brockman, Fred J.; Chandler, Darrell P.

    1999-01-01

    The purpose of this work is to develop a rapid, automated system for nucleic acid purification and concentration from environmental and food processing samples. Our current approach involves off-line filtration and cell lysis (ballistic disintegration) functions in appropriate buffers followed by automated nucleic acid capture and purification on renewable affinity matrix microcolumns. Physical cell lysis and renewable affinity microcolumns eliminate the need for toxic organic solvents, enzyme digestions or other time- consuming sample manipulations. Within the renewable affinity microcolumn, we have examined nucleic acid capture and purification efficiency with various microbead matrices (glass, polymer, paramagnetic), surface derivitization (sequence-specific capture oligonucleotides or peptide nucleic acids), and DNA target size and concentration under variable solution conditions and temperatures. Results will be presented comparing automated system performance relative to benchtop procedures for both clean (pure DNA from a laboratory culture) and environmental (soil extract) samples, including results which demonstrate 8 minute purification and elution of low-copy nucleic acid targets from a crude soil extract in a form suitable for PCR or microarray-based detectors. Future research will involve the development of improved affinity reagents and complete system integration, including upstream cell concentration and cell lysis functions and downstream, gene-based detectors. Results of this research will ultimately lead to improved processes and instrumentation for on-line, automated monitors for pathogenic micro-organisms in food, water, air, and soil samples.

  19. Plasma cortisol and norepinephrine concentrations in pigs: automated sampling of freely moving pigs housed in the PigTurn versus manually sampled and restrained pigs

    USDA-ARS?s Scientific Manuscript database

    Minimizing effects of restraint and human interaction on the endocrine physiology of animals is essential for collection of accurate physiological measurements. Our objective was to compare stress-induced cortisol (CORT) and norepinephrine (NE) responses in automated versus manual blood sampling. A ...

  20. Plasma cortisol and noradrenalin concentrations in pigs: automated sampling of freely moving pigs housed in PigTurn versus manually sampled and restrained pigs

    USDA-ARS?s Scientific Manuscript database

    Minimizing the effects of restraint and human interaction on the endocrine physiology of animals is essential for collection of accurate physiological measurements. Our objective was to compare stress-induced cortisol (CORT) and noradrenalin (NorA) responses in automated versus manual blood sampling...

  1. Quantification of 4-beta-hydroxycholesterol in human plasma using automated sample preparation and LC-ESI-MS/MS analysis.

    PubMed

    Goodenough, Angela K; Onorato, Joelle M; Ouyang, Zheng; Chang, Shu; Rodrigues, A David; Kasichayanula, Sreeneeranj; Huang, Shu-Pang; Turley, Wesley; Burrell, Richard; Bifano, Marc; Jemal, Mohammed; LaCreta, Frank; Tymiak, Adrienne; Wang-Iverson, David

    2011-09-19

    It has recently been proposed that plasma levels of 4β-hydroxycholesterol (4βHC) may be indicative of cytochrome P450 3A4 (P450 3A) activity and therefore could be used to probe for P450 3A-mediated drug-drug interactions. With this in mind, we describe a highly sensitive and precise liquid chromatography-electrospray ionization-tandem mass spectrometry method for the measurement of 4βHC in human plasma with a lower limit of quantification established at 2 ng/mL using 50 μL of plasma. The entire sample preparation scheme including saponification and derivatization of 4βHC to the corresponding dipicolinyl ester (DPE) was completed in less than 8 h using an automated sample preparation scheme enabling higher-throughput capabilities. Chromatographic resolution of 4βHC from 4α-hydroxycholesterol and other endogenous isobaric species was achieved in 11-min using an isocratic gradient on a C18 column. Because of endogenous concentrations of 4βHC in plasma, a stable isotope labeled (SIL) analogue, d7-4βHC, was used as a surrogate analyte and measured in the standard curve and quality control samples prepared in plasma. A second SIL analogue, d4-4βHC, was used as the internal standard. The intraday and interday accuracy for the assay was within 6% of nominal concentrations, and the precision for these measurements was less than 5% relative standard deviation. Rigorous stability assessments demonstrated adequate stability of endogenous 4βHC in plasma and the corresponding DPE derivative for the analysis of clinical study samples. The results from clinical samples following treatment with a potent P450 3A inducer (rifampin) or inhibitor (ketoconazole) are reported and demonstrate the potential future application for this highly precise and robust analytical assay.

  2. Automated extraction and quantitation of oncogenic HPV genotypes from cervical samples by a real-time PCR-based system.

    PubMed

    Broccolo, Francesco; Cocuzza, Clementina E

    2008-03-01

    Accurate laboratory assays for the diagnosis of persistent oncogenic HPV infection are being recognized increasingly as essential for clinical management of women with cervical precancerous lesions. HPV viral load has been suggested to be a surrogate marker of persistent infection. Four independent real-time quantitative TaqMan PCR assays were developed for: HPV-16, -31, -18 and/or -45 and -33 and/or -52, -58, -67. The assays had a wide dynamic range of detection and a high degree of accuracy, repeatability and reproducibility. In order to minimize material and hands-on time, automated nucleic acid extraction was performed using a 96-well plate format integrated into a robotic liquid handler workstation. The performance of the TaqMan assays for HPV identification was assessed by comparing results with those obtained by means of PCR using consensus primers (GP5+/GP6+) and sequencing (296 samples) and INNO-LiPA analysis (31 samples). Good agreement was found generally between results obtained by real-time PCR assays and GP(+)-PCR system (kappa statistic=0.91). In conclusion, this study describes four newly developed real-time PCR assays that provide a reliable and high-throughput method for detection of not only HPV DNA but also HPV activity of the most common oncogenic HPV types in cervical specimens.

  3. Development of an automated multiple-target mask CD disposition system to enable new sampling strategy

    NASA Astrophysics Data System (ADS)

    Ma, Jian; Farnsworth, Jeff; Bassist, Larry; Cui, Ying; Mammen, Bobby; Padmanaban, Ramaswamy; Nadamuni, Venkatesh; Kamath, Muralidhar; Buckmann, Ken; Neff, Julie; Freiberger, Phil

    2006-03-01

    Traditional mask critical dimension (CD) disposition systems with only one or two targets is being challenged by the new requirements from mask-users as the wafer process control becomes more complicated in the newer generation of technologies. Historically, the mask shop does not necessarily measure and disposition off the same kind of CD structures that wafer fabs do. Mask disposition specifications and structures come from the frame-design and the tapeout, while wafer-level CD dispositions are mainly based on the historical process window established per CD-skew experiments and EOL (end of line) yield. In the current high volume manufacturing environment, the mask CDs are mainly dispositioned off their mean-to-target (MTT) and uniformity (6sigma) on one or two types of pre-determined structures. The disposition specification is set to ensure the printed mask will meet the design requirements and to ensure minimum deviation from them. The CD data are also used to adjust the dose of the mask exposure tools to control CD MTT. As a result, the mask CD disposition automation system was built to allow only one or two kinds of targets at most. In contrast, wafer-fabs measure a fairly wide range of different structures to ensure their process is on target and in control. The number of such structures that are considered critical is increasing due the growing complexity of the technology. To fully comprehend the wafer-level requirements, it is highly desirable to align the mask CD sample site and disposition to be the same as that of the wafer-fabs, to measure the OPC (optical proximity correction) structures or equivalent whenever possible, and to establish the true correlation between mask CD measurements vs. wafer CD measurement. In this paper, the development of an automated multiple-target mask CD disposition system with the goal of enabling new sampling strategy is presented. The pros and cons of its implementation are discussed. The new system has been inserted in

  4. Carotid Catheterization and Automated Blood Sampling Induce Systemic IL-6 Secretion and Local Tissue Damage and Inflammation in the Heart, Kidneys, Liver and Salivary Glands in NMRI Mice

    PubMed Central

    Teilmann, Anne Charlotte; Rozell, Björn; Kalliokoski, Otto; Hau, Jann; Abelson, Klas S. P.

    2016-01-01

    Automated blood sampling through a vascular catheter is a frequently utilized technique in laboratory mice. The potential immunological and physiological implications associated with this technique have, however, not been investigated in detail. The present study compared plasma levels of the cytokines IL-1β, IL-2, IL-6, IL-10, IL-17A, GM-CSF, IFN-γ and TNF-α in male NMRI mice that had been subjected to carotid artery catheterization and subsequent automated blood sampling with age-matched control mice. Body weight and histopathological changes in the surgical area, including the salivary glands, the heart, brain, spleen, liver, kidneys and lungs were compared. Catheterized mice had higher levels of IL-6 than did control mice, but other cytokine levels did not differ between the groups. No significant difference in body weight was found. The histology revealed inflammatory and regenerative (healing) changes at surgical sites of all catheterized mice, with mild inflammatory changes extending into the salivary glands. Several catheterized mice had multifocal degenerative to necrotic changes with inflammation in the heart, kidneys and livers, suggesting that thrombi had detached from the catheter tip and embolized to distant sites. Thus, catheterization and subsequent automated blood sampling may have physiological impact. Possible confounding effects of visceral damage should be assessed and considered, when using catheterized mouse models. PMID:27832170

  5. Automated dispersive liquid-liquid microextraction coupled to high performance liquid chromatography - cold vapour atomic fluorescence spectroscopy for the determination of mercury species in natural water samples.

    PubMed

    Liu, Yao-Min; Zhang, Feng-Ping; Jiao, Bao-Yu; Rao, Jin-Yu; Leng, Geng

    2017-04-14

    An automated, home-constructed, and low cost dispersive liquid-liquid microextraction (DLLME) device that directly coupled to a high performance liquid chromatography (HPLC) - cold vapour atomic fluorescence spectroscopy (CVAFS) system was designed and developed for the determination of trace concentrations of methylmercury (MeHg(+)), ethylmercury (EtHg(+)) and inorganic mercury (Hg(2+)) in natural waters. With a simple, miniaturized and efficient automated DLLME system, nanogram amounts of these mercury species were extracted from natural water samples and injected into a hyphenated HPLC-CVAFS for quantification. The complete analytical procedure, including chelation, extraction, phase separation, collection and injection of the extracts, as well as HPLC-CVAFS quantification, was automated. Key parameters, such as the type and volume of the chelation, extraction and dispersive solvent, aspiration speed, sample pH, salt effect and matrix effect, were thoroughly investigated. Under the optimum conditions, linear range was 10-1200ngL(-1) for EtHg(+) and 5-450ngL(-1) for MeHg(+) and Hg(2+). Limits of detection were 3.0ngL(-1) for EtHg(+) and 1.5ngL(-1) for MeHg(+) and Hg(2+). Reproducibility and recoveries were assessed by spiking three natural water samples with different Hg concentrations, giving recoveries from 88.4-96.1%, and relative standard deviations <5.1%.

  6. Automated assessment of the aortic root dimensions with multidetector row computed tomography.

    PubMed

    Delgado, Victoria; Ng, Arnold C T; Schuijf, Joanne D; van der Kley, Frank; Shanks, Miriam; Tops, Laurens F; van de Veire, Nico R L; de Roos, Albert; Kroft, Lucia J M; Schalij, Martin J; Bax, Jeroen J

    2011-03-01

    Accurate aortic root measurements and evaluation of spatial relationships with coronary ostia are crucial in preoperative transcatheter aortic valve implantation assessments. Standardization of measurements may increase intraobserver and interobserver reproducibility to promote procedural success rate and reduce the frequency of procedurally related complications. This study evaluated the accuracy and reproducibility of a novel automated multidetector row computed tomography (MDCT) imaging postprocessing software, 3mensio Valves (version 4.1.sp1, Medical Imaging BV, Bilthoven, The Netherlands), in the assessment of patients with severe aortic stenosis candidates for transcatheter aortic valve implantation. Ninety patients with aortic valve disease were evaluated with 64-row and 320-row MDCT. Aortic valve annular size, aortic root dimensions, and height of the coronary ostia relative to the aortic valve annular plane were measured with the 3mensio Valves software. The measurements were compared with those obtained manually by the Vitrea2 software (Vital Images, Minneapolis, MN). Assessment of aortic valve annulus and aortic root dimensions were feasible in all the patients using the automated 3mensio Valves software. There were excellent agreements with minimal bias between automated and manual MDCT measurements as demonstrated by Bland-Altman analysis and intraclass correlation coefficients ranging from 0.97 to 0.99. The automated 3mensio Valves software had better interobserver reproducibility and required less image postprocessing time than manual assessment. Novel automated MDCT postprocessing imaging software (3mensio Valves) permits reliable, reproducible, and automated assessments of the aortic root dimensions and spatial relations with the surrounding structures. This has important clinical implications for preoperative assessments of patients undergoing transcatheter aortic valve implantation. Copyright © 2011 The Society of Thoracic Surgeons. Published by

  7. High-resolution laboratory lysimeter for automated sampling of tracers through a 0.5 m soil block

    PubMed Central

    Johnson, A.; Mathews, T. J.; Patel, D.; Worsfold, P. J.; Andrew, K. N.

    2003-01-01

    A computer-controlled, automated sample collection from a 0.5-m lysimeter, designed to give superior temporal and spatial resolution for monitoring the movement of chemical tracers through a large undisturbed soil block, is described. The soil block, 0.520.520.5 m, was monitored for saturation using eight time domain reflectometry probes. Rainfall was applied at approximately 1600 ml hm1 using a 12212 array of 23-gauge (0.318 mm internal diameter) hypodermic needles. Soil leachates were collected at the base of the soil block using a machined aluminium collection plate with a 10210 grid of funnels that passed leachates to sample collection palettes. Sample collection was automated using a personal computer equipped with National Instruments LabVIEW™ software and linked to sensors for palette tracking. The automation of the lysimeter allowed sample collection and storage over a user-defined period with no human interaction. As an example of the use of the automated lysimeter, results show the distribution of phosphate within the soil. The eluted phosphate showed an initial and secondary peak, and only emerged from preferential flow channels. PMID:18924715

  8. Personality Assessment in a Diverse Urban Sample

    PubMed Central

    Sutin, Angelina R.; Costa, Paul T.; Evans, Michele K.; Zonderman, Alan B.

    2013-01-01

    The present research examined the data quality and replicability of the Revised NEO Personality Inventory (NEO-PI-R) factor structure in a sample that varied in ethnicity, socioeconomic status, and literacy. Participants (N=546), drawn from the Healthy Aging in Neighborhoods of Diversity across the Life Span study, were African American (58%) and White (42%) urban dwellers living above (49%) and below (51%) 125% of the federal poverty line. The NEO-PI-R, administered via telephone, was evaluated for data quality (percent valid, acquiescence, internal consistency), congruence with the normative factor structure, and readability. All indices of data quality and factor congruence were excellent in the full sample. Literacy was the most consistent predictor of data quality. A slightly worse structure was found for the Openness to Experience and Extraversion factors among lower SES African American and White participants. The overall index of factor congruence, however, supports replication of the normative structure well beyond chance levels even among those with lower literacy. Despite the challenges of low literacy, the present findings indicate that personality traits can be assessed reliably in socioeconomically diverse populations that include those living in poverty. PMID:23815114

  9. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

    PubMed

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

  10. AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

    PubMed Central

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

  11. Manual and automated enrichment procedures for biological samples using lipophilic gels.

    PubMed

    Uusijärvi, J; Egestad, B; Sjövall, J

    1989-03-17

    Aspects of the use of lipophilic gels in manual sample preparation procedures are reviewed. Neutral gels with a controlled hydrophobicity are used for sorbent extraction of non-polar and medium polarity compounds from biological fluids. Acidic amphiphilic compounds can be extracted as ion-pairs with decyltrimethylammonium ions. Solvent or detergent extracts of tissues or faeces can be mixed with hydrophobic gels for transfer of analytes from a solvent to a gel phase, permitting subsequent sample preparation in gel bed systems. Hydrophobic gels, alkyl-bonded silica and polystyrene matrices can be used in series for extraction of compounds with a wide range of polarities. Group fractionations are performed on neutral and ion-exchanging lipophilic gels to yield fractions of neutral, basic and acidic metabolites within selected polarity ranges. Selective isolation of phenolic acids on a strong anion exchanger, of ethynylic steroids on a strong cation exchanger in silver form and of oximes of ketonic steroids on a strong cation exchanger in hydrogen form is possible. A computerized system for automatic sample preparation is also described. It consists of an extraction bed, a cation-exchange column and an anion-exchange column. The pumps and switching valves are arranged so that the columns can operate in series or parallel for isolation of neutral, basic and acidic metabolites of amphiphilic compounds and for regeneration of the column beds. Fractions can be collected, or the effluent from the column beds can be diluted with water to permit sorption on a solid phase. The applicability of the automated method to the analysis of bile acids and metabolites of mono(2-ethylhexyl) phthalate is demonstrated.

  12. IHC Profiler: An Open Source Plugin for the Quantitative Evaluation and Automated Scoring of Immunohistochemistry Images of Human Tissue Samples

    PubMed Central

    Malhotra, Renu; De, Abhijit

    2014-01-01

    In anatomic pathology, immunohistochemistry (IHC) serves as a diagnostic and prognostic method for identification of disease markers in tissue samples that directly influences classification and grading the disease, influencing patient management. However, till today over most of the world, pathological analysis of tissue samples remained a time-consuming and subjective procedure, wherein the intensity of antibody staining is manually judged and thus scoring decision is directly influenced by visual bias. This instigated us to design a simple method of automated digital IHC image analysis algorithm for an unbiased, quantitative assessment of antibody staining intensity in tissue sections. As a first step, we adopted the spectral deconvolution method of DAB/hematoxylin color spectra by using optimized optical density vectors of the color deconvolution plugin for proper separation of the DAB color spectra. Then the DAB stained image is displayed in a new window wherein it undergoes pixel-by-pixel analysis, and displays the full profile along with its scoring decision. Based on the mathematical formula conceptualized, the algorithm is thoroughly tested by analyzing scores assigned to thousands (n = 1703) of DAB stained IHC images including sample images taken from human protein atlas web resource. The IHC Profiler plugin developed is compatible with the open resource digital image analysis software, ImageJ, which creates a pixel-by-pixel analysis profile of a digital IHC image and further assigns a score in a four tier system. A comparison study between manual pathological analysis and IHC Profiler resolved in a match of 88.6% (P<0.0001, CI = 95%). This new tool developed for clinical histopathological sample analysis can be adopted globally for scoring most protein targets where the marker protein expression is of cytoplasmic and/or nuclear type. We foresee that this method will minimize the problem of inter-observer variations across labs and further help in

  13. Computerized Analytical Data Management System and Automated Analytical Sample Transfer System at the COGEMA Reprocessing Plants in La Hague

    SciTech Connect

    Flament, T.; Goasmat, F.; Poilane, F.

    2002-02-25

    Managing the operation of large commercial spent nuclear fuel reprocessing plants, such as UP3 and UP2-800 in La Hague, France, requires an extensive analytical program and the shortest possible analysis response times. COGEMA, together with its engineering subsidiary SGN, decided to build high-performance laboratories to support operations in its plants. These laboratories feature automated equipment, safe environments for operators, and short response times, all in centralized installations. Implementation of a computerized analytical data management system and a fully automated pneumatic system for the transfer of radioactive samples was a key factor contributing to the successful operation of the laboratories and plants.

  14. Automated sample preparation techniques for the determination of drug enantiomers in biological fluids using liquid chromatography with chiral stationary phases.

    PubMed

    Ceccato, A; Toussaint, B; Chiap, P; Hubert, P; Crommen, J

    1999-01-01

    The determination of drug enantiomers has become of prime importance in the field of pharmaceutical and biomedical analysis. Liquid chromatography (LC) is one of the most frequently used techniques for achieving the separation and quantitation of the enantiomers of drug compounds. In the bioanalytical field, the integrated systems present an interesting alternative to time-consuming sample preparation techniques such as liquid-liquid extraction. Solid phase extraction (SPE) on disposable cartridges, dialysis or column switching are sample preparation techniques that can be fully automated and applied to enantioselective analysis in biological fluids. The selection of the most appropriate LC mode and chiral stationary phase for enantioseparations in bioanalysis is discussed and some aspects of these automated sample preparation procedures are compared, such as selectivity, detectability, elution of the analytes from the extraction sorbent, sample volume and analyte stability.

  15. Assessment of Automated Disease Detection in Diabetic Retinopathy Screening Using Two-Field Photography

    PubMed Central

    Goatman, Keith; Charnley, Amanda; Webster, Laura; Nussey, Stephen

    2011-01-01

    Aim To assess the performance of automated disease detection in diabetic retinopathy screening using two field mydriatic photography. Methods Images from 8,271 sequential patient screening episodes from a South London diabetic retinopathy screening service were processed by the Medalytix iGrading™ automated grading system. For each screening episode macular-centred and disc-centred images of both eyes were acquired and independently graded according to the English national grading scheme. Where discrepancies were found between the automated result and original manual grade, internal and external arbitration was used to determine the final study grades. Two versions of the software were used: one that detected microaneurysms alone, and one that detected blot haemorrhages and exudates in addition to microaneurysms. Results for each version were calculated once using both fields and once using the macula-centred field alone. Results Of the 8,271 episodes, 346 (4.2%) were considered unassessable. Referable disease was detected in 587 episodes (7.1%). The sensitivity of the automated system for detecting unassessable images ranged from 97.4% to 99.1% depending on configuration. The sensitivity of the automated system for referable episodes ranged from 98.3% to 99.3%. All the episodes that included proliferative or pre-proliferative retinopathy were detected by the automated system regardless of configuration (192/192, 95% confidence interval 98.0% to 100%). If implemented as the first step in grading, the automated system would have reduced the manual grading effort by between 2,183 and 3,147 patient episodes (26.4% to 38.1%). Conclusion Automated grading can safely reduce the workload of manual grading using two field, mydriatic photography in a routine screening service. PMID:22174741

  16. High-Throughput Serum 25-Hydroxy Vitamin D Testing with Automated Sample Preparation.

    PubMed

    Stone, Judy

    2016-01-01

    Serum from bar-coded tubes, and then internal standard, are pipetted to 96-well plates with an 8-channel automated liquid handler (ALH). The first precipitation reagent (methanol:ZnSO4) is added and mixed with the 8-channel ALH. A second protein precipitating agent, 1 % formic acid in acetonitrile, is added and mixed with a 96-channel ALH. After a 4-min delay for larger precipitates to settle to the bottom of the plate, the upper 36 % of the precipitate/supernatant mix is transferred with the 96-channel ALH to a Sigma Hybrid SPE(®) plate and vacuumed through for removal of phospholipids and precipitated proteins. The filtrate is collected in a second 96-well plate (collection plate) which is foil-sealed, placed in the autosampler (ALS), and injected into a multiplexed LC-MS/MS system running AB Sciex Cliquid(®) and MPX(®) software. Two Shimadzu LC stacks, with multiplex timing controlled by MPX(®) software, inject alternately to one AB Sciex API-5000 MS/MS using positive atmospheric pressure chemical ionization (APCI) and a 1.87 min water/acetonitrile LC gradient with a 2.1 × 20 mm, 2.7 μm, C18 fused core particle column (Sigma Ascentis Express). LC-MS/MS through put is ~44 samples/h/LC-MS/MS system with dual-LC channel multiplexing. Plate maps are transferred electronically from the ALH and reformatted into LC-MS/MS sample table format using the Data Innovations LLC (DI) Instrument Manager middleware application. Before collection plates are loaded into the ALS, the plate bar code is manually scanned to download the sample table from the DI middleware to the LC-MS/MS. After acquisition-LC-MS/MS data is analyzed with AB Sciex Multiquant(®) software using customized queries, and then results are transferred electronically via a DI interface to the LIS. 2500 samples/day can be extracted by two analysts using four ALHs in 4-6 h. LC-MS/MS analysis of those samples on three dual-channel LC multiplexed LC-MS/MS systems requires 19-21 h and data analysis can be

  17. A semi-automated measurement technique for the assessment of radiolucency.

    PubMed

    Pegg, E C; Kendrick, B J L; Pandit, H G; Gill, H S; Murray, D W

    2014-07-06

    The assessment of radiolucency around an implant is qualitative, poorly defined and has low agreement between clinicians. Accurate and repeatable assessment of radiolucency is essential to prevent misdiagnosis, minimize cases of unnecessary revision, and to correctly monitor and treat patients at risk of loosening and implant failure. The purpose of this study was to examine whether a semi-automated imaging algorithm could improve repeatability and enable quantitative assessment of radiolucency. Six surgeons assessed 38 radiographs of knees after unicompartmental knee arthroplasty for radiolucency, and results were compared with assessments made by the semi-automated program. Large variation was found between the surgeon results, with total agreement in only 9.4% of zones and a kappa value of 0.602; whereas the automated program had total agreement in 81.6% of zones and a kappa value of 0.802. The software had a 'fair to excellent' prediction of the presence or the absence of radiolucency, where the area under the curve of the receiver operating characteristic curves was 0.82 on average. The software predicted radiolucency equally well for cemented and cementless implants (p = 0.996). The identification of radiolucency using an automated method is feasible and these results indicate that it could aid the definition and quantification of radiolucency.

  18. Automated assessment of exclusion criteria for DXA lumbar spine scans.

    PubMed

    Barden, Howard S; Markwardt, Paul; Payne, Randy; Hawkins, Brent; Frank, Matt; Faulkner, Kenneth G

    2003-01-01

    Modern bone densitometry systems using dual-energy X-ray absorptiometry (DXA) automatically analyze lumbar spine scans and provide clinically important information concerning spine bone mineral density (BMD) and fracture risk. Lumbar spine BMD accurately reflects skeletal health and fracture risk in most cases, but degenerative diseases associated with aging may lead to the formation of reactive bone (osteophytes) and other confounding conditions that elevate BMD without a concomitant increase in bone strength or decrease in fracture risk. Automated densitometry software known as computer-aided densitometry (CAD) (GE Medical Systems Lunar) assists the user in identifying scans with common acquisition and analysis irregularities known to influence BMD values. Visual examination of 231 female spine scans measured with DXA found abnormal conditions that could influence BMD results in 29% of scans. The sensitivity and specificity of several criteria for identifying scans with conditions that could influence BMD were determined. A good criterion for identifying scans with abnormal conditions was a T-score difference of greater than 0.9 or 1.0 between L1-L4 mean and individual vertebrae. Criteria for excluding affected vertebrae were determined. Exclusion of affected vertebrae resulted in a mean BMD decrease of nearly 0.6 SD (T-score) among affected scans.

  19. Automated Tissue Classification Framework for Reproducible Chronic Wound Assessment

    PubMed Central

    Mukherjee, Rashmi; Manohar, Dhiraj Dhane; Das, Dev Kumar; Achar, Arun; Mitra, Analava; Chakraborty, Chandan

    2014-01-01

    The aim of this paper was to develop a computer assisted tissue classification (granulation, necrotic, and slough) scheme for chronic wound (CW) evaluation using medical image processing and statistical machine learning techniques. The red-green-blue (RGB) wound images grabbed by normal digital camera were first transformed into HSI (hue, saturation, and intensity) color space and subsequently the “S” component of HSI color channels was selected as it provided higher contrast. Wound areas from 6 different types of CW were segmented from whole images using fuzzy divergence based thresholding by minimizing edge ambiguity. A set of color and textural features describing granulation, necrotic, and slough tissues in the segmented wound area were extracted using various mathematical techniques. Finally, statistical learning algorithms, namely, Bayesian classification and support vector machine (SVM), were trained and tested for wound tissue classification in different CW images. The performance of the wound area segmentation protocol was further validated by ground truth images labeled by clinical experts. It was observed that SVM with 3rd order polynomial kernel provided the highest accuracies, that is, 86.94%, 90.47%, and 75.53%, for classifying granulation, slough, and necrotic tissues, respectively. The proposed automated tissue classification technique achieved the highest overall accuracy, that is, 87.61%, with highest kappa statistic value (0.793). PMID:25114925

  20. Risk assessment from automated feature analysis of digitized mammograms

    NASA Astrophysics Data System (ADS)

    Byng, Jeffrey W.; Yaffe, Martin J.; Little, L.; Lockwood, G.; Jong, Roberta A.; Fishell, E.; Tritchler, D.; Boyd, Norman F.

    1995-05-01

    The identification of women at increased risk for breast cancer has important implications in both the surveillance for cancer and research into causes of the disease. The parenchymal pattern of the breast, revealed by mammography, and rated subjectively by observer, has been found to provide strong factors of risk for breast cancer. To provide a more quantitative measure of the proportion of mammographically dense tissue in the breast, we have previously described and evaluated an interactive technique in which an observer selects a threshold brightness level to separate dense from fatty tissue in the image. Measurement of mammographic density in this way provides an estimate of relative risk of 4, that is among leading indicators of the risk of developing breast cancer. To remove the variability associated with identification of thresholds by observer, we are investigating an automated threshold prediction based on independent features characterizing mammographic parenchyma. These features are based on regional measurements of image brightness variations (histogram analysis) and texture variations (fractal analysis) within digitized mammographic images. Preliminary results from an investigative model are presented.

  1. Automated Quality Assessment of Structural Magnetic Resonance Brain Images Based on a Supervised Machine Learning Algorithm.

    PubMed

    Pizarro, Ricardo A; Cheng, Xi; Barnett, Alan; Lemaitre, Herve; Verchinski, Beth A; Goldman, Aaron L; Xiao, Ena; Luo, Qian; Berman, Karen F; Callicott, Joseph H; Weinberger, Daniel R; Mattay, Venkata S

    2016-01-01

    High-resolution three-dimensional magnetic resonance imaging (3D-MRI) is being increasingly used to delineate morphological changes underlying neuropsychiatric disorders. Unfortunately, artifacts frequently compromise the utility of 3D-MRI yielding irreproducible results, from both type I and type II errors. It is therefore critical to screen 3D-MRIs for artifacts before use. Currently, quality assessment involves slice-wise visual inspection of 3D-MRI volumes, a procedure that is both subjective and time consuming. Automating the quality rating of 3D-MRI could improve the efficiency and reproducibility of the procedure. The present study is one of the first efforts to apply a support vector machine (SVM) algorithm in the quality assessment of structural brain images, using global and region of interest (ROI) automated image quality features developed in-house. SVM is a supervised machine-learning algorithm that can predict the category of test datasets based on the knowledge acquired from a learning dataset. The performance (accuracy) of the automated SVM approach was assessed, by comparing the SVM-predicted quality labels to investigator-determined quality labels. The accuracy for classifying 1457 3D-MRI volumes from our database using the SVM approach is around 80%. These results are promising and illustrate the possibility of using SVM as an automated quality assessment tool for 3D-MRI.

  2. Assessing Writing in MOOCs: Automated Essay Scoring and Calibrated Peer Review™

    ERIC Educational Resources Information Center

    Balfour, Stephen P.

    2013-01-01

    Two of the largest Massive Open Online Course (MOOC) organizations have chosen different methods for the way they will score and provide feedback on essays students submit. EdX, MIT and Harvard's non-profit MOOC federation, recently announced that they will use a machine-based Automated Essay Scoring (AES) application to assess written work in…

  3. Automated Quality Assessment of Structural Magnetic Resonance Brain Images Based on a Supervised Machine Learning Algorithm

    PubMed Central

    Pizarro, Ricardo A.; Cheng, Xi; Barnett, Alan; Lemaitre, Herve; Verchinski, Beth A.; Goldman, Aaron L.; Xiao, Ena; Luo, Qian; Berman, Karen F.; Callicott, Joseph H.; Weinberger, Daniel R.; Mattay, Venkata S.

    2016-01-01

    High-resolution three-dimensional magnetic resonance imaging (3D-MRI) is being increasingly used to delineate morphological changes underlying neuropsychiatric disorders. Unfortunately, artifacts frequently compromise the utility of 3D-MRI yielding irreproducible results, from both type I and type II errors. It is therefore critical to screen 3D-MRIs for artifacts before use. Currently, quality assessment involves slice-wise visual inspection of 3D-MRI volumes, a procedure that is both subjective and time consuming. Automating the quality rating of 3D-MRI could improve the efficiency and reproducibility of the procedure. The present study is one of the first efforts to apply a support vector machine (SVM) algorithm in the quality assessment of structural brain images, using global and region of interest (ROI) automated image quality features developed in-house. SVM is a supervised machine-learning algorithm that can predict the category of test datasets based on the knowledge acquired from a learning dataset. The performance (accuracy) of the automated SVM approach was assessed, by comparing the SVM-predicted quality labels to investigator-determined quality labels. The accuracy for classifying 1457 3D-MRI volumes from our database using the SVM approach is around 80%. These results are promising and illustrate the possibility of using SVM as an automated quality assessment tool for 3D-MRI. PMID:28066227

  4. A Survey of Automated Assessment Approaches for Programming Assignments

    ERIC Educational Resources Information Center

    Ala-Mutka, Kirsti M.

    2005-01-01

    Practical programming is one of the basic skills pursued in computer science education. On programming courses, the coursework consists of programming assignments that need to be assessed from different points of view. Since the submitted assignments are executable programs with a formal structure, some features can be assessed automatically. The…

  5. Fully automated decomposition of Raman spectra into individual Pearson's type VII distributions applied to biological and biomedical samples.

    PubMed

    Schulze, H Georg; Atkins, Chad G; Devine, Dana V; Blades, Michael W; Turner, Robin F B

    2015-01-01

    Rapid technological advances have made the acquisition of large numbers of spectra not only feasible, but also routine. As a result, a significant research effort is focused on semi-automated and fully automated spectral processing techniques. However, the need to provide initial estimates of the number of peaks, their band shapes, and the initial parameters of these bands presents an obstacle to the full automation of peak fitting and its incorporation into fully automated spectral-preprocessing workflows. Moreover, the sensitivity of peak-fit routines to initial parameter settings and the resultant variations in solution quality further impede user-free operation. We have developed a technique to perform fully automated peak fitting on fully automated preconditioned spectra-specifically, baseline-corrected and smoothed spectra that are free of cosmic-ray-induced spikes. Briefly, the tallest peak in a spectrum is located and a Gaussian peak-fit is performed. The fitted peak is then subtracted from the spectrum, and the procedure is repeated until the entire spectrum has been processed. In second and third passes, all the peaks in the spectrum are fitted concurrently, but are fitted to a Pearson Type VII model using the parameters for the model established in the prior pass. The technique is applied to a synthetic spectrum with several peaks, some of which have substantial overlap, to test the ability of the method to recover the correct number of peaks, their true shape, and their appropriate parameters. Finally the method is tested on measured Raman spectra collected from human embryonic stem cells and samples of red blood cells.

  6. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOGICAL MODELING TOOL FOR WATERSHED MANAGEMENT AND LANDSCAPE ASSESSMENT

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment (http://www.epa.gov/nerlesd1/land-sci/agwa/introduction.htm and www.tucson.ars.ag.gov/agwa) tool is a GIS interface jointly developed by the U.S. Environmental Protection Agency, USDA-Agricultural Research Service, and the University ...

  7. AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT (AGWA): A GIS-BASED HYDROLOGICAL MODELING TOOL FOR WATERSHED MANAGEMENT AND LANDSCAPE ASSESSMENT

    EPA Science Inventory

    The Automated Geospatial Watershed Assessment (http://www.epa.gov/nerlesd1/land-sci/agwa/introduction.htm and www.tucson.ars.ag.gov/agwa) tool is a GIS interface jointly developed by the U.S. Environmental Protection Agency, USDA-Agricultural Research Service, and the University ...

  8. Assessment of Automated Measurement and Verification (M&V) Methods

    SciTech Connect

    Granderson, Jessica; Touzani, Samir; Custodio, Claudine; Sohn, Michael; Fernandes, Samuel; Jump, David

    2015-07-01

    This report documents the application of a general statistical methodology to assess the accuracy of baseline energy models, focusing on its application to Measurement and Verification (M&V) of whole-building energy savings.

  9. Advances toward fully automated in vivo assessment of oral epithelial dysplasia by nuclear endomicroscopy-A pilot study.

    PubMed

    Liese, Jan; Winter, Karsten; Glass, Änne; Bertolini, Julia; Kämmerer, Peer Wolfgang; Frerich, Bernhard; Schiefke, Ingolf; Remmerbach, Torsten W

    2017-07-04

    Uncertainties in detection of oral epithelial dysplasia (OED) frequently result from sampling error especially in inflammatory oral lesions. Endomicroscopy allows non-invasive, "en face" imaging of upper oral epithelium, but parameters of OED are unknown. Mucosal nuclei were imaged in 34 toluidine blue-stained oral lesions with a commercial endomicroscopy. Histopathological diagnosis showed four biopsies in "dys-/neoplastic," 23 in "inflammatory," and seven in "others" disease groups. Strength of different assessment strategies of nuclear scoring, nuclear count, and automated nuclear analysis were measured by area under ROC curve (AUC) to identify histopathological "dys-/neoplastic" group. Nuclear objects from automated image analysis were visually corrected. Best-performing parameters of nuclear-to-image ratios were the count of large nuclei (AUC=0.986) and 6-nearest neighborhood relation (AUC=0.896), and best parameters of nuclear polymorphism were the count of atypical nuclei (AUC=0.996) and compactness of nuclei (AUC=0.922). Excluding low-grade OED, nuclear scoring and count reached 100% sensitivity and 98% specificity for detection of dys-/neoplastic lesions. In automated analysis, combination of parameters enhanced diagnostic strength. Sensitivity of 100% and specificity of 87% were seen for distances of 6-nearest neighbors and aspect ratios even in uncorrected objects. Correction improved measures of nuclear polymorphism only. The hue of background color was stronger than nuclear density (AUC=0.779 vs 0.687) to detect dys-/neoplastic group indicating that macroscopic aspect is biased. Nuclear-to-image ratios are applicable for automated optical in vivo diagnostics for oral potentially malignant disorders. Nuclear endomicroscopy may promote non-invasive, early detection of dys-/neoplastic lesions by reducing sampling error. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. Inter-operator variability in perfusion assessment of tumors in MRI using automated AIF detection.

    PubMed

    Ashton, Edward; McShane, Teresa; Evelhoch, Jeffrey

    2005-01-01

    A method is presented for the calculation of perfusion parameters in dynamic contrast enhanced MRI. This method requires identification of enhancement curves for both tumor tissue and plasma. Inter-operator variability in the derived rate constant between plasma and extra-cellular extra-vascular space is assessed in both canine and human subjects using semi-automated tumor margin identification with both manual and automated arterial input function (AIF) identification. Experimental results show a median coefficient of variability (CV) for parameter measurement with manual AIF identification of 21.5% in canines and 11% in humans, with a median CV for parameter measurement with automated AIF identification of 6.7% in canines and 6% in humans.

  11. QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data

    PubMed Central

    2012-01-01

    new R packages for importing manually gated flow cytometry data and performing flexible and robust quality assessment checks. The pipeline addresses the increasing demand for tools capable of performing quality checks on large flow data sets generated in typical clinical trials. The QUAliFiER tool objectively, efficiently, and reproducibly identifies outlier samples in an automated manner by monitoring cell population statistics from gated or ungated flow data conditioned on experiment–level metadata. PMID:23020243

  12. Assessment of two automated imaging systems in evaluating estrogen receptor status in breast carcinoma.

    PubMed

    Gokhale, Sumita; Rosen, Daniel; Sneige, Nour; Diaz, Leslie K; Resetkova, Erika; Sahin, Aysegul; Liu, Jinsong; Albarracin, Constance T

    2007-12-01

    Immunohistochemical staining for estrogen receptor (ER) status is widely used in the management of breast cancer. These stains have traditionally been scored manually, which results in generally good agreement among observers when the cases are strongly positive. However, significant interobserver and intraobserver differences in scoring can occur in borderline or weakly staining cases. Recently, automated systems have been proposed to provide a more sensitive and objective method of ER quantification. The ChromaVision Automated Cellular Imaging System and the Applied Imaging Ariol SL-50 quantify the color intensity of the immunoreactive product. To assess the accuracy of these 2 automated systems and to compare them to one another and to manual scoring, we performed immunostaining for ER on 64 cases of breast cancer. The percentages of positive cells were scored manually by 4 pathologists and by the 2 imaging systems. A discrepancy in scoring was defined as that which resulted in the reclassification of a case from negative to positive or vice versa. Our results showed significant agreement between the 2 automated systems. When automated scores were compared with the manual scores, only 5 of the 64 cases (7%) were discrepant. In 4 of these, the percentage of cells staining for ER was low (0% to 20%). Overall, the 2 systems were comparable, and discrepant results were most frequently seen when analyzing tumors with low levels of ER positive cells.

  13. Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging

    NASA Astrophysics Data System (ADS)

    Bassan, Paul; Sachdeva, Ashwin; Shanks, Jonathan H.; Brown, Mick D.; Clarke, Noel W.; Gardner, Peter

    2014-03-01

    Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. FT-IR chemical imaging allows the spatial distribution of chemistry to be rapidly imaged at a high (diffraction-limited) spatial resolution where each pixel represents an area of 5.5 × 5.5 μm2 and contains a full infrared spectrum providing a chemical fingerprint which studies have shown contains the diagnostic potential to discriminate between different cell-types, and even the benign or malignant state of prostatic epithelial cells. We report a label-free (i.e. no chemical de-waxing, or staining) method of imaging large pieces of prostate tissue (typically 1 cm × 2 cm) in tens of minutes (at a rate of 0.704 × 0.704 mm2 every 14.5 s) yielding images containing millions of spectra. Due to refractive index matching between sample and surrounding paraffin, minimal signal processing is required to recover spectra with their natural profile as opposed to harsh baseline correction methods, paving the way for future quantitative analysis of biochemical signatures. The quality of the spectral information is demonstrated by building and testing an automated cell-type classifier based upon spectral features.

  14. Automated 3-dimensional aortic annular assessment by multidetector computed tomography in transcatheter aortic valve implantation.

    PubMed

    Watanabe, Yusuke; Morice, Marie-Claude; Bouvier, Erik; Leong, Tora; Hayashida, Kentaro; Lefèvre, Thierry; Hovasse, Thomas; Romano, Mauro; Chevalier, Bernard; Donzeau-Gouge, Patrick; Farge, Arnaud; Cormier, Bertrand; Garot, Philippe

    2013-09-01

    This study sought to evaluate the accuracy, reproducibility, and predictive value for post-procedural aortic regurgitation (AR) of an automated multidetector computed tomography (MDCT) post-processing imaging software, 3mensio Valves (version 5.1.sp1, 3mensio Medical Imaging BV, the Netherlands), in the assessment of patients undergoing transcatheter aortic valve implantation (TAVI). Accurate pre-operative aortic annulus measurements are crucial for patients undergoing TAVI. One hundred five patients undergoing MDCT screening before TAVI were evaluated. Aortic annular measurement was compared between automated 3mensio Valves software and manual data post-processing software on a dedicated workstation; we analyzed the discrimination value of annulus measurement for post-procedural AR in 44 recipients of a self-expanding valve. The automated 3mensio Valves software showed good concordance with manual MDCT measurements as demonstrated by Bland-Altman analysis. The automated software provided equally good reproducibility as manual measurement, especially for measurement of aortic annulus area (intraobserver intraclass correlation coefficients 0.98 vs. 0.97, interobserver 0.98 vs. 0.95). In 44 patients after implantation of a self-expanding valve, the valve diameter/CT-measured geometric mean annulus diameter ratio by automated 3mensio Valves software showed moderate and better discrimination ability in predicting post-procedural AR compared with manual measurement (p = 0.12, area under the curve 0.77, 95% confidence interval: 0.63 to 0.91, area under the curve 0.68, 95% confidence interval: 0.50 to 0.86, respectively). The automated 3mensio Valves software demonstrated reliable, reproducible aortic annulus measurement and better predictive value for post-procedural AR, suggesting important clinical implications for pre-operative assessment of patients undergoing TAVI. Copyright © 2013 American College of Cardiology Foundation. Published by Elsevier Inc. All rights

  15. Method and Apparatus for Automated Isolation of Nucleic Acids from Small Cell Samples

    NASA Technical Reports Server (NTRS)

    Sundaram, Shivshankar; Prabhakarpandian, Balabhaskar; Pant, Kapil; Wang, Yi

    2014-01-01

    RNA isolation is a ubiquitous need, driven by current emphasis on microarrays and miniaturization. With commercial systems requiring 100,000 to 1,000,000 cells for successful isolation, there is a growing need for a small-footprint, easy-to-use device that can harvest nucleic acids from much smaller cell samples (1,000 to 10,000 cells). The process of extraction of RNA from cell cultures is a complex, multi-step one, and requires timed, asynchronous operations with multiple reagents/buffers. An added complexity is the fragility of RNA (subject to degradation) and its reactivity to surface. A novel, microfluidics-based, integrated cartridge has been developed that can fully automate the complex process of RNA isolation (lyse, capture, and elute RNA) from small cell culture samples. On-cartridge cell lysis is achieved using either reagents or high-strength electric fields made possible by the miniaturized format. Traditionally, silica-based, porous-membrane formats have been used for RNA capture, requiring slow perfusion for effective capture. In this design, high efficiency capture/elution are achieved using a microsphere-based "microfluidized" format. Electrokinetic phenomena are harnessed to actively mix microspheres with the cell lysate and capture/elution buffer, providing important advantages in extraction efficiency, processing time, and operational flexibility. Successful RNA isolation was demonstrated using both suspension (HL-60) and adherent (BHK-21) cells. Novel features associated with this development are twofold. First, novel designs that execute needed processes with improved speed and efficiency were developed. These primarily encompass electric-field-driven lysis of cells. The configurations include electrode-containing constructs, or an "electrode-less" chip design, which is easy to fabricate and mitigates fouling at the electrode surface; and the "fluidized" extraction format based on electrokinetically assisted mixing and contacting of microbeads

  16. Automated sample preparation coupled to sequential injection chromatography: on-line filtration and dilution protocols prior to separation.

    PubMed

    Zacharis, Constantinos K; Verdoukas, Aspasia; Tzanavaras, Paraskevas D; Themelis, Demetrius G

    2009-04-05

    Sequential injection chromatography (SIC) is a valuable tool in analytical chemistry as it can combine the automation capabilities of low pressure continuous flow techniques and the separation power of HPLC into a single instrumental configuration. The present study reports an automated SI setup allowing on-line filtration and dilution of the samples before separation through a short monolithic column. The applicability of the procedure was evaluated by studying the behavior of acyclovir formulations under forced degradation conditions. Minimal sample preparation is required prior to analysis. Thorough validation of the on-line dilution SIC assay was carried out and proved its validity in terms of critical parameters such as precision, accuracy and robustness. The results were evaluated by parallel experiments and analysis using the procedure recommended by the USP based on conventional HPLC using particulate-based column.

  17. Assessing Creative Problem-Solving with Automated Text Grading

    ERIC Educational Resources Information Center

    Wang, Hao-Chuan; Chang, Chun-Yen; Li, Tsai-Yen

    2008-01-01

    The work aims to improve the assessment of creative problem-solving in science education by employing language technologies and computational-statistical machine learning methods to grade students' natural language responses automatically. To evaluate constructs like creative problem-solving with validity, open-ended questions that elicit…

  18. Comparison of Automated and Manual DNA Isolation Methods for DNA Methylation Analysis of Biopsy, Fresh Frozen, and Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Samples.

    PubMed

    Kalmár, Alexandra; Péterfia, Bálint; Wichmann, Barnabás; Patai, Árpád V; Barták, Barbara K; Nagy, Zsófia B; Furi, István; Tulassay, Zsolt; Molnár, Béla

    2015-12-01

    Automated DNA isolation can decrease hands-on time in routine pathology. Our aim was to apply automated DNA isolation and perform DNA methylation analyses. DNA isolation was performed manually from fresh frozen (CRC = 10, normal = 10) specimens and colonic biopsies (CRC = 10, healthy = 10) with QIAamp DNA Mini Kit and from FFPE blocks (CRC = 10, normal = 10) with QIAamp DNA FFPET Kit. Automated DNA isolation was performed with MagNA Pure DNA and Viral NA SV kit on MagNA Pure 96 system. DNA methylation of MAL, SFRP1, and SFRP2 were analyzed with methylation-specific high-resolution melting analysis. Yield of automatically isolated samples was equal in fresh frozens and significantly lower compared to manually isolated biopsy and FFPE samples. OD260/280 of fresh frozen and biopsy samples were similar after both isolations, automated isolation resulted in lower purity in FFPE samples. Both protocols resulted in similar OD260/230 from fresh frozens, automated isolation method was superior in biopsies and manual protocol in FFPE samples. DNA methylation of biopsies, fresh frozen samples were highly similar after both methods, results of automatically and manually isolated FFPE samples were different. Automated DNA isolation from fresh frozen samples can be suitable for high-throughput laboratories. © 2015 Society for Laboratory Automation and Screening.

  19. Falcon: automated optimization method for arbitrary assessment criteria

    DOEpatents

    Yang, Tser-Yuan; Moses, Edward I.; Hartmann-Siantar, Christine

    2001-01-01

    FALCON is a method for automatic multivariable optimization for arbitrary assessment criteria that can be applied to numerous fields where outcome simulation is combined with optimization and assessment criteria. A specific implementation of FALCON is for automatic radiation therapy treatment planning. In this application, FALCON implements dose calculations into the planning process and optimizes available beam delivery modifier parameters to determine the treatment plan that best meets clinical decision-making criteria. FALCON is described in the context of the optimization of external-beam radiation therapy and intensity modulated radiation therapy (IMRT), but the concepts could also be applied to internal (brachytherapy) radiotherapy. The radiation beams could consist of photons or any charged or uncharged particles. The concept of optimizing source distributions can be applied to complex radiography (e.g. flash x-ray or proton) to improve the imaging capabilities of facilities proposed for science-based stockpile stewardship.

  20. Automated Cognitive Health Assessment Using Smart Home Monitoring of Complex Tasks.

    PubMed

    Dawadi, Prafulla N; Cook, Diane J; Schmitter-Edgecombe, Maureen

    2013-11-01

    One of the many services that intelligent systems can provide is the automated assessment of resident well-being. We hypothesize that the functional health of individuals, or ability of individuals to perform activities independently without assistance, can be estimated by tracking their activities using smart home technologies. In this paper, we introduce a machine learning-based method for assessing activity quality in smart homes. To validate our approach we quantify activity quality for 179 volunteer participants who performed a complex, interweaved set of activities in our smart home apartment. We observed a statistically significant correlation (r=0.79) between automated assessment of task quality and direct observation scores. Using machine learning techniques to predict the cognitive health of the participants based on task quality is accomplished with an AUC value of 0.64. We believe that this capability is an important step in understanding everyday functional health of individuals in their home environments.

  1. Automated Cognitive Health Assessment Using Smart Home Monitoring of Complex Tasks

    PubMed Central

    Dawadi, Prafulla N.; Cook, Diane J.; Schmitter-Edgecombe, Maureen

    2014-01-01

    One of the many services that intelligent systems can provide is the automated assessment of resident well-being. We hypothesize that the functional health of individuals, or ability of individuals to perform activities independently without assistance, can be estimated by tracking their activities using smart home technologies. In this paper, we introduce a machine learning-based method for assessing activity quality in smart homes. To validate our approach we quantify activity quality for 179 volunteer participants who performed a complex, interweaved set of activities in our smart home apartment. We observed a statistically significant correlation (r=0.79) between automated assessment of task quality and direct observation scores. Using machine learning techniques to predict the cognitive health of the participants based on task quality is accomplished with an AUC value of 0.64. We believe that this capability is an important step in understanding everyday functional health of individuals in their home environments. PMID:25530925

  2. Random Sample Consensus: A Paradigm for Model Fitting with Applications to Image Analysis and Automated Cartography

    DTIC Science & Technology

    1980-03-01

    interpreting/smoothing data containing a significant percentage of gross errors, and thus is ideally suited for applications in automated image ... analysis where interpretation is based on the data provided by error-prone feature detectors. A major portion of the paper describes the application of

  3. ARAM: an automated image analysis software to determine rosetting parameters and parasitaemia in Plasmodium samples.

    PubMed

    Kudella, Patrick Wolfgang; Moll, Kirsten; Wahlgren, Mats; Wixforth, Achim; Westerhausen, Christoph

    2016-04-18

    Rosetting is associated with severe malaria and a primary cause of death in Plasmodium falciparum infections. Detailed understanding of this adhesive phenomenon may enable the development of new therapies interfering with rosette formation. For this, it is crucial to determine parameters such as rosetting and parasitaemia of laboratory strains or patient isolates, a bottleneck in malaria research due to the time consuming and error prone manual analysis of specimens. Here, the automated, free, stand-alone analysis software automated rosetting analyzer for micrographs (ARAM) to determine rosetting rate, rosette size distribution as well as parasitaemia with a convenient graphical user interface is presented. Automated rosetting analyzer for micrographs is an executable with two operation modes for automated identification of objects on images. The default mode detects red blood cells and fluorescently labelled parasitized red blood cells by combining an intensity-gradient with a threshold filter. The second mode determines object location and size distribution from a single contrast method. The obtained results are compared with standardized manual analysis. Automated rosetting analyzer for micrographs calculates statistical confidence probabilities for rosetting rate and parasitaemia. Automated rosetting analyzer for micrographs analyses 25 cell objects per second reliably delivering identical results compared to manual analysis. For the first time rosette size distribution is determined in a precise and quantitative manner employing ARAM in combination with established inhibition tests. Additionally ARAM measures the essential observables parasitaemia, rosetting rate and size as well as location of all detected objects and provides confidence intervals for the determined observables. No other existing software solution offers this range of function. The second, non-malaria specific, analysis mode of ARAM offers the functionality to detect arbitrary objects

  4. Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples.

    PubMed

    Uyaguari-Diaz, Miguel I; Slobodan, Jared R; Nesbitt, Matthew J; Croxen, Matthew A; Isaac-Renton, Judith; Prystajecky, Natalie A; Tang, Patrick

    2015-04-17

    Next-generation sequencing of environmental samples can be challenging because of the variable DNA quantity and quality in these samples. High quality DNA libraries are needed for optimal results from next-generation sequencing. Environmental samples such as water may have low quality and quantities of DNA as well as contaminants that co-precipitate with DNA. The mechanical and enzymatic processes involved in extraction and library preparation may further damage the DNA. Gel size selection enables purification and recovery of DNA fragments of a defined size for sequencing applications. Nevertheless, this task is one of the most time-consuming steps in the DNA library preparation workflow. The protocol described here enables complete automation of agarose gel loading, electrophoretic analysis, and recovery of targeted DNA fragments. In this study, we describe a high-throughput approach to prepare high quality DNA libraries from freshwater samples that can be applied also to other environmental samples. We used an indirect approach to concentrate bacterial cells from environmental freshwater samples; DNA was extracted using a commercially available DNA extraction kit, and DNA libraries were prepared using a commercial transposon-based protocol. DNA fragments of 500 to 800 bp were gel size selected using Ranger Technology, an automated electrophoresis workstation. Sequencing of the size-selected DNA libraries demonstrated significant improvements to read length and quality of the sequencing reads.

  5. AutoMate Express™ forensic DNA extraction system for the extraction of genomic DNA from biological samples.

    PubMed

    Liu, Jason Y; Zhong, Chang; Holt, Allison; Lagace, Robert; Harrold, Michael; Dixon, Alan B; Brevnov, Maxim G; Shewale, Jaiprakash G; Hennessy, Lori K

    2012-07-01

    The AutoMate Express™ Forensic DNA Extraction System was developed for automatic isolation of DNA from a variety of forensic biological samples. The performance of the system was investigated using a wide range of biological samples. Depending on the sample type, either PrepFiler™ lysis buffer or PrepFiler BTA™ lysis buffer was used to lyse the samples. After lysis and removal of the substrate using LySep™ column, the lysate in the sample tubes were loaded onto AutoMate Express™ instrument and DNA was extracted using one of the two instrument extraction protocols. Our study showed that DNA was recovered from as little as 0.025 μL of blood. DNA extracted from casework-type samples was free of detectable PCR inhibitors and the short tandem repeat profiles were complete, conclusive, and devoid of any PCR artifacts. The system also showed consistent performance from day-to-day operation. 2012 American Academy of Forensic Sciences. Published 2012. This article is a U.S. Government work and is in the public domain in the U.S.A.

  6. Bayesian stratified sampling to assess corpus utility

    SciTech Connect

    Hochberg, J.; Scovel, C.; Thomas, T.; Hall, S.

    1998-12-01

    This paper describes a method for asking statistical questions about a large text corpus. The authors exemplify the method by addressing the question, ``What percentage of Federal Register documents are real documents, of possible interest to a text researcher or analyst?`` They estimate an answer to this question by evaluating 200 documents selected from a corpus of 45,820 Federal Register documents. Bayesian analysis and stratified sampling are used to reduce the sampling uncertainty of the estimate from over 3,100 documents to fewer than 1,000. A possible application of the method is to establish baseline statistics used to estimate recall rates for information retrieval systems.

  7. Automation impact study of Army training management 2: Extension of sampling and collection of installation resource data

    SciTech Connect

    Sanquist, T.F.; McCallum, M.C.; Hunt, P.S.; Slavich, A.L.; Underwood, J.A.; Toquam, J.L.; Seaver, D.A.

    1989-05-01

    This automation impact study of Army training management (TM) was performed for the Army Development and Employment Agency (ADEA) and the Combined Arms Training Activity (CATA) by the Battelle Human Affairs Research Centers and the Pacific Northwest Laboratory. The primary objective of the study was to provide the Army with information concerning the potential costs and savings associated with automating the TM process. This study expands the sample of units surveyed in Phase I of the automation impact effort (Sanquist et al., 1988), and presents data concerning installation resource management in relation to TM. The structured interview employed in Phase I was adapted to a self-administered survey. The data collected were compatible with that of Phase I, and both were combined for analysis. Three US sites, one reserve division, one National Guard division, and one unit in the active component outside the continental US (OCONUS) (referred to in this report as forward deployed) were surveyed. The total sample size was 459, of which 337 respondents contributed the most detailed data. 20 figs., 62 tabs.

  8. SAMPLING DESIGN FOR ASSESSING RECREATIONAL WATER QUALITY

    EPA Science Inventory

    Current U.S. EPA guidelines for monitoring recreatoinal water quality refer to the geometric mean density of indicator organisms, enterococci and E. coli in marine and fresh water, respectively, from at least five samples collected over a four-week period. In order to expand thi...

  9. Automated Retroillumination Photography Analysis for Objective Assessment of Fuchs Corneal Dystrophy.

    PubMed

    Eghrari, Allen O; Mumtaz, Aisha A; Garrett, Brian; Rezaei, Mahsa; Akhavan, Mina S; Riazuddin, S Amer; Gottsch, John D

    2017-01-01

    Retroillumination photography analysis is an objective tool for the assessment of the number and distribution of guttae in eyes affected with Fuchs corneal dystrophy (FCD). Current protocols include manual processing of images; here, we assess validity and interrater reliability of automated analysis across various levels of FCD severity. Retroillumination photographs of 97 FCD-affected corneas were acquired, and total counts of guttae were previously summated manually. For each cornea, a single image was loaded into ImageJ software. We reduced color variability and subtracted background noise. Reflection of light from each gutta was identified as a local area of maximum intensity and counted automatically. Noise tolerance level was titrated for each cornea by examining a small region of each image with automated overlay to ensure appropriate coverage of individual guttae. We tested interrater reliability of automated counts of guttae across a spectrum of clinical and educational experience. A set of 97 retroillumination photographs was analyzed. Clinical severity as measured by a modified Krachmer scale ranged from a severity level of 1 to 5 in the set of analyzed corneas. Automated counts by an ophthalmologist correlated strongly with Krachmer grading (R = 0.79) and manual counts (R = 0.88). Intraclass correlation coefficients demonstrated strong correlation at 0.924 (95% CI, 0.870-0.958) among cases analyzed by 3 students, and 0.869 (95% CI, 0.797-0.918) among cases for which images were analyzed by an ophthalmologist and 2 students. Automated retroillumination photography analysis allows for grading of FCD severity with high resolution across a spectrum of disease severity.

  10. Automated Peripheral Neuropathy Assessment Using Optical Imaging and Foot Anthropometry.

    PubMed

    Siddiqui, Hafeez-U R; Spruce, Michelle; Alty, Stephen R; Dudley, Sandra

    2015-08-01

    A large proportion of individuals who live with type-2 diabetes suffer from plantar sensory neuropathy. Regular testing and assessment for the condition is required to avoid ulceration or other damage to patient's feet. Currently accepted practice involves a trained clinician testing a patient's feet manually with a hand-held nylon monofilament probe. The procedure is time consuming, labor intensive, requires special training, is prone to error, and repeatability is difficult. With the vast increase in type-2 diabetes, the number of plantar sensory neuropathy sufferers has already grown to such an extent as to make a traditional manual test problematic. This paper presents the first investigation of a novel approach to automatically identify the pressure points on a given patient's foot for the examination of sensory neuropathy via optical image processing incorporating plantar anthropometry. The method automatically selects suitable test points on the plantar surface that correspond to those repeatedly chosen by a trained podiatrist. The proposed system automatically identifies the specific pressure points at different locations, namely the toe (hallux), metatarsal heads and heel (Calcaneum) areas. The approach is generic and has shown 100% reliability on the available database used. The database consists of Chinese, Asian, African, and Caucasian foot images.

  11. An automated digital microradiography system for assessing tooth demineralization

    NASA Astrophysics Data System (ADS)

    Darling, Cynthia L.; Le, Charles Q.; Featherstone, John D. B.; Fried, Daniel

    2009-02-01

    Digital Transverse microradiography (TMR) offers several advantages over film based methods including real-time image acquisition, excellent linearity with exposure, and it does not require expensive specialized film. The purpose of this work was to demonstrate that a high-resolution digital microradiography system can be used to measure the volume percent mineral loss for sound and demineralized enamel and dentin thin sections from 150-350-µm in thickness. A custom fabricated digital microradiography system with ~ 2-µm spatial resolution consisting of a digital x-ray imaging camera, a computerized high-speed motion control system and a high-intensity copper Kα x-ray source was used to determine the volume percent mineral content of sound and demineralized tooth sections. The volume percent mineral loss was compared with cross-sectional microhardness measurements on sound extracted human teeth. The correlation between microhardness and microradiography was excellent (Pr=0.99) for section thickness ranging from 59-319-µm (n=11). The attenuation was linear with varying exposure time from 1-10 seconds. Digital TMR is an effective and rapid method for the assessment of the mineral content of enamel and dentin thin sections.

  12. Using after-action review based on automated performance assessment to enhance training effectiveness.

    SciTech Connect

    Stevens-Adams, Susan Marie; Gieseler, Charles J.; Basilico, Justin Derrick; Abbott, Robert G.; Forsythe, James Chris

    2010-09-01

    Training simulators have become increasingly popular tools for instructing humans on performance in complex environments. However, the question of how to provide individualized and scenario-specific assessment and feedback to students remains largely an open question. In this work, we follow-up on previous evaluations of the Automated Expert Modeling and Automated Student Evaluation (AEMASE) system, which automatically assesses student performance based on observed examples of good and bad performance in a given domain. The current study provides a rigorous empirical evaluation of the enhanced training effectiveness achievable with this technology. In particular, we found that students given feedback via the AEMASE-based debrief tool performed significantly better than students given only instructor feedback on two out of three domain-specific performance metrics.

  13. Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis.

    PubMed

    Besse, P; Taylor, G; Carroll, B; Berding, N; Burner, D; McIntyre, C L

    1998-10-01

    An assessment of genetic diversity within and between Saccharum, Old World Erianthus sect. Ripidium, and North American E.giganteus (S.giganteum) was conducted using Amplified Fragment Length Polymorphism (AFLP(TM)) markers. An automated gel scoring system (GelCompar(TM)) was successfully used to analyse the complex AFLP patterns obtained in sugarcane and its relatives. Similarity coefficient calculations and clustering revealed a genetic structure for Saccharum and Erianthus sect. Ripidium that was identical to the one previously obtained using other molecular marker types, showing the appropriateness of AFLP markers and the associated automated analysis in assessing genetic diversity in sugarcane. A genetic structure that correlated with cytotype (2n=30, 60, 90) was revealed within the North American species, E. giganteus (S.giganteum). Complex relationships among Saccharum, Erianthus sect. Ripidium, and North American E.giganteus were revealed and are discussed in the light of a similar study which involved RAPD markers.

  14. A device for automated direct sampling and quantitation from solid-phase sorbent extraction cards by electrospray tandem mass spectrometry.

    PubMed

    Wachs, Timothy; Henion, Jack

    2003-04-01

    A new solid-phase extraction (SPE) device in the 96-well format (SPE Card) has been employed for automated off-line sample preparation of low-volume urine samples. On-line automated analyte elution via SPE and direct quantitation by micro ion spray mass spectrometry is reported. This sample preparation device has the format of a microtiter plate and is molded in a plastic frame which houses 96 separate sandwiched 3M Empore sorbents (0.5-mm-thickness, 8-microm particles) covered on both sides by a microfiber support material. Ninety-six discrete SPE zones, each 7 mm in diameter, are imbedded into the sheet in the conventional 9-mm pitch (spacing) of a 96-well microtiter plate. In this study one-quarter of an SPE Card (24 individual zones) was used merely as a convenience. After automated off-line interference elution of applied human urine from 24 samples, a section of SPE Card is mounted vertically on a computer-controlled X, Y, Z positioner in front of a micro ion spray direct sampling tube equipped with a beveled tip. The beveled tip of this needle robotically penetrates each SPE elution zone (sorbent disk) or stationary phase in a serial fashion. The eluted analytes are sequentially transferred directly to a microelectrosprayer to obtain tandem mass spectrometric (MS/MS) analysis. This strategy precludes any HPLC separation and the associated method development. The quantitative determination of Ritalin (methylphenidate) from fortified human urine samples is demonstrated. A trideuterated internal standard of methylphenidate was used to obtain ion current response ratios between the parent drug and the internal standard. Human control urine samples fortified from 6.6 to 3300 ng/mL (normal therapeutic levels have been determined in other studies to be between 50 and 100 ng/mL urine) were analyzed and a linear calibration curve was obtained with a correlation coefficient of 0.9999, where the precision of the quality control (QC) samples ranged from 9.6% at the 24

  15. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis

    PubMed Central

    Haile, Simon; Pandoh, Pawan; McDonald, Helen; Corbett, Richard D.; Tsao, Philip; Kirk, Heather; MacLeod, Tina; Jones, Martin; Bilobram, Steve; Brooks, Denise; Smailus, Duane; Steidl, Christian; Scott, David W.; Bala, Miruna; Hirst, Martin; Miller, Diane; Moore, Richard A.; Mungall, Andrew J.; Coope, Robin J.; Ma, Yussanne; Zhao, Yongjun; Holt, Rob A.; Jones, Steven J.

    2017-01-01

    Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95–100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting. PMID:28570594

  16. Lab on valve-multisyringe flow injection system (LOV-MSFIA) for fully automated uranium determination in environmental samples.

    PubMed

    Avivar, Jessica; Ferrer, Laura; Casas, Montserrat; Cerdà, Víctor

    2011-06-15

    The hyphenation of lab-on-valve (LOV) and multisyringe flow analysis (MSFIA), coupled to a long path length liquid waveguide capillary cell (LWCC), allows the spectrophotometric determination of uranium in different types of environmental sample matrices, without any manual pre-treatment, and achieving high selectivity and sensitivity levels. On-line separation and preconcentration of uranium is carried out by means of UTEVA resin. The potential of the LOV-MSFIA makes possible the fully automation of the system by the in-line regeneration of the column. After elution, uranium(VI) is spectrophotometrically detected after reaction with arsenazo-III. The determination of levels of uranium present in environmental samples is required in order to establish an environmental control. Thus, we propose a rapid, cheap and fully automated method to determine uranium(VI) in environmental samples. The limit of detection reached is 1.9 ηg of uranium and depending on the preconcentrated volume; it results in ppt levels (10.3 ηg L(-1)). Different water sample matrices (seawater, well water, freshwater, tap water and mineral water) and a phosphogypsum sample (with natural uranium content) were satisfactorily analyzed.

  17. Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis.

    PubMed

    Haile, Simon; Pandoh, Pawan; McDonald, Helen; Corbett, Richard D; Tsao, Philip; Kirk, Heather; MacLeod, Tina; Jones, Martin; Bilobram, Steve; Brooks, Denise; Smailus, Duane; Steidl, Christian; Scott, David W; Bala, Miruna; Hirst, Martin; Miller, Diane; Moore, Richard A; Mungall, Andrew J; Coope, Robin J; Ma, Yussanne; Zhao, Yongjun; Holt, Rob A; Jones, Steven J; Marra, Marco A

    2017-01-01

    Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95-100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.

  18. Comparison of manual, semi- and fully automated heart segmentation for assessing global left ventricular function in multidetector computed tomography.

    PubMed

    Plumhans, Cedric; Keil, Sebastian; Ocklenburg, Christina; Mühlenbruch, Georg; Behrendt, Florian F; Günther, Rolf W; Mahnken, Andreas H

    2009-08-01

    To evaluate the reliability of global left ventricular (LV) function and mass measurements with the aid of a semi-automated (Circulation; Siemens, Forchheim, Germany) and a new fully automated software (Philips Research Europe, Aachen, Germany) versus an established manual segmentation method (Argus; Siemens). Forty-one patients (31 men, 10 women; mean age: 62 +/- 5 years) with known or suspected coronary heart disease underwent contrast-enhanced Dual-Source computed tomography of the heart (120 kV, 410 mAs/rotation, collimation 2 x 32 x 0.6 mm, gantry rotation time 0.33 milliseconds). Global LV function measurements of end-diastolic volume (EDV), end-systolic volume (ESV), stroke volume, ejection fraction (EF), and LV mass were each assessed with a manual, a semi- and fully automated method. The latter were compared with the manual contour tracing method, which was considered as standard of reference. Postprocessing time for each method was recorded. For statistical analysis, repeated-measures analysis of variance, post hoc t test, and concordance correlation coefficients were calculated. Bland-Altman plots were generated. In general, ESV and EF assessed with the semi-automated and with the fully automated prototype version agreed well with the manual contour tracing method. The mean ESV (+/-SD) calculated from the manual, the semi-automated, and the fully automated method was 67 +/- 43 mL, 74 +/- 54 mL, and 75 +/- 48 mL, respectively. No statistically significant differences between the methods were found for ESV and EF. In contrast, significant variations (P < 0.05) among the different segmentation methods were shown for EDV, stroke volume, and LV mass. This variation was predominantly due to variation in endocardial delineations among the different techniques. Concordance correlation coefficients demonstrated a better accuracy for the fully automated method than for the semi-automated technique when compared with the manual drawing method. Furthermore, fully

  19. Automated Multiple-Sample Tray Manipulation Designed and Fabricated for Atomic Oxygen Facility

    NASA Technical Reports Server (NTRS)

    Sechkar, Edward A.; Stueber, Thomas J.; Dever, Joyce A.; Banks, Bruce A.; Rutledge, Sharon K.

    2000-01-01

    Extensive improvements to increase testing capacity and flexibility and to automate the in situ Reflectance Measurement System (RMS) are in progress at the Electro-Physics Branch s Atomic Oxygen (AO) beam facility of the NASA Glenn Research Center at Lewis Field. These improvements will triple the system s capacity while placing a significant portion of the testing cycle under computer control for added reliability, repeatability, and ease of use.

  20. Automated Processing of Plasma Samples for Lipoprotein Separation by Rate-Zonal Ultracentrifugation.

    PubMed

    Peters, Carl N; Evans, Iain E J

    2016-12-01

    Plasma lipoproteins are the primary means of lipid transport among tissues. Defining alterations in lipid metabolism is critical to our understanding of disease processes. However, lipoprotein measurement is limited to specialized centers. Preparation for ultracentrifugation involves the formation of complex density gradients that is both laborious and subject to handling errors. We created a fully automated device capable of forming the required gradient. The design has been made freely available for download by the authors. It is inexpensive relative to commercial density gradient formers, which generally create linear gradients unsuitable for rate-zonal ultracentrifugation. The design can easily be modified to suit user requirements and any potential future improvements. Evaluation of the device showed reliable peristaltic pump accuracy and precision for fluid delivery. We also demonstrate accurate fluid layering with reduced mixing at the gradient layers when compared to usual practice by experienced laboratory personnel. Reduction in layer mixing is of critical importance, as it is crucial for reliable lipoprotein separation. The automated device significantly reduces laboratory staff input and reduces the likelihood of error. Overall, this device creates a simple and effective solution to formation of complex density gradients. © 2015 Society for Laboratory Automation and Screening.

  1. Automated Sampling and Imaging of Analytes Separated on Thin-Layer Chromatography Plates Using Desorption Electrospray Ionization Mass Spectrometry

    SciTech Connect

    Van Berkel, Gary J; Kertesz, Vilmos

    2006-01-01

    Modest modifications to the atmospheric sampling capillary of a commercial electrospray mass spectrometer and upgrades to an in-house developed surface positioning control software package (HandsFree TLC/MS ) were used to enable the automated sampling and imaging of analytes on and/or within large area surface substrates using desorption electrospray ionization mass spectrometry. Sampling and imaging of rhodamine dyes separated on TLC plates were used to illustrate some of the practical applications of this system. Examples are shown for user-defined spot sampling from separated bands on a TLC plate (one or multiple spots), scanning of a complete development lane (one or multiple lanes), or imaging of analyte bands in a development lane (i.e. multiple lane scans with close spacing). The post data processing and data display aspects of the software system are also discussed.

  2. A compact tritium enrichment unit for large sample volumes with automated re-filling and higher enrichment factor.

    PubMed

    Kumar, B; Han, L-F; Wassenaar, L I; Klaus, P M; Kainz, G G; Hillegonds, D; Brummer, D; Ahmad, M; Belachew, D L; Araguás, L; Aggarwal, P

    2016-12-01

    Tritium ((3)H) in natural waters is a powerful tracer of hydrological processes, but its low concentrations require electrolytic enrichment before precise measurements can be made with a liquid scintillation counter. Here, we describe a newly developed, compact tritium enrichment unit which can be used to enrich up to 2L of a water sample. This allows a high enrichment factor (>100) for measuring low (3)H contents of <0.05TU. The TEU uses a small cell (250mL) with automated re-filling and a CO2 bubbling technique to neutralize the high alkalinity of enriched samples. The enriched residual sample is retrieved from the cell under vacuum by cryogenic distillation at -20°C and the tritium enrichment factor for each sample is accurately determined by measuring pre- and post- enrichment (2)H concentrations with laser spectrometry.

  3. Evaluation of an Automated Instrument for Inoculating and Spreading Samples onto Agar Plates▿

    PubMed Central

    Glasson, J. H.; Guthrie, L. H.; Nielsen, D. J.; Bethell, F. A.

    2008-01-01

    The findings from a preliminary assessment of a new instrument designed for the inoculation and spreading of specimens for microbiological analysis onto agar plates are described. The study found that the instrument was able to select full or biplates from a number of input cassettes, each containing different agar types. Samples were then inoculated by the instrument onto the agar surfaces and spread by a novel plastic applicator. Following this, the instrument labeled the plates and sorted them into a number of specified output stations. It was found that the instrument was able to inoculate and spread samples over a greater proportion of the agar plate surface than the manual loop-to-plate method. As a consequence, up to 44% more usable colonies were produced per plate from clinical specimens and standard cultures. Viable counts showed that the instrument was able to detect as few as 102 CFU/ml in fluids and also facilitated the enumeration of organisms, particularly in specimens such as urine. PMID:18272700

  4. Automated Image Sampling and Classification Can Be Used to Explore Perceived Naturalness of Urban Spaces.

    PubMed

    Hyam, Roger

    2017-01-01

    The psychological restorative effects of exposure to nature are well established and extend to just viewing of images of nature. A previous study has shown that Perceived Naturalness (PN) of images correlates with their restorative value. This study tests whether it is possible to detect degree of PN of images using an image classifier. It takes images that have been scored by humans for PN (including a subset that have been assessed for restorative value) and passes them through the Google Vision API image classification service. The resulting labels are assigned to broad semantic classes to create a Calculated Semantic Naturalness (CSN) metric for each image. It was found that CSN correlates with PN. CSN was then calculated for a geospatial sampling of Google Street View images across the city of Edinburgh. CSN was found to correlate with PN in this sample also indicating the technique may be useful in large scale studies. Because CSN correlates with PN which correlates with restorativeness it is suggested that CSN or a similar measure may be useful in automatically detecting restorative images and locations. In an exploratory aside CSN was not found to correlate with an indicator of socioeconomic deprivation.

  5. Evaluation of an Automated Instrument for Inoculating and Spreading Samples onto Agar Plates.

    PubMed

    Glasson, J H; Guthrie, L H; Nielsen, D J; Bethell, F A

    2008-04-01

    The findings from a preliminary assessment of a new instrument designed for the inoculation and spreading of specimens for microbiological analysis onto agar plates are described. The study found that the instrument was able to select full or biplates from a number of input cassettes, each containing different agar types. Samples were then inoculated by the instrument onto the agar surfaces and spread by a novel plastic applicator. Following this, the instrument labeled the plates and sorted them into a number of specified output stations. It was found that the instrument was able to inoculate and spread samples over a greater proportion of the agar plate surface than the manual loop-to-plate method. As a consequence, up to 44% more usable colonies were produced per plate from clinical specimens and standard cultures. Viable counts showed that the instrument was able to detect as few as 10(2) CFU/ml in fluids and also facilitated the enumeration of organisms, particularly in specimens such as urine.

  6. Automated Image Sampling and Classification Can Be Used to Explore Perceived Naturalness of Urban Spaces

    PubMed Central

    2017-01-01

    The psychological restorative effects of exposure to nature are well established and extend to just viewing of images of nature. A previous study has shown that Perceived Naturalness (PN) of images correlates with their restorative value. This study tests whether it is possible to detect degree of PN of images using an image classifier. It takes images that have been scored by humans for PN (including a subset that have been assessed for restorative value) and passes them through the Google Vision API image classification service. The resulting labels are assigned to broad semantic classes to create a Calculated Semantic Naturalness (CSN) metric for each image. It was found that CSN correlates with PN. CSN was then calculated for a geospatial sampling of Google Street View images across the city of Edinburgh. CSN was found to correlate with PN in this sample also indicating the technique may be useful in large scale studies. Because CSN correlates with PN which correlates with restorativeness it is suggested that CSN or a similar measure may be useful in automatically detecting restorative images and locations. In an exploratory aside CSN was not found to correlate with an indicator of socioeconomic deprivation. PMID:28052110

  7. A Fully Automated Drosophila Olfactory Classical Conditioning and Testing System for Behavioral Learning and Memory Assessment

    PubMed Central

    Jiang, Hui; Hanna, Eriny; Gatto, Cheryl L.; Page, Terry L.; Bhuva, Bharat; Broadie, Kendal

    2016-01-01

    Background Aversive olfactory classical conditioning has been the standard method to assess Drosophila learning and memory behavior for decades, yet training and testing are conducted manually under exceedingly labor-intensive conditions. To overcome this severe limitation, a fully automated, inexpensive system has been developed, which allows accurate and efficient Pavlovian associative learning/memory analyses for high-throughput pharmacological and genetic studies. New Method The automated system employs a linear actuator coupled to an odorant T-maze with airflow-mediated transfer of animals between training and testing stages. Odorant, airflow and electrical shock delivery are automatically administered and monitored during training trials. Control software allows operator-input variables to define parameters of Drosophila learning, short-term memory and long-term memory assays. Results The approach allows accurate learning/memory determinations with operational fail-safes. Automated learning indices (immediately post-training) and memory indices (after 24 hours) are comparable to traditional manual experiments, while minimizing experimenter involvement. Comparison with Existing Methods The automated system provides vast improvements over labor-intensive manual approaches with no experimenter involvement required during either training or testing phases. It provides quality control tracking of airflow rates, odorant delivery and electrical shock treatments, and an expanded platform for high-throughput studies of combinational drug tests and genetic screens. The design uses inexpensive hardware and software for a total cost of ~$500US, making it affordable to a wide range of investigators. Conclusions This study demonstrates the design, construction and testing of a fully automated Drosophila olfactory classical association apparatus to provide low-labor, high-fidelity, quality-monitored, high-throughput and inexpensive learning and memory behavioral assays

  8. A fully automated Drosophila olfactory classical conditioning and testing system for behavioral learning and memory assessment.

    PubMed

    Jiang, Hui; Hanna, Eriny; Gatto, Cheryl L; Page, Terry L; Bhuva, Bharat; Broadie, Kendal

    2016-03-01

    Aversive olfactory classical conditioning has been the standard method to assess Drosophila learning and memory behavior for decades, yet training and testing are conducted manually under exceedingly labor-intensive conditions. To overcome this severe limitation, a fully automated, inexpensive system has been developed, which allows accurate and efficient Pavlovian associative learning/memory analyses for high-throughput pharmacological and genetic studies. The automated system employs a linear actuator coupled to an odorant T-maze with airflow-mediated transfer of animals between training and testing stages. Odorant, airflow and electrical shock delivery are automatically administered and monitored during training trials. Control software allows operator-input variables to define parameters of Drosophila learning, short-term memory and long-term memory assays. The approach allows accurate learning/memory determinations with operational fail-safes. Automated learning indices (immediately post-training) and memory indices (after 24h) are comparable to traditional manual experiments, while minimizing experimenter involvement. The automated system provides vast improvements over labor-intensive manual approaches with no experimenter involvement required during either training or testing phases. It provides quality control tracking of airflow rates, odorant delivery and electrical shock treatments, and an expanded platform for high-throughput studies of combinational drug tests and genetic screens. The design uses inexpensive hardware and software for a total cost of ∼$500US, making it affordable to a wide range of investigators. This study demonstrates the design, construction and testing of a fully automated Drosophila olfactory classical association apparatus to provide low-labor, high-fidelity, quality-monitored, high-throughput and inexpensive learning and memory behavioral assays. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    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

  10. The Effects of Finite Sampling Corrections on State Assessment Sample Requirements. NAEP Validity Studies (NVS).

    ERIC Educational Resources Information Center

    Chromy, James R.

    States participating in the National Assessment of Educational Progress State Assessment program (state NAEP) are required to sample at least 2,500 students from at least 100 schools per subject assessed. In this ideal situation, 25 students are assessed for a subject in each school selected for that subject. Two problems have arisen: some states…

  11. Assessing Tumor Angiogenesis in Histological Samples.

    PubMed

    Pang, Jia-Min; Jene, Nicholas; Fox, Stephen B

    2016-01-01

    Tumor neovascularization acquires their vessels through a number of processes including angiogenesis, vasculogenesis, vascular remodeling, intussusception, and possibly vascular mimicry in certain tumors. The end result of the tumor vasculature has been quantified by counting the number of immunohistochemically identified microvessels in areas of maximal vascularity, so-called hot spot. Other techniques have been developed such as Chalkley counting and the use of image analysis systems that are robust and reproducible as well as being more objective. Many of the molecular pathways that govern tumor neovascularization have been identified and many reagents are now available to study these tissue sections. These include angiogenic growth factors and their receptors and cell adhesion molecules, proteases, and markers of activated, proliferating, cytokine-stimulated, or angiogenic vessels, such as CD105. It is also possible to differentiate quiescent from active vessels. Other reagents that can identify proteins involved in microenvironmental influences such as hypoxia have also been generated. Although the histological assessment of tumor vascularity is used mostly in the research context, it may also have clinical applications if appropriate methodology and trained observers perform the studies.

  12. Automated assessment of bilateral breast volume asymmetry as a breast cancer biomarker during mammographic screening

    SciTech Connect

    Williams, Alex C; Hitt, Austin N; Voisin, Sophie; Tourassi, Georgia

    2013-01-01

    The biological concept of bilateral symmetry as a marker of developmental stability and good health is well established. Although most individuals deviate slightly from perfect symmetry, humans are essentially considered bilaterally symmetrical. Consequently, increased fluctuating asymmetry of paired structures could be an indicator of disease. There are several published studies linking bilateral breast size asymmetry with increased breast cancer risk. These studies were based on radiologists manual measurements of breast size from mammographic images. We aim to develop a computerized technique to assess fluctuating breast volume asymmetry in screening mammograms and investigate whether it correlates with the presence of breast cancer. Using a large database of screening mammograms with known ground truth we applied automated breast region segmentation and automated breast size measurements in CC and MLO views using three well established methods. All three methods confirmed that indeed patients with breast cancer have statistically significantly higher fluctuating asymmetry of their breast volumes. However, statistically significant difference between patients with cancer and benign lesions was observed only for the MLO views. The study suggests that automated assessment of global bilateral asymmetry could serve as a breast cancer risk biomarker for women undergoing mammographic screening. Such biomarker could be used to alert radiologists or computer-assisted detection (CAD) systems to exercise increased vigilance if higher than normal cancer risk is suspected.

  13. Automated assessment of bilateral breast volume asymmetry as a breast cancer biomarker during mammographic screening

    NASA Astrophysics Data System (ADS)

    Williams, Alex C.; Hitt, Austin; Voisin, Sophie; Tourassi, Georgia

    2013-03-01

    The biological concept of bilateral symmetry as a marker of developmental stability and good health is well established. Although most individuals deviate slightly from perfect symmetry, humans are essentially considered bilaterally symmetrical. Consequently, increased fluctuating asymmetry of paired structures could be an indicator of disease. There are several published studies linking bilateral breast size asymmetry with increased breast cancer risk. These studies were based on radiologists' manual measurements of breast size from mammographic images. We aim to develop a computerized technique to assess fluctuating breast volume asymmetry in screening mammograms and investigate whether it correlates with the presence of breast cancer. Using a large database of screening mammograms with known ground truth we applied automated breast region segmentation and automated breast size measurements in CC and MLO views using three well established methods. All three methods confirmed that indeed patients with breast cancer have statistically significantly higher fluctuating asymmetry of their breast volumes. However, statistically significant difference between patients with cancer and benign lesions was observed only for the MLO views. The study suggests that automated assessment of global bilateral asymmetry could serve as a breast cancer risk biomarker for women undergoing mammographic screening. Such biomarker could be used to alert radiologists or computer-assisted detection (CAD) systems to exercise increased vigilance if higher than normal cancer risk is suspected.

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

    USGS Publications Warehouse

    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/).

  15. A new automated sample transfer system for instrumental neutron activation analysis.

    PubMed

    Ismail, S S

    2010-01-01

    A fully automated and fast pneumatic transport system for short-time activation analysis was recently developed. It is suitable for small nuclear research reactors or laboratories that are using neutron generators and other neutron sources. It is equipped with a programmable logic controller, software package, and 12 devices to facilitate optimal analytical procedures. 550 ms were only necessary to transfer the irradiated capsule (diameter: 15 mm, length: 50 mm, weight: 4 gram) to the counting chamber at a distance of 20 meters using pressurized air (4 bars) as a transport gas.

  16. A New Automated Sample Transfer System for Instrumental Neutron Activation Analysis

    PubMed Central

    Ismail, S. S.

    2010-01-01

    A fully automated and fast pneumatic transport system for short-time activation analysis was recently developed. It is suitable for small nuclear research reactors or laboratories that are using neutron generators and other neutron sources. It is equipped with a programmable logic controller, software package, and 12 devices to facilitate optimal analytical procedures. 550 ms were only necessary to transfer the irradiated capsule (diameter: 15 mm, length: 50 mm, weight: 4 gram) to the counting chamber at a distance of 20 meters using pressurized air (4 bars) as a transport gas. PMID:20369063

  17. Immunosuppressant therapeutic drug monitoring by LC-MS/MS: workflow optimization through automated processing of whole blood samples.

    PubMed

    Marinova, Mariela; Artusi, Carlo; Brugnolo, Laura; Antonelli, Giorgia; Zaninotto, Martina; Plebani, Mario

    2013-11-01

    Although, due to its high specificity and sensitivity, LC-MS/MS is an efficient technique for the routine determination of immunosuppressants in whole blood, it involves time-consuming manual sample preparation. The aim of the present study was therefore to develop an automated sample-preparation protocol for the quantification of sirolimus, everolimus and tacrolimus by LC-MS/MS using a liquid handling platform. Six-level commercially available blood calibrators were used for assay development, while four quality control materials and three blood samples from patients under immunosuppressant treatment were employed for the evaluation of imprecision. Barcode reading, sample re-suspension, transfer of whole blood samples into 96-well plates, addition of internal standard solution, mixing, and protein precipitation were performed with a liquid handling platform. After plate filtration, the deproteinised supernatants were submitted for SPE on-line. The only manual steps in the entire process were de-capping of the tubes, and transfer of the well plates to the HPLC autosampler. Calibration curves were linear throughout the selected ranges. The imprecision and accuracy data for all analytes were highly satisfactory. The agreement between the results obtained with manual and those obtained with automated sample preparation was optimal (n=390, r=0.96). In daily routine (100 patient samples) the typical overall total turnaround time was less than 6h. Our findings indicate that the proposed analytical system is suitable for routine analysis, since it is straightforward and precise. Furthermore, it incurs less manual workload and less risk of error in the quantification of whole blood immunosuppressant concentrations than conventional methods. © 2013.

  18. Fully automated Liquid Extraction-Based Surface Sampling and Ionization Using a Chip-Based Robotic Nanoelectrospray Platform

    SciTech Connect

    Kertesz, Vilmos; Van Berkel, Gary J

    2010-01-01

    A fully automated liquid extraction-based surface sampling device utilizing an Advion NanoMate chip-based infusion nanoelectrospray ionization system is reported. Analyses were enabled for discrete spot sampling by using the Advanced User Interface of the current commercial control software. This software interface provided the parameter control necessary for the NanoMate robotic pipettor to both form and withdraw a liquid microjunction for sampling from a surface. The system was tested with three types of analytically important sample surface types, viz., spotted sample arrays on a MALDI plate, dried blood spots on paper, and whole-body thin tissue sections from drug dosed mice. The qualitative and quantitative data were consistent with previous studies employing other liquid extraction-based surface sampling techniques. The successful analyses performed here utilized the hardware and software elements already present in the NanoMate system developed to handle and analyze liquid samples. Implementation of an appropriate sample (surface) holder, a solvent reservoir, faster movement of the robotic arm, finer control over solvent flow rate when dispensing and retrieving the solution at the surface, and the ability to select any location on a surface to sample from would improve the analytical performance and utility of the platform.

  19. Validation of a fully automated robotic setup for preparation of whole blood samples for LC-MS toxicology analysis.

    PubMed

    Andersen, David; Rasmussen, Brian; Linnet, Kristian

    2012-05-01

    A fully automated setup was developed for preparing whole blood samples using a Tecan Evo workstation. By integrating several add-ons to the robotic platform, the flexible setup was able to prepare samples from sample tubes to a 96-well sample plate ready for injection on liquid chromatography-mass spectrometry using several preparation techniques, including protein precipitation, solid-phase extraction and centrifugation, without any manual intervention. Pipetting of a known aliquot of whole blood was achieved by integrating a balance and performing gravimetric measurements. The system was able to handle 1,073 of 1,092 (98.3%) samples of whole blood from forensic material, including postmortem samples, without any need for repeating sample preparation. Only three samples required special treatment such as dilution. The addition of internal and calibration standards were validated by pipetting a solution of Orange G and measuring the weight and absorbance. Internal standard (20 µL) was added in a multi-pipetting sequence with an accuracy of 99.9% and imprecision (coefficient of variation) of 1.6%. Calibration standards were added with high accuracy at volumes as low as 6.00 µL (±0.21 µL). The general setup of the offline sample preparation and key validation parameters of a quantitative analysis of Δ(9)-tetrahydrocannabinol is presented.

  20. High-frequency, long-duration water sampling in acid mine drainage studies: a short review of current methods and recent advances in automated water samplers

    USGS Publications Warehouse

    Chapin, Thomas

    2015-01-01

    Hand-collected grab samples are the most common water sampling method but using grab sampling to monitor temporally variable aquatic processes such as diel metal cycling or episodic events is rarely feasible or cost-effective. Currently available automated samplers are a proven, widely used technology and typically collect up to 24 samples during a deployment. However, these automated samplers are not well suited for long-term sampling in remote areas or in freezing conditions. There is a critical need for low-cost, long-duration, high-frequency water sampling technology to improve our understanding of the geochemical response to temporally variable processes. This review article will examine recent developments in automated water sampler technology and utilize selected field data from acid mine drainage studies to illustrate the utility of high-frequency, long-duration water sampling.

  1. An Assessment of the Technology of Automated Rendezvous and Capture in Space

    NASA Technical Reports Server (NTRS)

    Polites, M. E.

    1998-01-01

    This paper presents the results of a study to assess the technology of automated rendezvous and capture (AR&C) in space. The outline of the paper is as follows. First, the history of manual and automated rendezvous and capture and rendezvous and dock is presented. Next, the need for AR&C in space is established. Then, today's technology and ongoing technology efforts related to AR&C in space are reviewed. In light of these, AR&C systems are proposed that meet NASA's future needs, but can be developed in a reasonable amount of time with a reasonable amount of money. Technology plans for developing these systems are presented; cost and schedule are included.

  2. Sensitivity testing of trypanosome detection by PCR from whole blood samples using manual and automated DNA extraction methods.

    PubMed

    Dunlop, J; Thompson, C K; Godfrey, S S; Thompson, R C A

    2014-11-01

    Automated extraction of DNA for testing of laboratory samples is an attractive alternative to labour-intensive manual methods when higher throughput is required. However, it is important to maintain the maximum detection sensitivity possible to reduce the occurrence of type II errors (false negatives; failure to detect the target when it is present), especially in the biomedical field, where PCR is used for diagnosis. We used blood infected with known concentrations of Trypanosoma copemani to test the impact of analysis techniques on trypanosome detection sensitivity by PCR. We compared combinations of a manual and an automated DNA extraction method and two different PCR primer sets to investigate the impact of each on detection levels. Both extraction techniques and specificity of primer sets had a significant impact on detection sensitivity. Samples extracted using the same DNA extraction technique performed substantially differently for each of the separate primer sets. Type I errors (false positives; detection of the target when it is not present), produced by contaminants, were avoided with both extraction methods. This study highlights the importance of testing laboratory techniques with known samples to optimise accuracy of test results.

  3. An automated procedure for the simultaneous determination of specific conductance and pH in natural water samples

    USGS Publications Warehouse

    Eradmann, D.E.; Taylor, H.E.

    1978-01-01

    An automated, continuous-flow system is utilized to determine specific conductance and pH simultaneously in natural waters. A direct electrometric procedure is used to determine values in the range pH 4-9. The specific conductance measurements are made with an electronically modified, commercially available conductivity meter interfaced to a separate module containing the readout control devices and printer. The system is designed to switch ranges automatically to accommodate optimum analysis of widely varying conductances ranging from a few ??mhos cm-1 to 15,000 ??mho cm-1. Thirty samples per hour can be analyzed. Comparison of manual and automated procedures for 40 samples showed that the average differences were 1.3% for specific conductance and 0.07 units for pH. The relative standard deviation for 25 replicate values for each of five samples was significantly less than 1% for the specific conductance determination; the standard deviation for the pH determination was ??? 0.06 pH units. ?? 1978.

  4. Interdisciplinary development of manual and automated product usability assessments for older adults with dementia: lessons learned.

    PubMed

    Boger, Jennifer; Taati, Babak; Mihailidis, Alex

    2016-10-01

    The changes in cognitive abilities that accompany dementia can make it difficult to use everyday products that are required to complete activities of daily living. Products that are inherently more usable for people with dementia could facilitate independent activity completion, thus reducing the need for caregiver assistance. The objectives of this research were to: (1) gain an understanding of how water tap design impacted tap usability and (2) create an automated computerized tool that could assess tap usability. 27 older adults, who ranged from cognitively intact to advanced dementia, completed 1309 trials on five tap designs. Data were manually analyzed to investigate tap usability as well as used to develop an automated usability analysis tool. Researchers collaborated to modify existing techniques and to create novel ones to accomplish both goals. This paper presents lessons learned through the course of this research, which could be applicable in the development of other usability studies, automated vision-based assessments and the development of assistive technologies for cognitively impaired older adults. Collaborative interdisciplinary teamwork, which included older adult with dementia participants, was key to enabling innovative advances that achieved the projects' research goals. Implications for Rehabilitation Products that are implicitly familiar and usable by older adults could foster independent activity completion, potentially reducing reliance on a caregiver. The computer-based automated tool can significantly reduce the time and effort required to perform product usability analysis, making this type of analysis more feasible. Interdisciplinary collaboration can result in a more holistic understanding of assistive technology research challenges and enable innovative solutions.

  5. Reproducibility of a novel echocardiographic 3D automated software for the assessment of mitral valve anatomy.

    PubMed

    Aquila, Iolanda; González, Ariana; Fernández-Golfín, Covadonga; Rincón, Luis Miguel; Casas, Eduardo; García, Ana; Hinojar, Rocio; Jiménez-Nacher, José Julio; Zamorano, José Luis

    2016-05-17

    3D transesophageal echocardiography (TEE) is superior to 2D TEE in quantitative anatomic evaluation of the mitral valve (MV) but it shows limitations regarding automatic quantification. Here, we tested the inter-/intra-observer reproducibility of a novel full-automated software in the evaluation of MV anatomy compared to manual 3D assessment. Thirty-six out of 61 screened patients referred to our Cardiac Imaging Unit for TEE were retrospectively included. 3D TEE analysis was performed both manually and with the automated software by two independent operators. Mitral annular area, intercommissural distance, anterior leaflet length and posterior leaflet length were assessed. A significant correlation between both methods was found for all variables: intercommissural diameter (r = 0.84, p < 0.01), mitral annular area (r = 0.94, p > 0, 01), anterior leaflet length (r = 0.83, p < 0.01) and posterior leaflet length (r = 0.67, p < 0.01). Interobserver variability assessed by the intraclass correlation coefficient was superior for the automatic software: intercommisural distance 0.997 vs. 0.76; mitral annular area 0.957 vs. 0.858; anterior leaflet length 0.963 vs. 0.734 and posterior leaflet length 0.936 vs. 0.838. Intraobserver variability was good for both methods with a better level of agreement with the automatic software. The novel 3D automated software is reproducible in MV anatomy assessment. The incorporation of this new tool in clinical MV assessment may improve patient selection and outcomes for MV interventions as well as patient diagnosis and prognosis stratification. Yet, high-quality 3D images are indispensable.

  6. An Automated System for Skeletal Maturity Assessment by Extreme Learning Machines.

    PubMed

    Mansourvar, Marjan; Shamshirband, Shahaboddin; Raj, Ram Gopal; Gunalan, Roshan; Mazinani, Iman

    2015-01-01

    Assessing skeletal age is a subjective and tedious examination process. Hence, automated assessment methods have been developed to replace manual evaluation in medical applications. In this study, a new fully automated method based on content-based image retrieval and using extreme learning machines (ELM) is designed and adapted to assess skeletal maturity. The main novelty of this approach is it overcomes the segmentation problem as suffered by existing systems. The estimation results of ELM models are compared with those of genetic programming (GP) and artificial neural networks (ANNs) models. The experimental results signify improvement in assessment accuracy over GP and ANN, while generalization capability is possible with the ELM approach. Moreover, the results are indicated that the ELM model developed can be used confidently in further work on formulating novel models of skeletal age assessment strategies. According to the experimental results, the new presented method has the capacity to learn many hundreds of times faster than traditional learning methods and it has sufficient overall performance in many aspects. It has conclusively been found that applying ELM is particularly promising as an alternative method for evaluating skeletal age.

  7. Towards Automating Clinical Assessments: A Survey of the Timed Up and Go (TUG)

    PubMed Central

    Sprint, Gina; Cook, Diane; Weeks, Douglas

    2016-01-01

    Older adults often suffer from functional impairments that affect their ability to perform everyday tasks. To detect the onset and changes in abilities, healthcare professionals administer standardized assessments. Recently, technology has been utilized to complement these clinical assessments to gain a more objective and detailed view of functionality. In the clinic and at home, technology is able to provide more information about patient performance and reduce subjectivity in outcome measures. The timed up and go (TUG) test is one such assessment recently instrumented with technology in several studies, yielding promising results towards the future of automating clinical assessments. Potential benefits of technological TUG implementations include additional performance parameters, generated reports, and the ability to be self-administered in the home. In this paper, we provide an overview of the TUG test and technologies utilized for TUG instrumentation. We then critically review the technological advancements and follow up with an evaluation of the benefits and limitations of each approach. Finally, we analyze the gaps in the implementations and discuss challenges for future research towards automated, self-administered assessment in the home. PMID:25594979

  8. A Framework to Automate Assessment of Upper-Limb Motor Function Impairment: A Feasibility Study

    PubMed Central

    Otten, Paul; Kim, Jonghyun; Son, Sang Hyuk

    2015-01-01

    Standard upper-limb motor function impairment assessments, such as the Fugl-Meyer Assessment (FMA), are a critical aspect of rehabilitation after neurological disorders. These assessments typically take a long time (about 30 min for the FMA) for a clinician to perform on a patient, which is a severe burden in a clinical environment. In this paper, we propose a framework for automating upper-limb motor assessments that uses low-cost sensors to collect movement data. The sensor data is then processed through a machine learning algorithm to determine a score for a patient’s upper-limb functionality. To demonstrate the feasibility of the proposed approach, we implemented a system based on the proposed framework that can automate most of the FMA. Our experiment shows that the system provides similar FMA scores to clinician scores, and reduces the time spent evaluating each patient by 82%. Moreover, the proposed framework can be used to implement customized tests or tests specified in other existing standard assessment methods. PMID:26287206

  9. An Automated System for Skeletal Maturity Assessment by Extreme Learning Machines

    PubMed Central

    Mansourvar, Marjan; Shamshirband, Shahaboddin; Raj, Ram Gopal; Gunalan, Roshan; Mazinani, Iman

    2015-01-01

    Assessing skeletal age is a subjective and tedious examination process. Hence, automated assessment methods have been developed to replace manual evaluation in medical applications. In this study, a new fully automated method based on content-based image retrieval and using extreme learning machines (ELM) is designed and adapted to assess skeletal maturity. The main novelty of this approach is it overcomes the segmentation problem as suffered by existing systems. The estimation results of ELM models are compared with those of genetic programming (GP) and artificial neural networks (ANNs) models. The experimental results signify improvement in assessment accuracy over GP and ANN, while generalization capability is possible with the ELM approach. Moreover, the results are indicated that the ELM model developed can be used confidently in further work on formulating novel models of skeletal age assessment strategies. According to the experimental results, the new presented method has the capacity to learn many hundreds of times faster than traditional learning methods and it has sufficient overall performance in many aspects. It has conclusively been found that applying ELM is particularly promising as an alternative method for evaluating skeletal age. PMID:26402795

  10. "Aged sample" software on automated routine hematology analyzer enables differentiation between pathological and non-pathological WBC flagging in aging samples.

    PubMed

    Ulset, Ragna Aaram; Petrasch, Eveline; Saker, Jarob; Linssen, Jo; Kimura, Konobu; Uchihashi, Kinya; Philipsen, Paul; Eide, Arne

    2014-01-01

    Storing K(x)EDTA-conjugated blood samples at room temperature or under insufficient cooling conditions results in various morphological changes such as swelling of the blood cells. These changes are reproducible and have already been described well. However, they can lead to incorrect flagging when using automated hematology analyzers for complete blood counts and white blood cell differentials. The aim of this study was to determine if those changes can be detected automatically and used to prevent false positive flagging. 150 blood samples were aged under controlled conditions and the impact on the "Aged sample" software was checked retrospectively. The results were verified in a second retrospective study including 6288 routine samples. When tested in a routine laboratory, the "Aged sample" software was able to reduce overall flagging by 23% without increasing false negative flagging. The "Aged sample" software of XN-Series analyzers does not only detect and flag samples that are aging or were stored under suboptimal conditions but also prevents false positive flagging.

  11. Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

    NASA Astrophysics Data System (ADS)

    Rahman, Nur Aira Abd; Yussup, Nolida; Salim, Nazaratul Ashifa Bt. Abdullah; Ibrahim, Maslina Bt. Mohd; Mokhtar, Mukhlis B.; Soh@Shaari, Syirrazie Bin Che; Azman, Azraf B.; Ismail, Nadiah Binti

    2015-04-01

    Neutron Activation Analysis (NAA) had been established in Nuclear Malaysia since 1980s. Most of the procedures established were done manually including sample registration. The samples were recorded manually in a logbook and given ID number. Then all samples, standards, SRM and blank were recorded on the irradiation vial and several forms prior to irradiation. These manual procedures carried out by the NAA laboratory personnel were time consuming and not efficient. Sample registration software is developed as part of IAEA/CRP project on `Development of Process Automation in the Neutron Activation Analysis (NAA) Facility in Malaysia Nuclear Agency (RC17399)'. The objective of the project is to create a pc-based data entry software during sample preparation stage. This is an effective method to replace redundant manual data entries that needs to be completed by laboratory personnel. The software developed will automatically generate sample code for each sample in one batch, create printable registration forms for administration purpose, and store selected parameters that will be passed to sample analysis program. The software is developed by using National Instruments Labview 8.6.

  12. Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

    SciTech Connect

    Rahman, Nur Aira Abd Yussup, Nolida; Ibrahim, Maslina Bt. Mohd; Mokhtar, Mukhlis B.; Soh Shaari, Syirrazie Bin Che; Azman, Azraf B.; Salim, Nazaratul Ashifa Bt. Abdullah; Ismail, Nadiah Binti

    2015-04-29

    Neutron Activation Analysis (NAA) had been established in Nuclear Malaysia since 1980s. Most of the procedures established were done manually including sample registration. The samples were recorded manually in a logbook and given ID number. Then all samples, standards, SRM and blank were recorded on the irradiation vial and several forms prior to irradiation. These manual procedures carried out by the NAA laboratory personnel were time consuming and not efficient. Sample registration software is developed as part of IAEA/CRP project on ‘Development of Process Automation in the Neutron Activation Analysis (NAA) Facility in Malaysia Nuclear Agency (RC17399)’. The objective of the project is to create a pc-based data entry software during sample preparation stage. This is an effective method to replace redundant manual data entries that needs to be completed by laboratory personnel. The software developed will automatically generate sample code for each sample in one batch, create printable registration forms for administration purpose, and store selected parameters that will be passed to sample analysis program. The software is developed by using National Instruments Labview 8.6.

  13. Evaluation of a software package for automated quality assessment of contrast detail images—comparison with subjective visual assessment

    NASA Astrophysics Data System (ADS)

    Pascoal, A.; Lawinski, C. P.; Honey, I.; Blake, P.

    2005-12-01

    Contrast detail analysis is commonly used to assess image quality (IQ) associated with diagnostic imaging systems. Applications include routine assessment of equipment performance and optimization studies. Most frequently, the evaluation of contrast detail images involves human observers visually detecting the threshold contrast detail combinations in the image. However, the subjective nature of human perception and the variations in the decision threshold pose limits to the minimum image quality variations detectable with reliability. Objective methods of assessment of image quality such as automated scoring have the potential to overcome the above limitations. A software package (CDRAD analyser) developed for automated scoring of images produced with the CDRAD test object was evaluated. Its performance to assess absolute and relative IQ was compared with that of an average observer. Results show that the software does not mimic the absolute performance of the average observer. The software proved more sensitive and was able to detect smaller low-contrast variations. The observer's performance was superior to the software's in the detection of smaller details. Both scoring methods showed frequent agreement in the detection of image quality variations resulting from changes in kVp and KERMAdetector, which indicates the potential to use the software CDRAD analyser for assessment of relative IQ.

  14. Method for Effective Calibration of Temperature Loggers with Automated Data Sampling and Evaluation

    NASA Astrophysics Data System (ADS)

    Ljungblad, S.; Josefson, L. E.; Holmsten, M.

    2011-12-01

    A highly automated calibration method for temperature loggers is presented. By using an automated procedure, a time- and cost-efficient calibration of temperature loggers is made possible. The method is directed at loggers that lack the function/property of direct reading from a display. This type of logger has to be connected to a computer for the setting-up of the measurement and again for collection of the measurement results. During the calibration, the loggers are offline. This method has been developed for temperature loggers from Gemini Data loggers, but the software and method could be modified to suit other types of loggers as well. Calibration is performed by comparison to a reference thermometer in liquid baths; and for loggers which have external sensors, only the sensor is normally placed in the bath. Loggers with internal sensors are protected from the liquid by placing them in an exterior plastic or metallic cover, and thereafter the entire loggers are placed in the bath. A digital thermometer measures the reference temperature of the bath and transmits it to a computer by way of Bluetooth. The developed calibration software, SPTempLogger, controls the logger software, and thus the communication protocol of the logger software does not need to be known. The previous method, with manual handling of the start and termination of every measuring sequence, evaluation of the resulting data and its corresponding uncertainty components, can be replaced by this automated method. Both the logger and reference measurement data are automatically downloaded once the logger has been connected to a computer after the calibration, and the calibration software started. The data are then evaluated automatically, and by statistical analysis of the confidence coefficient and standard deviation, the temperature plateaus that the calibration includes are identified. If a number of control parameters comply with the requirements, then the correction, resolution, and short

  15. Non-destructive automated sampling of mycotoxins in bulk food and feed - A new tool for required harmonization.

    PubMed

    Spanjer, M; Stroka, J; Patel, S; Buechler, S; Pittet, A; Barel, S

    2001-06-01

    Mycotoxins contamination is highly non-uniformly distributed as is well recog-nized by the EC, by not only setting legal limits in a series of commodities, but also schedule a sampling plan that takes this heterogeneity into account. In practice however, it turns out that it is very difficult to carry out this sampling plan in a harmonised way. Applying the sampling plan to a container filled with pallets of bags (i.e. with nuts or coffee beans) varies from very laborious to almost impossible. The presented non-destructive automated method to sample bulk food could help to overcome these practical problems and to enforcing of EC directives. It is derived from a tested and approved technology for detection of illicit substances in security applications. It has capability to collect and iden-tify ultra trace contaminants, i.e. from a fingerprint of chemical substance in a bulk of goods, a cargo pallet load (~ 1000 kg) with boxes and commodities.The technology, patented for explosives detection, uses physical and chemistry processes for excitation and remote rapid enhanced release of contaminant residues, vapours and particulate, of the inner/outer surfaces of inspected bulk and collect them on selective probes. The process is automated, takes only 10 minutes, is non-destructive and the bulk itself remains unharmed. The system design is based on applicable international regulations for shipped cargo hand-ling and transportation by road, sea and air. After this process the pallet can be loaded on a truck, ship or plane. Analysis can be carried out before the cargo leaves the place of shipping. The potent application of this technology for myco-toxins detection, has been demonstrated by preliminary feasibility experiments. Aflatoxins were detected in pistachios and ochratoxin A in green coffee beans bulk. Both commodities were naturally contaminated, priory found and confirm-ed by common methods as used at routine inspections. Once the contaminants are extracted from a

  16. ARAM-W Automated Risk Assessment Methodology for Water and Wastewater

    SciTech Connect

    Dang, Tam; Jaeger, Calvin D.; Roehrig, Nathaniel S.; Torres, Teresa M.

    2015-06-04

    The Automated Risk Assessment Methodology for Water and Wastewater Utilities, ARAM-W, is a systematic, risk-based approach used to evaluate water and wastewater utilities from a range of threats that could cause an undesired event. It leverages the automated RAM-CI (critical infrastructure) prototype tool completed in September 2008, the manual RC RAM-W (RAMCAP compliant) approach completed in September 2007, the manual RAM-W, version 2, approach completed in 2002, and the requirements and needs of the Water Sector, EPA and DHS. The ARAM-W tool is a user-friendly tool which provides a sound scientific and technical framework to look at the total protection system. The ARAM-W tool provides the user the ability to determine a relative risk based on the threat, consequences and protection system effectiveness/vulnerability. It is a stand-alone PC-based tool which is compatible with the NIPP risk assessment methodology criteria as well as RAMPCAP. The ARAM-W process provides through a series of steps the ability to plan for the risk assessment; characterize the utility, facilities and assets; define the threat; identify undesired events and consequences; evaluate protection system effectiveness; determine risk; propose and evaluate upgrades if the risk is not acceptable and report on the assessment results.

  17. Assessing V and V Processes for Automation with Respect to Vulnerabilities to Loss of Airplane State Awareness

    NASA Technical Reports Server (NTRS)

    Whitlow, Stephen; Wilkinson, Chris; Hamblin, Chris

    2014-01-01

    Automation has contributed substantially to the sustained improvement of aviation safety by minimizing the physical workload of the pilot and increasing operational efficiency. Nevertheless, in complex and highly automated aircraft, automation also has unintended consequences. As systems become more complex and the authority and autonomy (A&A) of the automation increases, human operators become relegated to the role of a system supervisor or administrator, a passive role not conducive to maintaining engagement and airplane state awareness (ASA). The consequence is that flight crews can often come to over rely on the automation, become less engaged in the human-machine interaction, and lose awareness of the automation mode under which the aircraft is operating. Likewise, the complexity of the system and automation modes may lead to poor understanding of the interaction between a mode of automation and a particular system configuration or phase of flight. These and other examples of mode confusion often lead to mismanaging the aircraftâ€"TM"s energy state or the aircraft deviating from the intended flight path. This report examines methods for assessing whether, and how, operational constructs properly assign authority and autonomy in a safe and coordinated manner, with particular emphasis on assuring adequate airplane state awareness by the flight crew and air traffic controllers in off-nominal and/or complex situations.

  18. Automated retinal image quality assessment on the UK Biobank dataset for epidemiological studies.

    PubMed

    Welikala, R A; Fraz, M M; Foster, P J; Whincup, P H; Rudnicka, A R; Owen, C G; Strachan, D P; Barman, S A

    2016-04-01

    Morphological changes in the retinal vascular network are associated with future risk of many systemic and vascular diseases. However, uncertainty over the presence and nature of some of these associations exists. Analysis of data from large population based studies will help to resolve these uncertainties. The QUARTZ (QUantitative Analysis of Retinal vessel Topology and siZe) retinal image analysis system allows automated processing of large numbers of retinal images. However, an image quality assessment module is needed to achieve full automation. In this paper, we propose such an algorithm, which uses the segmented vessel map to determine the suitability of retinal images for use in the creation of vessel morphometric data suitable for epidemiological studies. This includes an effective 3-dimensional feature set and support vector machine classification. A random subset of 800 retinal images from UK Biobank (a large prospective study of 500,000 middle aged adults; where 68,151 underwent retinal imaging) was used to examine the performance of the image quality algorithm. The algorithm achieved a sensitivity of 95.33% and a specificity of 91.13% for the detection of inadequate images. The strong performance of this image quality algorithm will make rapid automated analysis of vascular morphometry feasible on the entire UK Biobank dataset (and other large retinal datasets), with minimal operator involvement, and at low cost.

  19. Laboratory and field testing of an automated atmospheric particle-bound reactive oxygen species sampling-analysis system.

    PubMed

    Wang, Yungang; Hopke, Philip K; Sun, Liping; Chalupa, David C; Utell, Mark J

    2011-01-01

    In this study, various laboratory and field tests were performed to develop an effective automated particle-bound ROS sampling-analysis system. The system uses 2' 7'-dichlorofluorescin (DCFH) fluorescence method as a nonspecific, general indicator of the particle-bound ROS. A sharp-cut cyclone and a particle-into-liquid sampler (PILS) were used to collect PM(2.5) atmospheric particles into slurry produced by a DCFH-HRP solution. The laboratory results show that the DCFH and H(2)O(2) standard solutions could be kept at room temperature for at least three and eight days, respectively. The field test in Rochester, NY, shows that the average ROS concentration was 8.3 ± 2.2 nmol of equivalent H(2)O(2) m(-3) of air. The ROS concentrations were observed to be greater after foggy conditions. This study demonstrates the first practical automated sampling-analysis system to measure this ambient particle component.

  20. Laboratory and Field Testing of an Automated Atmospheric Particle-Bound Reactive Oxygen Species Sampling-Analysis System

    PubMed Central

    Wang, Yungang; Hopke, Philip K.; Sun, Liping; Chalupa, David C.; Utell, Mark J.

    2011-01-01

    In this study, various laboratory and field tests were performed to develop an effective automated particle-bound ROS sampling-analysis system. The system uses 2′ 7′-dichlorofluorescin (DCFH) fluorescence method as a nonspecific, general indicator of the particle-bound ROS. A sharp-cut cyclone and a particle-into-liquid sampler (PILS) were used to collect PM2.5 atmospheric particles into slurry produced by a DCFH-HRP solution. The laboratory results show that the DCFH and H2O2 standard solutions could be kept at room temperature for at least three and eight days, respectively. The field test in Rochester, NY, shows that the average ROS concentration was 8.3 ± 2.2 nmol of equivalent H2O2 m−3 of air. The ROS concentrations were observed to be greater after foggy conditions. This study demonstrates the first practical automated sampling-analysis system to measure this ambient particle component. PMID:21577270

  1. Automated method for simultaneous lead and strontium isotopic analysis applied to rainwater samples and airborne particulate filters (PM10).

    PubMed

    Beltrán, Blanca; Avivar, Jessica; Mola, Montserrat; Ferrer, Laura; Cerdà, Víctor; Leal, Luz O

    2013-09-03

    A new automated, sensitive, and fast system for the simultaneous online isolation and preconcentration of lead and strontium by sorption on a microcolumn packed with Sr-resin using an inductively coupled plasma mass spectrometry (ICP-MS) detector was developed, hyphenating lab-on-valve (LOV) and multisyringe flow injection analysis (MSFIA). Pb and Sr are directly retained on the sorbent column and eluted with a solution of 0.05 mol L(-1) ammonium oxalate. The detection limits achieved were 0.04 ng for lead and 0.03 ng for strontium. Mass calibration curves were used since the proposed system allows the use of different sample volumes for preconcentration. Mass linear working ranges were between 0.13 and 50 ng and 0.1 and 50 ng for lead and strontium, respectively. The repeatability of the method, expressed as RSD, was 2.1% and 2.7% for Pb and Sr, respectively. Environmental samples such as rainwater and airborne particulate (PM10) filters as well as a certified reference material SLRS-4 (river water) were satisfactorily analyzed obtaining recoveries between 90 and 110% for both elements. The main features of the LOV-MSFIA-ICP-MS system proposed are the capability to renew solid phase extraction at will in a fully automated way, the remarkable stability of the column which can be reused up to 160 times, and the potential to perform isotopic analysis.

  2. An automated sample preparation system with mini-reactor to isolate and process submegabase fragments of bacterial DNA.

    PubMed

    Mollova, Emilia T; Patil, Vishal A; Protozanova, Ekaterina; Zhang, Meng; Gilmanshin, Rudolf

    2009-08-15

    Existing methods for extraction and processing of large fragments of bacterial genomic DNA are manual, time-consuming, and prone to variability in DNA quality and recovery. To solve these problems, we have designed and built an automated fluidic system with a mini-reactor. Balancing flows through and tangential to the ultrafiltration membrane in the reactor, cells and then released DNA can be immobilized and subjected to a series of consecutive processing steps. The steps may include enzymatic reactions, tag hybridization, buffer exchange, and selective removal of cell debris and by-products of the reactions. The system can produce long DNA fragments (up to 0.5 Mb) of bacterial genome restriction digest and perform DNA tagging with fluorescent sequence-specific probes. The DNA obtained is of high purity and floating free in solution, and it can be directly analyzed by pulsed-field gel electrophoresis (PFGE) or used in applications requiring submegabase DNA fragments. PFGE-ready samples of DNA restriction digests can be produced in as little as 2.1 h and require less than 10(8) cells. All fluidic operations are automated except for the injection of the sample and reagents.

  3. Development in release testing of topical dosage forms: use of the Enhancer Cell with automated sampling.

    PubMed

    Rege, P R; Vilivalam, V D; Collins, C C

    1998-09-01

    The aim of this study was to evaluate an automated method using the Enhancer Cell and compare the release of the corticosteroid triamcinolone acetonide (TA) from commercial semisolid formulations. The method used a modified USP Apparatus 2 using the Enhancer Cell in 200 ml capacity flasks instead of the standard 900 ml flasks. The additional equipment included an adapter plate to position the flasks in the center, a cover to reduce the receptor phase evaporation and smaller sized (1/4 in.) shaft and collets. All products were evaluated prior to their expiration date. Effects of system variables such as the temperature and composition of the receptor medium, stirring speed, and the choice of membrane on the drug release were evaluated. Statistical analysis was carried out using SAS Ver. 6.07 and the slopes and intercepts (of the cumulative release/unit area versus square root of time plots) were compared. TA release was a linear function of the square root of time (P < or = 0.0001), in accordance with Higuchi's model (r2 > or = 0.9 in most cases). Temperature (32 and 37 degrees C) did not affect the drug release (P > 0.32) but a significantly higher release rate was observed (P < or = 0.0001) at 50 degrees C. Stirring speed (50, 100, 200 rpm) (P > 0.26) and receptor media composition (38 and 76% ethanol) (P > 0.68) did not significantly alter the release rates. Membrane selection (regenerated cellulose, polyethylene, and rat skin) was found to be a significant variable (P < or = 0.004). This study demonstrates the use of the Enhancer Cell as an automated quality control tool in the in vitro release testing procedure for semisolid drug formulations.

  4. Iterative User Interface Design for Automated Sequential Organ Failure Assessment Score Calculator in Sepsis Detection.

    PubMed

    Aakre, Christopher Ansel; Kitson, Jaben E; Li, Man; Herasevich, Vitaly

    2017-05-18

    The new sepsis definition has increased the need for frequent sequential organ failure assessment (SOFA) score recalculation and the clerical burden of information retrieval makes this score ideal for automated calculation. The aim of this study was to (1) estimate the clerical workload of manual SOFA score calculation through a time-motion analysis and (2) describe a user-centered design process for an electronic medical record (EMR) integrated, automated SOFA score calculator with subsequent usability evaluation study. First, we performed a time-motion analysis by recording time-to-task-completion for the manual calculation of 35 baseline and 35 current SOFA scores by 14 internal medicine residents over a 2-month period. Next, we used an agile development process to create a user interface for a previously developed automated SOFA score calculator. The final user interface usability was evaluated by clinician end users with the Computer Systems Usability Questionnaire. The overall mean (standard deviation, SD) time-to-complete manual SOFA score calculation time was 61.6 s (33). Among the 24% (12/50) usability survey respondents, our user-centered user interface design process resulted in >75% favorability of survey items in the domains of system usability, information quality, and interface quality. Early stakeholder engagement in our agile design process resulted in a user interface for an automated SOFA score calculator that reduced clinician workload and met clinicians' needs at the point of care. Emerging interoperable platforms may facilitate dissemination of similarly useful clinical score calculators and decision support algorithms as "apps." A user-centered design process and usability evaluation should be considered during creation of these tools.

  5. An ultrasound automated method for non-invasive assessment of carotid artery pulse wave velocity.

    PubMed

    Zardi, Enrico Maria; Di Geso, Luca; Afeltra, Antonella; Zardi, Domenico Maria; Giorgi, Chiara; Salaffi, Fausto; Carotti, Marina; Gutierrez, Marwin; Filippucci, Emilio; Grassi, Walter

    2017-09-02

    To validate the clinical applicability and feasibility of an automated ultrasound (US) method in measuring the arterial stiffness of patients with chronic inflammatory rheumatic diseases, comparing automated measurements performed by a rheumatologist without experience in vascular sonography with those obtained by a sonographer experienced in vascular US, using a standardized manual method.Twenty subjects affected by different chronic inflammatory rheumatic disorders were consecutively recruited. For each patient, the arterial stiffness of both common carotids was manually calculated. Subsequently, the measure of the pulse wave velocity (PWV) was obtained using an US device called Radio Frequency - Quality Arterial Stiffness (RF-QAS), provided by the same US system (ie, My Lab 70 XVG, Esaote SpA, Genoa, Italy) equipped with a 4-13 MHz linear probe. The reliability comparison between the two US methods was calculated using the intraclass correlation coefficient (ICC). ICC between the values obtained with the two methods for calculating the arterial stiffness resulted 0.789. A significant positive correlation between the two methods was also established with Pearson's (r=0.62, p<0.0001) and Spearman's analysis (r=0.66, p=0.001). A significant performance comparison was seen using Bland-Altman plot. The acquisition of the arterial stiffness parameter with the automated method required about 2 min for each patient. Clinical applicability of this US automated method to assess PWV at common carotid level by a rheumatologist is reliable and feasible in comparison with a conventional manual method. © American Federation for Medical Research (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  6. Automated Assessment of Patients' Self-Narratives for Posttraumatic Stress Disorder Screening Using Natural Language Processing and Text Mining.

    PubMed

    He, Qiwei; Veldkamp, Bernard P; Glas, Cees A W; de Vries, Theo

    2017-03-01

    Patients' narratives about traumatic experiences and symptoms are useful in clinical screening and diagnostic procedures. In this study, we presented an automated assessment system to screen patients for posttraumatic stress disorder via a natural language processing and text-mining approach. Four machine-learning algorithms-including decision tree, naive Bayes, support vector machine, and an alternative classification approach called the product score model-were used in combination with n-gram representation models to identify patterns between verbal features in self-narratives and psychiatric diagnoses. With our sample, the product score model with unigrams attained the highest prediction accuracy when compared with practitioners' diagnoses. The addition of multigrams contributed most to balancing the metrics of sensitivity and specificity. This article also demonstrates that text mining is a promising approach for analyzing patients' self-expression behavior, thus helping clinicians identify potential patients from an early stage.

  7. Automated Ground-Water Sampling and Analysis of Hexavalent Chromium using a “Universal” Sampling/Analytical System

    PubMed Central

    Burge, Scott R.; Hoffman, Dave A.; Hartman, Mary J.; Venedam, Richard J.

    2005-01-01

    The capabilities of a “universal platform” for the deployment of analytical sensors in the field for long-term monitoring of environmental contaminants were expanded in this investigation. The platform was previously used to monitor trichloroethene in monitoring wells and at groundwater treatment systems (1,2). The platform was interfaced with chromium (VI) and conductivity analytical systems to monitor shallow wells installed adjacent to the Columbia River at the 100-D Area of the Hanford Site, Washington. A groundwater plume of hexavalent chromium is discharging into the Columbia River through the gravels beds used by spawning salmon. The sampling/analytical platform was deployed for the purpose of collecting data on subsurface hexavalent chromium concentrations at more frequent intervals than was possible with the previous sampling and analysis methods employed a the Site.

  8. Pharmacokinetic Studies of Chinese Medicinal Herbs Using an Automated Blood Sampling System and Liquid Chromatography-mass Spectrometry

    PubMed Central

    Wu, Yu-Tse; Wu, Ming-Tsang; Lin, Chia-Chun; Chien, Chao-Feng; Tsai, Tung-Hu

    2012-01-01

    The safety of herbal products is one of the major concerns for the modernization of traditional Chinese medicine, and pharmacokinetic data of medicinal herbs guide us to design the rational use of the herbal formula. This article reviews the advantages of the automated blood sampling (ABS) systems for pharmacokinetic studies. In addition, three commonly used sample preparative methods, protein precipitation, liquid-liquid extraction and solid-phase extraction, are introduced. Furthermore, the definition, causes and evaluation of matrix effects in liquid chromatography-mass spectrometry (LC/MS) analysis are demonstrated. Finally, we present our previous works as practical examples of the application of ABS systems and LC/MS for the pharmacokinetic studies of Chinese medicinal herbs. PMID:24716112

  9. Automated essay scoring and the future of educational assessment in medical education.

    PubMed

    Gierl, Mark J; Latifi, Syed; Lai, Hollis; Boulais, André-Philippe; De Champlain, André

    2014-10-01

    Constructed-response tasks, which range from short-answer tests to essay questions, are included in assessments of medical knowledge because they allow educators to measure students' ability to think, reason, solve complex problems, communicate and collaborate through their use of writing. However, constructed-response tasks are also costly to administer and challenging to score because they rely on human raters. One alternative to the manual scoring process is to integrate computer technology with writing assessment. The process of scoring written responses using computer programs is known as 'automated essay scoring' (AES). An AES system uses a computer program that builds a scoring model by extracting linguistic features from a constructed-response prompt that has been pre-scored by human raters and then, using machine learning algorithms, maps the linguistic features to the human scores so that the computer can be used to classify (i.e. score or grade) the responses of a new group of students. The accuracy of the score classification can be evaluated using different measures of agreement. Automated essay scoring provides a method for scoring constructed-response tests that complements the current use of selected-response testing in medical education. The method can serve medical educators by providing the summative scores required for high-stakes testing. It can also serve medical students by providing them with detailed feedback as part of a formative assessment process. Automated essay scoring systems yield scores that consistently agree with those of human raters at a level as high, if not higher, as the level of agreement among human raters themselves. The system offers medical educators many benefits for scoring constructed-response tasks, such as improving the consistency of scoring, reducing the time required for scoring and reporting, minimising the costs of scoring, and providing students with immediate feedback on constructed-response tasks. © 2014

  10. Efficiency of short individualised CPR self-learning sessions with automated assessment and feedback.

    PubMed

    Mpotos, Nicolas; De Wever, Bram; Cleymans, Nick; Raemaekers, Joris; Valcke, Martin; Monsieurs, Koenraad G

    2013-09-01

    Regular assessments are recommended to identify individuals requiring additional resuscitation training. We developed a strategy of short CPR self-learning sessions followed by automated assessment with feedback and investigated its efficiency to achieve a pre-defined level of compression skills. Four hundred and four students in pharmacy and educational sciences participated. Initial training (max. 40 min) consisted of a 15 min learning-while-watching video followed by manikin exercises with computer voice feedback. At baseline and after training, performance was measured using an automated test. To be judged competent participants had to achieve ≥ 70% compressions with depth ≥ 50 mm and ≥ 70% compressions with complete release (<5mm) and a compression rate between 100 and 120 min(-1) within a two month period. Automated feedback was provided and failed participants had to retrain within two weeks. Retraining (max. 20 min and max. three times) was done with voice feedback exercises. Before retraining, the previous test result was displayed together with feedforward. After five months all participants were invited for a retention test. After one to four sessions, 99% (401/404) of all participants achieved competency. After five months 48% (137/288) of the students participating in the retention test was still competent. The percentage competent participants was 80% (230/288) for compression depth, 97% (279/288) for complete release and 60% (172/288) for mean rate. One or multiple short self-learning sessions were highly efficient to successfully train 99% of participants. After five months, retention of compression depth and complete release was very high. However, only 48% still achieved a 70% combined score for compression skills, highlighting the importance of regular assessment and retraining. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  11. Fully automated determination of cannabinoids in hair samples using headspace solid-phase microextraction and gas chromatography-mass spectrometry.

    PubMed

    Musshoff, Frank; Junker, Heike P; Lachenmeier, Dirk W; Kroener, Lars; Madea, Burkhard

    2002-01-01

    This paper describes a fully automated procedure using alkaline hydrolysis and headspace solid-phase microextraction (HS-SPME) followed by on-fiber derivatization and gas chromatographic-mass spectrometric (GC-MS) detection of cannabinoids in human hair samples. Ten milligrams of hair was washed with deionized water, petroleum ether, and dichloromethane. After the addition of deuterated internal standards the sample was hydrolyzed with sodium hydroxide and directly submitted to HS-SPME. After absorption of analytes for an on-fiber derivatization procedure the fiber was directly placed into the headspace of a second vial containing N-methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) before GC-MS analysis. The limit of detection was 0.05 ng/mg for delta9-tetrahydrocannabinol (THC), 0.08 ng/mg for cannabidiol (CBD), and 0.14 ng/mg for cannabinol (CBN). Absolute recoveries were in the range between 0.3 and 7.5%. Linearity was proved over a range from 0.1 to 20 ng/mg with coefficients of correlation from 0.998 to 0.999. Validation of the whole procedure revealed excellent results. In comparison with conventional methods of hair analysis this automated HS-SPME-GC-MS procedure is substantially faster. It is easy to perform without use of solvents and with minimal sample quantities, but with the same degree of sensitivity and reproducibility. The applicability was demonstrated by the analysis of 25 hair samples from several forensic cases. The following concentration ranges were determined: THC 0.29-2.20 (mean 1.7) ng/mg, CBN 0.55-4.54 (mean 1.2) ng/mg, and CBD 0.53-18.36 (mean 1.3) ng/mg. 11-nor-Delta9-tetrahydrocannabinol-9-carboxylic acid could not be detected with this method.

  12. Extending laboratory automation to the wards: effect of an innovative pneumatic tube system on diagnostic samples and transport time.

    PubMed

    Suchsland, Juliane; Winter, Theresa; Greiser, Anne; Streichert, Thomas; Otto, Benjamin; Mayerle, Julia; Runge, Sören; Kallner, Anders; Nauck, Matthias; Petersmann, Astrid

    2017-02-01

    The innovative pneumatic tube system (iPTS) transports one sample at a time without the use of cartridges and allows rapid sending of samples directly into the bulk loader of a laboratory automation system (LAS). We investigated effects of the iPTS on samples and turn-around time (TAT). During transport, a mini data logger recorded the accelerations in three dimensions and reported them in arbitrary area under the curve (AUC) units. In addition representative quantities of clinical chemistry, hematology and coagulation were measured and compared in 20 blood sample pairs transported by iPTS and courier. Samples transported by iPTS were brought to the laboratory (300 m) within 30 s without adverse effects on the samples. The information retrieved from the data logger showed a median AUC of 7 and 310 arbitrary units for courier and iPTS transport, respectively. This is considerably below the reported limit for noticeable hemolysis of 500 arbitrary units. iPTS reduces TAT by reducing the hands-on time and a fast transport. No differences in the measurement results were found for any of the investigated 36 analytes between courier and iPTS transport. Based on these findings the iPTS was cleared for clinical use in our hospital.

  13. IntelliCages and automated assessment of learning in group-housed mice

    NASA Astrophysics Data System (ADS)

    Puścian, Alicja; Knapska, Ewelina

    2014-11-01

    IntelliCage is a fully automated, computer controlled system, which can be used for long-term monitoring of behavior of group-housed mice. Using standardized experimental protocols we can assess cognitive abilities and behavioral flexibility in appetitively and aversively motivated tasks, as well as measure social influences on learning of the subjects. We have also identified groups of neurons specifically activated by appetitively and aversively motivated learning within the amygdala, function of which we are going to investigate optogenetically in the future.

  14. Automated assessment of noninvasive filling pressure using color Doppler M-mode echocardiography

    NASA Technical Reports Server (NTRS)

    Greenberg, N. L.; Firstenberg, M. S.; Cardon, L. A.; Zuckerman, J.; Levine, B. D.; Garcia, M. J.; Thomas, J. D.

    2001-01-01

    Assessment of left ventricular filling pressure usually requires invasive hemodynamic monitoring to follow the progression of disease or the response to therapy. Previous investigations have shown accurate estimation of wedge pressure using noninvasive Doppler information obtained from the ratio of the wave propagation slope from color M-mode (CMM) images and the peak early diastolic filling velocity from transmitral Doppler images. This study reports an automated algorithm that derives an estimate of wedge pressure based on the spatiotemporal velocity distribution available from digital CMM Doppler images of LV filling.

  15. Deep learning for automated skeletal bone age assessment in X-ray images.

    PubMed

    Spampinato, C; Palazzo, S; Giordano, D; Aldinucci, M; Leonardi, R

    2017-02-01

    Skeletal bone age assessment is a common clinical practice to investigate endocrinology, genetic and growth disorders in children. It is generally performed by radiological examination of the left hand by using either the Greulich and Pyle (G&P) method or the Tanner-Whitehouse (TW) one. However, both clinical procedures show several limitations, from the examination effort of radiologists to (most importantly) significant intra- and inter-operator variability. To address these problems, several automated approaches (especially relying on the TW method) have been proposed; nevertheless, none of them has been proved able to generalize to different races, age ranges and genders. In this paper, we propose and test several deep learning approaches to assess skeletal bone age automatically; the results showed an average discrepancy between manual and automatic evaluation of about 0.8 years, which is state-of-the-art performance. Furthermore, this is the first automated skeletal bone age assessment work tested on a public dataset and for all age ranges, races and genders, for which the source code is available, thus representing an exhaustive baseline for future research in the field. Beside the specific application scenario, this paper aims at providing answers to more general questions about deep learning on medical images: from the comparison between deep-learned features and manually-crafted ones, to the usage of deep-learning methods trained on general imagery for medical problems, to how to train a CNN with few images.

  16. In vivo assessment of human burn scars through automated quantification of vascularity using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Liew, Yih Miin; McLaughlin, Robert A.; Gong, Peijun; Wood, Fiona M.; Sampson, David D.

    2013-06-01

    In scars arising from burns, objective assessment of vascularity is important in the early identification of pathological scarring, and in the assessment of progression and treatment response. We demonstrate the first clinical assessment and automated quantification of vascularity in cutaneous burn scars of human patients in vivo that uses optical coherence tomography (OCT). Scar microvasculature was delineated in three-dimensional OCT images using speckle decorrelation. The diameter and area density of blood vessels were automatically quantified. A substantial increase was observed in the measured density of vasculature in hypertrophic scar tissues (38%) when compared against normal, unscarred skin (22%). A proliferation of larger vessels (diameter≥100 μm) was revealed in hypertrophic scarring, which was absent from normal scars and normal skin over the investigated physical depth range of 600 μm. This study establishes the feasibility of this methodology as a means of clinical monitoring of scar progression.

  17. Automated sample preparation for monitoring groundwater pollution by carbamate insecticides and their transformation products.

    PubMed

    Chiron, S; Valverde, A; Fernandez-Alba, A; Barceló, D

    1995-01-01

    We investigated automated on-line solid-phase extraction (SPE) followed by liquid chromatographic (LC) techniques for monitoring carbamates and their transformation products. Analytical determinations were performed by LC with UV or postcolumn fluorescence detection (U.S. Environmental Protection Agency Method 531.1 for carbamate insecticides) after preconcentration with on-line SPE using C18 Empore extraction disks. On-line SPE/LC/thermospray mass spectrometry with time-scheduled selected-ion monitoring was used as confirmatory method. The method was used to determine pesticide traces in well waters of a typical aquifer in the Almeria area (Andalucia, south of Spain) from March 1993 to February 1994. The major pollutants, found in highest amounts, were carbofuran, methiocarb, and methomyl, at levels of 0.32, 0.3, and 0.8 micrograms/L, respectively. According to results of seasonal variation studies, pollution by carbamate insecticides is sporadic and exceeds the limit of 0.5 micrograms/L for total pesticides allowed by the European Economic Community Drinking Water Directive only twice a year. 3-Hydroxycarbofuran and methiocarb sulfone also were detected, showing the importance of including the main toxic break-down products of carbamate insecticides in future monitoring programs.

  18. Rapid and automated sample preparation for nucleic acid extraction on a microfluidic CD (compact disk)

    NASA Astrophysics Data System (ADS)

    Kim, Jitae; Kido, Horacio; Zoval, Jim V.; Gagné, Dominic; Peytavi, Régis; Picard, François J.; Bastien, Martine; Boissinot, Maurice; Bergeron, Michel G.; Madou, Marc J.

    2006-01-01

    Rapid and automated preparation of PCR (polymerase chain reaction)-ready genomic DNA was demonstrated on a multiplexed CD (compact disk) platform by using hard-to-lyse bacterial spores. Cell disruption is carried out while beadcell suspensions are pushed back and forth in center-tapered lysing chambers by angular oscillation of the disk - keystone effect. During this lysis period, the cell suspensions are securely held within the lysing chambers by heatactivated wax valves. Upon application of a remote heat to the disk in motion, the wax valves release lysate solutions into centrifuge chambers where cell debris are separated by an elevated rotation of the disk. Only debris-free DNA extract is then transferred to collection chambers by capillary-assisted siphon and collected for heating that inactivates PCR inhibitors. Lysing capacity was evaluated using a real-time PCR assay to monitor the efficiency of Bacillus globigii spore lysis. PCR analysis showed that 5 minutes' CD lysis run gave spore lysis efficiency similar to that obtained with a popular commercial DNA extraction kit (i.e., IDI-lysis kit from GeneOhm Sciences Inc.) which is highly efficient for microbial cell and spore lysis. This work will contribute to the development of an integrated CD-based assay for rapid diagnosis of infectious diseases.

  19. Solid recovered fuels in the cement industry--semi-automated sample preparation unit as a means for facilitated practical application.

    PubMed

    Aldrian, Alexia; Sarc, Renato; Pomberger, Roland; Lorber, Karl E; Sipple, Ernst-Michael

    2016-03-01

    One of the challenges for the cement industry is the quality assurance of alternative fuel (e.g., solid recovered fuel, SRF) in co-incineration plants--especially for inhomogeneous alternative fuels with large particle sizes (d95⩾100 mm), which will gain even more importance in the substitution of conventional fuels due to low production costs. Existing standards for sampling and sample preparation do not cover the challenges resulting from these kinds of materials. A possible approach to ensure quality monitoring is shown in the present contribution. For this, a specially manufactured, automated comminution and sample divider device was installed at a cement plant in Rohožnik. In order to prove its practical suitability with methods according to current standards, the sampling and sample preparation process were validated for alternative fuel with a grain size >30 mm (i.e., d95=approximately 100 mm), so-called 'Hotdisc SRF'. Therefore, series of samples were taken and analysed. A comparison of the analysis results with the yearly average values obtained through a reference investigation route showed good accordance. Further investigations during the validation process also showed that segregation or enrichment of material throughout the comminution plant does not occur. The results also demonstrate that compliance with legal standards regarding the minimum sample amount is not sufficient for inhomogeneous and coarse particle size alternative fuels. Instead, higher sample amounts after the first particle size reduction step are strongly recommended in order to gain a representative laboratory sample.

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

    NASA Astrophysics Data System (ADS)

    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

  1. Assessment for Operator Confidence in Automated Space Situational Awareness and Satellite Control Systems

    NASA Astrophysics Data System (ADS)

    Gorman, J.; Voshell, M.; Sliva, A.

    2016-09-01

    The United States is highly dependent on space resources to support military, government, commercial, and research activities. Satellites operate at great distances, observation capacity is limited, and operator actions and observations can be significantly delayed. Safe operations require support systems that provide situational understanding, enhance decision making, and facilitate collaboration between human operators and system automation both in-the-loop, and on-the-loop. Joint cognitive systems engineering (JCSE) provides a rich set of methods for analyzing and informing the design of complex systems that include both human decision-makers and autonomous elements as coordinating teammates. While, JCSE-based systems can enhance a system analysts' understanding of both existing and new system processes, JCSE activities typically occur outside of traditional systems engineering (SE) methods, providing sparse guidance about how systems should be implemented. In contrast, the Joint Director's Laboratory (JDL) information fusion model and extensions, such as the Dual Node Network (DNN) technical architecture, provide the means to divide and conquer such engineering and implementation complexity, but are loosely coupled to specialized organizational contexts and needs. We previously describe how Dual Node Decision Wheels (DNDW) extend the DNN to integrate JCSE analysis and design with the practicalities of system engineering and implementation using the DNN. Insights from Rasmussen's JCSE Decision Ladders align system implementation with organizational structures and processes. In the current work, we present a novel approach to assessing system performance based on patterns occurring in operational decisions that are documented by JCSE processes as traces in a decision ladder. In this way, system assessment is closely tied not just to system design, but the design of the joint cognitive system that includes human operators, decision-makers, information systems, and

  2. An Automated Quiet Sleep Detection Approach in Preterm Infants as a Gateway to Assess Brain Maturation.

    PubMed

    Dereymaeker, Anneleen; Pillay, Kirubin; Vervisch, Jan; Van Huffel, Sabine; Naulaers, Gunnar; Jansen, Katrien; De Vos, Maarten

    2017-09-01

    Sleep state development in preterm neonates can provide crucial information regarding functional brain maturation and give insight into neurological well being. However, visual labeling of sleep stages from EEG requires expertise and is very time consuming, prompting the need for an automated procedure. We present a robust method for automated detection of preterm sleep from EEG, over a wide postmenstrual age ([Formula: see text] age) range, focusing first on Quiet Sleep (QS) as an initial marker for sleep assessment. Our algorithm, CLuster-based Adaptive Sleep Staging (CLASS), detects QS if it remains relatively more discontinuous than non-QS over PMA. CLASS was optimized on a training set of 34 recordings aged 27-42 weeks PMA, and performance then assessed on a distinct test set of 55 recordings of the same age range. Results were compared to visual QS labeling from two independent raters (with inter-rater agreement [Formula: see text]), using Sensitivity, Specificity, Detection Factor ([Formula: see text] of visual QS periods correctly detected by CLASS) and Misclassification Factor ([Formula: see text] of CLASS-detected QS periods that are misclassified). CLASS performance proved optimal across recordings at 31-38 weeks (median [Formula: see text], median MF 0-0.25, median Sensitivity 0.93-1.0, and median Specificity 0.80-0.91 across this age range), with minimal misclassifications at 35-36 weeks (median [Formula: see text]). To illustrate the potential of CLASS in facilitating clinical research, normal maturational trends over PMA were derived from CLASS-estimated QS periods, visual QS estimates, and nonstate specific periods (containing QS and non-QS) in the EEG recording. CLASS QS trends agreed with those from visual QS, with both showing stronger correlations than nonstate specific trends. This highlights the benefit of automated QS detection for exploring brain maturation.

  3. Revisiting the Hubble sequence in the SDSS DR7 spectroscopic sample: a publicly available Bayesian automated classification

    NASA Astrophysics Data System (ADS)

    Huertas-Company, M.; Aguerri, J. A. L.; Bernardi, M.; Mei, S.; Sánchez Almeida, J.

    2011-01-01

    We present an automated morphological classification in 4 types (E, S0, Sab, Scd) of ~700 000 galaxies from the SDSS DR7 spectroscopic sample based on support vector machines. The main new property of the classification is that we associate a probability to each galaxy of being in the four morphological classes instead of assigning a single class. The classification is therefore better adapted to nature where we expect a continuous transition between different morphological types. The algorithm is trained with a visual classification and then compared to several independent visual classifications including the Galaxy Zoo first-release catalog. We find a very good correlation between the automated classification and classical visual ones. The compiled catalog is intended for use in different applications and is therefore freely available through a dedicated webpage* and soon from the CasJobs database. Full catalog is only available in electronic form at CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/525/A157 or via http://gepicom04.obspm.fr/sdss_morphology/Morphology_2010.html

  4. A novel high-throughput automated chip-based nanoelectrospray tandem mass spectrometric method for PAMPA sample analysis.

    PubMed

    Balimane, Praveen V; Pace, Ellen; Chong, Saeho; Zhu, Mingshe; Jemal, Mohammed; Pelt, Colleen K Van

    2005-09-01

    Parallel artificial membrane permeability assay (PAMPA) has recently gained popularity as a novel, high-throughput assay capable of rapidly screening compounds for their permeability characteristics in early drug discovery. The analytical techniques typically used for PAMPA sample analysis are HPLC-UV, LC/MS or more recently UV-plate reader. The LC techniques, though sturdy and accurate, are often labor and time intensive and are not ideal for high-throughput. On the other hand, UV-plate reader technique is amenable to high-throughput but is not sensitive enough to detect the lower concentrations that are often encountered in early drug discovery work. This article investigates a novel analytical method, a chip-based automated nanoelectrospray mass spectrometric method for its ability to rapidly analyze PAMPA permeability samples. The utility and advantages of this novel analytical method is demonstrated by comparing PAMPA permeability values obtained from nanoelectrospray to those from conventional analytical methods. Ten marketed drugs having a broad range of structural space, physico-chemical properties and extent of intestinal absorption were selected as test compounds for this investigation. PAMPA permeability and recovery experiments were conducted with model compounds followed by analysis by UV-plate reader, UV-HPLC as well as the automated nanoelectrospray technique (nanoESI-MS/MS). There was a very good correlation (r(2) > 0.9) between the results obtained using nanoelectrospray and the other analytical techniques tested. Moreover, the nanoelectrospray approach presented several advantages over the standard techniques such as higher sensitivity and ability to detect individual compounds in cassette studies, making it an attractive high-throughput analytical technique. Thus, it has been demonstrated that nanoelectrospray analysis provides a highly efficient and accurate analytical methodology to analyze PAMPA samples generated in early drug discovery.

  5. Automated radioanalytical system incorporating microwave-assisted sample preparation, chemical separation, and online radiometric detection for the monitoring of total 99Tc in nuclear waste processing streams.

    PubMed

    Egorov, Oleg B; O'Hara, Matthew J; Grate, Jay W

    2012-04-03

    An automated fluidic instrument is described that rapidly determines the total (99)Tc content of aged nuclear waste samples, where the matrix is chemically and radiologically complex and the existing speciation of the (99)Tc is variable. The monitor links microwave-assisted sample preparation with an automated anion exchange column separation and detection using a flow-through solid scintillator detector. The sample preparation steps acidify the sample, decompose organics, and convert all Tc species to the pertechnetate anion. The column-based anion exchange procedure separates the pertechnetate from the complex sample matrix, so that radiometric detection can provide accurate measurement of (99)Tc. We developed a preprogrammed spike addition procedure to automatically determine matrix-matched calibration. The overall measurement efficiency that is determined simultaneously provides a self-diagnostic parameter for the radiochemical separation and overall instrument function. Continuous, automated operation was demonstrated over the course of 54 h, which resulted in the analysis of 215 samples plus 54 hly spike-addition samples, with consistent overall measurement efficiency for the operation of the monitor. A sample can be processed and measured automatically in just 12.5 min with a detection limit of 23.5 Bq/mL of (99)Tc in low activity waste (0.495 mL sample volume), with better than 10% RSD precision at concentrations above the quantification limit. This rapid automated analysis method was developed to support nuclear waste processing operations planned for the Hanford nuclear site.

  6. ALVEOLAR BREATH SAMPLING AND ANALYSIS IN HUMAN EXPOSURE ASSESSMENT STUDIES

    EPA Science Inventory

    Alveolar breath sampling and analysis can be extremely useful in exposure assessment studies involving volatile organic compounds (VOCs). Over recent years scientists from the EPA's National Exposure Research Laboratory have developed and refined an alveolar breath collection ...

  7. ALVEOLAR BREATH SAMPLING AND ANALYSIS IN HUMAN EXPOSURE ASSESSMENT STUDIES

    EPA Science Inventory

    Alveolar breath sampling and analysis can be extremely useful in exposure assessment studies involving volatile organic compounds (VOCs). Over recent years scientists from the EPA's National Exposure Research Laboratory have developed and refined an alveolar breath collection ...

  8. Determination of selenium in marine biological tissues by transverse heated electrothermal atomic absorption spectrometry with longitudinal Zeeman background correction and automated ultrasonic slurry sampling.

    PubMed

    Méndez, H; Alava, F; Lavilla, I; Bendicho, C

    2001-01-01

    A fast, sensitive, and reliable method for determination of selenium in marine biological tissues by electrothermal atomic absorption spectrometry with slurry sampling was developed. Slurries were prepared from fresh and frozen seafood samples that were previously homogenized, dried, and ground; particle sizes <100 microm were taken for analysis. A 3% (v/v) HNO3 solution containing 0.01% (v/v) Triton X-100 was used as slurry diluent. Slurries were mixed on an automated ultrasonic slurry sampler at 20% amplitude for 30 s just before an aliquot was injected into the furnace. The method was successfully validated against the following certified reference materials: NRCC CRM DORM-2 (Dogfish muscle); NRCC CRM TORT-2 (Lobster hepatopancreas); NRCC CRM DOLT-2 (Dogfish liver); and BCR CRM 278 (Mussel tissue), and was subsequently applied to determination of Se in 10 marine biological samples. The influences of the drying procedure (oven-, microwave-, and freeze-drying), matrix modifier amount, mass of solid material in cup, and pipetting sequence are discussed. The limit of determination of Se was 0.16 microg/g and the repeatability, estimated as between-batch precision, was in the range of 4-8%. Se contents in the samples ranged from 0.6 to 2.8 microg/g. The proposed method should be useful for fast assessment of the daily dietary intake of Se.

  9. Sequential sampling: a novel method in farm animal welfare assessment.

    PubMed

    Heath, C A E; Main, D C J; Mullan, S; Haskell, M J; Browne, W J

    2016-02-01

    Lameness in dairy cows is an important welfare issue. As part of a welfare assessment, herd level lameness prevalence can be estimated from scoring a sample of animals, where higher levels of accuracy are associated with larger sample sizes. As the financial cost is related to the number of cows sampled, smaller samples are preferred. Sequential sampling schemes have been used for informing decision making in clinical trials. Sequential sampling involves taking samples in stages, where sampling can stop early depending on the estimated lameness prevalence. When welfare assessment is used for a pass/fail decision, a similar approach could be applied to reduce the overall sample size. The sampling schemes proposed here apply the principles of sequential sampling within a diagnostic testing framework. This study develops three sequential sampling schemes of increasing complexity to classify 80 fully assessed UK dairy farms, each with known lameness prevalence. Using the Welfare Quality herd-size-based sampling scheme, the first 'basic' scheme involves two sampling events. At the first sampling event half the Welfare Quality sample size is drawn, and then depending on the outcome, sampling either stops or is continued and the same number of animals is sampled again. In the second 'cautious' scheme, an adaptation is made to ensure that correctly classifying a farm as 'bad' is done with greater certainty. The third scheme is the only scheme to go beyond lameness as a binary measure and investigates the potential for increasing accuracy by incorporating the number of severely lame cows into the decision. The three schemes are evaluated with respect to accuracy and average sample size by running 100 000 simulations for each scheme, and a comparison is made with the fixed size Welfare Quality herd-size-based sampling scheme. All three schemes performed almost as well as the fixed size scheme but with much smaller average sample sizes. For the third scheme, an overall

  10. An automated thermophoretic soot sampling device for laboratory-scale high-pressure flames.

    PubMed

    Leschowski, M; Dreier, T; Schulz, C

    2014-04-01

    Studying soot particle morphology in high-pressure flames via thermophoretic sampling critically depends on sampling precision, speed, and reproducibility. This is mainly limited by the challenges of applying pneumatically driven devices for burner chamber pressures higher than the pneumatic pressure. We present a pneumatically driven device for high-pressure applications up to 90 bars. The novelty is to separate the pneumatic driver section from the high-pressure environment in the burner chamber. The device was tested by sampling soot from a laminar high-pressure flame at 20 bars.

  11. Use of automated monitoring to assess behavioral toxicology in fish: Linking behavior and physiology

    USGS Publications Warehouse

    Brewer, S.K.; DeLonay, A.J.; Beauvais, S.L.; Little, E.E.; Jones, S.B.

    1999-01-01

    We measured locomotory behaviors (distance traveled, speed, tortuosity of path, and rate of change in direction) with computer-assisted analysis in 30 day posthatch rainbow trout (Oncorhynchus mykiss) exposed to pesticides. We also examined cholinesterase inhibition as a potential endpoint linking physiology and behavior. Sublethal exposure to chemicals often causes changes in swimming behavior, reflecting alterations in sensory and motor systems. Swimming behavior also integrates functions of the nervous system. Rarely are the connections between physiology and behavior made. Although behavior is often suggested as a sensitive, early indicator of toxicity, behavioral toxicology has not been used to its full potential because conventional methods of behavioral assessment have relied on manual techniques, which are often time-consuming and difficult to quantify. This has severely limited the application and utility of behavioral procedures. Swimming behavior is particularly amenable to computerized assessment and automated monitoring. Locomotory responses are sensitive to toxicants and can be easily measured. We briefly discuss the use of behavior in toxicology and automated techniques used in behavioral toxicology. We also describe the system we used to determine locomotory behaviors of fish, and present data demonstrating the system's effectiveness in measuring alterations in response to chemical challenges. Lastly, we correlate behavioral and physiological endpoints.

  12. Automated Algorithm for J-Tpeak and Tpeak-Tend Assessment of Drug-Induced Proarrhythmia Risk

    SciTech Connect

    Johannesen, Lars; Vicente, Jose; Hosseini, Meisam; Strauss, David G.

    2016-12-30

    Prolongation of the heart rate corrected QT (QTc) interval is a sensitive marker of torsade de pointes risk; however it is not specific as QTc prolonging drugs that block inward currents are often not associated with torsade. Recent work demonstrated that separate analysis of the heart rate corrected J-Tpeakc (J-Tpeakc) and Tpeak-Tend intervals can identify QTc prolonging drugs with inward current block and is being proposed as a part of a new cardiac safety paradigm for new drugs (the “CiPA” initiative). In this work, we describe an automated measurement methodology for assessment of the J-Tpeakc and Tpeak-Tend intervals using the vector magnitude lead. The automated measurement methodology was developed using data from one clinical trial and was evaluated using independent data from a second clinical trial. Comparison between the automated and the prior semi-automated measurements shows that the automated algorithm reproduces the semi-automated measurements with a mean difference of single-deltas <1 ms and no difference in intra-time point variability (p for all > 0.39). In addition, the time-profile of the baseline and placebo-adjusted changes are within 1 ms for 63% of the time-points (86% within 2 ms). Importantly, the automated results lead to the same conclusions about the electrophysiological mechanisms of the studied drugs. We have developed an automated algorithm for assessment of J-Tpeakc and Tpeak-Tend intervals that can be applied in clinical drug trials. Under the CiPA initiative this ECG assessment would determine if there are unexpected ion channel effects in humans compared to preclinical studies. In conclusion, the algorithm is being released as open-source software.

  13. Automated Algorithm for J-Tpeak and Tpeak-Tend Assessment of Drug-Induced Proarrhythmia Risk

    DOE PAGES

    Johannesen, Lars; Vicente, Jose; Hosseini, Meisam; ...

    2016-12-30

    Prolongation of the heart rate corrected QT (QTc) interval is a sensitive marker of torsade de pointes risk; however it is not specific as QTc prolonging drugs that block inward currents are often not associated with torsade. Recent work demonstrated that separate analysis of the heart rate corrected J-Tpeakc (J-Tpeakc) and Tpeak-Tend intervals can identify QTc prolonging drugs with inward current block and is being proposed as a part of a new cardiac safety paradigm for new drugs (the “CiPA” initiative). In this work, we describe an automated measurement methodology for assessment of the J-Tpeakc and Tpeak-Tend intervals using themore » vector magnitude lead. The automated measurement methodology was developed using data from one clinical trial and was evaluated using independent data from a second clinical trial. Comparison between the automated and the prior semi-automated measurements shows that the automated algorithm reproduces the semi-automated measurements with a mean difference of single-deltas <1 ms and no difference in intra-time point variability (p for all > 0.39). In addition, the time-profile of the baseline and placebo-adjusted changes are within 1 ms for 63% of the time-points (86% within 2 ms). Importantly, the automated results lead to the same conclusions about the electrophysiological mechanisms of the studied drugs. We have developed an automated algorithm for assessment of J-Tpeakc and Tpeak-Tend intervals that can be applied in clinical drug trials. Under the CiPA initiative this ECG assessment would determine if there are unexpected ion channel effects in humans compared to preclinical studies. In conclusion, the algorithm is being released as open-source software.« less

  14. Automated Algorithm for J-Tpeak and Tpeak-Tend Assessment of Drug-Induced Proarrhythmia Risk

    PubMed Central

    Johannesen, Lars; Vicente, Jose; Hosseini, Meisam; Strauss, David G.

    2016-01-01

    Background Prolongation of the heart rate corrected QT (QTc) interval is a sensitive marker of torsade de pointes risk; however it is not specific as QTc prolonging drugs that block inward currents are often not associated with torsade. Recent work demonstrated that separate analysis of the heart rate corrected J-Tpeakc (J-Tpeakc) and Tpeak-Tend intervals can identify QTc prolonging drugs with inward current block and is being proposed as a part of a new cardiac safety paradigm for new drugs (the “CiPA” initiative). Methods In this work, we describe an automated measurement methodology for assessment of the J-Tpeakc and Tpeak-Tend intervals using the vector magnitude lead. The automated measurement methodology was developed using data from one clinical trial and was evaluated using independent data from a second clinical trial. Results Comparison between the automated and the prior semi-automated measurements shows that the automated algorithm reproduces the semi-automated measurements with a mean difference of single-deltas <1 ms and no difference in intra-time point variability (p for all > 0.39). In addition, the time-profile of the baseline and placebo-adjusted changes are within 1 ms for 63% of the time-points (86% within 2 ms). Importantly, the automated results lead to the same conclusions about the electrophysiological mechanisms of the studied drugs. Conclusions We have developed an automated algorithm for assessment of J-Tpeakc and Tpeak-Tend intervals that can be applied in clinical drug trials. Under the CiPA initiative this ECG assessment would determine if there are unexpected ion channel effects in humans compared to preclinical studies. The algorithm is being released as open-source software. Trial Registration NCT02308748 and NCT01873950 PMID:28036330

  15. An automated gas exchange tank for determining gas transfer velocities in natural seawater samples

    NASA Astrophysics Data System (ADS)

    Schneider-Zapp, K.; Salter, M. E.; Upstill-Goddard, R. C.

    2014-02-01

    In order to advance understanding of the role of seawater surfactants in the air-sea exchange of climatically active trace gases via suppression of the gas transfer velocity (kw), we constructed a fully automated, closed air-water gas exchange tank and coupled analytical system. The system allows water-side turbulence in the tank to be precisely controlled with an electronically operated baffle. Two coupled gas chromatographs and an integral equilibrator, connected to the tank in a continuous gas-tight system, allow temporal changes in the partial pressures of SF6, CH4 and N2O to be measured simultaneously in the tank water and headspace at multiple turbulence settings, during a typical experimental run of 3.25 h. PC software developed by the authors controls all operations and data acquisition, enabling the optimisation of experimental conditions with high reproducibility. The use of three gases allows three independent estimates of kw for each turbulence setting; these values are subsequently normalised to a constant Schmidt number for direct comparison. The normalised kw estimates show close agreement. Repeated experiments with MilliQ water demonstrate a typical measurement accuracy of 4% for kw. Experiments with natural seawater show that the system clearly resolves the effects on kw of spatial and temporal trends in natural surfactant activity. The system is an effective tool with which to probe the relationships between kw, surfactant activity and biogeochemical indices of primary productivity, and should assist in providing valuable new insights into the air-sea gas exchange process.

  16. An automated gas exchange tank for determining gas transfer velocities in natural seawater samples

    NASA Astrophysics Data System (ADS)

    Schneider-Zapp, K.; Salter, M. E.; Upstill-Goddard, R. C.

    2014-07-01

    In order to advance understanding of the role of seawater surfactants in the air-sea exchange of climatically active trace gases via suppression of the gas transfer velocity (kw), we constructed a fully automated, closed air-water gas exchange tank and coupled analytical system. The system allows water-side turbulence in the tank to be precisely controlled with an electronically operated baffle. Two coupled gas chromatographs and an integral equilibrator, connected to the tank in a continuous gas-tight system, allow temporal changes in the partial pressures of SF6, CH4 and N2O to be measured simultaneously in the tank water and headspace at multiple turbulence settings, during a typical experimental run of 3.25 h. PC software developed by the authors controls all operations and data acquisition, enabling the optimisation of experimental conditions with high reproducibility. The use of three gases allows three independent estimates of kw for each turbulence setting; these values are subsequently normalised to a constant Schmidt number for direct comparison. The normalised kw estimates show close agreement. Repeated experiments with Milli-Q water demonstrate a typical measurement accuracy of 4% for kw. Experiments with natural seawater show that the system clearly resolves the effects on kw of spatial and temporal trends in natural surfactant activity. The system is an effective tool with which to probe the relationships between kw, surfactant activity and biogeochemical indices of primary productivity, and should assist in providing valuable new insights into the air-sea gas exchange process.

  17. Accelerated Evaluation of Automated Vehicles Safety in Lane-Change Scenarios Based on Importance Sampling Techniques

    PubMed Central

    Zhao, Ding; Lam, Henry; Peng, Huei; Bao, Shan; LeBlanc, David J.; Nobukawa, Kazutoshi; Pan, Christopher S.

    2016-01-01

    Automated vehicles (AVs) must be thoroughly evaluated before their release and deployment. A widely used evaluation approach is the Naturalistic-Field Operational Test (N-FOT), which tests prototype vehicles directly on the public roads. Due to the low exposure to safety-critical scenarios, N-FOTs are time consuming and expensive to conduct. In this paper, we propose an accelerated evaluation approach for AVs. The results can be used to generate motions of the other primary vehicles to accelerate the verification of AVs in simulations and controlled experiments. Frontal collision due to unsafe cut-ins is the target crash type of this paper. Human-controlled vehicles making unsafe lane changes are modeled as the primary disturbance to AVs based on data collected by the University of Michigan Safety Pilot Model Deployment Program. The cut-in scenarios are generated based on skewed statistics of collected human driver behaviors, which generate risky testing scenarios while preserving the statistical information so that the safety benefits of AVs in nonaccelerated cases can be accurately estimated. The cross-entropy method is used to recursively search for the optimal skewing parameters. The frequencies of the occurrences of conflicts, crashes, and injuries are estimated for a modeled AV, and the achieved accelerated rate is around 2000 to 20 000. In other words, in the accelerated simulations, driving for 1000 miles will expose the AV with challenging scenarios that will take about 2 to 20 million miles of real-world driving to encounter. This technique thus has the potential to greatly reduce the development and validation time for AVs. PMID:27840592

  18. An automated laboratory-scale methodology for the generation of sheared mammalian cell culture samples.

    PubMed

    Joseph, Adrian; Goldrick, Stephen; Mollet, Michael; Turner, Richard; Bender, Jean; Gruber, David; Farid, Suzanne S; Titchener-Hooker, Nigel

    2017-05-01

    Continuous disk-stack centrifugation is typically used for the removal of cells and cellular debris from mammalian cell culture broths at manufacturing-scale. The use of scale-down methods to characterise disk-stack centrifugation performance enables substantial reductions in material requirements and allows a much wider design space to be tested than is currently possible at pilot-scale. The process of scaling down centrifugation has historically been challenging due to the difficulties in mimicking the Energy Dissipation Rates (EDRs) in typical machines. This paper describes an alternative and easy-to-assemble automated capillary-based methodology to generate levels of EDRs consistent with those found in a continuous disk-stack centrifuge. Variations in EDR were achieved through changes in capillary internal diameter and the flow rate of operation through the capillary. The EDRs found to match the levels of shear in the feed zone of a pilot-scale centrifuge using the experimental method developed in this paper (2.4×10(5) W/Kg) are consistent with those obtained through previously published computational fluid dynamic (CFD) studies (2.0×10(5) W/Kg). Furthermore, this methodology can be incorporated into existing scale-down methods to model the process performance of continuous disk-stack centrifuges. This was demonstrated through the characterisation of culture hold time, culture temperature and EDRs on centrate quality. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Accelerated Evaluation of Automated Vehicles Safety in Lane-Change Scenarios Based on Importance Sampling Techniques.

    PubMed

    Zhao, Ding; Lam, Henry; Peng, Huei; Bao, Shan; LeBlanc, David J; Nobukawa, Kazutoshi; Pan, Christopher S

    2016-08-05

    Automated vehicles (AVs) must be thoroughly evaluated before their release and deployment. A widely used evaluation approach is the Naturalistic-Field Operational Test (N-FOT), which tests prototype vehicles directly on the public roads. Due to the low exposure to safety-critical scenarios, N-FOTs are time consuming and expensive to conduct. In this paper, we propose an accelerated evaluation approach for AVs. The results can be used to generate motions of the other primary vehicles to accelerate the verification of AVs in simulations and controlled experiments. Frontal collision due to unsafe cut-ins is the target crash type of this paper. Human-controlled vehicles making unsafe lane changes are modeled as the primary disturbance to AVs based on data collected by the University of Michigan Safety Pilot Model Deployment Program. The cut-in scenarios are generated based on skewed statistics of collected human driver behaviors, which generate risky testing scenarios while preserving the statistical information so that the safety benefits of AVs in nonaccelerated cases can be accurately estimated. The cross-entropy method is used to recursively search for the optimal skewing parameters. The frequencies of the occurrences of conflicts, crashes, and injuries are estimated for a modeled AV, and the achieved accelerated rate is around 2000 to 20 000. In other words, in the accelerated simulations, driving for 1000 miles will expose the AV with challenging scenarios that will take about 2 to 20 million miles of real-world driving to encounter. This technique thus has the potential to greatly reduce the development and validation time for AVs.

  20. Impact of Moderate Blast Exposures on Thrombin Biomarkers Assessed by Calibrated Automated Thrombography in Rats

    PubMed Central

    Serebruany, Victor L.; Svetlov, Artem; Hayes, Ronald L.

    2013-01-01

    Abstract Severe blast exposures are frequently complicated with fatal intracranial hemorrhages. However, many more sustain low level blasts without tissue damage detectable by brain imaging. To investigate effects of nonlethal blast on thrombin-related biomarkers, rats were subjected to two different types of head-directed blast: 1) moderate “composite” blast with strong head acceleration or 2) moderate primary blast, without head acceleration. Thrombin generation (TG) ex vivo after blast was studied by calibrated automated thrombography (CAT). In the same blood samples, we assessed maximal concentration of TG (TGmax), start time, peak time, mean time, and concentrations of protein markers for vascular/hemostatic dysfunctions: integrin α/β, soluble endothelial selectin (sE-selectin), soluble intercellular cell adhesion molecule-1 (sICAM-1), and matrix metalloproteinases (MMP)-2, MMP-8, and MMP-13. Blast remarkably affected all TG indices. In animals exposed to “composite” blast, TGmax peaked at 6 h (∼4.5-fold vs. control), sustained at day 1 (∼3.8-fold increase), and declined to a 2-fold increase over control at day 7 post-blast. After primary blast, TGmax also rose to ∼4.2-fold of control at 6 h, dropped to ∼1.7-fold of control at day 1, and then exhibited a slight secondary increase at 2-fold of control at day 7. Other TG indices did not differ significantly between two types of blast exposure. The changes were also observed in other microvascular/inflammatory/hemostatic biomarkers. Integrin α/β and sICAM-1 levels were elevated after both “composite” and primary blast at 6 h, 1 day, and 7 days. sE-selectin exhibited near normal levels after “composite” blast, but increased significantly at 7 days after primary blast; MMP-2, MMP-8, and MMP-13 slightly rose after “composite” blast and significantly increased (∼2-4-fold) after primary blast. In summary, CAT may have a clinical diagnostic utility in combination with selected

  1. Investigation of Mercury Wet Deposition Physicochemistry in the Ohio River Valley through Automated Sequential Sampling

    EPA Science Inventory

    Intra-storm variability and soluble fractionation was explored for summer-time rain events in Steubenville, Ohio to evaluate the physical processes controlling mercury (Hg) in wet deposition in this industrialized region. Comprehensive precipitation sample collection was conducte...

  2. Investigation of Mercury Wet Deposition Physicochemistry in the Ohio River Valley through Automated Sequential Sampling

    EPA Science Inventory

    Intra-storm variability and soluble fractionation was explored for summer-time rain events in Steubenville, Ohio to evaluate the physical processes controlling mercury (Hg) in wet deposition in this industrialized region. Comprehensive precipitation sample collection was conducte...

  3. Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

    PubMed

    Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

    2016-01-01

    Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample

  4. Automated transmission line fault analysis using synchronized sampling at two ends

    SciTech Connect

    Kezunovic, M.; Perunicic, B.

    1996-02-01

    This paper introduces a new approach to fault analysis using synchronized sampling. A digital fault recorder with Global Positioning System (GPS) satellite receiver is the source of data for this approach. Fault analysis functions, such as fault detection, classification and location are implemented for a transmission line using synchronized samples from two ends of a line. This technique can be extremely fast, selective and accurate, providing fault analysis performance that can not easily be matched by other known techniques.

  5. Automated transmission line fault analysis using synchronized sampling at two ends

    SciTech Connect

    Kezunovic, M.; Perunicic, B.

    1995-12-31

    This paper introduces a new approach to fault analysis using synchronized sampling. A digital fault recorder with Global Positioning System (GPS) satellite receiver is the source of data for this approach. Fault analysis functions, such as fault detection, classification and location are implemented for a transmission line using synchronized samples from two ends of a line. This technique can be extremely fast, selective and accurate, providing fault analysis performance that can not easily be matched by other known techniques.

  6. Automated sample preparation station for studying self-diffusion in porous solids with NMR spectroscopy

    SciTech Connect

    Hedin, Niklas; DeMartin, Gregory J.; Reyes, Sebastian C.

    2006-03-15

    In studies of gas diffusion in porous solids with nuclear magnetic resonance (NMR) spectroscopy the sample preparation procedure becomes very important. An apparatus is presented here that pretreats the sample ex situ and accurately sets the desired pressure and temperature within the NMR tube prior to its introduction in the spectrometer. The gas manifold that supplies the NMR tube is also connected to a microbalance containing another portion of the same sample, which is kept at the same temperature as the sample in the NMR tube. This arrangement permits the simultaneous measurement of the adsorption loading on the sample, which is required for the interpretation of the NMR diffusion experiments. Furthermore, to ensure a good seal of the NMR tube, a hybrid valve design composed of titanium, a Teflon registered seat, and Kalrez registered O-rings is utilized. A computer controlled algorithm ensures the accuracy and reproducibility of all the procedures, enabling the NMR diffusion experiments to be performed at well controlled conditions of pressure, temperature, and amount of gas adsorbed on the porous sample.

  7. High-throughput automated microfluidic sample preparation for accurate microbial genomics

    PubMed Central

    Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

    2017-01-01

    Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

  8. High-throughput automated microfluidic sample preparation for accurate microbial genomics.

    PubMed

    Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C

    2017-01-27

    Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.

  9. Detection of motile micro-organisms in biological samples by means of a fully automated image processing system

    NASA Astrophysics Data System (ADS)

    Alanis, Elvio; Romero, Graciela; Alvarez, Liliana; Martinez, Carlos C.; Hoyos, Daniel; Basombrio, Miguel A.

    2001-08-01

    A fully automated image processing system for detection of motile microorganism is biological samples is presented. The system is specifically calibrated for determining the concentration of Trypanosoma Cruzi parasites in blood samples of mice infected with Chagas disease. The method can be adapted for use in other biological samples. A thin layer of blood infected by T. cruzi parasites is examined in a common microscope in which the images of the vision field are taken by a CCD camera and temporarily stored in the computer memory. In a typical field, a few motile parasites are observable surrounded by blood red cells. The parasites have low contrast. Thus, they are difficult to detect visually but their great motility betrays their presence by the movement of the nearest neighbor red cells. Several consecutive images of the same field are taken, decorrelated with each other where parasites are present, and digitally processed in order to measure the number of parasites present in the field. Several fields are sequentially processed in the same fashion, displacing the sample by means of step motors driven by the computer. A direct advantage of this system is that its results are more reliable and the process is less time consuming than the current subjective evaluations made visually by technicians.

  10. Quantitative analysis of a biopharmaceutical protein in cell culture samples using automated capillary electrophoresis (CE) western blot.

    PubMed

    Xu, Dong; Marchionni, Kentaro; Hu, Yunli; Zhang, Wei; Sosic, Zoran

    2017-10-25

    An effective control strategy is critical to ensure the safety, purity and potency of biopharmaceuticals. Appropriate analytical tools are needed to realize such goals by providing information on product quality at an early stage to help understanding and control of the manufacturing process. In this work, a fully automated, multi-capillary instrument is utilized for size-based separation and western blot analysis to provide an early readout on product quality in order to enable a more consistent manufacturing process. This approach aims at measuring two important qualities of a biopharmaceutical protein, titer and isoform distribution, in cell culture harvest samples. The acquired data for isoform distribution can then be used to predict the corresponding values of the final drug substance, and potentially provide information for remedy through timely adjustment of the downstream purification process, should the expected values fall out of the accepted range. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  11. Measurement, Sampling, and Equating Errors in Large-Scale Assessments

    ERIC Educational Resources Information Center

    Wu, Margaret

    2010-01-01

    In large-scale assessments, such as state-wide testing programs, national sample-based assessments, and international comparative studies, there are many steps involved in the measurement and reporting of student achievement. There are always sources of inaccuracies in each of the steps. It is of interest to identify the source and magnitude of…

  12. Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

    PubMed Central

    Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2016-01-01

    Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

  13. Automated, Unobtrusive, Action-by-Action Assessment of Self-Regulation during Learning with an Intelligent Tutoring System

    ERIC Educational Resources Information Center

    Aleven, Vincent; Roll, Ido; McLaren, Bruce M.; Koedinger, Kenneth R.

    2010-01-01

    Assessment of students' self-regulated learning (SRL) requires a method for evaluating whether observed actions are appropriate acts of self-regulation in theEv specific learning context in which they occur. We review research that has resulted in an automated method for context-sensitive assessment of a specific SRL strategy, help seeking while…

  14. Performance on the Defense Automated Neurobehavioral Assessment across controlled environmental conditions.

    PubMed

    Haran, F Jay; Dretsch, Michael N; Bleiberg, Joseph

    2016-01-01

    Neurocognitive assessment tools (NCAT) are commonly used to screen for changes in cognitive functioning following a mild traumatic brain injury and to assist with a return to duty decision. As such, it is critical to determine if performance on the Defense Automated Neurobehavioral Assessment (DANA) is adversely affected by operationally-relevant field environments. Differences in DANA performance between a thermoneutral environment and three simulated operationally-relevant field environments across the thermal stress continuum were calculated for 16 healthy U.S. Navy service members. Practice effects associated with brief test-retest intervals were calculated within each environmental condition. There were no significant differences between the simulated environmental conditions suggesting that performance on the DANA Brief is not impacted by thermal stress. Additionally, there were no significant differences in performance within each simulated environmental condition associated with repeated administrations.

  15. High-throughput automated image analysis of neuroinflammation and neurodegeneration enables quantitative assessment of virus neurovirulence

    PubMed Central

    Maximova, Olga A.; Murphy, Brian R.; Pletnev, Alexander G.

    2010-01-01

    Historically, the safety of live attenuated vaccine candidates against neurotropic viruses was assessed by semi-quantitative analysis of virus-induced histopathology in the central nervous system of monkeys. We have developed a high-throughput automated image analysis (AIA) for the quantitative assessment of virus-induced neuroinflammation and neurodegeneration. Evaluation of the results generated by AIA showed that quantitative estimates of lymphocytic infiltration, microglial activation, and neurodegeneration strongly and significantly correlated with results of traditional histopathological scoring. In addition, we show that AIA is a targeted, objective, accurate, and time-efficient approach that provides reliable differentiation of virus neurovirulence. As such, it may become a useful tool in establishing consistent analytical standards across research and development laboratories and regulatory agencies, and may improve the safety evaluation of live virus vaccines. The implementation of this high-throughput AIA will markedly advance many fields of research including virology, neuroinflammation, neuroscience, and vaccinology. PMID:20688036

  16. The Effects of Finite Sampling on State Assessment Sample Requirements. NAEP Validity Studies. Working Paper Series.

    ERIC Educational Resources Information Center

    Chromy, James R.

    This study addressed statistical techniques that might ameliorate some of the sampling problems currently facing states with small populations participating in State National Assessment of Educational Progress (NAEP) assessments. The study explored how the application of finite population correction factors to the between-school component of…

  17. Use of single particle aerosol mass spectrometry for the automated nondestructive identification of drugs in multicomponent samples.

    PubMed

    Martin, Audrey N; Farquar, George R; Steele, Paul T; Jones, A Daniel; Frank, Matthias

    2009-11-15

    In this work, single particle aerosol mass spectrometry (SPAMS) was used to identify the active drug ingredients in samples of multicomponent over-the-counter (OTC) drug tablets with minimal damage to the tablets. OTC drug tablets in various formulations were analyzed including single active ingredient tablets and multi-ingredient tablets. Using a sampling apparatus developed in-house, micrometer-sized particles were simultaneously dislodged from tablets and introduced to the SPAMS, where dual-polarity mass spectra were obtained from individual particles. Active ingredients were identified from the parent ions and fragment ions formed from each sample, and alarm files were developed for each active ingredient, allowing successful automated identification of each compound in a mixture. The alarm algorithm developed for SPAMS correctly identified all drug compounds in all single-ingredient and multi-ingredient tablets studied. A further study demonstrated the ability of this technique to identify the active ingredient in a single tablet analyzed in the presence of several other nonidentical tablets. In situ measurements were also made by sampling directly from a drug sample in its original bottle. A single tablet embedded in 11 identical tablets of different composition was detected in this manner. Overall, this work demonstrates the ability of the SPAMS technique to detect a target drug compound both in complex tablets, i.e., multidrug ingredient tablets, and complex sampling environments, i.e., multitablet sampling sources. The technique is practically nondestructive, leaving the characteristic shape, color, and imprint of a tablet intact for further analysis. Applications of this technique may include forensic and pharmaceutical analysis.

  18. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

    PubMed Central

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  19. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    PubMed

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers.

  20. The T-lock: Automated compensation of radio-frequency induced sample heating

    PubMed Central

    Hiller, Sebastian; Arthanari, Haribabu; Wagner, Gerhard

    2009-01-01

    Modern high-field NMR spectrometers can stabilize the nominal sample temperature at a precision of less than 0.1 K. However, the actual sample temperature may differ from the nominal value by several degrees because the sample heating caused by high-power radio frequency pulses is not readily detected by the temperature sensors. Without correction, transfer of chemical shifts between different experiments causes problems in the data analysis. In principle, the temperature differences can be corrected by manual procedures but this is cumbersome and not fully reliable. Here, we introduce the concept of a „T-lock“, which automatically maintains the sample at the same reference temperature over the course of different NMR experiments. The T-lock works by continuously measuring the resonance frequency of a suitable spin and simultaneously adjusting the temperature control, thus locking the sample temperature at the reference value. For three different nuclei, 13C, 17O and 31P in the compounds alanine, water, and phosphate, respectively, the T-lock accuracy was found to be < 0.1 K. The use of dummy scan periods with variable lengths allows a reliable establishment of the thermal equilibrium before the acquisition of an experiment starts. PMID:19434373

  1. Rapid and automated detection of fluorescent total bacteria in water samples.

    PubMed

    Lepeuple, A-S; Gilouppe, S; Pierlot, E; De Roubin, M-R

    2004-05-01

    Traditional methods for the detection and enumeration of bacteria in water samples are growth-based and require several days to obtain the result. New techniques which reduce the time of analysis have been developed. The objective of this work was to test a rapid method for the detection and enumeration of total viable bacteria using direct fluorescent labelling and detection by laser scanning. This method (referred to as TVC for Total Viable Count) was compared to the R2A culture method and the cyano-ditolyl-tetrazolium chloride (CTC) staining method for the analysis of samples before the final chlorination (after GAC filtration) and drinking water samples. For the comparison of TVC and CTC, the outcome depends on the water type: for samples after GAC filtration, TVC counts were significantly lower than CTC counts by up to 2 log10 orders of magnitude. For chlorinated water samples, TVC counts were not significantly different from CTC counts. The comparison of TVC and R2A showed that TVC counts could be lower than R2A counts or equivalent depending on the type of water. For drinking water, the TVC method proved to yield results equivalent to those of the R2A method. The TVC method requires much shorter time frame than others. It is also simple to use and allows the analysis of large volumes (100 ml) of drinking water.

  2. Monitoring cognitive function and need with the automated neuropsychological assessment metrics in Decompression Sickness (DCS) research

    NASA Technical Reports Server (NTRS)

    Nesthus, Thomas E.; Schiflett, Sammuel G.

    1993-01-01

    Hypobaric decompression sickness (DCS) research presents the medical monitor with the difficult task of assessing the onset and progression of DCS largely on the basis of subjective symptoms. Even with the introduction of precordial Doppler ultrasound techniques for the detection of venous gas emboli (VGE), correct prediction of DCS can be made only about 65 percent of the time according to data from the Armstrong Laboratory's (AL's) hypobaric DCS database. An AL research protocol concerned with exercise and its effects on denitrogenation efficiency includes implementation of a performance assessment test battery to evaluate cognitive functioning during a 4-h simulated 30,000 ft (9144 m) exposure. Information gained from such a test battery may assist the medical monitor in identifying early signs of DCS and subtle neurologic dysfunction related to cases of asymptomatic, but advanced, DCS. This presentation concerns the selection and integration of a test battery and the timely graphic display of subject test results for the principal investigator and medical monitor. A subset of the Automated Neuropsychological Assessment Metrics (ANAM) developed through the Office of Military Performance Assessment Technology (OMPAT) was selected. The ANAM software provides a library of simple tests designed for precise measurement of processing efficiency in a variety of cognitive domains. For our application and time constraints, two tests requiring high levels of cognitive processing and memory were chosen along with one test requiring fine psychomotor performance. Accuracy, speed, and processing throughout variables as well as RMS error were collected. An automated mood survey provided 'state' information on six scales including anger, happiness, fear, depression, activity, and fatigue. An integrated and interactive LOTUS 1-2-3 macro was developed to import and display past and present task performance and mood-change information.

  3. Monitoring cognitive function and need with the automated neuropsychological assessment metrics in Decompression Sickness (DCS) research

    NASA Technical Reports Server (NTRS)

    Nesthus, Thomas E.; Schiflett, Sammuel G.

    1993-01-01

    Hypobaric decompression sickness (DCS) research presents the medical monitor with the difficult task of assessing the onset and progression of DCS largely on the basis of subjective symptoms. Even with the introduction of precordial Doppler ultrasound techniques for the detection of venous gas emboli (VGE), correct prediction of DCS can be made only about 65 percent of the time according to data from the Armstrong Laboratory's (AL's) hypobaric DCS database. An AL research protocol concerned with exercise and its effects on denitrogenation efficiency includes implementation of a performance assessment test battery to evaluate cognitive functioning during a 4-h simulated 30,000 ft (9144 m) exposure. Information gained from such a test battery may assist the medical monitor in identifying early signs of DCS and subtle neurologic dysfunction related to cases of asymptomatic, but advanced, DCS. This presentation concerns the selection and integration of a test battery and the timely graphic display of subject test results for the principal investigator and medical monitor. A subset of the Automated Neuropsychological Assessment Metrics (ANAM) developed through the Office of Military Performance Assessment Technology (OMPAT) was selected. The ANAM software provides a library of simple tests designed for precise measurement of processing efficiency in a variety of cognitive domains. For our application and time constraints, two tests requiring high levels of cognitive processing and memory were chosen along with one test requiring fine psychomotor performance. Accuracy, speed, and processing throughout variables as well as RMS error were collected. An automated mood survey provided 'state' information on six scales including anger, happiness, fear, depression, activity, and fatigue. An integrated and interactive LOTUS 1-2-3 macro was developed to import and display past and present task performance and mood-change information.

  4. Automation of preparation of nonmetallic samples for analysis by atomic absorption and inductively coupled plasma spectrometry

    NASA Technical Reports Server (NTRS)

    Wittmann, A.; Willay, G.

    1986-01-01

    For a rapid preparation of solutions intended for analysis by inductively coupled plasma emission spectrometry or atomic absorption spectrometry, an automatic device called Plasmasol was developed. This apparatus used the property of nonwettability of glassy C to fuse the sample in an appropriate flux. The sample-flux mixture is placed in a composite crucible, then heated at high temperature, swirled until full dissolution is achieved, and then poured into a water-filled beaker. After acid addition, dissolution of the melt, and filling to the mark, the solution is ready for analysis. The analytical results obtained, either for oxide samples or for prereduced iron ores show that the solutions prepared with this device are undistinguished from those obtained by manual dissolutions done by acid digestion or by high temperature fusion. Preparation reproducibility and analytical tests illustrate the performance of Plasmasol.

  5. ISRU: Automated Water Extraction Ffrom Mars Surface Soils for Sample Return Missions

    NASA Astrophysics Data System (ADS)

    Willson, D.

    2012-06-01

    An ISRU option for Mars sample return vehicles is to employ a Sojourner/MER sized bucket excavation rover that mines and extracts water from the top 5 cm of surface soils and delivers it to an ISRU on the lander. The option is mass competitive.

  6. A self-contained polymeric cartridge for automated biological sample preparation.

    PubMed

    Xu, Guolin; Lee, Daniel Yoke San; Xie, Hong; Chiew, Deon; Hsieh, Tseng-Ming; Ali, Emril Mohamed; Lun Looi, Xing; Li, Mo-Huang; Ying, Jackie Y

    2011-09-01

    Sample preparation is one of the most crucial processes for nucleic acids based disease diagnosis. Several steps are required for nucleic acids extraction, impurity washes, and DNA/RNA elution. Careful sample preparation is vital to the obtaining of reliable diagnosis, especially with low copies of pathogens and cells. This paper describes a low-cost, disposable lab cartridge for automatic sample preparation, which is capable of handling flexible sample volumes of 10 μl to 1 ml. This plastic cartridge contains all the necessary reagents for pathogen and cell lysis, DNA/RNA extraction, impurity washes, DNA/RNA elution and waste processing in a completely sealed cartridge. The entire sample preparation processes are automatically conducted within the cartridge on a desktop unit using a pneumatic fluid manipulation approach. Reagents transportation is achieved with a combination of push and pull forces (with compressed air and vacuum, respectively), which are connected to the pneumatic inlets at the bottom of the cartridge. These pneumatic forces are regulated by pinch valve manifold and two pneumatic syringe pumps within the desktop unit. The performance of this pneumatic reagent delivery method was examined. We have demonstrated the capability of the on-cartridge RNA extraction and cancer-specific gene amplification from 10 copies of MCF-7 breast cancer cells. The on-cartridge DNA recovery efficiency was 54-63%, which was comparable to or better than the conventional manual approach using silica spin column. The lab cartridge would be suitable for integration with lab-chip real-time polymerase chain reaction devices in providing a portable system for decentralized disease diagnosis.

  7. An assessment of fine-needle sampling techniques.

    PubMed

    Titoria, Puneet; Siva, Thiru M; Malik, Tass

    2010-07-01

    Fine-needle cytology sampling, when adequate, is highly sensitive and specific for tissue-type diagnosis, with figures of 94% and 88%, respectively. This study explores the technique of sampling to reduce interoperator variability and ensure maximal tissue yield. Apple cortical tissue was sampled as a proxy of human lymph node. A total of 200 samples, by four methods, with 50 by each sampling method, were taken using blue venepuncture needles and weighed to assess tissue yield. Results were analysed using one-way analysis of variance and Tukey's HSD test. Comparable yields, by mass, were achieved by both straight lance and coring techniques (P > 0.05). Significantly greater yield was achieved with a multiplanar technique (P < 0.05). Multiplanar sampling increases mass yield of tissue in fine-needle sampling. Coring appears to have little bearing on yield.

  8. Toxicity assessment of ionic liquids with Vibrio fischeri: an alternative fully automated methodology.

    PubMed

    Costa, Susana P F; Pinto, Paula C A G; Lapa, Rui A S; Saraiva, M Lúcia M F S

    2015-03-02

    A fully automated Vibrio fischeri methodology based on sequential injection analysis (SIA) has been developed. The methodology was based on the aspiration of 75 μL of bacteria and 50 μL of inhibitor followed by measurement of the luminescence of bacteria. The assays were conducted for contact times of 5, 15, and 30 min, by means of three mixing chambers that ensured adequate mixing conditions. The optimized methodology provided a precise control of the reaction conditions which is an asset for the analysis of a large number of samples. The developed methodology was applied to the evaluation of the impact of a set of ionic liquids (ILs) on V. fischeri and the results were compared with those provided by a conventional assay kit (Biotox(®)). The collected data evidenced the influence of different cation head groups and anion moieties on the toxicity of ILs. Generally, aromatic cations and fluorine-containing anions displayed higher impact on V. fischeri, evidenced by lower EC50. The proposed methodology was validated through statistical analysis which demonstrated a strong positive correlation (P>0.98) between assays. It is expected that the automated methodology can be tested for more classes of compounds and used as alternative to microplate based V. fischeri assay kits.

  9. Development of an Automated and Sensitive Microfluidic Device for Capturing and Characterizing Circulating Tumor Cells (CTCs) from Clinical Blood Samples

    PubMed Central

    Gogoi, Priya; Sepehri, Saedeh; Zhou, Yi; Gorin, Michael A.; Paolillo, Carmela; Capoluongo, Ettore; Gleason, Kyle; Payne, Austin; Boniface, Brian; Cristofanilli, Massimo; Morgan, Todd M.; Fortina, Paolo; Pienta, Kenneth J.; Handique, Kalyan; Wang, Yixin

    2016-01-01

    Current analysis of circulating tumor cells (CTCs) is hindered by sub-optimal sensitivity and specificity of devices or assays as well as lack of capability of characterization of CTCs with clinical biomarkers. Here, we validate a novel technology to enrich and characterize CTCs from blood samples of patients with metastatic breast, prostate and colorectal cancers using a microfluidic chip which is processed by using an automated staining and scanning system from sample preparation to image processing. The Celsee system allowed for the detection of CTCs with apparent high sensitivity and specificity (94% sensitivity and 100% specificity). Moreover, the system facilitated rapid capture of CTCs from blood samples and also allowed for downstream characterization of the captured cells by immunohistochemistry, DNA and mRNA fluorescence in-situ hybridization (FISH). In a subset of patients with prostate cancer we compared the technology with a FDA-approved CTC device, CellSearch and found a higher degree of sensitivity with the Celsee instrument. In conclusion, the integrated Celsee system represents a promising CTC technology for enumeration and molecular characterization. PMID:26808060

  10. A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants.

    PubMed

    Heub, Sarah; Tscharner, Noe; Kehl, Florian; Dittrich, Petra S; Follonier, Stéphane; Barbe, Laurent

    2016-01-01

    A new method for solid phase extraction (SPE) of environmental water samples is proposed. The developed prototype is cost-efficient and user friendly, and enables to perform rapid, automated and simple SPE. The pre-concentrated solution is compatible with analysis by immunoassay, with a low organic solvent content. A method is described for the extraction and pre-concentration of natural hormone 17β-estradiol in 100 ml water samples. Reverse phase SPE is performed with octadecyl-silica sorbent and elution is done with 200 µl of methanol 50% v/v. Eluent is diluted by adding di-water to lower the amount of methanol. After preparing manually the SPE column, the overall procedure is performed automatically within 1 hr. At the end of the process, estradiol concentration is measured by using a commercial enzyme-linked immune-sorbent assay (ELISA). 100-fold pre-concentration is achieved and the methanol content in only 10% v/v. Full recoveries of the molecule are achieved with 1 ng/L spiked de-ionized and synthetic sea water samples.

  11. Development of an Automated and Sensitive Microfluidic Device for Capturing and Characterizing Circulating Tumor Cells (CTCs) from Clinical Blood Samples.

    PubMed

    Gogoi, Priya; Sepehri, Saedeh; Zhou, Yi; Gorin, Michael A; Paolillo, Carmela; Capoluongo, Ettore; Gleason, Kyle; Payne, Austin; Boniface, Brian; Cristofanilli, Massimo; Morgan, Todd M; Fortina, Paolo; Pienta, Kenneth J; Handique, Kalyan; Wang, Yixin

    2016-01-01

    Current analysis of circulating tumor cells (CTCs) is hindered by sub-optimal sensitivity and specificity of devices or assays as well as lack of capability of characterization of CTCs with clinical biomarkers. Here, we validate a novel technology to enrich and characterize CTCs from blood samples of patients with metastatic breast, prostate and colorectal cancers using a microfluidic chip which is processed by using an automated staining and scanning system from sample preparation to image processing. The Celsee system allowed for the detection of CTCs with apparent high sensitivity and specificity (94% sensitivity and 100% specificity). Moreover, the system facilitated rapid capture of CTCs from blood samples and also allowed for downstream characterization of the captured cells by immunohistochemistry, DNA and mRNA fluorescence in-situ hybridization (FISH). In a subset of patients with prostate cancer we compared the technology with a FDA-approved CTC device, CellSearch and found a higher degree of sensitivity with the Celsee instrument. In conclusion, the integrated Celsee system represents a promising CTC technology for enumeration and molecular characterization.

  12. On-line sample preparation for the automated sequential determination of HG in blood, urine and waste water

    SciTech Connect

    Schlemmer, G.; Erler, W.

    1995-12-31

    The accurate determination of mercury in environmental and clinical samples such as waste water, urine or blood with the cold vapour technique requires a complete oxidation and stabilization of mercury in the liquid phase prior to its reduction. It has been shown that the oxidation of all relevant organo-mercury compounds in this type of matrix can be achieved on-line by an appropriate oxidizing agent used in an open microwave system coupled to a flow injection cold vapour system. The various matrices, however, are handled individually. Blood samples, for example are diluted and injected into a neutral carrier. The acid to start the reaction is added on-line only shortly before the sample enters the heating zone of the microwave oven. Urine and waste water on the other hand are acidified already in the autosampler vessel and the microwave digestion is used for completion of the oxidation only. In this application, blood, urine and waste water, three most commonly encountered matrices, were analyzed using the same FIAS and microwave parameters in an automated run. The time for one individual measurement including the on-line deposition is about 90s. The detection limits obtained with a mercury specific detector is about 20 nm/L for urine and waste water and 100 ng/L for blood.

  13. Automated sample-scanning methods for radiation damage mitigation and diffraction-based centering of macromolecular crystals.

    PubMed

    Hilgart, Mark C; Sanishvili, Ruslan; Ogata, Craig M; Becker, Michael; Venugopalan, Nagarajan; Stepanov, Sergey; Makarov, Oleg; Smith, Janet L; Fischetti, Robert F

    2011-09-01

    Automated scanning capabilities have been added to the data acquisition software, JBluIce-EPICS, at the National Institute of General Medical Sciences and the National Cancer Institute Collaborative Access Team (GM/CA CAT) at the Advanced Photon Source. A `raster' feature enables sample centering via diffraction scanning over two-dimensional grids of simple rectangular or complex polygonal shape. The feature is used to locate crystals that are optically invisible owing to their small size or are visually obfuscated owing to properties of the sample mount. The raster feature is also used to identify the best-diffracting regions of large inhomogeneous crystals. Low-dose diffraction images taken at grid positions are automatically processed in real time to provide a quick quality ranking of potential data-collection sites. A `vector collect' feature mitigates the effects of radiation damage by scanning the sample along a user-defined three-dimensional vector during data collection to maximize the use of the crystal volume and the quality of the collected data. These features are integrated into the JBluIce-EPICS data acquisition software developed at GM/CA CAT where they are used in combination with a robust mini-beam of rapidly changeable diameter from 5 µm to 20 µm. The powerful software-hardware combination is being applied to challenging problems in structural biology.

  14. Advancing haemostasis automation--successful implementation of robotic centrifugation and sample processing in a tertiary service hospital.

    PubMed

    Sédille-Mostafaie, Nazanin; Engler, Hanna; Lutz, Susanne; Korte, Wolfgang

    2013-06-01

    Laboratories today face increasing pressure to automate operations due to increasing workloads and the need to reduce expenditure. Few studies to date have focussed on the laboratory automation of preanalytical coagulation specimen processing. In the present study, we examined whether a clinical chemistry automation protocol meets the preanalytical requirements for the analyses of coagulation. During the implementation of laboratory automation, we began to operate a pre- and postanalytical automation system. The preanalytical unit processes blood specimens for chemistry, immunology and coagulation by automated specimen processing. As the production of platelet-poor plasma is highly dependent on optimal centrifugation, we examined specimen handling under different centrifugation conditions in order to produce optimal platelet deficient plasma specimens. To this end, manually processed models centrifuged at 1500 g for 5 and 20 min were compared to an automated centrifugation model at 3000 g for 7 min. For analytical assays that are performed frequently enough to be targets for full automation, Passing-Bablok regression analysis showed close agreement between different centrifugation methods, with a correlation coefficient between 0.98 and 0.99 and a bias between -5% and +6%. For seldom performed assays that do not mandate full automation, the Passing-Bablok regression analysis showed acceptable to poor agreement between different centrifugation methods. A full automation solution is suitable and can be recommended for frequent haemostasis testing.

  15. Rapid habitability assessment of Mars samples by pyrolysis-FTIR

    NASA Astrophysics Data System (ADS)

    Gordon, Peter R.; Sephton, Mark A.

    2016-02-01

    Pyrolysis Fourier transform infrared spectroscopy (pyrolysis FTIR) is a potential sample selection method for Mars Sample Return missions. FTIR spectroscopy can be performed on solid and liquid samples but also on gases following preliminary thermal extraction, pyrolysis or gasification steps. The detection of hydrocarbon and non-hydrocarbon gases can reveal information on sample mineralogy and past habitability of the environment in which the sample was created. The absorption of IR radiation at specific wavenumbers by organic functional groups can indicate the presence and type of any organic matter present. Here we assess the utility of pyrolysis-FTIR to release water, carbon dioxide, sulfur dioxide and organic matter from Mars relevant materials to enable a rapid habitability assessment of target rocks for sample return. For our assessment a range of minerals were analyzed by attenuated total reflectance FTIR. Subsequently, the mineral samples were subjected to single step pyrolysis and multi step pyrolysis and the products characterised by gas phase FTIR. Data from both single step and multi step pyrolysis-FTIR provide the ability to identify minerals that reflect habitable environments through their water and carbon dioxide responses. Multi step pyrolysis-FTIR can be used to gain more detailed information on the sources of the liberated water and carbon dioxide owing to the characteristic decomposition temperatures of different mineral phases. Habitation can be suggested when pyrolysis-FTIR indicates the presence of organic matter within the sample. Pyrolysis-FTIR, therefore, represents an effective method to assess whether Mars Sample Return target rocks represent habitable conditions and potential records of habitation and can play an important role in sample triage operations.

  16. Automated mineralogical analysis of PM10: new parameters for assessing PM toxicity.

    PubMed

    Williamson, Ben J; Rollinson, Gavyn; Pirrie, Duncan

    2013-06-04

    This work provides the first automated mineralogical/phase assessment of urban airborne PM10 and a new method for determining particle surface mineralogy (PSM), which is a major control on PM toxicity in the lung. PM10 was analyzed on a TEOM filter (Aug.-Sept. 2006 collection) from the London Air Quality Network Bexley, East London, U.K. A cross-section of the filter was analyzed using a QEMSCAN automated mineralogical analysis system which provided 381,981 points of analysis for 14,525 particles over a period of 9 h 54 min. The method had a detection limit for individual mineral components of 0.05 ppm (by area). Particle shape and mineralogical characteristics were determined for particles in the size ranges PM(10-4), PM(4-2.5), and PM(2.5-0.8). The PM(2.5-0.8) fraction contained 2 orders of magnitude more mineral particles than the PM(10-4) and PM(4-2.5) fractions, however the PM(10-4) fraction forms 94% and 79% of the mineral mass and surface area, respectively. PSM of the PM10 was dominated by gypsum (36%), plagioclase (16%), Na sulphates (8%), and Fe-S-O phases (8%) in the PM(10-2.5), which may be important in explaining the toxicity of the coarse fraction. The wider implications of the study are discussed.

  17. Automated on-line preconcentration of palladium on different sorbents and its determination in environmental samples.

    PubMed

    Sánchez Rojas, Fuensanta; Bosch Ojeda, Catalina; Cano Pavón, José Manuel

    2007-01-01

    The determination of noble metals in environmental samples is of increasing importance. Palladium is often employed as a catalyst in chemical industry and is also used with platinum and rhodium in motor car catalytic converters which might cause environmental pollution problems. Two different sorbents for palladium preconcentration in different samples were investigated: silica gel functionalized with 1,5-bis(di-2-pyridyl)methylene tbiocarbohydrazide (DPTH-gel) and [1,5-Bis(2-pyridyl)-3-sulphophenyI methylene thiocarbonohydrazide (PSTH) immobilised on an anion-exchange resin (Dowex lx8-200)]. The sorbents were tested in a micro-column, placed in the auto-sampler arm, at the flow rate 2.8 mL min(-1). Elution was performed with 4 M HCl and 4 M HNO3, respectively. Satisfactory results were obtained for two sorbents.

  18. Improving semi-automated segmentation by integrating learning with active sampling

    NASA Astrophysics Data System (ADS)

    Huo, Jing; Okada, Kazunori; Brown, Matthew

    2012-02-01

    Interactive segmentation algorithms such as GrowCut usually require quite a few user interactions to perform well, and have poor repeatability. In this study, we developed a novel technique to boost the performance of the interactive segmentation method GrowCut involving: 1) a novel "focused sampling" approach for supervised learning, as opposed to conventional random sampling; 2) boosting GrowCut using the machine learned results. We applied the proposed technique to the glioblastoma multiforme (GBM) brain tumor segmentation, and evaluated on a dataset of ten cases from a multiple center pharmaceutical drug trial. The results showed that the proposed system has the potential to reduce user interaction while maintaining similar segmentation accuracy.

  19. Fully automated breast density assessment from low-dose chest CT

    NASA Astrophysics Data System (ADS)

    Liu, Shuang; Margolies, Laurie R.; Xie, Yiting; Yankelevitz, David F.; Henschke, Claudia I.; Reeves, Anthony P.

    2017-03-01

    Breast cancer is the most common cancer diagnosed among US women and the second leading cause of cancer death 1 . Breast density is an independent risk factor for breast cancer and more than 25 states mandate its reporting to patients as part of the lay mammogram report 2 . Recent publications have demonstrated that breast density measured from low-dose chest CT (LDCT) correlates well with that measured from mammograms and MRIs 3-4 , thereby providing valuable information for many women who have undergone LDCT but not recent mammograms. A fully automated framework for breast density assessment from LDCT is presented in this paper. The whole breast region is first segmented using an anatomy-orientated novel approach based on the propagation of muscle fronts for separating the fibroglandular tissue from the underlying muscles. The fibroglandular tissue regions are then identified from the segmented whole breast and the percentage density is calculated based on the volume ratio of the fibroglandular tissue to the local whole breast region. The breast region segmentation framework was validated with 1270 LDCT scans, with 96.1% satisfactory outcomes based on visual inspection. The density assessment was evaluated by comparing with BI-RADS density grades established by an experienced radiologist in 100 randomly selected LDCT scans of female subjects. The continuous breast density measurement was shown to be consistent with the reference subjective grading, with the Spearman's rank correlation 0.91 (p-value < 0.001). After converting the continuous density to categorical grades, the automated density assessment was congruous with the radiologist's reading in 91% cases.

  20. Assessing the accuracy of an inter-institutional automated patient-specific health problem list

    PubMed Central

    2010-01-01

    Background Health problem lists are a key component of electronic health records and are instrumental in the development of decision-support systems that encourage best practices and optimal patient safety. Most health problem lists require initial clinical information to be entered manually and few integrate information across care providers and institutions. This study assesses the accuracy of a novel approach to create an inter-institutional automated health problem list in a computerized medical record (MOXXI) that integrates three sources of information for an individual patient: diagnostic codes from medical services claims from all treating physicians, therapeutic indications from electronic prescriptions, and single-indication drugs. Methods Data for this study were obtained from 121 general practitioners and all medical services provided for 22,248 of their patients. At the opening of a patient's file, all health problems detected through medical service utilization or single-indication drug use were flagged to the physician in the MOXXI system. Each new arising health problem were presented as 'potential' and physicians were prompted to specify if the health problem was valid (Y) or not (N) or if they preferred to reassess its validity at a later time. Results A total of 263,527 health problems, representing 891 unique problems, were identified for the group of 22,248 patients. Medical services claims contributed to the majority of problems identified (77%), followed by therapeutic indications from electronic prescriptions (14%), and single-indication drugs (9%). Physicians actively chose to assess 41.7% (n = 106,950) of health problems. Overall, 73% of the problems assessed were considered valid; 42% originated from medical service diagnostic codes, 11% from single indication drugs, and 47% from prescription indications. Twelve percent of problems identified through other treating physicians were considered valid compared to 28% identified through study

  1. High-throughput pharmacokinetics screen of VLA-4 antagonists by LC/MS/MS coupled with automated solid-phase extraction sample preparation.

    PubMed

    Tong, Xinchun S; Wang, Junying; Zheng, Song; Pivnichny, James V

    2004-06-29

    Automation of plasma sample preparation for pharmacokinetic studies on VLA-4 antagonists has been achieved by using 96-well format solid-phase extraction operated by Beckman Coulter Biomek 2000 liquid handling system. A Biomek 2000 robot is used to perform fully automated plasma sample preparation tasks that include serial dilution of standard solutions, pipetting plasma samples, addition of standard and internal standard solutions, performing solid-phase extraction (SPE) on Waters OASIS 96-well plates. This automated sample preparation process takes less than 2 h for a typical pharmacokinetic study, including 51 samples, 24 standards, 9 quality controls, and 3-6 dose checks with minimal manual intervention. Extensive validation has been made to ensure the accuracy and reliability of this method. A two-stage vacuum pressure controller has been incorporated in the program to improve SPE efficiency. This automated SPE sample preparation approach combined with liquid chromatography coupled with the high sensitivity and selectivity of tandem mass spectrometry (LC/MS)/MS has been successfully applied on both individual and cassette dosing for pharmacokinetic screening of a large number of VLA-4 antagonists with a limit of quantitation in the range of 1-5 ng/ml. Consequently, a significant throughput increase has been achieved along with an elimination of tedious labor and its consequential tendency to produce errors. Copyright 2004 Elsevier B.V.

  2. Reducing the cost of semi-automated in-gel tryptic digestion and GeLC sample preparation for high-throughput proteomics.

    PubMed

    Ruelcke, Jayde E; Loo, Dorothy; Hill, Michelle M

    2016-10-21

    Peptide generation by trypsin digestion is typically the first step in mass spectrometry-based proteomics experiments, including 'bottom-up' discovery and targeted proteomics using multiple reaction monitoring. Manual tryptic digest and the subsequent clean-up steps can add variability even before the sample reaches the analytical platform. While specialized filter plates and tips have been designed for automated sample processing, the specialty reagents required may not be accessible or feasible due to their high cost. Here, we report a lower-cost semi-automated protocol for in-gel digestion and GeLC using standard 96-well microplates. Further cost savings were realized by re-using reagent tips with optimized sample ordering. To evaluate the methodology, we compared a simple mixture of 7 proteins and a complex cell-lysate sample. The results across three replicates showed that our semi-automated protocol had performance equal to or better than a manual in-gel digestion with respect to replicate variability and level of contamination. In this paper, we also provide the Agilent Bravo method file, which can be adapted to other liquid handlers. The simplicity, reproducibility, and cost-effectiveness of our semi-automated protocol make it ideal for routine in-gel and GeLC sample preparations, as well as high throughput processing of large clinical sample cohorts. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Steady-State Vacuum Ultraviolet Exposure Facility With Automated Lamp Calibration and Sample Positioning Fabricated

    NASA Technical Reports Server (NTRS)

    Sechkar, Edward A.; Steuber, Thomas J.; Banks, Bruce A.; Dever, Joyce A.

    2000-01-01

    The Next Generation Space Telescope (NGST) will be placed in an orbit that will subject it to constant solar radiation during its planned 10-year mission. A sunshield will be necessary to passively cool the telescope, protecting it from the Sun s energy and assuring proper operating temperatures for the telescope s instruments. This sunshield will be composed of metalized polymer multilayer insulation with an outer polymer membrane (12 to 25 mm in thickness) that will be metalized on the back to assure maximum reflectance of sunlight. The sunshield must maintain mechanical integrity and optical properties for the full 10 years. This durability requirement is most challenging for the outermost, constantly solar-facing polymer membrane of the sunshield. One of the potential threats to the membrane material s durability is from vacuum ultraviolet (VUV) radiation in wavelengths below 200 nm. Such radiation can be absorbed in the bulk of these thin polymer membrane materials and degrade the polymer s optical and mechanical properties. So that a suitable membrane material can be selected that demonstrates durability to solar VUV radiation, ground-based testing of candidate materials must be conducted to simulate the total 10- year VUV exposure expected during the Next Generation Space Telescope mission. The Steady State Vacuum Ultraviolet exposure facility was designed and fabricated at the NASA Glenn Research Center at Lewis Field to provide unattended 24-hr exposure of candidate materials to VUV radiation of 3 to 5 times the Sun s intensity in the wavelength range of 115 to 200 nm. The facility s chamber, which maintains a pressure of approximately 5 10(exp -6) torr, is divided into three individual exposure cells, each with a separate VUV source and sample-positioning mechanism. The three test cells are separated by a water-cooled copper shield plate assembly to minimize thermal effects from adjacent test cells. Part of the interior sample positioning mechanism of one

  4. Effect of sampling frequency on shoreline microbiology assessments.

    PubMed

    Leecaster, M K; Weisberg, S B

    2001-11-01

    More than 80,000 shoreline bacteriological samples are collected annually in southern California to protect beachgoer health, but sampling frequency varies from daily to monthly among sampling sites. To assess the effectiveness of various sampling frequencies, we used five years of data from 24 Los Angeles area sites that have been monitored daily to simulate five alternative sampling strategies: five weekdays, five days per week including a weekend day, three days per week, weekly, and monthly. For each of these sampling strategies, we included in the simulation the local custom of adaptive sampling, in which a site is resampled the following day if bacterial concentrations exceed the State of California's beach water quality standards. We found that sampling five times per week resulted in observing about 80% of the events in which State standards were exceeded. This frequency dropped to 55%, 25%, and 5% for three times per week, weekly, and monthly sampling, respectively. Adaptive sampling was ineffective because nearly 70% of the water quality exceedences were single-day events, even at the most frequently contaminated sites. This high frequency of single-day events is of concern because the public is typically notified about water quality conditions 24-48 h after samples are collected, meaning that most warnings are out-of-date when they are issued.

  5. Improved automation of dissolved organic carbon sampling for organic-rich surface waters.

    PubMed

    Grayson, Richard P; Holden, Joseph

    2016-02-01

    In-situ UV-Vis spectrophotometers offer the potential for improved estimates of dissolved organic carbon (DOC) fluxes for organic-rich systems such as peatlands because they are able to sample and log DOC proxies automatically through time at low cost. In turn, this could enable improved total carbon budget estimates for peatlands. The ability of such instruments to accurately measure DOC depends on a number of factors, not least of which is how absorbance measurements relate to DOC and the environmental conditions. Here we test the ability of a S::can Spectro::lyser™ for measuring DOC in peatland streams with routinely high DOC concentrations. Through analysis of the spectral response data collected by the instrument we have been able to accurately measure DOC up to 66 mg L(-1), which is more than double the original upper calibration limit for this particular instrument. A linear regression modelling approach resulted in an accuracy >95%. The greatest accuracy was achieved when absorbance values for several different wavelengths were used at the same time in the model. However, an accuracy >90% was achieved using absorbance values for a single wavelength to predict DOC concentration. Our calculations indicated that, for organic-rich systems, in-situ measurement with a scanning spectrophotometer can improve fluvial DOC flux estimates by 6 to 8% compared with traditional sampling methods. Thus, our techniques pave the way for improved long-term carbon budget calculations from organic-rich systems such as peatlands.

  6. Automated adipose study for assessing cancerous human breast tissue using optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Gan, Yu; Yao, Xinwen; Chang, Ernest W.; Bin Amir, Syed A.; Hibshoosh, Hanina; Feldman, Sheldon; Hendon, Christine P.

    2017-02-01

    Breast cancer is the third leading cause of death in women in the United States. In human breast tissue, adipose cells are infiltrated or replaced by cancer cells during the development of breast tumor. Therefore, an adipose map can be an indicator of identifying cancerous region. We developed an automated classification method to generate adipose map within human breast. To facilitate the automated classification, we first mask the B-scans from OCT volumes by comparing the signal noise ratio with a threshold. Then, the image was divided into multiple blocks with a size of 30 pixels by 30 pixels. In each block, we extracted texture features such as local standard deviation, entropy, homogeneity, and coarseness. The features of each block were input to a probabilistic model, relevance vector machine (RVM), which was trained prior to the experiment, to classify tissue types. For each block within the B-scan, RVM identified the region with adipose tissue. We calculated the adipose ratio as the number of blocks identified as adipose over the total number of blocks within the B-scan. We obtained OCT images from patients (n = 19) in Columbia medical center. We automatically generated the adipose maps from 24 B-scans including normal samples (n = 16) and cancerous samples (n = 8). We found the adipose regions show an isolated pattern that in cancerous tissue while a clustered pattern in normal tissue. Moreover, the adipose ratio (52.30 ± 29.42%) in normal tissue was higher than the that in cancerous tissue (12.41 ± 10.07%).

  7. Automated cell viability assessment using a microfluidics based portable imaging flow analyzer

    PubMed Central

    Jagannadh, Veerendra Kalyan; Adhikari, Jayesh Vasudeva; Gorthi, Sai Siva

    2015-01-01

    In this work, we report a system-level integration of portable microscopy and microfluidics for the realization of optofluidic imaging flow analyzer with a throughput of 450 cells/s. With the use of a cellphone augmented with off-the-shelf optical components and custom designed microfluidics, we demonstrate a portable optofluidic imaging flow analyzer. A multiple microfluidic channel geometry was employed to demonstrate the enhancement of throughput in the context of low frame-rate imaging systems. Using the cell-phone based digital imaging flow analyzer, we have imaged yeast cells present in a suspension. By digitally processing the recorded videos of the flow stream on the cellphone, we demonstrated an automated cell viability assessment of the yeast cell population. In addition, we also demonstrate the suitability of the system for blood cell counting. PMID:26015835

  8. Quantitative Assessment of Mouse Mammary Gland Morphology Using Automated Digital Image Processing and TEB Detection.

    PubMed

    Blacher, Silvia; Gérard, Céline; Gallez, Anne; Foidart, Jean-Michel; Noël, Agnès; Péqueux, Christel

    2016-04-01

    The assessment of rodent mammary gland morphology is largely used to study the molecular mechanisms driving breast development and to analyze the impact of various endocrine disruptors with putative pathological implications. In this work, we propose a methodology relying on fully automated digital image analysis methods including image processing and quantification of the whole ductal tree and of the terminal end buds as well. It allows to accurately and objectively measure both growth parameters and fine morphological glandular structures. Mammary gland elongation was characterized by 2 parameters: the length and the epithelial area of the ductal tree. Ductal tree fine structures were characterized by: 1) branch end-point density, 2) branching density, and 3) branch length distribution. The proposed methodology was compared with quantification methods classically used in the literature. This procedure can be transposed to several software and thus largely used by scientists studying rodent mammary gland morphology.

  9. Evaluation of the appropriate time period between sampling and analyzing for automated urinalysis

    PubMed Central

    Dolscheid-Pommerich, Ramona C.; Klarmann-Schulz, Ute; Conrad, Rupert; Stoffel-Wagner, Birgit; Zur, Berndt

    2016-01-01

    Introduction Preanalytical specifications for urinalysis must be strictly adhered to avoid false interpretations. Aim of the present study is to examine whether the preanalytical factor ‘time point of analysis’ significantly influences stability of urine samples for urine particle and dipstick analysis. Materials and methods In 321 pathological spontaneous urine samples, urine dipstick (Urisys™2400, Combur-10-Test™strips, Roche Diagnostics, Mannheim, Germany) and particle analysis (UF-1000 i™, Sysmex, Norderstedt, Germany) were performed within 90 min, 120 min and 240 min after urine collection. Results For urine particle analysis, a significant increase in conductivity (120 vs. 90 min: P < 0.001, 240 vs. 90 min: P < 0.001) and a significant decrease in WBC (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), RBC (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), casts (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001) and epithelial cells (120 vs. 90 min P = 0.610, 240 vs. 90 min P = 0.041) were found. There were no significant changes for bacteria. Regarding urine dipstick analysis, misclassification rates between measurements were significant for pH (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), leukocytes (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), nitrite (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), protein (120 vs. 90 min P < 0.001, 240 vs. 90 min P<0.001), ketone (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), blood (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001), specific gravity (120 vs. 90 min P < 0.001, 240 vs. 90 min P < 0.001) and urobilinogen (120 vs. 90 min, P = 0.031). Misclassification rates were not significant for glucose and bilirubin. Conclusion Most parameters critically depend on the time window between sampling and analysis. Our study stresses the importance of adherence to early time points in urinalysis (within 90 min). PMID:26981022

  10. Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species.

    PubMed

    Gu, Qun; David, Frank; Lynen, Frédéric; Rumpel, Klaus; Dugardeyn, Jasper; Van Der Straeten, Dominique; Xu, Guowang; Sandra, Pat

    2011-05-27

    In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected.

  11. Dried Blood Spot Proteomics: Surface Extraction of Endogenous Proteins Coupled with Automated Sample Preparation and Mass Spectrometry Analysis

    NASA Astrophysics Data System (ADS)

    Martin, Nicholas J.; Bunch, Josephine; Cooper, Helen J.

    2013-08-01

    Dried blood spots offer many advantages as a sample format including ease and safety of transport and handling. To date, the majority of mass spectrometry analyses of dried blood spots have focused on small molecules or hemoglobin. However, dried blood spots are a potentially rich source of protein biomarkers, an area that has been overlooked. To address this issue, we have applied an untargeted bottom-up proteomics approach to the analysis of dried blood spots. We present an automated and integrated method for extraction of endogenous proteins from the surface of dried blood spots and sample preparation via trypsin digestion by use of the Advion Biosciences Triversa Nanomate robotic platform. Liquid chromatography tandem mass spectrometry of the resulting digests enabled identification of 120 proteins from a single dried blood spot. The proteins identified cross a concentration range of four orders of magnitude. The method is evaluated and the results discussed in terms of the proteins identified and their potential use as biomarkers in screening programs.

  12. Consistency of breast density categories in serial screening mammograms: A comparison between automated and human assessment.

    PubMed

    Holland, Katharina; van Zelst, Jan; den Heeten, Gerard J; Imhof-Tas, Mechli; Mann, Ritse M; van Gils, Carla H; Karssemeijer, Nico

    2016-10-01

    Reliable breast density measurement is needed to personalize screening by using density as a risk factor and offering supplemental screening to women with dense breasts. We investigated the categorization of pairs of subsequent screening mammograms into density classes by human readers and by an automated system. With software (VDG) and by four readers, including three specialized breast radiologists, 1000 mammograms belonging to 500 pairs of subsequent screening exams were categorized into either two or four density classes. We calculated percent agreement and the percentage of women that changed from dense to non-dense and vice versa. Inter-exam agreement (IEA) was calculated with kappa statistics. Results were computed for each reader individually and for the case that each mammogram was classified by one of the four readers by random assignment (group reading). Higher percent agreement was found with VDG (90.4%, CI 87.9-92.9%) than with readers (86.2-89.2%), while less plausible changes from non-dense to dense occur less often with VDG (2.8%, CI 1.4-4.2%) than with group reading (4.2%, CI 2.4-6.0%). We found an IEA of 0.68-0.77 for the readers using two classes and an IEA of 0.76-0.82 using four classes. IEA is significantly higher with VDG compared to group reading. The categorization of serial mammograms in density